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Webb JR, Andersson P, Sim E, Zahedi A, Donald A, Hoang T, Watt AE, Agius JE, Donato CM, Cummins ML, Zulfiqar T, Nghiem S, Lin C, Menouhos D, Leong LEX, Baird R, Kennedy K, Cooley L, Speers D, Lim CK, de Ligt J, Ferdinand A, Glass K, Kirk MD, Djordjevic SP, Sloggett C, Horan K, Seemann T, Sintchenko V, Jennison AV, Howden BP. Implementing a national programme of pathogen genomics for public health: the Australian Pathogen Genomics Program (AusPathoGen). THE LANCET. MICROBE 2024:100969. [PMID: 39389079 DOI: 10.1016/j.lanmic.2024.100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/19/2024] [Accepted: 07/31/2024] [Indexed: 10/12/2024]
Abstract
Delivering large-scale routine pathogen genomics surveillance for public health is of considerable interest, although translational research models that promote national-level implementation are not well defined. We describe the development and deployment of the Australian Pathogen Genomics Program (AusPathoGen), a comprehensive national partnership between academia, public health laboratories, and public health agencies that commenced in January, 2021. Successfully establishing and delivering a national programme requires inclusive and transparent collaboration between stakeholders, defined and clear focus on public health priorities, and support for strengthening national genomics capacity. Major enablers for delivering such a programme include technical solutions for data integration and analysis, such as the genomics surveillance platform AusTrakka, standard bioinformatic analysis methods, and national ethics and data sharing agreements that promote nationally integrated surveillance systems. Training of public health officials to interpret and act on genomic data is crucial, and evaluation and cost-effectiveness programmes will provide a benchmark and evidence for sustainable investment in genomics nationally and globally.
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Affiliation(s)
- Jessica R Webb
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Eby Sim
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Alireza Zahedi
- Public and Environmental Health, Pathology Queensland Queensland Health, Brisbane, QLD, Australia
| | - Angela Donald
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jessica E Agius
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Celeste M Donato
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, NSW, Australia
| | - Tehzeeb Zulfiqar
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Son Nghiem
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Chantel Lin
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | | | | | - Rob Baird
- Territory Pathology, Royal Darwin Hospital, Darwin, NT, Australia
| | - Karina Kennedy
- Department of Clinical Microbiology and Infectious Diseases, Canberra Health Services, Australian National University Medical School of Medicine and Psychology, Canberra, ACT, Australia
| | - Louise Cooley
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Tasmania, Australia; Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - David Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Perth, WA, Australia
| | - Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Joep de Ligt
- Institute of Environmental Science and Research, Kenepuru, Porirua, New Zealand
| | - Angeline Ferdinand
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia; Centre for Health Policy, School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Katie Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, NSW, Australia
| | - Clare Sloggett
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Amy V Jennison
- Public and Environmental Health, Pathology Queensland Queensland Health, Brisbane, QLD, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia.
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2
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Richardson D, Savary-Trathen A, Fitzpatrick C, Williams D. Estimated prevalence and associations of sexually transmissible bacterial enteric pathogens in asymptomatic men who have sex with men: a systematic review and meta-analysis. Sex Transm Infect 2024:sextrans-2024-056183. [PMID: 38902026 DOI: 10.1136/sextrans-2024-056183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024] Open
Abstract
OBJECTIVE The reservoir of sexually transmissible bacterial enteric pathogens in asymptomatic men who have sex with men (MSM) may impact future outbreaks, and the evolution of antimicrobial resistance. We aimed to estimate the pooled prevalence and explore any factors associated with Shigella spp, Campylobacter spp, diarrhoeagenic Escherichia coli and Salmonella spp in asymptomatic MSM using the random effects model. METHODS We searched Embase, MEDLINE, CINAHL and Web of Science Core Collections for manuscripts published up to February 2024. One author screened citations and abstracts; two authors independently conducted a full-text review. We included manuscripts which measured the prevalence of Shigella spp, Campylobacter spp, diarrhoeagenic E. coli and Salmonella spp in asymptomatic MSM. Quality and risk of bias was assessed independently by two authors using the Joanna Briggs Institute critical appraisal tools. We calculated pooled prevalence and CIs using the random effects model. RESULTS Six manuscripts were included in the final review. The manuscripts were from Australia (n=2), the UK (n=2), the Netherlands (n=1) and the USA (n=1) and included data from 3766 asymptomatic MSM tested for bacterial enteric pathogens. The prevalence of Shigella spp was 1.1% (95% CI 0.7% to 1.7%), Campylobacter spp 1.9% (95% CI 1.5% to 2.5%), diarrhoeagenic E. coli 3.8% (95% CI 2.1% to 6.7%) and Salmonella spp 0.3% (95% CI 0.1% to 0.6%). Two manuscripts demonstrated that the detection of bacterial enteric pathogen was more frequent in asymptomatic MSM using HIV-pre-exposure prophylaxis (PrEP), living with HIV, reporting <5 new sexual partners in the past 3 months, reporting insertive oral-anal sex and group sex compared with MSM testing negative. CONCLUSION Despite a small number of manuscripts, this review has estimated the pooled prevalence, and highlighted some possible associations with sexually transmissible bacterial enteric pathogens in asymptomatic MSM, which can inform future clinical guidelines, public health control strategies and research to increase our understanding of transmission and the evolution of antimicrobial resistance. PROSPERO REGISTRATION NUMBER CRD42024518700.
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Affiliation(s)
- Daniel Richardson
- Sexual Health & HIV medicine, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Global Health & Infection, Brighton and Sussex Medical School, Brighton, UK
| | - Amber Savary-Trathen
- Sexual Health & HIV medicine, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Colin Fitzpatrick
- Sexual Health & HIV medicine, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Deborah Williams
- Sexual Health & HIV medicine, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
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Chessell C, Rabuszko L, Richardson D, Llewellyn C. Factors associated with the sexual transmission of Strongyloides stercoralis in men who have sex with men: A systematic review. J Eur Acad Dermatol Venereol 2024; 38:673-679. [PMID: 38013501 DOI: 10.1111/jdv.19664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/09/2023] [Indexed: 11/29/2023]
Abstract
Strongyloides stercoralis is a parasitic worm with a complex life cycle and can cause significant morbidity, including a proctocolitis and life-threatening hyperinfection syndrome. Limited reports from non-endemic areas, including in men who have sex with men (MSM), suggest sexual transmission of S. stercoralis. In this systematic review of the published literature, we aimed to explore the associated factors of S. stercoralis in MSM. We systematically searched three bibliographical databases (MEDLINE, CINAHL and EMBASE) up to November 2022. We used a two-stage process to assess eligibility: the primary author conducted an initial screen of abstracts, and then three authors conducted independent full manuscripts to determine the final eligible manuscripts. We only included manuscripts written in English that contained data on specific factors associated with sexual transmission in MSM. We used the STROBE checklist to assess the risk of bias and synthesized the narrative data using the SWiM method. Seven manuscripts were eligible for this review (four case reports, one case series, one cross-sectional study and one experimental study), which included 22 individuals from Europe and the Americas. From these studies, S. stercoralis in MSM was associated with living with HIV (including having a low CD4 count and not using antiretrovirals), having a concomitant sexually transmitted infection (Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum and hepatitis C) and a concomitant (sexually transmitted) protozoal infection (Entamoeba histolytica, Giardia lamblia), travel to the S. stercoralis endemic area, multiple sexual partners from endemic areas, oro-anal sexual contact and chemsex. Although limited by the number of cases in the literature, we have highlighted some possible biological and behavioural risk factors associated with the sexual transmission of S. stercoralis in MSM that could be used to both target future research and S. stercoralis public health control interventions.
