ORCID Profile
0000-0002-1357-9520
Current Organisations
Universidad de Sevilla
,
University of New South Wales
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Monash University
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Publisher: Wiley
Date: 13-02-2022
DOI: 10.1111/RESP.14227
Abstract: See related Editorial
Publisher: Springer Science and Business Media LLC
Date: 24-02-2012
Publisher: Informa UK Limited
Date: 11-2020
DOI: 10.1111/CXO.13065
Publisher: Springer Science and Business Media LLC
Date: 11-01-2021
Publisher: Public Library of Science (PLoS)
Date: 28-09-2018
Publisher: MDPI AG
Date: 14-07-2021
DOI: 10.3390/PATHOGENS10070894
Abstract: Acanthamoeba Keratitis (AK) can lead to substantial vision loss and morbidity among contact lens wearers. Misdiagnosis or delayed diagnosis is a major factor contributing to poor outcomes of AK. This study aimed to assess the effect of two antibiotics and one anaesthetic drug used in the diagnosis and nonspecific management of keratitis on the autofluorescence patterns of Acanthamoeba and two common bacteria that may also cause keratitis. Acanthamoeba castellanii ATCC 30868, Pseudomonas aeruginosa ATCC 9027, and Staphylococcus aureus ATCC 6538 were grown then diluted in either PBS (bacteria) or ¼ strength Ringer’s solution (Acanthamoeba) to give final concentrations of 0.1 OD at 660 nm or 104 cells/mL. Cells were then treated with ciprofloxacin, tetracycline, tetracaine, or no treatment (naïve). Excitation–emission matrices (EEMs) were collected for each s le with excitation at 270–500 nm with increments in 5 nm steps and emission at 280–700 nm at 2 nm steps using a Fluoromax-4 spectrometer. The data were analysed using MATLAB software to produce smoothed color-coded images of the s les tested. Acanthamoeba exhibited a distinctive fluorescence pattern compared to bacteria. The addition of antibiotics and anaesthetic had variable effects on autofluorescence. Tetracaine altered the fluorescence of all three microorganisms, whereas tetracycline did not show any effect on the fluorescence. Ciprofloxacin produced changes to the fluorescence pattern for the bacteria, but not Acanthamoeba. Fluorescence spectroscopy was able to differentiate Acanthamoeba from P. aeruginosa and S. aureus in vitro. There is a need for further assessment of the fluorescence pattern for different strains of Acanthamoeba and bacteria. Additionally, analysis of the effects of anti-amoebic drugs on the fluorescence pattern of Acanthamoeba and bacteria would be prudent before in vivo testing of the fluorescence diagnostic approach in the animal models.
Publisher: Elsevier BV
Date: 04-2021
Publisher: MDPI AG
Date: 15-10-2018
DOI: 10.3390/ANTIBIOTICS7040088
Abstract: Background: The prevalence of disinfectant resistance in Pseudomonas aeruginosa is on the rise. P. aeruginosa is the most common bacteria isolated from cases of microbial keratitis. Many multi-purpose contact lens disinfectant solutions are available to decontaminate contact lenses before use and to help reduce the incidence of infections. However, with increasing disinfectant resistance, the effect of multi-purpose disinfectant solutions may diminish. The goal of this study was to examine genes associated with disinfectant resistance in ocular isolates of P. aeruginosa and understand the strain’s susceptibility to different multipurpose disinfectant solutions. Methods: Seven potential disinfectant resistance genes were used in BLASTn searches against the whole genomes of 13 eye isolates of P. aeruginosa. A microdilution broth method was used to examine susceptibility to four different multipurpose disinfectant solutions. Results: All strains possessed the sugE2, sugE3 and emrE (qacE) genes. The sugE1 and qacEdelta1 genes were present in 6/13 isolates. No strains contained the qacF or qacG genes. All tested disinfectant solutions had the ability to kill all test strains at 100% concentration, with some strains being susceptible at 1:8 dilutions of the disinfecting solutions. However, the presence of disinfectant resistance genes was not associated with susceptibility to multi-purpose disinfectants. Conclusion: All four tested contact lens disinfectant preparations are effective against P. aeruginosa isolates regardless of the presence of disinfectant resistance genes.
