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Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa

Salmonella enterica serovar Typhi (S. Typhi) is either widely distributed or proximally transmitted via fecally-contaminated food or water to cause typhoid fever. In Samoa, where endemic typhoid fever has persisted over decades despite water quality and sanitation improvements, the local patterns of...

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Autores principales: Sikorski, Michael J., Ma, Jianguo, Hazen, Tracy H., Desai, Sachin N., Tupua, Siaosi, Nimarota-Brown, Susana, Sialeipata, Michelle, Rambocus, Savitra, Ballard, Susan A., Valcanis, Mary, Thomsen, Robert E., Robins-Browne, Roy M., Howden, Benjamin P., Naseri, Take K., Levine, Myron M., Rasko, David A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9612817/
https://www.ncbi.nlm.nih.gov/pubmed/36251704
http://dx.doi.org/10.1371/journal.pntd.0010348
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author Sikorski, Michael J.
Ma, Jianguo
Hazen, Tracy H.
Desai, Sachin N.
Tupua, Siaosi
Nimarota-Brown, Susana
Sialeipata, Michelle
Rambocus, Savitra
Ballard, Susan A.
Valcanis, Mary
Thomsen, Robert E.
Robins-Browne, Roy M.
Howden, Benjamin P.
Naseri, Take K.
Levine, Myron M.
Rasko, David A.
author_facet Sikorski, Michael J.
Ma, Jianguo
Hazen, Tracy H.
Desai, Sachin N.
Tupua, Siaosi
Nimarota-Brown, Susana
Sialeipata, Michelle
Rambocus, Savitra
Ballard, Susan A.
Valcanis, Mary
Thomsen, Robert E.
Robins-Browne, Roy M.
Howden, Benjamin P.
Naseri, Take K.
Levine, Myron M.
Rasko, David A.
author_sort Sikorski, Michael J.
collection PubMed
description Salmonella enterica serovar Typhi (S. Typhi) is either widely distributed or proximally transmitted via fecally-contaminated food or water to cause typhoid fever. In Samoa, where endemic typhoid fever has persisted over decades despite water quality and sanitation improvements, the local patterns of S. Typhi circulation remain unclear. From April 2018-June 2020, epidemiologic data and GPS coordinates were collected during household investigations of 260 acute cases of typhoid fever, and 27 asymptomatic shedders of S. Typhi were detected among household contacts. Spatial and temporal distributions of cases were examined using Average Nearest Neighbor and space-time hotspot analyses. In rural regions, infections occurred in sporadic, focal clusters contrasting with persistent, less clustered cases in the Apia Urban Area. Restrictions to population movement during nationwide lockdowns in 2019–2020 were associated with marked reductions of cases. Phylogenetic analyses of isolates with whole genome sequences (n = 186) revealed one dominant genotype 3.5.4 (n = 181/186) that contains three Samoa-exclusive sub-lineages: 3.5.4.1, 3.5.4.2, and 3.5.4.3. Variables of patient sex, age, and geographic region were examined by phylogenetic groupings, and significant differences (p<0.05) associated genetically-similar isolates in urban areas with working ages (20–49 year olds), and in rural areas with age groups typically at home (<5, 50+). Isolates from asymptomatic shedders were among all three sub-lineages. Whole genome sequencing provided evidence of bacterial genetic similarity, which corroborated 10/12 putative epidemiologic linkages among cases and asymptomatic shedders, as well as 3/3 repeat positives (presumed relapses), with a median of one single nucleotide polymorphism difference. These findings highlight various patterns of typhoid transmission in Samoa that differ between urban and rural regions as well as genomic subtypes. Asymptomatic shedders, detectable only through household investigations, are likely an important reservoir and mobile agent of infection. This study advances a “Samoan S. Typhi framework” that supports current and future typhoid surveillance and control efforts in Samoa.
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spelling pubmed-96128172022-10-28 Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa Sikorski, Michael J. Ma, Jianguo Hazen, Tracy H. Desai, Sachin N. Tupua, Siaosi Nimarota-Brown, Susana Sialeipata, Michelle Rambocus, Savitra Ballard, Susan A. Valcanis, Mary Thomsen, Robert E. Robins-Browne, Roy M. Howden, Benjamin P. Naseri, Take K. Levine, Myron M. Rasko, David A. PLoS Negl Trop Dis Research Article Salmonella enterica serovar Typhi (S. Typhi) is either widely distributed or proximally transmitted via fecally-contaminated food or water to cause typhoid fever. In Samoa, where endemic typhoid fever has persisted over decades despite water quality and sanitation improvements, the local patterns of S. Typhi circulation remain unclear. From April 2018-June 2020, epidemiologic data and GPS coordinates were collected during household investigations of 260 acute cases of typhoid fever, and 27 asymptomatic shedders of S. Typhi were detected among household contacts. Spatial and temporal distributions of cases were examined using Average Nearest Neighbor and space-time hotspot analyses. In rural regions, infections occurred in sporadic, focal clusters contrasting with persistent, less clustered cases in the Apia Urban Area. Restrictions to population movement during nationwide lockdowns in 2019–2020 were associated with marked reductions of cases. Phylogenetic analyses of isolates with whole genome sequences (n = 186) revealed one dominant genotype 3.5.4 (n = 181/186) that contains three Samoa-exclusive sub-lineages: 3.5.4.1, 3.5.4.2, and 3.5.4.3. Variables of patient sex, age, and geographic region were examined by phylogenetic groupings, and significant differences (p<0.05) associated genetically-similar isolates in urban areas with working ages (20–49 year olds), and in rural areas with age groups typically at home (<5, 50+). Isolates from asymptomatic shedders were among all three sub-lineages. Whole genome sequencing provided evidence of bacterial genetic similarity, which corroborated 10/12 putative epidemiologic linkages among cases and asymptomatic shedders, as well as 3/3 repeat positives (presumed relapses), with a median of one single nucleotide polymorphism difference. These findings highlight various patterns of typhoid transmission in Samoa that differ between urban and rural regions as well as genomic subtypes. Asymptomatic shedders, detectable only through household investigations, are likely an important reservoir and mobile agent of infection. This study advances a “Samoan S. Typhi framework” that supports current and future typhoid surveillance and control efforts in Samoa. Public Library of Science 2022-10-17 /pmc/articles/PMC9612817/ /pubmed/36251704 http://dx.doi.org/10.1371/journal.pntd.0010348 Text en © 2022 Sikorski et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Sikorski, Michael J.
Ma, Jianguo
Hazen, Tracy H.
Desai, Sachin N.
Tupua, Siaosi
Nimarota-Brown, Susana
Sialeipata, Michelle
Rambocus, Savitra
Ballard, Susan A.
Valcanis, Mary
Thomsen, Robert E.
Robins-Browne, Roy M.
Howden, Benjamin P.
Naseri, Take K.
Levine, Myron M.
Rasko, David A.
Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa
title Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa
title_full Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa
title_fullStr Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa
title_full_unstemmed Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa
title_short Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa
title_sort spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in samoa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9612817/
https://www.ncbi.nlm.nih.gov/pubmed/36251704
http://dx.doi.org/10.1371/journal.pntd.0010348
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