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Affiliation(s)
- Callum Chessell
- Department of Primary Care and Public Health, Brighton and Sussex Medical School, Brighton, UK
| | - Lucy Rabuszko
- Department of Primary Care and Public Health, Brighton and Sussex Medical School, Brighton, UK
| | - Daniel Richardson
- Department of Primary Care and Public Health, Brighton and Sussex Medical School, Brighton, UK
- Department of Sexual Health and HIV, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Carrie Llewellyn
- Department of Primary Care and Public Health, Brighton and Sussex Medical School, Brighton, UK
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Hossain MA, Al Amin M, Khan MA, Refat MRR, Sohel M, Rahman MH, Islam A, Hoque MN. Genome-Wide Investigation Reveals Potential Therapeutic Targets in Shigella spp. BIOMED RESEARCH INTERNATIONAL 2024; 2024:5554208. [PMID: 38595330 PMCID: PMC11003385 DOI: 10.1155/2024/5554208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Shigella stands as a major contributor to bacterial dysentery worldwide scale, particularly in developing countries with inadequate sanitation and hygiene. The emergence of multidrug-resistant strains exacerbates the challenge of treating Shigella infections, particularly in regions where access to healthcare and alternative antibiotics is limited. Therefore, investigations on how bacteria evade antibiotics and eventually develop resistance could open new avenues for research to develop novel therapeutics. The aim of this study was to analyze whole genome sequence (WGS) of human pathogenic Shigella spp. to elucidate the antibiotic resistance genes (ARGs) and their mechanism of resistance, gene-drug interactions, protein-protein interactions, and functional pathways to screen potential therapeutic candidate(s). We comprehensively analyzed 45 WGS of Shigella, including S. flexneri (n = 17), S. dysenteriae (n = 14), S. boydii (n = 11), and S. sonnei (n = 13), through different bioinformatics tools. Evolutionary phylogenetic analysis showed three distinct clades among the circulating strains of Shigella worldwide, with less genomic diversity. In this study, 2,146 ARGs were predicted in 45 genomes (average 47.69 ARGs/genome), of which only 91 ARGs were found to be shared across the genomes. Majority of these ARGs conferred their resistance through antibiotic efflux pump (51.0%) followed by antibiotic target alteration (23%) and antibiotic target replacement (18%). We identified 13 hub proteins, of which four proteins (e.g., tolC, acrR, mdtA, and gyrA) were detected as potential hub proteins to be associated with antibiotic efflux pump and target alteration mechanisms. These hub proteins were significantly (p < 0.05) enriched in biological process, molecular function, and cellular components. Therefore, the finding of this study suggests that human pathogenic Shigella strains harbored a wide range of ARGs that confer resistance through antibiotic efflux pumps and antibiotic target modification mechanisms, which must be taken into account to devise and formulate treatment strategy against this pathogen. Moreover, the identified hub proteins could be exploited to design and develop novel therapeutics against MDR pathogens like Shigella.
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Affiliation(s)
- Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
- Department of Microbiology, Primeasia University, Dhaka 1213, Bangladesh
| | - Md. Al Amin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md. Arif Khan
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - Md. Rashedur Rahman Refat
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213, Bangladesh
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh
| | - Ariful Islam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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Wang M, Zeng J, Tan H, Guo Q, Li X, Ling X, Zhang J, Song S, Deng Y. Anti-virulence and bactericidal activities of Stattic against Shigella sonnei. Appl Environ Microbiol 2023; 89:e0107423. [PMID: 38032177 PMCID: PMC10734500 DOI: 10.1128/aem.01074-23] [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: 06/24/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Shigella sonnei is a major human enteric pathogen that causes bacillary dysentery. The increasing spread of drug-resistant S. sonnei strains has caused an emergent need for the development of new antimicrobial agents against this pathogenic bacterium. In this study, we demonstrate that Stattic employs two antibacterial mechanisms against S. sonnei. It exerted both anti-virulence activity and bactericidal activity against S. sonnei, suggesting that it shows advantages over traditional antibiotics. Moreover, Stattic showed excellent synergistic effects with kanamycin, ampicillin, chloramphenicol, and gentamicin against S. sonnei. Our findings suggest that Stattic has promising potential for development as a new antibiotic or as an adjuvant to antibiotics for infections caused by S. sonnei.
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Affiliation(s)
- Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jia Zeng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Huihui Tan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Quan Guo
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xia Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xiwen Ling
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jinyue Zhang
- School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Shihao Song
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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6
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Tansarli GS, Long DR, Waalkes A, Bourassa LA, Libby SJ, Penewit K, Almazan J, Matsumoto J, Bryson-Cahn C, Rietberg K, Dell BM, Hatley NV, Salipante SJ, Fang FC. Genomic reconstruction and directed interventions in a multidrug-resistant Shigellosis outbreak in Seattle, WA, USA: a genomic surveillance study. THE LANCET. INFECTIOUS DISEASES 2023; 23:740-750. [PMID: 36731480 PMCID: PMC10726761 DOI: 10.1016/s1473-3099(22)00879-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/09/2022] [Accepted: 12/09/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Shigella spp have been associated with community-wide outbreaks in urban settings. We analysed a sustained shigellosis outbreak in Seattle, WA, USA, to understand its origins and mechanisms of antimicrobial resistance, define ongoing transmission patterns, and optimise strategies for treatment and infection control. METHODS We did a retrospective study of all Shigella isolates identified from stool samples at the clinical laboratories at Harborview Medical Center and University of Washington Medical Center (Seattle, WA, USA) from May 1, 2017, to Feb 28, 2022. We characterised isolates by species identification, phenotypic susceptibility testing, and whole-genome sequencing. Demographic characteristics and clinical outcomes of the patients were retrospectively examined. FINDINGS 171 cases of shigellosis were included. 78 (46%) patients were men who have sex with men (MSM), and 88 (52%) were people experiencing homelessness (PEH). Although 84 (51%) isolates were multidrug resistant, 100 (70%) of 143 patients with data on antimicrobial therapy received appropriate empirical therapy. Phylogenomic analysis identified sequential outbreaks of multiple distinct lineages of Shigella flexneri and Shigella sonnei. Discrete clonal lineages (ten in S flexneri and nine in S sonnei) and resistance traits were responsible for infection in different at-risk populations (ie, MSM, PEH), enabling development of effective guidelines for empirical treatment. The most prevalent lineage in Seattle was probably introduced to Washington State via international travel, with subsequent domestic transmission between at-risk groups. INTERPRETATION An outbreak in Seattle was driven by parallel emergence of multidrug-resistant strains involving international transmission networks and domestic transmission between at-risk populations. Genomic analysis elucidated not only outbreak origin, but directed optimal approaches to testing, treatment, and public health response. Rapid diagnostics combined with detailed knowledge of local epidemiology can enable high rates of appropriate empirical therapy even in multidrug-resistant infection. FUNDING None.
