Urinary tract infections (UTIs) are among the most prevalent infectious diseases, yet there is still limited understanding of the epidemiology of Enterococcal strains isolated from UTI patients in Shanghai. This study aims to elucidate the antimicrobial resistance profiles, virulence gene carriage, and molecular epidemiology of selected Enterococcal strains from UTI patients in Shanghai. A cohort of 80 Enterococcus faecalis and 40 Enterococcus faecium clinical isolates were randomly selected from UTI patients from October 2022 to March 2023. No vancomycin-resistant strains were identified based on minimum inhibitory concentration (MIC) testing. However, five strains of linezolid-resistant E. faecalis were identified, all of which were confirmed to be optrA -positive through whole-genome sequencing (WGS), with ST300 being reported as the first instance of this ST type in China. Polymerase chain reaction (PCR) assays were employed to ascertain the presence of virulence genes and multi-locus sequence type (MLST). In E. faecalis , the most common virulence genes were asal (75%), gelE (65%), esp (52.5%), and cylA (47.5%). In contrast, E. faecium primarily exhibited esp (65%) and hyl (12.5%). Among the E. faecalis strains, 21 distinct MLST types were identified, with ST16 and ST179 prevailing. Conversely, E. faecium exhibited only five MLST types, with ST78 being predominant. The prevalence of E. faecalis CC16 and E. faecium CC17 further complicates the treatment landscape for Enterococcal UTIs. IMPORTANCE: This study highlighted the critical need to understand Enterococcal strains causing UTIs in Shanghai, given their high prevalence. By assessing antimicrobial resistance profiles, virulence gene presence, and molecular epidemiology, the research offered valuable insights into the local epidemiology of Enterococcus faecalis and Enterococcus. faecium . Identifying linezolid-resistant strains, all of which carry the optrA gene, including the first report of ST300 in China and recognizing dominant MLST types, such as ST16 and ST179 for E. faecalis and ST78 for E. faecium , are vital for guiding treatment and addressing the challenges these infections present. The data emphasize the need for ongoing surveillance and customized therapeutic approaches to combat emerging resistance and virulence factors in Enterococcal UTIs.

Rapid antimicrobial resistance (AMR) prediction from MALDI-TOF mass spectrometry (MS) remains challenging, particularly when training artificial intelligence (AI) models under small-sample constraints. Performance is often hampered by the high dimensionality of spectral data and the subtle nature of resistance-related signals: full-spectrum approaches risk overfitting to high-dimensional noise, whereas peak-selection strategies risk discarding structurally informative, low-intensity signals. Here, we propose ReShuffle-MS, a region-guided data augmentation framework for MS data. Each spectrum is partitioned into a Main Discriminative Region (MDR) and a Peripheral Peak Region (PPR). By recombining signals within the PPR across samples of the same class while keeping the MDR intact, ReShuffle-MS generates structure-preserving augmented samples. On a clinical dataset for Escherichia coli (E. coli) levofloxacin resistance prediction, ReShuffle-MS delivered significant and consistent performance gains. It improved the average accuracy of classical machine learning models by 3.7% and enabled a one-dimensional convolutional neural network (CNN) to achieve 83.25% accuracy and 97.28% recall. Visualization using Grad-CAM revealed a shift from sparse, peak-dependent attention toward broader and more meaningful spectral patterns. Validation on the external DRIAMS-C dataset for ceftriaxone resistance further demonstrated that the method generalizes to a distinct laboratory setting and a different antibiotic target. These findings suggest that ReShuffle-MS can enhance the robustness and clinical utility of AI-based AMR prediction from routinely acquired MALDI-TOF spectra.

