1
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Qiu S, Liu K, Yang C, Xiang Y, Min K, Zhu K, Liu H, Du X, Yang M, Wang L, Sun Y, Zhou H, Mahe M, Zhao J, Li S, Yu D, Hawkey J, Holt KE, Baker S, Yang J, Xu X, Song H. A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China. Nat Commun 2022; 13:7365. [PMID: 36450777 PMCID: PMC9709761 DOI: 10.1038/s41467-022-35136-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Antimicrobial resistance of Shigella sonnei has become a global concern. Here, we report a phylogenetic group of S. sonnei with extensive drug resistance, including a combination of multidrug resistance, coresistance to ceftriaxone and azithromycin (cefRaziR), reduced susceptibility to fluoroquinolones, and even colistin resistance (colR). This distinct clone caused six waterborne shigellosis outbreaks in China from 2015 to 2020. We collect 155 outbreak isolates and 152 sporadic isolates. The cefRaziR isolates, including outbreak strains, are mainly distributed in a distinct clade located in global Lineage III. The outbreak strains form a recently derived monophyletic group that may have emerged circa 2010. The cefRaziR and colR phenotypes are attributed to the acquisition of different plasmids, particularly the IncB/O/K/Z plasmid coharboring the blaCTX-M-14, mphA, aac(3)-IId, dfrA17, aadA5, and sul1 genes and the IncI2 plasmid with an mcr-1 gene. Genetic analyses identify 92 accessory genes and 60 single-nucleotide polymorphisms associated with the cefRaziR phenotype. Surveillance of this clone is required to determine its dissemination and threat to global public health.
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Affiliation(s)
- Shaofu Qiu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kangkang Liu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chaojie Yang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ying Xiang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiyuan Min
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Kunpeng Zhu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbo Liu
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinying Du
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Mingjuan Yang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ligui Wang
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yong Sun
- grid.410620.10000 0004 1757 8298Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Haijian Zhou
- grid.198530.60000 0000 8803 2373National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention and State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Muti Mahe
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Jiayong Zhao
- grid.418504.cHenan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Shijun Li
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Deshan Yu
- grid.508057.fGansu Provincial Center for Disease Control and Prevention, Lanzhou, China
| | - Jane Hawkey
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Monash University, Melbourne, VIC Australia
| | - Kathryn E. Holt
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Monash University, Melbourne, VIC Australia
| | - Stephen Baker
- grid.5335.00000000121885934University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Juntao Yang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xuebin Xu
- grid.430328.eShanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hongbin Song
- grid.488137.10000 0001 2267 2324The Chinese PLA Center for Disease Control and Prevention, Beijing, China
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2
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Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill FX, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M, Ingle DJ, Dallman TJ, Jenkins C, Williamson DA, Holt KE. Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nat Commun 2021; 12:2684. [PMID: 33976138 PMCID: PMC8113504 DOI: 10.1038/s41467-021-22700-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/23/2021] [Indexed: 01/20/2023] Open
Abstract
Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Kalani Paranagama
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kate S Baker
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Ecological and Veterinary Sciences, University of Liverpool, Liverpool, UK
| | - Rebecca J Bengtsson
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Ecological and Veterinary Sciences, University of Liverpool, Liverpool, UK
| | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Dept Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Louise Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Zamin Iqbal
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Martin Hunt
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | | | - Claire Jenkins
- National Infection Service, Public Health England, London, UK
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Dept Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
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3
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Chung The H, Bodhidatta L, Pham DT, Mason CJ, Ha Thanh T, Voong Vinh P, Turner P, Hem S, Dance DAB, Newton PN, Phetsouvanh R, Davong V, Thwaites GE, Thomson NR, Baker S, Rabaa MA. Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia. Commun Biol 2021; 4:353. [PMID: 33742111 PMCID: PMC7979695 DOI: 10.1038/s42003-021-01905-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Conventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s-1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.
