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Rivas L, Duncan D, Wang J, Miller H, Wright J. Using CHROMagar™ STEC medium exclusively does not recover all clinically relevant Shiga toxin-producing Escherichia coli in Aotearoa, New Zealand. Lett Appl Microbiol 2024; 77:ovae033. [PMID: 38569656 DOI: 10.1093/lambio/ovae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/28/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Diagnostic laboratories in Aotearoa, New Zealand (NZ) refer cultures from faecal samples positive for Shiga toxin genes to the national Enteric Reference Laboratory for isolation of Shiga toxin-producing Escherichia coli (STEC) for epidemiological typing. As there was variation in the culture media being referred, a panel of 75 clinical isolates of STEC, representing 28 different serotypes, was used to assess six commercially available media and provide guidance to clinical laboratories. Recommendations were subsequently tested for a 3-month period, where STEC isolations and confirmations were assessed by whole genome sequencing analysis against the culture media referred. CHROMagar™ STEC (CH-STEC; CHROMagar Microbiology, Paris, France) or CH-STEC plus cefixime-tellurite sorbitol MacConkey agar was confirmed inferior to CH-STEC plus blood agar with vancomycin, cefsulodin, and cefixime (BVCC). The former resulted in fewer STEC types (n = 18) being confirmed compared to those from a combination of CH-STEC and BVCC (n = 42). A significant (P < .05) association with an STEC's ability to grow on CH-STEC and the presence of the ter gene cluster, and eae was observed. Culturing screen positive STEC samples onto both CH-STEC and BVCC ensures a consistently higher recovery of STEC from all clinical samples in NZ than CH-STEC alone.
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Affiliation(s)
- Lucia Rivas
- Institute of Environmental Science and Research (ESR), Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - David Duncan
- Institute of Environmental Science and Research (ESR), Wallaceville Science Centre, 66 Ward Street, Wallaceville, Upper Hutt 5018, New Zealand
| | - Jing Wang
- Institute of Environmental Science and Research (ESR), Kenepuru Science Centre, 34 Kenepuru Drive, Kenepuru, Porirua 5022, New Zealand
| | - Hilary Miller
- Institute of Environmental Science and Research (ESR), Kenepuru Science Centre, 34 Kenepuru Drive, Kenepuru, Porirua 5022, New Zealand
| | - Jackie Wright
- Institute of Environmental Science and Research (ESR), Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
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2
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Monte DFM, Gonzalez-Escalona N, Cao G, Pedrosa GTDS, Saraiva MMS, Balkey M, Jin Q, Brown E, Allard M, Macarisin D, Magnani M. Genomic analysis of a cAmpC (CMY-41)-producing Citrobacter freundii ST64 isolated from patient. Lett Appl Microbiol 2024; 77:ovae010. [PMID: 38327245 DOI: 10.1093/lambio/ovae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
Antibiotic resistance in Citrobacter freundii is a public health concern. This study evaluated the closed genome of a C. freundii isolated from the stool of a hospitalized patient initially related to a Salmonella outbreak. Confirmation of the isolate was determined by whole-genome sequencing. Nanopore sequencing was performed using a MinION with a Flongle flow cell. Assembly using SPAdes and Unicycler yielded a closed genome annotated by National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline. Genomic analyses employed MLST 2.0, ResFinder4.1, PlasmidFinder2.1, and VFanalyzer. Phylogenetic comparison utilized the Center for Food Safety and Applied Nutrition (CFSAN)-single nucleotide polymorphism pipeline and Genetic Algorithm for Rapid Likelihood Inference. Antimicrobial susceptibility was tested by broth microdilution following Clinical and Laboratory Standards Institute criteria. Multi-locus sequence type in silico analysis assigned the C. freundii as sequence type 64 and the blaCMY-41 gene was detected in resistome investigation. The susceptibility to antibiotics, determined using Sensititre® plates, revealed resistance to aztreonam, colistin, cefoxitin, amoxicillin/clavulanic acid, sulfisoxazole, ampicillin, and streptomycin. The genetic relatedness of the C. freundii CFSAN077772 with publicly available C. freundii genomes revealed a close relationship to a C. freundii SRR1186659, isolated in 2009 from human stool in Tanzania. In addition, C. freundii CFSAN077772 is nested in the same cluster with C. freundii clinical strains isolated in Denmark, Mexico, Myanmar, and Canada, suggesting a successful intercontinental spread.
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Affiliation(s)
- Daniel F M Monte
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397000, Brazil
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Guojie Cao
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Geany Targino de Souza Pedrosa
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Paraíba, João Pessoa, PB 58059900, Brazil
| | - Mauro M S Saraiva
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900, Brazil
| | - Maria Balkey
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Qing Jin
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Eric Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Marc Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Dumitru Macarisin
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Marciane Magnani
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Paraíba, João Pessoa, PB 58059900, Brazil
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Yang S, Kozyreva VK, Timme RE, Hemarajata P. Editorial: Integration of NGS in clinical and public health microbiology workflows: applications, compliance, quality considerations. Front Public Health 2024; 12:1357098. [PMID: 38322128 PMCID: PMC10845330 DOI: 10.3389/fpubh.2024.1357098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 02/08/2024] Open
Affiliation(s)
- Shangxin Yang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Varvara K. Kozyreva
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, CA, United States
| | - Ruth E. Timme
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - Peera Hemarajata
- Association of Public Health Laboratories, Silver Spring, MD, United States
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Sampedro F, Garcés-Vega F, Strickland AJ, Hedberg CW. Developing a risk management framework to improve public health outcomes by enumerating and serotyping Salmonella in ground turkey. Epidemiol Infect 2024; 152:e12. [PMID: 38185825 PMCID: PMC10804136 DOI: 10.1017/s0950268823002029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Salmonella enterica continues to be a leading cause of foodborne morbidity worldwide. A quantitative risk assessment model was developed to evaluate the impact of pathogen enumeration and serotyping strategies on public health after consumption of undercooked contaminated ground turkey in the USA. The risk assessment model predicted more than 20,000 human illnesses annually that would result in ~700 annual reported cases. Removing ground turkey lots contaminated with Salmonella exceeding 10 MPN/g, 1 MPN/g, and 1 MPN/25 g would decrease the mean number of illnesses by 38.2, 73.1, and 95.0%, respectively. A three-class mixed sampling plan was tested to allow the detection of positive lots above threshold levels with 2-6 (c = 1) and 3-8 samples per lot (c = 2) using 25-g and 325-g sample sizes for a 95% probability of rejecting a contaminated lot. Removal of positive lots with the presence of highly virulent serotypes would decrease the number of illnesses by 44.2-87.0%. Based on these model prediction results, risk management strategies should incorporate pathogen enumeration and/or serotyping. This would have a direct impact on illness incidence linking public health outcomes with measurable food safety objectives, at the cost of diverting production lots.
