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Toyting J, Nuanmuang N, Utrarachkij F, Supha N, Thongpanich Y, Leekitcharoenphon P, Aarestrup FM, Sato T, Thapa J, Nakajima C, Suzuki Y. Genomic analysis of Salmonella isolated from canal water in Bangkok, Thailand. Microbiol Spectr 2024; 12:e0421623. [PMID: 38563788 DOI: 10.1128/spectrum.04216-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria, Salmonella enterica, isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was Salmonella Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including mcr-3.1, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine S. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of S. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.IMPORTANCEBangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant Salmonella is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of Salmonella strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant Salmonella and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of S. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.
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Affiliation(s)
- Jirachaya Toyting
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Narong Nuanmuang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Fuangfa Utrarachkij
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Neunghatai Supha
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Yuwanda Thongpanich
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Toyotaka Sato
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
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Chen Z, Toro M, Moreno-Switt AI, Adell AD, Delgado-Suárez EJ, Bonelli RR, Oliveira CJB, Reyes-Jara A, Huang X, Albee B, Grim CJ, Allard M, Tallent SM, Brown EW, Bell RL, Meng J. Unveiling the genomic landscape of Salmonella enterica serotypes Typhimurium, Newport, and Infantis in Latin American surface waters: a comparative analysis. Microbiol Spectr 2024; 12:e0004724. [PMID: 38546218 DOI: 10.1128/spectrum.00047-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/06/2024] [Indexed: 05/03/2024] Open
Abstract
Surface waters are considered ecological habitats where Salmonella enterica can persist and disseminate to fresh produce production systems. This study aimed to explore the genomic profiles of S. enterica serotypes Typhimurium, Newport, and Infantis from surface waters in Chile, Mexico, and Brazil collected between 2019 and 2022. We analyzed the whole genomes of 106 S. Typhimurium, 161 S. Newport, and 113 S. Infantis isolates. Our phylogenetic analysis exhibited distinct groupings of isolates by their respective countries except for a notable case involving a Chilean S. Newport isolate closely related to two Mexican isolates, showing 4 and 13 single nucleotide polymorphisms of difference, respectively. The patterns of the most frequently detected antimicrobial resistance genes varied across countries and serotypes. A strong correlation existed between integron carriage and genotypic multidrug resistance (MDR) across serotypes in Chile and Mexico (R > 0.90, P < 0.01), while integron(s) were not detected in any of the Brazilian isolates. By contrast, we did not identify any strong correlation between plasmid carriage and genotypic MDR across diverse countries and serotypes.IMPORTANCEUnveiling the genomic landscape of S. enterica in Latin American surface waters is pivotal for ensuring public health. This investigation sheds light on the intricate genomic diversity of S. enterica in surface waters across Chile, Mexico, and Brazil. Our research also addresses critical knowledge gaps, pioneering a comprehensive understanding of surface waters as a reservoir for multidrug-resistant S. enterica. By integrating our understanding of integron carriage as biomarkers into broader MDR control strategies, we can also work toward targeted interventions that mitigate the emergence and dissemination of MDR in S. enterica in surface waters. Given its potential implications for food safety, this study emphasizes the critical need for informed policies and collaborative initiatives to address the risks associated with S. enterica in surface waters.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Magaly Toro
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aiko D Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Facultad de Agronomía y Sistemas Naturales, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andrés Bello, Santiago, Chile
| | - Enrique J Delgado-Suárez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad de Nacional Autónoma de México, Mexico City, Mexico
| | - Raquel R Bonelli
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Celso J B Oliveira
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Brazil
| | - Angélica Reyes-Jara
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Xinyang Huang
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Brett Albee
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Christopher J Grim
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Sandra M Tallent
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca L Bell
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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3
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Afreen S, Ray P, Muthuvel R, Agarwal A, Angrup A. Salmonella enterica serovar Give causing brain abscess and bacteremia: A case report. Indian J Med Microbiol 2024; 48:100526. [PMID: 38176586 DOI: 10.1016/j.ijmmb.2024.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024]
Abstract
Non-typhoidal Salmonellosis are an important cause of gastroenteritis and invasive disease in developing countries, with increase resistance and mortality in paediatric age group. We report here, a rare case of bacteremia and brain abscess in a 3year old female child with Salmonella enterica serovar Give as a causative organism.
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Affiliation(s)
- Sana Afreen
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
| | - Pallab Ray
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
| | - R Muthuvel
- Dept of Pediatrics, PGIMER, Chandigassrh, India.
| | | | - Archana Angrup
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
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Woh PY, Yeung MPS, Goggins WB, Lo N, Wong KT, Chow V, Chau KY, Fung K, Chen Z, Ip M. Genomic Epidemiology of Multidrug-Resistant Nontyphoidal Salmonella in Young Children Hospitalized for Gastroenteritis. Microbiol Spectr 2021; 9:e0024821. [PMID: 34346743 PMCID: PMC8552638 DOI: 10.1128/spectrum.00248-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 01/21/2023] Open
Abstract
Nontyphoidal Salmonella (NTS) gastroenteritis in children remains a significant burden on health care and constitutes a majority of all admissions for Salmonella infections in public hospitals in Hong Kong. In this prospective study, 41% of 241 children hospitalized with gastroenteritis from three public hospitals during 2019 were culture confirmed to have NTS infection. These Salmonella isolates were whole-genome sequenced and in silico predicted for their serovars/serotypes using the Salmonella In Silico Typing Resource (SISTR) and SeqSero1, and the antimicrobial resistance (AMR) genes were determined. Phylogenetic analysis revealed three major clades belonging to Salmonella enterica serovar Enteritidis sequence type 11 (ST11) (43%), multidrug-resistant (MDR) S. Typhimurium ST19 (12%) and its monophasic variant ST34 (25%), and mostly singletons of 15 other serovars. MDR S. Typhimurium and its variant were more common in infants <24 months of age and possessed genotypic resistance to five antimicrobial agents, including ampicillin (A), chloramphenicol (C), aminoglycosides (Am), sulfonamides (Su), and tetracyclines (T). Older children were more often infected with S. Enteritidis, which possessed distinct genotypic resistance to AAmSu and fluoroquinolones. In addition, 3% of the isolates possessed extended-spectrum beta-lactamase (ESBL) CTX-M genes, while one isolate (1%) harboring the carbapenemase gene blaNDM-1 was identified. Our findings provide a more complete genomic epidemiological insight into NTS causing gastroenteritis and identify a wider spectrum of determinants of resistance to third-generation beta-lactams and carbapenems, which are often not readily recognized. With high rates of multidrug-resistant NTS from studies in the Asia-Pacific region, the rapid and reliable determination of serovars and resistance determinants using whole-genome sequencing (WGS) is invaluable for enhancing public health interventions for infection prevention and control. IMPORTANCE Nontyphoidal Salmonella (NTS) gastroenteritis is a foodborne disease with a large global burden. Antimicrobial resistance (AMR) among foodborne pathogens is an important public health concern, and multidrug-resistant (MDR) Salmonella is prevalent in Southeast Asia and China. Using whole-genome sequencing, this study highlights the relationship of the MDR Salmonella serotypes and the diverse range of Salmonella genotypes that contaminate our food sources and contribute to disease in this locality. The findings update our understanding of Salmonella epidemiology and associated MDR determinants to enhance the tracking of foodborne pathogens for public health and food safety.
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Affiliation(s)
- Pei Yee Woh
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - May Pui Shan Yeung
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - William Bernard Goggins
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Norman Lo
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region
| | - Kam Tak Wong
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region
| | - Viola Chow
- Department of Pathology, Alice Ho Miu Ling Nethersole Hospital, Tai Po, Hong Kong Special Administrative Region
| | - Ka Yee Chau
- Department of Pathology, United Christian Hospital, Kowloon, Hong Kong Special Administrative Region
| | - Kitty Fung
- Department of Pathology, United Christian Hospital, Kowloon, Hong Kong Special Administrative Region
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong Special Administrative Region
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5
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Vaid RK, Thakur Z, Anand T, Kumar S, Tripathi BN. Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes. PLoS One 2021; 16:e0255612. [PMID: 34411120 PMCID: PMC8375982 DOI: 10.1371/journal.pone.0255612] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.
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Affiliation(s)
- Rajesh Kumar Vaid
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Zoozeal Thakur
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Taruna Anand
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Sanjay Kumar
- Bacteriology Laboratory, ICAR-National Research Centre on Equines, Hisar, Haryana, India
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Ingle DJ, Ambrose RL, Baines SL, Duchene S, Gonçalves da Silva A, Lee DYJ, Jones M, Valcanis M, Taiaroa G, Ballard SA, Kirk MD, Howden BP, Pearson JS, Williamson DA. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia. Nat Commun 2021; 12:4786. [PMID: 34373455 PMCID: PMC8352879 DOI: 10.1038/s41467-021-25073-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
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Affiliation(s)
- Danielle J Ingle
- Research School of Population Health, Australian National University, Canberra, ACT, Australia.
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Rebecca L Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Darren Y J Lee
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miriam Jones
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martyn D Kirk
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia.
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Shariat NW, Timme RE, Walters AT. Phylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability. Microb Genom 2021; 7. [PMID: 33539276 PMCID: PMC8208698 DOI: 10.1099/mgen.0.000522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Salmonella enterica subspecies arizonae is frequently associated with animal reservoirs, particularly reptiles, and can cause illness in some mammals, including humans. Using whole-genome sequencing data, core genome phylogenetic analyses were performed using 112 S. enterica subsp. arizonae isolates, representing 46 of 102 described serovars. Nearly one-third of these are polyphyletic, including two serovars that appear in four and five distinct evolutionary lineages. Subspecies arizonae has a monophasic H antigen. Among the 46 serovars investigated, only 8 phase 1 H antigens were identified, demonstrating high conservation for this antigen. Prophages and plasmids were found throughout this subspecies, including five novel prophages. Polyphyly was also reflected in prophage content, although some clade-specific enrichment for some phages was observed. IncFII(S) was the most frequent plasmid replicon identified and was found in a quarter of S. enterica subsp. arizonae genomes. Salmonella pathogenicity islands (SPIs) 1 and 2 are present across all Salmonella, including this subspecies, although effectors sipA, sptP and arvA in SPI-1 and sseG and ssaI in SPI-2 appear to be lost in this lineage. SPI-20, encoding a type VI secretion system, is exclusive to this subspecies and is well maintained in all genomes sampled. A number of fimbral operons were identified, including the sas operon that appears to be a synapomorphy for this subspecies, while others exhibited more clade-specific patterns. This work reveals evolutionary patterns in S. enterica subsp. arizonae that make this subspecies a unique lineage within this very diverse species.
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Affiliation(s)
- Nikki W. Shariat
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
- *Correspondence: Nikki W. Shariat,
| | - Ruth E. Timme
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Abigail T. Walters
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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Sakoparnig T, Field C, van Nimwegen E. Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife 2021; 10:e65366. [PMID: 33416498 PMCID: PMC7884076 DOI: 10.7554/elife.65366] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/07/2021] [Indexed: 12/26/2022] Open
Abstract
Although recombination is accepted to be common in bacteria, for many species robust phylogenies with well-resolved branches can be reconstructed from whole genome alignments of strains, and these are generally interpreted to reflect clonal relationships. Using new methods based on the statistics of single-nucleotide polymorphism (SNP) splits, we show that this interpretation is incorrect. For many species, each locus has recombined many times along its line of descent, and instead of many loci supporting a common phylogeny, the phylogeny changes many thousands of times along the genome alignment. Analysis of the patterns of allele sharing among strains shows that bacterial populations cannot be approximated as either clonal or freely recombining but are structured such that recombination rates between lineages vary over several orders of magnitude, with a unique pattern of rates for each lineage. Thus, rather than reflecting clonal ancestry, whole genome phylogenies reflect distributions of recombination rates.
