Distribution and genetic characterization of fluoroquinolone resistance gene qnr among Salmonella strains from chicken in China

The prevalence and dissemination of the plasmid-mediated fluoroquinolone (FQ) resistance gene qnr in Salmonella are considered serious public health concerns worldwide. So far, no comprehensive large-scale studies have focused on the prevalence and genetic characteristics of the qnr gene in Salmonella isolated from chickens. Herein, this study aimed to investigate the prevalence, antimicrobial resistance (AMR) patterns, and molecular characteristics of chicken-originated qnr-positive Salmonella strains from chicken farms, slaughterhouses, and markets in 12 provinces of China in 2020-2021. The overall prevalence of the qnr gene was 21.13% (56/265), with the highest prevalence in markets (36.11%, 26/72), followed in farms (17.95%, 21/117), and slaughterhouses (10.53%, 9/76). Only the qnrS and qnrB genes were detected, and the prevalence rate of the qnrS gene (19.25%, 51/265) was higher than that of the qnrB gene (1.89%, 5/265). Whole genome sequencing identified 37 distinct AMR genes and 15 plasmid replicons, and the most frequent mutation in quinolone resistance determining regions was parC (T57S; 91.49%, 43/47). Meanwhile, four different qnrS and two qnrB genetic environments were discovered among 47 qnr-positive Salmonella strains. In total, 21.28% (10/47) of the strains were capable of conjugative transfer, and all were qnrS1-positive strains, with the majority of transferable plasmids being IncHI2 types (n = 4). Overall, the prevalence of qnr-positive Salmonella strains from chickens in China and their carriage of multiple resistance and virulence genes and transferable plasmids is a major concern, which calls for continuous surveillance of qnr-positive Salmonella and the development of measures to control its prevalence and transmission.IMPORTANCESalmonella is a common foodborne pathogen responsible for 155,000 deaths annually worldwide. Fluoroquinolones (FQs) are used as first-line drugs for the treatment of Salmonella infections in several countries and regions. However, the emergence and increasing prevalence of the FQ-resistant gene qnr in Salmonella isolated from chickens have been widely reported. Gaining insight into the genetic mechanisms of AMR genes in chicken could lead to the development of preventive measures to control and reduce the risk of drug resistance. In this study, we identified qnr-positive Salmonellae isolated from chickens in different regions of China and their AMR patterns and genome-wide characteristics, providing a theoretical basis for further control of their prevalence and transmission.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

Occurrence of plasmid-mediated quinolone resistance determinants among Escherichia coli strains isolated from animals in Tunisia: Specific pathovars acquired qnr genes

OBJECTIVES

The aim of this study was to characterise Escherichia coli strains harbouring plasmid-mediated quinolone resistance (PMQR) genes recovered from various samples (n = 116) from healthy and diarrhoeic animals in Tunisia.

METHODS

All nalidixic acid-resistant E. coli isolates were screened for the presence of PMQR genes. Isolates positive for PMQR genes were investigated by PCR for chromosomal mutations in the quinolone resistance-determining regions (QRDRs) of GyrA and ParC, the presence of class 1 and class 2 integrons, genes encoding tetracycline and sulfonamide resistance, genes encoding virulence factors, and phylogenetic group. Genetic relationships was determined by pulsed-field gel electrophoresis (PFGE).

RESULTS

Amongst 51 nalidixic acid-resistant isolates, 9 harboured PMQR genes (5 co-harbouredqnrS1 and qnrB1, 3 harboured qnrS1 and 1 harboured qnrB1). Two types of mutation in the QRDR of GyrA were observed: S83L and D87N (eight isolates) and S83L (one isolate). For the QRDR of ParC, the substitution S80I was observed in four isolates. A class 1 integron was found in six isolates. The tetA or tetB gene was observed in six isolates and both tetA and tetB were co-harboured by two isolates. The sul1, sul2 and sul3 genes were detected in six, four and one isolates, respectively. According to the presence of specific virulence genes, the nine strains were classified as UPEC (5), EAEC (3) and EPEC (1). Three isolates from turkey faeces were clonally related by PFGE.

CONCLUSION

These findings highlight the plausible role of the avian industry as a reservoir of human pathogenic E. coli strains.

Detection of different β-lactamases encoding genes, including blaNDM, and plasmid-mediated quinolone resistance genes in different water sources from Brazil

Bacterial resistance occurs by spontaneous mutations or horizontal gene transfer mediated by mobile genetic elements, which represents a great concern. Resistance to β-lactam antibiotics is mainly due to the production of β-lactamases, and an important mechanism of fluoroquinolone resistance is the acquisition plasmid determinants. The aim of this study was to verify the presence of β-lactamase-encoding genes and plasmid-mediated quinolone resistance genes in different water samples obtained from São Paulo state, Brazil. A high level of these resistance genes was detected, being the bla_SHV, bla_GES, and qnr the most prevalent. Besides that, the bla_NDM gene, which codify an important and hazardous metallo-β-lactamase, was detected.