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Affiliation(s)
- Hao Chung The
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ladaporn Bodhidatta
- grid.413910.e0000 0004 0419 1772Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Duy Thanh Pham
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Carl J. Mason
- grid.413910.e0000 0004 0419 1772Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tuyen Ha Thanh
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sopheak Hem
- grid.418537.cMedical Biology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - David A. B. Dance
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Paul N. Newton
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Rattanaphone Phetsouvanh
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Guy E. Thwaites
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R. Thomson
- grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK ,grid.10306.340000 0004 0606 5382The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- grid.5335.00000000121885934The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Maia A. Rabaa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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4
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Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, Duong VT, Nguyen PHL, Turner P, Wick R, Ceyssens PJ, Thwaites G, Holt KE, Thomson NR, Rabaa MA, Baker S. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nat Commun 2019; 10:4828. [PMID: 31645551 PMCID: PMC6811581 DOI: 10.1038/s41467-019-12823-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/25/2019] [Indexed: 02/08/2023] Open
Abstract
Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance. Shigella sonnei is one of the main species causing shigellosis worldwide. Here the authors analyse nearly 400 S. sonnei genome sequences and carry out experimental evolution experiments to shed light into the evolutionary processes underlying the recent emergence of fluoroquinolone resistance in this pathogen.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christine Boinett
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Niall De Lappe
- National Salmonella, Shigella, and Listeria monocytogenes Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl J Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Phat Voong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thuy Duong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phu Huong Lan Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK.,The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, The Department of Medicine, University of Cambridge, Cambridge, UK
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5
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Baker KS, Dallman TJ, Field N, Childs T, Mitchell H, Day M, Weill FX, Lefèvre S, Tourdjman M, Hughes G, Jenkins C, Thomson N. Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance. Sci Rep 2018; 8:7389. [PMID: 29743642 PMCID: PMC5943296 DOI: 10.1038/s41598-018-25764-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/27/2018] [Indexed: 12/11/2022] Open
Abstract
Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements. Here, we whole genome sequenced representative subsamples of S. flexneri 2a and S. sonnei (n = 366) from the United Kingdom from 2008 to 2014, and analysed these alongside publicly available data to make qualitative insights on the genomic epidemiology of shigellosis and its AMR within the broader global context. Combined phylogenetic, epidemiological and genomic anlayses revealed the presence of domestically-circulating sublineages in patient risk-groups and the importation of travel-related sublineages from both Africa and Asia, including ciprofloxacin-resistant sublineages of both species from Asia. Genomic analyses revealed common AMR determinants among travel-related and domestically-acquired isolates, and the evolution of mutations associated with reduced quinolone susceptibility in domestically-circulating sublineages. Collectively, this study provides unprecedented insights on the contribution and mobility of endemic and travel-imported sublineages and AMR determinants responsible for disease in a high-income nation.
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Affiliation(s)
- Kate S Baker
- Institute for Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, UCL, London, United Kingdom
| | - Tristan Childs
- Centre for Infectious Disease Surveillance and Control, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Holly Mitchell
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, UCL, London, United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | | | - Sophie Lefèvre
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Mathieu Tourdjman
- Santé Publique France, the French Public Health Agency, Saint-Maurice, France
| | - Gwenda Hughes
- Department of HIV and STIs, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Nicholas Thomson
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.
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6
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Chung The H, Baker S. Out of Asia: the independent rise and global spread of fluoroquinolone-resistant Shigella. Microb Genom 2018; 4. [PMID: 29595412 PMCID: PMC5989582 DOI: 10.1099/mgen.0.000171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Shigella are ranked among the most prevalent aetiologies of diarrhoeal disease worldwide, disproportionately affecting young children in developing countries and high-risk communities in developed settings. Antimicrobial treatment, most commonly with fluoroquinolones, is currently recommended for Shigella infections to alleviate symptoms and control disease transmission. Resistance to fluoroquinolones has emerged in differing Shigella species (S. dysenteriae, flexneri and sonnei) since the turn of the 21st century, originating in endemic areas, and latterly spreading into non-endemic regions. Despite occurring independently, the emergence of fluoroquinolone resistance in these different Shigella species shares striking similarities regarding their epidemiology and resistance mechanisms. Here, we review and discuss the current epidemiology of fluoroquinolone-resistant Shigella species, particularly in the light of recent genomic insights.
