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Ashonibare VJ, Akorede BA, Ashonibare PJ, Akhigbe TM, Akhigbe RE. Gut microbiota-gonadal axis: the impact of gut microbiota on reproductive functions. Front Immunol 2024; 15:1346035. [PMID: 38482009 PMCID: PMC10933031 DOI: 10.3389/fimmu.2024.1346035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/30/2024] [Indexed: 04/12/2024] Open
Abstract
The influence of gut microbiota on physiological processes is rapidly gaining attention globally. Despite being under-studied, there are available data demonstrating a gut microbiota-gonadal cross-talk, and the importance of this axis in reproduction. This study reviews the impacts of gut microbiota on reproduction. In addition, the possible mechanisms by which gut microbiota modulates male and female reproduction are presented. Databases, including Embase, Google scholar, Pubmed/Medline, Scopus, and Web of Science, were explored using relevant key words. Findings showed that gut microbiota promotes gonadal functions by modulating the circulating levels of steroid sex hormones, insulin sensitivity, immune system, and gonadal microbiota. Gut microbiota also alters ROS generation and the activation of cytokine accumulation. In conclusion, available data demonstrate the existence of a gut microbiota-gonadal axis, and role of this axis on gonadal functions. However, majority of the data were compelling evidences from animal studies with a great dearth of human data. Therefore, human studies validating the reports of experimental studies using animal models are important.
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Affiliation(s)
- Victory J. Ashonibare
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
| | - Bolaji A. Akorede
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Biomedical Sciences, University of Wyoming, Laramie, WY, United States
| | - Precious J. Ashonibare
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tunmise M. Akhigbe
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Breeding and Genetic Unit, Department of Agronomy, Osun State University, Ejigbo, Osun State, Nigeria
| | - Roland Eghoghosoa Akhigbe
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
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Aguirre-Sanchez JR, Vega-Lopez IF, Castro Del Campo N, Medrano-Felix JA, Martínez-Urtaza J, Chaidez-Quiroz C. Genomic-wide analysis approach revealed genomic similarity for environmental Mexican S. Oranienburg genomes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:956-967. [PMID: 36946386 DOI: 10.1080/09603123.2023.2191312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
As the human population grows, an increase in food trade is needed. This elevates the risk of epidemiological outbreaks. One of the prevalent pathogens associated with food production in Mexico has been Salmonella Oranienburg. Effective surveillance systems require microbial genetic knowledge. The objective of this work is to describe the genetic composition of Mexican S. Oranienburg genomes. For that, 53 strains from different environmental sources were isolated and sequenced. Additionally, 109 S. Oranienburg genomes were downloaded. Bioinformatic analyses were used to explore the clonal complex and genomic relatedness. A major clonal group formed by ST23 was identified comprising four STs. 202 SNPs were found the maximum difference among isolates. Virulence genes for host invasion and colonization as rpoS, fimbria type 1, and, T3SS were found common for all isolates. This study suggests that Mexican S. Oranienburg strains are potential pathogens circulating continuously in the region between host and non-host environments.
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Affiliation(s)
- J R Aguirre-Sanchez
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
| | - I F Vega-Lopez
- Laboratorio en Ciencia y Mineria de Datos, Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacán, México
| | - N Castro Del Campo
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
| | - J A Medrano-Felix
- Inocuidad Alimentaria, Investigadoras e Investigadores por México-Centro de Investigación en Alimentación y Desarrollo A.C, Culiacán, México
| | - J Martínez-Urtaza
- Departement of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - C Chaidez-Quiroz
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
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Khan AS, Pierneef RE, Gonzalez-Escalona N, Maguire M, Georges K, Abebe W, Adesiyun AA. Phylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago. Poult Sci 2022; 102:102322. [PMID: 36473385 PMCID: PMC9720344 DOI: 10.1016/j.psj.2022.102322] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/12/2022] Open
Abstract
This study was conducted to determine the phylogenies of Salmonella strains isolated from cross-sectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016-2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness. In addition, Salmonella strains isolated from human salmonellosis cases in Trinidad were analyzed for their relatedness to the isolates detected along the broiler production chain. The common source of these isolates of diverse serovars within farms, within processing plants, between processing plants and retail outlets, and among farm-processing plant-retail outlet continuum was well-supported (bootstrap value >70%) by the core genome phylogenies for the respective serovars. Also, genome analyses revealed clustering of Salmonella serovars of regional (intra-Caribbean) and international (extra-Caribbean) origin. Similarly, strains of S. Enteritidis and S. Infantis isolated from human clinical salmonellosis in 2019 from Trinidad and Tobago clustered with our processing plant isolates recovered in 2018. This study is the first phylogenetic analysis of Salmonella isolates using WGS from the broiler industry in the Caribbean region. The use of WGS confirmed the genetic relatedness and transmission of Salmonella serovars contaminating chickens in broiler processing, and retailing in the country, with zoonotic and food safety implications for humans.
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Affiliation(s)
- Anisa S. Khan
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Rian E. Pierneef
- Agricultural Research Council-Biotechnology Platform, Pretoria 0110, South Africa
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Meghan Maguire
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Karla Georges
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Woubit Abebe
- Department of Pathobiology, Center for Food Animal Health, Food Safety and Food Defense, Tuskegee University, College of Veterinary Medicine, Tuskegee, AL 36088, USA
| | - Abiodun A. Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago,Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa,Corresponding author:
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Rocha ADDL, Ferrari RG, Pereira WE, de Lima LA, Givisiez PEN, Moreno-Switt AI, Toro M, Delgado-Suárez EJ, Meng J, de Oliveira CJB. Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health. Front Microbiol 2022; 13:802625. [PMID: 35722289 PMCID: PMC9201643 DOI: 10.3389/fmicb.2022.802625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.
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Affiliation(s)
- Alan Douglas de Lima Rocha
- Departamento de Zootecnia, Laboratório de Avaliação de Produtos de Origem Animal (LAPOA), Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Rafaela Gomes Ferrari
- Departamento de Zootecnia, Laboratório de Avaliação de Produtos de Origem Animal (LAPOA), Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Walter Esfrain Pereira
- Departamento de Ciências Fundamentais e Sociais, Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Laiorayne Araújo de Lima
- Departamento de Zootecnia, Laboratório de Avaliação de Produtos de Origem Animal (LAPOA), Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Patrícia Emília Naves Givisiez
- Departamento de Zootecnia, Laboratório de Avaliação de Produtos de Origem Animal (LAPOA), Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Andrea Isabel Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestla, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Magaly Toro
- Laboratorio de Microbiologia y Probioticos, Instituto de Nutricion y Tecnologia de los Alimentos, Universidad de Chile, Santiago, Chile
| | | | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, College Park, MD, United States
| | - Celso José Bruno de Oliveira
- Departamento de Zootecnia, Laboratório de Avaliação de Produtos de Origem Animal (LAPOA), Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
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Maguire M, Khan AS, Adesiyun AA, Georges K, Gonzalez-Escalona N. Genomic Comparison of Eight Closed Genomes of Multidrug-Resistant Salmonella enterica Strains Isolated From Broiler Farms and Processing Plants in Trinidad and Tobago. Front Microbiol 2022; 13:863104. [PMID: 35620095 PMCID: PMC9127609 DOI: 10.3389/fmicb.2022.863104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/08/2022] [Indexed: 12/15/2022] Open
Abstract
Salmonella enterica is an important foodborne pathogen worldwide. We used long and short-read sequencing to close genomes of eight multidrug-resistant (MDR) S. enterica strains, belonging to serovars Infantis (2), Albany, Oranienburg, I 4,[5],12:i:-, Javiana, Schwarzengrund, and Kentucky from broiler chicken farms and processing plants in Trinidad and Tobago. They also belonged to seven different sequence types (STs- 32, 292, 1510, 19, 24, 152, and 96). Among the strains, seven had demonstrated multi-drug resistance with the presence of at least three AMR genes, whereas three isolates contained the quinolone resistance gene qnr B19 in plasmids (CFSAN103840, CFSAN103854, and CFSAN103872). The extended-spectrum β-lactamase genes bla CTX-M-65 (CFSAN103796) and bla TEM-1 (CFSAN103852) were detected in this study. The genomes closed in this study will be useful for future source tracking and outbreak investigations in Trinidad and Tobago and worldwide.
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Affiliation(s)
- Meghan Maguire
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Anisa S Khan
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Abiodun A Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Karla Georges
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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Characterisation of Salmonella Enteritidis ST11 and ST1925 Associated with Human Intestinal and Extra-Intestinal Infections in Singapore. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095671. [PMID: 35565065 PMCID: PMC9104914 DOI: 10.3390/ijerph19095671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/04/2022]
Abstract
Salmonella Enteritidis is a major foodborne pathogen worldwide. In this study, a total of 276 S. enteritidis isolates, collected between 2016 and 2017 from human, food and farm/slaughterhouse samples, were studied to enhance the understanding of the epidemiology of human salmonellosis in Singapore. Results showed all 276 isolates belonged either to ST1925 (70.3%) or ST11 (29.7%), with ST11 being significantly more frequent in extra-intestinal isolates and chicken isolates. Food isolates, most of which were from poultry, showed the highest prevalence of resistance (33–37%) against beta-lactams or beta-lactams/beta-lactamase inhibitor combination (ampicillin, piperacillin and ampicillin/sulbactam). The analysis showed the detection of genes associated with resistance to aminoglycoside genes (99.6%), tetracycline (55.1%), and beta-lactams (14.9%) of all isolates. Nine types of plasmids were found in 266 isolates; the most common incompatibility group profiles were IncFIB(S)-IncFII(S)-IncX1 (72.2%) and IncFIB(S)-IncFII(S) (15.8%). Most plasmid harbouring isolates from chicken (63.6%, 14/22) and from human (73.8%, 175/237) shared the same plasmid profile (IncFIB(S)-IncFII(S)-IncX1). SNP analysis showed clustering of several isolates from poultry food products and human isolates, suggesting phylogenetic relatedness among these isolates. Lastly, this study provides important epidemiological insights on the application of phenotypic and next-generation sequencing (NGS) tools for improved food safety and public health surveillance and outbreak investigation of S.enteritidis.