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Affiliation(s)
- Fernando Sampedro
- Environmental Health Sciences Division, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | | | - Ali J. Strickland
- Environmental Health Sciences Division, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Craig W. Hedberg
- Environmental Health Sciences Division, School of Public Health, University of Minnesota, Minneapolis, MN, USA
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Lim AYH, Ang MLT, Cho SSL, Ng DHL, Cutter J, Lin RTP. Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019-2022. Microb Genom 2023; 9. [PMID: 38010371 DOI: 10.1099/mgen.0.001139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
The National Tuberculosis Programme (NTBP) monitors the occurrence and spread of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) in Singapore. Since 2020, whole-genome sequencing (WGS) of Mycobacterium tuberculosis isolates has been performed at the National Public Health Laboratory (NPHL) for genomic surveillance, replacing spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeats analysis (MIRU-VNTR). Four thousand three hundred and seven samples were sequenced from 2014 to January 2023, initially as research projects and later developed into a comprehensive public health surveillance programme. Currently, all newly diagnosed culture-positive cases of TB in Singapore are prospectively sent for WGS, which is used to perform lineage classification, predict drug resistance profiles and infer genetic relationships between TB isolates. This paper describes NPHL's operational and technical experiences with implementing the WGS service in an urban TB-endemic setting, focusing on cluster detection and genomic drug susceptibility testing (DST). Cluster detection: WGS has been used to guide contact tracing by detecting clusters and discovering unknown transmission networks. Examples have been clusters in a daycare centre, housing apartment blocks and a horse-racing betting centre. Genomic DST: genomic DST prediction (gDST) identifies mutations in core genes known to be associated with TB drug resistance catalogued in the TBProfiler drug resistance mutation database. Mutations are reported with confidence scores according to a standardized approach referencing NPHL's internal gDST confidence database, which is adapted from the World Health Organization (WHO) TB drug mutation catalogue. Phenotypic-genomic concordance was observed for the first-line drugs ranging from 2959/2998 (98.7 %) (ethambutol) to 2983/2996 (99.6 %) (rifampicin). Aspects of internal database management, reporting standards and caveats in results interpretation are discussed.
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Affiliation(s)
- Ansel Yi Herh Lim
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Michelle L T Ang
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Sharol S L Cho
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Deborah H L Ng
- National Tuberculosis Programme, National Centre for Infectious Diseases, Singapore, Singapore
| | - Jeffery Cutter
- National Tuberculosis Programme, National Centre for Infectious Diseases, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
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Motro Y, Wajnsztajn D, Michael-Gayego A, Mathur S, Marano RB, Salah I, Rosenbluh C, Temper V, Strahilevitz J, Moran-Gilad J. Metagenomic sequencing for investigation of a national keratoconjunctivitis outbreak, Israel, 2022. Euro Surveill 2023; 28:2300010. [PMID: 37535472 PMCID: PMC10401915 DOI: 10.2807/1560-7917.es.2023.28.31.2300010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/20/2023] [Indexed: 08/05/2023] Open
Abstract
BackgroundEpidemics of keratoconjunctivitis may involve various aetiological agents. Microsporidia are an uncommon difficult-to-diagnose cause of such outbreaks.AimDuring the third quarter of 2022, a keratoconjunctivitis outbreak was reported across Israel, related to common water exposure to the Sea of Galilee. We report a comprehensive diagnostic approach that identified Vittaforma corneae as the aetiology, serving as proof of concept for using real-time metagenomics for outbreak investigation.MethodsCorneal scraping samples from a clinical case were subjected to standard microbiological testing. Samples were tested by calcofluor white staining and metagenomic short-read sequencing. We analysed the metagenome for taxonomical assignment and isolation of metagenome-assembled genome (MAG). Targets for a novel PCR were identified, and the assay was applied to clinical and environmental samples and confirmed by long-read metagenomic sequencing.ResultsFluorescent microscopy was suggestive of microsporidiosis. The most abundant species (96.5%) on metagenomics analysis was V. corneae. Annotation of the MAG confirmed the species assignment. A unique PCR target in the microsporidian rRNA gene was identified and validated against the clinical sample. The assay and metagenomic sequencing confirmed V. corneae in an environmental sludge sample collected at the exposure site.ConclusionsThe real-time utilisation of metagenomics allowed species detection and development of diagnostic tools, which aided in outbreak source tracking and can be applied for future cases. Metagenomics allows a fully culture-independent investigation and is an important modality for public health microbiology.
