This study aimed to determine the global distribution and molecular characteristics of carbapenemase-producing Pseudomonas aeruginosa isolates. A total of 328 (11.1%, 328/2953) carbapenemase-producing P. aeruginosa isolates from humans were obtained from public databases as of October 2019. Of which, the bla_VIM and bla_IMP genes were the most prevalent carbapenemases in the P. aeruginosa isolates. These carbapenemase-producing P. aeruginosa isolates possessed 34 distinct sequence types (STs) and six predominated: ST357, ST823, ST308, ST233, ST175 and ST111. The ST357 and ST823 isolates were primarily found detected in Asia and all ST175 isolates were found in Europe. The ST308, ST233 and ST111 isolates were spread worldwide. Further, all ST823 isolates and the majority of ST111, ST233 and ST175 isolates carried bla_VIM but ST357 isolates primarily carried bla_IMP. ST308 isolates provide a key reservoir for the spread of bla_VIM, bla_IMP and bla_NDM. WGS analysis revealed that ST111 carried a great diversity of ARG types (n = 23), followed by ST357 (n = 21), ST308 (n = 19), ST233 (n = 18), ST175 (n = 14) and ST823 (n = 10). The ST175 isolates carried a more diversity and frequent of aminoglycoside ARGs, and ST233 isolates harbored more tetracycline ARGs. Our findings revealed that different carbapenem resistance genes were distributed primarily in variant STs of P. aeruginosa isolates, these isolates also possessed an extensive geographical distribution that highlights the need for surveillance studies that detect carbapenemase-producing P. aeruginosa isolates in humans.

We determined the prevalence and molecular characteristics of fosfomycin-resistant Escherichia coli from a domestic pigeon farm. A total of 79 samples collected from pigeons and their surrounding environments were screened for the presence of fosfomycin resistant isolates and these included 49 E. coli isolates that displayed high-level resistance (MIC ≥ 256 mg L⁻¹) and carried the fosA3 gene on plasmids with sizes ranging from 80 to 370 kb. MLST analysis of these fosA3-positive E. coli isolates indicated the presence of nine sequence types (ST6856, ST8804, ST457, ST746, ST533, ST165, ST2614, ST362 and ST8805) of which ST6856 was the most prevalent (24.5%, 12/49). PFGE combined with genomic context comparative analyses indicated that the fosA3 gene was spread by horizontal transfer as well as via clonal transmission between E. coli in the pigeon farm, and IS26 played an important role in fosA3 transmission. The high prevalence of fosA3 in the pigeon farm and the high similarity of the fosA3 genomic environment between E. coli isolates from humans and pigeons indicated that the pigeon farm served as a potential reservoir for human infections. The pigeon farm was found to be an important reservoir for the fosA3 gene and this should be further monitored.

We determined the prevalence and molecular characteristics of bla_CTX-M-55-positive Escherichia coli (E. coli) isolated from duck–fish polyculture farms in Guangzhou, China. A total of 914 E. coli strains were isolated from 2008 duck and environmental samples (water, soil and plants) collected from four duck fish polyculture farms between 2017 and 2019. Among them, 196 strains were CTX-M-1G-positive strains by PCR, and 177 (90%) bla_CTX-M-1G-producing strains were bla_CTX-M-55-positive. MIC results showed that the 177 bla_CTX-M-55-positive strains were highly resistant to ciprofloxacin, ceftiofur and florfenicol, with antibiotic resistance rates above 95%. Among the 177 strains, 37 strains carrying the F18:A-:B1 plasmid and 10 strains carrying the F33:A-:B- plasmid were selected for further study. Pulse field gel electrophoresis (PFGE) combined with S1-PFGE, Southern hybridization and whole-genome sequencing (WGS) analysis showed that both horizontal transfer and clonal spread contributed to dissemination of the bla_CTX-M-55 gene among the E. coli. bla_CTX-M-55 was located on different F18:A-:B1 plasmids with sizes between ~76 and ~173 kb. In addition, the presence of bla_CTX-M-55 with other resistance genes (e.g., tetA, floR, fosA3, bla_TEM, aadA5 CmlA and InuF) on the same F18:A-:B1 plasmid may result in co-selection of resistance determinants and accelerate the dissemination of bla_CTX-M-55 in E. coli. In summary, the F18:A-:B1 plasmid may play an important role in the transmission of bla_CTX-M-55 in E. coli, and the continuous monitoring of the prevalence and transmission mechanism of bla_CTX-M-55 in duck–fish polyculture farms remains important.

We determined the longitudinal persistence of ceftiofur-resistant Escherichia coli from a chicken breeding farm in China. A total of 150 samples were collected from 5 breeding periods in a flock of layer hens, and the prevalence of ceftiofur-resistant E. coli fluctuated across the 5 chicken breeding stages: eggs, 3.33%; growing period, 100%; early laying period, 36.7%; peak laying period, 66.7% and late laying period, 80%. The most prevalent ceftiofur resistance genes were bla_CTX-M-55, bla_CMY and bla_NDM, and ST101 was the most prevalent and persistent sequence type across the breeding periods. Our results indicated that this breeder flock was heavily contaminated by ST101 ceftiofur-resistant E. coli and that its presence should be intensively monitored on chicken farms.

Heteroresistance has seriously affected the evaluation of antibiotic efficacy against pathogenic bacteria, causing misjudgment of antibiotics’ sensitivity in clinical therapy, leading to treatment failure, and posing a serious threat to current medical health. However, the mechanism of Staphylococcus aureus heteroresistance to ciprofloxacin remains unclear. In this study, heteroresistance to ciprofloxacin in S. aureus strain 529 was confirmed by antimicrobial susceptibility testing and population analysis profiling (PAP), with the resistance of subclonal 529_HR based on MIC being 8-fold that of the original bacteria. A 7-day serial MIC evaluation and growth curves demonstrate that their phenotype was stable, with 529_HR growing more slowly than 529, but reaching a plateau in a similar proportion. WGS analysis showed that there were 11 nonsynonymous mutations and one deletion gene between the two bacteria, but none of these SNPs were directly associated with ciprofloxacin resistance. Transcriptome data analysis showed that the expression of membrane potential related genes (qoxA, qoxB, qoxC, qoxD, mprF) was downregulated, and the expression of multidrug resistance efflux pump gene mepA was upregulated. The combination of ciprofloxacin and limonene restored the 529_HR MIC from 1 mg/L to 0.125 mg/L. Measurement of the membrane potential found that 529_HR had a lower potential, which may enable it to withstand the ciprofloxacin-induced decrease in membrane potential. In summary, we demonstrated that upregulation of mepA gene expression and a reduction in membrane potential are the main heteroresistance mechanisms of S. aureus to ciprofloxacin. Additionally, limonene may be a potentially effective agent to inhibit ciprofloxacin heteroresistance phenotypes.