Publisher: Elsevier BV
Date: 11-2022
Abstract: The opportunistic protist Acanthamoeba, which interacts with other microbes such as bacteria, fungi, and viruses, shows significant similarity in cellular and functional aspects to human macrophages. Intracellular survival of microbes in this microbivorous amoebal host may be a crucial step for initiation of infection in higher eukaryotic cells. Therefore, Acanthamoeba-microbe adaptations are considered an evolutionary model of macrophage-pathogen interactions. This paper reviews Acanthamoeba as an emerging human pathogen and different ecological interactions between Acanthamoeba and microbes that may serve as environmental training grounds and a genetic melting pot for the evolution, persistence, and transmission of potential human pathogens.
Publisher: European Respiratory Society (ERS)
Date: 10-12-2020
DOI: 10.1183/13993003.03666-2020
Abstract: Nosocomial transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a major feature of the COVID-19 pandemic. Evidence suggests patients can auto-emit aerosols containing viable viruses these aerosols could be further propagated when patients undergo certain treatments, including continuous positive airway pressure (PAP) therapy. Our aim was to assess 1) the degree of viable virus propagated from PAP circuit mask leak and 2) the efficacy of a ventilated plastic canopy to mitigate virus propagation. Bacteriophage phiX174 (10 8 copies·mL −1 ) was nebulised into a custom PAP circuit. Mask leak was systematically varied at the mask interface. Plates containing Escherichia coli host quantified viable virus ( via plaque forming unit) settling on surfaces around the room. The efficacy of a low-cost ventilated headboard created from a tarpaulin hood and a high-efficiency particulate air (HEPA) filter was tested. Mask leak was associated with virus contamination in a dose-dependent manner (χ 2 =58.24, df=4, p .001). Moderate mask leak (≥21 L·min −1 ) was associated with virus counts equivalent to using PAP with a vented mask. The highest frequency of viruses was detected on surfaces m away however, viable viruses were recorded up to 3.86 m from the source. A plastic hood with HEPA filtration significantly reduced viable viruses on all plates. HEPA exchange rates ≥170 m 3 ·h −1 eradicated all evidence of virus contamination. Mask leak from PAP may be a major source of environmental contamination and nosocomial spread of infectious respiratory diseases. Subclinical mask leak levels should be treated as an infectious risk. Low-cost patient hoods with HEPA filtration are an effective countermeasure.
Publisher: Elsevier BV
Date: 11-2020
Publisher: Springer Science and Business Media LLC
Date: 23-10-2018
DOI: 10.1038/S41598-018-34020-7
Abstract: The large and complex genome of Pseudomonas aeruginosa , which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic ergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were erse in terms of sequence type and dissimilar to that of global epidemic P . aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chlor henicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic ersity of P . aeruginosa isolated from two different infection types and countries.
Publisher: Cold Spring Harbor Laboratory
Date: 17-12-2018
DOI: 10.1101/497974
Abstract: Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of P. aeruginosa. We obtained the complete genome of the ocular isolate strain PA34 of P. aeruginosa utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The phenotypic properties of susceptibility to heavy metals and cytotoxicity were determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 GIs were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (aac(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.
Publisher: MDPI AG
Date: 18-02-2021
DOI: 10.3390/PATHOGENS10020225
Abstract: Acanthamoeba, an opportunistic pathogen is known to cause an infection of the cornea, central nervous system, and skin. Acanthamoeba feeds different microorganisms, including potentially pathogenic prokaryotes some of microbes have developed ways of surviving intracellularly and this may mean that Acanthamoeba acts as incubator of important pathogens. A systematic review of the literature was performed in order to capture a comprehensive picture of the variety of microbial species identified within Acanthamoeba following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Forty-three studies met the inclusion criteria, 26 studies (60.5%) examined environmental s les, eight (18.6%) studies examined clinical specimens, and another nine (20.9%) studies analysed both types of s les. Polymerase chain reaction (PCR) followed by gene sequencing was the most common technique used to identify the intracellular microorganisms. Important pathogenic bacteria, such as E. coli, Mycobacterium spp. and P. aeruginosa, were observed in clinical isolates of Acanthamoeba, whereas Legionella, adenovirus, mimivirus, and unidentified bacteria (Candidatus) were often identified in environmental Acanthamoeba. Increasing resistance of Acanthamoeba associated intracellular pathogens to antimicrobials is an increased risk to public health. Molecular-based future studies are needed in order to assess the microbiome residing in Acanthamoeba, as a research on the hypotheses that intracellular microbes can affect the pathogenicity of Acanthamoeba infections.