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Affiliation(s)
- Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
- These authors contributed equally to the manuscript and share first authorship
| | - Denise Wajnsztajn
- Department of Ophthalmology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- These authors contributed equally to the manuscript and share first authorship
| | - Ayelet Michael-Gayego
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Shubham Mathur
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Roberto Bm Marano
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Ikram Salah
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Chaggai Rosenbluh
- Department of Genetics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Violeta Temper
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Jacob Strahilevitz
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
- Clinical Microbiology Laboratory, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
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7
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Rossella B, Stefania P, Paradiso R, Semproni M, Lucia B. Survival of Different Microbial Strains in Pure and Diluted Tattoo Inks. Lett Appl Microbiol 2023:ovad078. [PMID: 37410617 DOI: 10.1093/lambio/ovad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Several microorganisms can be found in tattoo inks injected into the skin, despite the ink matrix being considered inhospitable to microbial growth. Studies on the microbial quality of tattoo inks have reported the presence of microorganisms in most of the samples. This study aimed to assess the survival of environmental and human microbial species, selected on the specific criteria, in tattoo inks. Undiluted sterile black ink and serial dilutions (10-fold/100-fold) were each separately seeded with four bacterial strains (S. aureus, P. aeruginosa, B. pumilus, M. fortuitum), one yeast (C. albicans), and one mold (F. solani). Their survival was periodically tested using cultural methods. No tested microorganisms were able to survive in undiluted ink, except for B. pumilus which survived up to 3 weeks. All the tested species, except for S. aureus, showed survivability for up to 10 weeks in 100-fold diluted inks, and P. aeruginosa, M. fortuitum and C. albicans were even able to grow. B. pumilus and F. solani had good rates of survival even at the smallest dilution. The ability of microorganisms to survive and grow in tattoo inks could have health implications if contaminated ink dilutions are used during tattooing practices and stored for a long time.
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Affiliation(s)
- Briancesco Rossella
- Department of Environment and Health, Italian National Institute of Health, 00161, Rome, Italy
| | - Paduano Stefania
- Department of Biomedical, Metabolic and Neural Sciences, Section of Public Health, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Rosa Paradiso
- Department of Environment and Health, Italian National Institute of Health, 00161, Rome, Italy
| | - Maurizio Semproni
- Department of Environment and Health, Italian National Institute of Health, 00161, Rome, Italy
| | - Bonadonna Lucia
- Department of Environment and Health, Italian National Institute of Health, 00161, Rome, Italy
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Abstract
With the adoption of infection science as an umbrella term for the disciplines that inform our ideas of infection, there is a need for a common language that links infection's constituent parts. This paper develops a conceptual framework for infection science from the major themes used to understand causal relationships in infectious diseases. The paper proposes using the four main themes from the Principia Aetiologica to classify infection knowledge into four corresponding domains: Clinical microbiology, Public health microbiology, Mechanisms of microbial disease and Antimicrobial countermeasures. This epistemology of infection gives form and process to a revised infection ontology and an infectious disease heuristic. Application of the proposed epistemology has immediate practical implications for organization of journal content, promotion of inter-disciplinary collaboration, identification of emerging priority themes, and integration of cross-disciplinary areas such as One Health topics and antimicrobial resistance. Starting with these foundations, we can build a coherent narrative around the idea of infection that shapes the practice of infection science.
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Affiliation(s)
- Timothy J J Inglis
- School of Medicine, University of Western Australia, Nedlands, WA 6009, Australia.,PathWest Laboratory Medicine WA, Nedlands,, WA 6009, Australia.,Western Australian Country Health Service, Perth, WA 6000, Australia
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Gabbassov E, Moreno-Molina M, Comas I, Libbrecht M, Chindelevitch L. SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data. Microb Genom 2021; 7. [PMID: 34165419 PMCID: PMC8461467 DOI: 10.1099/mgen.0.000607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The occurrence of multiple strains of a bacterial pathogen such as M. tuberculosis or C. difficile within a single human host, referred to as a mixed infection, has important implications for both healthcare and public health. However, methods for detecting it, and especially determining the proportion and identities of the underlying strains, from WGS (whole-genome sequencing) data, have been limited. In this paper we introduce SplitStrains, a novel method for addressing these challenges. Grounded in a rigorous statistical model, SplitStrains not only demonstrates superior performance in proportion estimation to other existing methods on both simulated as well as real M. tuberculosis data, but also successfully determines the identity of the underlying strains. We conclude that SplitStrains is a powerful addition to the existing toolkit of analytical methods for data coming from bacterial pathogens and holds the promise of enabling previously inaccessible conclusions to be drawn in the realm of public health microbiology.
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Affiliation(s)
- Einar Gabbassov
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
- *Correspondence: Einar Gabbassov,
| | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Valencia, Spain
| | - Maxwell Libbrecht
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, UK
- *Correspondence: Leonid Chindelevitch,
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Butt S, Smith-Palmer A, Shand A, McDonald E, Allison L, Maund J, Fernandes A, Vishram B, Greig DR, Jenkins C, Elson R; Outbreak Control Team. Evidence of on-going transmission of Shiga toxin-producing Escherichia coli O157:H7 following a foodborne outbreak. Epidemiol Infect 2021; 149:e147. [PMID: 34096488 DOI: 10.1017/S0950268821001278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In August 2019, public health surveillance systems in Scotland and England identified seven, geographically dispersed cases infected with the same strain (defined as isolates that fell within the same five single nucleotide polymorphism single linage cluster) of Shiga toxin-producing Escherichia coli O157:H7. Epidemiological analysis of enhanced surveillance questionnaire data identified handling raw beef and shopping from the same national retailer (retailer A) as the common exposure. Concurrently, a microbiological survey of minced beef at retail identified the same strain in a sample of minced beef sold by retailer A, providing microbiological evidence of the link. Between September and November 2019, a further four primary and two secondary cases infected with the same strain were identified; two cases developed haemolytic uraemic syndrome. None of the four primary cases reported consumption of beef from retailer A and the transmission route of these subsequent cases was not identified, although all four primary cases visited the same petting farm. Generally, outbreaks of STEC O157:H7 in the UK appear to be distinct, short-lived events; however, on-going transmission linked to contaminated food, animals or environmental exposures and person-to-person contact do occur. Although outbreaks of STEC caused by contaminated fresh produce are increasingly common, undercooked meat products remain a risk of infection.