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Affiliation(s)
- Thomas Sakoparnig
- Biozentrum, University of Basel, and Swiss Institute of BioinformaticsBaselSwitzerland
| | - Chris Field
- Biozentrum, University of Basel, and Swiss Institute of BioinformaticsBaselSwitzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel, and Swiss Institute of BioinformaticsBaselSwitzerland
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9
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Cuenca-Arias P, Montaño LA, Villarreal JM, Wiesner M. Molecular and phenotypic characterization of Salmonella Typhimurium monophasic variant (1,4,[5],12:i:-) from Colombian clinical isolates. Biomedica 2020; 40:722-733. [PMID: 33275350 PMCID: PMC7808771 DOI: 10.7705/biomedica.5417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/29/2020] [Indexed: 12/04/2022]
Abstract
Introduction. The Salmonella Typhimurium monophasic variant (1,4,[5],12:i:-) is currently the most commonly detected variant in Salmonella surveillance programs worldwide. In Colombia, the Salmonella enterica monophasic variant is the fourth most common clinical isolate recovered through the laboratory surveillance of the Grupo de Microbiología from the Instituto Nacional de Salud; however, it is unknown whether these isolates are closely related to the monophasic Typhimurium variant, which circulates globally, and their genetic and phenotypic characteristics have not been reported. Objective. To characterize monophasic Salmonella enterica isolates identified in Colombia from 2015 to 2018 by the Instituto Nacional de Salud. Materials and methods. Two hundred eighty-six clinical isolates of the monophasic Salmonella enterica variant were analyzed by PCR or whole-genome sequencing to confirm whether they corresponded to the Salmonella Typhimurium monophasic variant while the genetic structure of the operon encoding the second flagellar phase was determined in 54 isolates. Motility, growth, and expression of the outer membrane proteins were evaluated in 23 isolates. Results. During the study period in Colombia, 61% (n=174) of Salmonella monophasic isolates belonged to Salmonella Typhimurium serovar monophasic (1,4,[5],12:i-). Of these, 64.8% (n=35/54) were related to the European/Spanish clone and 13% (n=7/54) to the U.S. clone. Two isolates recovered from urine samples showed differences in motility, growth, and the absence of the OmpD porin in M9 minimal medium. Conclusions. Most of the monophasic Salmonella Typhimurium variants that have circulated in Colombia since 2015 lacked the second phase of operon fljAB, which is related to the European/Spanish clone. The results evidenced phenotypic changes in urine samples suggesting bacterial adaptation in the case of these invasive samples.
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Affiliation(s)
- Paloma Cuenca-Arias
- Grupo de Microbiología, Subdirección de Investigación Científica y Tecnológica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia.
| | - Lucy Angeline Montaño
- Grupo de Microbiología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, D. C., Colombia.
| | - José Miguel Villarreal
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, D. C., Colombia; Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá, D. C., Colombia.
| | - Magdalena Wiesner
- Grupo de Microbiología, Subdirección de Investigación Científica y Tecnológica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., Colombia.
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10
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AKINOLA STEPHENABIOLA, TSHIMPAMBA MPINDAEDOAURD, MWANZA MULUNDA, ATEBA COLLINSNJIE. Biofilm Production Potential of Salmonella Serovars Isolated from Chickens in North West Province, South Africa. Pol J Microbiol 2020; 69:427-439. [PMID: 33574871 PMCID: PMC7812364 DOI: 10.33073/pjm-2020-046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 11/05/2022] Open
Abstract
Bacterial biofilms have recently gained considerable interest in the food production and medical industries due to their ability to resist destruction by disinfectants and other antimicrobials. Biofilms are extracellular polymer matrices that may enhance the survival of pathogens even when exposed to environmental stress. The effect of incubation temperatures (25°C, 37°C, and 40°C) and Salmonella serotype on biofilm-forming potentials was evaluated. Previously typed Salmonella serotypes (55) isolated from the gut of chickens were accessed for biofilms formation using a standard assay. Salmonella Typhimurium ATCC 14028TM and Salmonella Enteritidis ATCC 13076TM (positive controls), Escherichia coli (internal control) and un-inoculated Luria Bertani (LB) broth (negative control) were used. The isolates formed no biofilm (11.86-13.56%), weak (11.86-45.76%), moderate (18.64-20.34%), strong biofilms (23.73-54.24%) across the various temperatures investigated. Serotypes, Salmonella Heidelberg and Salmonella Weltevreden were the strongest biofilm formers at temperatures (25°C, 37°C, and 40°C, respectively). The potential of a large proportion (80%) of Salmonella serotypes to form biofilms increased with increasing incubation temperatures but decreased at 40°C. Findings indicate that average temperature favours biofilm formation by Salmonella serotypes. However, the influence of incubation temperature on biofilm formation was greater when compared to serotype. A positive correlation exists between Salmonella biofilm formed at 25°C, 37°C and 40°C (p ≥ 0.01). The ability of Salmonella species to form biofilms at 25°C and 37°C suggests that these serotypes may present severe challenges to food-processing and hospital facilities.
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Affiliation(s)
- STEPHEN ABIOLA AKINOLA
- Department of Microbiology, Bacteriophage Therapy and Phage Bio-Control Laboratory, Faculty of Natural and Agricultural Sciences, North West University, Mmabatho, South Africa
- Phytochemical Food Network Research Group, Department of Crop Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - MPINDA EDOAURD TSHIMPAMBA
- Center for Animal Health Studies, Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North West University, Mmabatho, South Africa
| | - MULUNDA MWANZA
- Center for Animal Health Studies, Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North West University, Mmabatho, South Africa
| | - COLLINS NJIE ATEBA
- Department of Microbiology, Bacteriophage Therapy and Phage Bio-Control Laboratory, Faculty of Natural and Agricultural Sciences, North West University, Mmabatho, South Africa
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11
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Townsend A, Li S, Mann DA, Deng X. A quasimetagenomics method for concerted detection and subtyping of Salmonella enterica and E. coli O157:H7 from romaine lettuce. Food Microbiol 2020; 92:103575. [PMID: 32950159 DOI: 10.1016/j.fm.2020.103575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/25/2020] [Accepted: 06/16/2020] [Indexed: 11/29/2022]
Abstract
Quasimetagenomics refers to the sequencing of a modified food microbiome to facilitate combined detection and subtyping of targeted pathogens in a single workflow. Through quasimetagenomic sequencing, pathogens are detected and subtyped in a shortened time frame compared to traditional culture enrichment and whole genome sequencing-based analyses. While this method was previously used to detect and subtype Salmonella enterica from chicken, iceberg lettuce, and black pepper, it has not been applied to investigate multiple pathogens in one workflow. A quasimetagenomic method to concertedly detect and subtype Salmonella enterica and Escherichia coli O157:H7 from artificially contaminated romaine lettuce in a single workflow was developed. All quasimetagenomic samples with initial target pathogen inoculum levels of ~1 CFU/g were detected and serotyped after co-enrichment of the two pathogens for 12 h. Single nucleotide polymorphism typing was achievable for some initial pathogen inoculum levels as low as ~0.1 CFU/g. Our results suggest that this method can be used for concerted detection and subtyping of multiple bacterial pathogens from romaine lettuce even at low contamination levels.
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Affiliation(s)
- Anna Townsend
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, 1109 Experiment St, Griffin, GA, 30223, USA
| | - Shaoting Li
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, 1109 Experiment St, Griffin, GA, 30223, USA
| | - David A Mann
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, 1109 Experiment St, Griffin, GA, 30223, USA
| | - Xiangyu Deng
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, 1109 Experiment St, Griffin, GA, 30223, USA.
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12
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Elnekave E, Hong SL, Lim S, Johnson TJ, Perez A, Alvarez J. Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA. Microb Genom 2020; 6:mgen000425. [PMID: 32845830 PMCID: PMC7643971 DOI: 10.1099/mgen.0.000425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/03/2020] [Indexed: 01/21/2023] Open
Abstract
Serotyping has traditionally been used for subtyping of non-typhoidal Salmonella (NTS) isolates. However, its discriminatory power is limited, which impairs its use for epidemiological investigations of source attribution. Whole-genome sequencing (WGS) analysis allows more accurate subtyping of strains. However, because of the relative newness and cost of routine WGS, large-scale studies involving NTS WGS are still rare. We aimed to revisit the big picture of subtyping NTS with a public health impact by using traditional serotyping (i.e. reaction between antisera and surface antigens) and comparing the results with those obtained using WGS. For this purpose, we analysed 18 282 sequences of isolates belonging to 37 serotypes with a public health impact that were recovered in the USA between 2006 and 2017 from multiple sources, and were available at the National Center for Biotechnology Information (NCBI). Phylogenetic trees were reconstructed for each serotype using the core genome for the identification of genetic subpopulations. We demonstrated that WGS-based subtyping allows better identification of sources potentially linked with human infection and emerging subpopulations, along with providing information on the risk of dissemination of plasmids and acquired antimicrobial resistance genes (AARGs). In addition, by reconstructing a phylogenetic tree with representative isolates from all serotypes (n=370), we demonstrated genetic variability within and between serotypes, which formed monophyletic, polyphyletic and paraphyletic clades. Moreover, we found (in the entire data set) an increased detection rate for AARGs linked to key antimicrobials (such as quinolones and extended-spectrum cephalosporins) over time. The outputs of this large-scale analysis reveal new insights into the genetic diversity within and between serotypes; the polyphyly and paraphyly of certain serotypes may suggest that the subtyping of NTS to serotypes may not be sufficient. Moreover, the results and the methods presented here, leading to differentiation between genetic subpopulations based on their potential risk to public health, as well as narrowing down the possible sources of these infections, may be used as a baseline for subtyping of future NTS infections and help efforts to mitigate and prevent infections in the USA and globally.
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Affiliation(s)
- Ehud Elnekave
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel
| | - Samuel L. Hong
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, University of Leuven, Leuven, Belgium
| | - Seunghyun Lim
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Bioinformatics and Computational Biology Program, University of Minnesota, Rochester, Minnesota, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Julio Alvarez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- VISAVET Health Surveillance Center, Universidad Complutense, Madrid, Spain
- Department of Animal Health, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
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13
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Zhao S, Li C, Hsu CH, Tyson GH, Strain E, Tate H, Tran TT, Abbott J, McDermott PF. Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals. Genes (Basel) 2020; 11:genes11091025. [PMID: 32883017 PMCID: PMC7564550 DOI: 10.3390/genes11091025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/02/2022] Open
Abstract
Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.
