ORCID Profile
0000-0001-9823-6078
Current Organisation
Monash University
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Environmental Monitoring | Civil Engineering | Water Quality Engineering | Microbiology not elsewhere classified
Natural Hazards in Fresh, Ground and Surface Water Environments | Recreational Services | Environmental Health |
Publisher: Wiley
Date: 09-04-2023
DOI: 10.1111/RISA.14138
Abstract: C ylobacter jejuni and C ylobacter coli infections are the leading cause of foodborne gastroenteritis in high‐income countries. C ylobacter colonizes a variety of warm‐blooded hosts that are reservoirs for human c ylobacteriosis. The proportions of Australian cases attributable to different animal reservoirs are unknown but can be estimated by comparing the frequency of different sequence types in cases and reservoirs. C ylobacter isolates were obtained from notified human cases and raw meat and offal from the major livestock in Australia between 2017 and 2019. Isolates were typed using multi‐locus sequence genotyping. We used Bayesian source attribution models including the asymmetric island model, the modified Hald model, and their generalizations. Some models included an “uns led” source to estimate the proportion of cases attributable to wild, feral, or domestic animal reservoirs not s led in our study. Model fits were compared using the Watanabe–Akaike information criterion. We included 612 food and 710 human case isolates. The best fitting models attributed % of C ylobacter cases to chickens, with a greater proportion of C. coli ( %) than C. jejuni ( %). The best fitting model that included an uns led source attributed 14% (95% credible interval [CrI]: 0.3%–32%) to the uns led source and only 2% to ruminants (95% CrI: 0.3%–12%) and 2% to pigs (95% CrI: 0.2%–11%) The best fitting model that did not include an uns led source attributed 12% to ruminants (95% CrI: 1.3%–33%) and 6% to pigs (95% CrI: 1.1%–19%). Chickens were the leading source of human C ylobacter infections in Australia in 2017–2019 and should remain the focus of interventions to reduce burden.
Publisher: MDPI AG
Date: 11-06-2018
DOI: 10.3390/V10060319
Publisher: Elsevier BV
Date: 08-1999
DOI: 10.1016/S0168-1656(99)00111-X
Abstract: Pasteurella multocida is the causative agent of fowl cholera and other diseases of production animals. Isolates are classified into five groups based on capsular antigens and into 16 serotypes based on LPS antigens. Strains causing fowl cholera are most frequently designated A:1, A:3 or A:4. Whole cell bacterins can provide some degree of protection, but only against the homologous LPS serotype. There is good evidence that cross-protective antigens are expressed only under in vivo conditions. Empirically derived, live, attenuated vaccines can protect against heterologous serotypes, but because the basis for attenuation is undefined, reversion to virulence is not uncommon. Work in our laboratory is aimed at using a variety of approaches to identify potential protective antigens or virulence genes to be used as candidates for attenuating mutations or as the basis for vaccine antigen delivery systems. The gene encoding an outer membrane protein, Oma87, which is a homologue of the D15 protective antigen of Haemophilus influenzae, was cloned and sequenced. Rabbit antiserum prepared against recombinant Oma87 could passively protect mice against infection. Type 4 fimbriae form the basis of vaccines against ovine footrot and bovine keratoconjunctivitis. We have identified type 4 fimbriae on the surface of P. multocida, purified the fimbrial subunit protein, PtfA, and determined its N-terminal amino acid sequence. Subsequent cloning of the ptfA gene and its inactivation will now be used to assess the importance of type 4 fimbriae in virulence. There has long been anecdotal evidence for the importance of capsule in virulence, but unequivocal genetic evidence for such a role is lacking. We have cloned and characterised the capsule biosynthetic locus in P. multocida A:1 and identified four bex genes involved in capsule transport and genes encoding enzymes involved in the biosynthesis and transfer of the N-acetyl glucosamine and glucuronic acid components of the capsule. It has been suggested that the low concentration of available iron in vivo acts as an environmental cue for expression of cross-protective antigens. Accordingly, we have cloned and characterised the gene encoding transferrin binding protein, Tbpl, so that its role in immunity and virulence can be investigated. Although P. multocida is not normally considered haemolytic, we have observed haemolysis under anaerobic conditions. Standard library construction and screening resulted in the identification of the mesA gene which encodes an esterase enzyme resulting in a haemolytic phenotype under anaerobic conditions. Virulence studies with mesA- mutants were performed to assess its role in pathogenesis. Using a promoterless phoA gene vector system, the cloning of proteins homologous to known surface proteins of other species as well as proteins unique to P. multocida, allowing their potential as vaccine components to be assessed.
Publisher: Elsevier BV
Date: 06-2004
Publisher: BMJ
Date: 12-2018
DOI: 10.1136/BMJOPEN-2018-026630
Abstract: The C ySource project aims to identify risk factors for human C ylobacter infection in Australia. We will investigate locally relevant risk factors and those significant in international studies in a case–control study. Case isolates and contemporaneous isolates from food and animal sources will be sequenced to conduct source attribution modelling, and findings will be combined with the case–control study in a source-assigned analysis. The case–control study will include 1200 participants (600 cases and 600 controls) across three regions in Australia. Cases will be recruited from c ylobacteriosis notifications to health departments. Only those with a pure and viable C ylobacter isolate will be eligible for selection to allow for whole genome sequencing of isolates. Controls will be recruited from notified cases of influenza, frequency matched by sex, age group and geographical area of residence. All participants will be interviewed by trained telephone interviewers using a piloted questionnaire. We will collect C ylobacter isolates from retail meats and companion animals (specifically dogs), and all food, animal and human isolates will undergo whole genome sequencing. We will use sequence data to estimate the proportion of human infections that can be attributed to animal and food reservoirs (source attribution modelling), and to identify spatial clusters and temporal trends. Source-assigned analysis of the case–control study data will also be conducted where cases are grouped according to attributed sources. Human and animal ethics have been approved. Genomic data will be published in online archives accompanied by basic metadata. We anticipate several publications to come from this study.
Publisher: Elsevier BV
Date: 11-2012
DOI: 10.1016/J.VIROL.2012.08.008
Abstract: Kimberley virus (KIMV) is an arthropod-borne rhabdovirus that was isolated in 1973 and on several subsequent occasions from healthy cattle, mosquitoes (Culex annulirostris) and biting midges (Culicoides brevitarsis) in Australia. Malakal virus (MALV) is an antigenically related rhabdovirus isolated in 1963 from mosquitoes (Mansonia uniformis) in Sudan. We report here the complete genome sequences of KIMV (15442 nt) and MALV (15444 nt). The genomes have a similar organisation (3'-l-N-P-M-G-G(NS)-α1-α2-β-γ-L-t-5') to that of bovine ephemeral fever virus (BEFV). High levels of amino acid identity in each gene, similar gene expression profiles, clustering in phylogenetic analyses of the N, P, G and L proteins, and strong cross-neutralisation indicate that KIMV and MALV are geographic variants of the same ephemerovirus that, like BEFV, occurs in Africa, Asia and Australia.
Publisher: American Society for Microbiology
Date: 29-10-2019
Publisher: Wiley
Date: 27-05-2021
DOI: 10.1111/ZPH.12853
Abstract: C ylobacter jejuni is the leading cause of bacterial gastroenteritis globally, and infections are often transmitted through consumption of raw or undercooked poultry. C ylobacter jejuni ST50 is among the top ten sequence types (STs) reported in the collected isolates listed at PubMLST records from poultry, food and clinical sources for Asia, Europe, North America, Oceania and South America. This study was designed to determine the most commonly reported C. jejuni STs globally using the PubMLST database and assess similarities between genomes of C. jejuni ST50 isolates from geographically distinct locations. To gain a better understanding of C. jejuni ersity, we compared draft genome sequences of 182 ST50 isolates recovered from retail or caecal poultry s les in Oceania, Europe and North America that were collected over a period of 9 years (2010 to 2018). Overall, phylogenetic analysis revealed that isolates from geographically distinct locations tended to cluster based on the continent where the s le was collected. Among ST50 isolates from Europe and North America, we identified resistance determinants associated with phenotypic resistance to beta‐lactams (EU: 55% GB: 43.1%), tetracyclines (CA: 77.3% EU: 37.5% GB: 9.8% US: 43.5%) and fluoroquinolones (EU: 60.0% GB: 15.7%) no resistance determinants were identified in isolates from Australia. In general, the majority of the virulence genes, with rare exceptions such as wlaN , cj1138 , hddA and rfbC , were evenly distributed throughout the genomes of all ST50 isolates in this study. Genomic‐based characterization of C. jejuni ST50 isolates from poultry on three continents highlighted that geographically distinct isolates have evolved independently but only represent a glimpse into the ersity of C. jejuni .
Publisher: American Society for Microbiology
Date: 15-06-2012
DOI: 10.1128/JVI.00182-12
Abstract: Bluetongue virus (BTV) is transmitted by biting midges ( Culicoides spp.). It causes disease mainly in sheep and occasionally in cattle and other species. BTV has spread into northern Europe, causing disease in sheep and cattle. The introduction of new serotypes, changes in vector species, and climate change have contributed to these changes. Ten BTV serotypes have been isolated in Australia without apparent associated disease. Simplified methods for preferential isolation of double-stranded RNA (dsRNA) and template preparation enabled high-throughput sequencing of the 10 genome segments of all Australian BTV prototype serotypes. Phylogenetic analysis reinforced the Western and Eastern topotypes previously characterized but revealed unique features of several Australian BTVs. Many of the Australian BTV genome segments (Seg-) were closely related, clustering together within the Eastern topotypes. A novel Australian topotype for Seg-5 (NS1) was identified, with taxa spread across several serotypes and over time. Seg-1, -2, -3, -4, -6, -7, -9, and -10 of BTV_2_AUS_2008 were most closely related to the cognate segments of viruses from Taiwan and Asia and not other Australian viruses, supporting the conclusion that BTV_2 entered Australia recently. The Australian BTV_15_AUS_1982 prototype was revealed to be unusual among the Australian BTV isolates, with Seg-3 and -8 distantly related to other BTV sequences from all serotypes.
Publisher: Oxford University Press (OUP)
Date: 15-08-1999
Publisher: Oxford University Press (OUP)
Date: 23-09-2020
Abstract: Gardnerella vaginalis is detected in women with and without bacterial vaginosis (BV). Identification of 4 G. vaginalis clades raised the possibility that pathogenic and commensal clades exist. We investigated the association of behavioral practices and Nugent Score with G. vaginalis clade distribution in women who have sex with women (WSW). Longitudinal self-collected vaginal specimens were analyzed using established G. vaginalis species-specific and clade-typing polymerase chain reaction assays. Logistic regression assessed factors associated with detection of G. vaginalis clades, and multinomial regression assessed factors associated with number of clades. Clades 1, 2, and 3 and multiclade communities ( clades) were associated with Nugent-BV. Clade 1 (odds ratio [OR], 3.36 95% confidence interval [CI], 1.65–6.84) and multiclade communities (relative risk ratio [RRR], 9.51 95% CI, 4.36–20.73) were also associated with Lactobacillus-deficient vaginal microbiota. Clade 4 was neither associated with Nugent-BV nor Lactobacillus-deficient microbiota (OR, 1.49 95% CI, 0.67–3.33). Specific clades were associated with differing behavioral practices. Clade 1 was associated with increasing number of recent sexual partners and smoking, whereas clade 2 was associated with penile-vaginal sex and sharing of sex toys with female partners. Our results suggest that G. vaginalis clades have varying levels of pathogenicity in WSW, with acquisition occurring through sexual activity. These findings suggest that partner treatment may be an appropriate strategy to improve BV cure.