Publisher: Oxford University Press (OUP)
Date: 10-05-2022
Abstract: Healthcare workers (HCWs) are at risk from aerosol transmission of severe acute respiratory syndrome coronavirus 2. The aims of this study were to (1) quantify the protection provided by masks (surgical, fit-testFAILED N95, fit-testPASSED N95) and personal protective equipment (PPE), and (2) determine if a portable high-efficiency particulate air (HEPA) filter can enhance the benefit of PPE. Virus aerosol exposure experiments using bacteriophage PhiX174 were performed. An HCW wearing PPE (mask, gloves, gown, face shield) was exposed to nebulized viruses (108 copies/mL) for 40 minutes in a sealed clinical room. Virus exposure was quantified via skin swabs applied to the face, nostrils, forearms, neck, and forehead. Experiments were repeated with a HEPA filter (13.4 volume-filtrations/hour). Significant virus counts were detected on the face while the participants were wearing either surgical or N95 masks. Only the fit-testPASSED N95 resulted in lower virus counts compared to control (P = .007). Nasal swabs demonstrated high virus exposure, which was not mitigated by the surgical/fit-testFAILED N95 masks, although there was a trend for the fit-testPASSED N95 mask to reduce virus counts (P = .058). HEPA filtration reduced virus to near-zero levels when combined with fit-testPASSED N95 mask, gloves, gown, and face shield. N95 masks that have passed a quantitative fit-test combined with HEPA filtration protects against high virus aerosol loads at close range and for prolonged periods of time.
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2021
DOI: 10.1101/2021.09.02.21263008
Abstract: Healthcare workers (HCWs) are at risk from nosocomial transmission of SARS-CoV-2 from virus laden aerosols. This study aimed to: 1) quantify the degree of protection from virus aerosol provided by different types of mask (surgical, N95, fit-tested N95) and personal protective equipment (PPE) 2) determine if the use of a portable HEPA filter can enhance the effectiveness of PPE 3) determine the effectiveness of a decontamination shower to remove virus aerosol contamination of a HCW. Virus aerosol exposure experiments were conducted using bacteriophage PhiX174 (10 8 copies/mL). A HCW wearing PPE (mask, gloves, gown, faceshield) was exposed to nebulised viruses for 40mins in a sealed clinical room. After exiting, the HCW doffed PPE. Virus exposure was quantified via skin swabs applied to the face and nostrils, forearms, neck, and forehead. Experiments were performed with and without the presence of a portable HEPA filter (set to 470m3/hr). Swabs quantified significant virus exposure under the surgical and N95 mask. Only the fit-tested N95 resulted in lower virus counts compared to no mask control (p=0.027). Nasal swabs demonstrated very high virus exposure, which was not mitigated by the surgical or N95 masks, although there was a trend for the fit-tested N95 mask to reduce virus counts (p=0.058). The addition of HEPA filtration substantially reduced virus counts from all swab sites, and to near zero levels when combined with a fit-tested N95 mask, gloves, gown and faces shield. Virus counts were substantially reduced to near zero levels following a shower. These data demonstrate that quantitatively fit tested N95 masks combined with a HEPA filter can offer protection against high virus aerosol loads at close range and for prolonged periods of time. Skin contamination from virus aerosol can be effectively by removed by showering. Epworth Hospital Capacity Building Research Grant ID: EH2020-654
Publisher: MDPI AG
Date: 31-08-2022
DOI: 10.3390/LIFE12091353