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Affiliation(s)
- Giannoula S Tansarli
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Lori A Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephen J Libby
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jared Almazan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jason Matsumoto
- Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA; Infection Prevention and Control, Harborview Medical Center, Seattle, WA, USA
| | - Krista Rietberg
- Infection Prevention and Control, Harborview Medical Center, Seattle, WA, USA
| | - BreeAnna M Dell
- Public Health-Seattle & King County, Communicable Diseases, Epidemiology, and Immunizations, Seattle, WA, USA
| | - Noël V Hatley
- Public Health-Seattle & King County, Communicable Diseases, Epidemiology, and Immunizations, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Ferric C Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA; Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA; Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA, USA.
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7
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Richardson D, Pakianathan M, Ewens M, Mitchell H, Mohammed H, Wiseman E, Tweed M, Nichols K, Rawdah W, Cooper R, Macrowan R, Irish M, Evans A, Godbole G. British Association of Sexual Health and HIV (BASHH) United Kingdom national guideline for the management of sexually transmitted enteric infections 2023. Int J STD AIDS 2023:9564624231168217. [PMID: 37247427 DOI: 10.1177/09564624231168217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This is the first British Association of Sexual Health and HIV (BASHH) national guideline for the management of sexually transmitted enteric infections (STEI). This guideline is primarily aimed for level 3 sexual health clinics; however, it may also be applicable to other settings such as primary care or other hospital departments where individuals with STEI may present. This guideline makes recommendations on testing, management, partner notification and public health control of STEI.
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Affiliation(s)
- Daniel Richardson
- University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Brighton & Sussex Medical School, Brighton, UK
| | | | | | | | | | | | | | | | - Waseem Rawdah
- University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Richard Cooper
- University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | | | | | - Amy Evans
- University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
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8
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Mason LCE, Greig DR, Cowley LA, Partridge SR, Martinez E, Blackwell GA, Chong CE, De Silva PM, Bengtsson RJ, Draper JL, Ginn AN, Sandaradura I, Sim EM, Iredell JR, Sintchenko V, Ingle DJ, Howden BP, Lefèvre S, Njampeko E, Weill FX, Ceyssens PJ, Jenkins C, Baker KS. The evolution and international spread of extensively drug resistant Shigella sonnei. Nat Commun 2023; 14:1983. [PMID: 37031199 PMCID: PMC10082799 DOI: 10.1038/s41467-023-37672-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.
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Affiliation(s)
- Lewis C E Mason
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - David R Greig
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | | | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Elena Martinez
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Grace A Blackwell
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Charlotte E Chong
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Rebecca J Bengtsson
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Jenny L Draper
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Andrew N Ginn
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia
| | - Indy Sandaradura
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Eby M Sim
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Microbiology Research, Westmead Hospital, Westmead, NSW, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sophie Lefèvre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Elisabeth Njampeko
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | | | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | - Kate S Baker
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK.
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK.
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9
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Fernández Vecilla D, Zugazaga Inchaurza K, Lombide Aguirre I, Díaz de Tuesta Del Arco JL. Phenotypic and genotypic characterization of Shigella sonnei carrying the extended-spectrum beta-lactamase CTX-M-27. A report of two cases in Spain in men who have sex with men. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2023; 41:248-250. [PMID: 36868981 DOI: 10.1016/j.eimce.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 03/05/2023]
Affiliation(s)
- Domingo Fernández Vecilla
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain; Instituto de Investigación Sanitaria Biocruces, Barakaldo, Vizcaya, Spain.
| | - Kristina Zugazaga Inchaurza
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain; Instituto de Investigación Sanitaria Biocruces, Barakaldo, Vizcaya, Spain.
| | - Itxaso Lombide Aguirre
- Instituto de Investigación Sanitaria Biocruces, Barakaldo, Vizcaya, Spain; Servicio de Enfermedades Infecciosas, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain.
| | - José Luis Díaz de Tuesta Del Arco
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain; Instituto de Investigación Sanitaria Biocruces, Barakaldo, Vizcaya, Spain.
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10
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O'Flanagan H, Siddiq M, Llewellyn C, Richardson D. Antimicrobial resistance in sexually transmitted Shigella in men who have sex with men: A systematic review. Int J STD AIDS 2023; 34:374-384. [PMID: 36786731 DOI: 10.1177/09564624231154942] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
BACKGROUND Outbreaks of sexually transmitted Shigella flexneri and Shigella sonnei in men who have sex with men (MSM) are a major public health issue. While most cases can be managed conservatively, a minority require antimicrobial treatment. Recent reports have highlighted increasing antimicrobial resistant (AMR) strains of Shigella spp. in men who have sex with men. We aimed to systematically review antimicrobial resistance (and decreased antimicrobial sensitivity) in sexually transmitted shigella in men who have sex with men, focussing on macrolides, quinolones, and third generation cephalosporins. METHODS We systematically searched 4 bibliographical databases (EMBASE, medline, EMCARE and CINAHL) from January 2011 to November 2021. We used a 2-stage process to assess eligibility: the primary author conducted an initial screen and then 3 authors conducted independent full-text reviews to determine the final eligible manuscripts. We only included manuscripts in English which included men who have sex with men with sexually transmitted shigella where data on antimicrobial resistance was available. RESULTS Thirty-nine manuscripts met the inclusion criteria. A majority of the manuscripts (N = 34) described reduced susceptibility or antimicrobial resistant to macrolides, quinolones and third generation cephalosporins in circulating strains of shigella within sexual networks of men who have sex with men. Extensively drug resistant outbreaks of shigella in men who have sex with men have been reported containing genetic markers of ceftriaxone resistance (e.g. BlaCTX-M27) where isolates also contained markers of reduced susceptibility, and antimicrobial resistant to macrolides and quinolones. CONCLUSION There is little role for macrolides, quinolones or third generation cephalosporins in the management of sexually transmitted shigella in men who have sex with men. More research is needed to develop novel strategies for shigella control in men who have sex with men, as antimicrobial options are diminishing.
