601
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Ingle DJ, Tauschek M, Edwards DJ, Hocking DM, Pickard DJ, Azzopardi KI, Amarasena T, Bennett-Wood V, Pearson JS, Tamboura B, Antonio M, Ochieng JB, Oundo J, Mandomando I, Qureshi S, Ramamurthy T, Hossain A, Kotloff KL, Nataro JP, Dougan G, Levine MM, Robins-Browne RM, Holt KE. Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nat Microbiol 2016; 1:15010. [PMID: 27571974 DOI: 10.1038/nmicrobiol.2015.10] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/02/2015] [Indexed: 01/25/2023]
Abstract
Atypical enteropathogenic Escherichia coli (aEPEC) is an umbrella term given to E. coli that possess a type III secretion system encoded in the locus of enterocyte effacement (LEE), but lack the virulence factors (stx, bfpA) that characterize enterohaemorrhagic E. coli and typical EPEC, respectively. The burden of disease caused by aEPEC has recently increased in industrialized and developing nations, yet the population structure and virulence profile of this emerging pathogen are poorly understood. Here, we generated whole-genome sequences of 185 aEPEC isolates collected during the Global Enteric Multicenter Study from seven study sites in Asia and Africa, and compared them with publicly available E. coli genomes. Phylogenomic analysis revealed ten distinct widely distributed aEPEC clones. Analysis of genetic variation in the LEE pathogenicity island identified 30 distinct LEE subtypes divided into three major lineages. Each LEE lineage demonstrated a preferred chromosomal insertion site and different complements of non-LEE encoded effector genes, indicating distinct patterns of evolution of these lineages. This study provides the first detailed genomic framework for aEPEC in the context of the EPEC pathotype and will facilitate further studies into the epidemiology and pathogenicity of EPEC by enabling the detection and tracking of specific clones and LEE variants.
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Affiliation(s)
- Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.,Centre for Systems Genomics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marija Tauschek
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.,Centre for Systems Genomics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dianna M Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Derek J Pickard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kristy I Azzopardi
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Thakshila Amarasena
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Vicki Bennett-Wood
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Jaclyn S Pearson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Boubou Tamboura
- Centre pour le Développement des Vaccins du Mali, Bamako, Mali
| | - Martin Antonio
- Medical Research Council Unit (United Kingdom), Fajara, The Gambia
| | - John B Ochieng
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Joseph Oundo
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça, (CISM), CP 1929, Maputo, Mozambique.,Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi 74800, Pakistan
| | | | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, Bangladesh
| | - Karen L Kotloff
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - James P Nataro
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Myron M Levine
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Roy M Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia.,Murdoch Childrens Research Institute, Royal Children's Hospital, Victoria 3052, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.,Centre for Systems Genomics, The University of Melbourne, Parkville, Victoria 3010, Australia
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602
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Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol 2016; 7:353-74. [PMID: 26772415 DOI: 10.1146/annurev-food-041715-033259] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-called next-generation sequencing (NGS) technologies that have made whole-genome sequencing (WGS) of foodborne bacterial pathogens a realistic and superior alternative to traditional subtyping methods. Routine, real-time, and widespread application of WGS in food safety and public health is on the horizon. Technological, operational, and policy challenges are still present and being addressed by an international and multidisciplinary community of researchers, public health practitioners, and other stakeholders.