Abstract: Avian pathogenic Escherichia coli (APEC) is an important extra-intestinal pathogenic E. coli (ExPEC), which often causes systemic infection in poultry and causes great economic loss to the breeding industry. In addition, as a major source of human ExPEC infection, the potential zoonotic risk of APEC has been an ongoing concern. Previous studies have pointed out that APEC is a potential zoonotic pathogen, which has high homology with human pathogenic E. coli such as uro-pathogenic E. coli (UPEC) and neonatal meningitis E. coli (NMEC), shares multiple virulence factors and can cause mammalian diseases. Previous studies have reported that O18 and O78 could cause different degrees of meningitis in neonatal rats, and different serotypes had different degrees of zoonotic risk. Here, we compared APEC DE205B (O2:K1) with NMEC RS218 (O18:K1:H7) by phylogenetic analysis and virulence gene identification to analyze the potential risk of DE205B in zoonotic diseases. We found that DE205B possessed a variety of virulence factors associated with meningitis and, through phylogenetic analysis, had high homology with RS218. DE205B could colonize the cerebrospinal fluid (CSF) of rats, and cause meningitis and nerve damage. Symptoms and pathological changes in the brain were similar to RS218. In addition, we found that DE205B had a complete T6SS, of which Hcp protein was its important structural protein. Hcp1 induced cytoskeleton rearrangement in human brain microvascular endothelial cells (HBMECs), and Hcp2 was mainly involved in the invasion of DE205B in vitro. In the meningitis model of rats, deletion of hcp2 gene reduced survival in the blood and the brain invasiveness of DE205B. Compared with WT group, Δhcp2 group induced lower inflammation and neutrophils infiltration in brain tissue, alleviating the process of meningitis. Together, these results suggested that APEC DE205B had close genetic similarities to NMEC RS218, and a similar mechanism in causing meningitis and being a risk for zoonosis. This APEC serotype provided a basis for zoonotic research.
Publisher: American Society for Microbiology
Date: 29-06-2022
DOI: 10.1128/SPECTRUM.00232-22
Abstract: With the increasing severity of antibiotic resistance and other adverse consequences, animal experiments and clinical trials investigating the use of phages for the control and prevention of enteric bacterial infections are growing. However, the effects of phages and antibiotics on organisms when treating intestinal infections have not been precisely studied.
Publisher: Scientific Research Publishing, Inc.
Date: 2014
Publisher: Elsevier BV
Date: 06-2022
Publisher: Informa UK Limited
Date: 03-2018
DOI: 10.1111/CXO.12621
Abstract: Treatment of Pseudomonas aeruginosa eye infections often becomes a challenge due to the ability of this bacterium to be resistant to antibiotics via intrinsic and acquired mechanisms. Transfer of resistance due to interchangeable genetic elements is an important mechanism for the rapid transfer of antibiotic resistance in this pathogen. As a result, drug-resistant strains are becoming increasingly prevalent worldwide. This review systematically analyses data from recent publications to describe the global prevalence and antibiotic sensitivity of ocular P. aeruginosa. Thirty-seven studies were selected for review from PubMed-based searches using the criteria 'microbial keratitis OR eye infection AND Pseudomonas aeruginosa AND antibiotic resistance' and limiting to papers from 2011 onward, to demonstrate the antibiotic resistance from isolates from around the world. Subsequently, we reviewed the ways in which P. aeruginosa can become resistant to antibiotics. Both the rate of isolation of bacteria in general (79 per cent of cases), and prevalence of P. aeruginosa (68 per cent of all isolates) were highest in contact lens-related microbial keratitis. The average resistance rate to common ocular antibiotics such as ciprofloxacin (9 per cent), gentamicin (22 per cent) and ceftazidime (13 per cent) remained relatively low. However, there were large variations in resistance rates reported in studies from different countries, for ex le resistance to ciprofloxacin reached up to 33 per cent. We next reviewed the types of mobile genetic elements (MGEs) such as plasmids, integrons and transposons that are frequently associated with drug resistance in P. aeruginosa. MGEs are important for the transmission of resistance to beta-lactams and aminoglycosides and recently have been shown to be potential factors for the transmission of fluoroquinolone resistance. Studies on the molecular mechanisms of resistance transfer in ocular P. aeruginosa have begun to be reported and will provide valuable information on the emergence of new antibiotic resistance and potential to treat resistant strains.