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Greenman NA, Jurgensen SK, Holmes CP, Kapsak CJ, Davis RE, Maza WM, Edemba D, Esser BA, Hise SM, Keen TN, Larson HG, Lockwood DJ, Wang B, Harsh JA, Herrick JB. Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens. Front Microbiol 2021; 12:592422. [PMID: 33967968 PMCID: PMC8100199 DOI: 10.3389/fmicb.2021.592422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
We have developed and implemented an undergraduate microbiology course in which students isolate, characterize, and perform whole genome assembly and analysis of Salmonella enterica from stream sediments and poultry litter. In the development of the course and over three semesters, successive teams of undergraduate students collected field samples and performed enrichment and isolation techniques specific for the detection of S. enterica. Eighty-eight strains were confirmed using standard microbiological methods and PCR of the invA gene. The isolates' genomes were Illumina-sequenced by the Center for Food Safety and Applied Nutrition at the FDA and the Virginia state Division of Consolidated Laboratory Services as part of the GenomeTrakr program. Students used GalaxyTrakr and other web- and non-web-based platforms and tools to perform quality control on raw and assembled sequence data, assemble, and annotate genomes, identify antimicrobial resistance and virulence genes, putative plasmids, and other mobile genetic elements. Strains with putative plasmid-borne antimicrobial resistance genes were further sequenced by students in our research lab using the Oxford Nanopore MinIONTM platform. Strains of Salmonella that were isolated include human infectious serotypes such as Typhimurium and Infantis. Over 31 of the isolates possessed antibiotic resistance genes, some of which were located on large, multidrug resistance plasmids. Plasmid pHJ-38, identified in a Typhimurium isolate, is an apparently self-transmissible 183 kb IncA/C2 plasmid that possesses multiple antimicrobial resistance and heavy-metal resistance genes. Plasmid pFHS-02, identified in an Infantis isolate, is an apparently self-transmissible 303 kb IncF1B plasmid that also possesses numerous heavy-metal and antimicrobial resistance genes. Using direct and indirect measures to assess student outcomes, results indicate that course participation contributed to cognitive gains in relevant content knowledge and research skills such as field sampling, molecular techniques, and computational analysis. Furthermore, participants self-reported a deeper interest in scientific research and careers as well as psychosocial outcomes (e.g., sense of belonging and self-efficacy) commonly associated with student success and persistence in STEM. Overall, this course provided a powerful combination of field, wet lab, and computational biology experiences for students, while also providing data potentially useful in pathogen surveillance, epidemiological tracking, and for the further study of environmental reservoirs of S. enterica.
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Affiliation(s)
- Noah A. Greenman
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Sophie K. Jurgensen
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Charles P. Holmes
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Curtis J. Kapsak
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Raechel E. Davis
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - William M. Maza
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Desiree Edemba
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Bethany A. Esser
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Selena M. Hise
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Tara N. Keen
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Hunter G. Larson
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | | | - Brian Wang
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Joseph A. Harsh
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - James B. Herrick
- Department of Biology, James Madison University, Harrisonburg, VA, United States
- Center for Genome and Metagenome Studies, James Madison University, Harrisonburg, VA, United States
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Mikhail AFW, Pereboom M, Utsi L, Hawker J, Lighthill J, Aird H, Swindlehurst M, Greig DR, Jenkins C, Godbole G, Elson R. Utility of whole-genome sequencing during an investigation of multiple foodborne outbreaks of Shigella sonnei. Epidemiol Infect 2021; 149:e71. [PMID: 33641696 DOI: 10.1017/S0950268821000509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In April 2018, Public Health England was notified of cases of Shigella sonnei who had eaten food from three different catering outlets in England. The outbreaks were initially investigated as separate events, but whole-genome sequencing (WGS) showed they were caused by the same strain. The investigation included analyses of epidemiological data, the food chain and microbiological examination of food samples. WGS was used to determine the phylogenetic relatedness and antimicrobial resistance profile of the outbreak strain. Ultimately, 33 cases were linked to this outbreak; the majority had eaten food from seven outlets specialising in Indian or Middle Eastern cuisine. Five outlets were linked to two or more cases, all of which used fresh coriander although a shared supplier was not identified. An investigation at one of the venues recorded that 86% of cases reported eating dishes with coriander as an ingredient or garnish. Four cases were admitted to hospital and one had evidence of treatment failure with ciprofloxacin. Phylogenetic analysis showed that the outbreak strain was part of a wider multidrug-resistant clade associated with travel to Pakistan. Poor hygiene practices during cultivation, distribution or preparation of fresh produce are likely contributing factors.
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Baines SL, da Silva AG, Carter GP, Jennison A, Rathnayake I, Graham RM, Sintchenko V, Wang Q, Rockett RJ, Timms VJ, Martinez E, Ballard S, Tomita T, Isles N, Horan KA, Pitchers W, Stinear TP, Williamson DA, Howden BP, Seemann T. Complete microbial genomes for public health in Australia and the Southwest Pacific. Microb Genom 2020; 6:mgen000471. [PMID: 33180013 PMCID: PMC8116684 DOI: 10.1099/mgen.0.000471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.
