Genomics-based approach for detection and characterization of SARS-CoV-2 co-infections and diverse viral populations.

Unlabelled: Due to the continuous genetic diversification of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) over time, the co-circulation of two different lineages in the same region may lead to co-infections within a host, a situation known to contribute to the emergence of hybrid viral populations through genomic recombination. The aim of this study was to use a genomics-based approach to identify distinct viral populations of SARS-CoV-2 in patients with coronavirus disease 2019 (COVID-19), as an indicator of potential co-infections and recombination events. The cohort included 41,224 serial nasopharyngeal swabs positive for SARS-CoV-2 RNA, prospectively collected between January 2021 and April 2022 as part of the French national surveillance program.

Extensive dissemination of ESBL-producing Clonal Complex 14 Escherichia coli is likely spread through sexual transmission among men who have sex with men at risk of sexually transmitted infections.

Objectives: We characterized the genetic proximity of Sequence Type (ST) 131, 1193 and 14 Extended-Spectrum Beta-Lactamase-producing E. coli (ESBL-Ec) to assess human determinants of carriage in community settings.

Methods: In this cross-sectional study, we included individuals seeking care at a sexually transmitted infection (STI) or HIV outpatient clinic.

Evaluation of the contribution of shotgun metagenomics in the microbiological diagnosis of liver abscesses.

Background: Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA.