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Wu H, Ding C, Chi C, Liu S, Gao Z, Sun W, Zhao H, Song S. Lactobacillus crispatus 7-4 Mitigates Salmonella typhimurium-Induced Enteritis via the γ‑Glutamylcysteine-Mediated Nrf2 Pathway. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10294-4. [PMID: 38829566 DOI: 10.1007/s12602-024-10294-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
Salmonella typhimurium (S. typhimurium) constitutes a major public health concern. We have previously proven that Lactobacillus crispatus 7-4 (L. crispatus 7-4) can inhibit the growth of S. typhimurium and thus can be used as a biocontrol strategy to suppress foodborne S. typhimurium infections. However, the inhibitory effect and in-depth mechanism of L. crispatus 7-4 remain to be elucidated. In this study, we found that L. crispatus 7-4 can protect against S. typhimurium-induced ileum injury by promoting intestinal barrier integrity, maintaining intestinal mucosal barrier homeostasis, and reducing intestinal inflammatory response. Furthermore, we demonstrated that this probiotic strain can increase the abundance of Lactobacillus spp. to maintain microbial homeostasis and simultaneously increase the amount of γ‑glutamylcysteine (γ-GC) by activating the glutathione metabolic pathway. The increased γ-GC promoted the transcription of Nrf2 target genes, thereby improving the host antioxidant level, reducing reactive oxygen species (ROS) accumulation, and removing pro-inflammatory cytokines. In other words, L. crispatus 7-4 could activate the enterocyte Nrf2 pathway by improving γ-GC to protect against S. typhimurium-induced intestinal inflammation and oxidative damage.
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Affiliation(s)
- Huixian Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenchen Ding
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Chi
- Pure&Natural (Shanghai) Biotechnology Co., Ltd., Shanghai, 201112, China
| | - Shuhui Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhangshan Gao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weidong Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haiming Zhao
- Pure&Natural (Shanghai) Biotechnology Co., Ltd., Shanghai, 201112, China
| | - Suquan Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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2
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Le SNH, Nguyen Ngoc Minh C, de Sessions PF, Jie S, Tran Thi Hong C, Thwaites GE, Baker S, Pham DT, Chung The H. The impact of antibiotics on the gut microbiota of children recovering from watery diarrhoea. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:12. [PMID: 38686335 PMCID: PMC11057199 DOI: 10.1038/s44259-024-00030-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/15/2024] [Indexed: 05/02/2024]
Abstract
Infectious diarrhoeal diseases remain a substantial health burden in young children in low- and middle-income countries. The disease and its variable treatment options significantly alter the gut microbiome, which may affect clinical outcomes and overall gut health. Antibiotics are often prescribed, but their impact on the gut microbiome during recovery is unclear. Here, we used 16S rRNA sequencing to investigate changes in the gut microbiota in Vietnamese children with acute watery diarrhoea, and highlight the impact of antibiotic treatment on these changes. Our analyses identified that, regardless of treatment, recovery was characterised by reductions in Streptococcus and Rothia species and expansion of Bacteroides/Phocaeicola, Lachnospiraceae and Ruminococcacae taxa. Antibiotic treatment significantly delayed the temporal increases in alpha- and beta-diversity within patients, resulting in distinctive patterns of taxonomic change. These changes included a pronounced, transient overabundance of Enterococcus species and depletion of Bifidobacterium pseudocatenulatum. Our findings demonstrate that antibiotic treatment slows gut microbiota recovery in children following watery diarrhoea.
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Affiliation(s)
- Son-Nam H. Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | | | | | - Song Jie
- Genome Institute of Singapore, Singapore, Singapore
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, United Kingdom
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
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3
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Saini P, Bandsode V, Singh A, Mendem SK, Semmler T, Alam M, Ahmed N. Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment. mBio 2024; 15:e0354523. [PMID: 38376265 PMCID: PMC10936179 DOI: 10.1128/mbio.03545-23] [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: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations. IMPORTANCE Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.
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Affiliation(s)
- Poorvi Saini
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Viraj Bandsode
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Anuradha Singh
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Suresh Kumar Mendem
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Munirul Alam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Niyaz Ahmed
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
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4
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Wang X, Zhang H, Yu S, Li D, Gillings MR, Ren H, Mao D, Guo J, Luo Y. Inter-plasmid transfer of antibiotic resistance genes accelerates antibiotic resistance in bacterial pathogens. THE ISME JOURNAL 2024; 18:wrad032. [PMID: 38366209 PMCID: PMC10881300 DOI: 10.1093/ismejo/wrad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 02/18/2024]
Abstract
Antimicrobial resistance is a major threat for public health. Plasmids play a critical role in the spread of antimicrobial resistance via horizontal gene transfer between bacterial species. However, it remains unclear how plasmids originally recruit and assemble various antibiotic resistance genes (ARGs). Here, we track ARG recruitment and assembly in clinically relevant plasmids by combining a systematic analysis of 2420 complete plasmid genomes and experimental validation. Results showed that ARG transfer across plasmids is prevalent, and 87% ARGs were observed to potentially transfer among various plasmids among 8229 plasmid-borne ARGs. Interestingly, recruitment and assembly of ARGs occur mostly among compatible plasmids within the same bacterial cell, with over 88% of ARG transfers occurring between compatible plasmids. Integron and insertion sequences drive the ongoing ARG acquisition by plasmids, especially in which IS26 facilitates 63.1% of ARG transfer events among plasmids. In vitro experiment validated the important role of IS26 involved in transferring gentamicin resistance gene aacC1 between compatible plasmids. Network analysis showed four beta-lactam genes (blaTEM-1, blaNDM-4, blaKPC-2, and blaSHV-1) shuffling among 1029 plasmids and 45 clinical pathogens, suggesting that clinically alarming ARGs transferred accelerate the propagation of antibiotic resistance in clinical pathogens. ARGs in plasmids are also able to transmit across clinical and environmental boundaries, in terms of the high-sequence similarities of plasmid-borne ARGs between clinical and environmental plasmids. This study demonstrated that inter-plasmid ARG transfer is a universal mechanism for plasmid to recruit various ARGs, thus advancing our understanding of the emergence of multidrug-resistant plasmids.
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Affiliation(s)
- Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Hanhui Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shenbo Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Donghang Li
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Michael R Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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5
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Matanza XM, Clements A. Pathogenicity and virulence of Shigella sonnei: A highly drug-resistant pathogen of increasing prevalence. Virulence 2023; 14:2280838. [PMID: 37994877 PMCID: PMC10732612 DOI: 10.1080/21505594.2023.2280838] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023] Open
Abstract
Shigella spp. are the causative agent of shigellosis (or bacillary dysentery), a diarrhoeal disease characterized for the bacterial invasion of gut epithelial cells. Among the 4 species included in the genus, Shigella flexneri is principally responsible for the disease in the developing world while Shigella sonnei is the main causative agent in high-income countries. Remarkably, as more countries improve their socioeconomic conditions, we observe an increase in the relative prevalence of S. sonnei. To date, the reasons behind this change in aetiology depending on economic growth are not understood. S. flexneri has been widely used as a model to study the pathogenesis of the genus, but as more research data are collected, important discrepancies with S. sonnei have come to light. In comparison to S. flexneri, S. sonnei can be differentiated in numerous aspects; it presents a characteristic O-antigen identical to that of one serogroup of the environmental bacterium Plesiomonas shigelloides, a group 4 capsule, antibacterial mechanisms to outcompete and displace gut commensal bacteria, and a poorer adaptation to an intracellular lifestyle. In addition, the World Health Organization (WHO) have recognized the significant threat posed by antibiotic-resistant strains of S. sonnei, demanding new approaches. This review gathers knowledge on what is known about S. sonnei within the context of other Shigella spp. and aims to open the door for future research on understanding the increasing spread of this pathogen.