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Affiliation(s)
- Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Amy Jennison
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Irani Rathnayake
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Rikki M. Graham
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Verlaine J. Timms
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Nicole Isles
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Kristy A. Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - William Pitchers
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Communicable Diseases Genomics Network (CDGN)
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
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Bajoriniene A, Leitmeyer KC, Struelens MJ, Kokki MH. Investing in Public Health Microbiology Laboratories in Western Balkan Countries Enhances Health Security From Communicable Disease Threats in Europe. Front Public Health 2019; 7:8. [PMID: 30778382 PMCID: PMC6369834 DOI: 10.3389/fpubh.2019.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/10/2019] [Indexed: 11/29/2022] Open
Abstract
The European Centre for Disease Prevention and Control (ECDC), under the EU enlargement policy, has supported national efforts of Western Balkan countries to strengthen their communicable disease prevention and control systems. The new EU strategy “A credible enlargement perspective for and enhanced EU engagement with the Western Balkans” advocates transformation processes that will build the foundation of EU-oriented national reforms. Well-functioning public health microbiology laboratories are key for early detection and control of infectious diseases, and thus maintaining and enhancing health security in Europe. In order to help Western Balkan countries to improve their national capacities, ECDC facilitated needs assessments and identified key areas for advancement toward effective public health microbiology systems. Countries identified gaps in their laboratory data reporting and exchange systems. Harmonized and effective procedures for handling of highly contagious agents and cross-border transportation of biological samples were often lacking, as well as the systematic use of diagnostic testing at the primary care level or referral of patients, in particular for detection of antimicrobial resistance. There is a clear need to address the financial investment required for sustaining sufficient numbers of skilled laboratory workforce, laboratory supplies, and the development of new methods and techniques, including investment in emerging laboratory technologies, such as molecular typing by whole genome sequencing. This article highlights the key areas for investing in public health microbiology laboratories in Western Balkan countries needed to strengthen health security in Europe.
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Affiliation(s)
- Agne Bajoriniene
- International Relations Section, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Katrin C Leitmeyer
- Microbiology Coordination Section, Office of the Chief Scientist, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Marc J Struelens
- Microbiology Coordination Section, Office of the Chief Scientist, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Maarit H Kokki
- International Relations Section, European Centre for Disease Prevention and Control, Stockholm, Sweden
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15
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Albiger B, Revez J, Leitmeyer KC, Struelens MJ. Networking of Public Health Microbiology Laboratories Bolsters Europe's Defenses against Infectious Diseases. Front Public Health 2018; 6:46. [PMID: 29535998 PMCID: PMC5834927 DOI: 10.3389/fpubh.2018.00046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/07/2018] [Indexed: 11/13/2022] Open
Abstract
In an era of global health threats caused by epidemics of infectious diseases and rising multidrug resistance, microbiology laboratories provide essential scientific evidence for risk assessment, prevention, and control. Microbiology has been at the core of European infectious disease surveillance networks for decades. Since 2010, these networks have been coordinated by the European Centre for Disease Prevention and Control (ECDC). Activities delivered in these networks include harmonization of laboratory diagnostic, antimicrobial susceptibility and molecular typing methods, multicentre method validation, technical capacity mapping, training of laboratory staff, and continuing quality assessment of laboratory testing. Cooperation among the European laboratory networks in the past 7 years has proved successful in strengthening epidemic preparedness by enabling adaptive capabilities for rapid detection of emerging pathogens across Europe. In partnership with food safety authorities, international public health agencies and learned societies, ECDC-supported laboratory networks have also progressed harmonization of routinely used antimicrobial susceptibility and molecular typing methods, thereby significantly advancing the quality, comparability and precision of microbiological information gathered by ECDC for surveillance for zoonotic diseases and multidrug-resistant pathogens in Europe. ECDC continues to act as a catalyst for sustaining continuous practice improvements and strengthening wider access to laboratory capacity across the European Union. Key priorities include optimization and broader use of rapid diagnostics, further integration of whole-genome sequencing in surveillance and electronic linkage of laboratory and public health systems. This article highlights some of the network contributions to public health in Europe and the role that ECDC plays managing these networks.
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Affiliation(s)
- Barbara Albiger
- Scientific Advice Coordination Section, Office of the Chief Scientist, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Joana Revez
- Microbiology Coordination Section, Office of the Chief Scientist, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Katrin Claire Leitmeyer
- Microbiology Coordination Section, Office of the Chief Scientist, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Marc J. Struelens
- Microbiology Coordination Section, Office of the Chief Scientist, European Centre for Disease Prevention and Control, Stockholm, Sweden
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MIKHAIL AFW, JENKINS C, DALLMAN TJ, INNS T, DOUGLAS A, MARTÍN AIC, FOX A, CLEARY P, ELSON R, HAWKER J. An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations. Epidemiol Infect 2018; 146:187-196. [PMID: 29248018 PMCID: PMC9134740 DOI: 10.1017/s0950268817002874] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 11/06/2022] Open
Abstract
In August 2015, Public Health England detected an outbreak of Shiga toxin-producing Escherichia coli (STEC) serotype O157:H7 caused by contaminated salad leaves in a mixed leaf prepacked salad product from a national retailer. The implicated leaves were cultivated at five different farms and the zoonotic source of the outbreak strain was not determined. In March 2016, additional isolates from new cases were identified that shared a recent common ancestor with the outbreak strain. A case-case study involving the cases identified in 2016 revealed that ovine exposures were associated with illness (n = 16; AOR 8·24; 95% CI 1·55-39·74). By mapping the recent movement of sheep and lambs across the United Kingdom, epidemiological links were established between the cases reporting ovine exposures. Given the close phylogenetic relationship between the outbreak strain and the isolates from cases with ovine exposures, it is plausible that ovine faeces may have contaminated the salad leaves via untreated irrigation water or run-off from fields nearby. Timely and targeted veterinary and environmental sampling should be considered during foodborne outbreaks of STEC, particularly where ready to eat vegetables and salads are implicated.
