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Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018

The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serot...

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Autores principales: Singh, Nitya, Li, Xiaolong, Beshearse, Elizabeth, Blanton, Jason L., DeMent, Jamie, Havelaar, Arie H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8100233/
https://www.ncbi.nlm.nih.gov/pubmed/33968960
http://dx.doi.org/10.3389/fmed.2021.656827
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author Singh, Nitya
Li, Xiaolong
Beshearse, Elizabeth
Blanton, Jason L.
DeMent, Jamie
Havelaar, Arie H.
author_facet Singh, Nitya
Li, Xiaolong
Beshearse, Elizabeth
Blanton, Jason L.
DeMent, Jamie
Havelaar, Arie H.
author_sort Singh, Nitya
collection PubMed
description The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose “combination approach” comprising “HC5 clustering,” as efficient tool to trigger Salmonella outbreak investigations, and “SNP-based analysis,” for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017–2018. Several clusters of closely related isolates (0–4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.
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spelling pubmed-81002332021-05-07 Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018 Singh, Nitya Li, Xiaolong Beshearse, Elizabeth Blanton, Jason L. DeMent, Jamie Havelaar, Arie H. Front Med (Lausanne) Medicine The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose “combination approach” comprising “HC5 clustering,” as efficient tool to trigger Salmonella outbreak investigations, and “SNP-based analysis,” for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017–2018. Several clusters of closely related isolates (0–4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks. Frontiers Media S.A. 2021-04-22 /pmc/articles/PMC8100233/ /pubmed/33968960 http://dx.doi.org/10.3389/fmed.2021.656827 Text en Copyright © 2021 Singh, Li, Beshearse, Blanton, DeMent and Havelaar. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Medicine
Singh, Nitya
Li, Xiaolong
Beshearse, Elizabeth
Blanton, Jason L.
DeMent, Jamie
Havelaar, Arie H.
Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
title Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
title_full Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
title_fullStr Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
title_full_unstemmed Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
title_short Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
title_sort molecular epidemiology of salmonellosis in florida, usa, 2017–2018
topic Medicine
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8100233/
https://www.ncbi.nlm.nih.gov/pubmed/33968960
http://dx.doi.org/10.3389/fmed.2021.656827
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