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Affiliation(s)
- Hao Chung The
- Enteric Infections, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Enteric Infections, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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7
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Kozyreva VK, Jospin G, Greninger AL, Watt JP, Eisen JA, Chaturvedi V. Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance. mSphere 2016; 1:e00344-16. [PMID: 28028547 PMCID: PMC5177732 DOI: 10.1128/msphere.00344-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 01/08/2023] Open
Abstract
Shigella sonnei has caused unusually large outbreaks of shigellosis in California in 2014 and 2015. Preliminary data indicated the involvement of two distinct bacterial populations, one from San Diego and San Joaquin (SDi/SJo) and one from the San Francisco (SFr) Bay area. Whole-genome analysis and antibiotic susceptibility testing of 68 outbreak and archival isolates of S. sonnei were performed to investigate the microbiological factors related to these outbreaks. Both SDi/SJo and SFr populations, as well as almost all of the archival S. sonnei isolates belonged to sequence type 152 (ST152). Genome-wide single nucleotide polymorphism (SNP) analysis clustered the majority of California (CA) isolates to an earlier described lineage III. Isolates in the SDi/SJo population had a novel lambdoid bacteriophage carrying genes encoding Shiga toxin (STX) that were most closely related to that found in Escherichia coli O104:H4. However, the STX genes (stx1A and stx1B) from this novel phage had sequences most similar to the phages from Shigella flexneri and S. dysenteriae. The isolates in the SFr population were resistant to ciprofloxacin due to point mutations in gyrA and parC genes and were related to the fluoroquinolone-resistant S. sonnei clade within lineage III that originated in South Asia. The emergence of a highly virulent S. sonnei strain and introduction of a fluoroquinolone-resistant strain reflect the changing traits of this pathogen in California. An enhanced monitoring is advocated for early detection of future outbreaks caused by such strains. IMPORTANCE Shigellosis is an acute diarrheal disease causing nearly half a million infections, 6,000 hospitalizations, and 70 deaths annually in the United States. S. sonnei caused two unusually large outbreaks in 2014 and 2015 in California. We used whole-genome sequencing to understand the pathogenic potential of bacteria involved in these outbreaks. Our results suggest the persistence of a local S. sonnei SDi/SJo clone in California since at least 2008. Recently, a derivative of the original clone acquired the ability to produce Shiga toxin (STX) via exchanges of bacteriophages with other bacteria. STX production is connected with more severe disease, including bloody diarrhea. A second population of S. sonnei that caused an outbreak in the San Francisco area was resistant to fluoroquinolones and showed evidence of connection to a fluoroquinolone-resistant lineage from South Asia. These emerging trends in S. sonnei populations in California must be monitored for future risks of the spread of increasingly virulent and resistant clones.
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Affiliation(s)
- Varvara K. Kozyreva
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - Guillaume Jospin
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Alexander L. Greninger
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - James P. Watt
- Division of Communicable Disease Control, California Department of Public Health, Richmond, California, USA
| | - Jonathan A. Eisen
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Vishnu Chaturvedi
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
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8
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The HC, Thanh DP, Holt KE, Thomson NR, Baker S. The genomic signatures of Shigella evolution, adaptation and geographical spread. Nat Rev Microbiol 2016; 14:235-50. [PMID: 26923111 DOI: 10.1038/nrmicro.2016.10] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Nicholas R Thomson
- Bacterial Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK.,Department of Pathogen and Molecular Biology, The London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
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