Publisher: Humana Press
Date: 2006
Publisher: American Society for Microbiology
Date: 31-10-2014
Abstract: Footrot is a contagious, debilitating disease of sheep, causing major economic losses in most sheep-producing countries. The causative agent is the Gram-negative anaerobe Dichelobacter nodosus . Depending on the virulence of the infective bacterial strain, clinical signs vary from a mild interdigital dermatitis (benign footrot) to severe underrunning of the horn of the hoof (virulent footrot). The aim of this study was to investigate the genetic relationship between D. nodosus strains of different phenotypic virulences and between isolates from different geographic regions. Genome sequencing was performed on 103 D. nodosus isolates from eight different countries. Comparison of these genome sequences revealed that they were highly conserved, with % sequence identity. However, single nucleotide polymorphism analysis of the 31,627 nucleotides that were found to differ in one or more of the 103 sequenced isolates ided them into two distinct clades. Remarkably, this ision correlated with known virulent and benign phenotypes, as well as with the single amino acid difference between the AprV2 and AprB2 proteases, which are produced by virulent and benign strains, respectively. This ision was irrespective of the geographic origin of the isolates. However, within one of these clades, isolates from different geographic regions generally belonged to separate clusters. In summary, we have shown that D. nodosus has a bimodal population structure that is globally conserved and provide evidence that virulent and benign isolates represent two distinct forms of D. nodosus strains. These data have the potential to improve the diagnosis and targeted control of this economically significant disease. IMPORTANCE The Gram-negative anaerobic bacterium Dichelobacter nodosus is the causative agent of ovine footrot, a disease of major importance to the worldwide sheep industry. The known D. nodosus virulence factors are its type IV fimbriae and extracellular serine proteases. D. nodosus strains are designated virulent or benign based on the type of disease caused under optimal climatic conditions. These isolates have similar fimbriae but distinct extracellular proteases. To determine the relationship between virulent and benign isolates and the relationship of isolates from different geographical regions, a genomic study that involved the sequencing and subsequent analysis of 103 D. nodosus isolates was undertaken. The results showed that D. nodosus isolates are highly conserved at the genomic level but that they can be ided into two distinct clades that correlate with their disease phenotypes and with a single amino acid substitution in one of the extracellular proteases.
Publisher: Public Library of Science (PLoS)
Date: 15-04-2019
Publisher: Springer Science and Business Media LLC
Date: 04-03-2019
Publisher: Oxford University Press (OUP)
Date: 15-02-2017
Abstract: Acinetobacter baumannii is a pathogen of major importance in intensive care units worldwide, with the potential to cause problematic outbreaks and acquire high-level resistance to antibiotics. There is an urgent need to understand the mechanisms of A. baumannii pathogenesis for the future development of novel targeted therapies. In this study we performed an in vivo transcriptomic analysis of A. baumannii isolated from a mammalian host with bacteremia. Mice were infected with A. baumannii American Type Culture Collection 17978 using an intraperitoneal injection, and blood was extracted at 8 hours to purify bacterial RNA for RNA-Seq with an Illumina platform. Approximately one-quarter of A. baumannii protein coding genes were differentially expressed in vivo compared with in vitro (false discovery rate, ≤0.001 2-fold change) with 557 showing decreased and 329 showing increased expression. Gene groups with functions relating to translation and RNA processing were overrepresented in genes with increased expression, and those relating to chaperone and protein turnover were overrepresented in the genes with decreased expression. The most strongly up-regulated genes corresponded to the 3 recognized siderophore iron uptake clusters, reflecting the iron-restrictive environment in vivo. Metabolic changes in vivo included reduced expression of genes involved in amino acid and fatty acid transport and catabolism, indicating metabolic adaptation to a different nutritional environment. Genes encoding types I and IV pili, quorum sensing components, and proteins involved in biofilm formation all showed reduced expression. Many genes that have been reported as essential for virulence showed reduced or unchanged expression in vivo. This study provides the first insight into A. baumannii gene expression profiles during a life-threatening mammalian infection. Analysis of differentially regulated genes highlights numerous potential targets for the design of novel therapeutics.
Publisher: Springer Science and Business Media LLC
Date: 20-03-2021
DOI: 10.1186/S13099-021-00413-9
Abstract: Infections caused by multidrug-resistant shigellae resistant to broad-spectrum cephalosporins are becoming more prevalent in the Middle East. We report a case of severe diarrhea due to a multiresistant Shigella flexneri 1 strain carrying four different ß-lactamase genes. A one-year-old Syrian infant presented with severe acute diarrhea, vomiting and dehydration. She did not respond to empirical treatment with amoxicillin-clavulanic acid followed by cefotaxime. Later, stool culture revealed S. flexneri 1 resistant to both these drugs. The patient was successfully treated with meropenem to which S. flexneri 1 was susceptible. The isolate was resistant to eight classes of antibiotics, and the whole genome sequence (WGS) identified four ß-lactamase genes ( bla CTX-M-15 , bla EC-8 , bla OXA-1 , and bla TEM-1 ) along with genes mediating resistance to seven other antibiotic classes. The WGS also identified several virulence genes including senA that encodes ShET-2 which induces watery diarrhea. Phylogenetically, the isolate was closely related to isolates from South Asia. This report highlights the emergence of extremely resistant Shigella that has acquired multiple resistance genes to cephalosporins rendering these drugs ineffective.
Publisher: Springer International Publishing
Date: 2018
DOI: 10.1007/82_2018_87
Abstract: Until about 15 years ago, the molecular and cellular basis for pathogenesis in leptospirosis was virtually unknown. The determination of the first full genome sequence in 2003 was followed rapidly by other whole genome sequences, whose availability facilitated the development of transposon mutagenesis and then directed mutagenesis of pathogenic Leptospira spp. The combination of genomics, transcriptomics and mutant construction and characterisation has resulted in major progress in our understanding of the taxonomy and biology of Leptospira. The most recent advances are analysed and discussed in this chapter.
Publisher: PeerJ
Date: 28-02-2017
DOI: 10.7717/PEERJ.3047
Abstract: The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide. We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages. We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCC mec- IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β -lactams, tetracycline and chlor henicol. This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.
Publisher: Springer Science and Business Media LLC
Date: 03-1990
DOI: 10.1007/BF01318350
Publisher: Microbiology Society
Date: 03-2019
Publisher: Elsevier BV
Date: 09-2014
Publisher: Mary Ann Liebert Inc
Date: 04-2020
Publisher: American Society for Microbiology
Date: 07-03-2018
Abstract: A major virulence factor in Clostridium sordellii -mediated infection is the toxin TcsL, which is encoded within a region of the genome called the pathogenicity locus (PaLoc). C. sordellii isolates carry the PaLoc on the pCS1 family of plasmids, of which there are four characterized members. Here, we determined the potential mobility of pCS1 plasmids and characterized a fifth unique pCS1 member. Using a derivative of the pCS1-1 plasmid from strain ATCC 9714 which had been marked with the ermB erythromycin resistance gene, conjugative transfer into a recipient C. sordellii isolate, R28058, was demonstrated. Bioinformatic analysis of pCS1-1 identified a novel conjugation gene cluster defined as the C. sordellii transfer ( cst ) locus. Interruption of genes within the cst locus resulted in loss of pCS1-1 transfer, which was restored upon complementation in trans . These studies provided clear evidence that genes within the cst locus are essential for the conjugative transfer of pCS1-1. The cst locus is present on all pCS1 subtypes, and homologous loci were identified on toxin-encoding plasmids from Clostridium perfringens and Clostridium botulinum and also carried within genomes of Clostridium difficile isolates, indicating that it is a widespread clostridial conjugation locus. The results of this study have broad implications for the dissemination of toxin genes and, potentially, antibiotic resistance genes among members of a erse range of clostridial pathogens, providing these microorganisms with a survival advantage within the infected host. IMPORTANCE C. sordellii is a bacterial pathogen that causes severe infections in humans and animals, with high mortality rates. While the pathogenesis of C. sordellii infections is not well understood, it is known that the toxin TcsL is an important virulence factor. Here, we have shown the ability of a plasmid carrying the tcsL gene to undergo conjugative transfer between distantly related strains of C. sordellii , which has far-reaching implications for the ability of C. sordellii to acquire the capacity to cause disease. Plasmids that carry tcsL encode a previously uncharacterized conjugation locus, and in idual genes within this locus were shown to be required for conjugative transfer. Furthermore, homologues on toxin plasmids from other clostridial species were identified, indicating that this region represents a novel clostridial conjugation locus. The results of this study have broad implications for the dissemination of virulence genes among members of a erse range of clostridial pathogens.
Publisher: Cold Spring Harbor Laboratory
Date: 19-03-2020
DOI: 10.1101/2020.03.18.996223
Abstract: Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipids as an energy storage molecule. We used proteomics to understand the molecular basis for acclimation of M. gaditana to increased salinity levels (55 and 100 PSU (Practical Salinity Unit). Correspondence analysis (CA) was used for the identification of salinity-responsive proteins (SRPs). The highest number of altered proteins was observed in 100 PSU. Gene Ontology (GO) enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis was up-regulated in high saline conditions. However, concomitantly lipid oxidation pathways were also up-regulated at high saline conditions, providing acetyl-CoA for energy metabolism through the TCA cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected under high salinity conditions. Importantly, temporal proteome analysis of salinity-challenged M. gaditana revealed vital salinity-responsive proteins which could be used for strain engineering for improved salinity resistance.
Publisher: Elsevier BV
Date: 04-2018
Publisher: American Society for Microbiology
Date: 07-2000
DOI: 10.1128/IAI.68.7.3793-3798.2000
Abstract: Lipopolysaccharide (LPS) is a key antigen in immunity to leptospirosis. Its biosynthesis requires enzymes for the biosynthesis and polymerization of nucleotide sugars and the transport through and attachment to the bacterial membrane. The genes encoding these functions are commonly clustered into loci for Leptospira borgpetersenii serovar Hardjo subtype Hardjobovis, this locus, named rfb , spans 36.7 kb and contains 31 open reading frames, of which 28 have been assigned putative functions on the basis of sequence similarity. Characterization of the function of these genes is hindered by the fact that it is not possible to construct isogenic mutant strains in Leptospira . We used two approaches to circumvent this problem. The first was to clone the entire locus into a heterologous host system and determine if a “recombinant” LPS or polysaccharide was synthesized in the new host. The second approach used putative functions to identify mutants in other bacterial species whose mutations might be complemented by genes on the leptospiral rfb locus. This approach was used to investigate the function of three genes in the leptospiral rfb locus and demonstrated function for orfH10 , which complemented a wbpM strain of Pseudomonas aeruginosa , and orfH13 , which complemented an rfbW strain of Vibrio cholerae . However, despite the similarity of OrfH11 to WecC, a wecC strain of E. coli was not complemented by orfH11 . The predicted protein encoded by orfH8 is similar to GalE from a number of organisms. A Salmonella enterica serovar Typhimurium strain producing no GalE was used as a background in which orfH8 produced detectable GalE enzyme activity.
