ORCID Profile
0000-0002-4756-4810
Current Organisation
University of Technology Sydney
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Veterinary Microbiology (excl. Virology) | Infectious Agents | Proteomics and Intermolecular Interactions (excl. Medical Proteomics) | Genomics | Veterinary Immunology | Biochemistry and Cell Biology | Synthetic biology | Microbiology | Microbial genetics | Veterinary Sciences | Genetics | Systems Biology | Genomics | Bacteriology |
ANZSRC Socio-Economic Objective (SEO)
Control of Pests, Diseases and Exotic Species at Regional or Larger Scales | Control of Animal Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Animal Welfare | Expanding Knowledge in the Biological Sciences | Forest and Woodlands Flora, Fauna and Biodiversity
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Publications
Preliminary phylogenetic identification of virulent Chlamydophila pecorum strains
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.MEEGID.2008.06.009
Abstract: Chlamydophila pecorum is an obligate intracellular bacterium associated with different pathological conditions in ruminants, swine and koala, which is also found in the intestine of asymptomatic animals. A multi-virulence locus sequence typing (MVLST) system was developed using 19 C. pecorum strains (8 pathogenic and 11 non-pathogenic intestinal strains) isolated from ruminants of different geographical origins. To evaluate the ability of MVLST to distinguish the pathogenic from the non-pathogenic strains of C. pecorum, the sequences of 12 genes were analysed: 6 potential virulence genes (ompA, incA, incB, incC, mip and copN), 5 housekeeping genes (recA, hemD, aroC, efp, gap), and the ORF663 gene encoding a hypothetical protein (HP) that includes a variant 15-nucleotides coding tandem repeat (CTR). MVLST provided high discriminatory power (100%) in allowing to distinguish 6 of 8 pathogenic strains in a single group, and overall more discriminatory than MLST targeting housekeeping genes. ompA was the most polymorphic gene and the phylogenetic tree based only on its sequence differentiated 4 groups with high bootstrap values. The number of CTRs (rich in serine, proline and lysine) in ORF663 detected in the pathogenic strains was generally lower than that found in the intestinal strains. MVLST appears to be a promising method for the differential identification of virulent C. pecorum strains, and the ompA, incA and ORF663 genes appear to be good molecular markers for further epidemiological investigation of C. pecorum.
Divergence without difference: phylogenetics and taxonomy ofChlamydiaresolved
Publisher: Oxford University Press (OUP)
Date: 03-2009
Analysis of Complete Genome Sequence of Acinetobacter baumannii Strain ATCC 19606 Reveals Novel Mobile Genetic Elements and Novel Prophage
Publisher: MDPI AG
Date: 24-11-2020
DOI: 10.3390/MICROORGANISMS8121851
Abstract: Acinetobacter baumannii isolate ATCC 19606 was recovered in the US prior to 1948. It has been used as a reference and model organism in many studies involving antibiotic resistance and pathogenesis of A. baumannii, while, until recently, a complete genome of this strain was not available. Here, we present an analysis of the complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina) and long-read sequencing (MinION), and show it contains two small cryptic plasmids and a novel complete prophage of size 41.2 kb. We also characterised several regions of the ATCC 19606 genome, leading to the identification of a novel cadmium/mercury transposon, which was named Tn6551. ATCC 19606 is an antibiotic-sensitive strain, but a comparative analysis of all publicly available ST52 strains predicts a resistance to modern antibiotics by the accumulation of antibiotic-resistance genes via plasmids in recent isolates that belong to this sequence type.
Predicting Phenotype and Emerging Strains amongChlamydia trachomatisInfections
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 09-2009
Regulation of Type IV Fimbrial Biogenesis in Dichelobacter nodosus
Publisher: American Society for Microbiology
Date: 07-2006
DOI: 10.1128/JB.00255-06
Abstract: Type IV fimbriae are expressed by several bacterial pathogens and are essential for virulence in Dichelobacter nodosus , which causes ovine footrot. We have identified a two-component signal transduction system (PilR/S) and an alternative sigma factor (σ 54 ) that were shown by insertional inactivation to be required for the regulation of fimbrial biogenesis in D. nodosus . Western blots showed that in both pilR and rpoN mutants, fimbrial subunit production was significantly reduced by a process that was shown to occur at a PilR- and σ 54 -dependent promoter. The mutants lacked surface fimbriae, which were shown to be required for the adherence of D. nodosus cells to tissue culture monolayers. The reduction in fimbrial subunit production in these mutants also resulted in a concomitant loss of the ability to secrete extracellular proteases. A maltose binding protein-PilR fusion protein was purified and was shown to bind specifically to a region located 234 to 594 bp upstream of the fimA transcriptional start point. To determine additional targets of PilR and σ 54 , genome-wide transcriptional profiling was performed using a whole-genome oligonucleotide microarray. The results indicated that PilR and σ 54 regulated genes other than fimA these genes appear to encode surface-exposed proteins whose role in virulence is unknown. In conclusion, this study represents a significant advancement in our understanding of how the ability of D. nodosus to cause ovine footrot is regulated, as we have shown that the biogenesis of type IV fimbriae in D. nodosus is regulated by a σ 54 -dependent PilR/S system that also indirectly controls protease secretion.
Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism
Publisher: Public Library of Science (PLoS)
Date: 13-05-2009
Genome Sequences of the Zoonotic Pathogens Chlamydia psittaci 6BC and Cal10
Publisher: American Society for Microbiology
Date: 08-2011
DOI: 10.1128/JB.05277-11
Abstract: Chlamydia psittaci is a highly prevalent avian pathogen and the cause of a potentially lethal zoonosis, causing life-threatening pneumonia in humans. We report the genome sequences of C. psittaci 6BC, the prototype strain of the species, and C. psittaci Cal10, a widely used laboratory strain.
Evidence that HumanChlamydia pneumoniaeWas Zoonotically Acquired
Publisher: American Society for Microbiology
Date: 06-2009
DOI: 10.1128/JB.00746-09
Abstract: Zoonotic infections are a growing threat to global health. Chlamydia pneumoniae is a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease. C. pneumoniae was first identified solely in human populations however, its host range now includes other mammals, marsupials, hibians, and reptiles. Australian koalas ( Phascolarctos cinereus ) are widely infected with two species of Chlamydia , C. pecorum and C. pneumoniae . Transmission of C. pneumoniae between animals and humans has not been reported however, two other chlamydial species, C. psittaci and C. abortus , are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain of C. pneumoniae (LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates of C. pneumoniae show that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) of C. pneumoniae which adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.
Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex.
Publisher: Informa UK Limited
Date: 2020
Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species
Publisher: Springer Science and Business Media LLC
Date: 21-07-2010
Abstract: Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal ( 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain ersity and evolution of this species. We performed in idual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic ersity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae , genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes). We have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
Publisher: Proceedings of the National Academy of Sciences
Date: 02-04-2004
Abstract: We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum . The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.
A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro
Publisher: Frontiers Media SA
Date: 21-09-2017
Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus
Publisher: Springer Science and Business Media LLC
Date: 05-2007
DOI: 10.1038/NBT1302
Abstract: Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.
Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-03-2003
Abstract: The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
Genetic Variation In Vitro and In Vivo of an Attenuated Lassa Vaccine Candidate
Publisher: American Society for Microbiology
Date: 15-03-2014
DOI: 10.1128/JVI.03035-13
Abstract: The attenuated Lassa vaccine candidate ML29 is a laboratory-produced reassortant between Lassa and Mopeia viruses, two Old World arenaviruses that differ by 40% in nucleic acid sequence. In our previous studies, ML29 elicited sterilizing immunity against Lassa virus challenge in guinea pigs and marmosets and virus-specific cell-mediated immunity in both simian immunodeficiency virus (SIV)-infected and uninfected rhesus macaques. Here, we show that ML29 is stable after 12 passages in vitro without losing its plaque morphology or its attenuated phenotype in suckling mice. Additionally, we used deep sequencing to characterize the viral population comprising the original stock of ML29, the stock of ML29 after 12 passages in Vero cells, and the ML29 isolates obtained from vaccinated animals. Twenty-seven isolates bore approximately 77 mutations that exceeded 20% of the single-nucleotide polymorphism (SNP) changes at any single locus. Of these 77 mutations, 5 appeared to be host specific, for ex le, appearing in mice but not in primates. None of these mutations were reversions of ML29 to the sequences of the parental Lassa and Mopeia viruses. The host-specific mutations indicate viral adaptations to virus-host interactions, and such interactions make reasonable targets for antiviral approaches. Variants capable of chronic infection did not emerge from any of the primate infections, even in immune-deficient animals, indicating that the ML29 reassortant is reasonably stable in vivo . In conclusion, the preclinical studies of ML29 as a Lassa virus vaccine candidate have been advanced, showing high levels of protection in nonhuman primates and acceptable stability both in vitro and in vivo .
Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments
Publisher: Oxford University Press (OUP)
Date: 23-05-2017
DOI: 10.1093/BIB/BBX043
Two carbapenem-resistant ST1:ST231:KL1:OCL1 Acinetobacter baumannii strains recovered in Tehran, Iran, carry AbaR31 in the chromosome and AbaR4 and TnaphA6 in a RepAci6 plasmid
Publisher: Oxford University Press (OUP)
Date: 12-07-2021
Abstract: To analyse the context of genes conferring antibiotic resistance in two carbapenem-resistant Acinetobacter baumannii isolates recovered in Tehran, Iran. The antibiotic resistance phenotype for 28 antibiotics was determined using disc diffusion. The whole genome sequences of ABH008 and ABS200 were determined using the Illumina HiSeq X Ten platform. Resistance genes were identified using ResFinder and multilocus sequence types were determined using the Oxford and Institut Pasteur schemes. Isolates ABH008 and ABS200, recovered in 2012 and 2013, respectively, in two different Tehran hospitals, belong to the common global clone 1 lineage, ST1IP and ST231OX. They are resistant to sulfamethoxazole, tetracycline, gentamicin, amikacin, third-generation cephalosporins and carbapenems. Despite being isolated in different hospitals, phylogenetic analysis indicated they are closely related. Consistent with this, both isolates carry catA1, sul1, aacC1 and aadA1 in a novel variant of the AbaR3-type resistance island, named AbaR31. Both isolates are resistant to amikacin and carbapenems owing to aphA6 and oxa23, respectively. The oxa23 gene is located in the AbaR4 resistance island, and aphA6 in TnaphA6, and both mobile elements are in an ∼90 kbp plasmid encoding the putative RepAci6 replication initiation protein. Resistance to third-generation cephalosporins is due to the acquisition by homologous recombination of a 5 kb DNA segment that contains ISAba1- C from a ST623 strain. The resistance gene complements of ABH008 and ABS200 were found in AbaR31 and a plasmid that encodes RepAci6. The close genetic relationship of ABH008 and ABS200, despite each being recovered from different hospitals, indicates transmission between the two hospitals.
Unity in Variety--The Pan-Genome of the Chlamydiae
Publisher: Oxford University Press (OUP)
Date: 20-06-2011
A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women.
Publisher: Wiley
Date: 26-12-2018
DOI: 10.1111/AJO.12754
Genome Sequence of Chlamydia suis MD56, Isolated from the Conjunctiva of a Weaned Piglet
Publisher: American Society for Microbiology
Date: 26-06-2014
Abstract: Chlamydia suis is a natural pathogen of pigs ( Sus scrofa ) and causes conjunctivitis, pneumonia, enteritis, and various reproductive disorders that adversely impact this economically important animal. Here, we report the first C. suis genome, that of C. suis MD56, isolated from a conjunctival swab of a weaned piglet.
Development of aChlamydia suis-specific antibody enzyme-linked immunosorbent assay based on the use of a B-cell epitope of the polymorphic membrane protein C
Publisher: Hindawi Limited
Date: 04-01-2018
DOI: 10.1111/TBED.12783
Abstract: Chlamydia suis infections lead to economic loss in the pork industry. Chlamydia suis infections could be successfully treated with tetracyclines until the appearance of a tetracycline resistant phenotype, which was acquired via horizontal gene transfer of the tet(C) gene. Given the importance of C. suis as a swine pathogen and as a recently emerged tetracycline resistant pathogen with zoonotic potential, our aim was to develop a sensitive C. suis-specific antibody ELISA based on the polymorphic membrane proteins (Pmps). Chlamydia Pmps are important virulence factors and candidate antigens for serodiagnosis. We identified nine Pmps (PmpA to I) in C. suis strain MD56 using a recently developed Hidden-Markov model. PmpC was the most promising candidate for the development of a C. suis-specific antibody ELISA as the protein was absent in C. abortus, C. pecorum and C. psittaci which also infect pigs and as the protein contained C. suis-specific amino acid regions, absent in C. trachomatis PmpC. We identified an immunodominant B-cell epitope in C. suis PmpC using experimental porcine sera. The sensitivity and specificity of the PmpC ELISA was compared to the complement fixation test (CFT) and to a recombinant MOMP ELISA using experimental sera. The PmpC ELISA detected all positive control sera and was in contrast to CFT and the rMOMP ELISA 100% C. suis specific as positive control sera against other Chlamydia species did not react in the PmpC ELISA. The test was successfully validated using slaughterhouse sera and sera from clinically affected pigs. The PmpC ELISA could assist in diminishing the spread of C. suis infections in the pork industry.
Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG
Publisher: Oxford University Press (OUP)
Date: 29-07-2014
DOI: 10.1093/BIOINFORMATICS/BTU505
Abstract: Summary: Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It includes a library of circular track types and predefined configuration files for common use-cases, including. (i) visualizing gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene conservation in related microbial strains, (iii) showing Single Nucleotide Polymorphisms (SNPs) and indels relative to a reference genome and gene set and (iv) viewing RNA-Seq plots. Availability and implementation: Circleator is freely available under the Artistic License 2.0 from jonathancrabtree.github.io/Circleator/ and is integrated with the CloVR cloud-based sequence analysis Virtual Machine (VM), which can be downloaded from clovr.org or run on Amazon EC2. Contact: jcrabtree@som.umaryland.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov.
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.SYAPM.2013.12.004
Abstract: The family Chlamydiaceae with the recombined single genus Chlamydia currently comprises nine species, all of which are obligate intracellular organisms distinguished by a unique biphasic developmental cycle. Anecdotal evidence from epidemiological surveys in flocks of poultry, pigeons and psittacine birds have indicated the presence of non-classified chlamydial strains, some of which may act as pathogens. In the present study, phylogenetic analysis of ribosomal RNA and ompA genes, as well as multi-locus sequence analysis of 11 field isolates were conducted. All independent analyses assigned the strains into two different clades of monophyletic origin corresponding to pigeon and psittacine strains or poultry isolates, respectively. Comparative genome analysis involving the type strains of currently accepted Chlamydiaceae species and the designated type strains representing the two new clades confirmed that the latter could be classified into two different species as their average nucleotide identity (ANI) values were always below 94%, both with the closest relative species and between themselves. In view of the evidence obtained from the analyses, we propose the addition of two new species to the current classification: Chlamydia avium sp. nov. comprising strains from pigeons and psittacine birds (type strain 10DC88(T) DSMZ: DSM27005(T), CSUR: P3508(T)) and Chlamydia gallinacea sp. nov. comprising strains from poultry (type strain 08-1274/3(T) DSMZ: DSM27451(T), CSUR: P3509(T)).
A high efficiency cloning and expression system for proteomic analysis
Publisher: Wiley
Date: 07-2006
Abstract: The recent description of the complete genomes of the two most pathogenic species of Brucella opens the way for genome-based analysis of the antigenicity of their proteins. In the present report, we describe a bench-level high-efficiency cloning and expression system (HECES) that allow expression of large numbers of Brucella proteins based on genomic sequence information. Purified proteins are produced with high efficiency in a microarray format conducive to analysis of their sero-reactivity against serum from immunized animals. This method is applicable at either small or large scale of protein processing. While it does not require robotics, the format is amenable to robotic implementation for all aspects of the process and subsequent analysis of protein characteristics. This method will allow selection of new reagents for diagnosis of brucellosis and development of vaccine against Brucella, an important zoonotic disease and biothreat agent.
Genomic Plasticity of the rrn-nqrF Intergenic Segment in the Chlamydiaceae
Publisher: American Society for Microbiology
Date: 03-2007
DOI: 10.1128/JB.00378-06
Abstract: In Chlamydiaceae , the nucleotide sequence between the 5S rRNA gene and the gene for subunit F of the Na + -translocating NADH-quinone reductase ( nqrF or dmpP ) has varied lengths and gene contents. We analyzed this site in 45 Chlamydiaceae strains having erse geographical and pathological origins and including members of all nine species.