Enhanced Bacterial Fitness Under Residual Fluoroquinolone Concentrations Is Associated With Increased Gene Expression in Wastewater-Derived qnr Plasmid-Harboring Strains

Plasmids harboring qnr genes confer resistance to low fluoroquinolone concentrations. These genes are of significant clinical, evolutionary and environmental importance, since they are widely distributed in a diverse array of natural and clinical environments. We previously extracted and sequenced a large (∼185 Kbp) qnrB-harboring plasmid, and several small (∼8 Kbp) qnrS-harboring plasmids, from Klebsiella pneumoniae isolates from municipal wastewater biosolids, and hypothesized that these plasmids provide host bacteria a selective advantage in wastewater treatment plants (WWTPs) that often contain residual concentrations of fluoroquinolones. The objectives of this study were therefore to determine the effect of residual fluoroquinolone concentrations on the growth kinetics of qnr plasmid-harboring bacteria; and on the copy number of qnr plasmids and expression of qnr genes. Electrotransformants harboring either one of the two types of plasmids could grow at ciprofloxacin concentrations exceeding 0.5 μg ml^-1, but growth was significantly decreased at concentrations higher than 0.1 μg ml^-1. In contrast, plasmid-free strains failed to grow even at 0.05 μg ml^-1. No differences were observed in plasmid copy number under the tested ciprofloxacin concentrations, but qnr expression increased incrementally from 0 to 0.4 μg ml^-1, suggesting that the transcription of this gene is regulated by antibiotic concentration. This study reveals that wastewater-derived qnr plasmids confer a selective advantage in the presence of residual fluoroquinolone concentrations and provides a mechanistic explanation for this phenomenon.

Quinolone susceptibility and genetic characterization of Salmonella enterica subsp. enterica isolated from pet turtles

Turtle-borne Salmonella enterica owns significance as a leading cause in human salmonellosis. The current study aimed to determine the quinolone susceptibility and the genetic characteristics of 21 strains of S. enterica subsp. enterica isolated from pet turtles. Susceptibility of four antimicrobials including nalidixic acid, ciprofloxacin, ofloxacin, and levofloxacin was examined in disk diffusion and MIC tests where the majority of the isolates were susceptible to all tested quinolones. In genetic characterization, none of the isolates were positive for qnr or aac(6')-Ib genes and no any target site mutations could be detected in gyrA, gyrB, and parC quinolone resistance determining regions (QRDR). In addition, neighbor-joining phylogenetic tree derived using gyrA gene sequences exhibited two distinct clads comprising; first, current study isolates, and second, quinolone-resistant isolates of human and animal origin. All results suggest that studied strains of S. enterica subsp. enterica isolated from pet turtles are susceptible to quinolones and genetically more conserved with regards to gyrA gene region.

Plasmid-Mediated Quinolone-Resistance (qnr) Genes in Clinical Isolates of Escherichia coli Collected from Several Hospitals of Qazvin and Zanjan Provinces, Iran

Objectives

Escherichia coli is regarded as the most important etiological agent of urinary tract infections. Fluoroquinolones are routinely used in the treatment of these infections; however, in recent years, a growing rate of resistance to these drugs has been reported globally. The aims of this study were to detect plasmid-mediated qnrA, qnrB, and qnrS genes among the quinolone-nonsusceptible E. coli isolates and to investigate their clonal relatedness in Qazvin and Zanjan Provinces, Iran.

Methods

A total of 200 clinical isolates of E. coli were collected from hospitalized patients. The bacterial isolates were identified through standard laboratory protocols and further confirmed using API 20E test strips. Antimicrobial susceptibility was determined by the standard disk diffusion method. Polymerase chain reaction (PCR) and sequencing were used for detecting qnrA, qnrB, and qnrS genes and the clonal relatedness of qnr-positive isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) method.

Results

In total, 136 (68%) isolates were nonsusceptible to quinolone compounds, among which 45 (33.1%) and 71 (52.2%) isolates showed high- and low-level quinolone resistance, respectively. Of the 136 isolates, four (2.9%) isolates were positive for the qnrS1 gene. The results from ERIC-PCR revealed that two (50%) cases of qnr-positive isolates were related genetically.

Conclusion

Our study results were indicative of the presence of low frequency of qnr genes among the clinical isolates of E. coli in Qazvin and Zanjan Provinces, which emphasizes the need for establishing tactful policies associated with infection-control measures in our hospital settings.