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Vogt NA, Hetman BM, Vogt AA, Pearl DL, Reid-Smith RJ, Parmley EJ, Kadykalo S, Janecko N, Bharat A, Mulvey MR, Ziebell K, Robertson J, Nash J, Allen V, Majury A, Ricker N, Bondo KJ, Allen SE, Jardine CM. Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data. Front Vet Sci 2022; 9:840416. [PMID: 35280127 PMCID: PMC8914089 DOI: 10.3389/fvets.2022.840416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Non-typhoidal Salmonella infections represent a substantial burden of illness in humans, and the increasing prevalence of antimicrobial resistance among these infections is a growing concern. Using a combination of Salmonella isolate short-read whole-genome sequence data from select human cases, raccoons, livestock and environmental sources, and an epidemiological framework, our objective was to determine if there was evidence for potential transmission of Salmonella and associated antimicrobial resistance determinants between these different sources in the Grand River watershed in Ontario, Canada. Logistic regression models were used to assess the potential associations between source type and the presence of select resistance genes and plasmid incompatibility types. A total of 608 isolates were obtained from the following sources: humans (n = 58), raccoons (n = 92), livestock (n = 329), and environmental samples (n = 129). Resistance genes of public health importance, including blaCMY−2, were identified in humans, livestock, and environmental sources, but not in raccoons. Most resistance genes analyzed were significantly more likely to be identified in livestock and/or human isolates than in raccoon isolates. Based on a 3,002-loci core genome multi-locus sequence typing (cgMLST) scheme, human Salmonella isolates were often more similar to isolates from livestock and environmental sources, than with those from raccoons. Rare instances of serovars S. Heidelberg and S. Enteritidis in raccoons likely represent incidental infections and highlight possible acquisition and dissemination of predominantly poultry-associated Salmonella by raccoons within these ecosystems. Raccoon-predominant serovars were either not identified among human isolates (S. Agona, S. Thompson) or differed by more than 350 cgMLST loci (S. Newport). Collectively, our findings suggest that the rural population of raccoons on swine farms in the Grand River watershed are unlikely to be major contributors to antimicrobial resistant human Salmonella cases in this region.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- *Correspondence: Nadine A. Vogt
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
| | | | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, Guelph, ON, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Stefanie Kadykalo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | | | - Anna Majury
- Public Health Ontario, Kingston, ON, Canada
- Department of Biomedical and Molecular Science, Queen's University, Kingston, ON, Canada
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
| | - Samantha E. Allen
- Wyoming Game and Fish Department, Laramie, WY, United States
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, United States
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, ON, Canada
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Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type. Appl Environ Microbiol 2022; 88:e0197921. [PMID: 35108089 PMCID: PMC8939312 DOI: 10.1128/aem.01979-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is typically considered a host generalist; however, certain isolates are associated with specific hosts and show genetic features of host adaptation. Here, we sequenced 131 S. Typhimurium isolates from wild birds collected in 30 U.S. states during 1978–2019. We found that isolates from broad taxonomic host groups including passerine birds, water birds (Aequornithes), and larids (gulls and terns) represented three distinct lineages and certain S. Typhimurium CRISPR types presented in individual lineages. We also showed that lineages formed by wild bird isolates differed from most isolates originating from domestic animal sources, and that genomes from these lineages substantially improved source attribution of Typhimurium genomes to wild birds by a machine learning classifier. Furthermore, virulence gene signatures that differentiated S. Typhimurium from passerines, water birds, and larids were detected. Passerine isolates tended to lack S. Typhimurium-specific virulence plasmids. Isolates from the passerine, water bird, and larid lineages had close genetic relatedness with human clinical isolates, including those from a 2021 U.S. outbreak linked to passerine birds. These observations indicate that S. Typhimurium from wild birds in the United States are likely host-adapted, and the representative genomic data set examined in this study can improve source prediction and facilitate outbreak investigation. IMPORTANCE Within-host evolution of S. Typhimurium may lead to pathovars adapted to specific hosts. Here, we report the emergence of disparate avian S. Typhimurium lineages with distinct virulence gene signatures. The findings highlight the importance of wild birds as a reservoir for S. Typhimurium and contribute to our understanding of the genetic diversity of S. Typhimurium from wild birds. Our study indicates that S. Typhimurium may have undergone adaptive evolution within wild birds in the United States. The representative S. Typhimurium genomes from wild birds, together with the virulence gene signatures identified in these bird isolates, are valuable for S. Typhimurium source attribution and epidemiological surveillance.
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Whole-Genome Analysis of Multidrug-Resistant Salmonella Enteritidis Strains Isolated from Poultry Sources in Korea. Pathogens 2021; 10:pathogens10121615. [PMID: 34959570 PMCID: PMC8707440 DOI: 10.3390/pathogens10121615] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022] Open
Abstract
The Salmonella Enterica subsp. Enterica serovar Enteritidis is one of main serovars isolated from human patients with food poisoning and poultry without clinical signs. Consumption of poultry products contaminated with Salmonella Enteritidis is a common source of human salmonellosis; 82 Salmonella spp. were isolated from 291 samples of retail chicken meat, 201 one-day-old chicks, 30 internal organs of chickens, 156 chicken eggs, 100 duck eggs, 38 straw bedding samples, 18 samples of retail duck meat, and 19 swab samples from slaughterhouses in 2019 and 2020. An antibiotic susceptibility test was performed for all isolates, revealing 33 multidrug-resistant (MDR) strains. The whole genome of 33 MDR strains isolated in 2019 and 2020 and 10 strains isolated in 2011, 2012, and 2017 was sequenced using the MinION sequencing protocol. Within these 43 samples, 5 serovars were identified: S. Enteritidis, S. Agona, S. Virchow, S. Albany, and S. Bareilly. The most common serovar was S. Enteritidis (26/43), which showed the highest resistance to ampicillin (100%), followed by nalidixic acid (90%) and colistin (83%). Core genome multilocus sequence typing analysis showed that the S. Enteritidis strains isolated from different sources and in different years were clustered together. In addition, the S. Enteritidis strains isolated since 2011 consistently harbored the same antibiotic resistance patterns.
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10
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Vogt NA, Hetman BM, Pearl DL, Vogt AA, Reid-Smith RJ, Parmley EJ, Janecko N, Bharat A, Mulvey MR, Ricker N, Bondo KJ, Allen SE, Jardine CM. Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada. PLoS One 2021; 16:e0260234. [PMID: 34793571 PMCID: PMC8601536 DOI: 10.1371/journal.pone.0260234] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022] Open
Abstract
To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Adam A. Vogt
- Independent Researcher, Mississauga, Ontario, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Samantha E. Allen
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
- Wyoming Game and Fish Department, Laramie, Wyoming, United States of America
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, United States of America
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, Ontario, Canada
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11
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Papić B, Kušar D, Mićunović J, Vidrih Š, Pirš M, Ocepek M, Avberšek J. Genomic insights into Salmonella Choleraesuis var. Kunzendorf outbreak reveal possible interspecies transmission. Vet Microbiol 2021; 263:109282. [PMID: 34785475 DOI: 10.1016/j.vetmic.2021.109282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Salmonella enterica serovar Choleraesuis is a host-adapted serovar that causes serious infections in domestic pigs and wild boars. Here, we investigated an outbreak of salmonellosis in domestic pigs in Slovenia, 2018-2019. To assess the outbreak, 18 isolates from domestic pigs, wild boars, wild boar meat and a human patient underwent whole-genome sequencing (WGS). All isolates were of sequence type (ST) 145 and harbored no antimicrobial resistance genes or AMR-associated mutations. A single transmission cluster (≤ 6 alleles) of spatially (< 100 km) and temporally linked isolates was observed, comprising isolates of pig (n = 9), wild boar (n = 2) and human (n = 1) origin, and suggesting possible interspecies transmission. In all outbreak-related animal cases, septicemic salmonellosis was observed, accompanied in some cases by enteric symptoms. All pig isolates were linked to a single intensive breeding farm that distributed growers to small family farms. The same transport vehicles were used to distribute growers to family farms and also to transport livestock between neighboring countries. Both isolates that originated from the imported wild boar meat were genetically distant (≥ 122 alleles) from the outbreak cluster. The present results indicate the importance of screening domestic pigs and proper disinfection of transport vehicles to control the spread of S. Choleraesuis.
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Affiliation(s)
- Bojan Papić
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, SI-1000 Ljubljana, Slovenia.
| | - Darja Kušar
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
| | - Jasna Mićunović
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
| | - Špela Vidrih
- University of Ljubljana, Veterinary Faculty, National Veterinary Institute, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
| | - Mateja Pirš
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Zaloška 4, SI-1000 Ljubljana, Slovenia
| | - Matjaž Ocepek
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
| | - Jana Avberšek
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
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12
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Hubálek Z. Pathogenic microorganisms associated with gulls and terns (Laridae). JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zdeněk Hubálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail:
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13
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Zeballos-Gross D, Rojas-Sereno Z, Salgado-Caxito M, Poeta P, Torres C, Benavides JA. The Role of Gulls as Reservoirs of Antibiotic Resistance in Aquatic Environments: A Scoping Review. Front Microbiol 2021; 12:703886. [PMID: 34367104 PMCID: PMC8343230 DOI: 10.3389/fmicb.2021.703886] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/21/2021] [Indexed: 12/04/2022] Open
Abstract
The role of wildlife with long-range dispersal such as gulls in the global dissemination of antimicrobial resistance (AMR) across natural and anthropogenic aquatic environments remains poorly understood. Antibiotic-resistant bacteria have been detected in resident and migratory gulls worldwide for more than a decade, suggesting gulls as either sentinels of AMR pollution from anthropogenic sources or independent reservoirs that could maintain and disperse AMR across aquatic environments. However, confirming either of these roles remains challenging and incomplete. In this review, we present current knowledge on the geographic regions where AMR has been detected in gulls, the molecular characterization of resistance genes, and the evidence supporting the capacity of gulls to disperse AMR across regions or countries. We identify several limitations of current research to assess the role of gulls in the spread of AMR including most studies not identifying the source of AMR, few studies comparing bacteria isolated in gulls with other wild or domestic species, and almost no study performing longitudinal sampling over a large period of time to assess the maintenance and dispersion of AMR by gulls within and across regions. We suggest future research required to confirm the role of gulls in the global dispersion of AMR including the standardization of sampling protocols, longitudinal sampling using advanced satellite tracking, and whole-genome sequencing typing. Finally, we discuss the public health implications of the spread of AMR by gulls and potential solutions to limit its spread in aquatic environments.