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14
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Kosznik-Kwaśnicka K, Ciemińska K, Grabski M, Grabowski Ł, Górniak M, Jurczak-Kurek A, Węgrzyn G, Węgrzyn A. Characteristics of a Series of Three Bacteriophages Infecting Salmonella enterica Strains. Int J Mol Sci 2020; 21:ijms21176152. [PMID: 32858954 PMCID: PMC7503781 DOI: 10.3390/ijms21176152] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 01/07/2023] Open
Abstract
Molecular and functional characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, infecting various Salmonella enterica serovars and strains is presented. All these phages were able to develop lytically while not forming prophages. Moreover, they were able to survive at pH 3. The phages revealed different host ranges within serovars and strains of S. enterica, different adsorption rates on host cells, and different lytic growth kinetics at various temperatures (in the range of 25 to 42 °C). They efficiently reduced the number of cells in the bacterial biofilm and decreased the biofilm mass. Whole genome sequences of these phages have been determined and analyzed, including their phylogenetic relationships. In conclusion, we have demonstrated detailed characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, which reveal favorable features in light of their potential use in phage therapy of humans and animals, as well as for food protection purposes.
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Affiliation(s)
- Katarzyna Kosznik-Kwaśnicka
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
| | - Karolina Ciemińska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (K.C.); (M.G.); (G.W.)
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (K.C.); (M.G.); (G.W.)
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Łukasz Grabowski
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
| | - Marcin Górniak
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (A.J.-K.)
| | - Agata Jurczak-Kurek
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (A.J.-K.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (K.C.); (M.G.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
- Correspondence: ; Tel.: +48-58-523-6024
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15
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Richards AK, Hopkins BA, Shariat NW. Conserved CRISPR arrays in Salmonella enterica serovar Infantis can serve as qPCR targets to detect Infantis in mixed serovar populations. Lett Appl Microbiol 2020; 71:138-145. [PMID: 32333808 DOI: 10.1111/lam.13296] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Abstract
Salmonellosis is a leading bacterial cause of foodborne illness, and numerous Salmonella enterica serovars have been responsible for foodborne outbreaks. In the United States outbreaks are often linked to poultry and poultry-related products. The prevalence of Salmonella serovar Infantis has been increasing in poultry processing facilities over the past few years and in 2018 was identified as the causative agent for a large multistate outbreak linked to raw chicken. CRISPR-typing is a subtyping approach based on PCR and the sequencing of two Salmonella loci, CRISPR1 and CRISPR2. CRISPR-typing was used to interrogate 138 recent (2018-2019) isolates and genomes of ser. Infantis. Results show that the CRISPR elements are remarkably conserved in this serovar. The most conserved spacers, and those also unique to ser. Infantis, were used as targets to develop a ser. Infantis-specific qPCR assay. This assay was able to detect ser. Infantis in mixed serovar cultures of Salmonella, down to 0·1% of the population, highlighting the utility of this molecular approach in improving surveillance sensitivity for this important food safety pathogen. SIGNIFICANCE AND IMPACT OF THE STUDY: The incidence of human salmonellosis cases caused by Salmonella enterica serovar Infantis (ser. Infantis) has been increasing, as has its prevalence in broiler chickens, which are a frequent reservoir of Salmonella. A cluster of ser. Infantis genetically linked to an outbreak strain have been identified in numerous processing facilities. A qPCR assay targeting CRISPR elements that are unique to ser. Infantis has been developed and can detect this serovar directly from mixed cultures. This assay is sensitive enough to reveal ser. Infantis within a mixed Salmonella population where it constitutes only 0·1% of the population. The rapid nature of qPCR lends this assay to high-throughput screening of poultry samples to detect this important pathogen.
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Affiliation(s)
- A K Richards
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - B A Hopkins
- International Technical Animal Production and Processing Solutions (iTAPPS), Overland Park, KS, USA
| | - N W Shariat
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
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Chen Z, Kuang D, Xu X, González-Escalona N, Erickson DL, Brown E, Meng J. Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies. PLoS One 2020; 15:e0235641. [PMID: 32614888 PMCID: PMC7332006 DOI: 10.1371/journal.pone.0235641] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/19/2020] [Indexed: 01/04/2023] Open
Abstract
We sequenced 25 isolates of phenotypically multidrug-resistant Salmonella Indiana (n = 11), Typhimurium (n = 8), and Enteritidis (n = 6) using both MinION long-read [SQK-LSK109 and flow cell (R9.4.1)] and MiSeq short-read (Nextera XT and MiSeq Reagent Kit v2) sequencing technologies to determine the advantages of each approach in terms of the characteristics of genome structure, antimicrobial resistance (AMR), virulence potential, whole-genome phylogeny, and pan-genome. The MinION reads were base-called in real-time using MinKnow 3.4.8 integrated with Guppy 3.0.7. The long-read-only assembly, Illumina-only assembly, and hybrid assembly pipelines of Unicycler 0.4.8 were used to generate the MinION, MiSeq, and hybrid assemblies, respectively. The MinION assemblies were highly contiguous compared to the MiSeq assemblies but lacked accuracy, a deficiency that was mitigated by adding the MiSeq short reads through the Unicycler hybrid assembly which corrected erroneous single nucleotide polymorphisms (SNPs). The MinION assemblies provided similar predictions of AMR and virulence potential compared to the MiSeq and hybrid assemblies, although they produced more total false negatives of AMR genotypes, primarily due to failure in identifying tetracycline resistance genes in 11 of the 19 MinION assemblies of tetracycline-resistant isolates. The MinION assemblies displayed a large genetic distance from their corresponding MiSeq and hybrid assemblies on the whole-genome phylogenetic tree, indicating that the lower read accuracy of MinION sequencing caused incorrect clustering. The pan-genome of the MinION assemblies contained significantly more accessory genes and less core genes compared to the MiSeq and hybrid assemblies, suggesting that although these assemblies were more contiguous, their sequencing errors reduced accurate genome annotations. Our research demonstrates that MinION sequencing by itself provides an efficient assessment of the genome structure, antimicrobial resistance, and virulence potential of Salmonella; however, it is not sufficient for whole-genome phylogenetic and pan-genome analyses. MinION in combination with MiSeq facilitated the most accurate genomic analyses.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, United States of Amrica
| | - Dai Kuang
- Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Narjol González-Escalona
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - David L. Erickson
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, United States of Amrica
| | - Eric Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, United States of Amrica
- * E-mail:
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17
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Müştak İB, Müştak HK, Sarıçam S. Molecular characterisation of hydrogen sulfide negative Salmonella enterica serovar Havana. Antonie Van Leeuwenhoek 2020; 113:1241-1246. [PMID: 32607922 DOI: 10.1007/s10482-020-01432-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/28/2020] [Indexed: 11/26/2022]
Abstract
Hydrogen sulfide (H2S) detection is a screening method for distinguishing and identifying Salmonella strains from other bacteria in the intestine. Incidences of H2S-negative Salmonella have recently been reported in different countries. Although a high resistance rate against antimicrobial agents has been reported for H2S-positive Salmonella in many regions of the world, there is increasing evidence that high resistance to antibiotics has also increased in many H2S-negative Salmonella isolates. In this study, molecular characterisation of three H2S-negative Salmonella Havana, isolated from cloacal swab samples of broiler chickens, was performed. The phsA, phsB and phsC genes of the phs operon, which is responsible for hydrogen sulfide production, were amplified. Sequence analysis was then performed to identify mutations in the gene cluster. The antimicrobial resistance profiles of the isolates were determined by disc diffusion. Molecular characterisation was performed by multilocus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE). The sequence analysis showed identified five point mutations in the phsA gene and one point mutation in the phsC gene in all isolates. The antibiotic resistance profile showed that the strains were resistant to cefoxitin and ceftazidime. MLST analysis showed that all strains belonged to sequence type (ST) 1621. This study is the first to report the H2S-negative S. Havana serotype.
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Affiliation(s)
- İnci Başak Müştak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Şehit Ömer Halisdemir Bulv. Dışkapı, Ankara, 06110, Turkey
| | - Hamit Kaan Müştak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Şehit Ömer Halisdemir Bulv. Dışkapı, Ankara, 06110, Turkey.
| | - Seyyide Sarıçam
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Şehit Ömer Halisdemir Bulv. Dışkapı, Ankara, 06110, Turkey
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18
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Lu J, Li L, Pan F, Zuo G, Yu D, Liu R, Fan H, Ma Z. PagC is involved in salmonella pullorum OMVs production and affects biofilm production. Vet Microbiol 2020; 247:108778. [PMID: 32768224 DOI: 10.1016/j.vetmic.2020.108778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/05/2020] [Accepted: 06/20/2020] [Indexed: 12/12/2022]
Abstract
The pagC gene is ubiquitously distributed in Salmonella, but there is limited information regarding its function. Pullorum disease (PD) is a septicemic disease caused by Salmonella Pullorum, which also harbors the pagC gene. In this study, we constructed an S. Pullorum pagC gene deletion strain and its complemented strain. First, we confirmed that the pagC gene does not participate in bacterial growth regulation or environmental pH adaptation. Interestingly, the results of subsequent analyses indicated that the pagC gene defect led to increased bacterial colonization in the intestine (especially in the cecum) and increased biofilm formation, while the number of outer-membrane vesicles (OMVs) in the bacterial culture decreased. Purified OMVs were able to reduce S. Pullorum biofilm formation in vitro. In addition, the results of a mass spectrometry analysis of purified OMVs indicated that some enzymes harbored by OMVs may be involved in biofilm degradation. Based on these results, we conclude that deletion of the pagC gene leads to reduced S. Pullorum OMVs production, which subsequently promotes biofilm stability, increases bacterial colonization in the intestine, and potentially inhibits the switch from sessile to planktonic growth.
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Affiliation(s)
- Jiaxing Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Ministry of Agriculture Key Laboratory of Animal Bacteriology, Nanjing, 210095, China
| | - Lianyue Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Ministry of Agriculture Key Laboratory of Animal Bacteriology, Nanjing, 210095, China
| | - Fei Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Ministry of Agriculture Key Laboratory of Animal Bacteriology, Nanjing, 210095, China
| | - Gengliang Zuo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Ministry of Agriculture Key Laboratory of Animal Bacteriology, Nanjing, 210095, China
| | - Dandan Yu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Ministry of Agriculture Key Laboratory of Animal Bacteriology, Nanjing, 210095, China
| | - Runxia Liu
- South Dakota State University, Brookings, SD, 57007, USA
| | - Hongjie Fan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Ministry of Agriculture Key Laboratory of Animal Bacteriology, Nanjing, 210095, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Zhe Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Ministry of Agriculture Key Laboratory of Animal Bacteriology, Nanjing, 210095, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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Miller EA, Elnekave E, Flores-Figueroa C, Johnson A, Kearney A, Munoz-Aguayo J, Tagg KA, Tschetter L, Weber BP, Nadon CA, Boxrud D, Singer RS, Folster JP, Johnson TJ. Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America. mSphere 2020; 5:e00056-20. [PMID: 32295868 PMCID: PMC7160679 DOI: 10.1128/msphere.00056-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/26/2020] [Indexed: 01/09/2023] Open
Abstract
Two separate human outbreaks of Salmonella enterica serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole-genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade, isolates clustered into three subclades, including an "emergent" clade that contained only isolates dated 2016 or later, with many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades, suggesting that the apparent success of currently circulating subclades is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source.IMPORTANCE Increasingly, outbreak investigations involving foodborne pathogens are difficult due to the interconnectedness of food animal production and distribution, and homogeneous nature of industry integration, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole-genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincided with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in commercial turkeys and ability to cause illness in humans.
