Assessing the occurrence and transfer dynamics of ESBL/pAmpC-producing Escherichia coli across the broiler production pyramid

Abstract

Extended-spectrum β-lactamase (ESBL)- and plasmid mediated AmpC-type cephalosporinase (pAmpC)-producing Escherichia coli (ESBL/pAmpC E. coli) in food-producing animals is a major public health concern. This study aimed at quantifying ESBL/pAmpC-E. coli occurrence and transfer in Italy's broiler production pyramid. Three production chains of an integrated broiler company were investigated. Cloacal swabs were taken from parent stock chickens and offspring broiler flocks in four fattening farms per chain. Carcasses from sampled broiler flocks were collected at slaughterhouse. Samples were processed on selective media, and E. coli colonies were screened for ESBL/pAmpC production. ESBL/pAmpC genes and E. coli phylogroups were determined by PCR and sequencing. Average pairwise overlap of ESBL/pAmpC E. coli gene and phylogroup occurrences between subsequent production stages was estimated using the proportional similarity index, modelling uncertainty in a Monte Carlo simulation setting. In total, 820 samples were processed, from which 513 ESBL/pAmpC E. coli isolates were obtained. We found a high prevalence (92.5%, 95%CI 72.1-98.3%) in day-old parent stock chicks, in which blaCMY-2 predominated; prevalence then dropped to 20% (12.9-29.6%) at laying phase. In fattening broilers, prevalence was 69.2% (53.6-81.3%) at the start of production, 54.2% (38.9-68.6%) at slaughter time, and 61.3% (48.1-72.9%) in carcasses. Significantly decreasing and increasing trends for respectively blaCMY-2 and blaCTX-M-1 gene occurrences were found across subsequent production stages. ESBL/pAmpC E. coli genetic background appeared complex and bla-gene/phylogroup associations indicated clonal and horizontal transmission. Modelling revealed that the average transfer of ESBL/pAmpC E. coli genes between subsequent production stages was 47.7% (42.3-53.4%). We concluded that ESBL/pAmpC E. coli in the broiler production pyramid is prevalent, with substantial transfer between subsequent production levels.

Fig 1. Prevalence of ESBL/pAmpC E. coli in the broiler production pyramid.

From left to right: PS chicks, PS breeders, broiler chicks, broilers and carcasses. Bars represent corresponding 95% confidence intervals.

Fig 2

Distribution of ESBL/pAmpC genes (A) and E. coli phylogroups (B) in the broiler production pyramid. (A) cAmpC, isolates with chromosomal mutations in the ampC promoter/attenuator. (A) and (B) from left to right: PS chicks, PS breeders, broiler chicks, broilers and carcasses.

Fig 3. Detected isolates by phylogroup/bla-gene combination and corresponding production stages.

Size of segments on the right represent the number of isolates with a specific combination. Size of segments on the left represent the number of isolates detected in different production stages. Ribbons connecting left and right segments represent the number of isolates with a specific combination found on the respective production stage. Chord diagram generated with CIRCOS [29].

Fig 4. Transfer of ESBL/pAmpC E. coli across the production pyramid.

BrS1, PS chicks; BrS2, PS breeders; F1-4S1, farm 1–4 broiler chicks; F1-4S2, farm 1–4 broilers; F1-4Sc, farm 1–4 carcasses. Arrows and text boxes indicate the overlap of genotyping data in subsequent sampling stages (bold) at three levels (M1-M3) of increasing stratification. Underlined text indicates the time elapsed between sampling two consecutive stages.