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Affiliation(s)
- Xosé M. Matanza
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, UK
| | - Abigail Clements
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, UK
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6
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Stenhouse GE, Keddy KH, Bengtsson RJ, Hall N, Smith AM, Thomas J, Iturriza-Gómara M, Baker KS. The genomic epidemiology of shigellosis in South Africa. Nat Commun 2023; 14:7715. [PMID: 38001075 PMCID: PMC10673971 DOI: 10.1038/s41467-023-43345-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.
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Affiliation(s)
- George E Stenhouse
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
| | | | - Rebecca J Bengtsson
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Miren Iturriza-Gómara
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Kate S Baker
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
- Department of Genetics, University of Cambridge, CB23EH, Cambridge, UK.
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7
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Jones NK, Thu TNH, de Alwis R, Thompson C, Tuyen HT, Nhu TDH, Phat VV, Trung PD, Lam PK, Tien BTT, Tuyet HTD, Vi LL, Van Vinh Chau N, Le Thi Quynh N, Baker S. The seroincidence of childhood Shigella sonnei infection in Ho Chi Minh City, Vietnam. PLoS Negl Trop Dis 2023; 17:e0011728. [PMID: 37903147 PMCID: PMC10635567 DOI: 10.1371/journal.pntd.0011728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/09/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Shigella sonnei is a pathogen of growing global importance as a cause of diarrhoeal illness in childhood, particularly in transitional low-middle income countries (LMICs). Here, we sought to determine the incidence of childhood exposure to S. sonnei infection in a contemporary transitional LMIC population, where it represents the dominant Shigella species. METHODS Participants were enrolled between the age of 12-36 months between June and December 2014. Baseline characteristics were obtained through standardized electronic questionnaires, and serum samples were collected at 6-month intervals over two years of follow-up. IgG antibody against S. sonnei O-antigen (anti-O) was measured using an enzyme-linked immunosorbent assay (ELISA). A four-fold increase in ELISA units (EU) with convalescent IgG titre >10.3 EU was taken as evidence of seroconversion between timepoints. RESULTS A total of 3,498 serum samples were collected from 748 participants; 3,170 from the 634 participants that completed follow-up. Measures of anti-O IgG varied significantly by calendar month (p = 0.03). Estimated S. sonnei seroincidence was 21,451 infections per 100,000 population per year (95% CI 19,307-23,834), with peak incidence occurring at 12-18 months of age. Three baseline factors were independently associated with the likelihood of seroconversion; ever having breastfed (aOR 2.54, CI 1.22-5.26), history of prior hospital admission (aOR 0.57, CI 0.34-0.95), and use of a toilet spray-wash in the household (aOR 0.42, CI 0.20-0.89). CONCLUSIONS Incidence of S. sonnei exposure in Ho Chi Minh City is substantial, with significant reduction in the likelihood of exposure as age increases beyond 2 years.
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Affiliation(s)
- Nick K. Jones
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ruklanthi de Alwis
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Corinne Thompson
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Thanh Tuyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Voong Vinh Phat
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Duc Trung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phung Khanh Lam
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Vo Van Kiet, Ho Chi Minh City, Vietnam
| | | | - Nhi Le Thi Quynh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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8
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Tok S, Guzel M, Soyer Y. Emerging Increase in Colistin Resistance Rates in Escherichia coli and Salmonella enterica from Türkiye. Curr Microbiol 2023; 80:222. [PMID: 37221339 DOI: 10.1007/s00284-023-03323-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Foodborne infections caused by drug-resistant Salmonella spp. are a global health concern. Moreover, commensal Escherichia coli is considered risky due to the presence of antimicrobial resistance genes. Colistin is considered a last-resort antibiotic against Gram-negative bacterial infections. Colistin resistance can be transferred both vertically, and horizontally via conjugation between bacterial species. Plasmid-mediated resistance has been associated with mcr-1 to mcr-10 genes. In this study, we collected food samples (n = 238), and isolated E. coli (n = 36) and Salmonella (n = 16), representing recent isolates. We included previously collected Salmonella (n = 197) and E. coli (n = 56) from various sources from 2010 to 2015 in Türkiye as representing historical isolates to investigate colistin-resistance over time. In all isolates, colistin resistance was screened phenotypically by minimum inhibitory concentration (MIC), and then in resistant isolates, mcr-1 to mcr-5 genes were further screened. In addition, the antibiotic resistance of recent isolates was determined, and antibiotic resistance genes were investigated. We found that in total 20 Salmonella isolates (9.38%) and 23 of the E. coli isolates (25%) showed phenotypic colistin resistance. Interestingly, the majority of colistin-resistant isolates (N:32) had resistance levels above 128 mg/L. Furthermore 75% of commensal E. coli isolates recently isolated were resistant at least 3 antibiotics. Overall, we found that the colistin resistance has been increased from 8.12 to 25% in Salmonella isolates, and 7.14% to 52.8% in E. coli isolates over time. However, none of these resistant isolates carried mcr genes, most likely indicating emerging chromosomal colistin resistance.
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Affiliation(s)
- Seray Tok
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara, Turkey
| | - Mustafa Guzel
- Department of Food Engineering, Hitit University, Çorum, Turkey
- Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| | - Yeşim Soyer
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara, Turkey.
- Department of Biotechnology, Middle East Technical University, Ankara, Turkey.
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9
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Baker S, Scott TA. Antimicrobial-resistant Shigella: where do we go next? Nat Rev Microbiol 2023:10.1038/s41579-023-00906-1. [PMID: 37188805 PMCID: PMC10184058 DOI: 10.1038/s41579-023-00906-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
- International AIDS Vaccine Initiative, Chelsea and Westminster Hospital, London, UK.
| | - Timothy A Scott
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
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10
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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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11
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Irulappan M, Mutreja A, Veeraraghavan B. Genomic surveillance for comprehensive Shigella management. THE LANCET. INFECTIOUS DISEASES 2023; 23:645-647. [PMID: 36731479 DOI: 10.1016/s1473-3099(23)00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 02/02/2023]
Affiliation(s)
- Madhumathi Irulappan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, India
| | - Ankur Mutreja
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, India.
