Prevalence of qnrS-positive Escherichia coli from chicken in Thailand and possible co-selection of isolates with plasmids carrying qnrS and trimethoprim-resistance genes under farm use of trimethoprim

Strict relationship between phenotypic and plasmid-associated genotypic of multidrug-resistant Escherichia coli isolated from Taihe Black-Boned Silky Fowl farms

Taihe Black-Boned Silky Fowl (TBSF) is a unique breed in China, characterized by a high concentration of melanin deposited throughout its body. Compared to broiler chickens, many antibiotics exhibit significantly longer withdrawal periods in TBSF. Given that antibiotic exposure is widely recognized as the primary selective pressure driving the persistence and dissemination of antibiotic resistance genes (ARGs) across diverse environments, it is crucial to investigate the occurrence and prevalence of ARGs within TBSF farming systems. In this study, 34 Escherichia coli strains isolated from 22 TBSF farms were subjected to phenotypic and genotypic analyses. The isolates were tested for susceptibility to 28 antimicrobial drugs representing nine antibiotic classes to determine their antimicrobial resistance phenotypes. Draft genome sequences of these E. coli strains were obtained, and the ARGs carried by mobile genetic elements, particularly plasmids, were analyzed for their association with susceptibility phenotype. The genetic context of key ARGs in these E. coli isolates was further characterized. Network analysis was employed to investigate the correlations between ARGs, phenotypes, and drug residues. The results demonstrated that high rates of antimicrobial resistance were observed, with 100 % and 29.4 % of isolates exhibiting resistance to four or more and eight or more antibiotic classes, respectively. According to whole-genome sequencing, a total of 143 ARGs were identified. The antimicrobial resistance phenotypes were consistently correlated with the presence of corresponding ARGs in the 34 E. coli genomes. 100 % of the β-lactams antibiotics resistant mechanism could be attributed to the presence of the resistance gene blaTEM and/or blaOXA-10. Similarly, resistance to tetracyclines, chloramphenicols, aminoglycosides, and fluoroquinolones was fully explained by the presence of tetR and/or tetA, floR and/or cmlA, ant(3'')-IIa, aph(3'')-Ib, aph(6)-Id, aac(3)-IId, and aadA, and qnrS and/or mutant gyrA/parC/mdtH. The majority of these key ARGs were found to be plasmid-associated. This study verified and highlighted the prevalent horizontal gene transfer of ARGs in TBSF farms. Factors such as hygiene status, biosecurity measures, and other environmental conditions might play a more significant role than antimicrobial usage in facilitating the horizontal gene transfer of ARGs in TBSF farms. Appropriate measures should be taken to control the transmission and dissemination of these mobile genetic elements associated ARGs and prevent their entry into the human clinical environment from TBSF breeding environment.

Bacterial Contamination and Antimicrobial Resistance in Two-Spotted (Gryllus bimaculatus) and House (Acheta domesticus) Cricket Rearing and Harvesting Processes