Publisher: Public Library of Science (PLoS)
Date: 15-04-2019
Publisher: Springer Science and Business Media LLC
Date: 07-02-2020
DOI: 10.1186/S41182-020-0194-1
Abstract: Dengue is a mosquito-borne viral infection. Since the first reported incidence in 2004, several sporadic outbreaks of dengue have been recorded from both tropical and subtropical regions of Nepal, including the capital city Kathmandu. However, in the last 5 years, the incidence of dengue cases has risen alarmingly. The largest-ever outbreak was reported in 2019, which killed six people. The global warming, unplanned urbanization, increased transportation, and lack of efficient mosquito control are presumably associated with the spread of dengue and its vector to the plane and hilly regions of this country. With the ongoing Nepalese government c aign “Visit Nepal Year 2020” to attract two million tourists in mind, effective dengue control measures must be implemented to control potential future outbreaks.
Publisher: Association for Research in Vision and Ophthalmology (ARVO)
Date: 23-03-2021
DOI: 10.1167/IOVS.62.3.33
Publisher: Cold Spring Harbor Laboratory
Date: 29-07-2022
DOI: 10.1101/2022.07.24.22277784
Abstract: Healthcare workers treating patients with SARS-CoV-2 are at risk of infection from patient-emitted virus-laden aerosols. We quantified the reduction of airborne infectious virus in a simulated hospital room when a ventilated patient isolation (McMonty) hood was in use. We nebulised 10 9 plaque forming units (PFU) of bacteriophage PhiX174 virus into a 35.1m 3 room with a hood active or inactive. The airborne concentration of infectious virus was measured by BioSpot-VIVAS and settle plates using plaque assay quantification on the bacterial host Escherichia coli C . The particle number concentration (PNC) was monitored continuously using an optical particle sizer. Median airborne viral concentration in the room reached 1.41 × 10 5 PFU.m -3 with the hood inactive. Using the active hood as source containment reduced infectious virus concentration by 374-fold in air s les. This was associated with a 109-fold reduction in total airborne particle number escape rate. The deposition of infectious virus on the surface of settle plates was reduced by 87-fold. The isolation hood significantly reduced airborne infectious virus exposure in a simulated hospital room. Our findings support the use of the hood to limit exposure of healthcare workers to airborne virus in clinical environments. COVID-19 patients exhale aerosol particles which can potentially carry infectious viruses into the hospital environment, putting healthcare workers at risk of infection. This risk can be reduced by proper use of personal protective equipment (PPE) to protect workers from virus exposure. More effective strategies, however, aim to provide source control, reducing the amount of virus-contaminated air that is exhaled into the hospital room. The McMonty isolation hood has been developed to trap and decontaminate the air around an infected patient. We tested the efficacy of the hood using a live virus model to mimic a COVID-19 patient in a hospital room. Using the McMonty hood reduced the amount of exhaled air particles in the room by over 109-times. In our tests, people working in the room were exposed to 374-times less infectious virus in the air, and room surfaces were 87-times less contaminated. Our study supports using devices like the McMonty hood in combination with PPE to keep healthcare workers safe from virus exposure at work.