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Affiliation(s)
| | - C. JENKINS
- National Infection Service, Public Health England, London, UK
| | - T. J. DALLMAN
- National Infection Service, Public Health England, London, UK
| | - T. INNS
- Field Epidemiology Services, Public Health England, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, London, UK
| | - A. DOUGLAS
- National Infection Service, Public Health England, London, UK
| | - A. I. C. MARTÍN
- European Program for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - A. FOX
- National Infection Service, Public Health England, London, UK
| | - P. CLEARY
- Field Epidemiology Services, Public Health England, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, London, UK
| | - R. ELSON
- National Infection Service, Public Health England, London, UK
| | - J. HAWKER
- Field Epidemiology Services, Public Health England, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, London, UK
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Currie SL, Stephenson N, Palmer AS, Jones BL, Hawkins G, Alexander CL. Under-reporting giardiasis: time to consider the public health implications. Epidemiol Infect 2017; 145:3007-11. [PMID: 28879824 DOI: 10.1017/S0950268817001959] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Giardiasis is a treatable disease, caused by the flagellated protozoan parasite, Giardia duodenalis (G. duodenalis). It is one of the most common enteric parasites found globally to cause gastrointestinal disturbances, and infections may result in long-term irritable bowel syndrome-like symptoms. It is a common misconception that giardiasis is associated with foreign travel, which results in locally acquired cases in the UK being underdiagnosed. This report highlights the findings from one large Scottish Health Board, arising from a change in testing methodology, which resulted in the screening of all stools submitted for enteric investigations for G. duodenalis. Previous selection criteria were restricted to patients with a travel history to specific regions of the world, or on the basis of certain clinical details. In this report, clinical details were recorded from samples shown to be positive using two methods: an ELISA-based antigen detection assay and microscopy. Clinical details were assessed for a total of 28 laboratory-confirmed positive cases against the original selection criteria. Twenty-six cases (93%) would have been excluded from Giardia testing if the previous selection criteria had been applied. Although nine cases stated foreign travel, only two had been to regions deemed to be 'high risk'. Therefore, those seven cases that travelled to perceived 'low-risk' regions would have been excluded from testing for this reason. This summary highlights the need for significant improvements to the selection criteria for Giardia testing. Laboratories should be encouraged towards the testing of all routinely submitted stools for this neglected pathogen to ensure cases that are acquired locally are properly identified and treated effectively.
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18
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McCARTHY KL, Kidd TJ, Paterson DL. Pseudomonas aeruginosa blood stream infection isolates from patients with recurrent blood stream infection: Is it the same genotype? Epidemiol Infect 2017; 145:3040-6. [PMID: 28826423 DOI: 10.1017/S0950268817001832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The type identity of strains of Pseudomonas aeruginosa from primary and recurrent blood stream infection (BSI) has not been widely studied. Twenty-eight patients were identified retrospectively from 2008 to 2013 from five different laboratories; available epidemiological, clinical and microbiological data were obtained for each patient. Isolates were genotyped by iPLEX MassARRAY MALDI-TOF MS and rep-PCR. This showed that recurrent P. aeruginosa BSI was more commonly due to the same genotypically related strain as that from the primary episode. Relapse due to a genotypically related strain occurred earlier in time than a relapsing infection from an unrelated strain (median time: 26 vs. 91 days, respectively). Line related infections were the most common source of suspected BSI and almost half of all BSI episodes were associated with neutropenia, possibly indicating translocation of the organism from the patient's gut in this setting. Development of meropenem resistance occurred in two relapse isolates, which may suggest that prior antibiotic therapy for the primary BSI was a driver for the subsequent development of resistance in the recurrent isolate.
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BUTCHER H, ELSON R, CHATTAWAY MA, FEATHERSTONE CA, WILLIS C, JORGENSEN F, DALLMAN TJ, JENKINS C, McLAUCHLIN J, BECK CR, HARRISON S. Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk. Epidemiol Infect 2016; 144:2812-23. [PMID: 27338677 PMCID: PMC9150458 DOI: 10.1017/s0950268816000509] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 01/29/2016] [Accepted: 02/21/2016] [Indexed: 11/06/2022] Open
Abstract
Five cases of STEC O157 phage type (PT) 21/28 reported consumption of raw cows' drinking milk (RDM) produced at a dairy farm in the South West of England. STEC O157 PT21/28 was isolated from faecal specimens from milking cows on the implicated farm. Whole genome sequencing (WGS) showed that human and cattle isolates were the same strain. Further analysis of WGS data confirmed that sequences of isolates from an additional four cases (who did not report consumption of RDM when first questioned) fell within the same five single nucleotide polymorphism cluster as the initial five cases epidemiologically linked to the consumption of RDM. These four additional cases identified by WGS were investigated further and were, ultimately, associated with the implicated farm. The RDM outbreak strain encoded stx2a, which is associated with increased pathogenicity and severity of symptoms. Further epidemiological analysis showed that 70% of isolates within a wider cluster containing the outbreak strain were from cases residing in, or linked to, the same geographical region of England. During this RDM outbreak, use of WGS improved case ascertainment and provided insights into the evolution of a highly pathogenic clade of STEC O157 PT21/28 stx2a associated with the South West of England.