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Affiliation(s)
| | | | | | - Daniel Richardson
- 12190Brighton and Sussex Medical School, Brighton, UK.,8721University Hospitals Sussex NHS Foundation Trust, Brighton, UK
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11
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Moreno-Mingorance A, Mir-Cros A, Goterris L, Rodriguez-Garrido V, Sulleiro E, Barberà MJ, Alberny M, Hoyos-Mallecot Y, Descalzo V, Bravo A, Roca-Grande J, Viñado B, Pumarola T, Larrosa MN, González-López JJ. Increasing trend of antimicrobial resistance in Shigella associated with MSM transmission in Barcelona, 2020-21: outbreak of XRD Shigella sonnei and dissemination of ESBL-producing Shigella flexneri. J Antimicrob Chemother 2023; 78:975-982. [PMID: 36760088 PMCID: PMC10068420 DOI: 10.1093/jac/dkad031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Several countries have recently reported the detection of ESBL-producing Shigella sonnei associated with transmission among MSM. In a previous study by our group, 2.8% of Shigella spp. obtained from MSM in Barcelona between 2015 and 2019 were ESBL producers. OBJECTIVES To describe and characterize the emerging ESBL-producing Shigella spp. associated with sexual transmission among MSM detected from 2020 to 2021 in Barcelona, elucidating their connectivity with contemporaneous ESBL-producing Shigella spp. from other countries. RESULTS From 2020 to 2021, we identified that among MSM, 68% of S. sonnei were XDR harbouring blaCTX-M-27 and 14% of Shigella flexneri were MDR harbouring blaCTX-M-27. WGS analysis showed that the ESBL-producing S. sonnei were part of a monophyletic cluster, which included isolates responsible for the prolonged outbreak occurring in the UK. Our data also reveal the first emergence and clonal dissemination of ESBL-producing and fluoroquinolone-resistant S. flexneri 2a among MSM. CONCLUSIONS We report an increasing trend of antimicrobial resistance in Shigella spp. among MSM in Barcelona since 2021, mainly as a consequence of the dissemination of XDR ESBL-producing S. sonnei, previously reported in the UK. These results highlight the importance of international collaborative surveillance of MDR/XDR S. sonnei and S. flexneri for rapid identification of their emergence and the prevention of the transmission of these pathogens.
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Affiliation(s)
- Albert Moreno-Mingorance
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alba Mir-Cros
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Lidia Goterris
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Virginia Rodriguez-Garrido
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Elena Sulleiro
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - M Jesús Barberà
- Drassanes-Vall d'Hebron Sexually Transmitted Infections Unit, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Mireia Alberny
- Primary Health-Care Division, Catalan Institute of Health, Barcelona, Spain
| | - Yannick Hoyos-Mallecot
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Vicente Descalzo
- Drassanes-Vall d'Hebron Sexually Transmitted Infections Unit, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Albert Bravo
- Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Roca-Grande
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Belén Viñado
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Tomàs Pumarola
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - M Nieves Larrosa
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Juan José González-López
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
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12
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Siddiq M, O'Flanagan H, Richardson D, Llewellyn CD. Factors associated with sexually transmitted shigella in men who have sex with men: a systematic review. Sex Transm Infect 2023; 99:58-63. [PMID: 36283806 DOI: 10.1136/sextrans-2022-055583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Outbreaks of sexually transmitted shigella have been reported in men who have sex with men (MSM) since the 1970s and present a major public health issue. Understanding the factors associated with the sexual transmission of shigella may inform future control strategies. METHODS We systematically searched four bibliographical databases (January 2000-February 2022) for manuscripts in English. We used a two-stage process to assess eligibility: the primary author conducted an initial screen and then three authors conducted independent full-text reviews to determine the final eligible manuscripts. We only included manuscripts that included MSM diagnosed with sexually transmitted shigella where specific factors associated with transmission were identified. RESULTS Thirteen manuscripts met the inclusion criteria that included 547 individuals. Sexually transmitted shigella in MSM was associated with: residing in a capital city/urban region, living with HIV (including engaging in seroadaptive sexual behaviour, having a low CD4 count, having a HIV viral load >100 000 and not engaging with HIV care), using HIV pre-exposure prophylaxis, use of geospatial mobile phone applications to meet sexual partners, visiting sex on premises venues, chemsex and recreational drug use, sexual behaviour (including multiple non-regular sexual partners and oral-anal sexual contact) and concomitant STIs. CONCLUSION We have highlighted some important risk behaviours and factors that are associated with sexually transmitted shigella in MSM that can be used to target future shigella control interventions.
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Affiliation(s)
| | | | - Daniel Richardson
- Brighton and Sussex Medical School, Brighton, UK .,Department of Sexual Health & HIV, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Carrie D Llewellyn
- Department of Primary Care & Public Health, Brighton and Sussex Medical School, Brighton, Brighton and Hove, UK
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13
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Chen MY, Williamson DA. Sexually acquired enteric infections among men who have sex with men. THE LANCET. INFECTIOUS DISEASES 2023; 23:644-645. [PMID: 36731482 DOI: 10.1016/s1473-3099(22)00813-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Marcus Y Chen
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC 3053, Australia; Central Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University, Melbourne, VIC, Australia.
| | - Deborah A Williamson
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Melbourne, VIC, Australia; Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
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14
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Sherry NL, Horan KA, Ballard SA, Gonҫalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, Seemann T. An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nat Commun 2023; 14:60. [PMID: 36599823 DOI: 10.1038/s41467-022-35713-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
Realising the promise of genomics to revolutionise identification and surveillance of antimicrobial resistance (AMR) has been a long-standing challenge in clinical and public health microbiology. Here, we report the creation and validation of abritAMR, an ISO-certified bioinformatics platform for genomics-based bacterial AMR gene detection. The abritAMR platform utilises NCBI's AMRFinderPlus, as well as additional features that classify AMR determinants into antibiotic classes and provide customised reports. We validate abritAMR by comparing with PCR or reference genomes, representing 1500 different bacteria and 415 resistance alleles. In these analyses, abritAMR displays 99.9% accuracy, 97.9% sensitivity and 100% specificity. We also compared genomic predictions of phenotype for 864 Salmonella spp. against agar dilution results, showing 98.9% accuracy. The implementation of abritAMR in our institution has resulted in streamlined bioinformatics and reporting pathways, and has been readily updated and re-verified. The abritAMR tool and validation datasets are publicly available to assist laboratories everywhere harness the power of AMR genomics in professional practice.
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Affiliation(s)
- Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Kristy A Horan
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Anders Gonҫalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Claire L Gorrie
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Mark B Schultz
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Michelle L Sait
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia.
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia.