Identification of a Dichelobacter nodosus Ferric Uptake Regulator and Determination of Its Regulatory Targets
Publisher: American Society for Microbiology
Date: 2005
DOI: 10.1128/JB.187.1.366-375.2005
Abstract: The expression of iron regulated genes in bacteria is typically controlled by the ferric uptake regulator (Fur) protein, a global transcriptional repressor that regulates functions as erse as iron acquisition, oxidative stress, and virulence. We have identified a fur homologue in Dichelobacter nodosus , the causative agent of ovine footrot, and shown that it complements an Escherichia coli fur mutant. Homology modeling of the D. nodosus Fur protein with the recently solved crystal structure of Fur from Pseudomonas aeruginosa indicated extensive structural conservation. As Southern hybridization analysis of different clinical isolates of D. nodosus indicated that the fur gene was present in all of these strains, the fur gene was insertionally inactivated to determine its functional role. Analysis of these mutants by various techniques did not indicate any significant differences in the expression of known virulence genes or in iron-dependent growth. However, we determined several Fur regulatory targets by two-dimensional gel electrophoresis coupled with mass spectrometry. Analysis of proteins from cytoplasmic, membrane, and extracellular fractions revealed numerous differentially expressed proteins. The transcriptional basis of these differences was analyzed by using quantitative reverse transcriptase PCR. Proteins with increased expression in the fur mutant were homologues of the periplasmic iron binding protein YfeA and a cobalt chelatase, CbiK. Down-regulated proteins included a putative manganese superoxide dismutase and ornithine decarboxylase. Based on these data, it is suggested that in D. nodosus the Fur protein functions as a regulator of iron and oxidative metabolism.
Chlamydia pneumoniae is genetically diverse in animals and appears to have crossed the host barrier to humans on (at least) two occasions
Publisher: Public Library of Science (PLoS)
Date: 20-05-2010
Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells
Publisher: Public Library of Science (PLoS)
Date: 04-12-2013
The Pangenome Structure ofEscherichia coli: Comparative Genomic Analysis ofE. coliCommensal and Pathogenic Isolates
Publisher: American Society for Microbiology
Date: 15-10-2200
DOI: 10.1128/JB.00619-08
Abstract: Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli . Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli , enteropathogenic E. coli , and enteroaggregative E. coli . We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli . Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic ersity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli , while descriptive, should provide the basis for future functional work on this important group of pathogens.
Cloning, expression, and purification of Brucella suis outer membrane proteins
Publisher: Elsevier BV
Date: 03-2005
DOI: 10.1016/J.PEP.2004.12.017
Abstract: Brucella, an aerobic, nonsporeforming, nonmotile Gram-negative coccobacillus, is a NIH/CDC category B bioterror threat agent that causes incapacitating human illness. Medical defense against the bioterror threat posed by Brucella would be strengthened by development of a human vaccine and improved diagnostic tests. Central to advancement of these goals is discovery of bacterial constituents that are immunogenic or antigenic for humans. Outer membrane proteins (OMPs) are particularly attractive for this purpose. In this study, we cloned, expressed, and purified seven predicted OMPs of Brucella suis. The recombinant proteins were fused with 6-His and V5 epitope tags at their C termini to facilitate detection and purification. The B. suis surface genes were PCR synthesized based on their ORF sequences and directly cloned into an entry vector. The recombinant entry constructs were propagated in TOP 10 cells, recombined into a destination vector, pET-DEST42, then transformed into Escherichia coli BL21 cells for IPTG-induced protein expression. The expressed recombinant proteins were confirmed with Western blot analysis using anti-6-His antibody conjugated with alkaline phosphatase. These B. suis OMPs were captured and purified using a HisGrab plate. The purified recombinant proteins were examined for their binding activity with antiserum. Serum derived from a rabbit immunized intramuscularly with dialyzed cell lysate of Brucella rough mutant WRR51. The OMPs were screened using the rabbit antiserum and purified IgG. The results suggested that recombinant B. suis OMPs were successfully cloned, expressed and purified. Some of the expressed OMPs showed high binding activity with immunized rabbit antiserum.
Full Genome Sequences of All Nine Chlamydia psittaci Genotype Reference Strains
Publisher: American Society for Microbiology
Date: 15-12-2012
DOI: 10.1128/JB.01828-12
Abstract: Chlamydia psittaci primarily infects birds, but zoonotic transmission occurs in people in close contact with infected birds. The clinical outcome ranges from inapparent disease to pneumonia. Here we report the genome sequences of all 9 Chlamydia psittaci genotype reference strains.
Dual RNA-Seq analysis of in vitro infection multiplicity in Chlamydia-infected epithelial cells
Publisher: Cold Spring Harbor Laboratory
Date: 22-10-2020
DOI: 10.1101/2020.10.21.347906
Abstract: Dual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq to Chlamydia trachomatis infected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 hours), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host-pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights.
Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection
Publisher: American Society for Microbiology
Date: 07-2014
Abstract: It is not currently possible to predict the probability of whether a woman with a chlamydial genital infection will develop pelvic inflammatory disease (PID). To determine if specific biomarkers may be associated with distinct chlamydial pathotypes, we utilized two Chlamydia muridarum variants ( C. muridarum Var001 [CmVar001] and CmVar004) that differ in their abilities to elicit upper genital tract pathology in a mouse model. CmVar004 has a lower growth rate in vitro and induces pathology in only 20% of C57BL/6 mouse oviducts versus 83.3% of oviducts in CmVar001-infected mice. To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. CmVar004 infection induced significantly lower levels of CXCL1, CXCL2, tumor necrosis factor alpha (TNF-α), and CCL2 in comparison to CmVar001 infection with similar rRNA ( rs16 ) levels for Chlamydiae . A combination of microRNA (miRNA) sequencing and quantitative real-time PCR (qRT-PCR) analysis of 134 inflammation-related miRNAs was performed 24 h postinfection to determine if the chemokine/cytokine responses would also be reflected in miRNA expression profiles. Interestingly, 12 miRNAs (miR-135a-5p, miR298-5p, miR142-3p, miR223-3p, miR299a-3p, miR147-3p, miR105, miR325-3p, miR132-3p, miR142-5p, miR155-5p, and miR-410-3p) were overexpressed during CmVar004 infection compared to CmVar001 infection, inversely correlating with the respective chemokine/cytokine responses. To our knowledge, this is the first report demonstrating that early biomarkers elicited in the host can differentiate between two pathological variants of chlamydiae and be predictive of upper tract disease. IMPORTANCE It is apparent that an infecting chlamydial population consists of multiple genetic variants with differing capabilities of eliciting a pathological response thus, it may be possible to identify biomarkers specific for a given virulence pathotype. miRNAs are known to regulate genes that in turn regulate signaling pathways involved in disease pathogenesis. Importantly, miRNAs are stable and can reflect a tissue response and therefore have the potential to be biomarkers of disease severity. Currently, with respect to chlamydial infections, there is no way to predict whether an infected patient is more or less likely to develop PID. However, data presented in this study indicate that the expression of a specific miRNA profile associated with a virulent variant early in the infection course may be predictive of an increased risk of pelvic inflammatory disease, allowing more aggressive treatment before significant pathology develops.
Visualization of comparative genomic analyses by BLAST score ratio
Publisher: Springer Science and Business Media LLC
Date: 2005
Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital
Publisher: Microbiology Society
Date: 05-2020
Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes
Publisher: Springer Science and Business Media LLC
Date: 14-01-2014
Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells
Publisher: Cold Spring Harbor Laboratory
Date: 06-01-2017
DOI: 10.1101/098715
Abstract: Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA-Seq technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. We pioneered dRNA-Seq to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with bacteria, using in vitro Chlamydia -infected epithelial cells as proof of principle. Here we provide a detailed laboratory and bioinformatics protocol for dRNA-seq that is readily adaptable to any host-bacteria system of interest.
Genus-optimized strategy for the identification of chlamydial type III secretion substrates
Publisher: Oxford University Press (OUP)
Date: 14-08-2013
Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution.
Publisher: Frontiers Media SA
Date: 19-11-2019
Expression of two novel proteins in Chlamydia trachomatis during natural infection
Publisher: Elsevier BV
Date: 08-2000
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment
Publisher: Proceedings of the National Academy of Sciences
Date: 05-09-2006
Abstract: Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.
Non-pathogenic bacteria take center stage: a lesson in contrasts
Publisher: Elsevier BV
Date: 07-2004
Chromatin accessibility dynamics of Chlamydia-infected epithelial cells
Publisher: Springer Science and Business Media LLC
Date: 27-10-2020
DOI: 10.1186/S13072-020-00368-2
Abstract: Chlamydia are Gram-negative, obligate intracellular bacterial pathogens responsible for a broad spectrum of human and animal diseases. In humans, Chlamydia trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and is the causative agent of trachoma (infectious blindness) in disadvantaged populations. Over the course of its developmental cycle, Chlamydia extensively remodels its intracellular niche and parasitises the host cell for nutrients, with substantial resulting changes to the host cell transcriptome and proteome. However, little information is available on the impact of chlamydial infection on the host cell epigenome and global gene regulation. Regions of open eukaryotic chromatin correspond to nucleosome-depleted regions, which in turn are associated with regulatory functions and transcription factor binding. We applied formaldehyde-assisted isolation of regulatory elements enrichment followed by sequencing (FAIRE-Seq) to generate temporal chromatin maps of C. trachomatis -infected human epithelial cells in vitro over the chlamydial developmental cycle. We detected both conserved and distinct temporal changes to genome-wide chromatin accessibility associated with C. trachomatis infection. The observed differentially accessible chromatin regions include temporally-enriched sets of transcription factors, which may help shape the host cell response to infection. These regions and motifs were linked to genomic features and genes associated with immune responses, re-direction of host cell nutrients, intracellular signalling, cell–cell adhesion, extracellular matrix, metabolism and apoptosis. This work provides another perspective to the complex response to chlamydial infection, and will inform further studies of transcriptional regulation and the epigenome in Chlamydia -infected human cells and tissues.
