Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania

Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical <i>Campylobacter</i> populations from Tennessee (TN) and Pennsylvania (PA), u...

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Autores principales:	Lauren K. Hudson, William E. Andershock, Runan Yan, Mugdha Golwalkar, Nkuchia M. M’ikanatha, Irving Nachamkin, Linda S. Thomas, Christina Moore, Xiaorong Qian, Richard Steece, Katie N. Garman, John R. Dunn, Jasna Kovac, Thomas G. Denes
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Campylobacter</i> <i>Campylobacter jejuni</i> <i>Campylobacter coli</i> source attribution Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/54263b671a2740489517705fb7dadefc
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spelling	oai:doaj.org-article:54263b671a2740489517705fb7dadefc2021-11-25T18:24:57ZPhylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania10.3390/microorganisms91123002076-2607https://doaj.org/article/54263b671a2740489517705fb7dadefc2021-11-01T00:00:00Zhttps://www.mdpi.com/2076-2607/9/11/2300https://doaj.org/toc/2076-2607Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical <i>Campylobacter</i> populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. <i>Campylobacter</i> isolates studied (<i>n</i> = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were <i>C. jejuni</i> (<i>n</i> = 2132, 69.2%) and <i>C. coli</i> (<i>n</i> = 921, 29.9%), while the remaining were <i>C. lari</i> (0.4%), <i>C. upsaliensis</i> (0.3%), and <i>C. fetus</i> (0.1%). The <i>C. jejuni</i> group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The <i>C. coli</i> isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 <i>C. jejuni</i> and one <i>C. coli</i> potential outbreak clusters. The <i>C. jejuni</i> clusters contained 188 clinical isolates, 19.6% of the total <i>C. jejuni</i> clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.Lauren K. HudsonWilliam E. AndershockRunan YanMugdha GolwalkarNkuchia M. M’ikanathaIrving NachamkinLinda S. ThomasChristina MooreXiaorong QianRichard SteeceKatie N. GarmanJohn R. DunnJasna KovacThomas G. DenesMDPI AGarticle<i>Campylobacter</i><i>Campylobacter jejuni</i><i>Campylobacter coli</i>source attributionBiology (General)QH301-705.5ENMicroorganisms, Vol 9, Iss 2300, p 2300 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Campylobacter</i> <i>Campylobacter jejuni</i> <i>Campylobacter coli</i> source attribution Biology (General) QH301-705.5
spellingShingle	<i>Campylobacter</i> <i>Campylobacter jejuni</i> <i>Campylobacter coli</i> source attribution Biology (General) QH301-705.5 Lauren K. Hudson William E. Andershock Runan Yan Mugdha Golwalkar Nkuchia M. M’ikanatha Irving Nachamkin Linda S. Thomas Christina Moore Xiaorong Qian Richard Steece Katie N. Garman John R. Dunn Jasna Kovac Thomas G. Denes Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania
description	Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical <i>Campylobacter</i> populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. <i>Campylobacter</i> isolates studied (<i>n</i> = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were <i>C. jejuni</i> (<i>n</i> = 2132, 69.2%) and <i>C. coli</i> (<i>n</i> = 921, 29.9%), while the remaining were <i>C. lari</i> (0.4%), <i>C. upsaliensis</i> (0.3%), and <i>C. fetus</i> (0.1%). The <i>C. jejuni</i> group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The <i>C. coli</i> isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 <i>C. jejuni</i> and one <i>C. coli</i> potential outbreak clusters. The <i>C. jejuni</i> clusters contained 188 clinical isolates, 19.6% of the total <i>C. jejuni</i> clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.
format	article
author	Lauren K. Hudson William E. Andershock Runan Yan Mugdha Golwalkar Nkuchia M. M’ikanatha Irving Nachamkin Linda S. Thomas Christina Moore Xiaorong Qian Richard Steece Katie N. Garman John R. Dunn Jasna Kovac Thomas G. Denes
author_facet	Lauren K. Hudson William E. Andershock Runan Yan Mugdha Golwalkar Nkuchia M. M’ikanatha Irving Nachamkin Linda S. Thomas Christina Moore Xiaorong Qian Richard Steece Katie N. Garman John R. Dunn Jasna Kovac Thomas G. Denes
author_sort	Lauren K. Hudson
title	Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania
title_short	Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania
title_full	Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania
title_fullStr	Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania
title_full_unstemmed	Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania
title_sort	phylogenetic analysis reveals source attribution patterns for <i>campylobacter</i> spp. in tennessee and pennsylvania
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/54263b671a2740489517705fb7dadefc
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Phylogenetic Analysis Reveals Source Attribution Patterns for <i>Campylobacter</i> spp. in Tennessee and Pennsylvania

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