Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
DOI: | 10.3389/fcimb.2022.772829 |
Texto Completo: | http://dx.doi.org/10.3389/fcimb.2022.772829 http://hdl.handle.net/11449/241290 |
Resumo: | Since its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated. |
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Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africaantimicrobial resistancefoodborne pathogengenetic diversitySalmonella pathogenicity islandssalmonellosiswhole genome sequencingSince its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Financiadora de Estudos e ProjetosCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Department of Pathology Theriogenology and One Health Sao Paulo State University (FCAV-Unesp)Department of Preventive Veterinary Medicine College of Veterinary Medicine The Ohio State UniversityDepartment of Animal Science Center for Agricultural Sciences Federal University of Paraiba (CCA/UFPB)Department of Technology Sao Paulo State University (FCAV-Unesp)Department of Preventive Veterinary Medicine Veterinary School Federal University of Minas Gerais (UFMG)Facultad de Medicina Veterinaria y Zootecnia Universidad Nacional Autónoma de México (UNAM)Aklilu Lemma Institute of Pathobiology Addis Ababa UniversityCentre for Microbiology Research Kenya Medical Research InstituteGlobal One Health Initiative (GOHi) The Ohio State UniversityDepartment of Pathology Theriogenology and One Health Sao Paulo State University (FCAV-Unesp)Department of Technology Sao Paulo State University (FCAV-Unesp)CAPES: 88881.131934/2016-01CAPES: 88881.311776/2018-01CAPES: Finance Code 001Universidade Estadual Paulista (UNESP)The Ohio State UniversityUniversidade Federal da Paraíba (UFPB)Universidade Federal de Minas Gerais (UFMG)Universidad Nacional Autónoma de México (UNAM)Addis Ababa UniversityKenya Medical Research InstituteSaraiva, Mauro de Mesquita Sousa [UNESP]Benevides, Valdinete Pereira [UNESP]Silva, Núbia Michelle Vieira daVarani, Alessandro de Mello [UNESP]Freitas Neto, Oliveiro Caetano deBerchieri, Ângelo [UNESP]Delgado-Suárez, Enrique JesúsRocha, Alan Douglas de LimaEguale, TadesseMunyalo, Janet AgnesKariuki, SamuelGebreyes, Wondwossen AbebeOliveira, Celso José Bruno de2023-03-01T20:55:26Z2023-03-01T20:55:26Z2022-06-20info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fcimb.2022.772829Frontiers in Cellular and Infection Microbiology, v. 12.2235-2988http://hdl.handle.net/11449/24129010.3389/fcimb.2022.7728292-s2.0-85133613488Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Cellular and Infection Microbiologyinfo:eu-repo/semantics/openAccess2024-06-07T15:32:22Zoai:repositorio.unesp.br:11449/241290Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:59:37.221082Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa |
title |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa |
spellingShingle |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa Saraiva, Mauro de Mesquita Sousa [UNESP] antimicrobial resistance foodborne pathogen genetic diversity Salmonella pathogenicity islands salmonellosis whole genome sequencing Saraiva, Mauro de Mesquita Sousa [UNESP] antimicrobial resistance foodborne pathogen genetic diversity Salmonella pathogenicity islands salmonellosis whole genome sequencing |
title_short |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa |
title_full |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa |
title_fullStr |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa |
title_full_unstemmed |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa |
title_sort |
Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa |
author |
Saraiva, Mauro de Mesquita Sousa [UNESP] |
author_facet |
Saraiva, Mauro de Mesquita Sousa [UNESP] Saraiva, Mauro de Mesquita Sousa [UNESP] Benevides, Valdinete Pereira [UNESP] Silva, Núbia Michelle Vieira da Varani, Alessandro de Mello [UNESP] Freitas Neto, Oliveiro Caetano de Berchieri, Ângelo [UNESP] Delgado-Suárez, Enrique Jesús Rocha, Alan Douglas de Lima Eguale, Tadesse Munyalo, Janet Agnes Kariuki, Samuel Gebreyes, Wondwossen Abebe Oliveira, Celso José Bruno de Benevides, Valdinete Pereira [UNESP] Silva, Núbia Michelle Vieira da Varani, Alessandro de Mello [UNESP] Freitas Neto, Oliveiro Caetano de Berchieri, Ângelo [UNESP] Delgado-Suárez, Enrique Jesús Rocha, Alan Douglas de Lima Eguale, Tadesse Munyalo, Janet Agnes Kariuki, Samuel Gebreyes, Wondwossen Abebe Oliveira, Celso José Bruno de |
author_role |
author |
author2 |
Benevides, Valdinete Pereira [UNESP] Silva, Núbia Michelle Vieira da Varani, Alessandro de Mello [UNESP] Freitas Neto, Oliveiro Caetano de Berchieri, Ângelo [UNESP] Delgado-Suárez, Enrique Jesús Rocha, Alan Douglas de Lima Eguale, Tadesse Munyalo, Janet Agnes Kariuki, Samuel Gebreyes, Wondwossen Abebe Oliveira, Celso José Bruno de |
author2_role |
author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) The Ohio State University Universidade Federal da Paraíba (UFPB) Universidade Federal de Minas Gerais (UFMG) Universidad Nacional Autónoma de México (UNAM) Addis Ababa University Kenya Medical Research Institute |
dc.contributor.author.fl_str_mv |
Saraiva, Mauro de Mesquita Sousa [UNESP] Benevides, Valdinete Pereira [UNESP] Silva, Núbia Michelle Vieira da Varani, Alessandro de Mello [UNESP] Freitas Neto, Oliveiro Caetano de Berchieri, Ângelo [UNESP] Delgado-Suárez, Enrique Jesús Rocha, Alan Douglas de Lima Eguale, Tadesse Munyalo, Janet Agnes Kariuki, Samuel Gebreyes, Wondwossen Abebe Oliveira, Celso José Bruno de |
dc.subject.por.fl_str_mv |
antimicrobial resistance foodborne pathogen genetic diversity Salmonella pathogenicity islands salmonellosis whole genome sequencing |
topic |
antimicrobial resistance foodborne pathogen genetic diversity Salmonella pathogenicity islands salmonellosis whole genome sequencing |
description |
Since its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-06-20 2023-03-01T20:55:26Z 2023-03-01T20:55:26Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3389/fcimb.2022.772829 Frontiers in Cellular and Infection Microbiology, v. 12. 2235-2988 http://hdl.handle.net/11449/241290 10.3389/fcimb.2022.772829 2-s2.0-85133613488 |
url |
http://dx.doi.org/10.3389/fcimb.2022.772829 http://hdl.handle.net/11449/241290 |
identifier_str_mv |
Frontiers in Cellular and Infection Microbiology, v. 12. 2235-2988 10.3389/fcimb.2022.772829 2-s2.0-85133613488 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in Cellular and Infection Microbiology |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1822218415517990912 |
dc.identifier.doi.none.fl_str_mv |
10.3389/fcimb.2022.772829 |