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12
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Lefèvre S, Njamkepo E, Feldman S, Ruckly C, Carle I, Lejay-Collin M, Fabre L, Yassine I, Frézal L, Pardos de la Gandara M, Fontanet A, Weill FX. Rapid emergence of extensively drug-resistant Shigella sonnei in France. Nat Commun 2023; 14:462. [PMID: 36709320 PMCID: PMC9883819 DOI: 10.1038/s41467-023-36222-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/19/2023] [Indexed: 01/30/2023] Open
Abstract
Shigella sonnei, the main cause of bacillary dysentery in high-income countries, has become increasingly resistant to antibiotics. We monitored the antimicrobial susceptibility of 7121 S. sonnei isolates collected in France between 2005 and 2021. We detected a dramatic increase in the proportion of isolates simultaneously resistant to ciprofloxacin (CIP), third-generation cephalosporins (3GCs) and azithromycin (AZM) from 2015. Our genomic analysis of 164 such extensively drug-resistant (XDR) isolates identified 13 different clusters within CIP-resistant sublineage 3.6.1, which was selected in South Asia ∼15 years ago. AZM resistance was subsequently acquired, principally through IncFII (pKSR100-like) plasmids. The last step in the development of the XDR phenotype involved various extended-spectrum beta-lactamase genes (blaCTX-M-3, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaCTX-M-134) carried by different plasmids (IncFII, IncI1, IncB/O/K/Z) or even integrated into the chromosome, and encoding resistance to 3GCs. This rapid emergence of XDR S. sonnei, including an international epidemic strain, is alarming, and good laboratory-based surveillance of shigellosis will be crucial for informed decision-making and appropriate public health action.
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Affiliation(s)
- 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 Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Sarah Feldman
- Institut Pasteur, Université Paris Cité, Unité Epidémiologie des maladies émergentes, Paris, F-75015, France.,National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Corinne Ruckly
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Isabelle Carle
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Monique Lejay-Collin
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Laëtitia Fabre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Iman Yassine
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Lise Frézal
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Maria Pardos de la Gandara
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Arnaud Fontanet
- Institut Pasteur, Université Paris Cité, Unité Epidémiologie des maladies émergentes, 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.
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13
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:fuac031. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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14
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Bumbangi FN, Llarena AK, Skjerve E, Hang’ombe BM, Mpundu P, Mudenda S, Mutombo PB, Muma JB. Evidence of Community-Wide Spread of Multi-Drug Resistant Escherichia coli in Young Children in Lusaka and Ndola Districts, Zambia. Microorganisms 2022; 10:1684. [PMID: 36014101 PMCID: PMC9416312 DOI: 10.3390/microorganisms10081684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 12/23/2022] Open
Abstract
Increased antimicrobial resistance (AMR) has been reported for pathogenic and commensal Escherichia coli (E. coli), hampering the treatment, and increasing the burden of infectious diarrhoeal diseases in children in developing countries. This study focused on exploring the occurrence, patterns, and possible drivers of AMR E. coli isolated from children under-five years in Zambia. A hospital-based cross-sectional study was conducted in the Lusaka and Ndola districts. Rectal swabs were collected from 565 and 455 diarrhoeic and healthy children, respectively, from which 1020 E. coli were cultured and subjected to antibiotic susceptibility testing. Nearly all E. coli (96.9%) were resistant to at least one antimicrobial agent tested. Further, 700 isolates were Multi-Drug Resistant, 136 were possibly Extensively-Drug Resistant and nine were Pan-Drug-Resistant. Forty percent of the isolates were imipenem-resistant, mostly from healthy children. A questionnaire survey documented a complex pattern of associations between and within the subgroups of the levels of MDR and socio-demographic characteristics, antibiotic stewardship, and guardians' knowledge of AMR. This study has revealed the severity of AMR in children and the need for a community-specific-risk-based approach to implementing measures to curb the problem.
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Affiliation(s)
- Flavien Nsoni Bumbangi
- School of Medicine, Eden University, Lusaka P.O. Box 37727, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia
| | - Ann-Katrin Llarena
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Eystein Skjerve
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Bernard Mudenda Hang’ombe
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia
| | - Prudence Mpundu
- Department of Environmental and Occupational Health, Levy Mwanawasa Medical University, Lusaka P.O. Box 33991, Zambia
| | - Steward Mudenda
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka P.O. Box 50110, Zambia
| | - Paulin Beya Mutombo
- Kinshasa School of Public Health, Faculty of Medicine, University of Kinshasa, Kinshasa 834, Congo
| | - John Bwalya Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia
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15
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Chowdhury G, Ramamurthy T, Das B, Ghosh D, Okamoto K, Miyoshi SI, Dutta S, Mukhopadhyay AK. Characterization of NDM-5 Carbapenemase-Encoding Gene ( bla NDM-5) - Positive Multidrug Resistant Commensal Escherichia coli from Diarrheal Patients. Infect Drug Resist 2022; 15:3631-3642. [PMID: 35837541 PMCID: PMC9275505 DOI: 10.2147/idr.s364526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/21/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose The multidrug resistance Enterobacteriaceae cause many serious infections resulting in prolonged hospitalization, increased treatment charges and mortality rate. In this study, we characterized bla NDM-5-positive multidrug resistance commensal Escherichia coli (CE) isolated from diarrheal patients in Kolkata, India. Methods Three CE strains were isolated from diarrheal stools, which were negative for different pathogroups of diarrheagenic E. coli (DEC). The presence of carbapenemases encoding genes and other antimicrobial resistance genes (ARGs) was detected using PCR. The genetic arrangement adjoining bla NDM-5 was investigated by plasmid genome sequencing. The genetic relatedness of the strains was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) methods. Results In addition to colistin, the bla NDM-5-positive CE strains showed resistance to most of the antibiotics. Higher MICs were detected for ciprofloxacin (>32 mg/L) and imipenem (8 mg/L). Molecular typing revealed that three CE strains belonged to two different STs (ST 101 and ST 648) but they were 95% similar in the PFGE analysis. Screening for ARGs revealed that CE strains harbored Int-1, bla TEM, blaC TX-M3, bla OXA-1, bla OXA-7, bla OXA-9, tetA, strA, aadA1, aadB, sul2, floR, mph(A), and aac(6´)-Ib-cr. In conjugation experiment, transfer frequencies ranged from 2.5×10-3 to 8.4x10-5. The bla NDM-5 gene was located on a 94-kb pNDM-TC-CE-89 type plasmid, which is highly similar to the IncFII plasmid harboring an IS26-IS30-bla NDM-5-ble MBL-trpF-dsbd-IS91-dhps structure. Conclusion To the best of our knowledge, this is the first report on carbapenem resistance involving the bla NDM-5 gene in CE from diarrheal patients. The circulation of bla NDM-5 gene in CE is worrisome, since it has the potential to transfer bla NDM-5 gene to other enteric pathogens.