Publisher: Microbiology Society
Date: 10-2013
Abstract: The molecular basis for leptospirosis infection and colonization remains poorly understood, with no efficient methods available for screening libraries of mutants for attenuation. We analysed the attenuation of leptospiral transposon mutants in vivo using a high-throughput method by infecting animals with pooled sets of transposon mutants. A total of 95 mutants was analysed by this method in the hamster model of acute infection, and one mutant was identified as attenuated (M1233, lb058 mutant). All virulence factors identified in Leptospira to date have been characterized in the acute model of infection, neglecting the carrier host. To address this, a BALB/c mouse colonization model was established. The lb058 mutant and two mutants defective in LPS synthesis were colonization deficient in the mouse model. By applying the high-throughput screening method, a further five colonization-deficient mutants were identified for the mouse model these included two mutants in genes encoding proteins with a predicted role in iron uptake (LB191/HbpA and LB194). Two attenuated mutants had transposon insertions in either la0589 or la2786 (encoding proteins of unknown function). The final attenuated mutant had an unexpected deletion of genes la0969 – la0975 at the point of transposon insertion. This is the first description of defined, colonization-deficient mutants in a carrier host for Leptospira . These mutants were either not attenuated or only weakly attenuated in the hamster model of acute leptospirosis, thus illustrating that different factors that may be required in the carrier and acute models of leptospiral infection. High-throughput screening can reduce the number of animals used in virulence studies and increase the capacity to screen mutants for attenuation, thereby enhancing the likelihood of detecting unique virulence factors. A comparison of virulence factors required in the carrier and acute models of infection will help to unravel colonization and dissemination mechanisms of leptospirosis.
Publisher: American Society for Microbiology
Date: 08-2013
DOI: 10.1128/IAI.00531-13
Abstract: Leptospirosis is a worldwide zoonosis caused by pathogenic Leptospira spp., but knowledge of leptospiral pathogenesis remains limited. However, the development of mutagenesis systems has allowed the investigation of putative virulence factors and their involvement in leptospirosis. LipL41 is the third most abundant lipoprotein found in the outer membranes of pathogenic leptospires and has been considered a putative virulence factor. LipL41 is encoded on the large chromosome 28 bp upstream of a small open reading frame encoding a hypothetical protein of unknown function. This gene was named lep , for L ipL41 e xpression p artner. In this study, lipL41 was found to be cotranscribed with lep . Two transposon mutants were characterized: a lipL41 mutant and a lep mutant. In the lep mutant, LipL41 protein levels were reduced by approximately 90%. Lep was shown through cross-linking and coexpression experiments to bind to LipL41. Lep is proposed to be a molecular chaperone essential for the stable expression of LipL41. The roles of LipL41 and Lep in the pathogenesis of Leptospira interrogans were investigated surprisingly, neither of these two unique proteins was essential for acute leptospirosis.
Publisher: Elsevier BV
Date: 09-2016
Publisher: American Chemical Society (ACS)
Date: 16-08-2021
Publisher: Cold Spring Harbor Laboratory
Date: 09-06-2020
DOI: 10.1101/2020.06.07.139238
Abstract: Microalgae can tolerate a wide range of environmental conditions and have been exploited for their lipid and carbohydrate accumulating properties. The utility of this process could be further enhanced through understanding the critical gene regulatory networks that govern the acclimatization process. Advancements in systems biology and sequencing tools now enable us to obtain a genome-wide overview of gene expression under particular conditions of interest. Under salinity stress, Microchloropsis gaditana CCMP526, a commercially important alga has been previously reported to accumulate carbohydrate and lipid. To understand the mechanism of acclimatization, here we report a temporal transcriptomic analysis of M. gaditana under two different salinity levels (55 and 100 PSU). The short term (0, 1 and 6 h) and long term (24 and 72 h) responses of the salt-induced transcript pool were used to identify salinity-inducible genes using correspondence analysis. The transcript abundance of genes involved in triacylglycerol biosynthesis, membrane lipid modification, carbon assimilation and shunting, and osmolyte biosynthesis indicated that M. gaditana employs a two-stage acclimatization strategy during hypersaline conditions.
Publisher: Informa UK Limited
Date: 1988
DOI: 10.1080/03079458808436477
Abstract: DNA from 10 Mycoplasma gallisepticum strains and one strain each of M. synoviae and M. gallinarum were studied by restriction endo-nuclease DNA analysis using endonucleases Eco RI, HindIII, BglII, BamHI, KpnI, and XhoI. Digestion patterns of DNA in agarose gels allowed easy differentiation of M. gallisepticum strains from different sources, while patterns obtained from one strain at the 6th and 100th in vitro passage levels were identical. The F strain and a field derivative obtained from a poultry farm where F strain vaccine had been previously used had almost identical patterns. This technique should be useful for comparing and differentiating M. gallisepticum strains in epidemiological and other studies. Strain differences were also noted by DNA-DNA hybridisation using a probe containing mycoplasma ribosomal RNA genes.
Publisher: Public Library of Science (PLoS)
Date: 16-09-2016
Publisher: American Society for Microbiology
Date: 12-2010
DOI: 10.1128/JB.00972-10
Abstract: We report the resequencing and revised annotation of the Mycobacterium avium subsp. paratuberculosis K10 genome. A total of 90 single-nucleotide errors and a 51-bp indel in the original K10 genome were corrected, and the whole genome annotation was revised. Correction of these sequencing errors resulted in 28 frameshift alterations. The amended genome sequence is accessible via the supplemental section of study SRR060191 in the NCBI Sequence Read Archive and will serve as a valuable reference genome for future studies.
Publisher: American Society for Microbiology
Date: 05-2002
DOI: 10.1128/IAI.70.5.2311-2318.2002
Abstract: Recombinant leptospiral outer membrane proteins (OMPs) can elicit immunity to leptospirosis in a hamster infection model. Previously characterized OMPs appear highly conserved, and thus their potential to stimulate heterologous immunity is of critical importance. In this study we undertook a global analysis of leptospiral OMPs, which were obtained by Triton X-114 extraction and phase partitioning. Outer membrane fractions were isolated from Leptospira interrogans serovar Lai grown at 20, 30, and 37°C with or without 10% fetal calf serum and, finally, in iron-depleted medium. The OMPs were separated by two-dimensional gel electrophoresis. Gel patterns from each of the five conditions were compared via image analysis, and 37 gel-purified proteins were tryptically digested and characterized by mass spectrometry (MS). Matrix-assisted laser desorption ionization-time-of-flight MS was used to rapidly identify leptospiral OMPs present in sequence databases. Proteins identified by this approach included the outer membrane lipoproteins LipL32, LipL36, LipL41, and LipL48. No known proteins from any cellular location other than the outer membrane were identified. Tandem electrospray MS was used to obtain peptide sequence information from eight novel proteins designated pL18, pL21, pL22, pL24, pL45, pL47/49, pL50, and pL55. The expression of LipL36 and pL50 was not apparent at temperatures above 30°C or under iron-depleted conditions. The expression of pL24 was also downregulated after iron depletion. The leptospiral major OMP LipL32 was observed to undergo substantial cleavage under all conditions except iron depletion. Additionally, significant downregulation of these mass forms was observed under iron limitation at 30°C, but not at 30°C alone, suggesting that LipL32 processing is dependent on iron-regulated extracellular proteases. However, separate cleavage products responded differently to changes in growth temperature and medium constituents, indicating that more than one process may be involved in LipL32 processing. Furthermore, under iron-depleted conditions there was no concomitant increase in the levels of the intact form of LipL32. The temperature- and iron-regulated expression of LipL36 and the iron-dependent cleavage of LipL32 were confirmed by immunoblotting with specific antisera. Global analysis of the cellular location and expression of leptospiral proteins will be useful in the annotation of genomic sequence data and in providing insight into the biology of Leptospira .
Publisher: Public Library of Science (PLoS)
Date: 08-12-2009
Publisher: Public Library of Science (PLoS)
Date: 18-02-2016
Publisher: Mary Ann Liebert Inc
Date: 11-2017
Abstract: Proteomics is a crucial postgenomic biotechnology for functional and systems scale analyses in cell and integrative biology, not to mention clinical and precision medicine research. However, a fundamental requirement for an accurate examination of the protein complement of cells is an efficient method for extracting the proteins. This study reports on the evaluation of three protein extraction methods: trichloroacetic acid (TCA)-acetone, phenol, and TRIzol, in the eustigmatophyte alga Microchloropsis gaditana CCMP526 for proteomic analysis. M. gaditana is a potential candidate for algal-based biofuels. This industrially important strain is also rich in dietary oil and pigments and is used as feed in the aquaculture industry. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analysis was performed for proteins obtained using the three extraction methods and their effects were examined by the abundance ratio. Protein yield was higher using the TCA-acetone and phenol methods than with the TRIzol method. The TCA method was superior than other methods examined here in terms of protein coverage and abundance. Subcellular localization of the identified proteins revealed no significant difference among the extraction methods. Importantly, each method revealed a unique set of proteins. To the best of our knowledge, this is the first report on evaluation of protein extraction methods for the proteomic analysis of M. gaditana CCMP526. These observations underscore the importance of using multiple protein extraction methods for comprehensive proteome coverage, as the field of proteomics edges toward erse applications in biofuels, aquaculture industry, marine biology, and agriculture.
Publisher: Elsevier BV
Date: 04-2018
DOI: 10.1016/J.BIORTECH.2018.01.062
Abstract: Evaporation from culture ponds and raceways can subject algae to hypersalinity stress, and this is exacerbated by global warming. We investigated the effect of salinity on a marine microalga, Microchloropsis gaditana, which is of industrial significance because of its high lipid-accumulating capability. Both short-term (hours) and medium-term (days) effects of salinity were studied across various salinities (37.5, 55, 70 and 100 PSU). Salinity above 55 PSU suppressed cell growth and specific growth rate was significantly reduced at 100 PSU. Photosynthesis (F
Publisher: Hindawi Limited
Date: 30-08-2019
DOI: 10.1111/TBED.13322
Abstract: The genus Capripoxvirus in the subfamily Chordopoxvirinae, family Poxviridae, comprises sheeppox virus (SPPV), goatpox virus (GTPV) and lumpy skin disease virus (LSDV), which cause the eponymous diseases across parts of Africa, the Middle East and Asia. These diseases cause significant economic losses and can have a devastating impact on the livelihoods and food security of small farm holders. So far, only live classically attenuated SPPV, GTPV and LSDV vaccines are commercially available and the history, safety and efficacy of many have not been well established. Here, we report 13 new capripoxvirus genome sequences, including the hairpin telomeres, from both pathogenic field isolates and vaccine strains. We have also updated the genome annotations to incorporate recent advances in our understanding of poxvirus biology. These new genomes and genes grouped phenetically with other previously sequenced capripoxvirus strains, and these new alignments collectively identified several recurring alterations in genes thought to modulate virulence and host range. In particular, some of the many large capripoxvirus ankyrin and kelch-like proteins are commonly mutated in vaccine strains, while the variola virus B22R-like gene homolog has also been disrupted in many vaccine isolates. Among these vaccine isolates, frameshift mutations are especially common and clearly present a risk of reversion to wild type in vaccines bearing these mutations. A consistent pattern of gene inactivation from LSDV to GTPV and then SPPV is also observed, much like the pattern of gene loss in orthopoxviruses, but, rather surprisingly, the overall genome size of ~150 kbp remains relatively constant. These data provide new insights into the evolution of capripoxviruses and the determinants of pathogenicity and host range. They will find application in the development of new vaccines with better safety, efficacy and trade profiles.