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
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15
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Berbers B, Vanneste K, Roosens NHCJ, Marchal K, Ceyssens PJ, De Keersmaecker SCJ. Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium. Microb Genom 2023; 9:mgen000925. [PMID: 36748573 PMCID: PMC9973847 DOI: 10.1099/mgen.0.000925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/03/2022] [Indexed: 01/25/2023] Open
Abstract
For antimicrobial resistance (AMR) surveillance, it is important not only to detect AMR genes, but also to determine their plasmidic or chromosomal location, as this will impact their spread differently. Whole-genome sequencing (WGS) is increasingly used for AMR surveillance. However, determining the genetic context of AMR genes using only short-read sequencing is complicated. The combination with long-read sequencing offers a potential solution, as it allows hybrid assemblies. Nevertheless, its use in surveillance has so far been limited. This study aimed to demonstrate its added value for AMR surveillance based on a case study of extended-spectrum beta-lactamases (ESBLs). ESBL genes have been reported to occur also on plasmids. To gain insight into the diversity and genetic context of ESBL genes detected in clinical isolates received by the Belgian National Reference Center between 2013 and 2018, 100 ESBL-producing Shigella and 31 ESBL-producing Salmonella were sequenced with MiSeq and a representative selection of 20 Shigella and six Salmonella isolates additionally with MinION technology, allowing hybrid assembly. The bla CTX-M-15 gene was found to be responsible for a rapid rise in the ESBL Shigella phenotype from 2017. This gene was mostly detected on multi-resistance-carrying IncFII plasmids. Based on clustering, these plasmids were determined to be distinct from the circulating plasmids before 2017. They were spread to different Shigella species and within Shigella sonnei between multiple genotypes. Another similar IncFII plasmid was detected after 2017 containing bla CTX-M-27 for which only clonal expansion occurred. Matches of up to 99 % to plasmids of various bacterial hosts from all over the world were found, but global alignments indicated that direct or recent ESBL-plasmid transfers did not occur. It is most likely that travellers introduced these in Belgium and subsequently spread them domestically. However, a clear link to a specific country could not be made. Moreover, integration of bla CTX-M in the chromosome of two Shigella isolates was determined for the first time, and shown to be related to ISEcp1. In contrast, in Salmonella, ESBL genes were only found on plasmids, of which bla CTX-M-55 and IncHI2 were the most prevalent, respectively. No matching ESBL plasmids or cassettes were detected between clinical Shigella and Salmonella isolates. The hybrid assembly data allowed us to check the accuracy of plasmid prediction tools. MOB-suite showed the highest accuracy. However, these tools cannot replace the accuracy of long-read and hybrid assemblies. This study illustrates the added value of hybrid assemblies for AMR surveillance and shows that a strategy where even just representative isolates of a collection used for hybrid assemblies could improve international AMR surveillance as it allows plasmid tracking.
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Affiliation(s)
- Bas Berbers
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | | | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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16
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Antimicrobial resistance in shigellosis: A surveillance study among urban and rural children over 20 years in Bangladesh. PLoS One 2022; 17:e0277574. [PMID: 36409683 PMCID: PMC9678309 DOI: 10.1371/journal.pone.0277574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Antimicrobial resistance against shigellosis is increasingly alarming. However, evidence-based knowledge gaps regarding the changing trends of shigellosis in Bangladesh exist due to the scarcity of longitudinal data on antimicrobial resistance. Our study evaluated the last 20 years antimicrobial resistance patterns against shigellosis among under-5 children in the urban and rural sites of Bangladesh. Data were extracted from the Diarrheal Disease Surveillance System (DDSS) of Dhaka Hospital (urban site) and Matlab Hospital (rural site) of the International Centre for Diarrheal Disease Research, Bangladesh (icddr,b) between January 2001 and December 2020. We studied culture-confirmed shigellosis cases from urban Dhaka Hospital (n = 883) and rural Matlab Hospital (n = 1263). Since 2001, a declining percentage of shigellosis in children observed in urban and rural sites. Moreover, higher isolation rates of Shigella were found in the rural site [1263/15684 (8.1%)] compared to the urban site [883/26804 (3.3%)] in the last 20 years. In both areas, S. flexneri was the predominant species. The upward trend of S. sonnei in both the study sites was statistically significant after adjusting for age and sex. WHO-recommended 1st line antibiotic ciprofloxacin resistance gradually reached more than 70% in both the urban and rural site by 2020. In multiple logistic regression after adjusting for age and sex, ciprofloxacin, azithromycin, mecillinam, ceftriaxone, and multidrug resistance (resistance to any two of these four drugs) among under-5 children were found to be increasing significantly (p<0.01) in the last 20 years in both sites. The study results underscore the importance of therapeutic interventions for shigellosis by appropriate drugs based on their current antibiogram for under-5 children. These observations may help policymakers in formulating better case management strategies for shigellosis.
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17
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Prevalence of Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Producing Shigella Species in Asia: A Systematic Review and Meta-Analysis. Antibiotics (Basel) 2022; 11:antibiotics11111653. [PMID: 36421297 PMCID: PMC9687025 DOI: 10.3390/antibiotics11111653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Shigellosis remains one of the leading causes of morbidity and mortality worldwide and is the second leading cause of diarrheal mortality among all age groups. However, the global emergence of antimicrobial-resistant Shigella strains, limiting the choice of effective drugs for shigellosis, has become the major challenge in the treatment of Shigella infections. The aim of this systematic review and meta-analysis was to provide an updated picture of the prevalence of antimicrobial-resistant Shigella species in Asia. A comprehensive and systematic search was performed on three electronic databases (PubMed, ScienceDirect and Scopus), in which 63 eligible studies published between 2010 and 2022 were identified. From our meta-analysis of proportions using a random-effects model, the overall prevalence of Shigella spp. in Asian patients was estimated to be 8.0% (95% CI: 5.5–10.5). The pooled prevalence rates of multidrug-resistant (MDR) and extended-spectrum beta-lactamase (ESBL)-producing Shigella strains were 68.7% (95% CI: 59.9–77.5) and 23.9% (95% CI: 12.9–34.8), respectively. Concerning recommended antimicrobial drugs for Shigella, the prevalence of resistance was highest for ciprofloxacin (29.8%) and azithromycin (29.2%), followed by ceftriaxone (23.8%), in spite of their importance as first- and second-line treatments for shigellosis. In contrast, resistance to carbapenems, such as ertapenem (0.0%), imipenem (0.1%) and meropenem (0.0%), was almost non-existent among the 49 tested antibiotics. The significantly high prevalence estimation suggests that the multidrug-resistant Shigella is a pressing threat to public health worthy of careful and justified interventions. Effective antibiotic treatment strategies, which may lead to better outcomes for the control and treatment of shigellosis in Asia, are essential.