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Affiliation(s)
- Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.,Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Bhabatosh Das
- Department of Infection and Immunology, Translational Health Science and Technology Institute, Faridabad, India
| | - Debjani Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Keinosuke Okamoto
- Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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16
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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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17
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Limosilactobacillus reuteri SLZX19-12 Protects the Colon from Infection by Enhancing Stability of the Gut Microbiota and Barrier Integrity and Reducing Inflammation. Microbiol Spectr 2022; 10:e0212421. [PMID: 35658572 PMCID: PMC9241593 DOI: 10.1128/spectrum.02124-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Limosilactobacillus reuteri plays an important role in regulating intestinal functions and maintaining barrier integrity in animals. In this study, Limosilactobacillus reuteri strain SLZX19-12 was isolated from the fecal microbiota of Tibetan pigs, and it was found that this strain is sensitive to common antibiotics and has strong resistance to stress. Upon being administered by gavage at different doses, including low, medium, and high doses, for 14 days, Limosilactobacillus reuteri SLZX19-12 may enhance the intestinal barrier. After administration of a high dose of SLZX19-12, mice were challenged with Salmonella enterica serovar Typhimurium SL1344. Infection with Salmonella Typhimurium SL1344 led to disordered colonic microbiotas, colonic inflammation through the S100A8/S100A9-NF-κB pathway and potential apoptosis, and translocation of pathogens to parenteral visceral organs in mice. However, the mice pretreated with Limosilactobacillus reuteri SLZX19-12 showed lower loads of Salmonella in visceral organs, less colonic inflammation, and higher barrier integrity. More importantly, the administration of strain SLZX19-12 resulted in a more stable microbiota structure of the colon, in which the abundance of Alloprevotella was greatly enhanced. Therefore, this study suggests that Limosilactobacillus reuteri SLZX19-12 can protect the colon from infection by enhancing the stability of gut microbiota and barrier integrity and reducing inflammation. IMPORTANCE The use of antibiotics to treat bacterial infections leads to a series of side effects. As an alternative method, the biocontrol strategy, which uses probiotics to suppress pathogens, is considered a potential way to deal with bacterial infections in gut. However, there are few probiotics that are currently safe and can protect against infection. In this study, Limosilactobacillus reuteri strain SLZX19-12 was obtained from Tibetan pigs, which have higher resistance to infection. This strain is sensitive to conventional antibiotics, secretes a wide spectrum of enzymes, and also promotes the intestinal barrier function in mice. In addition, Limosilactobacillus reuteri SLZX19-12 can promote the stability of the gut microbiota to avoid or alleviate the occurrence or development of foodborne infections.
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18
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Fernández Álvaro E, Voong Vinh P, de Cozar C, Willé DR, Urones B, Cortés A, Price A, Tran Do Hoang N, Ha Thanh T, McCloskey M, Shaheen S, Dayao D, Martinot A, de Mercado J, Castañeda P, García-Perez A, Singa B, Pavlinac P, Walson J, Martínez-Martínez MS, Arnold SLM, Tzipori S, Ballell Pages L, Baker S. The repurposing of Tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug-resistant Shigella spp. eLife 2022; 11:e69798. [PMID: 35289746 PMCID: PMC8959600 DOI: 10.7554/elife.69798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 03/09/2022] [Indexed: 11/18/2022] Open
Abstract
Background Diarrhoea remains one of the leading causes of childhood mortality globally. Recent epidemiological studies conducted in low-middle income countries (LMICs) identified Shigella spp. as the first and second most predominant agent of dysentery and moderate diarrhoea, respectively. Antimicrobial therapy is often necessary for Shigella infections; however, we are reaching a crisis point with efficacious antimicrobials. The rapid emergence of resistance against existing antimicrobials in Shigella spp. poses a serious global health problem. Methods Aiming to identify alternative antimicrobial chemicals with activity against antimicrobial resistant Shigella, we initiated a collaborative academia-industry drug discovery project, applying high-throughput phenotypic screening across broad chemical diversity and followed a lead compound through in vitro and in vivo characterisation. Results We identified several known antimicrobial compound classes with antibacterial activity against Shigella. These compounds included the oral carbapenem Tebipenem, which was found to be highly potent against broadly susceptible Shigella and contemporary MDR variants for which we perform detailed pre-clinical testing. Additional in vitro screening demonstrated that Tebipenem had activity against a wide range of other non-Shigella enteric bacteria. Cognisant of the risk for the development of resistance against monotherapy, we identified synergistic behaviour of two different drug combinations incorporating Tebipenem. We found the orally bioavailable prodrug (Tebipenem pivoxil) had ideal pharmacokinetic properties for treating enteric pathogens and was effective in clearing the gut of infecting organisms when administered to Shigella-infected mice and gnotobiotic piglets. Conclusions Our data highlight the emerging antimicrobial resistance crisis and shows that Tebipenem pivoxil (licenced for paediatric respiratory tract infections in Japan) should be accelerated into human trials and could be repurposed as an effective treatment for severe diarrhoea caused by MDR Shigella and other enteric pathogens in LMICs. Funding Tres Cantos Open Lab Foundation (projects TC239 and TC246), the Bill and Melinda Gates Foundation (grant OPP1172483) and Wellcome (215515/Z/19/Z).
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Affiliation(s)
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | | | | | | | | | - Alan Price
- GSK Global Health, Tres CantosMadridSpain
| | - Nhu Tran Do Hoang
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Molly McCloskey
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | - Shareef Shaheen
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | - Denise Dayao
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary MedicineNorth GraftonUnited States
| | - Amanda Martinot
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary MedicineNorth GraftonUnited States
| | | | | | | | | | - Patricia Pavlinac
- Department of Global Health, University of WashingtonSeattleUnited States
| | - Judd Walson
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | | | - Samuel LM Arnold
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary MedicineNorth GraftonUnited States
| | | | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
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19
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Yan W, Hall AB, Jiang X. Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters. NPJ Biofilms Microbiomes 2022; 8:1. [PMID: 35013297 PMCID: PMC8748976 DOI: 10.1038/s41522-021-00260-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/26/2021] [Indexed: 12/21/2022] Open
Abstract
Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.
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Affiliation(s)
- Wei Yan
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - A Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
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20
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Ghorbani A, Khoshbakht R, Kaboosi H, Shirzad-Aski H, Peyravii Ghadikolaii F. Study on antibiotic resistance and phylogenetic comparison of avian-pathogenic Escherichia coli (APEC) and uropathogenic Escherichia coli (UPEC) isolates. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2022; 13:569-576. [PMID: 36686883 PMCID: PMC9840809 DOI: 10.30466/vrf.2021.527563.3160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/16/2021] [Indexed: 01/24/2023]
Abstract
Avian pathogenic Escherichia coli (APEC) and uropathogenic E. coli (UPEC) can cause vast infections in humans and poultry. The present study was conducted to compare the isolates of the APEC and UPEC pathotypes on the basis phenotypic and genotypic features of antibiotic resistance and phylogenetic differences. Total number of 70 identified E. coli strains, including 35 APEC and 35 UPEC isolates, were isolated from avian colibacillosis and human urinary tract infection (UTI), and were subjected to the antimicrobial susceptibility testing, polymerase chain reaction (PCR) detection of the resistance genes, phylogenetic grouping and DNA fingerprinting with enterobacterial repetitive intergenic consensus PCR (ERIC - PCR) to survey the variability of the isolates. The most resistance rates among all E. coli isolates were, respectively, obtained for Ampicillin (84.20%) and sulfamethoxazole-trimethoprim (65.70%). The APEC and UPEC isolates showed the most susceptibility to imipenem and gentamycin, respectively. Among 70 APEC and UPEC isolates 34.20%, 32.80%, 20.00%, and 12.80% belonged to the A, B2, D, and B1 phylogenetic groups, respectively. Analysis of the DNA fingerprinting phylogenetic tree showed 10 specific clusters of APEC and UPEC isolates. According to the results, the most effective antibiotics and the phenotypic and genotypic predominant resistance patterns of the APEC and UPEC isolates were different. Moreover, APECs and UPECs showed various dominant phylogenetic groups. With all descriptions, the APEC isolates still are potential candidates for carrying important resistance genes and can be one of the possible strains related to human infections.
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Affiliation(s)
- Alireza Ghorbani
- Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran;
| | - Rahem Khoshbakht
- Department of Pathobiology, Faculty of Veterinary Medicine, Amol University of Special Modern Technologies, Amol, Iran; ,Correspondence Rahem Khoshbakht. DVM, PhD Department of Pathobiology, Faculty of Veterinary Medicine, Amol University of Special Modern Technologies, Amol, Iran. E-mail:
| | - Hami Kaboosi
- Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran;
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21
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Nguyen Q, Nguyen TTN, Pham P, Chau V, Nguyen LPH, Nguyen TD, Ha TT, Le NTQ, Vu DT, Baker S, Thwaites GE, Rabaa MA, Pham DT. Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam. Microb Genom 2021; 7. [PMID: 34904942 PMCID: PMC8767341 DOI: 10.1099/mgen.0.000733] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) ST1193, a globally emergent fluoroquinolone-resistant clone, has become an important cause of bloodstream infections (BSIs) associated with significant morbidity and mortality. Previous studies have reported the emergence of fluoroquinolone-resistant ExPEC ST1193 in Vietnam; however, limited data exist regarding the genetic structure, antimicrobial resistance (AMR) determinants and transmission dynamics of this pandemic clone. Here, we performed genomic and phylogenetic analyses of 46 ST1193 isolates obtained from BSIs and healthy individuals in Ho Chi Minh City, Vietnam, to investigate the pathogen population structure, molecular mechanisms of AMR and potential transmission patterns. We further examined the phylogenetic structure of ST1193 isolates in a global context. We found that the endemic E. coli ST1193 population was heterogeneous and highly dynamic, largely driven by multiple strain importations. Several well-supported phylogenetic clusters (C1-C6) were identified and associated with distinct bla CTX-M variants, including bla CTXM-27 (C1-C3, C5), bla CTXM-55 (C4) and bla CTXM-15 (C6). Most ST1193 isolates were multidrug-resistant and carried an extensive array of AMR genes. ST1193 isolates also exhibited the ability to acquire further resistance while circulating in Vietnam. There were phylogenetic links between ST1193 isolates from BSIs and healthy individuals, suggesting these organisms may both establish long-term colonization in the human intestinal tract and induce infections. Our study uncovers factors shaping the population structure and transmission dynamics of multidrug-resistant ST1193 in Vietnam, and highlights the urgent need for local One Health genomic surveillance to capture new emerging ExPEC clones and to better understand the origins and transmission patterns of these pathogens.
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Affiliation(s)
- Quynh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Phuong Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Chau
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Tuyen Thanh Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhi Thi Quynh Le
- The University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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22
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Mai SNT, Bodhidatta L, Turner P, Wangchuk S, Ha Thanh T, Voong Vinh P, Pham DT, Rabaa MA, Thwaites GE, Thomson NR, Baker S, Chung The H. The evolutionary history of Shigella flexneri serotype 6 in Asia. Microb Genom 2021; 7. [PMID: 34904947 PMCID: PMC8767353 DOI: 10.1099/mgen.0.000736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Shigella flexneri serotype 6 is an understudied cause of diarrhoeal diseases in developing countries, and has been proposed as one of the major targets for vaccine development against shigellosis. Despite being named as S. flexneri, Shigella flexneri serotype 6 is phylogenetically distinct from other S. flexneri serotypes and more closely related to S. boydii. This unique phylogenetic relationship and its low sampling frequency have hampered genomic research on this pathogen. Herein, by utilizing whole genome sequencing (WGS) and analyses of Shigella flexneri serotype 6 collected from epidemiological studies (1987–2013) in four Asian countries, we revealed its population structure and evolutionary history in the region. Phylogenetic analyses supported the delineation of Asian Shigella flexneri serotype 6 into two phylogenetic groups (PG-1 and −2). Notably, temporal phylogenetic approaches showed that extant Asian S. flexneri serotype 6 could be traced back to an inferred common ancestor arising in the 18th century. The dominant lineage PG-1 likely emerged in the 1970s, which coincided with the times to most recent common ancestors (tMRCAs) inferred from other major Southeast Asian S. flexneri serotypes. Similar to other S. flexneri serotypes in the same period in Asia, genomic analyses showed that resistance to first-generation antimicrobials was widespread, while resistance to more recent first-line antimicrobials was rare. These data also showed a number of gene inactivation and gene loss events, particularly on genes related to metabolism and synthesis of cellular appendages, emphasizing the continuing role of reductive evolution in the adaptation of the pathogen to an intracellular lifestyle. Together, our findings reveal insights into the genomic evolution of the understudied Shigella flexneri serotype 6, providing a new piece in the puzzle of Shigella epidemiology and evolution.
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Affiliation(s)
- Si-Nguyen T Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | | | - Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sonam Wangchuk
- Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R Thomson
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,London School of Hygiene and Tropical Medicine, Bloomsbury, London WC1E 7HT, UK
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, UK
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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23
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Bernaquez I, Gaudreau C, Pilon PA, Bekal S. Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks. Microb Genom 2021; 7. [PMID: 34730485 PMCID: PMC8743557 DOI: 10.1099/mgen.0.000672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus sequence typing (MLST)-based allele differences and/or core genome single-nucleotide variants (SNVs). In addition to being a food- and travel-associated outbreak pathogen, most
Shigella
spp. cases occur through continuous person-to-person transmission, predominantly involving men who have sex with men (MSM), leading to long-term and recurrent outbreaks. Continuous transmission patterns coupled to genetic evolution under antibiotic treatment pressure require an assessment of existing WGS-based subtyping methods and interpretation criteria for cluster inclusion/exclusion. An evaluation of 4 WGS-based subtyping methods [SNVPhyl, coreMLST, core genome MLST (cgMLST) and whole-genome MLST (wgMLST)] was performed on 9 foodborne-, travel- and MSM-related retrospective outbreaks from a collection of 91
Shigella flexneri
and 232
Shigella sonnei
isolates to determine the methods’ epidemiological concordance, discriminatory power, robustness and ability to generate stable interpretation criteria. The discriminatory powers were ranked as follows: coreMLST<SNVPhyl<cgMLST<wgMLST (range: 0.970–1.000). The genetic differences observed for non-MSM-related
Shigella
spp. outbreaks respect the standard 0–10 allele/SNV guideline; however, mobile genetic element (MGE)-encoded loci caused inflated genetic variation and discrepant phylogenies for prolonged MSM-related
S. sonnei
outbreaks via wgMLST. The
S. sonnei
correlation coefficients of wgMLST were also the lowest at 0.680, 0.703 and 0.712 for SNVPhyl, coreMLST and cgMLST, respectively. Plasmid maintenance, mobilization and conjugation-associated genes were found to be the main source of genetic distance inflation in addition to prophage-related genes. Duplicated alleles arising from the repeated nature of IS elements were also responsible for many false cg/wgMLST differences. The coreMLST approach was shown to be the most robust, followed by SNVPhyl and wgMLST for inter-laboratory comparability. Our results highlight the need for validating species-specific subtyping methods based on microbial genome plasticity and outbreak dynamics in addition to the importance of filtering confounding MGEs for cluster detection.
