Identification and characterization of plasmid-mediated quinolone resistance determinants in Enterobacteriaceae isolated from healthy poultry in Brazil

Abstract

The expression of plasmid-mediated quinolone resistance (PMQR) genes confers low-level quinolone and fluoroquinolones resistance alone. However, the association to chromosomal resistance mechanisms determines an expressively higher resistance in Enterobacteriaceae. These mechanisms are horizontally disseminated within plasmids and have contributed to the emergence of bacteria with reduced susceptibility or resistant to therapies worldwide. The epidemiological characterization of PMQR dissemination is highly relevant in the scientific and medical context, to investigate the dissemination within enterobacteria, from different populations, including humans and food-producing animals. In the present study, 200 Enterobacteriaceae isolates were harvested from poultry with cloacal swabs and identified as Escherichia coli (90.5%), Escherichia fergusonii (5.5%), Klebsiella oxytoca (2.5%) and Klebsiella pneumoniae (1.5%). Among isolates evaluated, 46 (23%) harboured PMQR genes including qnrB (43/200), qnrS (2/200) and aac(6')-Ib-cr (1/200). All isolates carrying PMQR genes showed multidrug-resistance phenotype. The 36 E. coli isolates showed 18 different PFGE types. All E. fergusonii isolates showed the same PFGE type. The two Klebsiella oxytoca belonged to two different PFGE types. The phylogenetic groups A, B1, and D were found among the E. coli harboring PMQR genes. Based on the phylogenetic analysis and PFGE, the population structure of E. coli isolates was diverse, even within the same farm. All isolates carrying qnrB and qnrS genes also harboured ColE-like plasmids. The Southern blot hybridization using the S1-PFGE revealed that the qnrB genes were located on low molecular weight plasmids, smaller than 10Kb. Resistance plasmids were sequenced and showed 100% identity with plasmid pPAB19-3. The association of PMQR genes with mobile genetic elements, such as transferable plasmids, favours the selection and dissemination of (fluoro) quinolones resistant bacteria among food-producing animals, and may play an important role in the current increased prevalence of resistant bacteria in different environments reported worldwide.

Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview

“…The same was noticed for qnrS. Although Ferreira et al described this gene in ColE plasmids, it was also described in a 49kb IncX1 plasmid carried by E. coli, co-located with bla CTX-M-15 [157,177].…”

“…Different qnrB variants (when specified recognized as qnrB2, qnrB5, qnrB19) have been reported in E. coli, E. fergusonii, K oxytoca, S. Corvallis, S. Schwarzengund, and S. Newport isolates obtained from chicken or chicken meat [36,140,147,[175][176][177][178]. qnrS was reported in E. coli obtained from chicken meat and swabs from healthy poultry and pork [140,177,179]. More recently, qnrE was detected in an MDR S. Typhimurium strain isolated from a swine carcass [180].…”

“…The occurrence of qnrA in animal-derived samples was no reported in the studies covered by this review. The genetic occurrence of qnrB seems to be strongly associated with low molecular weight ColE plasmids [36,147,177]. Nevertheless, in Salmonella, the gene has also been detected in large 280 kb IncHI2A plasmids, co-located with bla CTX-M-2 [36].…”

Genome wide characterization of enterotoxigenic Escherichia coli serogroup O6 isolates from multiple outbreaks and sporadic infections from 1975-2016

“…coli and Shigella . ) [34]. The MIC for ciprofloxacin in 2015EL-1279-2 was 0.25 μg/mL which is in the expected range for qnr + E .…”

“…colistin) and fluoroquinolone (e.g. ciprofloxacin) classes of antibiotics [33, 34] were discovered after the initial screening. Determinants present on contigs with low sequencing coverage (defined as less than 5x) were omitted from further analysis as these are sometimes the result of carryover contamination or sample bleed over on the Illumina platform [35].…”