Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia

Abstract

Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistanceassociated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but tenfold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.

Susceptibility of Campylobacter Strains to Selected Natural Products and Frontline Antibiotics

“…There have been increased reports about high-level resistance to frontline and alternative antimicrobials, including macrolides, fluoroquinolones, aminoglycosides, and tetracyclines, among Campylobacter strains [ 7 , 8 ]. Increased antimicrobial resistance (AMR) among pathogens has been associated with many factors, including the unrestricted use of antimicrobials in various fields [ 9 , 10 ]. The main mechanisms of AMR include mutations in specific genes and acquiring efflux pumps [ 11 ].…”

Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance in Salmonella enterica subsp. enterica serovar Heidelberg

“…In the past decade, it has become increasingly common for studies to assert a 'genomic epidemiology' paradigm by superimposing geographic or source metadata onto descriptive results from WGS in the form of dendrograms or similar visualisations. Recently, studies have begun applying an analytical epidemiology framework to measure associations between the epidemiology of a pathogen and its genomic features [42,43]. By including considerations for sampling and controlling for confounding at the analysis stage, conclusions generated from results from bioinformatic and genomic analyses can be more readily extrapolated to the level of the target population [16].…”

Situational analysis on fluoroquinolones use and characterization of high-level ciprofloxacin-resistant Enterococcus faecalis by integrated broiler operations in South Korea

“…The plasmids carrying mobile resistance genes are easily transferable from one bacteria to another by conjugation, sharing genetic information ( 49 , 50 ). Moreover, the externalization of antimicrobials via efflux pumps responsible for the outflow of the antimicrobials can simultaneously confer resistance to several antimicrobials, and their overexpression can lead to high levels of resistance and MDR ( 51 – 53 ).…”