Phenotypic and genotypic characteristics of Escherichia coli with non-susceptibility to quinolones isolated from environmental samples on pig farms

Abstract

Background In the last decade, the growth of the pig-farming industry has led to an increase in antibiotic use, including several used in human medicine, e.g. (fluoro)quinolones. Data from several studies suggest that there is a link between the agricultural use of antibiotics and the prevalence of antibiotic-resistant bacteria in the pig farm environment, including (fluoro)quinolone resistance. This poses a threat to human and animal health. Our goal was to phenotypically and genotypically characterize 174 E. coli showing non-susceptibility to quinolones isolated from environmental samples from pig farms. Antimicrobial susceptibility testing (AST) was performed using the disk diffusion method. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of gyrA and the isolates were screened for the presence of the plasmid-mediated quinolone resistance (PMQR) genes aac-(6')-Ib-cr , qepA , qnrA , qnrB , qnrC , qnrD and qnrS . Strain relatedness was assessed by phylogenetic classification and multilocus sequence typing (MLST). Results Of 174 isolates, 81% ( n = 141) were resistant to nalidixic acid, and 19% ( n = 33) were intermediately resistant. Overall, 68.4% ( n = 119) were multidrug resistant. This study revealed a prevalence of 79.9% ( n = 139) for gyrA QRDR mutations, and detected 21.8% ( n = 38) isolates with at least one PMQR gene. The two most frequently detected PMQR genes were qnrB and qnrS (13.8% ( n = 24) and 9.8% ( n = 17, respectively). E. coli belonging to phylogenetic group A (48.3%/ n = 84) and group B1 (33.3% / n = 58) were the most frequent. E. coli ST10 ( n = 20) and ST297 (n = 20) were the most common STs. Conclusions E. coli with non-susceptibility to quinolones are widespread among the environment of Swiss pig farms and are often associated with an MDR phenotype. In several cases these isolates possess at least one PMQR gene, which could spread by horizontal gene transfer. E. coli from pig farms have diverse STs, some of which are associated with human and animal disease. Electronic supplementary material The online version of this article (10.1186/s40813-019-0116-y) contains supplementary material, which is available to authoriz...

Phenotypic and Genotypic Properties of Fluoroquinolone-Resistant, qnr-Carrying Escherichia coli Isolated from the German Food Chain in 2017

“…While CIP and NAL resistance were reported by several European countries at high levels in broiler and turkey, the EU medians in pigs and calves were rather low (6.2% and 4.2% for NAL and 7.4% and 8.4% for CIP per matrix, respectively) [ 43 ]. Regarding the detection of specific qnr genes, our result is in good agreement with previous reports in which qnrS and qnrB were the most frequently detected qnr genes in livestock sources [ 44 , 45 ]. In contrast to livestock, qnrA genes are often present in isolates from hospitalised patients [ 46 ].…”

Occurrence and Antimicrobial Resistance Traits of Escherichia coli from Wild Birds and Rodents in Singapore

“…In our study, PMQR genes were detected in four MDR E. coli isolates (C1742, C1758, C1805_1 and 8645_0135) which were, however, phenotypically susceptible to the Quinolones tested. This is congruent with a study on E. coli from environmental samples in pig farms, which reported that PMQR genes alone are insufficient to confer resistance to Quinolones [ 62 ]. As discussed in the previous paragraph, further mechanisms such as mutations in QRDR regions would confer resistance to Quinolones.…”

Prevalence and Characterization of Quinolone-Resistance Determinants in Escherichia coli Isolated from Food-Producing Animals and Animal-Derived Food in the Philippines

“…In the present study, all ST10 isolates were multidrug-resistant and mostly carried qnrs and a virulence gene, whereas ST117 was recovered from two different samples (chicken and pork), with both isolates being multidrug-resistant with mutations in QRDRs. ST117 is a well-recognized avian pathogenic E. coli with zoonotic potential [ 53 ]. In addition, in the present work, 13 STs were observed in multiple sources, seemingly indicating a possible interspecies transmission that potentially poses a risk to humans via direct contact with food-producing animals and/or consumption of contaminated animal-derived food.…”

“…Although E. coli belonging to phylogenetic groups A and B1 are classified as environmental and commensal E. coli , strains that belong to group D are classified as potential extraintestinal pathogenic strains [ 54 ]. In the present work, it was found that 15.7% of E. coli isolates harboring mutations in QRDR and/or PMQR genes belonged to phylogenetic group D. These isolates include E. coli clonal lineages (ST38, ST117, and ST354), which are human-associated, fluoroquinolone-resistant lineages that cause extraintestinal infection [ 53 , 55 ]. These findings indicate that these isolates may also carry pathogenic characteristics of ExPEC strains.…”