Metagenomic insights into the influence of mobile genetic elements on ARGs along typical wastewater treatment system on pig farms in China.

The wastewater treatment processes (WTP) on pig farms are heavily contaminated by antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) play an important role in shaping ARG profiles. Here we first employed metagenomic sequencing to follow the diversities and shifts of ARG associated mobile genetic elements (AAMGEs) including insertion sequences (ISs) and plasmids along the WTP for three pig farms in southeast China. The IS average relative abundance rose from the initial pig feces source to the wastewater storage lagoon (WSL) but decreased in the influent and rose in the effluent of the anaerobic digestor (AD). In contrast, plasmids were eliminated rapidly along this process. These results indicated that the AD reduced plasmid copies while IS abundance increased. We found a great diversity ISs, including IS91, ISNCY, IS630 and IS701, were large contributors to the transfer of multi-drug resistance. In addition, the tetracycline resistance genes co-occurred with a greater diversity of ISs than other ARG classes and this likely contributed to the high abundance of tetracycline resistance genes we found. The transfer of ARGs mediated by MGEs along the WTP of pig farms was a key contributor for the ARGs persistence in the environment of pig farms. Collectively, our findings demonstrated different fates for ISs and plasmids along the WTP for pig farms and suggested that AAMGE monitoring served as an important role in controlling ARGs in pig waste.

Prevalence and Persistence of Ceftiofur-Resistant Escherichia coli in A Chicken Layer Breeding Program.

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 blaCTX-M-55, blaCMY and blaNDM, 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.

Source Tracking and Global Distribution of the Tigecycline Non-Susceptible tet(X).

The emergence of tet(X) genes has compromised the clinical use of the last-line antibiotic tigecycline. We identified 322 (1.21%) tet(X) positive samples from 12,829 human microbiome samples distributed in four continents (Asia, Europe, North America, and South America) using retrospective data from worldwide. These tet(X) genes were dominated by tet(X2)-like orthologs but we also identified 12 samples carrying novel tet(X) genes, designed tet(X45), tet(X46), and tet(X47), were resistant to tigecycline. The metagenomic analysis indicated these tet(X) genes distributed in anaerobes dominated by Bacteroidaceae (78.89%) of human-gut origin. Two mobile elements ISBf11 and IS4351 were most likely to promote the transmission of these tet(X2)-like orthologs between Bacteroidaceae and Riemerella anatipestifer. tet(X2)-like orthologs was also developed during transmission by mutation to high-level tigecycline resistant genes tet(X45), tet(X46), and tet(X47). Further tracing these tet(X) in single bacterial isolate from public repository indicated tet(X) genes were present as early as 1960s in R. anatipestifer that was the primary tet(X) carrier at early stage (before 2000). The tet(X2) and non-tet(X2) orthologs were primarily distributed in humans and food animals respectively, and non-tet(X2) were dominated by tet(X3) and tet(X4). Genomic comparison indicated these tet(X) genes were likely to be generated during tet(X) transmission between Flavobacteriaceae and E. coli/Acinetobacter spp., and ISCR2 played a key role in the transmission. These results suggest R. anatipestifer was the potential ancestral source of tet(X). In addition, Bacteroidaceae of human-gut origin was an important hidden reservoir and mutational incubator for the mobile tet(X) genes that enabled spread to facultative anaerobes and aerobes. IMPORTANCE The emergence of the tigecycline resistance gene tet(X) has posed a severe threat to public health. However, reports of its origin and distribution in human remain rare. Here, we explore the origin and distribution of tet(X) from large-scale metagenomic data of human-gut origin and public repository. This study revealed the emergency of tet(X) gene in 1960s, which has refreshed a previous standpoint that the earliest presence of tet(X) was in 1980s. The metagenomic analysis from data mining covered the unculturable bacteria, which has overcome the traditional bacteria isolating and purificating technologies, and the analysis indicated that the Bacteroidaceae of human-gut origin was an important hidden reservoir for tet(X) that enabled spread to facultative anaerobes and aerobes. The continuous monitoring of mobile tigecycline resistance determinants from both culturable and unculturable microorganisms is imperative for understanding and tackling the dissemination of tet(X) genes in both the health care and agricultural sectors.

Molecular Epidemiology of Fosfomycin Resistant E. coli from a Pigeon Farm in China.

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.