Characterization of ciprofloxacin-resistant isolates from a wastewater treatment plant and its receiving river

In this study we characterised the ciprofloxacin-resistant strains isolated in biofilm and sediments from a wastewater treatment plant (WWTP) discharge point and its receiving river. We also examined the prevalence of qnrA, qnrB, qnrS and aac(6')-Ib-cr genes in these isolates and determined whether they harbour plasmid-encoded β-lactamases such as TEM, SHV and CTX-M. Moreover, antibiotic concentrations were also measured to evaluate the level of contamination of these pharmaceuticals in the sampling area. Antibiotics were found in the range of ng L(-1) in WWTP effluents, but most of them were no longer found in downstream river. However, some fluoroquinolones were detected in sediment downstream demonstrating their high persistence and their capacity to be retained in the river sediments. Most of the ciprofloxacin-resistant isolates belonged to the Gammaproteobacteria class and 17 of them, 8 (7.6%) from the first sampling and 9 (6.1%) from the second sampling, carried a qnr gene. In particular, 15 isolates carried the qnrS gene and 2 carried the qnrB gene. Among the qnr-positive isolates, 12 harboured the aac(6')-lb-cr gene and 2 of them also carried a β-lactamase on the same plasmid, indicating that they may be transferred simultaneously. It is also noteworthy that all qnr-positive isolates identified as Aeromonas species harboured the same qnrS allele, namely the qnrS2. This study reinforces the importance of environmental bacteria as vehicles for dissemination of antibiotic resistance genes.

Incidence, clinical presentation, and antimicrobial resistance trends in Salmonella and Shigella infections from children in Yucatan, Mexico

BACKGROUND

Salmonella and Shigella cause significant morbidity and mortality among children worldwide. Increased antimicrobial resistance results in greater burden of disease.

MATERIALS AND METHODS

From 2005 to 2011, Salmonella and Shigella isolates collected from ill children at a major hospital in Yucatan, Mexico, were subjected to serotyping and antimicrobial susceptibility testing by disk diffusion and agar dilution. The identification of bla CTX, bla CMY, bla SHV, bla TEM, and bla OXA and qnr resistance genes was conducted by PCR and sequencing.

RESULTS

Among 2344 children with acute gastroenteritis, salmonellosis decreased from 17.7% in 2005 to 11.2% in 2011 (p < 0.001). In contrast, shigellosis increased from 8.3% in 2010 to 12.1% in 2011. Compared to children with Salmonella, those with Shigella had significantly more bloody stools (59 vs 36%, p < 0.001), dehydration (27 vs 15%, p = 0.031), and seizures (11 vs 3%, p = 0.03). In Salmonella (n = 365), there was a significant decrease in resistance to ampicillin (43 to 16%, p < 0.001), trimethoprim-sulfamethoxazole (44 to 26%, p = 0.014), and extended-spectrum cephalosporins (27 to 10%, p = 0.009). Reduced susceptibility to ciprofloxacin in Salmonella rose from 30 to 41% (p < 0.001). All ceftriaxone-resistant isolates harbored the bla CMY-2 gene. qnr genes were found in 42 (36%) of the 117 Salmonella isolates with a ciprofloxacin MIC ≥ 0.125 μg/ml. Four were qnrA1 and 38 were qnrB19. Resistance to ampicillin (40%) and trimethoprim-sulfamethoxazole (58%) was common in Shigella (n = 218), but isolates remained fully susceptible to ceftriaxone and ciprofloxacin.

CONCLUSION

Illness from Salmonella has decreased while severe Shigella infections have increased among children with gastroenteritis in the Yucatan Peninsula. While Shigella resistance to clinically important antibiotics remained unchanged, resistance to most of these, except ciprofloxacin, declined in Salmonella. bla CMY-2 and qnr genes are common in Salmonella isolates.

The first attempt of an active integrated laboratory-based Salmonella surveillance programme in the north-eastern region of Nigeria

AIM

To identify the sources of Salmonella contamination, distribution, prevalence and antimicrobial susceptibility patterns, which have significant impact on public and animal health, and international trade.

METHODS AND RESULTS

A total of 1888 samples were collected by stratified random sampling from 2009 to 2011 from cattle, camels, poultry, fish, vegetables and humans. All identified Salmonella isolates were serotyped and tested for antimicrobial susceptibility by MIC determinations. A total of 149 Salmonella isolates comprising 17 different serovars were obtained (7·9% prevalence). Salmonella Hadar (37%), S. Eko (17%), S. Enteritidis (10%), S. Kentucky (7%) and S. Uganda (7%) were isolated from different sources. The occurrence of antimicrobial resistance was generally low, but S. Enteritidis and S. Eko showed variable antimicrobial resistance patterns, while all S. Kentucky isolates were resistant to seven of 17 tested antimicrobials, including ciprofloxacin and nalidixic acid. Three S. Hadar isolates revealed reduced susceptibility to ciprofloxacin and susceptibility to nalidixic acid and harboured the plasmid-mediated quinolone resistance gene qnrS1.

CONCLUSIONS

Salmonella serovars Hadar, Enteritidis and the previously very rarely reported Eko were the major serovars associated with human infections, animal and environmental contamination in the north-eastern region of Nigeria.

SIGNIFICANCE AND IMPACT OF THE STUDY

These serovars constitute a health risk to poultry, environment and human population in the region.