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Ortiz de la Rosa JM, Rodríguez-Villodres Á, Casimiro-Soriguer CS, Ruiz-Pérez De Pipaón M, Briones E, Aznar Fernández M, Lepe JA. MDR Shigella sonnei in Spain: an ever-evolving emerging threat? JAC Antimicrob Resist 2022; 4:dlac090. [PMID: 36072302 PMCID: PMC9442613 DOI: 10.1093/jacamr/dlac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Background Seven CTX-M-27-producing Shigella sonnei strains were isolated at the University Hospital Virgen del Rocío (Seville, Spain) microbiology service from October to November 2021. Objectives To offer extensive information on the microbiological and molecular epidemiology results of the seven S. sonnei isolates and compare them with other previously documented CTX-M-27-producing S. sonnei associated with MSM transmission. Methods S. sonnei isolated from stool samples of patients with acute diarrhoea were identified through biochemical and serological typing. Whole characterization of the seven isolates was performed by sequencing with MinION Mk1C followed by genomic and molecular analysis. Results All the isolates were resistant to penicillins, cephalosporins, fluoroquinolones, cotrimoxazole and azithromycin. Sequencing showed the presence of several resistance determinants, outstanding blaCTX-M-27, azithromycin resistance genes [ermB and mph(A)], qnrB19 and mutations in the QRDRs. All isolates belonged to the same hierarchical clustering of cgMLST (HierCC) with five allele distance (HC5) scheme v1 from EnteroBase. However, they presented differences in plasmid composition, with all seven isolates harbouring IncFII, IncB/O/K/Z and ColE1-like while SH2, SH6 and SH7 had IncFIB only. Our isolates were closely related to others from Spain (HC5; 98748), Australia (HC5; 98748) and the UK (HC5; 98748), which were also associated with MSM transmission. Nevertheless, the structure of the non-chromosomal genetic elements and the genetic context of blaCTX-M-27 presented a certain variability compared with isolates from other countries and among them. Conclusions This study confirms the emergence of CTX-M-27-producing S. sonnei (ST152) associated with MSM transmission in Spain, adding it to the Europe outbreak list and reinforcing the necessity of active surveillance and control of this high-risk clone.
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Affiliation(s)
- José Manuel Ortiz de la Rosa
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío , Seville , Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville , Seville , Spain
| | - Ángel Rodríguez-Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío , Seville , Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville , Seville , Spain
| | - Carlos S Casimiro-Soriguer
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío , Seville , Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville , Seville , Spain
| | - Maite Ruiz-Pérez De Pipaón
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío , Seville , Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville , Seville , Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC) , Madrid , Spain
| | - Eduardo Briones
- Epidemiology and Public Health Unit, Sevilla Health District , Seville , Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP) , Seville , Spain
| | - María Aznar Fernández
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío , Seville , Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville , Seville , Spain
| | - José Antonio Lepe
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío , Seville , Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville , Seville , Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC) , Madrid , Spain
- Department of Microbiology, University of Seville , Seville , Spain
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Fernández Vecilla D, Zugazaga Inchaurza K, Lombide Aguirre I, Díaz de Tuesta del Arco JL. Caracterización fenotípica y genotípica de Shigella sonnei portadora de la betalactamasa de espectro extendido CTX-M-27. A propósito de dos casos en España en hombres que tienen sexo con hombres. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Characterization of Extended-Spectrum β-Lactamase-Producing Shigella sonnei in Spain: Expanding the Geographic Distribution of Sequence Type 152/CTX-M-27 Clone. Antimicrob Agents Chemother 2022; 66:e0033422. [PMID: 35762798 PMCID: PMC9295536 DOI: 10.1128/aac.00334-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We describe the first occurrence in Spain of community cases of CTX-M-27-producing Shigella sonnei sequence type 152 (ST152), resistant to quinolones and azithromycin. The cases included adult males and also one pediatric case. The isolates were clustered together with an Australian isolate and differed from other outbreak-causing strains in England by more than 50 alleles. They carried the blaCTX-M-27 gene on an 83-Kb F2:A-:B- plasmid, similar to that found in a British isolate.
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Charles H, Prochazka M, Thorley K, Crewdson A, Greig DR, Jenkins C, Painset A, Fifer H, Browning L, Cabrey P, Smith R, Richardson D, Waters L, Sinka K, Godbole G, Corkin H, Abrahams A, LeBlond H, Lo J, Holgate A, Saunders J, Plahe G, Vusirikala A, Green F, King M, Tewolde R, Jajja A. Outbreak of sexually transmitted, extensively drug-resistant Shigella sonnei in the UK, 2021–22: a descriptive epidemiological study. THE LANCET INFECTIOUS DISEASES 2022; 22:1503-1510. [DOI: 10.1016/s1473-3099(22)00370-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/23/2022]
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22
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Gaudreau C, Bernaquez I, Pilon PA, Goyette A, Yared N, Bekal S. Clinical and Genomic Investigation of an International Ceftriaxone- and Azithromycin-Resistant Shigella sonnei Cluster among Men Who Have Sex with Men, Montréal, Canada 2017-2019. Microbiol Spectr 2022; 10:e0233721. [PMID: 35647695 PMCID: PMC9241791 DOI: 10.1128/spectrum.02337-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/06/2022] [Indexed: 12/29/2022] Open
Abstract
Multidrug-resistant (MDR) Shigella sonnei have become prevalent among men who have sex with men and have become a global public health concern. From June 2017 to April 2019, 32 men were infected with MDR S. sonnei acquired locally, in Montréal, which was suggestive of an outbreak. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), phylogenetic analysis, antimicrobial resistance and virulence characterization, and association to international clusters were performed. The outbreak strain was ceftriaxone- and azithromycin-resistant due to the acquisition of blaCTX-M-27, and mphA and ermB genes, respectively, with reduced susceptibility to ciprofloxacin due to a single point mutation (gyrA S83L). One out of 27 patients treated with a fluoroquinolone experienced microbiological failure. Epidemiological evidence first supported by a rare unique MDR Shigella sonnei documented only in men in 2017 followed by similar pulsed-field gel electrophoresis profiles was confirmed by WGS. A core genome high-quality single-nucleotide variant (hqSNV)-based phylogeny found a median of 6 hqSNV differences among isolates. Virulence gene content was investigated, but no Shiga toxins were detected. An international cluster of highly related isolates was identified (PDS000019750.208) and belonged to the 3.7.29.1.4.1 S. sonnei genotype (Global III VN2.KH1.Aus). Genomic analysis revealed that this Montréal cluster was connected to other documented outbreaks in Australia, the United States, and the United Kingdom. This study highlights the urgent need for public health measures to focus on the prevention and the early detection of S. sonnei, since global transmission patterns of MDR strains is concerning and few antimicrobial treatment options are available. IMPORTANCE Shigella sonnei, an important foodborne pathogen, recently became a frequent sexually transmitted agent involved in large and persistent outbreaks globally among men who have sex with men. Most strains also harbor several multidrug-resistant (MDR) determinants of particular concern. This study characterizes an outbreak strain at the source of an important MDR cluster identified in Montréal in 2017. Associations were made to many high-profile international outbreaks, and the causative S. sonnei lineage of these clusters was identified, which was not evident in past reports. The worldwide occurrence of this strain is of concern since treatment with antimicrobials like ceftriaxone and azithromycin may not be effective, and rare microbiological failures have been documented in patients treated with ciprofloxacin. Our investigation highlights the threats of Shigella spp. infection and the necessity for antimicrobial susceptibility monitoring in order to mitigate S. sonnei's impact on public health and to avoid transmission to other at-risk communities.