Publisher: American Society for Microbiology
Date: 08-2013
DOI: 10.1128/AEM.01097-13
Abstract: High concentrations of free metal ions in the environment can be detrimental to bacterial survival. However, bacteria utilize strategies, including the activation of stress response pathways and immobilizing chemical elements on their surface, to limit this toxicity. In this study, we characterized LA4131, the HtpX-like M48 metalloprotease from Leptospira interrogans , with a putative role in bacterial stress response and membrane homeostasis. Growth of the la4131 transposon mutant strain (L522) in 360 μM FeSO 4 (10-fold the normal in vitro concentration) resulted in the production of an amorphous iron precipitate. Atomic force microscopy and transmission electron microscopy analysis of the strain demonstrated that precipitate production was associated with the generation and release of outer membrane vesicles (OMVs) from the leptospiral surface. Transcriptional studies indicated that inactivation of la4131 resulted in altered expression of a subset of metal toxicity and stress response genes. Combining these findings, this report describes OMV production in response to environmental stressors and associates OMV production with the in vitro activity of an HtpX-like metalloprotease.
Publisher: American Society for Microbiology
Date: 11-2015
DOI: 10.1128/AAC.01643-15
Abstract: Bacitracins are mixtures of structurally related cyclic polypeptides with antibiotic properties. They act by interfering with the biosynthesis of the bacterial cell wall. In this study, we analyzed an avian necrotic enteritis strain of Clostridium perfringens that was resistant to bacitracin and produced NetB toxin. We identified a bacitracin resistance locus that resembled a bacitracin resistance determinant from Enterococcus faecalis . It contained the structural genes bcrABD and a putative regulatory gene, bcrR . Mutagenesis studies provided evidence that both bcrA and bcrB are essential for bacitracin resistance, and that evidence was supported by the results of experiments in which the introduction of both the bcrA and bcrB genes into a bacitracin-susceptible C. perfringens strain was required to confer bacitracin resistance. The wild-type strain was shown to contain at least three large, putatively conjugative plasmids, and the bcrRABD locus was localized to an 89.7-kb plasmid, pJIR4150. This plasmid was experimentally shown to be conjugative and was sequenced. The sequence revealed that it also carries a tpeL toxin gene and is related to the pCW3 family of conjugative antibiotic resistance and toxin plasmids from C. perfringens . The bcr genes were located on a genetic element, ICE Cp1 , which is related to the Tn 916 family of integrative conjugative elements (ICEs). ICE Cp1 appears to be the first Tn 916 -like element shown to confer bacitracin resistance. In summary, we identified in a toxin-producing C. perfringens strain a novel mobile bacitracin resistance element which was experimentally shown to be essential for bacitracin resistance and is carried by a putative ICE located on a conjugative plasmid.
Publisher: American Society for Microbiology
Date: 07-2006
DOI: 10.1128/JB.00298-06
Abstract: Clostridium perfringens causes fatal human infections, such as gas gangrene, as well as gastrointestinal diseases in both humans and animals. Detailed molecular analysis of the tetracycline resistance plasmid pCW3 from C. perfringens has shown that it represents the prototype of a unique family of conjugative antibiotic resistance and virulence plasmids. We have identified the pCW3 replication region by deletion and transposon mutagenesis and showed that the essential rep gene encoded a basic protein with no similarity to any known plasmid replication proteins. An 11-gene conjugation locus containing 5 genes that encoded putative proteins with similarity to proteins from the conjugative transposon Tn 916 was identified, although the genes’ genetic arrangements were different. Functional genetic studies demonstrated that two of the genes in this transfer clostridial plasmid ( tcp ) locus, tcpF and tcpH , were essential for the conjugative transfer of pCW3, and comparative analysis confirmed that the tcp locus was not confined to pCW3. The conjugation region was present on all known conjugative plasmids from C. perfringens , including an enterotoxin plasmid and other toxin plasmids. These results have significant implications for plasmid evolution, as they provide evidence that a nonreplicating Tn 916 -like element can evolve to become the conjugation locus of replicating plasmids that carry major virulence genes or antibiotic resistance determinants.
Publisher: Elsevier BV
Date: 2001
Publisher: Wiley
Date: 07-2001
Publisher: Springer Science and Business Media LLC
Date: 26-02-2020
DOI: 10.1186/S13099-020-00351-Y
Abstract: The human gut microbiome has an important role in health and disease. There is extensive geographical variation in the composition of the gut microbiome, however, little is known about the gut microbiome composition of people from the Arabian Peninsula. In this study, we describe the gut microbiome of Arab Kuwaitis. The gut microbiome of 25 native adult Arab Kuwaitis was characterised using 16S rRNA gene sequencing of the V3–V4 regions. Sequencing data were analysed using DADA2. Phylogeny analysis was performed using licon sequence variants (ASVs) assigned to the Bacteroides genus and 16S rRNA sequences of Bacteroides type strains to understand the relationships among Bacteroides ASVs. About 63% of participants were overweight/obese reflecting normal Kuwaiti population. Firmicutes and Bacteroidetes were the dominant phyla detected in the gut microbiome (representing 48% and 46% of total sequencing reads respectively). At the genus level, Bacteroides was the most abundant genus in 22 of 25 participants. A total of 223 ASVs were assigned to the Bacteroides genus, eleven of which were present in 50% or more of study participants, reflecting a high ersity of this genus. Phylogenetic analysis revealed that the Bacteroides dorei/vulgatus group was the most abundant phylogenetic group (representing 11.91% of all sequence reads) and was detected in all 25 in iduals. Bacteroides was the most abundant genus in the gut microbiome of native Arab Kuwaiti adults, with Bacteroides dorei/vulgatus forming the predominant phylogenetic group. The microbiome composition would also have been influenced by the nutritional status of participants.
Publisher: Elsevier BV
Date: 04-2012
DOI: 10.1016/J.VIROL.2012.01.004
Abstract: Kotonkan virus (KOTV) and Obodhiang virus (OBOV) are rhabdoviruses that were isolated from arthropods in Africa and formerly classified as lyssaviruses. KOTV causes clinical bovine ephemeral fever in cattle the ecology and pathogenicity of OBOV is poorly understood. In this paper, we report the complete genome sequences of KOTV and OBOV, their gene expression profiles, and their serological and phylogenetic relationships to other rhabdoviruses. The 15,870 nt KOTV genome (3'-l-N-P-M-G-G(NS)-α1-α2-β-γ-δ-L-t-5') is similar to that of bovine ephemeral fever virus but encodes an additional protein (δ) that shares homology with the pleckstrin homology domain of coactivator-associated arginine methyltransferase. The 14,717 nt OBOV genome (3'-l-N-P-M-G-G(NS)-α1-α2-β-L-t-5') is similar to that of Adelaide River virus from which it is distinguishable serologically. In each virus, all ORFs, except α1 and α2, are transcribed as monocistronic mRNA. Genetic and serological data indicate that KOTV and OBOV should be classified as new species in the genus Ephemerovirus.
Publisher: Public Library of Science (PLoS)
Date: 20-04-2012
Publisher: American Society for Microbiology
Date: 26-10-2021
Abstract: Recurrence of BV following standard treatment is unacceptably high. Posttreatment recurrence is distressing for women, and it imposes a considerable burden on the health care system.
Publisher: Elsevier BV
Date: 2011
Publisher: Elsevier BV
Date: 05-1997
Abstract: The icillin resistance gene from Shigella flexneri 2a strain YSH6000 was cloned and shown by Southern hybridization analysis to be closely linked to the previously cloned streptomycin, chlor henicol, and tetracycline resistance determinants, which are borne on a chromosomally integrated 99-kb element. Analysis of this chromosomal multi-antibiotic resistance locus revealed that it had a high level of sequence and organizational similarity to an equivalent region of the Shigella R-plasmid, NR1. However, the chromosomal locus exhibited several differences, including the presence of two stretches of sequence derived from IS elements, the precise insertion of a beta-lactamase encoding oxal cassette into the Tn21-borne integron In2, a possible 17.5-kb deletion, and the loss or inactivation of the mercury resistance determinant. Based on these data, it is proposed that the chromosomal locus arose following integration of an NR1-like plasmid.
Publisher: American Society for Microbiology
Date: 11-2014
DOI: 10.1128/JCM.01775-14
Abstract: H 2 S-producing multiresistant Salmonella enterica serovar Kentucky strain sequence type (ST) 198 and its non-H 2 S-producing variant were isolated from a patient. Whole-genome comparison showed a base addition in the gene encoding molybdenum cofactor biosynthesis protein C, which could affect H 2 S production in the variant. Lack of H 2 S production has implications for diagnosis of salmonella.
Publisher: Frontiers Media SA
Date: 06-10-2017
Publisher: American Society for Microbiology
Date: 06-2006
DOI: 10.1128/IAI.02000-05
Abstract: The enteric, anaerobic spirochete Brachyspira hyodysenteriae is the causative agent of swine dysentery, a severe mucohemorrhagic diarrheal disease of pigs that has economic significance in every major pork-producing country. Recent investigation into potential vaccine candidates has focused on the outer membrane proteins of B. hyodysenteriae . Bhmp39 (formerly Vsp39) is the most abundant surface-exposed outer membrane protein of B. hyodysenteriae its predicted gene sequence has previously been shown to share sequence similarity to eight genes ided evenly between two paralogous loci. The peptide sequence suggested that Bhmp39 is encoded by one of these genes, bhmp39h . The biological significance of maintaining eight homologous bhmp39 genes is unclear, though it has been proposed that this may play a role in antigenic variation. In this study, real-time, reverse transcription-PCR was used to demonstrate that bhmp39f and bhmp39h were the transcripts most abundantly expressed by B. hyodysenteriae strain B204 cultured under in vitro growth conditions. Mass spectrometry data of the purified 39-kDa membrane protein showed that both Bhmp39f and Bhmp39h were present. Northern blot analysis across predicted Rho-independent terminators demonstrated that the genes of the bhmp39efgh locus result in monocistronic transcripts.
