Antimicrobial resistance and genomic diversity of Campylobacter jejuni isolates from broiler caeca and neck skin samples collected at key stages during processing

Phenotypic antimicrobial resistance testing of 160 Campylobacter jejuni isolates from broiler caeca and neck skin samples collected at key stages during processing from 32 batches was conducted to: (i) determine the prevalence of antimicrobial resistance in C. jejuni isolates (ii) investigate if C. jejuni strains with particular resistance profiles were more frequently recovered at the end of processing, (iii) to establish if multiple strains with different resistance profiles were present within individual batches of broilers and (iv) to determine the virulence profiles of isolates. C. jejuni isolates were tested for resistance to erythromycin (ERY), ciprofloxacin (CIP), tetracycline (TET), gentamicin (GEN), nalidixic acid (NAL) and streptomycin (STR) using a broth dilution phenotypic method. Resistance to TET was most prevalent (46%), followed by resistance to CIP and NAL (29%). All isolates were susceptible to ERY and GEN, while resistance to STR was low (2%). Strains with different resistance profiles were found within 8 individual batches of broilers. Both resistant and susceptible strains were present within 4 individual batches of broilers. Whole genome sequencing of 132 C. jejuni isolates was conducted to: (i) determine relationship between resistant phenotypes and genotypes, (ii) examine genomic diversity of strains present in caeca and in neck skin samples collected at different processing stages and (iii) gain insights into the genomic profiles, including the resistome and virulome of C. jejuni isolates. A high level of correlation between resistant phenotypes and genotypes was observed (99.2%). Resistance determinants identified in sequenced isolates using ResFinder included the tet(O) gene, tet(O/32/O) gene, gyrA p. T86I mutation and bla(OX)(A-)(61) like genes. A high correlation between sequence type (ST) and antimicrobial resistance was observed. The 132 sequenced C. jejuni isolates were assigned to 10 sequence types (STs), which belonged to 7 clonal complexes, based on multi-locus sequence typing (MLST). ST-257 was prevalent with 58 isolates assigned to it, followed by ST-51 with 25 isolates, ST-10089 with 16 isolates, ST-48 with 13 isolates and ST-50 with 12 isolates. Four isolates were assigned to ST-354, while 1 isolate was assigned to STs 464, 42, 1489 and 6209. All sequenced isolates were assigned to 17 cgSTs. Virulence genes which might have a role in Campylobacter survival and environmental adaptation during key processing stages and a number of virulence genes associated with human infection and colonization of broilers were detected. This study is one of the first to provide data on genomic diversity of C. jejuni isolates from broilers collected during processing in Ireland.