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Machado M, Panzenhagen P, Aburjaile FF, Brenig B, Costa MMD, Azevedo VADC, Figueiredo EEDS, Conte-Junior CA. Evolution of pathogenic Escherichia coli harboring the transmissible locus of stress tolerance: from food sources to clinical environments. Sci Rep 2025; 15:5014. [PMID: 39934272 PMCID: PMC11814101 DOI: 10.1038/s41598-025-89066-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 02/03/2025] [Indexed: 02/13/2025] Open
Abstract
Escherichia coli (E. coli) carrying the transmissible locus of stress tolerance (tLST) are able to overcome numerous environmental challenges. In our in-silico study, we aimed to characterize tLST in terms of its variants in 793 genomes of E. coli from Brazil originating from food, environmental and clinical (animal and human) sources, and to perform a temporal analysis in order to identify the historical moment of its emergence. We also analyzed the presence of two Yersinia high pathogenicity island (HPI) variants in E. coli genomes, describing other genes and accessory for resistance, persistence, mobile elements (plasmids) and sequence types. The prevalence of the tLST was 10% in E. coli from Brazil, predominantly observed in milk-originating genomes, within the prevalent tLSTCP010237 variant. In E. coli from other sources (clinical/environmental), only part of the tLST was present. Remarkably, our temporal analysis pinpointed the emergence of tLST back to around 1914, coinciding with major societal events. Regarding virulence genes, we found a prevalence of 38.5% for HPI of Y. pestis across genomes from all sources. Our global analysis also showed a high diversity of other virulence genes for milk E. coli (+ 100 genes). These genomes also stood out from the overall metadata for presenting a greater variety of resistance genes to other stresses, such as metals, biocides and acids, as well as persistence genes (biofilm formation). This study demonstrated the historical background of E. coli with tLST genes dating back more than 100 years, and the acquisition of a wide range of virulence and resistance genes that allow it to circulate in different environments: from food to clinic or from clinic to food, making this bacterium a pathogen that requires rigorous surveillance and strategic interventions to mitigate potential risks.
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Affiliation(s)
- Maxsueli Machado
- Food Science Program (PPGCAL), Chemistry Institute (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-909, Brazil
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Flávia Figueira Aburjaile
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, 31270- 901, Minas Gerais, Brazil
| | | | - Mateus Matiuzzi da Costa
- Animal Science Program, Federal University of Vale do São Francisco (UNIVASF), Pernambuco, 56300-000, Brazil
| | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, 31270- 901, Minas Gerais, Brazil
| | - Eduardo Eustáquio de Souza Figueiredo
- Animal Science Program (PPGCA), Federal University of Mato Grosso (UFMT), Cuiabá, 78060-900, Mato Grosso, Brazil
- Nutrition, Food and Metabolism Program (PPGNAM), Federal University of Mato Grosso (UFMT), Cuiabá, 78060-900, Mato Grosso, Brazil
| | - Carlos Adam Conte-Junior
- Food Science Program (PPGCAL), Chemistry Institute (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-909, Brazil.
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
- Horacio Macedo. Avenue, Cidade Universitária, Ilha do Fundão, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-598, RJ, Brazil.