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Affiliation(s)
- Danae Zeballos-Gross
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Zulma Rojas-Sereno
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Facultad de Ciencias de la Vida, Centro de Investigación para la Sustentabilidad, Universidad Andrés Bello, Santiago, Chile
| | - Marília Salgado-Caxito
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - Patricia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, Lisbon, Portugal.,Veterinary and Animal Research Centre, Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Carmen Torres
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Julio A Benavides
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Facultad de Ciencias de la Vida, Centro de Investigación para la Sustentabilidad, Universidad Andrés Bello, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
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14
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Rivera D, Allel K, Dueñas F, Tardone R, Soza P, Hamilton-West C, Moreno-Switt AI. Screening the Presence of Non-Typhoidal Salmonella in Different Animal Systems and the Assessment of Antimicrobial Resistance. Animals (Basel) 2021; 11:ani11061532. [PMID: 34074040 PMCID: PMC8225015 DOI: 10.3390/ani11061532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 01/14/2023] Open
Abstract
Salmonella is a major bacterial foodborne pathogen that causes the majority of worldwide food-related outbreaks and hospitalizations. Salmonellosis outbreaks can be caused by multidrug-resistant (MDR) strains, emphasizing the importance of maintaining public health and safer food production. Nevertheless, the drivers of MDR Salmonella serovars have remained poorly understood. In this study, we compare the resistance profiles of Salmonella strains isolated from 4047 samples from domestic and wild animals in Chile. A total of 106 Salmonella strains (2.61%) are isolated, and their serogroups are characterized and tested for susceptibility to 16 different antimicrobials. The association between antimicrobial resistance (AMR) and a subset of independent variables is evaluated using multivariate logistic models. Our results show that 47 antimicrobial-resistant strains were found (44.3% of the total strains). Of the 47, 28 correspond to single-drug resistance (SDR = 26.4%) and 19 are MDR (17.9%). S. Enteritidis is highly persistent in animal production systems; however, we report that serogroup D strains are 18 times less likely to be resistant to at least one antimicrobial agent than the most common serogroup (serogroup B). The antimicrobials presenting the greatest contributions to AMR are ampicillin, streptomycin and tetracycline. Additionally, equines and industrial swine are more likely to acquire Salmonella strains with AMR. This study reports antimicrobial-susceptible and resistant Salmonella in Chile by expanding the extant literature on the potential variables affecting antimicrobial-resistant Salmonella.
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Affiliation(s)
- Dácil Rivera
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 7550000, Chile;
| | - Kasim Allel
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 7550000, Chile;
- Department of Disease Control, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Antimicrobial Resistance Centre, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Fernando Dueñas
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
| | - Rodolfo Tardone
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
| | - Paula Soza
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
| | - Christopher Hamilton-West
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santa Rosa 11735, La Pintana, Santiago 8820000, Chile;
| | - Andrea I. Moreno-Switt
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 7550000, Chile;
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago 7810000, Chile
- Correspondence:
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15
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Tracking Salmonella enterica by whole genome sequencing of isolates recovered from broiler chickens in a poultry production system. Int J Food Microbiol 2021; 350:109246. [PMID: 34034079 DOI: 10.1016/j.ijfoodmicro.2021.109246] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/27/2021] [Accepted: 05/09/2021] [Indexed: 01/12/2023]
Abstract
Salmonella enterica is a major cause of foodborne diseases, and is also an important pathogenic bacterium in poultry industry. Whole genome sequencing (WGS) has become a crucial molecular typing technology used for the surveillance of the pathogenic bacteria. In the present study, we adopted WGS for tracking transmission of S. enterica in the production chain of broiler chickens. A total of 74 S. enterica strains were isolated from the different steps of breeding and slaughtering in a large production enterprise in Sichuan Province, China. The isolation rate of Salmonella was the highest in procedure of defeathering (50.0%) and evisceration (36.7%). Serotype identification showed that 74 Salmonella isolates included 7 serotypes, among which Mbandaka accounted for the highest proportions (35.1%). WGS revealed that 74 strains belonged to 7 different sequence types (STs), as well as 7 different ribosomal STs and 35 core genome STs. cgMLST-based Minimum Spanning Trees and phylogenetic tree based on the SNPs indicated that three serotypes, Mbandaka, Indiana and Kentucky, could be clonally transmitted between broiler farm and slaughterhouse. Heterogeneous resistant phenotypes and genotypes were found in two serotypes, Indiana and Kentucky. Our study indicated WGS in an accurate tool for molecular typing of S. enterica. Routine surveillance of S. enterica in the production chain of broiler chickens is needed.
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16
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Mascitti AK, Kipper D, Dos Reis RO, da Silva JS, Fonseca ASK, Ikuta N, Tondo EC, Lunge VR. Retrospective whole-genome comparison of Salmonella enterica serovar Enteritidis from foodborne outbreaks in Southern Brazil. Braz J Microbiol 2021; 52:1523-1533. [PMID: 33990934 DOI: 10.1007/s42770-021-00508-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 04/24/2021] [Indexed: 01/14/2023] Open
Abstract
Salmonella enterica serovar Enteritidis is frequently isolated from animal-source foods associated with human salmonellosis outbreaks. This serovar was spread to animal (mainly poultry) farms worldwide in the 1980s, and it is still detected in foods produced in many countries, including Brazil. The present study reports a retrospective genome-wide comparison of S. Enteritidis from foodborne outbreaks in Southern Brazil in the last two decades. Fifty-two S. Enteritidis isolates were obtained from foodborne outbreaks occurring in different cities of the Brazilian southernmost State, Rio Grande do Sul (RS), from 2003 to 2015. Whole-genome sequences (WGS) from these isolates were obtained and comparatively analyzed with 65 additional genomes from NCBI. Phylogenetic and Bayesian analyses were performed to study temporal evolution. Genes related to antibiotic resistance and virulence were also evaluated. The results demonstrated that all S. Enteritidis isolates from Southern Brazil clustered in the global epidemic clade disseminated worldwide originally in the 1980s. Temporal analysis demonstrated that all Brazilian isolates had a tMRCA (time to most recent common ancestor) in 1986 with an effective population size (Ne) increase soon after until 1992, then becoming constant up to now. In Southern Brazil, there was a significant decrease in the spreading of S. Enteritidis in the last decade. In addition, three antibiotic resistance genes were detected in all isolates: aac(6')-Iaa, mdfA, and tet(34). These results demonstrate the high frequency of one only specific S. Enteritidis lineage (global epidemic clade) in foodborne outbreaks from Southern Brazil in the last two decades.
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Affiliation(s)
- Andréa K Mascitti
- Lutheran University of Brazil, 8001, Canoas, Rio Grande Do Sul, 92425-020, Brazil
| | - Diéssy Kipper
- Lutheran University of Brazil, 8001, Canoas, Rio Grande Do Sul, 92425-020, Brazil
| | - Rafael O Dos Reis
- Lutheran University of Brazil, 8001, Canoas, Rio Grande Do Sul, 92425-020, Brazil
| | - Juliana S da Silva
- Lutheran University of Brazil, 8001, Canoas, Rio Grande Do Sul, 92425-020, Brazil
| | | | - Nilo Ikuta
- Simbios Biotechnology, Cachoeirinha, Rio Grande do Sul, Brazil
| | - Eduardo C Tondo
- Institute of Food Science and Technology, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Vagner R Lunge
- Lutheran University of Brazil, 8001, Canoas, Rio Grande Do Sul, 92425-020, Brazil.
- Simbios Biotechnology, Cachoeirinha, Rio Grande do Sul, Brazil.
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17
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Wang Z, Xu H, Chu C, Tang Y, Li Q, Jiao X. Genomic Identification of Multidrug-Resistant Salmonella Virchow Monophasic Variant Causing Human Septic Arthritis. Pathogens 2021; 10:pathogens10050536. [PMID: 33947106 PMCID: PMC8146543 DOI: 10.3390/pathogens10050536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/25/2021] [Accepted: 04/28/2021] [Indexed: 11/21/2022] Open
Abstract
The monophasic variant of Salmonella Typhimurium has emerged and increased rapidly worldwide during the past two decades. The loss of genes encoding the second-phase flagella and the acquirement of the multi-drug resistance cassette are the main genomic characteristics of the S. Typhimurium monophasic variant. In this study, two Salmonella strains were isolated from the knee effusion and feces of a 4-year-old girl who presented with a case of septic arthritis and fever, respectively. Primary serovar identification did not detect the second-phase flagellar antigens of the strains using the classical slide agglutination test. Whole-genome sequencing analysis was performed to reveal that the replacement of the fljAB operon by a 4.8-kb cassette from E. coli caused the non-expression of phase-2 flagellar antigens of the strains, which were confirmed to be a novel S. Virchow monophasic variant (Salmonella 6,7,14:r:-) by core-genome multi-locus sequence typing (cgMLST). Compared to the 16 published S. Virchow genomes, the two strains shared a unique CRISPR type of VCT12, and showed a close genetic relationship to S. Virchow BCW_2814 and BCW_2815 strains, isolated from Denmark and China, respectively, based on cgMLST and CRISPR typing. Additionally, the acquisition of Salmonella genomic island 2 (SGI2) with an antimicrobial resistance gene cassette enabled the strains to be multidrug-resistant to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole. The emergence of the multidrug-resistant S. Virchow monophasic variant revealed that whole-genome sequencing and CRISPR typing could be applied to identify the serovaraints of Salmonella enterica strains in the national Salmonella surveillance system.
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Affiliation(s)
- Zhenyu Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
| | - Haiyan Xu
- Nantong Center for Disease Control and Prevention, Gongnong South Road 189, Nantong 226007, China;
| | - Chao Chu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
| | - Yuanyue Tang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Correspondence: (Q.L.); (X.J.); Tel.: +86-514-87971136 (Q.L.); +86-514-87971136 (X.J.)
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Correspondence: (Q.L.); (X.J.); Tel.: +86-514-87971136 (Q.L.); +86-514-87971136 (X.J.)