Publisher: American Society for Microbiology
Date: 07-2018
DOI: 10.1128/AAC.02442-17
Abstract: Colistin is a crucial last-line drug used for the treatment of life-threatening infections caused by multidrug-resistant strains of the Gram-negative bacterium Acinetobacter baumannii . However, colistin-resistant A. baumannii isolates can still be isolated following failed colistin therapy. Resistance is most often mediated by the addition of phosphoethanolamine (pEtN) to lipid A by PmrC, following missense mutations in the pmrCAB operon encoding PmrC and the two-component signal transduction system PmrA/PmrB. We recovered a pair of A. baumannii isolates from a single patient before (6009-1) and after (6009-2) failed colistin treatment. These strains displayed low and very high levels of colistin resistance (MICs, 8 to 16 μg/ml and 128 μg/ml), respectively. To understand how increased colistin resistance arose, we sequenced the genome of each isolate, which revealed that 6009-2 had an extra copy of the insertion sequence element IS Aba125 within a gene encoding an H-NS family transcriptional regulator. To confirm the role of H-NS in colistin resistance, we generated an hns deletion mutant in 6009-1 and showed that colistin resistance increased upon the deletion of hns . We also provided 6009-2 with an intact copy of hns and showed that the strain was no longer resistant to high concentrations of colistin. Transcriptomic analysis of the clinical isolates identified more than 150 genes as being differentially expressed in the colistin-resistant hns mutant 6009-2. Importantly, the expression of eptA , encoding a second lipid A-specific pEtN transferase but not pmrC , was increased in the hns mutant. This is the first time an H-NS family transcriptional regulator has been associated with a pEtN transferase and colistin resistance.
Publisher: Public Library of Science (PLoS)
Date: 11-12-3202
Publisher: American Society for Microbiology
Date: 06-2007
DOI: 10.1128/IAI.01619-06
Abstract: Transmission of pathogenic Leptospira between mammalian hosts usually involves dissemination via soil or water contaminated by the urine of carrier animals. The ability of Leptospira to adapt to the erse conditions found inside and outside the host is reflected in its relatively large genome size and high percentage of signal transduction genes. An exception is Leptospira borgpetersenii serovar Hardjo, which is transmitted by direct contact and appears to have lost genes necessary for survival outside the mammalian host. Invasion of host tissues by Leptospira interrogans involves a transition from a low osmolar environment outside the host to a higher physiologic osmolar environment within the host. Expression of the lipoprotein LigA and LigB adhesins is strongly induced by an upshift in osmolarity to the level found in mammalian host tissues. These data suggest that Leptospira utilizes changes in osmolarity to regulate virulence characteristics. To better understand how L. interrogans serovar Copenhageni adapts to osmolar conditions that correspond with invasion of a mammalian host, we quantified alterations in transcript levels using whole-genome microarrays. Overnight exposure in leptospiral culture medium supplemented with sodium chloride to physiologic osmolarity significantly altered the transcript levels of 6% of L. interrogans genes. Repressed genes were significantly more likely to be absent or pseudogenes in L. borgpetersenii , suggesting that osmolarity is relevant in studying the adaptation of L. interrogans to host conditions. Genes induced by physiologic osmolarity encoded a higher than expected number of proteins involved in signal transduction. Further, genes predicted to encode lipoproteins and those coregulated by temperature were overrepresented among both salt-induced and salt-repressed genes. In contrast, leptospiral homologues of hyperosmotic or general stress genes were not induced at physiologic osmolarity. These findings suggest that physiologic osmolarity is an important signal for regulation of gene expression by pathogenic leptospires during transition from ambient conditions to the host tissue environment.
Publisher: Public Library of Science (PLoS)
Date: 22-07-2011
Publisher: Springer Science and Business Media LLC
Date: 05-08-2020
DOI: 10.1007/S00248-019-01419-2
Abstract: Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 s les in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment s les, respectively. The combined detection increased from 15% in winter to 32% in summer (p < 0.05) indicating seasonal variation as potential part of public health risk assessments. Further, pathogenic potential of the Salmonella isolates was characterised via the quantification of attachment and invasion capacity using human epithelial colorectal cell line Caco-2 on a subset of isolates (n = 62). While all of these isolates could attach and invade Caco-2 cells, 52% and 13% of these showed greater attachment and invasiveness, respectively, than the corresponding mean values for S. Typhimurium ATCC14028 control. Isolates from winter were on average more invasive (seven out of eight isolates with the highest invasiveness recovered from the colder s ling period) than the isolates from summer, and Salmonella collected during summer showed lower invasion (p < 0.05) compared with the control. Similar low invasion compared with the same control was observed for isolates recovered from bank sediment (p < 0.05). While the higher prevalence in summer may imply higher risks during these peak recreational periods, it is essential that this information is used in combination with quantitative microbial risk assessments to fully understand the health risks posed by Salmonella in microtidal estuaries.
Publisher: Springer International Publishing
Date: 2015
Publisher: American Society for Microbiology
Date: 10-2006
DOI: 10.1128/IAI.00755-06
Abstract: Leptospirosis is an important zoonosis of worldwide distribution. Humans become infected via exposure to pathogenic Leptospira spp. from infected animals or contaminated water or soil. The availability of genome sequences for Leptospira interrogans , serovars Lai and Copenhageni, has opened up opportunities to examine global transcription profiles using microarray technology. Temperature is a key environmental factor known to affect leptospiral protein expression. Leptospira spp. can grow in artificial media at a range of temperatures reflecting conditions found in the environment and the mammalian host. Therefore, transcriptional changes were compared between cultures grown at 20°C, 30°C, 37°C, and 39°C to represent ambient temperatures in the environment, growth under laboratory conditions, and temperatures in healthy and febrile hosts. Data from direct pairwise comparisons of the four temperatures were consolidated to examine transcriptional changes at two generalized biological conditions representing mammalian physiological temperatures (37°C and 39°C) versus environmental temperatures (20°C and 30°C). Additionally, cultures grown at 30°C then shifted overnight to 37°C were compared with those grown long-term at 30°C and 37°C to identify genes potentially expressed in the early stages of infection. Comparison of data sets from physiological versus environmental experiments with upshift experiments provided novel insights into possible transcriptional changes at different stages of infection. Changes included differential expression of chemotaxis and motility genes, signal transduction systems, and genes encoding proteins involved in alteration of the outer membrane. These findings indicate that temperature is an important factor regulating expression of proteins that facilitate invasion and establishment of disease.
Publisher: Elsevier BV
Date: 12-2020
Publisher: Springer Science and Business Media LLC
Date: 30-06-2022
DOI: 10.1186/S12879-022-07553-6
Abstract: We aimed to identify risk factors for sporadic c ylobacteriosis in Australia, and to compare these for C ylobacter jejuni and C ylobacter coli infections. In a multi-jurisdictional case–control study, we recruited culture-confirmed cases of c ylobacteriosis reported to state and territory health departments from February 2018 through October 2019. We recruited controls from notified influenza cases in the previous 12 months that were frequency matched to cases by age group, sex, and location. C ylobacter isolates were confirmed to species level by public health laboratories using molecular methods. We conducted backward stepwise multivariable logistic regression to identify significant risk factors. We recruited 571 cases of c ylobacteriosis (422 C. jejuni and 84 C. coli ) and 586 controls. Important risk factors for c ylobacteriosis included eating undercooked chicken (adjusted odds ratio [aOR] 70, 95% CI 13–1296) or cooked chicken (aOR 1.7, 95% CI 1.1–2.8), owning a pet dog aged 6 months (aOR 6.4, 95% CI 3.4–12), and the regular use of proton-pump inhibitors in the 4 weeks prior to illness (aOR 2.8, 95% CI 1.9–4.3). Risk factors remained similar when analysed specifically for C. jejuni infection . Unique risks for C. coli infection included eating chicken pâté (aOR 6.1, 95% CI 1.5–25) and delicatessen meats (aOR 1.8, 95% CI 1.0–3.3). Eating any chicken carried a high population attributable fraction for c ylobacteriosis of 42% (95% CI 13–68), while the attributable fraction for proton-pump inhibitors was 13% (95% CI 8.3–18) and owning a pet dog aged 6 months was 9.6% (95% CI 6.5–13). The population attributable fractions for these variables were similar when analysed by c ylobacter species. Eating delicatessen meats was attributed to 31% (95% CI 0.0–54) of cases for C. coli and eating chicken pâté was attributed to 6.0% (95% CI 0.0–11). The main risk factor for c ylobacteriosis in Australia is consumption of chicken meat. However, contact with young pet dogs may also be an important source of infection. Proton-pump inhibitors are likely to increase vulnerability to infection.
Publisher: Oxford University Press (OUP)
Date: 04-09-2018
DOI: 10.1093/JAC/DKY331
Abstract: Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Australia, there has been a recent concerning increase in bacteraemia associated with the vanA genotype, prompting investigation into the genomic epidemiology of VREfm. A population-level study of VREfm (10 November-9 December 2015) was conducted. A total of 321 VREfm isolates (from 286 patients) across Victoria State were collected and sequenced with Illumina NextSeq. SNPs were used to assess relatedness. STs and genes associated with resistance and virulence were identified. The vanA-harbouring plasmid from an isolate from each ST was assembled using long-read data. Illumina reads from remaining isolates were then mapped to these assemblies to identify their probable vanA-harbouring plasmid. vanA-VREfm comprised 17.8% of isolates. ST203, ST80 and a pstS(-) clade, ST1421, predominated (30.5%, 30.5% and 37.2%, respectively). Most vanB-VREfm were ST796 (77.7%). vanA-VREfm were more closely related within hospitals versus between them [core SNPs 10 (IQR 1-357) versus 356 (179-416), respectively], suggesting discrete introductions of vanA-VREfm, with subsequent intra-hospital transmission. In contrast, vanB-VREfm had similar core SNP distributions within versus between hospitals, due to widespread dissemination of ST796. Different vanA-harbouring plasmids were found across STs. With the exception of ST78 and ST796, Tn1546 transposons also varied. Phylogenetic analysis revealed Australian strains were often interspersed with those from other countries, suggesting ongoing cross-continental transmission. Emerging vanA-VREfm in Australia is polyclonal, indicating repeat introductions of vanA-VREfm into hospitals and subsequent dissemination. The close relationship to global strains reinforces the need for ongoing screening and control of VREfm in Australia and abroad.
Publisher: Oxford University Press (OUP)
Date: 24-06-2010
DOI: 10.1111/J.1574-6968.2010.02029.X
Abstract: A lipopolysaccharide mutant of Leptospira interrogans (LaiMut) was obtained by growth in the presence of an agglutinating monoclonal antibody (mAb) against lipopolysaccharide. Agglutination reactions with anti-lipopolysaccharide mAbs and polyclonal antibodies showed that LaiMut had lost some serogroup Icterohaemorrhagiae agglutinating epitopes. However, LaiMut displayed an increased reactivity to antisera against related serogroups, suggesting that the disruption of some lipopolysaccharide epitopes resulted in greater exposure to cross-reactive epitopes, not accessible to antibodies in the wild type (LaiWT). Comparison of the nucleotide sequences of the lipopolysaccharide loci of LaiMut and Lai wild type (LaiWT) strains showed an inframe stop mutation in the gene encoding undecaprenyl-galactosyltransferase, a protein that provides a fundamental and nonredundant function essential for lipopolysaccharide biosynthesis. Despite this, the biosynthesis of lipopolysaccharide agglutinating antigens was not abolished by the mutation. Based on the phenotype of LaiMut and analysis of the domain structure of the undecaprenyl-galactosyltransferase in relation to the mutation, we propose that the mutation results in the expression of two functional proteins in place of the undecaprenyl-galactosyltransferase. We hypothesize that the loss of coordination of the coupled function afforded by the intact dual function protein present in the parent strain results in an inefficient production of lipopolysaccharide in LaiMut.