Publisher: Springer Science and Business Media LLC
Date: 29-09-2022
DOI: 10.1186/S12879-022-07741-4
Abstract: Acanthamoeba is an emerging pathogen, infamous for its resilience against antiprotozoal compounds, disinfectants and harsh environments. It is known to cause keratitis, a sight-threatening, painful and difficult to treat corneal infection which is often reported among contact lens wearers and patients with ocular trauma. Acanthamoeba comprises over 24 species and currently 23 genotypes (T1-T23) have been identified. This retrospective study was designed to examine the Acanthamoeba species and genotypes recovered from patients with Acanthamoeba keratitis (AK), determine the presence of endosymbionts in ocular isolates of Acanthamoeba and review the clinical presentations. Thirteen culture-confirmed AK patients treated in a tertiary eye care facility in Hyderabad, India from February to October 2020 were included in this study. The clinical manifestations, medications and visual outcomes of all patients were obtained from medical records. The Acanthamoeba isolates were identified by sequencing the ribosomal nuclear subunit ( rns ) gene. Acanthamoeba isolates were assessed for the presence of bacterial or fungal endosymbionts using molecular assays, PCR and fluorescence in situ hybridization (FISH). The mean age of the patients was 33 years (SD ± 17.4 95% CI 22.5 to 43.5 years). Six (46.2%) cases had AK associated risk factors four patients had ocular trauma and two were contact lens wearers. A. culbertsoni (6/13, 46.2%) was the most common species, followed by A. polyphaga and A. triangularis . Most of the isolates (12/13) belonged to genotype T4 and one was a T12 three sub-clusters T4A, T4B, and T4F were identified within the T4 genotype. There was no significant association between Acanthamoeba types and clinical outcomes. Eight (61.5%) isolates harboured intracellular bacteria and one contained Malassezia restricta . The presence of intracellular microbes was associated with a higher proportion of stromal infiltrates (88.9%, 8/9), epithelial defect (55.6%, 5/9) and hypopyon (55.6%, 5/9) compared to 50% (2/4), 25% (1/4) and 25% (1/4) AK cases without intracellular microbes, respectively. Genotype T4 was the predominant isolate in southern India. This is the second report of T12 genotype identified from AK patient in India, which is rarely reported worldwide. The majority of the Acanthamoeba clinical isolates in this study harboured intracellular microbes, which may impact clinical characteristics of AK.
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MA19048
Publisher: Oxford University Press (OUP)
Date: 13-03-2018
DOI: 10.1093/JAC/DKY073
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2020
DOI: 10.1101/2020.09.04.20187922
Abstract: Nosocomial transmission of SARS-CoV-2 has been a major cause of morbidity and mortality in the COVID-19 pandemic. Emerging evidence suggests patients auto-emit aerosols containing viable respiratory viruses. These aerosols could be further propagated when patients undergo certain treatments including continuous positive airway pressure (PAP) therapy. This study aimed to assess the degree of viable virus propagated from mask leak in a PAP circuit and the mitigation of virus propagation by an air filter combined with a plastic canopy. Bacteriophage PhiX174 (10 8 copies/mL) was nebulised into a custom PAP circuit within a non-vented clinical room. Mask leak was systematically varied to allow 0, 7, 21, 28 and 42 L/min at the mask interface. Plates containing Escherichia coli host assessed the degree of viable virus (via plaque forming unit) settling on surfaces around the room. In order to contain virus spread, the efficacy of a simple, low-cost ventilated headboard, created from a plastic tarpaulin hood and a high efficiency particulate air (HEPA) filter was tested. Increasing mask leak was associated with virus contamination in a dose response manner (χ 2 = 58.24, df = 4, p 0.001). Clinically relevant levels of leak (≥21 L/min) were associated with virus counts equivalent to using PAP with a standard vented mask. The highest frequency of viruses was detected on surfaces 1m from the leak source, however, viable viruses were recorded on all plates (up to 3.86m from source). A plastic hood with HEPA filtration significantly reduced viable viruses on all plates. HEPA exchange rates of 170 and 470m 3 /hr eradicated all evidence of virus contamination. Mask leak from PAP circuits may be a major source of environmental contamination and nosocomial spread of infectious respiratory diseases. Subclinical levels of leak should be treated as an infectious risk. Cheap and low-cost patient hoods with HEPA filtration are an effective countermeasure. National Health and Medical Research Council of Australia (1139745). Nosocomial spread of SARS-CoV-2 results in increased infection rates among healthcare workers compared to the general population. Those workers involved in the delivery of non-invasive ventilation are at higher risk based on evidence from previous SARS outbreaks. However, little is known about virus aerosol spread and environmental contamination from respiratory interventions like non-invasive ventilation, which is one of few life-saving treatments for COVID-19 patients. We therefore searched through PubMed with no language restrictions