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18
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Ewbank AC, Esperón F, Sacristán C, Sacristán I, Neves E, Costa-Silva S, Antonelli M, Rocha Lorenço J, Kolesnikovas CKM, Catão-Dias JL. Occurrence and Quantification of Antimicrobial Resistance Genes in the Gastrointestinal Microbiome of Two Wild Seabird Species With Contrasting Behaviors. Front Vet Sci 2021; 8:651781. [PMID: 33829054 PMCID: PMC8019699 DOI: 10.3389/fvets.2021.651781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/24/2021] [Indexed: 01/24/2023] Open
Abstract
Antimicrobial resistance genes (ARGs) are environmental pollutants and anthropization indicators. We evaluated human interference in the marine ecosystem through the ocurrence and quantification (real-time PCRs) of 21 plasmid-mediated ARGs in enema samples of 25 wild seabirds, upon admission into rehabilitation: kelp gull (Larus dominicanus, n = 14) and Magellanic penguin (Spheniscus magellanicus, n = 11). Overall, higher resistance values were observed in kelp gulls (non-migratory coastal synanthropic) in comparison with Magellanic penguins (migratory pelagic non-synanthropic). There were significant differences between species (respectively, kelp gull and Magellanic penguin): ARGs occurrence (bla TEM [p = 0.032]; tetM [p = 0.015]; tetA [p = 0.003]; and sulII [p = 0.007]), mean number of ARGs per sample (p = 0.031), ARGs mean load percentage (aadA [p = 0.045], tetA [p = 0.031], tetM [p = 0.016], bla TEM [p = 0.032], sulII [p = 0.008]), percentage of genes conferring resistance to an antimicrobial class (betalactams [p = 0.036] and sulfonamides [p = 0.033]), mean number of genes conferring resistance to one or more antimicrobial classes (p = 0.024]), percentage of multiresistant microbiomes (p = 0.032), and clustering (p = 0.006). These differences are likely due to these species' contrasting biology and ecology - key factors in the epidemiology of ARGs in seabirds. Additionally, this is the first report of mecA in seabirds in the Americas. Further studies are necessary to clarify the occurrence and diversity of ARGs in seabirds, and their role as potential sources of infection and dispersal within the One Health chain of ARGs.
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Affiliation(s)
- Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Esperón
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain
| | - Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Irene Sacristán
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Elena Neves
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain
| | | | | | | | | | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
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19
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Kubicek-Sutherland JZ, Xie G, Shakya M, Dighe PK, Jacobs LL, Daligault H, Davenport K, Stromberg LR, Stromberg ZR, Cheng Q, Kempaiah P, Ong’echa JM, Otieno V, Raballah E, Anyona S, Ouma C, Chain PSG, Perkins DJ, Mukundan H, McMahon BH, Doggett NA. Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya. PLoS Negl Trop Dis 2021; 15:e0008991. [PMID: 33524010 PMCID: PMC7877762 DOI: 10.1371/journal.pntd.0008991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 02/11/2021] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003-2010. Nine isolates were identified as S. Typhimurium sequence type 313 while the other two were S. Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S. Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.
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Affiliation(s)
| | - Gary Xie
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Migun Shakya
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Priya K. Dighe
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | - Lindsey L. Jacobs
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | - Karen Davenport
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
| | | | | | - Qiuying Cheng
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Prakasha Kempaiah
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John Michael Ong’echa
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Vincent Otieno
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Evans Raballah
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Laboratory Science, School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Samuel Anyona
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, Kenya
| | - Collins Ouma
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | | | - Douglas J. Perkins
- Center for Global Health, University of New Mexico, Albuquerque, New Mexico, United States of America
- University of New Mexico/KEMRI Laboratories of Parasitic and Viral Diseases, Kenya Medical Research Institute, Kisumu, Kenya
| | - Harshini Mukundan
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
- * E-mail:
| | | | - Norman A. Doggett
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States
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20
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Ewbank AC, Esperón F, Sacristán C, Sacristán I, Krul R, Cavalcante de Macedo E, Calatayud O, Bueno I, de Francisco Strefezzi R, Catão-Dias JL. Seabirds as anthropization indicators in two different tropical biotopes: A One Health approach to the issue of antimicrobial resistance genes pollution in oceanic islands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142141. [PMID: 32920402 DOI: 10.1016/j.scitotenv.2020.142141] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/12/2023]
Abstract
Antimicrobial resistance is a quintessential One Health issue, among the most serious 21st century global threats to human health. Seabirds may act as sentinels of natural and anthropogenic changes in the marine ecosystem health, including pollution by antimicrobial resistance genes (ARGs). We used real time PCR to identify and quantify 22 plasmid-mediated ARGs in the gastrointestinal microbiome of six wild seabird species, comparing an anthropized (Fernando de Noronha Archipelago - FNA) and a pristine biotope (Rocas Atoll - ROA), Brazil. Of 257 birds, 218 (84.8%) were positive to at least one ARG. ARG classes encoding resistance to tetracyclines (75.1%), quinolones (10.5%) and phenicols (10.5%) were the most prevalent, with tetracyclines significantly greater than the remaining classes (p < 0.05). Genes tet(S) (29.2%), tet(A) (28.8%), and tet(B) (24.9%) were the most commonly found and had a significantly greater prevalence when compared to the remaining ARGs (p < 0.05). The anthropized biotope presented statistically significant higher prevalence of sulfonamide- and quinolone-encoding ARGs in comparison with the pristine (respectively, p = 0.01 and p = 0.03), and higher sulII gene prevalence (p = 0.04), consistent with anthropogenic pressure. Migratory species (only present in ROA) showed statistically significant higher mcr-1 (polymyxins) and blaTEM (betalactam) prevalences (respectively, p = 0.009 and p = 0.02), and mcr-1 percentage load (p = 0.0079) in comparison with non-migratory. To our knowledge, this is the largest ARGs survey based on direct detection and quantification in seabirds worldwide, and the first to evaluate non-synanthropic species in oceanic islands. This is the first detection of mcr-1 in wild free-ranging seabirds in Brazil and in free-ranging migratory non-synanthropic seabirds worldwide. Our findings show the importance of biological and ecological factors, highlighting the role of seabirds as anthropization sentinels and ARGs-pollution environmental indicators (even in a pristine biotope), and their involvement in the One Health epidemiological chain of ARGs.
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Affiliation(s)
- Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
| | - Fernando Esperón
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain.
| | - Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
| | - Irene Sacristán
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Ricardo Krul
- Ornithology Laboratory, Center for Studies of the Sea, Paraná State University, Paraná State, Brazil.
| | - Eduardo Cavalcante de Macedo
- Chico Mendes Institute for Biodiversity Conservation (ICMBio) - Brazilian Ministry of the Environment, Rocas Atol Biological Reserve, Rio Grande do Norte, Brazil.
| | - Olga Calatayud
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain.
| | - Irene Bueno
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States.
| | - Ricardo de Francisco Strefezzi
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil.
| | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
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21
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Whole-Genome Sequencing Analysis of Salmonella
Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010-2017. Pathogens 2021; 10:pathogens10010045. [PMID: 33430364 PMCID: PMC7825753 DOI: 10.3390/pathogens10010045] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/26/2020] [Accepted: 01/04/2021] [Indexed: 01/17/2023] Open
Abstract
Salmonella enterica subsp. enterica serotype Enteritidis (SE) is recognized as a major cause of human salmonellosis worldwide, and most human salmonellosis is due to the consumption of contaminated poultry meats and poultry byproducts. Whole-genome sequencing (data were obtained from 96 SE isolates from poultry sources, including an integrated broiler supply chain, farms, slaughterhouses, chicken transporting trucks, and retail chicken meats in South Korea during 2010–2017. Antimicrobial resistance and virulence genes were investigated using WGS data, and the phylogenetic relationship of the isolates was analyzed using single-nucleotide polymorphism (SNP) typing and core genome multilocus sequence typing (cgMLST). All isolates carried aminoglycoside resistance genes, aac(6’)-Iaa, and 56 isolates carried multiple antimicrobial resistance genes. The most frequent virulence gene profile, pef-fim-sop-inv.-org-sip-spa-sif-fli-flg-hil-ssa-sse-prg-pag-spv, was found in 90 isolates. The SNP analysis provided a higher resolution than the cgMLST analysis, but the cgMLST analysis was highly congruent with the SNP analysis. The phylogenetic results suggested the presence of resident SE within the facility of processing plants, environments of slaughterhouses, and the integrated broiler supply chain, and the phylogenetically related isolates were found in retail meats. In addition, the SE isolates from different origins showed close genetic relationships indicating that these strains may have originated from a common source. This study could be valuable reference data for future traceback investigations in South Korea.
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22
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Quino W, Caro-Castro J, Mestanza O, Hurtado CV, Zamudio ML, Gavilan RG. Phylogenetic structure of Salmonella Enteritidis provides context for a foodborne outbreak in Peru. Sci Rep 2020; 10:22080. [PMID: 33328486 PMCID: PMC7745040 DOI: 10.1038/s41598-020-78808-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 11/27/2020] [Indexed: 11/09/2022] Open
Abstract
Salmonella Enteritidis, an important foodborne zoonosis, has a dramatically increased number of cases around the world. To explore the phylogenetic structure of Peruvian Salmonella Enteritidis strains and their relationship with an outbreak occurred in 2018, we analyzed a comprehensive strains of S. Enteritidis received by the National Institute of Health during the period 2000-2018. A total of 180 strains were characterized by microbiological procedures, serotyping and whole genome sequencing. Based on genome sequences annotated, virulence factors and accessory genes were identified. Phylogenetic and population structure analysis were also analyzed based on SNPs. The phylogenetic analysis grouped the genomes into two well-supported clades that were consistent with population structure analysis. The clinical and food strains corresponding to the outbreak were included in the same cluster, which presented the sdhA gene, related to the increase of the virulence of this pathogen. The phylogenetic relationship of Peruvian S. Enteritidis suggests the presence of four S. enteritidis population with high epidemiological importance.
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Affiliation(s)
- Willi Quino
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Junior Caro-Castro
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Orson Mestanza
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Carmen V Hurtado
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Maria L Zamudio
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Ronnie G Gavilan
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru. .,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru.