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Affiliation(s)
- Isabelle Bernaquez
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
| | - Christiane Gaudreau
- Microbiologie médicale et infectiologie, Centre Hospitalier de l’Université de Montréal (CHUM), Montreal, QC, H2X 3E4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, QC, H3C 3J7, 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, Montreal, QC, H2L 4M1, Canada
- Département de médecine sociale et préventive, Université de Montréal, Montreal, QC, H3N 1X9, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, QC, H3C 3J7, Canada
- *Correspondence: Sadjia Bekal,
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24
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Pereira-Dias J, Nguyen Ngoc Minh C, Tran Thi Hong C, Nguyen Thi Nguyen T, Ha Thanh T, Zellmer C, Chung The H, Pike L, Higginson EE, Baker S. The gut microbiome of healthy Vietnamese adults and children is a major reservoir for resistance genes against critical antimicrobials. J Infect Dis 2021; 224:S840-S847. [PMID: 34374428 PMCID: PMC8687120 DOI: 10.1093/infdis/jiab398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Antimicrobials are a key group of therapeutic agents. Given the animal/human population density and high antimicrobial consumption rate in Southeast Asia, the region is a focal area for monitoring antimicrobial resistance (AMR). Hypothesizing that the gastrointestinal tract of healthy individuals in Vietnam is a major source of AMR genes that may be transferred to pathogens, we performed shotgun metagenomic sequencing on fecal samples from 42 healthy Vietnamese people (21 children and 21 adults). We compared their microbiome profiles by age group and determined the composition of AMR genes. An analysis of the taxonomic profiles in the gut microbiome showed a clear differentiation by age, with young children (age <2 years) exhibiting a unique structure in comparison to adults and older children. We identified a total of 132 unique AMR genes, with macrolide, lincosamide, and streptogramin class resistance genes (ermB and lnuC) and tetracycline resistance genes being almost ubiquitous across the study population. Notably, samples from younger children were significantly associated with a greater number of AMR genes than other age groups, including key signature genes associated with AMR pathogens (eg, blaCTX-M, mphA). Our data suggest that the gut microbiome of those living in Vietnam, particularly young children, is a substantial reservoir of AMR genes, which can be transferred to circulating enteric pathogens. Our data support the generation of longitudinal cohort studies of those living in urban and rural areas of developing countries to understand the behavior of these AMR reservoirs and their role in generating multidrug-resistant and extensively drug-resistant pathogens.
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Affiliation(s)
- Joana Pereira-Dias
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | | | | | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Caroline Zellmer
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Lindsay Pike
- The Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Ellen E Higginson
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
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25
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Ingle DJ, Ambrose RL, Baines SL, Duchene S, Gonçalves da Silva A, Lee DYJ, Jones M, Valcanis M, Taiaroa G, Ballard SA, Kirk MD, Howden BP, Pearson JS, Williamson DA. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia. Nat Commun 2021; 12:4786. [PMID: 34373455 PMCID: PMC8352879 DOI: 10.1038/s41467-021-25073-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
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Affiliation(s)
- Danielle J Ingle
- Research School of Population Health, Australian National University, Canberra, ACT, Australia.
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Rebecca L Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Darren Y J Lee
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miriam Jones
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martyn D Kirk
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, 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
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, 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.
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia.
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26
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Sridhar S, Forrest S, Pickard D, Cormie C, Lees EA, Thomson NR, Dougan G, Baker S. Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium. mBio 2021; 12:e0109321. [PMID: 34154399 PMCID: PMC8262899 DOI: 10.1128/mbio.01093-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance (AMR) is a pressing global health crisis, which has been fueled by the sustained use of certain classes of antimicrobials, including fluoroquinolones. While the genetic mutations responsible for decreased fluoroquinolone (ciprofloxacin) susceptibility are known, the implications of ciprofloxacin exposure on bacterial growth, survival, and interactions with host cells are not well described. Aiming to understand the influence of inhibitory concentrations of ciprofloxacin in vitro, we subjected three clinical isolates of Salmonella enterica serovar Typhimurium to differing concentrations of ciprofloxacin, dependent on their MICs, and assessed the impact on bacterial growth, morphology, and transcription. We further investigated the differential morphology and transcription that occurred following ciprofloxacin exposure and measured the ability of ciprofloxacin-treated bacteria to invade and replicate in host cells. We found that ciprofloxacin-exposed S. Typhimurium is able to recover from inhibitory concentrations of ciprofloxacin and that the drug induces specific morphological and transcriptional signatures associated with the bacterial SOS response, DNA repair, and intracellular survival. In addition, ciprofloxacin-treated S. Typhimurium has increased capacity for intracellular replication in comparison to that of untreated organisms. These data suggest that S. Typhimurium undergoes an adaptive response under ciprofloxacin perturbation that promotes cellular survival, a consequence that may justify more measured use of ciprofloxacin for Salmonella infections. The combination of multiple experimental approaches provides new insights into the collateral effects that ciprofloxacin and other antimicrobials have on invasive bacterial pathogens. IMPORTANCE Antimicrobial resistance is a critical concern in global health. In particular, there is rising resistance to fluoroquinolones, such as ciprofloxacin, a first-line antimicrobial for many Gram-negative pathogens. We investigated the adaptive response of clinical isolates of Salmonella enterica serovar Typhimurium to ciprofloxacin, finding that the bacteria adapt in short timespans to high concentrations of ciprofloxacin in a way that promotes intracellular survival during early infection. Importantly, by studying three clinically relevant isolates, we were able to show that individual isolates respond differently to ciprofloxacin and that for each isolate, there was a heterogeneous response under ciprofloxacin treatment. The heterogeneity that arises from ciprofloxacin exposure may drive survival and proliferation of Salmonella during treatment and lead to drug resistance.
