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. 2023 Jul 13:14:1197579.
doi: 10.3389/fmicb.2023.1197579. eCollection 2023.

The emergence of multi-drug resistant and virulence gene carrying Escherichia coli strains in the dairy environment: a rising threat to the environment, animal, and public health

Muhammad Shoaib  1 , Zhoulin He  1 , Xiang Geng  1 , Minjia Tang  1 , Ruochen Hao  1 , Shengyi Wang  1 , Ruofeng Shang  1 , Xuehong Wang  1 , Hongjuan Zhang  1 , Wanxia Pu  1
Affiliations

The emergence of multi-drug resistant and virulence gene carrying Escherichia coli strains in the dairy environment: a rising threat to the environment, animal, and public health

Muhammad Shoaib et al. Front Microbiol. .

Abstract

Escherichia coli is a common inhabitant of the intestinal microbiota and is responsible for udder infection in dairy cattle and gastro-urinary tract infections in humans. We isolated E. coli strains from a dairy farm environment in Xinjiang, China, and investigated their epidemiological characteristics, phenotypic and genotypic resistance to antimicrobials, virulence-associated genes, and phylogenetic relationship. A total of 209 samples were collected from different sources (feces, slurry, water, milk, soil) and cultured on differential and selective agar media (MAC and EMB). The presumptive identification was done by the VITEK2 system and confirmed by 16S rRNA gene amplification by PCR. Antimicrobial susceptibility testing was done by micro-dilution assay, and genomic characterization was done by simple and multiplex polymerase chain reaction (PCR). A total of 338 E. coli strains were identified from 141/209 (67.5%) of the samples. Most of the E. coli strains were resistant to sulfamethoxazole/trimethoprim (62.43%), followed by cefotaxime (44.08%), ampicillin (33.73%), ciprofloxacin (31.36%), tetracycline (28.99%), and a lesser extent to florfenicol (7.99%), gentamicin (4.44%), amikacin (1.77%), and fosfomycin (1.18%). All of the strains were susceptible to meropenem, tigecycline, and colistin sulfate. Among the resistant strains, 44.4% were identified as multi-drug resistant (MDR) showing resistance to at least one antibiotic from ≥3 classes of antibiotics. Eighteen out of 20 antibiotic-resistance genes (ARGs) were detected with sul2 (67.3%), blaTEM (56.3%), gyrA (73.6%), tet(B) (70.4%), aph(3)-I (85.7%), floR (44.4%), and fosA3 (100%, 1/1) being the predominant genes among different classes of antibiotics. Among the virulence-associated genes (VAGs), ompA was the most prevalent (86.69%) followed by ibeB (85.0%), traT (84.91%), ompT (73.96%), fyuA (23.1%), iroN (23.1%), and irp2 gene (21.9%). Most of the E. coli strains were classified under phylogenetic group B1 (75.45%), followed by A (18.34%), C (2.96%), D (1.18%), E (1.18%), and F (0.30%). The present study identified MDR E. coli strains carrying widely distributed ARGs and VAGs from the dairy environment. The findings suggested that the dairy farm environment may serve as a source of mastitis-causing pathogens in animals and horizontal transfer of antibiotic resistance and virulence genes carrying bacterial strains to humans via contaminated milk and meat, surface water and agricultural crops.

Keywords: Escherichia coli; antibiotic resistance genes (ARGs); antimicrobial resistance; dairy environment; multi-drug resistance; virulence associated genes.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Distribution of samples collected from different sources.
Figure 2
Figure 2
Isolation of Escherichia coli strains in different sampling years and sources. (A) Total number of E. coli strains isolated in different years. (B) Distribution of E. coli strains isolated from different sources in different years; **, indicate non-significant difference (p > 0.05); *, indicate not applicable; ***, indicate significant difference (p < 0.05).
Figure 3
Figure 3
Antimicrobial susceptibility of the 338 E. coli strains isolated from the dairy environment. (A) The overall resistant (R) and susceptible (S) E. coli strains. (B) The overall antimicrobial susceptibility of 338 E. coli strains against individual antibiotic tested. (C) The comparison of antimicrobial susceptibility of E. coli strains from different sampling years. AMP, ampicillin; CTX, cefotaxime; MEM, meropenem; SXT, trimethoprim-sulfamethoxazole; CIP, ciprofloxacin; AMK, amikacin; GEN, gentamicin; TET, tetracycline; TIG, tigecycline; FFC, florfenicol; FOS, fosfomycin; CS, colistin sulfate; **, indicate non-significant difference (p > 0.05); *, indicate not applicable; ***, indicate significant difference (p < 0.05).
Figure 4
Figure 4
AMR rates of E. coli strains isolated from different sources. (A) fecal sample. (B) manure slurry from the storage tank. (C) raw milk. (D) blank soil. (E) crop field soil. AMP, ampicillin; CTX, cefotaxime; MEM, meropenem; CIP, ciprofloxacin; AMK, amikacin; GEN, gentamicin; TET, tetracycline; TIG, tigecycline; SXT, trimethoprim/sulfamethoxazole; FOS, fosfomycin; COL, colistin; FFC, florfenicol; **, indicate non-significant difference (p > 0.05); *, indicate not applicable; ***, indicate significant difference (p < 0.05).
Figure 5
Figure 5
Drug-resistance spectrum of E. coli strains isolated from the dairy environment. (A) proportions of MDR and non-MDR strains. (B) Percentage resistance spectrum of 284 E. coli strains to 1 ~ 8 antibiotics.
Figure 6
Figure 6
Percentage distribution of ARGs among E. coli strains.
Figure 7
Figure 7
Escherichia coli strains carrying virulence-associated genes (VAGs). (A) Overall percentage and number of positive E. coli strains to carry VAGs. (B) Percentage distribution of VAGs among the E. coli strains isolated from different sources.
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References

    1. Afema J. A., Ahmed S., Besser T. E., Jones L. P., Sischo W. M., Davis M. A. (2018). Molecular epidemiology of dairy cattle-associated Escherichia coli carrying Bla CTX-M genes in Washington state. Appl. Environ. Microbiol. 84, e02430–e02417. doi: 10.1128/AEM.02430-17 - DOI - PMC - PubMed
    1. Alfinete N. W., Bolukaoto J. Y., Heine L., Potgieter N., Barnard T. G. (2022). Virulence and phylogenetic analysis of enteric pathogenic Escherichia coli isolated from children with diarrhoea in South Africa. Int. J. Infect. Dis. 114, 226–232. doi: 10.1016/j.ijid.2021.11.017, PMID: - DOI - PubMed
    1. Amézquita-López B. A., Soto-Beltrán M., Lee B. G., Yambao J. C., Quiñones B. (2018). Isolation, genotyping and antimicrobial resistance of Shiga toxin-producing Escherichia coli. J. Microbiol. Immunol. Infect. 51, 425–434. doi: 10.1016/j.jmii.2017.07.004 - DOI - PubMed
    1. Bacanlı M., Başaran N. (2019). Importance of antibiotic residues in animal food. Food Chem. Toxicol. 125, 462–466. doi: 10.1016/j.fct.2019.01.033 - DOI - PubMed
    1. Beattie R. E., Bakke E., Konopek N., Thill R., Munson E., Hristova K. R. (2020). Antimicrobial resistance traits of Escherichia coli isolated from dairy manure and freshwater ecosystems are similar to one another but differ from associated clinical isolates. Microorganisms 8:747. doi: 10.3390/microorganisms8050747, PMID: - DOI - PMC - PubMed

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