Food safety for cricket production is a crucial factor in producing edible crickets with safety for consumers and sustainability for two-spotted (Gryllus bimaculatus) as well as house (Acheta domesticus) cricket production. This study was conducted by simultaneously rearing two cricket species, comprising two-spotted crickets (G. bimaculatus) and house crickets (A. domesticus). A total of 16 rearing crates were used for the present study, which were allocated into 8 rearing crates for each studied cricket species, including paper egg cartons. Cricket eggs were incubated in the rearing crates. Once the crickets hatched, tap water and powdered feed were provided ad libitum throughout the experiment. At the end of this study (35 and 42 days for the two-spotted and house crickets, respectively), all crickets were harvested, rinsed in tap water, and boiled in water for 5 min. During the rearing and harvesting processes, samples were collected from various potential contamination points for bacteria, including E. coli and Salmonella spp. There were samples of the initial input (feed, drinking water, and staff hands), rearing environment (water pipe, crate wall, living cartons, frass, and cricket surface), and harvesting crickets (harvested, washed, and boiled crickets), with a 2-week sampling interval, except for the last round of sampling for the two-spotted crickets. Subsequently, all samples were submitted to isolate and identify contaminated bacteria. The samples from the last round of sampling for both kinds of crickets were submitted to quantify the level of contamination for E. coli and Salmonella spp., including antimicrobial resistance by the disk diffusion method for the positive isolate. The results showed that bacterial contamination was found in the rearing of both cricket species, primarily involving Klebsiella spp. and Enterobacter spp., mainly found in prepared drinking water and the water pipes of drinking water supply equipment, which are potential sources of contamination with cricket frass. E. coli was found in 4.8% and 4.3% of the two-spotted and house crickets, respectively, while no presence of Salmonella spp. was detected in any submitted samples. The quantification of E. coli and Salmonella spp. indicated E. coli contamination near the water pipe and the frass of two-spotted crickets, but Salmonella spp. was undetectable in both two-spotted and house crickets. The antimicrobial resistance of isolated E. coli mainly involved penicillin G, amoxicillin, ampicillin, erythromycin, lincomycin, and tiamulin. Thus, good farm management with proper sanitation practices (such as cleaning and keeping the environment dry), as well as boiling crickets during the harvesting process, may help ensure the safety of edible cricket production.

Phenotypic and Genotypic Characterization of Multidrug-Resistant Enterobacter hormaechei Carrying qnrS Gene Isolated from Chicken Feed in China

Multidrug resistance (MDR) in Enterobacteriaceae including resistance to quinolones is rising worldwide. The plasmid-mediated quinolone resistance (PMQR) gene qnrS is prevalent in Enterobacteriaceae. However, the qnrS gene is rarely found in Enterobacter hormaechei (E. hormaechei). Here, we reported one multidrug resistant E. hormaechei strain M1 carrying the qnrS1 and blaTEM-1 genes. This study was to analyze the characteristics of MDR E. hormaechei strain M1. The E. hormaechei strain M1 was identified as Enterobacter cloacae complex by biochemical assay and 16S rRNA sequencing. The whole genome was sequenced by the Oxford Nanopore method. Taxonomy of the E. hormaechei was based on multilocus sequence typing (MLST). The qnrS with the other antibiotic resistance genes were coexisted on IncF plasmid (pM1). Besides, the virulence factors associated with pathogenicity were also located on pM1. The qnrS1 gene was located between insertion element IS2A (upstream) and transposition element ISKra4 (downstream). The comparison result of IncF plasmids revealed that they had a common plasmid backbone. Susceptibility experiment revealed that the E. hormaechei M1 showed extensive resistance to the clinical antimicrobials. The conjugation transfer was performed by filter membrane incubation method. The competition and plasmid stability assays suggested the host bacteria carrying qnrS had an energy burden. As far as we know, this is the first report that E. hormaechei carrying qnrS was isolated from chicken feed. The chicken feed and poultry products could serve as a vehicle for these MDR bacteria, which could transfer between animals and humans through the food chain. We need to pay close attention to the epidemiology of E. hormaechei and prevent their further dissemination. IMPORTANCE Enterobacter hormaechei is an opportunistic pathogen. It can cause infections in humans and animals. Plasmid-mediated quinolone resistance (PMQR) gene qnrS can be transferred intergenus, which is leading to increase the quinolone resistance levels in Enterobacteriaceae. Chicken feed could serve as a vehicle for the MDR E. hormaechei. Therefore, antibiotic-resistance genes (ARGs) might be transferred to the intestinal flora after entering the gastrointestinal tract with the feed. Furthermore, antibiotic-resistant bacteria (ARB) were also excreted into environment with feces, posing a huge threat to public health. This requires us to monitor the ARB and antibiotic-resistant plasmids in the feed. Here, we demonstrated the characteristics of one MDR E. hormaechei isolate from chicken feed. The plasmid carrying the qnrS gene is a conjugative plasmid with transferability. The presence of plasmid carrying antibiotic-resistance genes requires the maintenance of antibiotic pressure. In addition, the E. hormaechei M1 belonged to new sequence type (ST). These data show the MDR E. hormaechei M1 is a novel strain that requires our further research.