Isolation of a New Chlamydia species from the Feral Sacred Ibis (Threskiornis aethiopicus): Chlamydia ibidis
Publisher: Public Library of Science (PLoS)
Date: 20-09-2013
Dual RNA-Seq of Chlamydia and Host Cells
Publisher: Springer New York
Date: 2019
DOI: 10.1007/978-1-4939-9694-0_9
Abstract: During the infection of a host cell by a bacterial pathogen, a cascading series of gene expression changes occurs as each organism manipulates or responds to the other via defense or survival strategies. Unraveling this complex interplay is key for our understanding of bacterial virulence and host response pathways for the development of novel therapeutics. Dual RNA sequencing (dual RNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. Leveraging the sensitivity and resolution allowed by RNA-seq, dual RNA-Seq can be applied to any bacteria-eukaryotic host interaction. We pioneered dual RNA-Seq to simultaneously capture Chlamydia and host expression profiles during an in vitro infection as proof of principle. Here we provide a detailed laboratory protocol and bioinformatics analysis guidelines for dual RNA-seq experiments focusing on Chlamydia as the organism of interest.
High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA)
Publisher: Elsevier BV
Date: 03-2008
DOI: 10.1016/J.MEEGID.2007.12.002
Abstract: A multilocus VNTR analysis (MLVA) system for detection of tandem repeats across the whole genome of Chlamydophila psittaci has been developed. Twenty selected genetic loci were initially tested on 9 avian reference strains including representatives of all major serotypes (A to F). Thereafter, 8 loci were retained for a more complete study performed on over 150 C. psittaci isolates from different bird species and geographical origins. Comparative analysis of the MLVA results and those obtained from currently available methods including serotyping and/or ompA sequencing indicate that the MLVA system provides an additional level of discrimination, with 20 distinct patterns identified to date. The newly developed MLVA system therefore provides a highly sensitive, high resolution test for the differentiation of C. psittaci isolates from different origins that is suitable for molecular epidemiological studies.
The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences<b> </b>as well as the Most Conserved Pmp Protein Differ within and across <b><i>Chlamydia<
Publisher: S. Karger AG
Date: 2016
DOI: 10.1159/000447092
Abstract: Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of i mp /i coding sequences differs between i Chlamydia /i species, but it is unknown whether the number of i mp /i coding sequences is constant within a i Chlamydia /i species. The level of conservation of the Pmp proteins has previously only been determined for i Chlamydia trachomatis. /i As different Pmp proteins might be indispensible for the pathogenesis of different i Chlamydia /i species, this study investigated the conservation of Pmp proteins both within and across i C. trachomatis, /i i C. pneumoniae, /i i C. abortus, /i and i C. psittaci. /i The i mp /i coding sequences were annotated in 16 i C. trachomatis, /i 6 i C. pneumoniae, /i 2 i C. abortus, /i and 16 i C. psittaci /i genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed i Chlamydia /i species. The length of coding sequences of i mpA, /i i mpB, /i and i mpH /i was conserved among all analyzed genomes, while the length of i mpE/F /i and i mpG, /i and remarkably also of the subtype i mpD, /i differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in i C. trachomatis, /i i C. pneumoniae, /i i C. abortus, /i and i C. psittaci /i , respectively. PmpB was the most conserved Pmp across the 4 analyzed i Chlamydia /i species.
Genome Sequence of the Obligate Intracellular Animal Pathogen Chlamydia pecorum E58
Publisher: American Society for Microbiology
Date: 13-05-2011
DOI: 10.1128/JB.00454-11
Type III secretion à la Chlamydia
Publisher: Elsevier BV
Date: 06-2007
DOI: 10.1016/J.TIM.2007.04.005
Abstract: Type III secretion (T3S) is a mechanism that is central to the biology of the Chlamydiaceae and many other pathogens whose virulence depends on the translocation of toxic effector proteins to cytosolic targets within infected eukaryotic cells. Biomathematical simulations, using a previously described model of contact-dependent, T3S-mediated chlamydial growth and late differentiation, suggest that chlamydiae contained in small non-fusogenic inclusions will persist. Here, we further discuss the model in the context of in vitro-persistent, stress-induced aberrantly enlarged forms and of recent studies using small molecule inhibitors of T3S. A general mechanism is emerging whereby both early- and mid-cycle T3S-mediated activities and late T3S inactivation upon detachment of chlamydiae from the inclusion membrane are crucial for chlamydial intracellular development.
Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota
Publisher: Oxford University Press (OUP)
Date: 11-03-2015
Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens
Publisher: Cold Spring Harbor Laboratory
Date: 06-07-2006
DOI: 10.1101/GR.5238106
Abstract: Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic ersity with unique “genomic islands” identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.
Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5
Publisher: Springer Science and Business Media LLC
Date: 07-2005
DOI: 10.1038/NBT1110
Strain and Virulence Diversity in the Mouse Pathogen Chlamydia muridarum
Publisher: American Society for Microbiology
Date: 08-2009
DOI: 10.1128/IAI.00147-09
Abstract: The mouse chlamydial pathogen Chlamydia muridarum has been used as a model organism for the study of human Chlamydia trachomatis urogenital and respiratory tract infections. To date, two commonly used C. muridarum isolates have been used interchangeably and are essentially taken to be identical. Herein, we present data that indicate that this is not the case. The C. muridarum Weiss isolate and C. muridarum Nigg isolate varied significantly in their virulences in vivo and possessed different growth characteristics in vitro. Distinct differences were observed in intravaginal 50% infectious doses and in challenge infections, with the Weiss isolate displaying greater virulence. Respiratory infection by the intranasal route also indicated a greater virulence of the Weiss isolate. In vitro, morphometric analysis revealed that the Weiss isolate produced consistently smaller inclusions in human cervical adenocarcinoma cells (HeLa 229) and smaller plaques in monolayers of mouse fibroblasts (L929) than did the Nigg isolate. In addition, the Weiss isolate possessed significantly higher replicative yields in vitro than did the Nigg isolate. In plaque-purified isolates derived from our stocks of these two strains, total genomic sequencing identified several unique nonsynonymous single nucleotide polymorphisms and insertion/deletion mutations when our Weiss ( n = 4) and Nigg ( n = 5) isolates were compared with the published Nigg sequence. In addition, the two isolates shared 11 mutations compared to the published Nigg sequence. These results prove that there is genotypic and virulence ersity among C. muridarum isolates. These findings can be exploited to determine factors related to chlamydial virulence and immunity.
Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1
Publisher: Microbiology Society
Date: 07-12-2021
Abstract: Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these in idual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn 6022 ::ISAba42, and L4 and L5 associated with Tn 6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more erse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.
An Integrated Proteomic and Transcriptomic Analysis Reveals the Venom Complexity of the Bullet Ant Paraponera clavata
Publisher: MDPI AG
Date: 14-05-2020
Abstract: A critical hurdle in ant venom proteomic investigations is the lack of databases to comprehensively and specifically identify the sequence and function of venom proteins and peptides. To resolve this, we used venom gland transcriptomics to generate a sequence database that was used to assign the tandem mass spectrometry (MS) fragmentation spectra of venom peptides and proteins to specific transcripts. This was performed alongside a shotgun liquid chromatography–mass spectrometry (LC-MS/MS) analysis of the venom to confirm that these assigned transcripts were expressed as proteins. Through the combined transcriptomic and proteomic investigation of Paraponera clavata venom, we identified four times the number of proteins previously identified using 2D-PAGE alone. In addition to this, by mining the transcriptomic data, we identified several novel peptide sequences for future pharmacological investigations, some of which conform with inhibitor cysteine knot motifs. These types of peptides have the potential to be developed into pharmaceutical or bioinsecticide peptides.
Related Organisations
Australian Genome Research Facility Ltd Melbourne
Location: Australia
The Institute For Genomic Research
Location: United States of America
University Of Maryland School Of Medicine
Location: United States of America
Related Funding Activities
Discovery Projects - Grant ID: DP130102066
Start Date: 2013
End Date: 06-2016
Amount: $360,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP150101485
Start Date: 2015
End Date: 02-2018
Amount: $458,600.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE160100204
Start Date: 2016
End Date: 12-2016
Amount: $550,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE230100090
Start Date: 2023
End Date: 12-2023
Amount: $682,792.00
Funder: Australian Research Council
View Funded Activity