Risk of Transmission of Antimicrobial Resistant Escherichia coli from Commercial Broiler and Free-Range Retail Chicken in India

Abstract

Multidrug-resistant Escherichia coli infections are a growing public health concern. This study analyzed the possibility of contamination of commercial poultry meat (broiler and free-range) with pathogenic and or multi-resistant E. coli in retail chain poultry meat markets in India. We analyzed 168 E. coli isolates from broiler and free-range retail poultry (meat/ceca) sampled over a wide geographical area, for their antimicrobial sensitivity, phylogenetic groupings, virulence determinants, extended-spectrum-β-lactamase (ESBL) genotypes, fingerprinting by Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and genetic relatedness to human pathogenic E. coli using whole genome sequencing (WGS). The prevalence rates of ESBL producing E. coli among broiler chicken were: meat 46%; ceca 40%. Whereas, those for free range chicken were: meat 15%; ceca 30%. E. coli from broiler and free-range chicken exhibited varied prevalence rates for multi-drug resistance (meat 68%; ceca 64% and meat 8%; ceca 26%, respectively) and extraintestinal pathogenic E. coli (ExPEC) contamination (5 and 0%, respectively). WGS analysis confirmed two globally emergent human pathogenic lineages of E. coli, namely the ST131 (H30-Rx subclone) and ST117 among our poultry E. coli isolates. These results suggest that commercial poultry meat is not only an indirect public health risk by being a possible carrier of non-pathogenic multi-drug resistant (MDR)-E. coli, but could as well be the carrier of human E. coli pathotypes. Further, the free-range chicken appears to carry low risk of contamination with antimicrobial resistant and extraintestinal pathogenic E. coli (ExPEC). Overall, these observations reinforce the understanding that poultry meat in the retail chain could possibly be contaminated by MDR and/or pathogenic E. coli.

Keywords: antibiotic resistance; food borne pathogens; poultry; whole genome sequencing; zoonosis.

FIGURE 1

Dendrogram representing genetic relationships of 38 broiler and 22 free-range chicken Escherichia coli isolates based on ERIC-PCR fingerprints. The clustering was performed by UPGMA algorithm based on Dice similarity coefficients. The genotypic patterns generated by ERIC-PCR were analyzed at 80% cutoff. Among the eight identical clades (C1 to C8), six clades corresponded consistently to geographic and isolation source.

FIGURE 2

Phylogenetic tree of 50 E. coli strains: the core genome based consensus Maximum Likelihood phylogenetic tree of 10 in-house poultry E. coli isolates together with 40 other publicly available human and animal disease associated E. coli isolates generated using Harvest. The output of Harvest was visualized using iTOL tool (http://itol.embl.de/). Despite genetic diversity, the phylogenetic tree on the whole was able to diffusely group isolates belonging to different pathotypes.

FIGURE 3

Distribution of EC958 genomic islands (GIs) in 6 ST131 E. coli genomes: results show that the 22 GIs of EC958 are well-conserved among three human and one in-house ST131 poultry E. coli genome (NAEC1) but partially present in the commensal ST131 (SE15) and the poultry E. coli genome from Germany (IHIT25637). Detail description of the genomes analyzed are as follows- JJ1886; CP006784.1 (Human ExPEC, United States), NA114; GCA_000214765.3 (Human ExPEC, India), NA097; GCA_001029415.1 (Human ExPEC, India), SE15; GCA_000010485.1 (Human commensal, Japan), IHIT25637; GCA_001676995.1 (Avian ExPEC, Germany).

FIGURE 4

Gene cluster results for 50 E. coli isolates: the presence (Black Square) and the absence (Gray Square) of virulence genes (A) and resistance genes (B) are represented in the image. Gene names are listed on the left. E. coli pathotypes are listed below the image (APEC: avian pathogenic E. coli, ExPEC: extraintestinal pathogenic E. coli, IPEC: intestinal pathogenic E. coli, PEC: healthy poultry E. coli, NA_PEC: in-house poultry E. coli). Results of resistance clustering indicated that only 50% of our poultry E. coli shared resistance genes with other E. coli pathotypes (distributed in mixed clusters 1a and 1b) and the rest formed a separate group (cluster 2, B). However, the virulence based cluster diagram showed that the in-house poultry (NAPEC) shared more virulence similarity with ExPEC and APEC genomes compared to intestinal pathogenic E. coli (IPEC), as cluster 2 of (A) was dominated by enteric E. coli genomes without any poultry E. coli genome.