Norovirus GII causes a substantial global burden of acute gastroenteritis, and genotype-resolved wastewater surveillance offers a complementary approach for monitoring community circulation beyond cases captured by routine clinical surveillance. We monitored four municipal wastewater treatment plants in Beijing, China, from October 2023 to September 2024 and compared weekly GII genotype profiles with contemporaneous sporadic-case and outbreak surveillance. Strict-weekly genotype comparisons were the primary inference and used moving-block bootstrap confidence intervals, block-sign tests, and false-discovery-rate correction; centred 3-week profiles were used for description and sensitivity analysis. Bray-Curtis dissimilarity quantified compositional concordance, and same-week and lagged Spearman correlations compared wastewater GII concentration with clinical surveillance activity. In the centred 3-week wastewater series, GII.4 had the highest mean read-based relative abundance (31.1%), followed by GII.17 (17.5%) and GII.7 (15.2%). In strict-weekly comparisons, wastewater had lower GII.17 representation than sporadic cases (−32.6 percentage points) and lower GII.7 representation than outbreaks (−14.0 percentage points). Wastewater had higher GII.3, GII.4, GII.6, and GII.9 representation than sporadic cases and higher GII.9 and GII.13 representation than outbreaks; the GII.4 and GII.7 differences were sensitive to analytical specification, and the GII.13 effect was small. Mean strict-weekly Bray-Curtis dissimilarities were 0.590–0.679 in 32 common weeks. Same-week and lagged wastewater concentration correlations with sporadic-case positivity and outbreak case counts were not significant after temporal-dependence and multiplicity correction. Genotype-resolved wastewater surveillance documented co-circulating GII genotypes and recurrent source-specific differences, while read-based relative abundance remained dependent on catchment coverage and genotype-specific analytical performance.
Acinetobacter baumannii sequence type 2 (Pasteur ST2), associated with international clone 2, is a major antimicrobial-resistant lineage, but its within-lineage population structure and accessory resistance variation remain incompletely resolved. We analyzed 5612 quality-filtered public genomes from an existing global dataset using PopPUNK, core-genome SNP analysis, AMRFinderPlus, MobileElementFinder and MOB-suite. A dominant PopPUNK cluster contained 5604 genomes (99.86%). Its SNP phylogeny showed dense short-distance relationships within a connected lineage; pairwise distances had a median of 314 SNPs. Four antibiotic classes—beta-lactams, aminoglycosides, phenicols and fosfomycin—were detected in at least 95% of dominant-cluster genomes. The median antibiotic-class annotation hit count was 14 per genome (IQR, 13–15), including intrinsic and lineage-associated determinants. Predicted conjugative and mobilizable plasmid signatures occurred in 52.6% and 42.7% of dominant-cluster genomes, respectively. Across the full cohort, mobile-element and antibiotic-class hit counts were weakly positively correlated (Spearman ρ = 0.191). This unadjusted association was absent among 700 representatives selected one per ≤10-SNP component (ρ = −0.0721; p = 0.0567), and a component-bootstrap interval included zero. Assembly-adjusted associations differed between the full cohort and representatives. The small positive unadjusted collection-year association was not robust to location adjustment and was unsupported in dated representatives. Complete-genome annotations documented both chromosomal and plasmid blaOXA-23 copies and upstream ISAba1 proximity, without establishing promoter activity or resistance phenotype. These findings describe a cohesive ST2 lineage with heterogeneous accessory resistance and plasmid-mobility signatures, while emphasizing the sensitivity of genome-wide associations to assembly characteristics and clonal and geographic sampling.
Objective To characterize the genomic phylogeny and antimicrobial resistance (AMR) genotypes of the ORN-1-producing R. ornithinolytica B16451B, and to elucidate the transfer mechanisms of resistance genes at the genomic level. Methods The genome of R. ornithinolytica B16451B was sequenced using the Illumina HiSeq 4000 and PacBio RSII sequencing platforms. A global phylogenetic analysis of the genomic data was conducted by the Center for Genomic Epidemiology (CGE), incorporating information on geographical distribution, isolation sources, and host associations. A comparative phylogenomic analysis was performed using the BLAST Ring Image Generator (BRIG). Genome annotation was performed using Glimmer and the Rapid Annotation using Subsystem Technology (RAST) server. Mobile genetic elements were predicted using TnCentral, ISFinder, and PHASTER. The antibiotic resistance genes (ARGs) were analyzed using the Comprehensive Antibiotic Resistance Database (CARD), while the virulence factors genes (VFGs) were analyzed using the Virulence Factor Database (VFDB). Gene transfer experiments were conducted in the intestinal tract of mice. Transconjugants were identified using 16S rRNA metagenomic sequencing, and drug-resistance genes were amplified by PCR. Results A chromosome (designated chromosome 01) was first identified in strain B16451B. A carrying IS4 insertion sequence distinct resistance region within this chromosome, designated B1645–1B-RG, harbors the β-lactamase gene blaORN-1. Three intact prophages, designated prophage YC1, YC2, and YC3, were also first identified. The blaORN-1 gene was successfully transferred from strain B16451B to Escherichia coli (designated B1645–1BLMY1) and Klebsiella pneumoniae (designated B1645–1BYCF2) in the intestines of mice. The strain B16451B harbored 25 antimicrobial resistance genes and 8 classes of virulence factor genes. Based on comparative genomic analysis of strains retrieved from the NCBI Genome Database, 98 antimicrobial resistance genes (ARGs) (e.g., sul1, blaKPC-2, blaNDM-1) among 234 R. ornithinolytica strains were identified to exhibit significantly higher prevalence in human isolates than in non-human host sources (e.g., water, animals, plants). Conclusions The chromosome 01 was identified in a multi-drug resistant ORN-1-producing the strain B16451B isolated from China. The genome of strain B16451B harbors three integrated prophages: YC1 (42.2 kb), YC2 (60.5 kb), and YC3 (23.8 kb) was identified. The IS4 insertion might promote blaORN-1 gene transfer within the intestinal flora of mice. Among these 234 R. ornithinolytica strains analyzed in this study, most virulence factor genes (e.g., ompa, yagx/ecpc) and resistance genes (e.g., blaKPC, blaNDM) exhibited higher prevalence in Homo sapiens isolates than in strains from non-human sources including water, animals and plants. These findings provide valuable references for clinicians optimize the management of R. ornithinolytica infections and guide clinical treatment.
We report six lactose-fermenting Salmonella Strathcona isolates carrying a lac operon on an IncHI2/IncHI2A plasmid. Whole-genome sequencing revealed intact lacI–lacZ–lacY and truncated lacA genes. These isolates represent the first detection of lactose-fermenting S. Strathcona, highlighting a risk of diagnostic errors due to reliance on lactose fermentation–based phenotypic identification.