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23
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Ben Hassena A, Haendiges J, Zormati S, Guermazi S, Gdoura R, Gonzalez-Escalona N, Siala M. Virulence and resistance genes profiles and clonal relationships of non-typhoidal food-borne Salmonella strains isolated in Tunisia by whole genome sequencing. Int J Food Microbiol 2020; 337:108941. [PMID: 33181420 DOI: 10.1016/j.ijfoodmicro.2020.108941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/30/2020] [Accepted: 10/15/2020] [Indexed: 12/22/2022]
Abstract
Whole genome sequencing (WGS) has made impressive progress in the field of molecular biology. Its most common application for public health is in the area of surveillance of food-borne diseases. WGS has the potential for providing a large amount of information, such as the identification of the strain type, the characterization of antibiotic resistance and virulence, and phylogeny. In our study, thirty-nine non-typhoidal Salmonella strains were isolated from diverse sources in Tunisia. Non-typhoidal Salmonella are among the most common pathogens contaminating food animals. The presence of virulence and antimicrobial resistance determinants in those strains were investigated using whole genome sequencing (WGS) and appropriate data analysis. The genomes were screened for several Salmonella virulence genes using the Virulence Factor Database VFDB. Twelve different virulence profiles, which correspond to the 12 identified serovars, were recognized. Several antimicrobial resistance genes were also detected: aac (6')-Iaa, sul1, tetA, bla-TEM and qnrS genes. Phylogenetic relationships among the strains were further assessed by a cgMLST analysis. The resulting phylogenetic tree consisted of several clusters consistently with the in silico multilocus sequence typing (MLST) and serotyping. Our findings demonstrated that WGS and subsequent data analysis provided an accurate tool for genetic characterization of bacterial strains compared to usual molecular typing techniques. To the best of our knowledge, this is the first report of an application of WGS for genetic characterization of food-borne Tunisian strains.
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Affiliation(s)
- Amal Ben Hassena
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Julie Haendiges
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Sonia Zormati
- Regional Center of Veterinary research of Sfax, Tunisia
| | - Sonda Guermazi
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Radhouane Gdoura
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Mariam Siala
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax, Sfax, Tunisia; Department of Biology, Preparatory Institute for Engineering Studies of Sfax, University of Sfax, Tunisia.
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24
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Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia. Eur J Clin Microbiol Infect Dis 2020; 40:597-606. [PMID: 33030625 DOI: 10.1007/s10096-020-04055-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/30/2020] [Indexed: 10/23/2022]
Abstract
We sought to determine the relative value of conventional molecular methods and whole-genome sequencing (WGS) for subtyping Salmonella enterica serovar Enteritidis recovered from 2000 to 2015 in Tunisia and to investigate the genetic diversity of this serotype. A total of 175 Salmonella Enteritidis isolates were recovered from human, animal, and foodborne outbreak samples. Pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing were performed. Eight pulsotypes were detected for all isolates with PFGE (DI = 0.518). Forty-five Salmonella Enteritidis isolates were selected for the MLVA and WGS techniques. Eighteen MLVA profiles were identified and classified into two major clusters (DI = 0.889). Core genome multilocus typing (cgMLST) analysis revealed 16 profiles (DI = 0.785). Whole-genome analysis indicated 660 single-nucleotide polymorphism (SNP) divergences dividing these isolates into 43 haplotypes (DI = 0.997). The phylogenetic tree supported the classification of Salmonella Enteritidis isolates into two distinct lineages subdivided into five clades and seven subclades. Pairwise SNP differences between the isolates ranged between 302 and 350. We observed about 311 SNP differences between the two foodborne outbreaks, while only less or equal to 4 SNP differences within each outbreak. SNP-based WGS typing showed an excellent discriminatory power comparing with the conventional methods such as PFGE and MLVA. Besides, we demonstrate the added value of WGS as a complementary subtyping method to discriminate outbreak from non-outbreak isolates belonging to common subtypes. It is important to continue the survey of Salmonella Enteritidis lineages in Tunisia using WGS.
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25
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Patchanee P, Tanamai P, Tadee P, Hitchings MD, Calland JK, Sheppard SK, Meunsene D, Pascoe B, Tadee P. Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand. PeerJ 2020. [DOI: 10.7717/peerj.9700] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background
Monophasic Salmonella Typhimurium or S. enterica 1,4,[5],12:i:- is among the top five serotypes reported in Thailand. In this study, nineteen monophasic S. Typhimurium from the pig production chain in Chiang Mai and Lamphun provinces during 2011–2014 were sequenced and compared to a globally disseminated clone. Isolates were probed in silico for the presence of antimicrobial resistance genes and Salmonella virulence factors, including Pathogenicity Islands.
Results
All isolates were from sequence type 34 (ST-34) and clustered similarly in core and pangenome genealogies. The two closest related isolates showed differences in only eighteen loci from whole-genome multilocus sequence typing analysis. All 19 isolates carried aminoglycoside and beta-lactam class resistance genes and genes for five or more different antibiotic classes. Seven out of 14 known SPIs were detected, including SPI-5, SPI-13 and SPI-14, which were detected in all isolates.
Conclusions
The multi-drug resistant clone, ST-34 was sampled at all stages of pork production. This clone has infiltrated global agricultural processes and poses a significant public health risk. Differences in the core and accessory genomes of the isolates we collected suggest that strains persist though the pork production process, with evidence of mutation within the core-genome and horizontal acquisition of genes, potentially via sharing of pathogenicity islands and plasmids. This highlights the importance of surveillance and targeted intervention measures to successfully control Salmonella contamination.
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Affiliation(s)
- Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Department of Food and Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prawitchaya Tanamai
- Integrative Research Center for Veterinary Preventive Medicine, Department of Food and Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai, Thailand
| | | | - Jessica K. Calland
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Dethaloun Meunsene
- Department of Veterinary Medicine, Faculty of Agriculture, National University of Laos, Vientiane, Loas PDR
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Pakpoom Tadee
- Integrative Research Center for Veterinary Preventive Medicine, Department of Food and Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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26
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Monte DFM, Nethery MA, Barrangou R, Landgraf M, Fedorka-Cray PJ. Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources. Food Microbiol 2020; 93:103601. [PMID: 32912589 DOI: 10.1016/j.fm.2020.103601] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
For decades, Salmonella Typhimurium and Salmonella Enteritidis have prevailed in several countries as agents of salmonellosis outbreaks. In Brazil, the largest exporter of poultry meat, relatively little attention has been paid to infrequent serovars. Here, we report the emergence and characterization of rare serovars isolated from food and related sources collected between 2014 and 2016 in Brazil. Twenty-two Salmonella enterica isolates were analyzed through the use of whole-genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats (CRISPR) genotyping. These isolates were classified into 10 infrequent serovars, including S. Abony, S. Isangi, S. Rochdale, S. Saphra, S. Orion, S. Ouakam, S. Grumpensis, S. Carrau, S. Abaetetuba, and S. Idikan. The presence of six antimicrobial resistance (AMR) genes, qnrB19, blaCMY-2, tetA, aac(6')-Iaa, sul2 and fosA7, which encode resistance to quinolones, third-generation cephalosporin, tetracycline, aminoglycoside, sulfonamide and fosfomycin, respectively, were confirmed by WGS. All S. Isangi harbored qnrB19 with conserved genomic context across strains, while S. Abony harbored blaCMY-2. Twelve (54.5%) strains displayed chromosomal mutations in parC (Thr57→Ser). Most serovars were classified as independent lineages, except S. Abony and S. Abaetetuba, which phylogenetically nested with Salmonella strains from different countries. CRISPR analysis revealed that the spacer content was strongly correlated with serovar and multi-locus sequence type for all strains, independently confirming the observed phylogenetic patterns, and highlighting the value of CRISPR-based genotyping for Salmonella. These findings add valuable information to the epidemiology of S. enterica in Brazil, where the emergency of antibiotic-resistant Salmonella continues to evolve.
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Affiliation(s)
- Daniel F M Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil; Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.
| | - Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.
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Genetic diversity of clinical Salmonella enterica serovar Typhimurium in a university hospital of south Tunisia, 2000-2013. INFECTION GENETICS AND EVOLUTION 2020; 85:104436. [PMID: 32569743 DOI: 10.1016/j.meegid.2020.104436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/28/2020] [Accepted: 06/16/2020] [Indexed: 01/06/2023]
Abstract
Typhimurium is one of the main Salmonella serovar responsible for non-typhoidal gastro-enteritis in Tunisia. Here, we aimed to assess the genetic diversity of 88 clinical Salmonella Typhimurium strains recovered during 14 years from 2000 to 2013. Phage typing, CRISPR polymorphisms (CRISPOL), pulsed-field gel electrophoresis (PFGE), multi-locus variable-number tandem repeat analysis (MLVA) and Whole genome sequencing (WGS) were used to study the relatedness and spatio-temporal evolution of Salmonella Typhimurium populations (Typhimurium (n = 81), monophasic (n = 3) and nonmotile (n = 4) variants). Seven-locus MLST from whole genome assemblies showed that all isolates, except one, belonged to ST19. The isolates were divided into 10 definitive phage (DT) types, dominated by DT104-L (39.8%), DT41 (14.8%), DT116 (11.4%) and DT120 (5.7%). Fifty-seven MLVA patterns (DI, 0.978) were obtained compared to 11 different CRISPOL types and 15 PFGE types (DI,0.845). For cgMLST analysis, 20 profiles were found. A total of 3056 SNPs were identified from the whole genome of the 88 Salmonella Typhimurium isolates. These SNPs resolved these isolates into 86 SNP haplotypes. The phylogeny result allocated most Salmonella Typhimurium isolates into four distinct clades and seven subclades. Genetic diversity between the four clades ranged in the order of 249 to 720 nucleotide changes. The prevalent phage type DT104L formed a major clade on the phylogenetic tree. Pairwise SNP differences between the strains of this clade ranged between 0 and 59. SNP-based WGS typing seems to be the most valuable molecular markers for studying the evolutionary relationships of homogeneous serovar Typhimurium isolates.
