Biology subjects

Velmurugan, A.

Publications and source records attributed to Velmurugan, A..

3 recordsLinked to original sources

bioRxiv2026

Three Plasmid Strategies, One Intermediate Convergence State: Lineage-Specific Resistance, Virulence Architecture in Dominant Indian Carbapenem-Resistant Klebsiella pneumoniae Clones

Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a critical global healthcare threat driven by high-risk multidrug-resistant (MDR) clones that acquire hypervirulence genes. Although resistance-virulence co-occurrence is extensively documented, the plasmid-level mechanisms facilitating this convergence remain unclear. In this study, we utilized hybrid short- and long-read whole-genome sequencing of 376 clinical CRKp strains to define the evolutionary trajectories and structural plasmid dynamics of three predominant high-risk clones: ST147 (n=157), ST231 (n=108), and ST2096 (n=111). Carbapenemase genes were present in 90% of isolates, predominantly blaOXA-48-like and blaNDM-5 co-harbored with blaCTX-M-15. Virulence profiling indicated high aerobactin (iuc) prevalence (62.7%), while salmochelin and colibactin were undetected. Hypermucoviscosity occurred infrequently (6.6%) and was independent of rmpA/rmpA2, confirming a clear genotype-phenotype discordance. Comparative plasmid mapping revealed three distinct, lineage-specific plasmid configurations underlying this intermediate convergent pathotype: ST147 exhibited dynamic, mosaic hybrid IncFIB-IncHI1B plasmids; ST2096 showed structurally stabilized hybrids; and ST231 retained virulence and resistance determinants on separate, segregated plasmids. These findings show that convergence is regulated by multiple, clone-specific evolutionary routes rather than a single path, highlighting the critical need for more in-depth genomic surveillance capable of identifying convergent plasmids along with high-risk lineages

microbiology↗

bioRxiv2026

Development and validation of a genome-informed multiplex PCR for specific detection of typhoidal Salmonella serovars

Enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi A, B and C remains a major public health burden in endemic regions. Existing molecular assays frequently demonstrate limited specificity due to cross-reactivity with non-typhoidal Salmonella (NTS). In this study, we developed and validated a genomics-informed multiplex PCR assay capable of simultaneously differentiating all four typhoidal Salmonella serovars. A curated dataset of 3,239 Salmonella genomes, including S. Typhi (n=361), S. Paratyphi A (n=453), S. Paratyphi B (n=511), S. Paratyphi C (n=62), and NTS genomes (n=1,853), was used for comparative genomic analysis. Thirty published PCR targets were evaluated in silico, followed by pangenome and SNP analyses to identify discriminatory loci for mismatch amplification mutation assay (MAMA)-based primer design. Candidate primers were validated using in silico PCR, BLASTn analysis, and laboratory testing against a panel of typhoidal Salmonella, clinical NTS isolates, and non-Salmonella bacterial pathogens. In silico evaluation demonstrated substantial cross-reactivity among many published targets, whereas SNP-informed primer design targeting staG (S. Typhi), SPA0152 (S. Paratyphi A), SPAB_03490 (S. Paratyphi B), and SPC_0571 (S. Paratyphi C) achieved predicted specificities of 98-100% while retaining high analytical sensitivity (>97%) across target genomes. Combined with a pan-Salmonella invA target, the multiplex assay precisely identified all target serovars in vitro with minimal cross-reactivity. These findings demonstrate that genomics-informed SNP-based primer design enables reliable multiplex differentiation of typhoidal Salmonella serovars and provides a scalable framework for improving enteric fever diagnosis and surveillance in endemic settings. ImportanceTyphoidal Salmonella serovars remain major causes of enteric fever in endemic regions, yet molecular differentiation from non-typhoidal Salmonella (NTS) remains challenging because of extensive genomic conservation and cross-reactivity of commonly used diagnostic targets. In this study, we combined large-scale comparative genomics of 3,239 Salmonella genomes with SNP-informed primer design to develop a multiplex PCR assay capable of simultaneously differentiating all four typhoidal serovars (S. Typhi, S. Paratyphi A, B, and C) from NTS and other non-Salmonella pathogens. Unlike conventional gene-content-based assays, this approach incorporated lineage-specific SNPs and mismatch amplification strategies to improve specificity while maintaining high analytical sensitivity. In silico evaluation demonstrated high diagnostic performance across diverse global lineages, while in vitro testing confirmed accurate serovar-level discrimination with minimal cross-reactivity. These findings demonstrate the value of population-scale genomics for molecular assay development and provide a scalable framework for improving diagnosis and surveillance of enteric fever in endemic settings.

molecular biology↗

bioRxiv2022

ompC/F mutations drive XDR phenotype and lineage defining super clones of E. coli: Sequential events and consequences

Multi-drug resistant Escherichia coli is an increasing public health problem. Though, PBP3 insertions with blaNDM, blaCMY and blaOXA-48 like is restricted to South-East Asia with few reports from USA. The study suggests ompC/F variants as a core factor to classify ESBL (E), non-ESBL (NE), and ESBL with PBP3 and carbapenemases (EPBP3) clones. EPBP3 results in treatment complication, as most of the time, E. coli with PBP3 insertions co-carries blaNDM (87.5%), blaCMY (96.3%) and blaOXA-48 like (88.8%) implicating it as a predisposing factor for carbapenemase gene acquirement. Cefiderocol and cefepime/zidebactam are the choice against EPBP3 E. coli. Evolutionary BEAST analysis revealed consecutive events of YRIN and YRIK insertions in PBP3 gene leading to a surge in MDR E. coli clones. Further, emergence of the super clones STs 410, 405, 167 and 617 featuring these phenotypes is a major threat for developing and developed countries, which needs close monitoring. ImportanceThe manuscript describes various E. coli resistant genotypes across the globe and their importance in the choice of antimicrobial for treatment. The study identified six clades based on ompC and ompF mutations with a strong correlation to PBP3 insertions co-carried with beta-lactamases including blaNDM. Though, the ompC and ompF mutations were reported to precede the acquisition of carbapenemases in E. coli, clade segregation based on AMR genes as observed in this study reveals the ompC and ompF genes as a potential biomarker for AMR clade identification in E. coli. Currently, cefiderocol and cefepime/zidebactam seems to be the only choice to cover the AMR mechanism mediated by PBP3 insertions. Further, emergence of the super clones STs 410, 405, 167 and 617 featuring these PBP3 phenotypes is a major threat for developing and developed countries, which needs close monitoring.

genomics↗