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Affiliation(s)
- Elizabeth A Miller
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ehud Elnekave
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | | | - Abigail Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ashley Kearney
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Jeannette Munoz-Aguayo
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
| | | | - Lorelee Tschetter
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Bonnie P Weber
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Celine A Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Dave Boxrud
- Minnesota Department of Health, Saint Paul, Minnesota, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jason P Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
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Mohamed A, Taha O, El-Sherif HM, Connerton PL, Hooton SP, Bassim ND, Connerton IF, El-Shibiny A. Bacteriophage ZCSE2 is a Potent Antimicrobial Against Salmonella enterica Serovars: Ultrastructure, Genomics and Efficacy. Viruses 2020; 12:v12040424. [PMID: 32283768 PMCID: PMC7232530 DOI: 10.3390/v12040424] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/22/2020] [Accepted: 04/07/2020] [Indexed: 02/04/2023] Open
Abstract
Developing novel antimicrobials capable of controlling multidrug-resistant bacterial pathogens is essential to restrict the use of antibiotics. Bacteriophages (phages) constitute a major resource that can be harnessed as an alternative to traditional antimicrobial therapies. Phage ZCSE2 was isolated among several others from raw sewage but was distinguished by broad-spectrum activity against Salmonella serovars considered pathogenic to humans and animals. Lytic profiles of ZCSE2 against a panel of Salmonella were determined together with low temperature activity and pH stability. The morphological features of the phage and host infection processes were characterized using a combination of transmission electron and atomic force microscopies. Whole genome sequencing of ZCSE2 produced a complete DNA sequence of 53,965 bp. No known virulence genes were identified in the sequence data, making ZCSE2 a good candidate for phage-mediated biological control purposes. ZCSE2 was further tested against S. Enteritidis in liquid culture and was observed to reduce the target bacterium to below the limits of detection from initial concentrations of 107–108 Colony Forming Units (CFU)/mL. With a broad host-range against pathogenic Salmonella serovars, phage ZCSE2 constitutes a potential tool against a major cause of human and animal disease.
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Affiliation(s)
- Ahmed Mohamed
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; (A.M.); (O.T.)
| | - Omar Taha
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; (A.M.); (O.T.)
| | - Hesham M. El-Sherif
- Mechanical Design and Production Engineering Department, Faculty of Engineering, Cairo University, Giza 12613, Egypt;
- Materials Science and Engineering Department, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada;
| | - Phillippa L. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK; (P.L.C.); (S.P.T.H.)
| | - Steven P.T. Hooton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK; (P.L.C.); (S.P.T.H.)
| | - Nabil D. Bassim
- Materials Science and Engineering Department, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada;
| | - Ian F. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK; (P.L.C.); (S.P.T.H.)
- Correspondence: (I.F.C.); (A.E.-S.)
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt; (A.M.); (O.T.)
- Faculty of Environmental Agricultural Sciences, Arish University, Arish 45615, Egypt
- Correspondence: (I.F.C.); (A.E.-S.)
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21
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Mastrorilli E, Petrin S, Orsini M, Longo A, Cozza D, Luzzi I, Ricci A, Barco L, Losasso C. Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. BMC Genomics 2020; 21:202. [PMID: 32131727 PMCID: PMC7057659 DOI: 10.1186/s12864-020-6588-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars. RESULTS 179 S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum β-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans. CONCLUSIONS Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.
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Affiliation(s)
- Eleonora Mastrorilli
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
- Present address: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Sara Petrin
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy.
| | - Alessandra Longo
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Debora Cozza
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Ida Luzzi
- Istituto Superiore di Sanità, Rome, Italy
| | - Antonia Ricci
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Lisa Barco
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Carmen Losasso
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
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Sia CM, Greig DR, Day M, Hartman H, Painset A, Doumith M, Meunier D, Jenkins C, Chattaway MA, Hopkins KL, Woodford N, Godbole G, Dallman TJ. The characterization of mobile colistin resistance ( mcr) genes among 33 000 Salmonella enterica genomes from routine public health surveillance in England. Microb Genom 2020; 6:e000331. [PMID: 32003708 PMCID: PMC7067213 DOI: 10.1099/mgen.0.000331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/05/2020] [Indexed: 12/15/2022] Open
Abstract
To establish the prevalence of mobile colistin resistance (mcr) genes amongst Salmonella enterica isolates obtained through public health surveillance in England (April 2014 to September 2017), 33 205 S. enterica genome sequences obtained from human, food, animal and environmental isolates were screened for the presence of mcr variants 1 to 8. The mcr-positive genomes were assembled, annotated and characterized according to plasmid type. Nanopore sequencing was performed on six selected isolates with putative novel plasmids, and phylogenetic analysis was used to provide an evolutionary context for the most commonly isolated clones. Fifty-two mcr-positive isolates were identified, of which 32 were positive for mcr-1, 19 for mcr-3 and 1 for mcr-5. The combination of Illumina and Nanopore sequencing identified three novel mcr-3 plasmids and one novel mcr-5 plasmid, as well as the presence of chromosomally integrated mcr-1 and mcr-3. Monophasic S. enterica serovar Typhimurium accounted for 27/52 (52 %) of the mcr-positive isolates, with the majority clustering in clades associated with travel to Southeast Asia. Isolates in these clades were associated with a specific plasmid range and an additional extended-spectrum beta-lactamase genotype. Routine whole-genome sequencing for public health surveillance provides an effective screen for novel and emerging antimicrobial determinants, including mcr. Complementary long-read technologies elucidated the genomic context of resistance determinants, offering insights into plasmid dissemination and linkage to other resistance genes.
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Affiliation(s)
| | - David R. Greig
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Martin Day
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Hassan Hartman
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Anais Painset
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Michel Doumith
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Daniele Meunier
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | | | - Katie L. Hopkins
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Neil Woodford
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Gauri Godbole
- National Infection Service, Public Health England, London, NW9 5EQ, UK
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Abstract
Non-typhoidal Salmonella (NTS) infection is a major pathogen causing gastroenteritis among immunocompetent adults. NTS infection is mainly transmitted by contaminated food and water, but some cases are transmitted by animal contact. Salmonella enterica subsp. enterica serovar Poona (S. Poona) is an NTS usually transmitted by reptiles, and cases including outbreaks of gastroenteritis have been reported previously. However, invasive infections due to this organism among immunocompetent adults are rare. We herein report a case of a 39-year-old man who was admitted to our hospital for a fever and headache. Blood cultures were positive for S. Poona, although he did not recall any exposure to reptiles. He was treated successfully with intravenous ceftriaxone without any subsequent complications. This case implies that NTS bacteremia can occur in immunocompetent adults, and the diagnosis may be challenging since there may be no clear exposure or focal physical signs.
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Affiliation(s)
- Kazuaki Fukushima
- Department of Infectious Diseases, Tokyo Metropolitan Komagome Hospital, Japan
| | - Naoki Yanagisawa
- Bureau of International Health Cooperation, National Center for Global Health and Medicine, Japan
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, USA
| | - Noritaka Sekiya
- Department of Infection Prevention and Control, Tokyo Metropolitan Komagome Hospital, Japan
- Department of Clinical Laboratory, Tokyo Metropolitan Komagome Hospital, Japan
| | - Hidemasa Izumiya
- Department of Bacteriology 1, National Institute of Infectious Diseases, Japan
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Abstract
Salmonella enterica serotype I 4,[5],12:i:- has been increasingly isolated from swine. However, its pathogenic potential is not well characterized. Analysis of swine cases confirmed a strong positive association between isolation of I 4,[5],12:i:- and lesions of enteric salmonellosis and suggested a similar pathogenic potential as that for Salmonella Typhimurium.
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Breurec S, Reynaud Y, Frank T, Farra A, Costilhes G, Weill FX, Le Hello S. Serotype distribution and antimicrobial resistance of human Salmonella enterica in Bangui, Central African Republic, from 2004 to 2013. PLoS Negl Trop Dis 2019; 13:e0007917. [PMID: 31790418 PMCID: PMC6907862 DOI: 10.1371/journal.pntd.0007917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/12/2019] [Accepted: 11/11/2019] [Indexed: 01/30/2023] Open
Abstract
Background Limited epidemiological and antimicrobial resistance data are available on Salmonella enterica from sub-Saharan Africa. We determine the prevalence of resistance to antibiotics in isolates in the Central African Republic (CAR) between 2004 and 2013 and the genetic basis for resistance to third-generation cephalosporin (C3G). Methodology/Principal findings A total of 582 non-duplicate human clinical isolates were collected. The most common serotype was Typhimurium (n = 180, 31% of the isolates). A randomly selected subset of S. Typhimurium isolates were subtyped by clustered regularly interspaced short palindromic repeat polymorphism (CRISPOL) typing. All but one invasive isolate tested (66/68, 96%) were associated with sequence type 313. Overall, the rates of resistance were high to traditional first-line drugs (18–40%) but low to many other antimicrobials, including fluoroquinolones (one resistant isolate) and C3G (only one ESBL-producing isolate). The extended-spectrum beta-lactamase (ESBL)-producing isolate and three additional ESBL isolates from West Africa were studied by whole genome sequencing. The blaCTX-M-15 gene and the majority of antimicrobial resistance genes found in the ESBL isolate were present in a large conjugative IncHI2 plasmid highly similar (> 99% nucleotide identity) to ESBL-carrying plasmids found in Kenya (S. Typhimurium ST313) and also in West Africa (serotypes Grumpensis, Havana, Telelkebir and Typhimurium). Conclusions/Significance Although the prevalence of ESBL-producing Salmonella isolates was low in CAR, we found that a single IncHI2 plasmid-carrying blaCTX-M-15 was widespread among Salmonella serotypes from sub-Saharan Africa, which is of concern. Salmonella enterica infections are common causes of bloodstream infection in sub-Saharan Africa and associated with a high mortality rate. Levels of multidrug resistance have become alarmingly high. Then, third-generation cephalosporin (C3G) and fluoroquinolones have become standard for first-line empirical treatment. Recently, C3G-resistant Salmonella populations have emerged and spread over all continents. This resistance is mainly mediated by acquired extended-spectrum beta-lactamase (ESBL) genes carried by mobile genetic elements such as plasmids. We report here the prevalence of resistance to antibiotics in isolates in the Central African Republic (CAR) between 2004 and 2013 and the genetic basis for resistance to C3G. Overall, resistance rates to antimicrobials were low during the study period, for all classes other than conventional antimicrobials, confirming recommendations for first-line treatment based on C3G and fluoroquinolones. Only one ESBL-producing isolate was recovered. The ESBL gene and the majority of antimicrobial resistance genes found were present in a large plasmid highly similar to ESBL-carrying plasmids found in East and West Africa, highlighting its significant role in the spread of ESBL genes in Salmonella isolates in sub-Saharan Africa. These finding have implications for treatment of salmonellosis and support the growing necessity for increased microbiological surveillance based on networks of clinical laboratories in order to control dissemination of antibiotic resistance among Salmonella isolates.
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Affiliation(s)
- Sebastien Breurec
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
- Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, France
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
- * E-mail:
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Thierry Frank
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
| | - Alain Farra
- Laboratoire de Bactériologie, Institut Pasteur, Bangui, Central African Republic
| | - Geoffrey Costilhes
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, World Health Organization Collaborative Centre for typing and antibiotic resistance of Salmonella, Institut Pasteur, Paris, France
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Gymoese P, Kiil K, Torpdahl M, Østerlund MT, Sørensen G, Olsen JE, Nielsen EM, Litrup E. WGS based study of the population structure of Salmonella enterica serovar Infantis. BMC Genomics 2019; 20:870. [PMID: 31730461 PMCID: PMC6858691 DOI: 10.1186/s12864-019-6260-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. RESULTS We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed. CONCLUSIONS This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.