Publisher: Springer Science and Business Media LLC
Date: 11-09-2017
Publisher: American Society for Microbiology
Date: 05-2003
DOI: 10.1128/IAI.71.5.2414-2421.2003
Abstract: Leptospira is the etiologic agent of leptospirosis, a bacterial zoonosis distributed worldwide. Leptospiral lipopolysaccharide is a protective immunogen, but the extensive serological ersity of leptospires has inspired a search for conserved outer membrane proteins (OMPs) that may stimulate heterologous immunity. Previously, a global analysis of leptospiral OMPs (P. A. Cullen, S. J. Cordwell, D. M. Bulach, D. A. Haake, and B. Adler, Infect. Immun. 70: 2311-2318, 2002) identified pL21, a novel 21-kDa protein that is the second most abundant constituent of the Leptospira interrogans serovar Lai outer membrane proteome. In this study, we identified the gene encoding pL21 and found it to encode a putative lipoprotein accordingly, the protein was renamed LipL21. Southern hybridization analysis revealed the presence of lipL21 in all of the pathogenic species but in none of the saprophytic species examined. Alignment of the LipL21 sequence from six strains of Leptospira revealed 96 to 100% identity. When specific polyclonal antisera to recombinant LipL21 were used, LipL21 was isolated together with other known leptospiral OMPs by both Triton X-114 extraction and sucrose density gradient membrane fractionation. All nine strains of pathogenic leptospires investigated by Western blotting, whether culture attenuated or virulent, were found to express LipL21. In contrast, the expression of LipL21 or an antigenically related protein could not be detected in nonpathogenic L. biflexa . Infected hamster sera and two of eight human leptospirosis sera tested were found to react with recombinant LipL21. Native LipL21 was found to incorporate tritiated palmitic acid, consistent with the prediction of a lipoprotein signal peptidase cleavage site. Biotinylation of the leptospiral surface resulted in selective labeling of LipL21 and the previously known OMPs LipL32 and LipL41. These findings show that LipL21 is a surface-exposed, abundant outer membrane lipoprotein that is expressed during infection and conserved among pathogenic Leptospira species.
Publisher: Springer Science and Business Media LLC
Date: 24-12-2019
DOI: 10.1038/S41598-019-56233-0
Abstract: Human microbiomes are predicted to assemble in a reproducible and ordered manner yet there is limited knowledge on the development of the complex bacterial communities that constitute the oral microbiome. The oral microbiome plays major roles in many oral diseases including early childhood caries (ECC), which afflicts up to 70% of children in some countries. Saliva contains oral bacteria that are indicative of the whole oral microbiome and may have the ability to reflect the dysbiosis in supragingival plaque communities that initiates the clinical manifestations of ECC. The aim of this study was to determine the assembly of the oral microbiome during the first four years of life and compare it with the clinical development of ECC. The oral microbiomes of 134 children enrolled in a birth cohort study were determined at six ages between two months and four years-of-age and their mother’s oral microbiome was determined at a single time point. We identified and quantified 356 operational taxonomic units (OTUs) of bacteria in saliva by sequencing the V4 region of the bacterial 16S RNA genes. Bacterial alpha ersity increased from a mean of 31 OTUs in the saliva of infants at 1.9 months-of-age to 84 OTUs at 39 months-of-age. The oral microbiome showed a distinct shift in composition as the children matured. The microbiome data were compared with the clinical development of ECC in the cohort at 39, 48, and 60 months-of-age as determined by ICDAS-II assessment. Streptococcus mutans was the most discriminatory oral bacterial species between health and current disease, with an increased abundance in disease. Overall our study demonstrates an ordered temporal development of the oral microbiome, describes a limited core oral microbiome and indicates that saliva testing of infants may help predict ECC risk.
Publisher: Elsevier BV
Date: 08-1999
Publisher: American Society for Microbiology
Date: 10-2010
DOI: 10.1128/JVI.00930-10
Abstract: Full-genome sequencing of 11 Australian and 1 New Zealand avian influenza A virus isolate (all subtype H7) has enabled comparison of the sequences of each of the genome segments to those of other subtype H7 avian influenza A viruses. The inference of phylogenetic relationships for each segment has been used to develop a model of the natural history of these viruses in Australia. Phylogenetic analysis of the hemagglutinin segment indicates that the Australian H7 isolates form a monophyletic clade. This pattern is consistent with the long-term, independent evolution that is, in this instance, associated with geographic regions. On the basis of the analysis of the other H7 hemagglutinin sequences, three other geographic regions for which similar monophyletic clades have been observed were confirmed. These regions are Eurasia plus Africa, North America, and South America. Analysis of the neuraminidase sequences from the H7N1, H7N3, and H7N7 genomes revealed the same region-based relationships. This pattern of independent evolution of Australian isolates is supported by the results of analysis of each of the six remaining genomic segments. These results, in conjunction with the occurrence of five different combinations of neuraminidase subtypes (H7N2, H7N3, H7N4, H7N6, H7N7) among the 11 Australian isolates, suggest that the maintenance host(s) is nearly exclusively associated with Australia. The single lineage of Australian H7 hemagglutinin sequences, despite the occurrence of multiple neuraminidase types, suggests the existence of a genetic pool from which a variety of reassortants arise rather than the presence of a small number of stable viral clones. This pattern of evolution is likely to occur in each of the regions mentioned above.
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.PLASMID.2018.04.001
Abstract: Clostridioides (Clostridium) difficile is a major bacterial pathogen of both humans and animals. Several species of pathogenic clostridia are known to harbour large plasmids with combinations of virulence, antibiotic resistance and metabolism determinants. Small cryptic plasmids have been previously identified in C. difficile, but there is a lack of recent work examining the prevalence and heterogeneity of plasmids in this erse bacterial species. A survey of clinical and historical isolates of C. difficile showed that several strains carry large plasmids. Following whole-genome sequencing of these erse strains, 42-47 kb plasmids with high nucleotide identity were found to be carried in 4.9% (n = 451) of isolates, with no firm connection to the strain backgrounds. These plasmids appear to have arisen as a result of recombination with a bacteriophage, but contain key plasmid features, such as a putative plasmid replication and partitioning locus. As no virulence factors or antibiotic resistance determinants were identified, further work is required to identify the selective advantage that must exist for the host isolates to maintain these large plasmids.
Publisher: Elsevier BV
Date: 05-1997
DOI: 10.1016/S0168-1702(97)01454-8
Abstract: Nucleotide sequence analysis of the Helicoverpa zea S-type nucleopolyhedrovirus (HzSNPV) genomic interval between the polh and iel genes has revealed an open reading frame (HOAR ORF) that contains a complex A 1-T rich triplet repeat region (RAT-repeats). HOAR ORF is predicted to encode an acidic, arginine residue rich. 712 aa protein, with a C3HC4 (RING-finger) zinc binding motif. RAT-repeats, distributed over 450 bp. consist of GAT. AAT, and GTT codons, correspond to Asp, Asn and Val residues which display an extreme codon bias not seen with nine other genes of this virus. A survey of four other (field) isolates of Helicoverpa sp. NPVs confirms a high incidence of mutation in the RAT-repeat region. A 158-bp conserved block, homologous to the pe38-ien promoter of AcMNPV, was identified upstream of HOAR ORF. The sub-region of the genome in which HOAR ORF is located is susceptible to rearrangement.
Publisher: Wiley
Date: 14-07-2021
Abstract: Corals are colonized by symbiotic microorganisms that profoundly influence the animal’s health. One noted symbiont is a single‐celled alga (in the dinoflagellate family Symbiodiniaceae ), which provides the coral with most of its fixed carbon. Thermal stress increases the production of reactive oxygen species (ROS) by Symbiodiniaceae during photosynthesis. ROS can both damage the algal symbiont’s photosynthetic machinery and inhibit its repair, causing a positive feedback loop for the toxic accumulation of ROS. If not scavenged by the antioxidant network, excess ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating in a process known as bleaching. We use Exaiptasia diaphana as a model for corals and constructed a consortium comprised of E. diaphana –associated bacteria capable of neutralizing ROS. We identified six strains with high free radical scavenging (FRS) ability belonging to the families Alteromonadaceae , Rhodobacteraceae , Flavobacteriaceae and Micrococcaceae . In parallel, we established a consortium of low FRS isolates consisting of genetically related strains. Bacterial whole genome sequences were used to identify key pathways that are known to influence ROS.
Publisher: Springer Science and Business Media LLC
Date: 29-04-2020
DOI: 10.1186/S13567-020-00781-1
Abstract: Bovine ephemeral fever is a vector-borne disease of ruminants that occurs in tropical and sub-tropical regions of Africa, Asia and Australia. The disease is caused by a rhabdovirus, bovine ephemeral fever virus (BEFV), which occurs as a single serotype globally. Although several other closely related ephemeroviruses have been isolated from cattle and/or arthropods, only kotonkan virus from Nigeria and (tentatively) Mavingoni virus from Mayotte Island in the Indian Ocean have been previously associated with febrile disease. Here, we report the isolation of a novel virus (Hayes Yard virus HYV) from blood collected in February 2000 from a bull ( Bos indicus ) in the Northern Territory of Australia. The animal was suffering from a severe ephemeral fever-like illness with neurological involvement, including recumbency and paralysis, and was euthanised. Histological examination of spinal cord and lung tissue identified extensive haemorrhage in the dura mata with moderate perineuronal oedema and extensive emphysema. HYV displayed cone-shaped morphology, typical of rhabdoviruses, and was found to be most closely related antigenically to Puchong virus (PUCV), isolated in 1965 from mosquitoes in Malaysia. Analysis of complete genome sequences of HYV (15 025 nt) and PUCV (14 932 nt) indicated that each has a complex organisation (3′ N-P-M-G-G NS -α1-α2-β-γ-L 5′) and expression strategy, similar to that of BEFV. Based on an alignment of complete L protein sequences, HYV and PUCV cluster with other rhabdoviruses in the genus Ephemerovirus and appear to represent two new species. Neutralising antibody to HYV was also detected in a retrospective survey of cattle sera collected in the Northern Territory.
Publisher: Elsevier BV
Date: 07-2015
Publisher: Springer Science and Business Media LLC
Date: 24-12-2019
DOI: 10.1038/S41598-019-55929-7
Abstract: Women-who-have-sex-with-women (WSW) are at increased risk of bacterial vaginosis (BV). We investigated the impact of practices and past BV on the vaginal microbiota within a two-year longitudinal cohort of Australian WSW. Self-collected vaginal swabs were used to characterise the vaginal microbiota using 16S-rRNA gene sequencing. Hierarchical clustering defined community state types (CSTs). Bacterial ersity was calculated using the Shannon ersity index and instability of the vaginal microbiota was assessed by change of CST and Bray-Curtis dissimilarity. Sex with a new partner increased the bacterial ersity (adjusted-coefficient = 0.41, 95%CI: 0.21,0.60, p 0.001) and instability of the vaginal microbiota, in terms of both change of CST (adjusted-odds-ratio = 2.65, 95%CI: 1.34,5.22, p = 0.005) and increased Bray-Curtis dissimilarity (adjusted-coefficient = 0.21, 95%CI: 0.11,0.31, p 0.001). Women reporting sex with a new partner were more likely than women reporting no new partner to have a vaginal microbiota characterised by Gardnerella vaginalis (adjusted-relative-risk-ratio[aRRR] = 3.45, 95%CI: 1.42,8.41, p = 0.006) or anaerobic BV-associated bacteria (aRRR = 3.62, 95%CI: 1.43,9.14, p = 0.007) relative to a Lactobacillus crispatus dominated microbiota. Sex with a new partner altered the vaginal microbiota of WSW by increasing the ersity and abundance of BV-associated bacteria. These findings highlight the influence of practices on the development of a non-optimal vaginal microbiota and provide microbiological support for the sexual exchange of bacteria between women.
