The occurrence and contamination of optrA-positive methicillin-resistant Staphylococcus aureus from duck farms in Guangdong, China

Study on molecular characteristics of Staphylococcus from yak milk-Xizang

This study investigated the biological characteristics of Staphylococcus strains isolated from Xizangan yak milk by examining the antibiotic resistance phenotypes of 69 isolates against 18 antibiotics, detecting 31 associated resistance genes, identifying 16 virulence genes, and assessing biofilm formation capability. Furthermore, molecular typing techniques including spa typing, multilocus sequence typing (MLST), and Staphylococcus cassette chromosome mec (SCCmec) were used for detailed characterization of the isolates. The findings revealed a high penicillin resistance rate of 72.46%. Resistance genes such as gyrA (100.00%), glrB (92.75%), and gyrB (44.93%) were prevalent. The detection rates were 81.16% and 55.07% for the beta-lactamase gene blaZ and the mecA gene, respectively. Among the tested virulence genes, lukS, lukF, hla, clfA, and icaD were detected in 40.58% of isolates, while sec was detected in 24.64%. MLST typing identified four isolates belonging to the ST62623 type and 24 other isolates representing novel ST types not reported on PubMLST.org. Spa typing revealed spa types t1940 (n = 9), t3022 (n = 8), t4558 (n = 6), t4236 (n = 3), t4445 (n = 1), and one unreported spa type. For SCCmec typing, 11 isolates were typed as SCCmec IVb and 9 as SCCmec V. These findings significantly enhance our understanding of the biological characteristics of Staphylococcus strains derived from Xizangan yak milk.

Long-read epicPCR enhances species-level host identification of clinically relevant antibiotic resistance genes in environmental microbial communities

Identifying clinically relevant antibiotic resistance gene (ARG) hosts in complex microbial communities is crucial for environmental health. EpicPCR (emulsion, paired isolation, and concatenation PCR), a single-cell technology, has advanced this field. However, its traditional format, which links target genes to the V4 region of 16S rRNA genes (∼300 bp), limits species-level identification. To overcome this, we developed "long-read" epicPCR, which links target genes to 16S segments spanning the V4-V9 regions (∼1000 bp) by refining primer pairing strategies to balance amplification length and specificity. We validated this approach by targeting seven clinically relevant ARGs (optrA, tet(X4), mcr-3, NDM-5, KPC-2, IMP-4, and VIM-1), an efflux pump gene (tmexD), and an insertion sequence gene (IS1216E), all confirming correct sequence fusion. Using the optrA gene as a model target, long-read epicPCR demonstrated greater precision and fewer false positives than the short-read method in mock communities. It also significantly improved the identification rate of optrA host species from 29.0 % to 54.4 % in anaerobic digestion reactors, while maintaining consistency with short-read epicPCR in profiling host bacterial communities. Moreover, long-read epicPCR identified two novel optrA host species, Lactobacillus amylotrophicus and Streptococcus alactolyticus, in anaerobic effluents, highlighting potential dissemination risks. Notably, this versatile method is envisioned to enhance targeted antimicrobial surveillance and microbial functional dynamics monitoring in the environment.

Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl

Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain's genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying "bird-specific" virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.