Antimicrobial resistance surveillance of Escherichia coli from chickens in the Qinghai Plateau of China

Abstract

Antimicrobial resistance (AMR) may lead to worldwide epidemics through human activities and natural transmission, posing a global public safety threat. Colistin resistance mediated by the mcr-1 gene is the most prevalent among animal-derived Escherichia coli, and mcr-1-carrying E. coli have been frequently detected in central-eastern China. However, animal-derived E. coli with AMR and the prevalence of mcr-1 in the Qinghai Plateau have been rarely investigated. Herein, 375 stool samples were collected from 13 poultry farms in Qinghai Province and 346 E. coli strains were isolated, of which eight carried mcr-1. The AMR rates of the E. coli strains to ampicillin, amoxicillin/clavulanic acid, and tetracycline were all above 90%, and the resistance rates to ciprofloxacin, cefotaxime, ceftiofur, and florfenicol were above 70%. Multidrug-resistant strains accounted for 95.66% of the total isolates. Twelve E. coli strains showed colistin resistance, from which a total of 46 AMR genes and 36 virulence factors were identified through whole-genome sequencing. The mcr-1 gene resided on the IncHI2, IncI2-type and IncY-type plasmids, and mcr-1 was located in the nikA-nikB-mcr-1-pap2 gene cassette (three strains) or the pap2-mcr-1-ISApl1 structure (one strain). Completed IncI2-type plasmid pMCR4D31-3 sequence (62,259 bp) revealed that it may cause the horizontal transmission of mcr-1 and may increase the risk of its spread through the food chain. Taken together, the AMR of chicken-derived E. coli in the plateau is of concern, suggesting that it is very necessary for us to strengthen the surveillance in various regions under the background of one health.

Keywords: Escherichia coli; Qinghai Plateau; antimicrobial resistance; genome sequences; mcr-1.

Figure 1

The sampling locations and susceptibility test results of 346 strains of Escherichia coli to 13 antibiotics. (A) Sampling areas in Qinghai Province, China. (B) AMR rates of E. coli. (C) The distribution of multidrug-resistant strains. (D) MIC distributions of 13 antibiotics in isolated E. coli strains.

Figure 2

Antimicrobial resistance profiles of 346 Escherichia coli strains. Vertical and horizontal trees represent clustering relationships. The abscissa is the antibiotic, and the ordinate is the E. coli isolate.

Figure 3

The insusceptibility of mcr-1-harboring Escherichia coli strains to colistin. (A) Bacterial viability of E. coli strains on LB plates containing different concentrations of colistin. The diluted suspension (10 μl) was inoculated onto the prepared LB plates. Escherichia coli ATCC 25922 was used as a negative control. (B) E-test to compare the MIC of colistin in E. coli strains. Escherichia coli ATCC 25922 was used as a negative control.

Figure 4

Acquired resistance genes, virulence genes, and plasmid replicon types of Escherichia coli strains with whole-genome sequences. (A) Antimicrobial resistance (AMR) gene profiles. Various types of AMR genes are labeled with different colors. White squares indicate no AMR genes. (B) Virulence gene profiles. Colored squares represent virulence genes, and white squares indicate no virulence genes. (C) Plasmid replicon profiles. Colored squares represent the presence of plasmids, and white squares indicate no plasmids.

Figure 5

Sequence alignment analysis of IncI2 (A) and IncHI2-type (B) plasmids carrying the mcr-1 gene. The arrows indicate the direction of gene transcription. Functional genes are shown in different colors. Regions of >95% nucleotide homology are indicated by colored shading.

Figure 6

Circular diagram of the IncI2 plasmids. Circles, from inside to outside, indicate the GC skew, GC content, and ORFs in the positive and negative DNA strands. Genes are shown in different colors.