Publisher: American Society for Microbiology
Date: 11-2012
DOI: 10.1128/JVI.00957-12
Abstract: Koi herpesvirus (KHV) (species Cyprinid herpesvirus 3 ) ORF134 was shown to transcribe a spliced transcript encoding a 179-amino-acid (aa) interleukin-10 (IL-10) homolog (khvIL-10) in koi fin (KF-1) cells. Pairwise sequence alignment indicated that the expressed product shares 25% identity with carp IL-10, 22 to 24% identity with mammalian (including primate) IL-10s, and 19.1% identity with European eel herpesvirus IL-10 (ahvIL-10). In phylogenetic analyses, khvIL-10 fell in a ergent position from all host IL-10 sequences, indicating extensive structural ergence following capture from the host. In KHV-infected fish, khvIL-10 transcripts were observed to be highly expressed during the acute and reactivation phases but to be expressed at very low levels during low-temperature-induced persistence. Similarly, KHV early (helicase [Hel] and DNA polymerase [DNAP]) and late (intercapsomeric triplex protein [ITP] and major capsid protein [MCP]) genes were also expressed at high levels during the acute and reactivation phases, but only low-level expression of the ITP gene was detected during the persistent phase. Injection of khvIL-10 mRNA into zebrafish ( Danio rerio ) embryos increased the number of lysozyme-positive cells to a similar degree as zebrafish IL-10. Downregulation of the IL-10 receptor long chain (IL-10R1) using a specific morpholino abrogated the response to both khvIL-10 and zebrafish IL-10 transcripts, indicating that, despite the structural ergence, khvIL-10 functions via this receptor. This is the first report describing the characteristics of a functional viral IL-10 gene in the Alloherpesviridae .
Publisher: American Society for Microbiology
Date: 02-2009
DOI: 10.1128/IAI.01293-08
Abstract: Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner -based transposon Himar1 to generate the first defined mutants in L. interrogans . In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans . This library provides a valuable resource for the study of gene function in L. interrogans . Combined with the genome sequences of L. interrogans , this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans .
Publisher: Oxford University Press (OUP)
Date: 22-11-2018
DOI: 10.1093/JAC/DKX405
Publisher: SAGE Publications
Date: 2017
Abstract: Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic ersity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.
Publisher: AMPCo
Date: 04-2016
DOI: 10.5694/MJA15.01222
Publisher: American Society for Microbiology
Date: 25-06-2015
Abstract: Leptospira interrogans serovar Bratislava infection occurs in multiple domestic and wildlife species and is associated with poor reproductive performance in swine and horses. We present the complete genome assembly of strain PigK151 comprising two chromosomes, CI (4.457 Mbp) and CII (358 kbp).
Publisher: American Society for Microbiology
Date: 06-2000
DOI: 10.1128/IAI.68.6.3780-3783.2000
Abstract: An unstable chromosomal element encoding multiple antibiotic resistance in Shigella flexneri serotype 2a was found to include sequences homologous to the csg genes encoding curli in Escherichia coli and Salmonella enterica serovar Typhimurium. As curli have been implicated in the virulence of serovar Typhimurium, we investigated the csg loci in all four species of Shigella . DNA sequencing and PCR analysis showed that the csg loci of a wide range of Shigella strains, of erse serotypes and different geographical distributions, were almost universally disrupted by deletions or insertions, indicating the existence of a strong selective pressure against the expression of curli. Strains of enteroinvasive E. coli (EIEC), which share virulence traits with Shigella spp. and cause similar diseases in humans, also possessed insertions or deletions in the csg locus or were otherwise unable to produce curli. Since the production of curli is a widespread trait in environmental isolates of E. coli , our results suggest that genetic lesions that abolish curli production in the closely related genus Shigella and in EIEC are pathoadaptive mutations.
Publisher: Cambridge University Press (CUP)
Date: 10-1998
DOI: 10.1017/S095026889800137X
Abstract: A set of 723 diagnostic sera from human patients, submitted for the microscopic agglutination test (MAT) for antibodies to a group of 6 leptospiral serovars, was also tested by MAT for antibodies to the recently-discovered Leptospira fainei serovar hurstbridge. MAT titres of [ges ]128 to serovar hurstbridge were detected in 13·4% of these sera, and titres of [ges ]512 in 7·2%. In contrast, none of 62 sera obtained from a control population of laboratory staff gave titres of [ges ]128. The difference between the number of titres of [ges ]128 given by the two groups of sera was highly significant ( P ·01). The titres observed may have been due to cross-reactions with other leptospiral serovars, but this could not be demonstrated. An alternative explanation is that serovar hurstbridge is present in the human population.
Publisher: Elsevier BV
Date: 2003
DOI: 10.1016/S0147-619X(02)00150-6
Abstract: Outer membrane lipoproteins are emerging as key targets for protective immunity to many bacterial pathogens. Heterologous expression of lipoproteins in Escherichia coli does not always result in high level expression of acylated recombinant protein. Thus, these proteins do not take up their correct membrane topology and are lacking the immunostimulatory properties endowed by the lipid. To this end, we have designed a lipoprotein expression vector (pDUMP) that results in the production of fusion proteins containing the E. coli major outer membrane lipoprotein (Lpp) signal sequence, lipoprotein signal peptidase recognition site, and the +2 outer membrane sorting signal at their N termini. To test the ability of pDUMP to express lipoproteins from heterologous hosts, the surface lipoprotein PsaA from the Gram-positive organism Streptococcus pneumoniae and the outer membrane lipoproteins MlpA from the Gram-negative Pasteurella multocida and BlpA from the spirochete Brachyspira hyodysenteriae were cloned into both hexahistidine fusion vectors and pDUMP. High level expression of antigenically active protein from both the hexahistidine fusion vectors and pDUMP resulted in abundant bands of the predicted molecular masses when analyzed by SDS-PAGE. When grown in the presence of 3[H]palmitic acid, proteins encoded by pDUMP were observed to incorporate palmitic acid whilst the hexahistidine fusion proteins did not. Using mass spectrometry and image analysis we determined the efficiency of lipidation between the three clones to vary from 31.7 to 100%. In addition, lipidated, but not hexahistidine, forms of the proteins were presented on the E. coli surface.
Publisher: Frontiers Media SA
Date: 26-01-2017
Publisher: Cold Spring Harbor Laboratory
Date: 28-03-2018
DOI: 10.1101/289975
Abstract: Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Australia, the vanB genotype is dominant however there has been a recent increase in the predominantly plasmid-encoded vanA genotype, prompting investigation into the genomic epidemiology of VREfm in this context. A cross-sectional study of VREfm in Victoria, Australia (Nov.10 th - Dec.9 th , 2015). A total of 321 VREfm isolates (from 286 patients) were collected and whole-genome sequenced with Illumina NextSeq. Single nucleotide polymorphisms (SNPs) were used to assess relatedness. Multi-locus sequence types (STs), and genes associated with resistance and virulence were identified. The vanA -harbouring plasmid from an isolate from each ST was assembled using long-read data. vanA -VREfm comprised 17.8% of isolates. ST203, ST80 and a pstS (-) clade, ST1421, predominated (30.5%, 30.5% and 37.2% of vanA -VREfm, respectively). Most vanB- VREfm were ST796 (77.7%). vanA -VREfm isolates were closely-related within hospitals vs. between them (core SNPs 10 [interquartile range 1-357] vs. 356 [179-416] respectively), suggesting discrete introductions of vanA -VREfm, with subsequent intra-hospital transmission. In contrast, vanB -VREfm had similar core SNP distributions within vs. between hospitals, due to widespread dissemination of ST796. Overall, vanA -harbouring plasmids differed across STs, and with exception of ST78 and ST796, Tn 1546 transposons also varied. vanA -VREfm in Victoria is associated with multiple STs, and is not solely mediated by a single shared plasmid/Tn 1546 transposon clonal transmission appears to play an important role, predominantly within, rather than between, hospitals. In contrast, vanB- VREfm appears to be well-established and widespread across Victorian healthcare institutions.
Publisher: Springer Science and Business Media LLC
Date: 13-11-2018
Publisher: Public Library of Science (PLoS)
Date: 16-07-2008
Publisher: Elsevier BV
Date: 04-2011
DOI: 10.1016/J.VETMIC.2010.09.036
Abstract: The Vsp proteins are the major outer membrane proteins of Brachyspira hyodysenteriae, the causative agent of swine dysentery. Eight vsp genes have been identified in B. hyodysenteriae strain B204, arranged into two four-gene loci, and at least two of the corresponding proteins are produced in vitro. The aims of this study were to characterise the vsp genes of the virulent Australian B. hyodysenteriae strain X576 and their corresponding proteins, Genomic sequence comparison with strains B204 and WA1 demonstrated that the number of vsp genes varies between B. hyodysenteriae strains, although the chromosomal locations of the vsp gene loci are consistent. We identified two additional vsp-like genes, designated vspI and vspJ, in each of the three strains. Double SDS-PAGE was used to demonstrate that Vsp proteins of B. hyodysenteriae strain X576 form multimeric protein complexes in the outer membrane that are stable in 6M urea but dissociate after boiling. The Vsp complexes primarily consisted of VspF but also contain VspE and VspI. VspD was also found in a series of complexes slightly larger than the more abundant VspF complexes. Vsp proteins are purported to be antigenic however little direct data are available to support this claim. In this study convalescent pig sera did not bind denatured Vsp proteins by Western blotting, but did bind the Vsp complexes on Western blots, showing that conformational epitopes may be important in immune recognition of these major outer membrane proteins. This is the first definitive demonstration of the antigenicity of these proteins in swine dysentery.
Publisher: Oxford University Press (OUP)
Date: 06-2007
DOI: 10.1111/J.1574-6968.2007.00711.X
Abstract: Molecular typing of leptospiral strains based on variation within putative O-antigen polymerase gene (wzy) was determined among reference strains and those isolated from patients. Using the PCR primers designed from the flanking gene of wzy derived from Leptospira interrogans serovar Copenhageni, all L. interrogans serovars as well as human and rodent leptospiral isolates from Thailand could be lified. The size of PCR product ranged from 1 to 1.5 kb. The limitation of these primer pairs was the inability to lify those strains whose sequences differ in the region of the primers, these included Leptospira biflexa (serovar Patoc), Leptospira borgpetersenii (serovar Tarassovi) and Leptospira kirschneri (serovar Bim, Bulgarica, Butembo). Notably, lification was not limited to L. interrogans as demonstrated by the lification of some strains from L. kirschneri, Leptospira meyeri, Leptospira noguchii, Leptospira santarosai, L. borgpetersenii and Leptospira weilii. The phylogenetic tree of wzy sequence, inferred by posterior probability of the Bayesian, enabled the categorization of leptospiral serovars into seven genetically related group, of which its differentiation power was better than that of the more highly conserved 16S rRNA gene, which is used extensively for genotyping.