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28
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Jayeola V, McClelland M, Porwollik S, Chu W, Farber J, Kathariou S. Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis. Front Microbiol 2020; 11:726. [PMID: 32499760 PMCID: PMC7242855 DOI: 10.3389/fmicb.2020.00726] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 01/11/2023] Open
Abstract
Salmonella enterica is the leading foodborne pathogen associated with outbreaks involving low-moisture foods (LMFs). However, the genes involved in Salmonella's long-term survival on LMFs remain poorly characterized. In this study, in-shell pistachios were inoculated with Tn5-based mutant libraries of S. Enteritidis P125109, S. Typhimurium 14028s, and S. Newport C4.2 at approximate 108 CFU/g and stored at 25°C. Transposon sequencing analysis (Tn-seq) was then employed to determine the relative abundance of each Tn5 insertion site immediately after inoculation (T0), after drying (T1), and at 120 days (T120). In S. Enteritidis, S. Typhimurium, and S. Newport mutant libraries, the relative abundance of 51, 80, and 101 Tn5 insertion sites, respectively, was significantly lower at T1 compared to T0, while in libraries of S. Enteritidis and S. Typhimurium the relative abundance of 42 and 68 Tn5 insertion sites, respectively, was significantly lower at T120 compared to T1. Tn5 insertion sites with reduced relative abundance in this competition assay were localized in DNA repair, lipopolysaccharide biosynthesis and stringent response genes. Twelve genes among those under strong negative selection in the competition assay were selected for further study. Whole gene deletion mutants in ten of these genes, sspA, barA, uvrB, damX, rfbD, uvrY, lrhA, yifE, rbsR, and ompR, were impaired for individual survival on pistachios. The findings highlight the value of combined mutagenesis and sequencing to identify novel genes important for the survival of Salmonella in low-moisture foods.
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Affiliation(s)
- Victor Jayeola
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Weiping Chu
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Jeffrey Farber
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Sophia Kathariou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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29
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Abstract
Salmonella enterica is one of the main causes of gastrointestinal disease worldwide. Wild birds are capable of harboring a variety of Salmonella serovars, which could have an important role in the epidemiology of salmonellosis in humans and production animals. We tested 519 fecal samples from raptors and aquatic birds from different regions of central (three rehabilitation centers for wildlife and the coastal area) and southern areas of Chile for Salmonella. All samples were obtained in 2015 and 2017, covering all four seasons. Salmonella was isolated from 12 of the 519 samples (2%) analyzed, from two carnivorous birds, four birds with generalist habits, and six waterfowl. Among the isolates obtained, one showed resistance to gentamicin, and one showed a multidrug-resistance phenotype, with resistance to ampicillin, ceftriaxone, ciprofloxacin, chloramphenicol, streptomycin, gentamicin, kanamycin, trimethoprim-sulfamethoxazole, and tetracycline. These results demonstrated the importance of characterizing Salmonella in wild birds because previous studies have shown genetic and phenotypic evidence suggesting interspecies transmission of Salmonella enterica that is resistant to antimicrobials between humans and wild and domestic birds.
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30
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Simpson KMJ, Mor SM, Ward MP, Collins J, Flint J, Hill-Cawthorne GA, Abd El Ghany M. Genomic characterisation of Salmonella enterica serovar Wangata isolates obtained from different sources reveals low genomic diversity. PLoS One 2020; 15:e0229697. [PMID: 32109266 PMCID: PMC7048276 DOI: 10.1371/journal.pone.0229697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica serovar Wangata is an important pathogen in New South Wales (NSW), Australia. The incidence of S. Wangata is increasing and transmission is suspected to be via a non-food source. A recent outbreak investigation of sources of S. Wangata recovered isolates from humans, domestic animals, wildlife and the environment. Here, we extend that investigation by characterising and describing the genomic determinates of these isolates. We found that Australian S. Wangata isolates from different sources exhibited similar virulence and antimicrobial resistance gene profiles. There were no major genomic differences between isolates obtained from different geographical regions within Australia or from different host species. In addition, we found evidence (low number of SNPs and identical virulence gene profiles) suggestive of an international transmission event between Australia and the United Kingdom. This study supports the hypothesis that S. Wangata is shared between different hosts in NSW, Australia and provides strong justification for the continued use of genomic surveillance of Salmonella.
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Affiliation(s)
- Kelly M. J. Simpson
- School of Veterinary Science, Faculty of Science, University of Sydney, Camden and Camperdown, Sydney, New South Wales, Australia
- * E-mail:
| | - Siobhan M. Mor
- School of Veterinary Science, Faculty of Science, University of Sydney, Camden and Camperdown, Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, New South Wales, Australia
- Institute for Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Michael P. Ward
- School of Veterinary Science, Faculty of Science, University of Sydney, Camden and Camperdown, Sydney, New South Wales, Australia
| | - Julie Collins
- Hunter New England Population Health, Wallsend, New South Wales, Australia
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, ACT, Australia
| | - James Flint
- Hunter New England Population Health, Wallsend, New South Wales, Australia
| | - Grant A. Hill-Cawthorne
- Westmead Institute for Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, New South Wales, Australia
- School of Public Health, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Moataz Abd El Ghany
- Westmead Institute for Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead, New South Wales, Australia
- Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
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31
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International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda. PLoS One 2020; 15:e0220484. [PMID: 31990938 PMCID: PMC6986767 DOI: 10.1371/journal.pone.0220484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
The growing occurrence of multidrug-resistant (MDR) Salmonella enterica in poultry has been reported with public health concern worldwide. We reported, recently, the occurrence of Escherichia coli and Salmonella enterica serovars carrying clinically relevant resistance genes in dairy cattle farms in the Wakiso District, Uganda, highlighting an urgent need to monitor food-producing animal environments. Here, we present the prevalence, antimicrobial resistance, and sequence type of 51 Salmonella isolates recovered from 379 environmental samples from chicken farms in Uganda. Among the Salmonella isolates, 32/51 (62.7%) were resistant to at least one antimicrobial, and 10/51 (19.6%) displayed multiple drug resistance. Through PCR, five replicon plasmids were identified among chicken Salmonella isolates including IncFIIS 17/51 (33.3%), IncI1α 12/51 (23.5%), IncP 8/51 (15.7%), IncX1 8/51 (15.7%), and IncX2 1/51 (2.0%). In addition, we identified two additional replicons through WGS (Whole Genome Sequencing; ColpVC and IncFIB). A significant seasonal difference between chicken sampling periods was observed (p = 0.0017). We conclude that MDR Salmonella highlights the risks posed to animals and humans. Implementing a robust, integrated surveillance system will aid in monitoring MDR zoonotic threats.
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Moreno-Switt AI, Pezoa D, Sepúlveda V, González I, Rivera D, Retamal P, Navarrete P, Reyes-Jara A, Toro M. Transduction as a Potential Dissemination Mechanism of a Clonal qnrB19-Carrying Plasmid Isolated From Salmonella of Multiple Serotypes and Isolation Sources. Front Microbiol 2019; 10:2503. [PMID: 31787939 PMCID: PMC6854032 DOI: 10.3389/fmicb.2019.02503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/17/2019] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial resistance is an increasing problem worldwide, and Salmonella spp. resistance to quinolone was classified by WHO in the high priority list. Recent studies in Europe and in the US reported the presence of small plasmids carrying quinolone resistance in Enterobacteriaceae isolated from poultry and poultry products. The aims of this study were to identify and characterize plasmid-mediated quinolone resistance in Salmonella spp. and to investigate transduction as a possible mechanism associated to its dissemination. First, we assessed resistance to nalidixic acid and/or ciprofloxacin in 64 Salmonella spp. and detected resistance in eight of them. Genomic analyses determined that six isolates of different serotypes and sources carried an identical 2.7-kb plasmid containing the gene qnrB19 which confers quinolone resistance. The plasmid detected also has high identity with plasmids reported in the US, Europe, and South America. The presence of similar plasmids was later surveyed by PCR in a local Salmonella collection (n = 113) obtained from diverse sources: food (eggs), wild and domestic animals (pigs, horse, chicken), and human clinical cases. qnrB19-carrying plasmids were found in 8/113 Salmonella tested strains. A bioinformatics analysis including Chilean and previously described plasmids revealed over 95.0% of nucleotide identity among all the sequences obtained in this study. Furthermore, we found that a qnrB19-carrying plasmid can be transferred between Salmonella of different serotypes through a P22-mediated transduction. Altogether our results demonstrate that plasmid-mediated quinolone resistance (PMQR) is widespread in Salmonella enterica of different serotypes isolated from human clinical samples, wild and domestic animals, and food in Chile and suggest that transduction could be a plausible mechanism for its dissemination. The occurrence of these antimicrobial resistance elements in Salmonella in a widespread area is of public health and food safety concern, and it indicates the need for increased surveillance for the presence of these plasmids in Salmonella strains and to assess their actual impact in the rise and spread of quinolone resistance.
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Affiliation(s)
- Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - David Pezoa
- Facultad de Ciencias, Escuela de Medicina Veterinaria, Universidad Mayor, Santiago, Chile
| | - Vanessa Sepúlveda
- Facultad de Ciencias, Escuela de Medicina Veterinaria, Universidad Mayor, Santiago, Chile
| | - Iván González
- Facultad de Ciencias, Escuela de Medicina Veterinaria, Universidad Mayor, Santiago, Chile
| | - Dácil Rivera
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Patricio Retamal
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Paola Navarrete
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Angélica Reyes-Jara
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Magaly Toro
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
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Prasertsee T, Chuammitri P, Deeudom M, Chokesajjawatee N, Santiyanont P, Tadee P, Nuangmek A, Tadee P, Sheppard SK, Pascoe B, Patchanee P. Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain. Int J Food Microbiol 2019; 304:68-74. [PMID: 31174037 DOI: 10.1016/j.ijfoodmicro.2019.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/02/2019] [Accepted: 05/25/2019] [Indexed: 02/02/2023]
Abstract
Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.
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Affiliation(s)
- Teerarat Prasertsee
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phongsakorn Chuammitri
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Manu Deeudom
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pannita Santiyanont
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pakpoom Tadee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Aniroot Nuangmek
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai 50290, Thailand
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom; Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom; Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand.
