Comparative Analysis of Phylogenetic Relationships and Virulence Factor Characteristics between Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Derived from Clinical Sites and Chicken Farms

Abstract

Antimicrobial resistance in bacteria is the most urgent global threat to public health, with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) being one of the most documented examples. Nonetheless, the ESBL-E. coli transmission relationship among clinical sites and chicken farms remains unclear. Here, 408 ESBL-E. coli strains were isolated from hospitals and chicken farms in Sichuan Province and Yunnan Province in 2021. We detected bla_CTX-M genes in 337 (82.62%) ESBL-E. coli strains. Although the isolation rate, prevalent sequence type (ST) subtypes, and bla_CTX-M gene subtypes of ESBL-E. coli varied based on regions and sources, a few strains of CTX-ESBL-E. coli derived from clinical sites and chicken farms in Sichuan Province displayed high genetic similarity. This indicates a risk of ESBL-E. coli transmission from chickens to humans. Moreover, we found that the high-risk clonal strains ST131 and ST1193 primarily carried bla_CTX-M-27. This indicates that drug-resistant E. coli from animal and human sources should be monitored. As well, the overuse of β-lactam antibiotics should be avoided in poultry farms to ensure public health and build an effective regulatory mechanism of "farm to fork" under a One Health perspective. IMPORTANCE Bacterial drug resistance has become one of the most significant threats to human health worldwide, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-E. coli). Timely and accurate epidemiological surveys can provide scientific guidance for the adoption of treatments in different regions and also reduce the formation of drug-resistant bacteria. Our study showed that the subtypes of ESBL-E. coli strains prevalent in different provinces are somewhat different, so it is necessary to individualize treatment regimens in different regions, and it is especially important to limit and reduce antibiotic use in poultry farming since chicken-derived ESBL-E. coli serves as an important reservoir of drug resistance genes and has the potential to spread to humans, thus posing a threat to human health. The use of antibiotics in poultry farming should be particularly limited and reduced.

Keywords: ESBL-E. coli; blaCTX-M; chicken farm; hospital; virulence factor.

FIG 1

Isolation and phylogenetic analysis of CTX-ESBL-E. coli. (a) Isolation rate of CTX-ESBL-E. coli in chicken farm-derived isolates and clinical isolates. (b) Isolation rate of CTX-ESBL-E. coli in chicken farm-derived isolates and clinical isolates in Sichuan Province and Yunnan Province. SCAE and YNAE indicate the chicken farm-derived CTX-ESBL-E. coli in Sichuan Province and Yunnan Province, respectively, SCHE and YNHE indicate the clinical CTX-ESBL-E. coli in Sichuan Province and Yunnan Province, respectively. (c) Distribution of 131 CTX-ESBL-E. coli isolates used for whole-genome sequencing. (d and e) Isolation rates of four phylogenetic groups of 131 CTX-ESBL-E. coli isolates.

FIG 2

Single nucleotide polymorphism evolutionary analysis of CTX-ESBL-E. coli isolates. The SNP evolution tree was created with CGE CSI Phylogeny 1.4, which was observed using the Interactive Tree Of Life (iTOL v6, https://itol.embl.de/). The genome sequence of E. coli C600 (EC600, GenBank accession no. CP031214.1) was used as a reference.

FIG 3

Minimum spanning tree analysis based on multilocus sequence typing analyses of CTX-ESBL-E. coli. (a) ST distribution of CTX-ESBL-E. coli isolates. (b to e) ST distribution of CTX-ESBL-E. coli isolates from different regions and sources. (f and g) Number of shared STs in the CTX-ESBL-E. coli isolates.

FIG 4

Antimicrobial sensitivity test, antimicrobial resistance genes, and plasmid replicon analysis of CTX-ESBL-E. coli. (a) Numbers of various drug resistance genes carried by CTX-ESBL-E. coli isolates from different regions and sources. The histogram in the upper right corner indicates the number of strains carrying different bla_CTX-M genes. ARG, antimicrobial resistance gene. (b) Comparative analysis of the number of drug resistance genes carried by CTX-ESBL-E. coli from different regions and sources. ***, P ≤ 0.001; ****, P ≤ 0.0001. (c) Antibiotic resistance phenotypes, antibiotic resistance genes, and plasmid replicon analysis of the CTX-ESBL-E. coli. The evolutionary tree was constructed using GrapeTree of the EnteroBase site based on the STs and visualized using iTOL v.6.

FIG 5

Analysis of virulence-associated genes. (a) Number of virulence-associated genes in CTX-ESBL-E. coli isolates from various sources. The histogram in the upper right corner indicates the number of the 24 virulence factors with the highest detection rate carried by the CTX-ESBL-E. coli isolates from different sources. (b) Comparative analysis of the number of virulence-associated genes carried by CTX-ESBL-E. coli isolates from different sources; *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001. (c) Virulence-associated gene distribution in the CTX-ESBL-E. coli isolates, the evolutionary tree was constructed using GrapeTree of the EnteroBase site based on the STs and visualized using iTOL v.6.

FIG 6

Comparison of the relationships between antimicrobial resistance genes, virulence genes, and STs. (a) Correlation between antibiotic resistance genes and virulence genes. VF, virulence factor. (b) Number of virulence factors in CTX-ESBL-E. coli isolates containing various bla_CTX-M genes. (c) Number of virulence factors in different STs of E. coli. (d and e) Correlation between bla_CTX-M genes and STs. *, 0.01 < P < 0.05; **, 0.001 < P < 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001. (f) Virulence factors in ST131 and ST1193 E. coli.