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Affiliation(s)
- Christiane Gaudreau
- Microbiologie médicale et infectiologie, Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, Quebec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Isabelle Bernaquez
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Pierre A. Pilon
- Direction régionale de santé publique, Centre intégré universitaire de santé et de services sociaux du Centre-Sud-de–l’île-de-Montréal, Montréal, Quebec, Canada
- Département de médecine sociale et préventive, Université de Montréal, Montréal, Quebec, Canada
| | - Alexandre Goyette
- Direction régionale de santé publique, Centre intégré universitaire de santé et de services sociaux du Centre-Sud-de–l’île-de-Montréal, Montréal, Quebec, Canada
| | - Nada Yared
- Microbiologie médicale et infectiologie, Hôpital Charles-Lemoyne, Greenfield Park, Quebec, Canada
| | - Sadjia Bekal
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
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Decreased Susceptibility of Shigella Isolates to Azithromycin in Children in Tehran, Iran. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:4503964. [PMID: 35386469 PMCID: PMC8977332 DOI: 10.1155/2022/4503964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
Abstract
Azithromycin (AZT) has widely been used for the treatment of shigellosis in children. Recent studies showed a high rate of decreased susceptibility to azithromycin due to different mechanisms of resistance in Shigella isolates. Accordingly, the purpose of this study was to investigate the role of azithromycin resistance mechanisms of Shigella isolates in Iran during a two-year period. In this study, we investigated the mechanisms of resistance among Shigella spp. that were isolated from children with shigellosis. The minimum inhibitory concentration (MIC) of Shigella isolates to azithromycin was determined by the agar dilution method in the presence and absence of Phe-Arg-β-naphthylamide inhibitor. The presence of 12 macrolide resistance genes was investigated for all isolates by PCR for the first time in Tehran province in Iran. Among the 120 Shigella spp., only the mph(A) gene (49.2%) was detected and other macrolide resistance genes were absent. The phenotypic activity of efflux pump was observed in 1.9% of isolates which were associated with over expression of both omp(A) and omp(W) genes. The high prevalence of the mph(A) gene among DSA isolates may indicate that azithromycin resistance has evolved as a result of antimicrobial selection pressures and inappropriate use of azithromycin.
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24
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Emergence of azithromycin and third-generation cephalosporins resistant Shigella isolated from Iranian children. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Pakbin B, Amani Z, Allahyari S, Mousavi S, Mahmoudi R, Brück WM, Peymani A. Genetic diversity and antibiotic resistance of Shigella spp. isolates from food products. Food Sci Nutr 2021; 9:6362-6371. [PMID: 34760266 PMCID: PMC8565218 DOI: 10.1002/fsn3.2603] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/02/2021] [Accepted: 09/12/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of multidrug-resistant Shigella is a significant threat to global public health. Limited studies have investigated the incidence, antimicrobial susceptibility, and genetic diversity of Shigella isolated from food products. Conventional culture-based, serologic, molecular, disk diffusion, PCR, and RAPD-PCR methods were used to determine the prevalence rate, phenotypic and genotypic antibiotic resistance profile, and genetic diversity of the Shigella isolates from food samples including vegetable salad, ground meat, and raw cow's milk (405 samples). The prevalence rate of Shigella in food samples was 4.44%. The incidence of S. sonnei (3.7%) was higher than that of S. flexneri (0.74%). S. dysenteriae and S. boydii were not detected in food samples examined. Also, no Shigella were recovered from raw cow's milk. This study showed that the Shigella isolates were resistant to sulfamethoxazole/trimethoprim (83.3%), amoxicillin (66.6%), streptomycin (66.6%), tetracycline (61.1%), ampicillin (50%), amoxicillin-clavulanic acid (50%), azithromycin (50%), and chloramphenicol (50%) and completely sensitive to cefoxitin, cefepime, amikacin, and gentamicin. All Shigella isolates were multidrug-resistant. We detected bla SHV resistance gene in all isolates; however, no isolate harbored bla TEM gene. RAPD-PCR categorized the Shigella isolates into five main clusters. The highest antibiotic resistance was observed in the isolates of cluster R4. The finding of this study also indicated an association between antimicrobial resistance profiles and genotyping properties of the isolates. Novel food monitoring systems, including surveillance of multidrug-resistant foodborne pathogens, especially in developing countries, are required to control the foodborne diseases.
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Affiliation(s)
- Babak Pakbin
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Zahra Amani
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Samaneh Allahyari
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Shaghayegh Mousavi
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Razzagh Mahmoudi
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Wolfram Manuel Brück
- Institute for Life TechnologiesUniversity of Applied Sciences Western Switzerland Valais‐WallisSwitzerland
| | - Amir Peymani
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
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26
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Fischer N, Maex M, Mattheus W, Van den Bossche A, Van Cauteren D, Laisnez V, Hammami N, Ceyssens PJ. Genomic epidemiology of persistently circulating MDR Shigella sonnei strains associated with men who have sex with men (MSM) in Belgium (2013-19). J Antimicrob Chemother 2021; 77:89-97. [PMID: 34673959 PMCID: PMC8730680 DOI: 10.1093/jac/dkab377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives Shigella sonnei resistant to first-line antibiotics azithromycin and ciprofloxacin are on the rise globally. The aim of this study was to describe the epidemiology of MDR S. sonnei in Belgium and to identify origins and circulating clusters through WGS. Methods We undertook demographic, temporal and geographical analysis of 930 S. sonnei isolates submitted to the Belgian National Reference Centre for Salmonella and Shigella between 2017 and 2019. Phylogenetic analysis of WGS data, genotyping and identification of genetic markers of antimicrobial resistance was performed on 372 Belgian isolates submitted between 2013 and 2019. Results S. sonnei was identified in 75% (930/1253) of Belgian Shigella isolates submitted between 2017 and 2019. Overall, 7% (69/930) of isolates were resistant to ciprofloxacin alone, 6% (57/930) showed reduced susceptibility to azithromycin alone, and 24% (223/930) exhibited both. Men were at higher risk of carrying a double resistant S. sonnei strain, compared with women (risk ratio = 8.6, 95% CI = 5.4–13.9). Phylogenetic analysis revealed four independent Belgian clusters of persistently circulating MDR strains, associated with men who have sex with men (MSM) and of the same genotypes as previously described international MSM-related clades. Belgian isolates carried various incompatibility (Inc)-type plasmids, the SpA plasmid and ESBL genes. Conclusions In Belgium, S. sonnei isolates from men are much more likely to be resistant to important first-line antibiotics than isolates from women. Multiple co-circulating MDR S. sonnei clusters of different genotypes were identified in the MSM community. Further studies on risk groups are needed for targeted prevention, improved clinical and public health management and antimicrobial stewardship in Belgium.