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Affiliation(s)
- Pernille Gymoese
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mia Torpdahl
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mark T. Østerlund
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Gitte Sørensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
| | - Eva M. Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
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Kasturi KN. A real-time PCR for rapid identification of Salmonella enterica Gaminara serovar. J Microbiol Methods 2019; 169:105729. [PMID: 31711901 DOI: 10.1016/j.mimet.2019.105729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/13/2019] [Accepted: 09/21/2019] [Indexed: 12/17/2022]
Abstract
Salmonella is one of the leading causes of foodborne illnesses in the USA. When a Salmonella outbreak occurs, rapid identification of the causative serovar is important for tracing the source of contamination and for preventing the further spread of the illness. Each serovar is characterized by the presence of a group-specific somatic O-antigen(s) and an assortment of flagellar phase-1 and phase-2 antigens. As the traditional serotyping protocol is time consuming, labor intensive, and expensive, faster and less expensive molecular diagnostic methods are needed. This report outlines the development of a rapid multiplex real-time PCR procedure that facilitates the identification of Salmonella serogroup I and the serovars of the group. Using Salmonella Gaminara serovar (O16:d:1,7) as an example, first the gene(s) responsible for expression of the somatic O antigen, O16, and the nucleotide sequence of the variable-region of genes encoding the flagellar phase-1 (d) and phase-2 (1,7) antigens were identified. Then, a multiplex real-time PCR was designed that incorporated primers and probes specific for the three target genes and confirmed the specificity. The assay had 100% inclusivity for all three gene targets, detecting 2 genomic DNA copies of O16 and 1,7 gene targets and 10 copies of d gene target. Importance: Rapid molecular methods to identify Salmonella serovars should increase the precision of routine surveillance of clinically important serovars and promote public health.
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Affiliation(s)
- Kuppuswamy N Kasturi
- U. S. Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Northeast Food and Feed Laboratory, Jamaica, New York 11433, USA.
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Meinen A, Simon S, Banerji S, Szabo I, Malorny B, Borowiak M, Hadziabdic S, Becker N, Luber P, Lohr D, Harms C, Plenge-Bönig A, Mellou K, Mandilara G, Mossong J, Ragimbeau C, Weicherding P, Hau P, Dědičová D, Šafaříková L, Nair S, Dallman TJ, Larkin L, McCormick J, De Pinna E, Severi E, Kotila S, Niskanen T, Rizzi V, Deserio D, Flieger A, Stark K. Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017. Euro Surveill 2019; 24:1800543. [PMID: 31507266 PMCID: PMC6737830 DOI: 10.2807/1560-7917.es.2019.24.36.1800543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/29/2019] [Indexed: 11/20/2022] Open
Abstract
In spring 2016, Greece reported an outbreak caused by a previously undescribed Salmonella enterica subsp. enterica serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presumptive vehicle. Subsequently, Germany, Czech Republic, Luxembourg and the United Kingdom (UK) reported infections with this novel serotype via EPIS-FWD. Concerned countries in collaboration with the European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA) adopted a common outbreak case definition. An outbreak case was defined as a laboratory-confirmed notification of the novel Salmonella serotype. Between March 2016 and April 2017, 47 outbreak cases were notified (Greece: n = 22; Germany: n = 13; Czech Republic: n = 5; Luxembourg: n = 4; UK: n = 3). Whole genome sequencing revealed the very close genetic relatedness of isolates from all affected countries. Interviews focusing on sesame product consumption, suspicious food item testing and trace-back analysis following Salmonella spp. detection in food products identified a company in Greece where sesame seeds from different countries were processed. Through European collaboration, it was possible to identify and recall sesame spread as one contaminated food item serving as vehicle of infection and trace it back to its origin.
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Affiliation(s)
- Anika Meinen
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
- These authors contributed equally
| | - Sandra Simon
- These authors contributed equally
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Sangeeta Banerji
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Istvan Szabo
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Sead Hadziabdic
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Natalie Becker
- Federal Office of Consumer Protection and Food Safety, Crisis Unit Office, Foodborne Outbreaks, Prevention, Berlin, Germany
| | - Petra Luber
- Federal Office of Consumer Protection and Food Safety, Crisis Unit Office, Foodborne Outbreaks, Prevention, Berlin, Germany
| | - Dorothee Lohr
- Baden-Wuerttemberg State Health Office, Stuttgart, Germany
| | - Carolin Harms
- Institute for Hygiene and Environment Hamburg, Department of Microbiology, Hamburg, Germany
| | - Anita Plenge-Bönig
- Institute for Hygiene and Environment Hamburg, Infectious Disease Surveillance Unit, Hamburg, Germany
| | - Kassiani Mellou
- Hellenic National Public Health Organization, Athens, Greece
| | - Georgia Mandilara
- National School of Public Health, National Reference Centre for Salmonella, Athens, Greece
| | - Joël Mossong
- Laboratoire National de Santé, Département de Microbiologie, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Département de Microbiologie, Dudelange, Luxembourg
| | | | - Patrick Hau
- Direction de la Santé, Luxembourg, Luxembourg
| | - Daniela Dědičová
- Státní zdravotní ústav (National Institute of Public Health), Prague, Czech Republic
| | - Lucie Šafaříková
- Státní zdravotní ústav (National Institute of Public Health), Prague, Czech Republic
| | | | | | | | | | | | - Ettore Severi
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | - Saara Kotila
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | - Taina Niskanen
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | | | | | - Antje Flieger
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Klaus Stark
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
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Brown AC, Chen JC, Watkins LKF, Campbell D, Folster JP, Tate H, Wasilenko J, Van Tubbergen C, Friedman CR. CTX-M-65 Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serotype Infantis, United States 1. Emerg Infect Dis 2019; 24:2284-2291. [PMID: 30457533 PMCID: PMC6256390 DOI: 10.3201/eid2412.180500] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Extended-spectrum β-lactamases (ESBLs) confer resistance to clinically important third-generation cephalosporins, which are often used to treat invasive salmonellosis. In the United States, ESBLs are rarely found in Salmonella. However, in 2014, the US Food and Drug Administration found blaCTX-M-65 ESBL-producing Salmonella enterica serotype Infantis in retail chicken meat. The isolate had a rare pulsed-field gel electrophoresis pattern. To clarify the sources and potential effects on human health, we examined isolates with this pattern obtained from human surveillance and associated metadata. Using broth microdilution for antimicrobial susceptibility testing and whole-genome sequencing, we characterized the isolates. Of 34 isolates, 29 carried the blaCTX-M-65 gene with <9 additional resistance genes on 1 plasmid. Of 19 patients with travel information available, 12 (63%) reported recent travel to South America. Genetically, isolates from travelers, nontravelers, and retail chicken meat were similar. Expanded surveillance is needed to determine domestic sources and potentially prevent spread of this ESBL-containing plasmid.
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Pulford CV, Wenner N, Redway ML, Rodwell EV, Webster HJ, Escudero R, Kröger C, Canals R, Rowe W, Lopez J, Hall N, Rowley PD, Timofte D, Harrison RA, Baker KS, Hinton JCD. The diversity, evolution and ecology of Salmonella in venomous snakes. PLoS Negl Trop Dis 2019; 13:e0007169. [PMID: 31163033 PMCID: PMC6548357 DOI: 10.1371/journal.pntd.0007169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Reptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles. METHODOLOGY/PRINCIPLE FINDINGS We used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella, and found that a diverse range of serovars (n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae. Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S. diarizonae, S. enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo-inositol and allantoin. SIGNIFICANCE We present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella, including serovars which have been associated with disease in humans such as S. Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis.
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Affiliation(s)
- Caisey V. Pulford
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nicolas Wenner
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Martha L. Redway
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ella V. Rodwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Hermione J. Webster
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Roberta Escudero
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Carsten Kröger
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Rocío Canals
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Will Rowe
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Javier Lopez
- Animal Health Department, Chester Zoo, Cheshire, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Paul D. Rowley
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Dorina Timofte
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Cheshire, United Kingdom
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Robert A. Harrison
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kate S. Baker
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Tay MY, Pathirage S, Chandrasekaran L, Wickramasuriya U, Sadeepanie N, Waidyarathna KD, Liyanage LDC, Seow KL, Hendriksen RS, Takeuchi MT, Schlundt J. Whole-Genome Sequencing Analysis of Nontyphoidal Salmonella enterica of Chicken Meat and Human Origin Under Surveillance in Sri Lanka. Foodborne Pathog Dis 2019; 16:531-537. [PMID: 31099590 PMCID: PMC6653781 DOI: 10.1089/fpd.2018.2604] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A total of 73 nontyphoidal Salmonella enterica isolates, 33 from raw chicken meat and 40 from routine clinical specimens, were collected between 2015 and 2017 from eight cities in Sri Lanka for a pilot study of whole-genome sequencing for Salmonella surveillance. The isolates were characterized by conventional serotyping and whole-genome sequencing. The raw sequenced data were assembled and analyzed to predict Salmonella serotypes, determine sequence type (ST) profiles of genome and plasmid, and identify plasmid replicon sequences and antimicrobial resistance (AMR) genes. The most common serovar isolated from chicken meat was Salmonella enterica serovar Agona of ST13 (n = 16), in contrast to Salmonella enterica serovar Enteritidis of ST11 (n = 21) in human. Salmonella enterica serovar Corvallis is the only serovar that was overlapping between human and chicken meat. The level of agreement between serotyping and serotype prediction results was 100%. Among the 33 chicken isolates, multidrug resistance (MDR) was observed in five isolates, including two Salmonella enterica serovar Kentucky ST314, which harbored six different classes of AMR determinants. Among the 40 human isolates, MDR was detected in two Salmonella enterica serovar Chester (ST2063) isolates containing five different antibiotic classes of AMR determinants. Out of 73 isolates, the only human Salmonella enterica serovar Typhimurium strain of ST36 was found to possess extended-spectrum beta-lactamase (ESBL) gene, blaCTX-M-15, and it was positive for ESBL production. In summary, this study identified S. enterica serovars that were dominating in chicken meat and human and showed the genomic differences among the chicken meat and human strains. It should be noted that the limited number of isolates and sampling at a different time period means that thorough source attribution is not possible. To the best of our knowledge, this is the first report on the use of whole-genome sequencing analysis of nontyphoidal S. enterica isolated from chicken meat and human in Sri Lanka.
