Becsei, A. | bioRxiv Science

bioRxiv2022

Porcine cytomegalovirus detection by nanopore-based metagenomic sequencing in a Hungarian pig farm

The rapid diagnosis of infectious diseases has an essential impact on their control, treatment and recovery. Oxford Nanopore Technologies (ONT) sequencing opens up a new dimension in applying clinical metagenomics. In a large-scale pig farm in Hungary, four fattening and one piglet nasal swab pooled samples were sequenced using ONT for metagenomic analysis. Long reads covering 53.69% of the porcine cytomegalovirus genome were obtained in the piglet sample. The 650 bp long read matching the glycoprotein B gene of the virus is sequentially most similar to Japanese, Chinese and Spanish isolates.

genomics↗

bioRxiv2021

Mobile antimicrobial resistance genes in probiotics

Even though people around the world tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they transfer. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.

genomics↗