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Affiliation(s)
- Xiangyu Deng
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, Georgia 30269;
| | - Henk C den Bakker
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas 79409
| | - Rene S Hendriksen
- National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, DK-2800 Denmark
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603
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Dearlove BL, Cody AJ, Pascoe B, Méric G, Wilson DJ, Sheppard SK. Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. ISME JOURNAL 2015; 10:721-9. [PMID: 26305157 PMCID: PMC4677457 DOI: 10.1038/ismej.2015.149] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/20/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022]
Abstract
Campylobacter jejuni and Campylobacter coli are the biggest causes of bacterial gastroenteritis in the developed world, with human infections typically arising from zoonotic transmission associated with infected meat. Because Campylobacter is not thought to survive well outside the gut, host-associated populations are genetically isolated to varying degrees. Therefore, the likely origin of most strains can be determined by host-associated variation in the genome. This is instructive for characterizing the source of human infection. However, some common strains, notably isolates belonging to the ST-21, ST-45 and ST-828 clonal complexes, appear to have broad host ranges, hindering source attribution. Here whole-genome sequencing has the potential to reveal fine-scale genetic structure associated with host specificity. We found that rates of zoonotic transmission among animal host species in these clonal complexes were so high that the signal of host association is all but obliterated, estimating one zoonotic transmission event every 1.6, 1.8 and 12 years in the ST-21, ST-45 and ST828 complexes, respectively. We attributed 89% of clinical cases to a chicken source, 10% to cattle and 1% to pig. Our results reveal that common strains of C. jejuni and C. coli infectious to humans are adapted to a generalist lifestyle, permitting rapid transmission between different hosts. Furthermore, they show that the weak signal of host association within these complexes presents a challenge for pinpointing the source of clinical infections, underlining the view that whole-genome sequencing, powerful though it is, cannot substitute for intensive sampling of suspected transmission reservoirs.
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Affiliation(s)
- Bethany L Dearlove
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
| | - Alison J Cody
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ben Pascoe
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK.,MRC CLIMB Consortium, Institute of Life Science, Swansea University, Swansea, UK
| | - Guillaume Méric
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK.,MRC CLIMB Consortium, Institute of Life Science, Swansea University, Swansea, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Samuel K Sheppard
- Department of Zoology, University of Oxford, Oxford, UK.,College of Medicine, Institute of Life Science, Swansea University, Swansea, UK.,MRC CLIMB Consortium, Institute of Life Science, Swansea University, Swansea, UK
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604
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Pettengill JB. The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence. PLoS One 2015; 10:e0128407. [PMID: 26273822 PMCID: PMC4537086 DOI: 10.1371/journal.pone.0128407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/17/2015] [Indexed: 11/18/2022] Open
Abstract
With the advent of more sophisticated models and increase in computational power, an ever-growing amount of information can be extracted from DNA sequence data. In particular, recent advances have allowed researchers to estimate the date of historical events for a group of interest including time to most recent common ancestor (TMRCA), dates of specific nodes in a phylogeny, and the date of divergence or speciation date. Here I use coalescent simulations and re-analyze an empirical dataset to illustrate the importance of taxon sampling, in particular, on correctly estimating such dates. I show that TMRCA of representatives of a single taxon is often not the same as divergence date due to issues such as incomplete lineage sorting. Of critical importance is when estimating divergence or speciation dates a representative from a different taxonomic lineage must be included in the analysis. Without considering these issues, studies may incorrectly estimate the times at which historical events occurred, which has profound impacts within both research and applied (e.g., those related to public health) settings.