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Affiliation(s)
- H. BUTCHER
- Devon, Cornwall and Somerset Public Health England Centre, Exeter, Devon, UK
| | - R. ELSON
- Gastrointestinal and Emerging Zoonotic Infections Department, Public Health England, UK
| | - M. A. CHATTAWAY
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, UK
| | - C. A. FEATHERSTONE
- Animal and Plant Health Agency, Veterinary Investigation Centre, Thirsk, Yorkshire, UK
| | - C. WILLIS
- Food Water and Environmental Microbiology Laboratory Services, Public Health England, UK
| | - F. JORGENSEN
- Food Water and Environmental Microbiology Laboratory Services, Public Health England, UK
| | - T. J. DALLMAN
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, UK
| | - C. JENKINS
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, UK
| | - J. McLAUCHLIN
- Food Water and Environmental Microbiology Laboratory Services, Public Health England, UK
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - C. R. BECK
- Field Epidemiology Service, Public Health England, UK
| | - S. HARRISON
- Devon, Cornwall and Somerset Public Health England Centre, Exeter, Devon, UK
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ROWELL S, KING C, JENKINS C, DALLMAN TJ, DECRAENE V, LAMDEN K, HOWARD A, FEATHERSTONE CA, CLEARY P. An outbreak of Shiga toxin-producing Escherichia coli serogroup O157 linked to a lamb-feeding event. Epidemiol Infect 2016; 144:2494-500. [PMID: 27297133 PMCID: PMC9150456 DOI: 10.1017/s0950268816001229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/29/2016] [Accepted: 05/25/2016] [Indexed: 11/07/2022] Open
Abstract
Fifteen confirmed cases and 15 possible cases of Shiga toxin-producing Escherichia coli (STEC) O157 phage type 21/28 were linked to direct contact with lambs at a 'Lambing Live' event in the North West of England between 29 March and 21 April 2014. Twenty-one (70%) of the cases were female, 23 (77%) were children aged <16 years, of whom 14 (46%) were in the 0-5 years age group. Five children developed haemolytic uraemic syndrome. Multilocus variable number tandem repeat analysis (MLVA) profiles on 14 human cases were indistinguishable, and 6/10 animal isolates had a MLVA profile identical to the outbreak profile. Whole-genome sequencing analysis revealed that all isolates, both human and animal, fell within a 5-single nucleotide polymorphism cluster indicating the isolates belonged to the same point source. On inspection of the premises, extensive and uncontrolled physical contact between visitors and animals was occuring within the animal pens and during bottle-feeding. Public areas were visibly contaminated with animal faeces. Information to visitors, and the infection control awareness demonstrated by staff, was inadequate. Managing the risk to visitors of STEC O157 infection at animal petting events and open farms requires implementation of stringent control measures by the operator, as outlined in the industry code of practice. Enforcement action is sometimes required to prevent high-risk activities taking place at both permanent and temporary attractions.
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Affiliation(s)
- S. ROWELL
- Cumbria and Lancashire Public Health England Centre, Chorley, Lancashire, UK
| | - C. KING
- Cumbria and Lancashire Public Health England Centre, Chorley, Lancashire, UK
| | - C. JENKINS
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - T. J. DALLMAN
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - V. DECRAENE
- Field Epidemiology Service North West, Public Health England, UK
| | - K. LAMDEN
- Cumbria and Lancashire Public Health England Centre, Chorley, Lancashire, UK
| | - A. HOWARD
- South Ribble Borough Council, Leyland, Lancashire, UK
| | - C. A. FEATHERSTONE
- Animal and Plant Health Agency, Veterinary Investigation Centre, Thirsk, North Yorkshire, UK
| | - P. CLEARY
- Field Epidemiology Service North West, Public Health England, UK
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21
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Affiliation(s)
- Cath Arnold
- a Head of Genomic Services and Development Unit , National Infection Service, Public Health England , London , UK
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22
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Campe H, Heinzinger S, Hartberger C, Sing A. Clinical symptoms cannot predict influenza infection during the 2013 influenza season in Bavaria, Germany. Epidemiol Infect 2016; 144:1045-51. [PMID: 26388141 DOI: 10.1017/S0950268815002228] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
For influenza surveillance and diagnosis typical clinical symptoms are traditionally used to discriminate influenza virus infections from infections by other pathogens. During the 2013 influenza season we performed a multiplex assay for 16 different viruses in 665 swabs from patients with acute respiratory infections (ARIs) to display the variety of different pathogens causing ARI and to test the diagnostic value of both the commonly used case definitions [ARI, and influenza like illness (ILI)] as well as the clinical judgement of physicians, respectively, to achieve a laboratory-confirmed influenza diagnosis. Fourteen different viruses were identified as causing ARI/ILI. Influenza diagnosis based on clinical signs overestimated the number of laboratory-confirmed influenza cases and misclassified cases. Furthermore, ILI case definition and physicians agreed in only 287/651 (44%) cases with laboratory confirmation. Influenza case management has to be supported by laboratory confirmation to allow evidence-based decisions. Epidemiological syndromic surveillance data should be supported by laboratory confirmation for reasonable interpretation.
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23
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Dallman TJ, Ashton PM, Byrne L, Perry NT, Petrovska L, Ellis R, Allison L, Hanson M, Holmes A, Gunn GJ, Chase-Topping ME, Woolhouse MEJ, Grant KA, Gally DL, Wain J, Jenkins C. Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK. Microb Genom 2015; 1:e000029. [PMID: 28348814 PMCID: PMC5320567 DOI: 10.1099/mgen.0.000029] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/22/2015] [Indexed: 11/18/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) O157:H7 is a recently emerged zoonotic pathogen with considerable morbidity. Since the emergence of this serotype in the 1980s, research has focussed on unravelling the evolutionary events from the E. coli O55:H7 ancestor to the contemporaneous globally dispersed strains observed today. In this study, the genomes of over 1000 isolates from both human clinical cases and cattle, spanning the history of STEC O157:H7 in the UK, were sequenced. Phylogenetic analysis revealed the ancestry, key acquisition events and global context of the strains. Dated phylogenies estimated the time to evolution of the most recent common ancestor of the current circulating global clone to be 175 years ago. This event was followed by rapid diversification. We show the acquisition of specific virulence determinates has occurred relatively recently and coincides with its recent detection in the human population. We used clinical outcome data from 493 cases of STEC O157:H7 to assess the relative risk of severe disease including haemolytic uraemic syndrome from each of the defined clades in the population and show the dramatic effect Shiga toxin repertoire has on virulence. We describe two strain replacement events that have occurred in the cattle population in the UK over the last 30 years, one resulting in a highly virulent strain that has accounted for the majority of clinical cases in the UK over the last decade. There is a need to understand the selection pressures maintaining Shiga-toxin-encoding bacteriophages in the ruminant reservoir and the study affirms the requirement for close surveillance of this pathogen in both ruminant and human populations.