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2
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Hawkey J, Frézal L, Tran Dien A, Zhukova A, Brown D, Chattaway MA, Simon S, Izumiya H, Fields PI, De Lappe N, Kaftyreva L, Xu X, Isobe J, Clermont D, Njamkepo E, Akeda Y, Issenhuth-Jeanjean S, Makarova M, Wang Y, Hunt M, Jenkins BM, Ravel M, Guibert V, Serre E, Matveeva Z, Fabre L, Cormican M, Yue M, Zhu B, Morita M, Iqbal Z, Silva Nodari C, Pardos de la Gandara M, Weill FX. Genomic perspective on the bacillus causing paratyphoid B fever. Nat Commun 2024; 15:10143. [PMID: 39658567 PMCID: PMC11632088 DOI: 10.1038/s41467-024-54418-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 11/11/2024] [Indexed: 12/12/2024] Open
Abstract
Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtained globally, between 1898 and 2021. We show that this pathogen existed in the 13th century, subsequently diversifying into 11 lineages and 38 genotypes with strong phylogeographic patterns. Following its discovery in 1896, it circulated across Europe until the 1970s, after which it was mostly reimported into Europe from South America, the Middle East, South Asia, and North Africa. Antimicrobial resistance recently emerged in various genotypes of SPB PG1, mostly through mutations of the quinolone-resistance-determining regions of gyrA and gyrB. This study provides an unprecedented insight into SPB PG1 and essential genomic tools for identifying and tracking this pathogen, thereby facilitating the global genomic surveillance of PTB.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Lise Frézal
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Alicia Tran Dien
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
- Bioinformatic Core Facility, UMS AMMICA, Gustave Roussy, Villejuif, F-94800, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, F-75015, France
| | - Derek Brown
- Scottish Microbiology Reference Laboratories (SMiRL), Glasgow, G31 2ER, UK
| | - Marie Anne Chattaway
- Gastrointestinal Bacteria Reference Unit (GBRU), United Kingdom Health Security Agency, London, NW9 5EQ, UK
| | - Sandra Simon
- Unit of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch-Institute, Wernigerode, 38855, Germany
| | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Patricia I Fields
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Niall De Lappe
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospitals, Galway, SW4 671, Ireland
| | - Lidia Kaftyreva
- Pasteur Institute of St Petersburg, St Petersburg, 197101, Russia
| | - Xuebin Xu
- Department of Microbiology, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, 200336, China
| | - Junko Isobe
- Department of Bacteriology, Toyama Institute of Health, Toyama, 939-0363, Japan
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), Paris, F-75015, France
| | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Sylvie Issenhuth-Jeanjean
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Mariia Makarova
- Pasteur Institute of St Petersburg, St Petersburg, 197101, Russia
| | - Yanan Wang
- International Joint Research Centre for National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Martin Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Brent M Jenkins
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Magali Ravel
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Véronique Guibert
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Estelle Serre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Zoya Matveeva
- Pasteur Institute of St Petersburg, St Petersburg, 197101, Russia
| | - Laëtitia Fabre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Martin Cormican
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospitals, Galway, SW4 671, Ireland
- School of Medicine, University of Galway, Galway, H91 TK33, Ireland
| | - Min Yue
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, 310058, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
- Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Carolina Silva Nodari
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - Maria Pardos de la Gandara
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France.
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3
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Tzfadia O, Gijsbers A, Vujkovic A, Snobre J, Vargas R, Dewaele K, Meehan CJ, Farhat M, Hakke S, Peters PJ, de Jong BC, Siroy A, Ravelli RBG. Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets. Microbiol Spectr 2024; 12:e0381623. [PMID: 38874407 PMCID: PMC11302016 DOI: 10.1128/spectrum.03816-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 06/15/2024] Open
Abstract
Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens. IMPORTANCE We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.
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Affiliation(s)
- Oren Tzfadia
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Abril Gijsbers
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alexandra Vujkovic
- Clinical Virology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- ADReM Data Lab, University of Antwerp, Antwerp, Belgium
| | - Jihad Snobre
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Klaas Dewaele
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sneha Hakke
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Peter J. Peters
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Axel Siroy
- Unité de soutien à l'Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM, IECB, US1, Université de Bordeaux, Pessac, France
| | - Raimond B. G. Ravelli
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
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4
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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5
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Vargas R, Luna MJ, Freschi L, Marin M, Froom R, Murphy KC, Campbell EA, Ioerger TR, Sassetti CM, Farhat MR. Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A 2023; 120:e2301394120. [PMID: 37399390 PMCID: PMC10334774 DOI: 10.1073/pnas.2301394120] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/03/2023] [Indexed: 07/05/2023] Open
Abstract
Phase variation induced by insertions and deletions (INDELs) in genomic homopolymeric tracts (HT) can silence and regulate genes in pathogenic bacteria, but this process is not characterized in MTBC (Mycobacterium tuberculosis complex) adaptation. We leverage 31,428 diverse clinical isolates to identify genomic regions including phase-variants under positive selection. Of 87,651 INDEL events that emerge repeatedly across the phylogeny, 12.4% are phase-variants within HTs (0.02% of the genome by length). We estimated the in-vitro frameshift rate in a neutral HT at 100× the neutral substitution rate at [Formula: see text] frameshifts/HT/year. Using neutral evolution simulations, we identified 4,098 substitutions and 45 phase-variants to be putatively adaptive to MTBC (P < 0.002). We experimentally confirm that a putatively adaptive phase-variant alters the expression of espA, a critical mediator of ESX-1-dependent virulence. Our evidence supports the hypothesis that phase variation in the ESX-1 system of MTBC can act as a toggle between antigenicity and survival in the host.
