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. 2021 Nov 5;9(11):2300.
doi: 10.3390/microorganisms9112300.

Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania

Lauren K Hudson  1 , William E Andershock  2 , Runan Yan  3 , Mugdha Golwalkar  4 , Nkuchia M M'ikanatha  5 , Irving Nachamkin  6 , Linda S Thomas  7 , Christina Moore  7 , Xiaorong Qian  7 , Richard Steece  7 , Katie N Garman  4 , John R Dunn  4 , Jasna Kovac  3 , Thomas G Denes  1
Affiliations

Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania

Lauren K Hudson et al. Microorganisms. .

Abstract

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 Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 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 C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni 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 C. coli 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 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.

Keywords: Campylobacter; Campylobacter coli; Campylobacter jejuni; source attribution.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Neighbor-joining phylogenetic tree of C. jejuni isolates. The optimal tree with the sum of branch length equal to 37,842.9 is shown. The tree is drawn to scale, with branch lengths representing core SNP distances. There were a total of 6132 core SNP positions in the final dataset. Symbols at the end of tree leaves indicate isolation location and source (see legend). Figure S1 is an alternate rendering of the tree with bootstrap values and additional information.
Figure 2
Figure 2
Neighbor-joining phylogenetic tree of C. coli isolates. The optimal tree with the sum of branch length equal to 73,485.2 is shown. The tree is drawn to scale, with branch lengths representing core SNP distances. There were a total of 11,628 core SNP positions in the final dataset. Symbols at the end of tree leaves indicate isolation location and source (see legend). Figure S2 is an alternate rendering of the tree with bootstrap values and additional information.
See this image and copyright information in PMC

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