from inception to August 21, 2020 using the search terms ([NIV] or [non-invasive ventilation] or [noninvasive ventilation] or [CPAP] or [continuous positive airways pressure] or [PAP] or [positive airways pressure]) and ([aerosol spread] or [aerosol dispersion] or [aerosol generation]). The search returned 130 publications of which 28 related to the generation or spread of aerosols. Of the 28 related papers, 17 were consensus or opinion papers, 4 were reviews and 7 were original research papers. All previous studies investigating aerosol propagation with respiratory interventions utilised particle sizers or smoke visualisation techniques. These methodological limitations mean that particles are counted or visualised close to the aerosol source and reveal little about wider aerosol spread. Furthermore, they ignore the inherent biological aspects of viral aerosol dispersion in that the aerosol needs to contain viable virus in order to be infectious. It has not been directly established that clinical respiratory interventions are capable of propagating viable virus aerosol and no attempt has been made to systematically quantify the degree of environmental contamination from viable virus aerosol escaping from non-invasive ventilation circuits. There are no current studies informing us as to the effectiveness of air filtration interventions at mitigating environmental contamination with viable virus aerosol escaping from non-invasive ventilation circuits. Our study quantifies the degree of viable virus aerosol spread from clinically relevant levels of noninvasive ventilator circuit mask leak, and demonstrates a risk mitigation strategy using a hood and air-purifier at completely eliminating viable virus aerosol environmental contamination. We developed a viable virus aerosol model utilising bacteriophage PhiX174 which is similar in size to SARS-CoV-2 and is harmless to humans. Through nebulising a solution of PhiX174 into a custom ventilation circuit with controllable mask leak settings, we were able to demonstrate that increasing circuit leak was associated with environmental virus contamination in a dose response manner (p 0.001). Even sub-clinically apparent levels of circuit leak ( 7L/min) were associated with detectable virus propagation up to 3.86 metres from the leak source. Deployment of a hood and air-purifier setup as described by the United States Centres for Disease Control and Prevention, completely eliminated environmental virus contamination from viral aerosol dispersion. Non-invasive ventilator circuit mask leak can propagate live virus containing aerosol and can lead to extensive environmental contamination up to 3.86 metres from the leak source, even at levels of leak that would be difficult to detect clinically. This raises important safety considerations for open wards delivering non-invasive ventilatory support and could explain the noted increased risk of nosocomial SARS infections in healthcare workers delivering non-invasive ventilation treatment. Point of emission air filtration with simple hood and air-purifier completely eliminates environmental contamination with viable virus and could be readily deployed to protect health care workers in the COVID-19 pandemic.
Publisher: Cold Spring Harbor Laboratory
Date: 18-08-2021
DOI: 10.1101/2021.08.15.21261997
Abstract: Rationale: We recently demonstrated that a patient hood with a high efficiency particulate air filter eliminates virus aerosol contamination when very large quantities of bacteriophage virus are aerosolised into a clinical room. While this containment method is relatively low cost, it is unclear whether similar efficacy can be achieved with lower cost/commercial grade air purifiers, or if such an approach protects healthcare workers against virus aerosol contamination. Method: A total of 109 (10 ml of 108) PhiX174 bacteriophages was nebulized into a sealed clinical room. Surface contamination was detected by settle plates left uncovered during exposure. A healthcare worker remained in the room, personal exposure was determined by skin swabs after exiting the room, following doffing of personal protective equipment (PPE). Four skin areas were swabbed: forearms/hands, neck, forehead, under N95 mask. Three conditions were tested, 1) hood with hospital grade air purifier (IQ Air Health Pro 250), 2) hood with commercial air purifier (Philips 1000i), and 3) control (no hood/air-purification). Findings: The control condition demonstrated extensive environmental and limited skin contamination underneath PPE, which was highest under an N95 mask. The commercial air purifier and hood provided environmental control of virus aerosol and almost zero skin contamination. In comparison, the hospital grade purifier provided complete environmental and skin contamination protection, despite a lower clean air filtration rate (240m3/hr vs 270m3/hr). Virus counts on plates and swabs were significantly lower for both air purifiers and across neck, forehead, and under the N95. There were no statistically significant differences in detected virus counts between air purifiers. Conclusion: This cheap and scalable method may be an effective way to reduce the spread of COVID-19 in hospitals by enhancing the effectiveness of PPE worn by health care workers who care for COVID-19 patients and who are exposed to virus aerosol.
