AUTHOR=Harrison Lucas , Mukherjee Sampa , Hsu Chih-Hao , Young Shenia , Strain Errol , Zhang Qijing , Tillman Glenn E. , Morales Cesar , Haro Jovita , Zhao Shaohua 

TITLE=Core Genome MLST for Source Attribution of Campylobacter coli

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.703890

DOI=10.3389/fmicb.2021.703890

ISSN=1664-302X

ABSTRACT=<p><italic>Campylobacter</italic> species are among the leading foodborne bacterial agents of human diarrheal illness. The majority of campylobacteriosis has been attributed to <italic>Campylobacter jejuni</italic> (85% or more), followed by <italic>Campylobacter coli</italic> (5–10%). The distribution of <italic>C. jejuni</italic> and <italic>C. coli</italic> varies by host organism, indicating that the contribution to human infection may differ between isolation sources. To address the relative contribution of each source to <italic>C. coli</italic> infections in humans, core genome multilocus sequence type with a 200-allele difference scheme (cgMLST<sub>200</sub>) was used to determine cgMLST type for 3,432 <italic>C. coli</italic> isolated from food animals (<italic>n</italic> = 2,613), retail poultry meats (<italic>n</italic> = 389), human clinical settings (<italic>n</italic> = 285), and environmental sources (<italic>n</italic> = 145). Source attribution was determined by analyzing the core genome with a minimal multilocus distance methodology (MMD). Using MMD, a higher proportion of the clinical <italic>C. coli</italic> population was attributed to poultry (49.6%) and environmental (20.9%) sources than from cattle (9.8%) and swine (3.2%). Within the population of <italic>C. coli</italic> clinical isolates, 70% of the isolates that were attributed to non-cecal retail poultry, dairy cattle, beef cattle and environmental waters came from two cgMLST<sub>200</sub> groups from each source. The most common antibiotic resistance genes among all <italic>C. coli</italic> were <italic>tetO</italic> (65.6%), <italic>bla</italic><sub><italic>OXA</italic></sub><sub>–</sub><sub>193</sub> (54.2%), <italic>aph(3′)-IIIa</italic> (23.5%), and <italic>aadE-Cc</italic> (20.1%). Of the antibiotic resistance determinants, only one gene was isolated from a single source: <italic>bla</italic><sub><italic>OXA</italic></sub><sub>–</sub><sub>61</sub> was only isolated from retail poultry. Within cgMLST<sub>200</sub> groups, 17/17 cgMLST<sub>200</sub>-435 and 89/92 cgMLST<sub>200</sub>-707 isolates encoded for <italic>aph(3’)-VIIa</italic> and 16/16 cgMLST<sub>200</sub>-319 harbored <italic>aph(2’)-If</italic> genes. Distribution of <italic>bla</italic><sub><italic>OXA</italic></sub> alleles showed 49/50 cgMLST<sub>200</sub>-5 isolates contained <italic>bla</italic><sub><italic>OXA</italic></sub><sub>–</sub><sub>498</sub> while <italic>bla</italic><sub><italic>OXA</italic></sub><sub>–</sub><sub>460</sub> was present in 37/38 cgMLST<sub>200</sub>-650 isolates. The cgMLST<sub>200</sub>-514 group revealed both <italic>ant</italic>(6)<italic>-Ia</italic> and <italic>sat4</italic> resistance genes in 23/23 and 22/23 isolates, respectively. Also, cgMLST<sub>200</sub>-266 and cgMLST<sub>200</sub>-84 had GyrAT86I mutation with 16/16 (100%) and 14/15 (93.3%), respectively. These findings illustrate how cgMLST and MMD methods can be used to evaluate the relative contribution of known sources of <italic>C. coli</italic> to the human burden of campylobacteriosis and how cgMLST typing can be used as an indicator of antimicrobial resistance in <italic>C. coli</italic>.</p>