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Affiliation(s)
- Roger Vargas
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA02115
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Michael J. Luna
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Maximillian Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY10065
| | - Kenan C. Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX77843
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Maha Reda Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA02114
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6
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Green AG, Vargas R, Marin MG, Freschi L, Xie J, Farhat MR. Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations. Mol Biol Evol 2023; 40:msad131. [PMID: 37352142 PMCID: PMC10292908 DOI: 10.1093/molbev/msad131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
Pathogenic microorganisms are in a perpetual struggle for survival in changing host environments, where host pressures necessitate changes in pathogen virulence, antibiotic resistance, or transmissibility. The genetic basis of phenotypic adaptation by pathogens is difficult to study in vivo. In this work, we develop a phylogenetic method to detect genetic dependencies that promote pathogen adaptation using 31,428 in vivo sampled Mycobacterium tuberculosis genomes, a globally prevalent bacterial pathogen with increasing levels of antibiotic resistance. We find that dependencies between mutations are enriched in antigenic and antibiotic resistance functions and discover 23 mutations that potentiate the development of antibiotic resistance. Between 11% and 92% of resistant strains harbor a dependent mutation acquired after a resistance-conferring variant. We demonstrate the pervasiveness of genetic dependency in adaptation of naturally evolving populations and the utility of the proposed computational approach.
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Affiliation(s)
- Anna G Green
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jiaqi Xie
- Department of Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
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7
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Commins N, Sullivan MR, McGowen K, Koch EM, Rubin EJ, Farhat M. Mutation rates and adaptive variation among the clinically dominant clusters of Mycobacterium abscessus. Proc Natl Acad Sci U S A 2023; 120:e2302033120. [PMID: 37216535 PMCID: PMC10235944 DOI: 10.1073/pnas.2302033120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Mycobacterium abscessus (Mab) is a multidrug-resistant pathogen increasingly responsible for severe pulmonary infections. Analysis of whole-genome sequences (WGS) of Mab demonstrates dense genetic clustering of clinical isolates collected from disparate geographic locations. This has been interpreted as supporting patient-to-patient transmission, but epidemiological studies have contradicted this interpretation. Here, we present evidence for a slowing of the Mab molecular clock rate coincident with the emergence of phylogenetic clusters. We performed phylogenetic inference using publicly available WGS from 483 Mab patient isolates. We implement a subsampling approach in combination with coalescent analysis to estimate the molecular clock rate along the long internal branches of the tree, indicating a faster long-term molecular clock rate compared to branches within phylogenetic clusters. We used ancestry simulation to predict the effects of clock rate variation on phylogenetic clustering and found that the degree of clustering in the observed phylogeny is more easily explained by a clock rate slowdown than by transmission. We also find that phylogenetic clusters are enriched in mutations affecting DNA repair machinery and report that clustered isolates have lower spontaneous mutation rates in vitro. We propose that Mab adaptation to the host environment through variation in DNA repair genes affects the organism's mutation rate and that this manifests as phylogenetic clustering. These results challenge the model that phylogenetic clustering in Mab is explained by person-to-person transmission and inform our understanding of transmission inference in emerging, facultative pathogens.
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Affiliation(s)
- Nicoletta Commins
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Mark R. Sullivan
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Kerry McGowen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Evan M. Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA02114
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