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Affiliation(s)
- Moon Y.F. Tay
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore, Singapore
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
- Address correspondence to: Moon Y.F. Tay, PhD, School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), 62 Nanyang Drive, Singapore 637459, Singapore
| | - Sujatha Pathirage
- Enteric Reference Laboratory, Department of Bacteriology, Medical Research Institute (MRI), Colombo, Sri Lanka
- Sujatha Pathirage, MD, Medical Research Institute (MRI), PO Box 527, Dr. Danister Silva Mawatha, Colombo 00800, Sri Lanka
| | - Lakshmi Chandrasekaran
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore, Singapore
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Uddami Wickramasuriya
- Enteric Reference Laboratory, Department of Bacteriology, Medical Research Institute (MRI), Colombo, Sri Lanka
| | - Nirasha Sadeepanie
- Enteric Reference Laboratory, Department of Bacteriology, Medical Research Institute (MRI), Colombo, Sri Lanka
| | - Kaushalya D.K. Waidyarathna
- Enteric Reference Laboratory, Department of Bacteriology, Medical Research Institute (MRI), Colombo, Sri Lanka
| | | | - Kelyn L.G. Seow
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore, Singapore
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Rene S. Hendriksen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Masami T. Takeuchi
- Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Joergen Schlundt
- School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore, Singapore
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
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Arnott A, Wang Q, Bachmann N, Sadsad R, Biswas C, Sotomayor C, Howard P, Rockett R, Wiklendt A, Iredell JR, Sintchenko V. Multidrug-Resistant Salmonella enterica 4,[5],12:i:- Sequence Type 34, New South Wales, Australia, 2016-2017. Emerg Infect Dis 2019; 24:751-753. [PMID: 29553318 PMCID: PMC5875280 DOI: 10.3201/eid2404.171619] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Multidrug- and colistin-resistant Salmonella enterica serotype 4,[5],12:i:- sequence type 34 is present in Europe and Asia. Using genomic surveillance, we determined that this sequence type is also endemic to Australia. Our findings highlight the public health benefits of genome sequencing–guided surveillance for monitoring the spread of multidrug-resistant mobile genes and isolates.
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Sabbatucci M, Dionisi AM, Pezzotti P, Lucarelli C, Barco L, Mancin M, Luzzi I. Molecular and Epidemiologic Analysis of Reemergent Salmonella enterica Serovar Napoli, Italy, 2011-2015. Emerg Infect Dis 2019; 24:562-565. [PMID: 29460759 PMCID: PMC5823338 DOI: 10.3201/eid2403.171178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Human infections with Salmonella enterica serovar Napoli are uncommon in Europe. However, these infections represented 5.9% of salmonellosis cases in Italy during 2014–2015. The source of infection is unknown. We analyzed surveillance data and compared strain genetic similarities and found that contaminated vegetables and surface water are probable sources of human infection.
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Siira L, Naseer U, Alfsnes K, Hermansen NO, Lange H, Brandal LT. Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016. Euro Surveill 2019; 24:1800186. [PMID: 30696528 PMCID: PMC6352000 DOI: 10.2807/1560-7917.es.2019.24.4.1800186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 11/06/2018] [Indexed: 11/20/2022] Open
Abstract
IntroductionDuring summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.AimOur aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.MethodsWe included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonella enterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.ResultsConfirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster. All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.ConclusionWhole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonella enterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.
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Affiliation(s)
- Lotta Siira
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Umaer Naseer
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
| | - Kristian Alfsnes
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
| | - Nils Olav Hermansen
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Heidi Lange
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
| | - Lin T Brandal
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health (NIPH), Oslo, Norway
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Abstract
The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.
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Affiliation(s)
- Ohad Gal-Mor
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Callahan MT, Van Kessel JA, Micallef SA. Salmonella enterica recovery from river waters of the Maryland Eastern Shore reveals high serotype diversity and some multidrug resistance. Environ Res 2019; 168:7-13. [PMID: 30253315 DOI: 10.1016/j.envres.2018.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
The Delmarva Peninsula, a major agricultural and recreational region for the U.S. states of Delaware, Maryland and Virginia, experiences recurrent salmonellosis disease. Previous studies point to water environments as a potential persistent environmental reservoir of Salmonella enterica. To evaluate this hypothesis, water from the four main rivers of the Maryland Eastern Shore on the Delmarva Peninsula was tested for the presence of S. enterica, and recovered isolates were characterized for antimicrobial resistance. Sampling was performed in autumn and spring to evaluate temporal persistence at twenty four sites along the Choptank, Nanticoke, Pocomoke and Wicomico Rivers. Water (10 L) was filtered through sterile modified Moore swabs in situ. Swabs were selectively enriched for S. enterica and presumptive salmonellae were confirmed by PCR amplification of the Salmonella-specific invA and hilA genes. The serogroup of 402 isolates was determined, followed by serotype characterization for 157 isolates selected to represent all the identified serogroups across all samples. S. enterica was isolated from all the rivers in both seasons and was detected in 35/46 (65%) of surface water samples, with equivalent recovery in spring (70%) and fall (61%). The likelihood of isolating S. enterica was higher for the Nanticoke and Pocomoke Rivers, χ2 (3, N = 46) = 12.75, p < 0.01. In total, 18 serotypes of S. enterica were identified, and serotype diversity differed between the fall and spring samplings. Newport was the most frequently isolated serotype, both overall and in the fall, identified in 8/46 samples (17%). Typhimurium was the predominant serotype in spring. Some temporal and biogeographic patterns were observed in S. enterica recovery, but 6/18 serotypes were identified in both seasons. The majority (84%) of isolates were pan-susceptible, including all those tested from the Wicomico River (N = 19). Twenty five isolates (16%) from 9 samples were resistant to at least one antimicrobial, including serotypes Typhimurium, Newport, Litchfield, III 17:z10: e,n,x,z15, III 60:I and IV_40:z4: z32: -. Of the isolates that were resistant to a single antimicrobial (N = 12), resistance was to streptomycin or sulfisoxazole. Thirteen isolates were multidrug resistant, nine exhibiting resistance to ampicillin, sulfisoxazole, tetracycline, amoxicillin/clavulanic acid, cefoxitin and ceftriaxone, and four to sulfisoxazole and tetracycline. The widespread presence and diversity of S. enterica in Delmarva rivers are concerning given the frequent use of rivers and tributaries as a source of irrigation and for recreation. Future research should seek to determine specific point sources of S. enterica for surface river waters, and risks associated with acquisition of antimicrobial resistance traits.
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Affiliation(s)
- Mary Theresa Callahan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Jo Ann Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, ARS-USDA, Beltsville, MD, USA
| | - Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA; Centre for Food Safety and Security Systems, University of Maryland, College Park, MD, USA.
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Thompson CP, Doak AN, Amirani N, Schroeder EA, Wright J, Kariyawasam S, Lamendella R, Shariat NW. High-Resolution Identification of Multiple Salmonella Serovars in a Single Sample by Using CRISPR-SeroSeq. Appl Environ Microbiol 2018; 84:e01859-18. [PMID: 30170999 PMCID: PMC6193385 DOI: 10.1128/aem.01859-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/21/2018] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica is represented by >2,600 serovars that can differ in routes of transmission, host colonization, and in resistance to antimicrobials. S. enterica is the leading bacterial cause of foodborne illness in the United States, with well-established detection methodology. Current surveillance protocols rely on the characterization of a few colonies to represent an entire sample; thus, minority serovars remain undetected. Salmonella contains two CRISPR loci, CRISPR1 and CRISPR2, and the spacer contents of these can be considered serovar specific. We exploited this property to develop an amplicon-based and multiplexed sequencing approach, CRISPR-SeroSeq (serotyping by sequencing of the CRISPR loci), to identify multiple serovars present in a single sample. Using mixed genomic DNA from two Salmonella serovars, we were able to confidently detect a serovar that constituted 0.01% of the sample. Poultry is a major reservoir of Salmonella spp., including serovars that are frequently associated with human illness, as well as those that are not. Numerous studies have examined the prevalence and diversity of Salmonella spp. in poultry, though these studies were limited to culture-based approaches and therefore only identified abundant serovars. CRISPR-SeroSeq was used to investigate samples from broiler houses and a processing facility. Ninety-one percent of samples harbored multiple serovars, and there was one sample in which four different serovars were detected. In another sample, reads for the minority serovar comprised 0.003% of the total number of Salmonella spacer reads. The most abundant serovars identified were Salmonella enterica serovars Montevideo, Kentucky, Enteritidis, and Typhimurium. CRISPR-SeroSeq also differentiated between multiple strains of some serovars. This high resolution of serovar populations has the potential to be utilized as a powerful tool in the surveillance of Salmonella species.IMPORTANCESalmonella enterica is the leading bacterial cause of foodborne illness in the United States and is represented by over 2,600 distinct serovars. Some of these serovars are pathogenic in humans, while others are not. Current surveillance for this pathogen is limited by the detection of only the most abundant serovars, due to the culture-based approaches that are used. Thus, pathogenic serovars that are present in a minority remain undetected. By exploiting serovar-specific differences in the CRISPR arrays of Salmonella spp., we have developed a high-throughput sequencing tool to be able to identify multiple serovars in a single sample and tested this in multiple poultry samples. This novel approach allows differences in the dynamics of individual Salmonella serovars to be measured and can have a significant impact on understanding the ecology of this pathogen with respect to zoonotic risk and public health.
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Affiliation(s)
- Cameron P Thompson
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Alexandra N Doak
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
- Department of Computer Science, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Naufa Amirani
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Erin A Schroeder
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Justin Wright
- Wright Labs, Juniata Center for Entrepreneurial Leadership, Huntingdon, Pennsylvania, USA
| | - Subhashinie Kariyawasam
- Department of Veterinary Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Regina Lamendella
- Wright Labs, Juniata Center for Entrepreneurial Leadership, Huntingdon, Pennsylvania, USA
- Biology Department, Juniata College, Huntingdon, Pennsylvania, USA
| | - Nikki W Shariat
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
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Methner U, Merbach S, Peters M. Salmonella enterica subspecies enterica serovar Choleraesuis in a German wild boar population: occurrence and characterisation. Acta Vet Scand 2018; 60:65. [PMID: 30373603 PMCID: PMC6206682 DOI: 10.1186/s13028-018-0422-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/24/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The swine-adapted serovar Choleraesuis of Salmonella enterica subspecies enterica is found rarely in domestic pigs in Germany. However, a considerable and increasing number of S. Choleraesuis organisms have been isolated from wild boars in Germany in recent years. To investigate a possible epidemiological context, S. Choleraesuis strains from a regional German wild boar population and other hosts were characterised by genotyping methods. RESULTS Macrorestriction analysis, biochemical differentiation and antimicrobial susceptibility typing enabled the identification of several clusters of S. Choleraesuis. Some clusters occurred almost permanently in a certain district, whereas other groups circulated among different wild boar herds in larger regions. Non-porcine hosts were infected with the same cluster as the wild boars. CONCLUSIONS The emergence of S. Choleraesuis in wild boars might be caused by a higher prevalence in the wild boar population, but also the higher awareness to infections with African swine fever may have resulted in a higher number of examined animals. Separation of wild boar populations and, as a result, also the diverse S. Choleraesuis organisms might be due to natural barriers and artificial barriers like arterial roads. The findings of S. Choleraesuis in domestic pigs emphasize the importance of strict biosecurity measures to prevent transmission from wild boars of this but also other pathogens. To avoid risks for humans by zoonotic pathogens regular inspections of meat from wildlife need to be conducted.
