Cargando…

A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing

BACKGROUND: Campylobacter is a leading global cause of bacterial gastroenteritis, motivating research to identify sources of human infection. Population genetic studies have been increasingly applied to this end, mainly using multilocus sequence typing (MLST) data. OBJECTIVES: This review aimed to s...

Descripción completa

Detalles Bibliográficos
Autores principales: Cody, Alison J, Maiden, Martin CJ, Strachan, Norval JC, McCarthy, Noel D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: European Centre for Disease Prevention and Control (ECDC) 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6820127/
https://www.ncbi.nlm.nih.gov/pubmed/31662159
http://dx.doi.org/10.2807/1560-7917.ES.2019.24.43.1800696
_version_ 1783463878732021760
author Cody, Alison J
Maiden, Martin CJ
Strachan, Norval JC
McCarthy, Noel D
author_facet Cody, Alison J
Maiden, Martin CJ
Strachan, Norval JC
McCarthy, Noel D
author_sort Cody, Alison J
collection PubMed
description BACKGROUND: Campylobacter is a leading global cause of bacterial gastroenteritis, motivating research to identify sources of human infection. Population genetic studies have been increasingly applied to this end, mainly using multilocus sequence typing (MLST) data. OBJECTIVES: This review aimed to summarise approaches and findings of these studies and identify best practice lessons for this form of genomic epidemiology. METHODS: We systematically reviewed publications using MLST data to attribute human disease isolates to source. Publications were from January 2001, when this type of approach began. Searched databases included Scopus, Web of Science and PubMed. Information on samples and isolate datasets used, as well as MLST schemes and attribution algorithms employed, was obtained. Main findings were extracted, as well as any results’ validation with subsequent correction for identified biases. Meta-analysis is not reported given high levels of heterogeneity. RESULTS: Of 2,109 studies retrieved worldwide, 25 were included, and poultry, specifically chickens, were identified as principal source of human infection. Ruminants (cattle or sheep) were consistently implicated in a substantial proportion of cases. Data sampling and analytical approaches varied, with five different attribution algorithms used. Validation such as self-attribution of isolates from known sources was reported in five publications. No publication reported adjustment for biases identified by validation. CONCLUSIONS: Common gaps in validation and adjustment highlight opportunities to generate improved estimates in future genomic attribution studies. The consistency of chicken as the main source of human infection, across high income countries, and despite methodological variations, highlights the public health importance of this source.
format Online
Article
Text
id pubmed-6820127
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher European Centre for Disease Prevention and Control (ECDC)
record_format MEDLINE/PubMed
spelling pubmed-68201272019-11-08 A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing Cody, Alison J Maiden, Martin CJ Strachan, Norval JC McCarthy, Noel D Euro Surveill Review BACKGROUND: Campylobacter is a leading global cause of bacterial gastroenteritis, motivating research to identify sources of human infection. Population genetic studies have been increasingly applied to this end, mainly using multilocus sequence typing (MLST) data. OBJECTIVES: This review aimed to summarise approaches and findings of these studies and identify best practice lessons for this form of genomic epidemiology. METHODS: We systematically reviewed publications using MLST data to attribute human disease isolates to source. Publications were from January 2001, when this type of approach began. Searched databases included Scopus, Web of Science and PubMed. Information on samples and isolate datasets used, as well as MLST schemes and attribution algorithms employed, was obtained. Main findings were extracted, as well as any results’ validation with subsequent correction for identified biases. Meta-analysis is not reported given high levels of heterogeneity. RESULTS: Of 2,109 studies retrieved worldwide, 25 were included, and poultry, specifically chickens, were identified as principal source of human infection. Ruminants (cattle or sheep) were consistently implicated in a substantial proportion of cases. Data sampling and analytical approaches varied, with five different attribution algorithms used. Validation such as self-attribution of isolates from known sources was reported in five publications. No publication reported adjustment for biases identified by validation. CONCLUSIONS: Common gaps in validation and adjustment highlight opportunities to generate improved estimates in future genomic attribution studies. The consistency of chicken as the main source of human infection, across high income countries, and despite methodological variations, highlights the public health importance of this source. European Centre for Disease Prevention and Control (ECDC) 2019-10-24 /pmc/articles/PMC6820127/ /pubmed/31662159 http://dx.doi.org/10.2807/1560-7917.ES.2019.24.43.1800696 Text en This article is copyright of the authors or their affiliated institutions, 2019. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence. You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence, and indicate if changes were made.
spellingShingle Review
Cody, Alison J
Maiden, Martin CJ
Strachan, Norval JC
McCarthy, Noel D
A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing
title A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing
title_full A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing
title_fullStr A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing
title_full_unstemmed A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing
title_short A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing
title_sort systematic review of source attribution of human campylobacteriosis using multilocus sequence typing
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6820127/
https://www.ncbi.nlm.nih.gov/pubmed/31662159
http://dx.doi.org/10.2807/1560-7917.ES.2019.24.43.1800696
work_keys_str_mv AT codyalisonj asystematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping
AT maidenmartincj asystematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping
AT strachannorvaljc asystematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping
AT mccarthynoeld asystematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping
AT codyalisonj systematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping
AT maidenmartincj systematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping
AT strachannorvaljc systematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping
AT mccarthynoeld systematicreviewofsourceattributionofhumancampylobacteriosisusingmultilocussequencetyping