Publisher: American Society for Microbiology
Date: 07-01-2021
DOI: 10.1128/MRA.01086-20
Abstract: C ylobacter spp. can survive and be transmitted from a range of environments. Here, we examine eight draft genome sequences of C ylobacter volucris , identified as part of an examination of waterborne C ylobacter species. This is the first report of environmental survival of C. volucris outside gull species.
Publisher: Springer Science and Business Media LLC
Date: 30-09-2021
DOI: 10.1186/S13099-021-00452-2
Abstract: The burden of Helicobacter pylori -induced gastric cancer varies based on predominant H. pylori population in various geographical regions. Vietnam is a high H. pylori burden country with the highest age-standardized incidence rate of gastric cancer (16.3 cases/100,000 for both sexes) in Southeast Asia, despite this data on the H. pylori population is scanty. We examined the global context of the endemic H. pylori population in Vietnam and present a contextual and comparative genomics analysis of 83 H. pylori isolates from patients in Vietnam. There are at least two major H. pylori populations are circulating in symptomatic Vietnamese patients. The majority of the isolates (~ 80%, 66/83) belong to the hspEastAsia and the remaining belong to hpEurope population (~ 20%, 17/83). In total, 66 isolates (66/83) were cagA positive, 64 were hspEastAsia isolates and two were hpEurope isolates . Examination of the second repeat region revealed that most of the cagA genes were ABD type (63/66 61 were hspEastAsia isolates and two were hpEurope isolates). The remaining three isolates (all from hspEastAsia isolates) were ABC or ABCC types. We also detected that 4.5% (3/66) cagA gene from hspEastAsia isolates contained EPIYA-like sequences, ESIYA at EPIYA-B segments. Analysis of the vacA allelic type revealed 98.8% (82/83) and 41% (34/83) of the strains harboured the s1 and m1 allelic variant, respectively 34/83 carried both s1m1 alleles. The most frequent genotypes among the cagA positive isolates were vacA s1m1/ cagA + and vacA s1m2/ cagA + , accounting for 51.5% (34/66) and 48.5% (32/66) of the isolates, respectively. There are two predominant lineages of H. pylori circulating in Vietnam most of the isolates belong to the hspEastAsia population. The hpEurope population is further ided into two smaller clusters.
Publisher: Elsevier BV
Date: 1999
Abstract: Two major clades, designated Groups I and II, of nucleopolyhedroviruses (NPVs) from lepidopteran hosts have been previously identified. To reveal more detailed relationships, a series of DNA polymerase nucleotide sequences from the taxa MbMNPV, SeMNPV, HzSNPV, HearNPV, SpltNPV, BusuNPV, and OranNPV have been determined using a polymerase chain reaction (PCR)-based approach. This technique enabled gene sequence determination using microliter s les of NPV-infected insect cadavers. Polyhedrin genes from HearNPV, OranNPV, SeMNPV, and SpltNPV were also isolated and sequenced using a similar approach. These sequences, together with other database entries, were aligned for positional homology of peptide sequences. Phylogenetic analysis of DNA polymerase molecular sequence alignments supports LdMNPV as a taxon of Group II and three Group II subclades, designated A, B, and C. Comparison of DNA polymerase trees with those estimated from occlusion protein molecular sequences enabled identification of three subclades of Group II. These are Subgroup II-A [MbMNPV, LeseNPV, MacoNPV, PaflNPV, SeMNPV, SpltNPV (India isolate), SfMNPV] Subgroup II-B [SpliNPV, SpltNPV (Japan isolate), SpltNPV (Queensland isolate), and possibly HzSNPV, HearNPV, and ManeNPV], and Subgroup II-C [OpSNPV, OranNPV (S-type), BusuNPV (S-type), and possibly EcobNPV (S-type)]. Notably, all Subgroup II-A taxa are from noctuid hosts. Correlations of virus and host evolution within Group II taxa are discussed. The methods and data developed in this study will allow rapid sequencing of NPV DNA polymerase genes.
Publisher: American Society for Microbiology
Date: 15-11-2016
DOI: 10.1128/AEM.02067-16
Abstract: We report the isolation and characterization of three new cytochrome P450 monooxygenases: CYP101J2, CYP101J3, and CYP101J4. These P450s were derived from Sphingobium yanoikuyae B2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. Genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding P450s. The P450 enzymes were cloned, heterologously expressed (N-terminally His 6 tagged) in Escherichia coli BL21(DE3), purified, and spectroscopically characterized. Recombinant whole-cell biotransformation in E. coli demonstrated that all three P450s hydroxylate 1,8-cineole using electron transport partners from E. coli to yield a product putatively identified as (1 S )-2α-hydroxy-1,8-cineole or (1 R )-6α-hydroxy-1,8-cineole. The new P450s belong to the CYP101 family and share 47% and 44% identity with other 1,8-cineole-hydroxylating members found in Novosphingobium aromaticivorans and Pseudomonas putida . Compared to P450 cin (CYP176A1), a 1,8-cineole-hydroxylating P450 from Citrobacter braakii , these enzymes share less than 30% amino acid sequence identity and hydroxylate 1,8-cineole in a different orientation. Expansion of the enzyme toolbox for modification of 1,8-cineole creates a starting point for use of hydroxylated derivatives in a range of industrial applications. IMPORTANCE CYP101J2, CYP101J3, and CYP101J4 are cytochrome P450 monooxygenases from S. yanoikuyae B2 that hydroxylate the monoterpenoid 1,8-cineole. These enzymes not only play an important role in microbial degradation of this plant-based chemical but also provide an interesting route to synthesize oxygenated 1,8-cineole derivatives for applications as natural flavor and fragrance precursors or incorporation into polymers. The P450 cytochromes also provide an interesting basis from which to compare other enzymes with a similar function and expand the CYP101 family. This could eventually provide enough bacterial parental enzymes with similar amino acid sequences to enable in vitro evolution via DNA shuffling.
Publisher: Elsevier BV
Date: 04-2003
DOI: 10.1016/S1286-4579(03)00027-3
Abstract: The identification of Brachyspira hyodysenteriae outer membrane proteins (OMPs) that may stimulate immunity to swine dysentery is important for vaccine development. We report here the analysis of a novel locus, blpGFEA, encoding four tandem paralogous proteins of approximately 30 kDa from B. hyodysenteriae. The four proteins share 31-39% sequence identity with lipoproteins from several species of bacterial pathogens, but the locus possesses a unique genetic organization. Using antisera raised to recombinant versions of each of these proteins, only BlpA and BlpE were found to be immunologically cross-reactive with the other proteins encoded by the locus. Northern hybridization indicated that only blpA was expressed under in vitro growth conditions. In addition, convalescent swine serum recognized recombinant BlpA in immunoblotting experiments, demonstrating that it is also expressed during infection. Analysis of the translated sequences of each of the genes revealed atypical spirochetal signal peptidase II recognition sites, and BlpA was shown to be a lipoprotein by incorporation of tritiated palmitic acid. Native BlpA was completely extracted by Triton X-114 (TX-114) and partitioned exclusively into the detergent phase during extraction of whole B. hyodysenteriae cells, implicating it as a component of the brachyspiral outer membrane. Consistent with the transcriptional and immunological data, analysis of the brachyspiral outer membrane proteome also revealed expression of only BlpA. Notably, inactivation of blpA homologs in Haemophilus influenzae and Salmonella enteritidis resulted in attenuation of virulence.
Publisher: Wiley
Date: 18-10-2021
DOI: 10.1111/HEL.12766
Publisher: Cold Spring Harbor Laboratory
Date: 03-07-2020
DOI: 10.1101/2020.07.02.185645
Abstract: Corals are colonized by symbiotic microorganisms that exert a profound influence on the animal’s health. One noted symbiont is a single-celled alga (from the family Symbiodiniaceae ), which provides the coral with most of its fixed carbon. During thermal stress, hyperactivity of photosynthesis results in a toxic accumulation of reactive oxygen species (ROS). If not scavenged by the antioxidant network, ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating this process is known as bleaching. Our goal was to construct a probiotic comprised of host-associated bacteria able to neutralize free radicals such as ROS. Using the coral model, the anemone Exaiptasia diaphana , and pure bacterial cultures isolated from the model animal, we identified six strains with high free radical scavenging ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae , and Micrococcaceae . In parallel, we established a “negative” probiotic consisting of genetically related strains with poor free radical scavenging capacities. From their whole genome sequences, we explored genes of interest that may contribute to their potential beneficial roles, which may help facilitate the therapeutic application of a bacterial probiotic. In particular, the occurrence of key pathways that are known to influence ROS in each of the strains has been inferred from the genomes sequences and are reported here. Coral bleaching is tightly linked to the production of reactive oxygen species (ROS), which accumulates to a toxic level in algae-harboring host cells leading to coral-algal dissociation. Interventions targeting ROS accumulation, such as the application of exogenous antioxidants, have shown promise for maintaining the coral-algal partnership. With the feasibility of administering antioxidants directly to corals being low, we aim to develop a probiotic to neutralize toxic ROS during a thermal stress event. This probiotic can be tested with corals or a coral model to assess its efficacy in improving coral resistance to environmental stress.
Publisher: Public Library of Science (PLoS)
Date: 23-03-2015
Publisher: American Society for Microbiology
Date: 02-2016
DOI: 10.1128/JCM.02344-15
Abstract: Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance of Listeria monocytogenes has the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423 L. monocytogenes isolates underwent WGS, and comparisons uncovered a erse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferred in silico from the WGS data were highly concordant ( %) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97 L. monocytogenes isolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospective L. monocytogenes surveillance and investigated for other pathogens relevant to public health.
Publisher: Public Library of Science (PLoS)
Date: 14-01-2015
Publisher: American Society for Microbiology
Date: 21-09-2017
Abstract: The draft genome sequences of two strains of a newly described species, Sphingobacterium cellulitidis , have been determined. The type strain originated from cellulitis of a toe of a patient and the other strain from the environment. The sequences will provide the reference genomes of the new Sphingobacterium species.
Publisher: Public Library of Science (PLoS)
Date: 07-05-2015
Publisher: Oxford University Press (OUP)
Date: 10-02-2016
Abstract: Previous studies suggest overrepresentation of particular polymorphisms within the Helicobacter pylori CagL hypervariable motif (CagLHM) in gastric cancer-associated isolates. However, these disease correlations were geographically variable and ambiguous. We compared the disease correlation of several hundred geographically erse CagL sequences and identified 33 CagLHM sequence combinations with disparate geographical distribution, revealing substantial worldwide CagLHM ersity, particularly within Asian countries. Notably, polymorphisms E59 and I60 were significantly overrepresented, whereas D58 and E62 were underrepresented, in gastric cancer-associated H. pylori isolates worldwide. Thus, CagLHM regional ersity may contribute to the varied prevalence of H. pylori-related gastric cancer observed in erse populations.
Publisher: Public Library of Science (PLoS)
Date: 30-07-2020
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 03-2017
Start Date: 2016
End Date: 2018
Funder: Australian Research Council
View Funded ActivityStart Date: 2016
End Date: 2019
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 12-2016
End Date: 12-2020
Amount: $435,000.00
Funder: Australian Research Council
View Funded Activity