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Affiliation(s)
- James B. Pettengill
- Division of rPublic Health Informatics and Analytics, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, United States of America
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605
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606
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Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CLC, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TEA. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. THE LANCET. INFECTIOUS DISEASES 2015; 15:1193-1202. [PMID: 26116186 PMCID: PMC4579482 DOI: 10.1016/s1473-3099(15)00062-6] [Citation(s) in RCA: 424] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/03/2015] [Accepted: 05/15/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drug-susceptibility testing is slow and expensive, and commercial genotypic assays screen only common resistance-determining mutations. We used whole-genome sequencing to characterise common and rare mutations predicting drug resistance, or consistency with susceptibility, for all first-line and second-line drugs for tuberculosis. METHODS Between Sept 1, 2010, and Dec 1, 2013, we sequenced a training set of 2099 Mycobacterium tuberculosis genomes. For 23 candidate genes identified from the drug-resistance scientific literature, we algorithmically characterised genetic mutations as not conferring resistance (benign), resistance determinants, or uncharacterised. We then assessed the ability of these characterisations to predict phenotypic drug-susceptibility testing for an independent validation set of 1552 genomes. We sought mutations under similar selection pressure to those characterised as resistance determinants outside candidate genes to account for residual phenotypic resistance. FINDINGS We characterised 120 training-set mutations as resistance determining, and 772 as benign. With these mutations, we could predict 89·2% of the validation-set phenotypes with a mean 92·3% sensitivity (95% CI 90·7-93·7) and 98·4% specificity (98·1-98·7). 10·8% of validation-set phenotypes could not be predicted because uncharacterised mutations were present. With an in-silico comparison, characterised resistance determinants had higher sensitivity than the mutations from three line-probe assays (85·1% vs 81·6%). No additional resistance determinants were identified among mutations under selection pressure in non-candidate genes. INTERPRETATION A broad catalogue of genetic mutations enable data from whole-genome sequencing to be used clinically to predict drug resistance, drug susceptibility, or to identify drug phenotypes that cannot yet be genetically predicted. This approach could be integrated into routine diagnostic workflows, phasing out phenotypic drug-susceptibility testing while reporting drug resistance early. FUNDING Wellcome Trust, National Institute of Health Research, Medical Research Council, and the European Union.
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Affiliation(s)
- Timothy M Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Thomas A Kohl
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - Shaheed V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Jessica Hedge
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Carlos Del Ojo Elias
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Phelim Bradley
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Silke Feuerriegel
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Katherine E Niehaus
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David A Clifton
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | | | - Camilla L C Ip
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Francis A Drobniewski
- Public Health England National Mycobacterial Reference Laboratory, Queen Mary's School of Medicine and Dentistry, London, UK; Department of Infectious Diseases, Imperial College, London, UK
| | | | | | | | - Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Airway Research Center North, Kiel, Germany
| | - Philip Supply
- Genoscreen, Lille, France; Centre National de la Recherche Scientifique, Lille, France; INSERM, Université de Lille, and Campus de l'Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - E Grace Smith
- Public Health England West Midlands Public Health Laboratory, Heartlands Hospital, Birmingham, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Stefan Niemann
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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607
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Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci. J Clin Microbiol 2015; 53:2271-85. [PMID: 25972423 PMCID: PMC4473186 DOI: 10.1128/jcm.00744-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/06/2015] [Indexed: 02/02/2023] Open
Abstract
The pneumococcus is a leading pathogen infecting children and adults. Safe, effective vaccines exist, and they work by inducing antibodies to the polysaccharide capsule (unique for each serotype) that surrounds the cell; however, current vaccines are limited by the fact that only a few of the nearly 100 antigenically distinct serotypes are included in the formulations. Within the serotypes, serogroup 6 pneumococci are a frequent cause of serious disease and common colonizers of the nasopharynx in children. Serotype 6E was first reported in 2004 but was thought to be rare; however, we and others have detected serotype 6E among recent pneumococcal collections. Therefore, we analyzed a diverse data set of ∼1,000 serogroup 6 genomes, assessed the prevalence and distribution of serotype 6E, analyzed the genetic diversity among serogroup 6 pneumococci, and investigated whether pneumococcal conjugate vaccine-induced serotype 6A and 6B antibodies mediate the killing of serotype 6E pneumococci. We found that 43% of all genomes were of serotype 6E, and they were recovered worldwide from healthy children and patients of all ages with pneumococcal disease. Four genetic lineages, three of which were multidrug resistant, described ∼90% of the serotype 6E pneumococci. Serological assays demonstrated that vaccine-induced serotype 6B antibodies were able to elicit killing of serotype 6E pneumococci. We also revealed three major genetic clusters of serotype 6A capsular sequences, discovered a new hybrid 6C/6E serotype, and identified 44 examples of serotype switching. Therefore, while vaccines appear to offer protection against serotype 6E, genetic variants may reduce vaccine efficacy in the longer term because of the emergence of serotypes that can evade vaccine-induced immunity.
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