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

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.

Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance

“…The relationship between STs, phenotypic resistance, seasonality and the presence of pTet plasmid was assessed using Fisher's exact test (GraphPad Prism 9.1.2). Source attribution patterns were assigned based on ST-ecotype associations described in recent publications [41][42][43]. Gene annotation was carried out from the draft assemblies using Prokka v.1.13 [44].…”

Phylogeny and Genomic Characterization of Clinical Salmonella enterica Serovar Newport Collected in Tennessee

“…This may indicate that there are more related cases than previously thought, similar to what was found in Campylobacter spp. ( 32 ). However, isolation dates and other epidemiological data were not taken into account when identifying potential clusters in the current study, as would be done for cluster detection by public health departments.…”

“…Putative clusters were identified as previously described ( 32 ). Candidate clusters of Salmonella Newport consisting of at least three isolates were identified using SNP distances from the lineage-specific phylogenetic analyses and a threshold of 15 SNPs.…”

Pathogen genomics and One Health: a scoping review of current practices in zoonotic disease research

“…In our study, evolutionary models that included three domains and/or above-average sample sizes did not necessarily translate to accurate model validation. In some cases, phylogenetic inference was relatively simple for studies including intense sampling efforts (e.g., Tsui et al , 2018; Sia et al , 2020; Hudson et al , 2021). Nevertheless, sampling effort and evolutionary model complexity should not be mistaken for realism; many studies may choose to focus on a lower sampling effort and on a single interface (i.e., human-animal or human-environment) and apply relatively simple phylogenetic methods which allowed them to accurately depict transmission dynamics.…”