Invasive group A streptococcal (iGAS) infections have been increasing in Europe, Australia, and the USA, but few data from China are available. This study intended to provide local data to highlight the characteristics of iGAS infections in China. A retrospective analysis was performed on clinical iGAS infection data from 2014 to 2023 in a tertiary hospital in Shanghai, China. Genomic analysis was conducted to characterize antimicrobial resistance, virulence, prophages, and integrative and conjugative elements (ICEs), as well as phylogenetic clusters. From 2014 to 2023, a total of 21 iGAS cases were discovered, with soft tissue infections accounting for 61.9% (13/21) and 85.7% (18/21) of isolates resistant to erythromycin and clindamycin, respectively. Three iGAS isolates from 2023 underwent genome sequencing, which indicated that two isolates were emm12 and one was emm28. Phylogenetic analysis showed that the two emm12 isolates were assigned to clade II and closely related to Chinese scarlet fever-causing isolates. The emm28 isolate was assigned to subclades of SC1A and discovered to possess a novel ICE (designated as ICE-SHemm28; Tn916-like) that carried both the ermB gene and the type IV secretion system. Emergence of an emm28 iGAS strain harboring a novel macrolide resistance-carrying type IV secretion system ICE was identified in invasive infections in Shanghai.

Non-O1/non-O139 Vibrio cholerae (NOVC) have been observed sporadically worldwide, causing a spectrum of illnesses ranging in severity from mild to life-threatening, despite the absence of the ctx virulence gene. Here, we report a fatal case of NOVC bacteremia in a 72-year-old woman with no obvious underlying diseases. The isolate, designated as V. cholerae vc973360, was classified as a novel sequence type 1665, by whole genome sequencing. Notably, vc973360 lacked the ctxAB genes but contained 147 other potential virulence factors, including hlyA, tlh, and rtx. Additionally, this isolate encodes three putative O-antigen ORFs of Yersinia origin, representing a unique genomic feature within the Vibrio genus. It also carried several resistance genes, such as qnrVC4, CRP, almE, almF, almG. However, the isolate’s susceptibility profile indicated that it was susceptible to the majority of antimicrobials tested except polymyxin B. Phylogenetic analysis revealed that vc973360 was most closely related to a clinical isolate recovered from human blood in Colombia. The patient had severe symptoms and succumbed to the infection, underscoring the need for comprehensive exploration of both clinical manifestations and epidemiological factors to facilitate early diagnosis and establish effective therapeutic strategies.

Background: Bloodstream infection (BSI) caused by Escherichia coli has become a growing clinical threat due to its high incidence and mortality rates. Despite its significant global health burden, the genomic diversity of E. coli in Shanghai has not been systematically investigated, with ramifications for treatment and prevention. This study aimed to assess the prevalence and genomic epidemiology of E. coli BSI isolates in Shanghai, delineate predominant lineages and their related phenotypic and genomic characteristics, and elucidate the population structure. Methods: A total of 136 E. coli strains were collected from a tertiary hospital in Shanghai between 2023 and 2024. We conducted comprehensive analyses, including multilocus sequence typing (MLST), core genome MLST (cgMLST), clonal complex assignment, serotype prediction, identification of antimicrobial resistance genes (ARGs) and plasmid-borne virulence genes, and plasmid mobility prediction. Results: The predominant clonal complex was CC131 (22.8%), followed by CC14 (14%). The highest resistance rate was observed for ampicillin (85.3%), whereas amikacin (3.7%), ertapenem (2.9%), imipenem (2.9%), minocycline (2.2%), and meropenem (2.2%) retained excellent in vitro activity. High resistance to ciprofloxacin (63.2%) and levofloxacin (62.5%) was observed, primarily mediated by mutations in gyrA (S83L, D87N) and parC (S80I), particularly in ST1193 strains. Plasmid-borne siderophore virulence genes co-occurred as gene modules, the majority of which were located on transferable IncFIB plasmids. However, this trend was not uniform across lineages, with the CC131 clones predominantly carrying mobilizable plasmids, while CC14 clones predominantly harbored non-mobilizable plasmids. Conclusions: Our findings reveal the dynamic genetic diversity of E. coli BSI isolates at a tertiary hospital in Shanghai, highlighting the importance of genomic surveillance and providing valuable insights for infection control.