Publisher: Elsevier BV
Date: 06-2023
Publisher: American Society for Microbiology
Date: 23-02-2021
DOI: 10.1128/MSYSTEMS.00990-20
Abstract: T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology, from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories.
Publisher: Cold Spring Harbor Laboratory
Date: 18-08-2023
DOI: 10.1101/2023.08.17.553642
Abstract: Large-scale metagenomic and data mining efforts have uncovered an expansive ersity of bacteriophages (phages) within the human gut 1–3 . These insights include broader phage populational dynamics such as temporal stability 4 , interin idual uniqueness 5,6 and potential associations to specific disease states 7,8 . However, the functional understanding of phage-host interactions and their impacts within this complex ecosystem have been limited due to a lack of cultured isolates for experimental validation. Here we characterise 125 active prophages originating from 252 erse human gut bacterial isolates using seven different induction conditions to substantially expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 17% of computationally predicted prophages were induced with common induction agents and these exhibited distinct gene patterns compared to non-induced predictions. Active Bacteroidota prophages were among the most prevalent members of the gut virome, with extensive use of ersity generating retroelements and exhibiting broad host ranges. Moreover, active polylysogeny was present in 52% of studied gut lysogens and led to coordinated prophage induction across erse conditions. This study represents a substantial expansion of experimentally validated gut prophages, providing key insights into their ersity and genetics, including a genetic pathway for prophage domestication and demonstration that differential induction was complex and influenced by ergent prophage integration sites. More broadly, it highlights the importance of experimental validation alongside genomic based computational prediction to enable further functional understanding of these commensal viruses within the human gut.
Publisher: Cold Spring Harbor Laboratory
Date: 25-09-2020
DOI: 10.1101/2020.09.24.312751
Abstract: T-series phages have been model organisms for molecular biology since the 1940s. Given that these phages have been stocked, distributed, and propagated for decades across the globe, there exists the potential for genetic drift to accumulate between stocks over time. Here we compared the temporal stability and genetic relatedness of laboratory-maintained phage stocks with a T-series collection from 1972. Only the T-even phages produced viable virions. We obtained complete genomes of these T-even phages, along with two contemporary T4 stocks. Performing comparative genomics, we found 12 and 16 nucleotide variations, respectively, in the genomes of T2 and T6 whereas there were ~172 nucleotide variations between T4-sublines when compared with NCBI RefSeq genome. To account for the possibility of artefacts in the NCBI RefSeq, we used the 1972 T4 stock as a reference and compared genetic and phenotypic variations between T4-sublines. Genomic analysis predicted nucleotide variations in genes associated with DNA metabolism and structural proteins. We did not however, observe any differences in growth characteristics or host range between the T4-sublines. Our study highlights the potential for genetic drift between in idually maintained T-series phage stocks, yet after 48-years, this has not resulted in phenotypic alternations in these important model organisms. T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology – from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories. However, we observed genetic variability when compared contemporary sublines of T4-phages to a 48-year old stock of T4. This may have effects in the comparability of results obtained using T4 phage. Here, we highlighted the genomic differences between T4 sublines and examined phenotypic differences in phage replication parameters. We observed limited genomic changes but no phenotypic variations between T4 sublines. Our research highlights the possibility of genetic drift in model bacteriophages.
Publisher: Public Library of Science (PLoS)
Date: 11-03-2020
Publisher: Elsevier BV
Date: 03-2022
Publisher: Elsevier BV
Date: 04-2013
No related grants have been discovered for Dinesh Subedi.