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Affiliation(s)
- Sushmita Sridhar
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sally Forrest
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Derek Pickard
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Claire Cormie
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Emily A. Lees
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
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27
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Abstract
Acute bacterial gastroenteritis is among the most common infections worldwide, with millions of infections annually in the United States. Much of the illness is foodborne, occurring as both sporadic cases and large multistate outbreaks. Pathogen evolution through genetic exchange of virulence traits and antibiotic resistance determinants poses challenges for empiric therapy. Culture-independent diagnostic tests in clinical laboratories afford rapid diagnosis and expanded identification of pathogens. However, cultures remain important to generate sensitivity data and strain archiving for outbreak investigations. Most infections are self-limited, permitting judicious selection of antibiotic use in more severe forms of illness.
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Affiliation(s)
- James M Fleckenstein
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine, Campus Box 8051, 660 South Euclid Avenue, Saint Louis, MO 63110, USA; Infectious Disease Section, Medicine Service, Veterans Affairs Saint Louis Health Care System, 915 North Grand Boulevard, Saint Louis, MO 63106, USA.
| | - F Matthew Kuhlmann
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine, Campus Box 8051, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
| | - Alaullah Sheikh
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine, Campus Box 8051, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
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28
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Antioxidant Molecules as a Source of Mitigation of Antibiotic Resistance Gene Dissemination. Antimicrob Agents Chemother 2021; 65:AAC.02658-20. [PMID: 33753335 DOI: 10.1128/aac.02658-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is the most commonly identified human pathogen and a prominent microorganism of the gut microbiota. Acquired resistance to antibiotics in this species is driven mainly by horizontal gene transfer and plasmid acquisition. Currently, the main concern is the acquisition of extended-spectrum β-lactamases of the CTX-M type in E. coli, a worldwide-observed phenomenon. Plasmids encoding CTX-M enzymes have different scaffolds and conjugate at different frequencies. Here, we show that the conjugation rates of several plasmid types encoding broad-spectrum β-lactamases are increased when the E. coli donor strain is exposed to subinhibitory concentrations of diverse orally given antibiotics, including fluoroquinolones, such as ciprofloxacin and levofloxacin, but also trimethoprim and nitrofurantoin. This study provides insights into underlying mechanisms leading to increased plasmid conjugation frequency in relation to DNA synthesis inhibitor-type antibiotics, involving reactive oxygen species (ROS) production and probably increased expression of genes involved in the SOS response. Furthermore, we show that some antioxidant molecules currently approved for unrelated clinical uses, such as edaravone, p-coumaric acid, and N-acetylcysteine, may antagonize the ability of antibiotics to increase plasmid conjugation rates. These results suggest that several antioxidative molecules might be used in combination with these "inducer" antibiotics to mitigate the unwanted increased resistance plasmid dissemination.
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Bengtsson RJ, Dallman TJ, Allen H, De Silva PM, Stenhouse G, Pulford CV, Bennett RJ, Jenkins C, Baker KS. Accessory Genome Dynamics and Structural Variation of Shigella from Persistent Infections. mBio 2021; 12:e00254-21. [PMID: 33906921 PMCID: PMC8092226 DOI: 10.1128/mbio.00254-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022] Open
Abstract
Shigellosis is a diarrheal disease caused mainly by Shigella flexneri and Shigella sonnei Infection is thought to be largely self-limiting, with short- to medium-term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM)-associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 and 1,862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM-associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart to shed light on the adaptation of these important pathogens during infection. We find that pairs likely associated with persistent infection/carriage and with a smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection, and with a greater SNP distance. We observed antimicrobial resistance acquisition during Shigella carriage, including the gain of an extended-spectrum beta-lactamase gene during carriage. Finally, we explored large chromosomal structural variations and rearrangements in seven (five chronic and two reinfection associated) pairs of S. flexneri 3a isolates from an MSM-associated epidemic sublineage, which revealed variations at several common regions across isolate pairs, mediated by insertion sequence elements and comprising a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection/carriage. In addition, we have also created a complete reference genome and biobanked isolate of the globally important pathogen, S. flexneri 3a.IMPORTANCEShigella spp. are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrheal illness among children under the age of five in low-income countries. In high-income countries, shigellosis is also a sexually transmissible disease among men who have sex with men. Within the latter setting, we have captured prolonged and/or recurrent infection with shigellae of the same serotype, challenging the belief that Shigella infection is short lived and providing an early opportunity to study the evolution of the pathogen over the course of infection. Using this recently emerged transmission scenario, we comprehensively characterize the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genomic regions, findings that have relevance for other Enterobacteriaceae.
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Affiliation(s)
- Rebecca J Bengtsson
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom
| | - Timothy J Dallman
- National Infection Service, Public Health England, Colindale, London, United Kingdom
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Hester Allen
- National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - P Malaka De Silva
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom
| | - George Stenhouse
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom
| | - Caisey V Pulford
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom
| | - Rebecca J Bennett
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom
| | - Claire Jenkins
- National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Kate S Baker
- Clinical Infection, Microbiology and Immunity, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom
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30
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Chung The H, Bodhidatta L, Pham DT, Mason CJ, Ha Thanh T, Voong Vinh P, Turner P, Hem S, Dance DAB, Newton PN, Phetsouvanh R, Davong V, Thwaites GE, Thomson NR, Baker S, Rabaa MA. Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia. Commun Biol 2021; 4:353. [PMID: 33742111 PMCID: PMC7979695 DOI: 10.1038/s42003-021-01905-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Conventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s-1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.
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Affiliation(s)
- Hao Chung The
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ladaporn Bodhidatta
- grid.413910.e0000 0004 0419 1772Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Duy Thanh Pham
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Carl J. Mason
- grid.413910.e0000 0004 0419 1772Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tuyen Ha Thanh
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sopheak Hem
- grid.418537.cMedical Biology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - David A. B. Dance
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Paul N. Newton
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Rattanaphone Phetsouvanh
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Guy E. Thwaites
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R. Thomson
- grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK ,grid.10306.340000 0004 0606 5382The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- grid.5335.00000000121885934The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Maia A. Rabaa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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31
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Ingle DJ, Howden BP, Duchene S. Development of Phylodynamic Methods for Bacterial Pathogens. Trends Microbiol 2021; 29:788-797. [PMID: 33736902 DOI: 10.1016/j.tim.2021.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/30/2022]
Abstract
Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until recently, a paucity of whole-genome sequence data sets with rich associated metadata. We posit that the increasing availability of bacterial genomes and epidemiological data means that the field is now ripe to lay the foundations for applying phylodynamics to bacterial pathogens. The development of new methods that integrate more complex genomic and ecological data will help to inform public heath surveillance and control strategies for bacterial pathogens that represent serious threats to human health.