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Affiliation(s)
- Ulrich Methner
- Institute of Bacterial Infections and Zoonoses at the Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Naumburger Str. 96a, 07743 Jena, Germany
| | - Sabine Merbach
- Chemisches und Veterinäruntersuchungsamt Westfalen, Zur Taubeneiche 10-12, 59821 Arnsberg, Germany
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, Zur Taubeneiche 10-12, 59821 Arnsberg, Germany
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Mokracka J, Krzymińska S, Ałtunin D, Wasyl D, Koczura R, Dudek K, Dudek M, Chyleńska ZA, Ekner-Grzyb A. In vitro virulence characteristics of rare serovars of Salmonella enterica isolated from sand lizards (Lacerta agilis L.). Antonie Van Leeuwenhoek 2018; 111:1863-1870. [PMID: 29779148 PMCID: PMC6153992 DOI: 10.1007/s10482-018-1079-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/31/2018] [Indexed: 01/24/2023]
Abstract
The aim of this study was to estimate virulence potential of Salmonella enterica strains colonizing the gut of free-living sand lizards (Lacerta agilis L.). The strains belonged to three Salmonella serovars: Abony, Schleissheim, and Telhashomer. Adhesion and invasion abilities of the strains were determined in quantitative assays using the gentamicin protection method. Induction of apoptosis was assessed using HeLa cell monolayers. PCR assays were used for detection of 26 virulence genes localised within mobile elements: pathogenicity islands, virulence plasmids, and prophage sequences. In vitro studies revealed that all strains had adhesion and invasion abilities to human epithelial cells. The isolates were cytotoxic and induced apoptosis of the cells. The serovars differed in the number of virulence-associated genes: up to 18 genes were present in Salmonella Schleissheim, 17 in Salmonella Abony, whereas as few as six genes were found in Salmonella Telhashomer. Generally, Salmonella Abony and Salmonella Schleissheim did not differ much in gene content connected with the presence SPI-1 to -5. All of the strains lacked genes localised within bacteriophages and plasmids. The presence of virulence-associated genes and in vitro pathogenicity assays suggest that Salmonella sp. strains originating from autochthonous, free-living lizards can potentially infect and cause disease in humans.
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Affiliation(s)
- Joanna Mokracka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznan, Poland.
| | - Sylwia Krzymińska
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznan, Poland
| | - Danił Ałtunin
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznan, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Partyzantów 57, 24-100, Puławy, Poland
| | - Ryszard Koczura
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznan, Poland
| | - Krzysztof Dudek
- Department of Zoology, Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71 C, 60-625, Poznan, Poland
- HiProMine S.A., ul. Poznańska 8, 62-023, Robakowo, Poland
| | - Monika Dudek
- Laboratory of Neurobiology, Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71 C, 60-625, Poznan, Poland
| | - Zofia Anna Chyleńska
- Department of Nature Education and Conservation, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznan, Poland
| | - Anna Ekner-Grzyb
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznan, Poland
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40
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Wheeler NE, Gardner PP, Barquist L. Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genet 2018; 14:e1007333. [PMID: 29738521 PMCID: PMC5940178 DOI: 10.1371/journal.pgen.1007333] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/24/2018] [Indexed: 11/18/2022] Open
Abstract
Emerging pathogens are a major threat to public health, however understanding how pathogens adapt to new niches remains a challenge. New methods are urgently required to provide functional insights into pathogens from the massive genomic data sets now being generated from routine pathogen surveillance for epidemiological purposes. Here, we measure the burden of atypical mutations in protein coding genes across independently evolved Salmonella enterica lineages, and use these as input to train a random forest classifier to identify strains associated with extraintestinal disease. Members of the species fall along a continuum, from pathovars which cause gastrointestinal infection and low mortality, associated with a broad host-range, to those that cause invasive infection and high mortality, associated with a narrowed host range. Our random forest classifier learned to perfectly discriminate long-established gastrointestinal and invasive serovars of Salmonella. Additionally, it was able to discriminate recently emerged Salmonella Enteritidis and Typhimurium lineages associated with invasive disease in immunocompromised populations in sub-Saharan Africa, and within-host adaptation to invasive infection. We dissect the architecture of the model to identify the genes that were most informative of phenotype, revealing a common theme of degradation of metabolic pathways in extraintestinal lineages. This approach accurately identifies patterns of gene degradation and diversifying selection specific to invasive serovars that have been captured by more labour-intensive investigations, but can be readily scaled to larger analyses.
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Affiliation(s)
- Nicole E. Wheeler
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- * E-mail: (NEW); (LB)
| | - Paul P. Gardner
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
- Helmholtz Institute for RNA-based Infection Research, Wuerzburg, Germany
- * E-mail: (NEW); (LB)
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Parry-Hanson Kunadu A, Holmes M, Miller EL, Grant AJ. Microbiological quality and antimicrobial resistance characterization of Salmonella spp. in fresh milk value chains in Ghana. Int J Food Microbiol 2018; 277:41-49. [PMID: 29680695 DOI: 10.1016/j.ijfoodmicro.2018.04.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/08/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022]
Abstract
Consumer perception of poor hygiene of fresh milk products is a major barrier to promotion of milk consumption as an intervention to alleviate the burden of malnutrition in Ghana. Fresh milk is retailed raw, boiled, or processed into unfermented cheese and spontaneously fermented products in unlicensed outlets. In this study, we have determined microbiological quality of informally retailed fresh milk products and characterized the genomic diversity and antimicrobial resistance (AMR) patterns of non-typhoidal Salmonella (NTS) in implicated products. A total of 159 common dairy products were purchased from five traditional milk markets in Accra. Samples were analysed for concentrations of aerobic bacteria, total and fecal coliforms, Escherichia coli, staphylococci, lactic acid bacteria and yeast and moulds. The presence of Salmonella, E. coli O157:H7, Listeria monocytogenes and Staphylococcus aureus were determined. AMR of Salmonella against 18 antibiotics was experimentally determined. Genome sequencing of 19 Salmonella isolates allowed determination of serovars, antigenic profiles, prediction of AMR genes in silico and inference of phylogenetic relatedness between strains. Raw and heat-treated milk did not differ significantly in overall bacterial quality (P = 0.851). E. coli O157:H7 and Staphylococcus aureus were present in 34.3% and 12.9% of dairy products respectively. Multidrug resistant (MDR) Salmonella enterica serovars Muenster and Legon were identified in 11.8% and 5.9% of unfermented cheese samples respectively. Pan genome analysis revealed a total of 3712 core genes. All Salmonella strains were resistant to Trimethoprim/Sulfamethoxazole, Cefoxitin, Cefuroxime Axetil and Cefuroxime. Resistance to Chloramphenicol (18%) and Ciprofloxacin (100%), which are first line antibiotics used in treatment of NTS bacteremia in Ghana, was evident. AMR was attributed to presence and/or mutations in the following genes: golS, sdiA for cephalosporins, aac(6')-Iy, ant(9) for aminoglycosides, mdtK, gyrA, gyrB, parC, parE for quinolones and cat1, cat4 for phenicols. Phylogenetic analysis based on accessory genes clustered S. Legon strains separately from the S. Muenster strains. These strains were from different markets suggesting local circulation of related strains. Our study justifies consumer resistance to consumption of unripened soft cheese without further lethal heat treatment, and provides evidence that supports the Ghana Health Service recommendation for use of 3rd generation cephalosporins for the treatment of MDR NTS infections.
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Affiliation(s)
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Eric L Miller
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
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Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ. Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:. PLoS One 2018; 13:e0192504. [PMID: 29408896 PMCID: PMC5800660 DOI: 10.1371/journal.pone.0192504] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/24/2018] [Indexed: 12/05/2022] Open
Abstract
Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp. enterica serovar Typhimurium and serovar 1,4,[5],12:i:- isolates including five isolates from a confirmed outbreak and three isolates obtained from the same patient at different time points. The analysis was carried out using the original (high-coverage) and a down-sampled (low-coverage) datasets and two different reference genomes. All three tested workflows, namely CSI Phylogeny-based workflow, CFSAN-based workflow and PHEnix-based workflow, were able to correctly group the confirmed outbreak isolates and isolates from the same patient with all combinations of reference genomes and datasets. However, the workflows differed strongly with respect to the SNP distances between isolates and sensitivity towards sequencing coverage, which could be linked to the specific data analysis strategies used therein. To demonstrate the effect of particular data analysis steps, several modifications of the existing workflows were also tested. This allowed us to propose data analysis schemes most suitable for routine SNP-based subtyping applied to S. Typhimurium and S. 1,4,[5],12:i:-. Results presented in this study illustrate the importance of using correct data analysis strategies and to define benchmark and fine-tune parameters applied within routine data analysis pipelines to obtain optimal results.
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Affiliation(s)
- Assia Saltykova
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | - Véronique Wuyts
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Wesley Mattheus
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Sophie Bertrand
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Nancy H. C. Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB, Ghent, Belgium
- University of Pretoria, Pretoria, South Africa
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43
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Usongo V, Berry C, Yousfi K, Doualla-Bell F, Labbé G, Johnson R, Fournier E, Nadon C, Goodridge L, Bekal S. Impact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg. PLoS One 2018; 13:e0192233. [PMID: 29401524 PMCID: PMC5798827 DOI: 10.1371/journal.pone.0192233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/18/2018] [Indexed: 12/15/2022] Open
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. The core genome single nucleotide variant pipeline (cgSNV) is one of several whole genome based sequence typing methods used for the laboratory investigation of foodborne pathogens. SNV detection using this method requires a reference genome. The purpose of this study was to investigate the impact of the choice of the reference genome on the cgSNV-informed phylogenetic clustering and inferred isolate relationships. We found that using a draft or closed genome of S. Heidelberg as reference did not impact the ability of the cgSNV methodology to differentiate among 145 S. Heidelberg isolates involved in foodborne outbreaks. We also found that using a distantly related genome such as S. Dublin as choice of reference led to a loss in resolution since some sporadic isolates were found to cluster together with outbreak isolates. In addition, the genetic distances between outbreak isolates as well as between outbreak and sporadic isolates were overall reduced when S. Dublin was used as the reference genome as opposed to S. Heidelberg.
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Affiliation(s)
- Valentine Usongo
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Department of Food Science and Agricultural Chemistry, Food Safety and Quality Program, McGill University, Ste Anne de Bellevue, Québec, Canada
| | - Chrystal Berry
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Khadidja Yousfi
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | | | - Genevieve Labbé
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Roger Johnson
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Celine Nadon
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, Food Safety and Quality Program, McGill University, Ste Anne de Bellevue, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Liakopoulos A, Geurts Y, Dierikx CM, Brouwer MSM, Kant A, Wit B, Heymans R, van Pelt W, Mevius DJ. Extended-Spectrum Cephalosporin-Resistant Salmonella enterica serovar Heidelberg Strains, the Netherlands(1). Emerg Infect Dis 2018; 22:1257-61. [PMID: 27314180 PMCID: PMC4918182 DOI: 10.3201/eid2207.151377] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg strains (JF6X01.0022/XbaI.0251, JF6X01.0326/XbaI.1966, JF6X01.0258/XbaI.1968, and JF6X01.0045/XbaI.1970) have been identified in the United States with pulsed-field gel electrophoresis. Our examination of isolates showed introduction of these strains in the Netherlands and highlight the need for active surveillance and intervention strategies by public health organizations.