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Affiliation(s)
- Natalie Fischer
- European Programme for Public Health Microbiology (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 169 73 Solna, Sweden.,Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - Margo Maex
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - Wesley Mattheus
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - An Van den Bossche
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - Dieter Van Cauteren
- Service Epidemiology of Infectious Diseases, Sciensano, Rue Ernest Blerot 1, 1070 Anderlecht, Belgium
| | - Valeska Laisnez
- Service Epidemiology of Infectious Diseases, Sciensano, Rue Ernest Blerot 1, 1070 Anderlecht, Belgium.,Agentschap Zorg en Gezondheid, Koning Albert-II-laan 35 bus 33, 1030 Brussels, Belgium
| | - Naïma Hammami
- Agentschap Zorg en Gezondheid, Koning Albert-II-laan 35 bus 33, 1030 Brussels, Belgium
| | - Pieter-Jan Ceyssens
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
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Dallman TJ, Charles H, Prochazka M, Sinka K, Hughes G, Godbole G, Jenkins C. Emergence of novel strains of Shigella flexneri associated with sexual transmission in adult men in England, 2019-2020. J Med Microbiol 2021; 70. [PMID: 34665107 PMCID: PMC8604172 DOI: 10.1099/jmm.0.001437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
National surveillance of shigellosis in England revealed an increase in sexually transmitted Shigella flexneri in adult males in 2019 that persisted throughout 2020. We observed a resurgence of azithromycin-resistant S. flexneri serotype 3a, and the emergence of two novel multidrug-resistant clades of S. flexneri 2a and S. flexneri 1b.
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Affiliation(s)
- Timothy J Dallman
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Hannah Charles
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Mateo Prochazka
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Katy Sinka
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Gwenda Hughes
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Gauri Godbole
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
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Locke RK, Greig DR, Jenkins C, Dallman TJ, Cowley LA. Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK. Microb Genom 2021; 7. [PMID: 34427554 PMCID: PMC8549364 DOI: 10.1099/mgen.0.000644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shigellosis in men who have sex with men (MSM) is caused by multidrug resistant Shigellae, exhibiting resistance to antimicrobials including azithromycin, ciprofloxacin and more recently the third-generation cephalosporins. We sequenced four blaCTX-M-27-positive MSM Shigella isolates (2018–20) using Oxford Nanopore Technologies; three S. sonnei (identified as two MSM clade 2, one MSM clade 5) and one S. flexneri 3a, to explore AMR context. All S. sonnei isolates harboured Tn7/Int2 chromosomal integrons, whereas S. flexneri 3a contained the Shigella Resistance Locus. All strains harboured IncFII pKSR100-like plasmids (67-83kbp); where present blaCTX-M-27 was located on these plasmids flanked by IS26 and IS903B, however blaCTX-M-27 was lost in S. flexneri 3a during storage between Illumina and Nanopore sequencing. IncFII AMR regions were mosaic and likely reorganised by IS26; three of the four plasmids contained azithromycin-resistance genes erm(B) and mph(A) and one harboured the pKSR100 integron. Additionally, all S. sonnei isolates possessed a large IncB/O/K/Z plasmid, two of which carried aph(3’)-Ib/aph(6)-Id/sul2 and tet(A). Monitoring the transmission of mobile genetic elements with co-located AMR determinants is necessary to inform empirical treatment guidance and clinical management of MSM-associated shigellosis.
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Affiliation(s)
| | - David R Greig
- Gastrointestinal Reference Services, Public Health England, London, UK.,Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Claire Jenkins
- Gastrointestinal Reference Services, Public Health England, London, UK
| | - Tim J Dallman
- Gastrointestinal Reference Services, Public Health England, London, UK.,Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
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Moreno-Mingorance A, Espinal P, Rodriguez V, Goterris L, Fàbrega A, Serra-Pladevall J, Barberà MJ, Alberny M, Martín-González H, Cornejo-Sánchez T, Armas M, Mir-Cros A, Raventós A, Viñado B, Pumarola T, Larrosa MN, González-López JJ. Circulation of multi-drug-resistant Shigella sonnei and Shigella flexneri among men who have sex with men in Barcelona, Spain, 2015-2019. Int J Antimicrob Agents 2021; 58:106378. [PMID: 34157402 DOI: 10.1016/j.ijantimicag.2021.106378] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/20/2021] [Accepted: 06/13/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND In high-income countries, shigellosis is mainly found in travellers to high-risk regions or in men who have sex with men (MSM). This study investigated the genomic characteristics and the features of antimicrobial resistance of MSM-associated Shigella flexneri and Shigella sonnei circulating in Barcelona, Spain, elucidating their connectivity with contemporaneous Shigella spp. from other countries. METHODS Antimicrobial susceptibility, whole-genome sequencing, genomic characterization and phylogenetic analysis were performed in MSM-associated Shigella spp. recovered from 2015 to 2019. Reference genomes of MSM-associated Shigella spp. were included for contextualization and to determine their connection with international outbreaks. RESULTS In total, 44 S. flexneri and 26 S. sonnei were identified among MSM. Overall, 80% showed resistance to azithromycin, 65.7% showed resistance to trimethoprim-sulphamethoxazole and 32.8% showed resistance to ciprofloxacin; 27.1% were resistant to all three antimicrobials. mphA and/or ermB, and qnrS and mutations in the quinolone resistance determining regions were found in the azithromycin- and ciprofloxacin-resistant isolates, respectively. Additionally, two isolates carried blaCTX-M-27. Single-nucleotide-polymorphism-based analysis revealed that the isolates were organized into different lineages, most of which were closely related to dominant MSM-associated lineages described previously in the UK and Australia. CONCLUSIONS This study investigated the circulation of lineages of S. flexneri and S. sonnei among MSM in Spain that were mainly resistant to first-/second-line oral treatments, and closely related to dominant MSM-associated lineages described previously in the UK and Australia. These data reinforce the urgent need for the implementation of public health measures focusing on the early detection and prevention of transmission of this emerging pathogen, which is contributing to the antimicrobial resistance crisis in sexually transmitted infections.
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Affiliation(s)
- Albert Moreno-Mingorance
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Paula Espinal
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Virginia Rodriguez
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Lidia Goterris
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Anna Fàbrega
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Judit Serra-Pladevall
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - M Jesús Barberà
- Drassanes-Vall d'Hebron Sexually Transmitted Infections Unit, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Mireia Alberny
- Primary Healthcare Division, Catalan Institute of Health, Barcelona, Spain
| | - Héctor Martín-González
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Thais Cornejo-Sánchez
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Mayuli Armas
- Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Alba Mir-Cros
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alex Raventós
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Belén Viñado
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Tomàs Pumarola
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - M Nieves Larrosa
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.
| | - Juan José González-López
- Vall d'Hebron Institut de Recerca, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Clinical Microbiology, Vall d'Hebron Hospital Universitari, Barcelona, Spain.
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