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34
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Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates. Appl Environ Microbiol 2019; 85:AEM.00139-19. [PMID: 30902850 DOI: 10.1128/aem.00139-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/07/2019] [Indexed: 12/17/2022] Open
Abstract
Municipal wastewater includes human waste that contains both commensal and pathogenic enteric microorganisms, and this collective community microbiome can be monitored for community diseases. In a previous study, we assessed the salmonellosis disease burden using municipal wastewater from Honolulu, Hawaii, which was monitored over a 54-week period. During that time, a strain of Salmonella enterica serovar Paratyphi B variant L(+) tartrate(+) (also known as Salmonella enterica serovar Paratyphi B variant Java) was identified; this strain was detected simultaneously with a clinically reported outbreak, and pulsed-field gel electrophoresis patterns were identical for clinical and municipal wastewater isolates. Months after the outbreak subsided, the same pulsotype was detected as the dominant pulsotype in municipal wastewater samples, with no corresponding clinical cases reported. Using genomic characterization (including core single-nucleotide polymorphism alignment, core genome multilocus sequence typing, and screening for virulence and antibiotic resistance genes), all S Java municipal wastewater isolates were determined to be clonal, indicating a resurgence of the original outbreak strain. This demonstrates the feasibility and utility of municipal wastewater surveillance for determining enteric disease outbreaks that may be missed by traditional clinical surveillance methods.IMPORTANCE Underdetection of microbial infectious disease outbreaks in human communities carries enormous health costs and is an ongoing problem in public health monitoring (which relies almost exclusively on data from health clinics). Surveillance of municipal wastewater for community-level monitoring of infectious disease burdens has the potential to fill this information gap, due to its easy access to the mixed community microbiome. In the present study, the genomes of 21 S Java isolates (collected from municipal wastewater in Honolulu) were analyzed; results showed that the same Salmonella strain that caused a known salmonellosis clinical outbreak in spring 2010 remerged as the most dominant strain in municipal wastewater in spring 2011, indicating a new outbreak that was not detected by health clinics. Our results show that wastewater monitoring holds great promise to inform the field of public health regarding outbreak status within communities.
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35
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Genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s. Genomics 2019; 112:528-544. [PMID: 30974149 DOI: 10.1016/j.ygeno.2019.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/22/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023]
Abstract
A total of 91 draft genome sequences were used to analyze isolates of Salmonella enterica serovar Enteritidis obtained from feral mice caught on poultry farms in Pennsylvania. One objective was to find mutations disrupting open reading frames (ORFs) and another was to determine if ORF-disruptive mutations were present in isolates obtained from other sources. A total of 83 mice were obtained between 1995-1998. Isolates separated into two genomic clades and 12 subgroups due to 742 mutations. Nineteen ORF-disruptive mutations were found, and in addition, bigA had exceptional heterogeneity requiring additional evaluation. The TRAMS algorithm detected only 6 ORF disruptions. The sefD mutation was the most frequently encountered mutation and it was prevalent in human, poultry, environmental and mouse isolates. These results confirm previous assessments of the mouse as a rich source of Salmonella enterica serovar Enteritidis that varies in genotype and phenotype.
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36
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Ball TA, Monte DF, Aidara-Kane A, Matheu-Alvarez J, Ru H, Thakur S, Horovitz J, Ejobi F, Lacher DW, Fedorka-Cray PJ. Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella enterica from Dairy Cattle Farms in the Wakiso District, Uganda: A Cross-Sectional Study. Foodborne Pathog Dis 2019; 16:54-59. [DOI: 10.1089/fpd.2018.2528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Takiyah A. Ball
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Daniel F. Monte
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Awa Aidara-Kane
- Department of Food Safety and Zoonoses, World Health Organization (WHO), Geneva, Switzerland
| | - Jorge Matheu-Alvarez
- Department of Food Safety and Zoonoses, World Health Organization (WHO), Geneva, Switzerland
| | - Hongyu Ru
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Joy Horovitz
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Francis Ejobi
- Department of Bio Security, Ecosystems, and Veterinary Public Health, College of Veterinary Medicine, Animal Resources & Biosecurity, Makerere University, Kampala, Uganda
| | - David W. Lacher
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Paula J. Fedorka-Cray
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
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37
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Closed Genome Sequence of Salmonella enterica Serovar Richmond Strain CFSAN000191, Obtained with Nanopore Sequencing. Microbiol Resour Announc 2018; 7:MRA01472-18. [PMID: 30574589 PMCID: PMC6298556 DOI: 10.1128/mra.01472-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
Here we report the genome sequence of Salmonella enterica serovar Richmond strain CFSAN000191, isolated from tilapia from Thailand in 2005. The genome was determined by a combination of long-read and short-read sequencing. Here we report the genome sequence of Salmonella enterica serovar Richmond strain CFSAN000191, isolated from tilapia from Thailand in 2005. The genome was determined by a combination of long-read and short-read sequencing. This strain was used for source tracking in a 2012 Salmonella enterica serovar Bareilly foodborne outbreak in the United States.
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38
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Toro M, Rivera D, Toledo V, Campos-Vargas R, Allard MW, Hamilton-West C, Moreno-Switt AI. Genomics of Salmonella contaminating backyard production systems reveals persistence and transmission of genetically related Salmonella on a farm basis. Zoonoses Public Health 2018; 65:1008-1014. [PMID: 30264433 DOI: 10.1111/zph.12526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/10/2018] [Accepted: 09/03/2018] [Indexed: 11/29/2022]
Abstract
Animals raised in backyard productive systems (BPS) have been frequently associated with Salmonella outbreaks. Several serovars have caused these events, showing that different BPSs can be contaminated by distinct Salmonella serovars. The aim of this study was to characterize the genomic diversity of Salmonella isolates obtained from BPSs in Central Chile to understand their genomic relatedness. A whole-genome SNP-based phylogenetic analysis of 22 Salmonella isolates from 12 locations revealed that S. Typhimurium isolates clustered based on the BPS that they were originally isolated from, and the same was established for S. Enteritidis isolates. Furthermore, our genomic analysis shows that animals from different species (i.e., a chicken, a duck and a pig) carried genetically related S. Typhimurium strains within the same BPS. Moreover, some of these genetically related isolates were obtained in different years (2013 and 2014), indicating that farm-specific Salmonella can persist in BPSs for multiple years and that interspecies transmission is plausible in this environment. Understanding the dynamics of interspecies transmission of Salmonella serovars within a contaminated BPS is fundamental to the design of mitigation strategies to reduce outbreaks of human Salmonella associated with backyard production systems.
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Affiliation(s)
- Magaly Toro
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dácil Rivera
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Viviana Toledo
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Reinaldo Campos-Vargas
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Marc W Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland
| | - Christopher Hamilton-West
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Nucleus on Interdisciplinary Approach to Antimicrobial Resistance, Santiago, Chile
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39
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Campioni F, Cao G, Kastanis G, Janies DA, Bergamini AMM, Rodrigues DDP, Stones R, Brown E, Allard MW, Falcão JP. Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses. Sci Rep 2018; 8:10478. [PMID: 29993044 PMCID: PMC6041339 DOI: 10.1038/s41598-018-28844-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
Salmonella Enteritidis became the main serovar isolated from gastroenteritis cases in Brazil after the 90's. In this study we used whole genome sequence analysis to determine the phylogenetic relationships among a collection of strains isolated in Brazil to identify possible genomic differences between the strains isolated in the pre and post-epidemic period. Also, we compared our data from strains isolated in Brazil to strains available in the public domain from other South American countries. Illumina technology was used to sequence the genome of 256 Salmonella Enteritidis strains isolated over a 48 year-period in Brazil, comprising the pre- and post-epidemic period. Phylogenetic analyses revealed distinct lineages for strains isolated before and after 1994. Moreover, the phage region SE20 that may be related to the emergence of Salmonella Enteritidis worldwide was present only in strains of the post-epidemic cluster. In conclusion, our results showed that the genomic profile of Salmonella Enteritidis strains isolated in Brazil shifted after 1994, replaced by a global epidemic group of strains. It may be hypothesized that the presence of the prophage SE20 might have conferred to these strains a better ability to colonize chicken and consequently to infect and cause disease in humans, which might better explain the increase in the number of S. Enteritidis cases in Brazil and other South American countries. However, to verify this hypothesis further studies are needed.
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Affiliation(s)
- Fábio Campioni
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/n°, Ribeirão Preto, SP, Brazil
| | - Guojie Cao
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - George Kastanis
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | | | - Dália Dos Prazeres Rodrigues
- Laboratório de Enterobactérias, FIOCRUZ/Fundação Instituto Oswaldo Cruz, Avenida Brasil, 4365, Pavilhão Rocha Lima, 3°andar, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Robert Stones
- Newcastle University, Newcastle upon Tyne, Newcastle, United Kingdom
| | - Eric Brown
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc W Allard
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA.
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/n°, Ribeirão Preto, SP, Brazil.
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40
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Cuypers WL, Jacobs J, Wong V, Klemm EJ, Deborggraeve S, Van Puyvelde S. Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Microb Genom 2018; 4. [PMID: 29975627 PMCID: PMC6113872 DOI: 10.1099/mgen.0.000195] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.
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Affiliation(s)
- Wim L Cuypers
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,2Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
| | - Jan Jacobs
- 3Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,4Department of Microbiology and Immunology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Vanessa Wong
- 5Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,6Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Stijn Deborggraeve
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Sandra Van Puyvelde
- 6Wellcome Trust Sanger Institute, Hinxton, UK.,1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
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41
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Carter L, Chase HR, Gieseker CM, Hasbrouck NR, Stine CB, Khan A, Ewing-Peeples LJ, Tall BD, Gopinath GR. Analysis of enterotoxigenic Bacillus cereus strains from dried foods using whole genome sequencing, multi-locus sequence analysis and toxin gene prevalence and distribution using endpoint PCR analysis. Int J Food Microbiol 2018; 284:31-39. [PMID: 29990637 DOI: 10.1016/j.ijfoodmicro.2018.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 06/08/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022]
Abstract
Bacillus cereus strains were isolated from dried foods, which included international brands of spices from South East Asia, Mexico and India purchased from several retail stores, samples of powdered infant formula (PIF), medicated fish feed and dietary supplements. The genetic diversity of 64 strains from spices and PIF was determined using a multiplex endpoint PCR assay designed to identify hemolysin BL, nonhemolytic enterotoxin, cytotoxin K, and enterotoxin FM toxin genes. Thirteen different B. cereus toxigenic gene patterns or profiles were identified among the strains. Randomly selected B. cereus strains were sequenced and compared with reference Genomic Groups from National Center Biotechnology Information using bioinformatics tools. A comprehensive multi-loci sequence analysis (MLSA) was designed using alleles from 25 known MLST genes specifically tailored for use with whole genome assemblies. A cohort of representative genomes of strains from a few FDA regulated commodities like dry foods and medicated fish feed was used to demonstrate the utility of the 25-MLSA approach for rapid clustering and identification of Genome Groups. The analysis clustered the strains from medicated fish feed, dry foods, and dietary supplements into phylogenetically-related groups. 25-MLSA also pointed to a greater diversity of B. cereus strains from foods and feed than previously recognized. Our integrated approach of toxin gene PCR, and to our knowledge, whole genome sequencing (WGS) based sequence analysis, may be the first of its kind that demonstrates enterotoxigenic potential and genomic diversity in parallel.