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Affiliation(s)
| | - Philip M Ashton
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Lisa Byrne
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Neil T Perry
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Liljana Petrovska
- Animal Laboratories and Plant Health Agency, Woodham Lane, Surrey KT15 3NB, UK
| | - Richard Ellis
- Animal Laboratories and Plant Health Agency, Woodham Lane, Surrey KT15 3NB, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Mary Hanson
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Anne Holmes
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - George J Gunn
- Future Farming Systems, R&D Division, SRUC, Drummondhill, Stratherrick Rd., Inverness IV2 4JZ, Scotland, UK
| | - Margo E Chase-Topping
- Centre for Immunity, Infection and Evolution, Kings Buildings, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Mark E J Woolhouse
- Centre for Immunity, Infection and Evolution, Kings Buildings, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kathie A Grant
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin EH25 9RG, UK
| | - John Wain
- University of East Anglia, Norwich NR4 7TJ, UK
| | - Claire Jenkins
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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Mohammed M, Delappe N, O'Connor J, McKeown P, Garvey P, Cormican M. Whole genome sequencing provides an unambiguous link between Salmonella Dublin outbreak strain and a historical isolate. Epidemiol Infect 2016; 144:576-81. [PMID: 26165314 DOI: 10.1017/S0950268815001636] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.
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Thomas P, Sekhar AC, Mujawar MM. Vulnerability of Bacillus spores and of related genera to physical impaction injury with particular reference to spread-plating. J Appl Microbiol 2014; 117:1358-72. [PMID: 25073977 DOI: 10.1111/jam.12613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/25/2014] [Accepted: 07/25/2014] [Indexed: 11/30/2022]
Abstract
AIMS To examine whether bacterial spores are vulnerable to impaction injury during standard spread-plating or to other modes of physical impaction. METHODS AND RESULTS Employing heat-challenged spores of Bacillus pumilus, Bacillus subtilis, Bacillus thuringiensis, Lysinibacillus, Paenibacillus and Brevibacillus spp. from day-4 to day-10 nutrient agar (NA) plates in 50% ethanol, plating the spore suspension to the extent of just drying the agar surface on fresh NA (50-60 s; SP-B) was tested in comparison with the spreader-independent approach of spotting-and-tilt-spreading (SATS), or a brief plating (<10 s; SP-A). Spore CFU was significantly reduced with SP-B in different organisms (23-40%) over SATS independent of the spore size. Comparing 4-, 7- and 10-day-old B. pumilus spores, the former two displayed significant CFU reduction in SP-B indicating a spore age-related effect. Continuous plating for 2-5 min showed a reduction in spore CFU in all organisms depending on plating duration. CFU reduction effect with SP-B was less manifest on refrigerated plates where no friction was experienced but acute on prewarmed and surface-dried plates. Spreader movement over agar surface subsequent to the exhaustion of free moisture proved highly detrimental to spores. A simulated plating study by plating the spores over a plastic film till drying showed a significant reduction in spore CFU. DAPI staining and glass bead-vortexing studies confirmed spore disruption through physical impaction. CONCLUSIONS Bacterial spores are vulnerable to injury during spread-plating or with other forms of physical impaction with variable effects on different genotypes independent of the spore size but altered by spore age. SIGNIFICANCE AND IMPACT OF THE STUDY Implications during spore CFU estimations employing spread-plating and during spore surveillance, and the recommendation of SATS as an easier and safer alternative for spore CFU enumeration.
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Affiliation(s)
- P Thomas
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
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26
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DINGSDAG S, COLEMAN NV. Bacterial communities on food court tables and cleaning equipment in a shopping mall. Epidemiol Infect 2013; 141:1647-51. [PMID: 22995219 PMCID: PMC9151585 DOI: 10.1017/s0950268812002142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/14/2012] [Accepted: 08/22/2012] [Indexed: 11/07/2022] Open
Abstract
The food court at a shopping mall is a potential transfer point for pathogenic microbes, but to date, this environment has not been the subject of detailed molecular microbiological study. We used a combination of culture-based and culture-independent approaches to investigate the types and numbers of bacteria present on food court tables, and on a food court cleaning cloth. Bacteria were found at 10²-10⁵ c.f.u./m² on food court tables and 10¹⁰ c.f.u./m² on the cleaning cloth. Tag-pyrosequencing of amplified 16S rRNA genes revealed that the dominant bacterial types on the cleaning cloth were genera known to include pathogenic species (Stenotrophomonas, Aeromonas), and that these genera were also evident at lower levels on table surfaces, suggesting possible cross-contamination. The evidence suggests a public health threat is posed by bacteria in the food court, and that this may be due to cross-contamination between cleaning equipment and table surfaces.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria, Aerobic/classification
- Bacteria, Aerobic/genetics
- Bacteria, Aerobic/isolation & purification
- Colony Count, Microbial/methods
- Commerce
- Environmental Microbiology
- Environmental Monitoring/methods
- New South Wales
- Polymerase Chain Reaction/methods
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Seasons
- Sequence Analysis, DNA
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Affiliation(s)
- S. DINGSDAG
- School of Molecular Bioscience, University of Sydney, Australia
| | - N. V. COLEMAN
- School of Molecular Bioscience, University of Sydney, Australia
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