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Affiliation(s)
- Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
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32
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Carey ME, Jain R, Yousuf M, Maes M, Dyson ZA, Thu TNH, Nguyen Thi Nguyen T, Ho Ngoc Dan T, Nhu Pham Nguyen Q, Mahindroo J, Thanh Pham D, Sandha KS, Baker S, Taneja N. Spontaneous Emergence of Azithromycin Resistance in Independent Lineages of Salmonella Typhi in Northern India. Clin Infect Dis 2021; 72:e120-e127. [PMID: 33515460 PMCID: PMC7935384 DOI: 10.1093/cid/ciaa1773] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The emergence and spread of antimicrobial resistance (AMR) pose a major threat to the effective treatment and control of typhoid fever. The ongoing outbreak of extensively drug-resistant Salmonella Typhi (S. Typhi) in Pakistan has left azithromycin as the only remaining broadly efficacious oral antimicrobial for typhoid in South Asia. Ominously, azithromycin-resistant S. Typhi organisms have been subsequently reported in Bangladesh, Pakistan, and Nepal. METHODS Here, we aimed to understand the molecular basis of AMR in 66 S. Typhi organisms isolated in a cross-sectional study performed in a suburb of Chandigarh in Northern India using whole-genome sequencing and phylogenetic analysis. RESULTS We identified 7 S. Typhi organisms with the R717Q mutation in the acrB gene that was recently found to confer resistance to azithromycin in Bangladesh. Six out of the seven azithromycin-resistant S. Typhi isolates also exhibited triple mutations in gyrA (S83F and D87N) and parC (S80I) genes and were resistant to ciprofloxacin. These contemporary ciprofloxacin/azithromycin-resistant isolates were phylogenetically distinct from each other and from those reported from Bangladesh, Pakistan, and Nepal. CONCLUSIONS The independent emergence of azithromycin-resistant typhoid in Northern India reflects an emerging broader problem across South Asia and illustrates the urgent need for the introduction of typhoid conjugate vaccines in the region.
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ruby Jain
- Civil Hospital, Manimajra, Chandigarh, India
| | - Mohammad Yousuf
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Zoe A Dyson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Trang Nguyen Hoang Thu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thanh Ho Ngoc Dan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Quynh Nhu Pham Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Jaspreet Mahindroo
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Duy Thanh Pham
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | | | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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33
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Wein T, Wang Y, Hülter NF, Hammerschmidt K, Dagan T. Antibiotics Interfere with the Evolution of Plasmid Stability. Curr Biol 2020; 30:3841-3847.e4. [DOI: 10.1016/j.cub.2020.07.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/29/2020] [Accepted: 07/07/2020] [Indexed: 01/08/2023]
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34
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Darton TC, Thi Hong Chau T, Parry CM, Campbell JI, Minh Ngoc N, Le Chau Ngoc T, Thanh Tuyen H, Thuy Duong V, Thanh Hoang Nhat L, van Minh P, Kestelyn E, Thwaites GE, Huu Tung T, Baker S. The CIPAZ study protocol: an open label randomised controlled trial of azithromycin versus ciprofloxacin for the treatment of children hospitalised with dysentery in Ho Chi Minh City, Vietnam. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.16093.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Diarrhoeal disease remains a common cause of illness and death in children <5 years of age. Faecal-oral infection by Shigella spp. causing bacillary dysentery is a leading cause of moderate-to-severe diarrhoea, particularly in low and middle-income countries. In Southeast Asia, S. sonnei predominates and infections are frequently resistant to first-line treatment with the fluoroquinolone, ciprofloxacin. While resistance to all antimicrobials is increasing, there may be theoretical and clinical benefits to prioritizing treatment of bacillary dysentery with the azalide, azithromycin. In this study we aim to measure the efficacy of treatment with azithromycin compared with ciprofloxacin, the current standard of care, for the treatment of children with bacillary dysentery. Methods and analysis: We will perform a multicentre, open-label, randomized controlled trial of two therapeutic options for the antimicrobial treatment of children hospitalised with dysentery. Children (6–60 months of age) presenting with symptoms and signs of dysentery at Children’s Hospital 2 in Ho Chi Minh City will be randomised (1:1) to treatment with either oral ciprofloxacin (15mg/kg/twice daily for 3 days, standard-of-care) or oral azithromycin (10mg/kg/daily for 3 days). The primary endpoint will be the proportion of treatment failure (defined by clinical and microbiological parameters) by day 28 (+3 days) and will be compared between study arms by logistic regression modelling using treatment allocation as the main variable. Ethics and dissemination: The study protocol (version 1.2 dated 27th December 2018) has been approved by the Oxford Tropical Research Ethics Committee (47–18) and the ethical review boards of Children's Hospital 2 (1341/NĐ2-CĐT). The study has also been approved by the Vietnamese Ministry of Health (5044/QĐ-BYT). Trial registration: Clinicaltrials.gov: NCT03854929 (February 26th 2019).
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35
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Hassan R, Tantawy M, Gouda NA, Elzayat MG, Gabra S, Nabih A, Diab AA, El-Hadidi M, Bakry U, Shoeb MR, Elanany M, Shalaby L, Sayed AA. Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt. Sci Rep 2020; 10:4165. [PMID: 32139767 PMCID: PMC7057982 DOI: 10.1038/s41598-020-61159-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 02/20/2020] [Indexed: 11/08/2022] Open
Abstract
Infection with multiple drug resistant (MDR) Escherichia coli poses a life threat to immunocompromised pediatric cancer patients. Our aim is to genotypically characterize the plasmids harbored in MDR E. coli isolates recovered from bacteremic patients of Children's Cancer Hospital in Egypt 57357 (CCHE 57357). In this study, 21 carbapenem-resistant E. coli (CRE) isolates were selected that exhibit Quinolones and Aminoglycosides resistance. Plasmid shot-gun sequencing was performed using Illumina next- generation sequencing platform. Isolates demonstrated resistant to all beta-lactams, carbapenems, aminoglycosides and quinolones. Of the 32 antimicrobial resistant genes identified that exceeded the analysis cutoff coverage, the highest represented genes were aph(6)-Id, sul2, aph(3″)-Ib, aph(3')-Ia, sul1, dfrA12, TEM-220, NDM-11. Isolates employed a wide array of resistance mechanisms including antibiotic efflux, antibiotic inactivation, antibiotic target replacements and antibiotic target alteration. Sequenced isolates displayed diverse insertion sequences, including IS26, suggesting dynamic reshuffling of the harbored plasmids. Most isolates carried plasmids originating from other bacterial species suggesting a possible horizontal gene transfer. Only two isolates showed virulence factors with iroA gene cluster which was found in only one of them. Outside the realms of nosocomial infections among patients in hospitals, our results indicate a transfer of resistant genes and plasmids across different organisms.
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Affiliation(s)
- Reem Hassan
- Molecular Microbiology Unit, Children's cancer hospital Egypt 57357, Cairo, Egypt
- Department of clinical pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Marwa Tantawy
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Nouran A Gouda
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Mariam G Elzayat
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Sara Gabra
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Amena Nabih
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Aya A Diab
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Mohamed El-Hadidi
- Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, Giza, Egypt
| | - Usama Bakry
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Mohamed R Shoeb
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Mervat Elanany
- Department of clinical pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
- Microbiology Unit, Children's cancer hospital Egypt 57357, Cairo, Egypt
| | - Lobna Shalaby
- Infectious disease unit, Children's cancer hospital Egypt 57357, Cairo, Egypt
- Department of pediatric oncology, National cancer Institute, Cairo University, Cairo, Egypt
| | - Ahmed A Sayed
- Genomics Program, Children's cancer hospital Egypt 57357, Cairo, Egypt.
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt.
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