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Affiliation(s)
- Laurenda Carter
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA.
| | - Hannah R Chase
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
| | - Charles M Gieseker
- U. S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Nicholas R Hasbrouck
- U. S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Cynthia B Stine
- U. S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Ashraf Khan
- Division of Microbiology, National Center for Toxicological Research, Jefferson, AR 72079, USA
| | - Laura J Ewing-Peeples
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
| | - Ben D Tall
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
| | - Gopal R Gopinath
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
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Alm EW, Daniels-Witt QR, Learman DR, Ryu H, Jordan DW, Gehring TM, Santo Domingo J. Potential for gulls to transport bacteria from human waste sites to beaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:123-130. [PMID: 28964987 PMCID: PMC6754825 DOI: 10.1016/j.scitotenv.2017.09.232] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 05/30/2023]
Abstract
Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape.
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Affiliation(s)
- Elizabeth W Alm
- Department of Biology & Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, United States.
| | - Quri R Daniels-Witt
- Department of Biology & Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Deric R Learman
- Department of Biology & Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Hodon Ryu
- U.S. Environmental Protection Agency, Office of Research and Development, Water Supply Water Resources Division, Cincinnati, OH 45268, United States
| | - Dustin W Jordan
- Department of Biology & Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Thomas M Gehring
- Department of Biology & Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Jorge Santo Domingo
- U.S. Environmental Protection Agency, Office of Research and Development, Water Supply Water Resources Division, Cincinnati, OH 45268, United States
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Wang H, Hoffmann M, Laasri A, Jacobson AP, Melka D, Curry PE, Hammack TS, Zheng J. Complete Genome Sequence of Salmonella enterica subsp. enterica serovar Minnesota Strain. Genome Biol Evol 2017. [PMCID: PMC5647791 DOI: 10.1093/gbe/evx209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mango has been implicated as food vehicle in several Salmonella-causing foodborne outbreaks. Here, Salmonella enterica subsp. enterica serovar Minnesota was isolated from fresh mango fruit imported from Mexico in 2014. The complete genome sequence of S. Minnesota CFSAN017963 was sequenced using single-molecule real-time DNA sequencing. Distinct prophage regions, Salmonella pathogenicity islands, and fimbrial gene clusters were observed in comparative genomic analysis on S. Minnesota CFSAN017963 with other phylogenetically closely related Salmonella serovars. Core genome multilocus sequencing typing analysis of all the S. Minnesota isolates in the Genbank and Enterobase also revealed a high genomic diversity among the genomes analyzed.
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Affiliation(s)
- Hua Wang
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
- Corresponding author: E-mail: .
| | - Maria Hoffmann
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Anna Laasri
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Andrew P. Jacobson
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - David Melka
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Phillip E. Curry
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Thomas S. Hammack
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Jie Zheng
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland
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Li J, Hao H, Cheng G, Wang X, Ahmed S, Shabbir MAB, Liu Z, Dai M, Yuan Z. The effects of different enrofloxacin dosages on clinical efficacy and resistance development in chickens experimentally infected with Salmonella Typhimurium. Sci Rep 2017; 7:11676. [PMID: 28916830 PMCID: PMC5601478 DOI: 10.1038/s41598-017-12294-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/07/2017] [Indexed: 12/05/2022] Open
Abstract
To investigate the optimal dosage which can improve clinical efficacy and minimize resistance, pharmacokinetics/pharmacodynamics model of enrofloxacin was established. Effect of enrofloxacin treatments on clearance of Salmonella in experimentally infected chickens and simultaneously resistance selection in Salmonella and coliforms were evaluated in three treatment groups (100, PK/PD designed dosage of 4, 0.1 mg/kg b.w.) and a control group. Treatment duration was three rounds of 7-day treatment alternated with 7-day withdrawal. Results showed that 100 mg/kg b.w. of enrofloxacin completely eradicated Salmonella, but resistant coliforms (4.0-60.8%) were selected from the end of the second round's withdrawal period till the end of the experiment (days 28-42). PK/PD based dosage (4 mg/kg b.w.) effectively reduced Salmonella for the first treatment duration. However upon cessation of medication, Salmonella repopulated chickens and persisted till the end with reduced susceptibility (MICCIP = 0.03-0.25 mg/L). Low frequency (5-9.5%) of resistant coliforms was selected (days 39-42). Enrofloxacin at dosage of 0.1 mg/kg b.w. was not able to eliminate Salmonella and selected coliforms with slight decreased susceptibility (MICENR = 0.25 mg/L). In conclusion, short time treatment (7 days) of enrofloxacin at high dosage (100 mg/kg b.w.) could be effective in treating Salmonella infection while minimizing resistance selection in both Salmonella and coliforms.
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Affiliation(s)
- Jun Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China.
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Xu Wang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China
| | - Saeed Ahmed
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China
| | - Muhammad Abu Bakr Shabbir
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China
| | - Zhenli Liu
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Menghong Dai
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China.
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, China.
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Browne HP, Neville BA, Forster SC, Lawley TD. Transmission of the gut microbiota: spreading of health. Nat Rev Microbiol 2017; 15:531-543. [PMID: 28603278 PMCID: PMC5837012 DOI: 10.1038/nrmicro.2017.50] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transmission of commensal intestinal bacteria between humans could promote health by establishing, maintaining and replenishing microbial diversity in the microbiota of an individual. Unlike pathogens, the routes of transmission for commensal bacteria remain unappreciated and poorly understood, despite the likely commonalities between both. Consequently, broad infection control measures that are designed to prevent pathogen transmission and infection, such as oversanitation and the overuse of antibiotics, may inadvertently affect human health by altering normal commensal transmission. In this Review, we discuss the mechanisms and factors that influence host-to-host transmission of the intestinal microbiota and examine how a better understanding of these processes will identify new approaches to nurture and restore transmission routes that are used by beneficial bacteria.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - B Anne Neville
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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Lorenz SC, Gonzalez-Escalona N, Kotewicz ML, Fischer M, Kase JA. Genome sequencing and comparative genomics of enterohemorrhagic Escherichia coli O145:H25 and O145:H28 reveal distinct evolutionary paths and marked variations in traits associated with virulence & colonization. BMC Microbiol 2017; 17:183. [PMID: 28830351 PMCID: PMC5567499 DOI: 10.1186/s12866-017-1094-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/14/2017] [Indexed: 12/14/2022] Open
Abstract
Background Enterohemorrhagic Escherichia coli (EHEC) O145 are among the top non-O157 serogroups associated with severe human disease worldwide. Two serotypes, O145:H25 and O145:H28 have been isolated from human patients but little information is available regarding the virulence repertoire, origin and evolutionary relatedness of O145:H25. Hence, we sequenced the complete genome of two O145:H25 strains associated with hemolytic uremic syndrome (HUS) and compared the genomes with those of previously sequenced O145:H28 and other EHEC strains. Results The genomes of the two O145:H25 strains were 5.3 Mbp in size; slightly smaller than those of O145:H28 and other EHEC strains. Both strains contained three nearly identical plasmids and several prophages and integrative elements, many of which differed significantly in size, gene content and organization as compared to those present in O145:H28 and other EHECs. Furthermore, notable variations were observed in several fimbrial gene cluster and intimin types possessed by O145:H25 and O145:H28 indicating potential adaptation to distinct areas of host colonization. Comparative genomics further revealed that O145:H25 are genetically more similar to other non-O157 EHEC strains than to O145:H28. Conclusion Phylogenetic analysis accompanied by comparative genomics revealed that O145:H25 and O145:H28 evolved from two separate clonal lineages and that horizontal gene transfer and gene loss played a major role in the divergence of these EHEC serotypes. The data provide further evidence that ruminants might be a possible reservoir for O145:H25 but that they might be impaired in their ability to establish a persistent colonization as compared to other EHEC strains. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1094-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra C Lorenz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, MD, 20740, USA. .,University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, 20146, Hamburg, Germany.
| | - Narjol Gonzalez-Escalona
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, MD, 20740, USA
| | - Michael L Kotewicz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Molecular Biology, Laurel, MD, 20708, USA
| | - Markus Fischer
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, 20146, Hamburg, Germany
| | - Julie A Kase
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, MD, 20740, USA
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Retamal P, Llanos-Soto S, Salas LM, López J, Vianna J, Hernández J, Medina-Vogel G, Castañeda F, Fresno M, González-Acuña D. Isolation of drug-resistant Salmonella enterica serovar enteritidis strains in gentoo penguins from Antarctica. Polar Biol 2017. [DOI: 10.1007/s00300-017-2163-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wang S, Weller D, Falardeau J, Strawn LK, Mardones FO, Adell AD, Moreno Switt AI. Food safety trends: From globalization of whole genome sequencing to application of new tools to prevent foodborne diseases. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.09.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy. J Clin Microbiol 2016; 54:2850-2853. [PMID: 27629902 DOI: 10.1128/jcm.01714-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant bacteria are responsible for substantial morbidity and mortality worldwide. Tracking the nosocomial spread of resistant bacteria is critical to infection control. Mellmann et al. (J. Clin. Microbiol. 54:2874-2881, 2016, http://dx.doi.org/10.1128/JCM.00790-16) have described prospective whole-genome sequencing with core genome multilocus sequencing typing (cgMLST) analysis for real-time surveillance and have addressed the practical aspects of implementing this type of operation in the hospital setting.
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