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45
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Maeda Y, Dobashi H, Sugiyama Y, Saeki T, Lim TK, Harada M, Matsunaga T, Yoshino T, Tanaka T. Colony fingerprint for discrimination of microbial species based on lensless imaging of microcolonies. PLoS One 2017; 12:e0174723. [PMID: 28369067 PMCID: PMC5378366 DOI: 10.1371/journal.pone.0174723] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/14/2017] [Indexed: 11/18/2022] Open
Abstract
Detection and identification of microbial species are crucial in a wide range of industries, including production of beverages, foods, cosmetics, and pharmaceuticals. Traditionally, colony formation and its morphological analysis (e.g., size, shape, and color) with a naked eye have been employed for this purpose. However, such a conventional method is time consuming, labor intensive, and not very reproducible. To overcome these problems, we propose a novel method that detects microcolonies (diameter 10–500 μm) using a lensless imaging system. When comparing colony images of five microorganisms from different genera (Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans), the images showed obvious different features. Being closely related species, St. aureus and St. epidermidis resembled each other, but the imaging analysis could extract substantial information (colony fingerprints) including the morphological and physiological features, and linear discriminant analysis of the colony fingerprints distinguished these two species with 100% of accuracy. Because this system may offer many advantages such as high-throughput testing, lower costs, more compact equipment, and ease of automation, it holds promise for microbial detection and identification in various academic and industrial areas.
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Affiliation(s)
- Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hironori Dobashi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yui Sugiyama
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tatsuya Saeki
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | | | - Tadashi Matsunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
- * E-mail:
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Keddy KH, Takuva S, Musekiwa A, Puren AJ, Sooka A, Karstaedt A, Klugman KP, Angulo FJ. An association between decreasing incidence of invasive non-typhoidal salmonellosis and increased use of antiretroviral therapy, Gauteng Province, South Africa, 2003-2013. PLoS One 2017; 12:e0173091. [PMID: 28264046 PMCID: PMC5338796 DOI: 10.1371/journal.pone.0173091] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/15/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND HIV-infected persons are at increased risk of opportunistic infections, including invasive nontyphoidal Salmonella (iNTS) infections; antiretroviral therapy (ART) reduces this risk. We explored changing iNTS incidence associated with increasing ART availability in South Africa. METHODS Laboratory-based surveillance for iNTS was conducted in Gauteng Province, South Africa, with verification using the National Health Laboratory Service's Central Data Warehouse (CDW), between 2003 and 2013. Isolates were serotyped at the Centre for Enteric Diseases. CDW data on patient numbers obtaining HIV viral load measurements provided estimates of numbers of HIV-infected patients receiving ART. A Poisson regression model was used to measure the changing incidence of iNTS infection from 2003 to 2013. The correlation between the incidence of iNTS and ART use from 2004 to 2013 was determined using Pearson's correlation coefficient. RESULTS From 2003-2013, the incidence of iNTS per 100,000 population per year decreased from 5.0 to 2.2 (p < .001). From 2004 to 2013, the incidence per 100,000 population of HIV viral load testing increased from 75.2 to 3,620.3 (p < .001). The most common serotypes causing invasive disease were Salmonella enterica serovar Typhimurium (Salmonella Typhimurium), and Salmonella Enteritidis: 2,469 (55.4%) and 1,156 (25.9%) of 4,459 isolates serotyped, respectively. A strong negative correlation was observed between decreasing iNTS incidence and increasing ART use from 2004 to 2013 (r = -0.94, p < .001). Similarly, decreasing incidence of invasive Salmonella Typhimurium infection correlated with increasing ART use (r = -0.93, p < .001). Incidence of invasive Salmonella Enteritidis infection increased, however (r = 0.95, p < .001). Between 2003 and 2004, fewer adult men than women presented with iNTS (male-to-female rate ratio 0.73 and 0.89, respectively). This was reversed from 2005 through 2013 (ranging from 1.07 in 2005 to 1.44 in 2013). Adult men accessed ART less (male-to-female rate ratio ranging from 0.61 [2004] to 0.67 [2013]). CONCLUSIONS The incidence of iNTS infections including Salmonella Typhimurium decreased significantly in Gauteng Province in association with increased ART utilization. Adult men accessed ART programs less than women, translating into increasing iNTS incidence in this group. Monitoring iNTS incidence may assist in monitoring the ART program. Increasing incidence of invasive Salmonella Enteritidis infections needs further elucidation.
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Affiliation(s)
- Karen H. Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Simbarashe Takuva
- CARTA Africa, Nairobi, Kenya
- Centre for HIV, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Alfred Musekiwa
- International Emerging Infections Program, South Africa Global Disease Detection Centre, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Adrian J. Puren
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arvinda Sooka
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Alan Karstaedt
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine, Chris Hani Baragwanath Hospital, Johannesburg, South Africa
| | - Keith P. Klugman
- Bill and Melinda Gates Foundation, Seattle, WA, United States of America
| | - Frederick J. Angulo
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Ho YN, Chou MY, Tsai HC, Huang TY, Fan CW, Hsu BM. Empirical testing of modified Salmonella MLST in aquatic environmental samples by in silico analysis. Sci Total Environ 2017; 581-582:378-385. [PMID: 28043703 DOI: 10.1016/j.scitotenv.2016.12.144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/15/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
Multilocus sequence typing (MLST) is an approach for prediction of Salmonella servoar and eBRUST groups (eBGs) based on seven typing scheme of housekeeping genes. Up to date, >220.000 allelic profiles and 65,973 Salmonella strains have been established in the MLST database. Several studies have modified MLST method with fewer targeted housekeeping genes for the purpose of economy and efficiency. Nevertheless, no study has conducted systematically to evaluate the correlation between the numbers of housekeeping genes targeted and the accuracy of prediction rate. In this study, we aimed to tackle this problem by extracting data from the MLST database as a whole using the software RStudio. Our results indicated that as the numbers of genes in MLST scheme increased, the accuracy of the eBGs prediction rate increased and reached 100% when the gene numbers are greater than or equal to 5. To examine the applicability of the approach, 395 environmental water samples were subjected to this study. A set of 52 Salmonella enterica isolates was initially used to develop MLST targeting seven housekeeping genes. A total of 29 sequence types, including 11 new sequence types were found among the 52 sequenced isolates that differentiated into 19 serotypes. Moreover, two novel sequence types did not belong to current classification. Our results show that the outcome in the three-gene sequence typing (aroC, hisD, and purE) was as accurate as in the seven-gene sequence typing for prediction of environmental Salmonella isolates. Our data suggested that this five-gene and reduced gene-number sequence-typing scheme can serve as an alternative modified MLST when effectiveness and financial management were the concerns.
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Affiliation(s)
- Ying-Ning Ho
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan, ROC; Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, ROC.
| | - Ming-Yuan Chou
- Department of Internal Medicine, Cheng Hsin General Hospital, Taipei, Taiwan, ROC.
| | - Hsin-Chi Tsai
- School of Medicine Tzu-Chi University, Hualien 970, Taiwan, ROC; Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan, ROC.
| | - Tung-Yi Huang
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan, ROC.
| | - Cheng-Wei Fan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan, ROC.
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan, ROC.
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48
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Xie X, Hu Y, Xu Y, Yin K, Li Y, Chen Y, Xia J, Xu L, Liu Z, Geng S, Li Q, Jiao X, Chen X, Pan Z. Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence. Vet Microbiol 2017; 203:81-87. [PMID: 28619172 DOI: 10.1016/j.vetmic.2017.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/20/2017] [Accepted: 02/20/2017] [Indexed: 11/19/2022]
Abstract
Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the cause of pullorum disease, characterized by white diarrhea, which leads to high mortality in poultry. In this study, we aimed to assess the genetic diversity of 655 S. Pullorum strains from 1962 to 2015 in China, Europe, and South America. A sequence typing scheme based on clustered regularly interspaced short palindromic repeats (CRISPR) was used to reveal the genetic relationships among these strains in this study. Overall, a total of 20 Pullorum sequence types (PSTs) of CRISPR were identified in the 655 isolates with PST7 (74%, 486/655) and PST3 (13%, 86/655) to be the most two frequent PSTs belonging to two different lineages, which confirmed the genetic conservation of S. Pullorum strains isolated from six provinces and two direct-controlled municipalities (Beijing and Shanghai) in China. However, the identification of seven new PSTs distributed in strains isolated since 2001 implied that genetic variation continues to develop in S. Pullorum. Interestingly, the whole-genome single-nucleotide polymorphism typing (WGST) of 96 strains out of the 655 isolates divided them into four lineages based on SNP analysis of core genomic sequence and exhibit good correspondence with the CRISPR subtyping method. Notably, 22 out of 26 isolates from Europe and South America were distributed in five distinctive PSTs (with no Chinese strains). Additionally, CRISPR data of spacers and their arrangement exhibit subtle but distinct specificity between different strains, and the dynamic adaptive nature of CRISPR loci provides critical insights into the evolution of S. Pullorum as the bacteria are influenced by their environment.
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Affiliation(s)
- Xiaolei Xie
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yachen Hu
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yaohui Xu
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Henan, China
| | - Kequan Yin
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yang Li
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yun Chen
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jie Xia
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lijuan Xu
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zijian Liu
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Shizhong Geng
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Qiuchun Li
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
| | - Xinan Jiao
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.
| | - Xiang Chen
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhiming Pan
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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49
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Uche IV, MacLennan CA, Saul A. A Systematic Review of the Incidence, Risk Factors and Case Fatality Rates of Invasive Nontyphoidal Salmonella (iNTS) Disease in Africa (1966 to 2014). PLoS Negl Trop Dis 2017; 11:e0005118. [PMID: 28056035 PMCID: PMC5215826 DOI: 10.1371/journal.pntd.0005118] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 10/19/2016] [Indexed: 11/19/2022] Open
Abstract
This study systematically reviews the literature on the occurrence, incidence and case fatality rate (CFR) of invasive nontyphoidal Salmonella (iNTS) disease in Africa from 1966 to 2014. Data on the burden of iNTS disease in Africa are sparse and generally have not been aggregated, making it difficult to describe the epidemiology that is needed to inform the development and implementation of effective prevention and control policies. This study involved a comprehensive search of PubMed and Embase databases. It documents the geographical spread of iNTS disease over time in Africa, and describes its reported incidence, risk factors and CFR. We found that Nontyphoidal Salmonella (NTS) have been reported as a cause of bacteraemia in 33 out of 54 African countries, spanning the five geographical regions of Africa, and especially in sub-Saharan Africa since 1966. Our review indicates that NTS have been responsible for up to 39% of community acquired blood stream infections in sub-Saharan Africa with an average CFR of 19%. Salmonella Typhimurium and Enteritidis are the major serovars implicated and together have been responsible for 91%% of the cases of iNTS disease, (where serotype was determined), reported in Africa. The study confirms that iNTS disease is more prevalent amongst Human Immunodeficiency Virus (HIV)-infected individuals, infants, and young children with malaria, anaemia and malnutrition. In conclusion, iNTS disease is a substantial cause of community-acquired bacteraemia in Africa. Given the high morbidity and mortality of iNTS disease in Africa, it is important to develop effective prevention and control strategies including vaccination.
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Affiliation(s)
| | | | - Allan Saul
- Novartis Vaccines Institute for Global Health, Siena, Italy
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50
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Moura Q, Fernandes MR, Cerdeira L, Ienne S, Souza TA, Negrão FJ, Lincopan N. Draft genome sequence of a multidrug-resistant CMY-2-producing Salmonella enterica subsp. enterica serovar Minnesota ST3088 isolated from chicken meat. J Glob Antimicrob Resist 2016; 8:67-69. [PMID: 28017672 DOI: 10.1016/j.jgar.2016.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 11/19/2022] Open
Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Susan Ienne
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio Juliano Negrão
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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