Balaji Veeraraghavan

Carbapenem-resistant Enterobacterales (CRE) are an increasing public health concern, particularly as carbapenemase-producing isolates, such as NDM and OXA-48-like producers, become more prevalent. Rapid and accurate identification of carbapenemases is crucial to guide appropriate antibiotic therapy. Although recent epidemiologic data show that CRE increasingly harbor multiple carbapenemases, the performance of common phenotypic tests—the modified carbapenem inactivation method (mCIM) and EDTA-modified CIM (eCIM)—has not been well defined in these isolates. We examined the performance of mCIM and eCIM among CRE-encoding NDM, OXA-48-like, or both. We included 172 genotypically confirmed carbapenemase-encoding CRE isolates from perirectal swabs collected from patients admitted to two intensive care units at a hospital in South India. Isolates included Escherichia coli (53.5%), Klebsiella pneumoniae (41.3%), and Enterobacter species (5.3%). Overall, 112 isolates (65.1%) encoded NDM alone, 23 (13.4%) encoded OXA-48-like alone, and 37 (21.5%) encoded both NDM and OXA-48-like. mCIM positivity was 98.2% for NDM, 47.8% for OXA-48-like, and 94.6% for NDM+OXA-48-like encoders; among mCIM-positive isolates, eCIM positivity rates were 99.1%, 91%, and 97.1%, respectively. When compared to molecular carbapenemase gene detection, mCIM/eCIM was highly sensitive for classifying isolates encoding NDM as metallo-β-lactamase (MBL) producers, but significantly misclassified isolates encoding OXA-48-like as having an MBL or lacking a carbapenemase. In the largest collection of NDM and OXA-48-like co-encoding CRE isolates to date, mCIM/eCIM typically reported these as MBL producers. IMPORTANCE: Carbapenemase-encoding Enterobacterales infections are associated with substantial adverse health outcomes, making rapid and accurate carbapenemase detection essential for guiding antibiotic therapy. Although Enterobacterales carrying multiple carbapenemases are increasingly reported worldwide, the performance of common phenotypic assays, mCIM and eCIM, remains insufficiently defined for these strains. In this study of 172 genotypically confirmed carbapenemase-encoding Enterobacterales isolates from hospitalized patients in South India, mCIM/eCIM consistently classified NDM-encoding isolates as metallo-β-lactamase encoders. Additionally, mCIM/eCIM frequently misclassified OXA-48-like-encoding isolates as either metallo-β-lactamase encoders or carbapenemase-negative, highlighting the need to better understand the mechanisms underlying this variable activity. In the largest collection of NDM and OXA co-encoding Enterobacterales isolates reported to date, mCIM/eCIM generally reported co-encoding isolates as metallo-β-lactamase producers. Our results suggest that mCIM/eCIM performance may vary geographically due to variable activity, distribution, and combinations of carbapenemases.

Background: Infections caused by carbapenem-resistant (CR) Gram-negative bacteria, particularly metallo-β-lactamase (MBL)-producers, have limited treatment options. Cefepime–zidebactam retains activity against these pathogens, but clinical data are limited. Methods: This prospective, open-label, single-arm, multicenter phase 2 trial enrolled adults with CR Gram-negative infections. Participants received intravenous cefepime–zidebactam for 7–21 days with renal dose adjustment. The Micro-ITT population included participants with a confirmed qualifying CR Gram-negative pathogen, and the CME population included those meeting prespecified evaluability criteria. The primary endpoint was investigator-assessed clinical cure at TOC in the CME population. Outcomes were also reviewed by an external adjudication committee. Results: Seventy-two participants received treatment; 68 were included in the Micro-ITT population and 60 in the CME population. Among 68 qualifying isolates, 56 (82.4%) were MBL producers, predominantly NDM-β-lactamase producers. Investigator-assessed clinical cure at test-of-cure in the CME population was 91.7% (95% confidence interval, 81.6%–97.2%), and favorable microbiological outcome at TOC was 90.0%. Among participants in the CME population with MBL-producing pathogens, clinical cure was 93.9% and favorable microbiological outcome was 91.8%. External adjudication in the CME population yielded clinical cure of 86.7% and favorable microbiological outcome of 85.0%. Twenty-eight-day mortality was 2.8%. Treatment-related adverse events occurred in 15.3%, and serious treatment-related adverse events occurred in 2.8%. Conclusions: In 60 evaluable adults with carbapenem-resistant Gram-negative infections, predominantly MBL-producing (81.7%) and cUTI/AP (58.3%), investigator-assessed TOC clinical cure was 91.7%; post hoc adjudicated cure was 86.7%. Day 28 all-cause mortality was 2.8%, and cefepime zidebactam was well tolerated.

Background: Pneumococcal disease imposes a substantial public health burden in India, particularly among older adults and individuals with chronic or immunocompromising conditions. Although the 13-valent pneumococcal conjugate vaccine (PCV13) and the 23-valent pneumococcal polysaccharide vaccine are available, the emergence of non-PCV13 serotypes has highlighted the need for broader serotype coverage. The approval of the 20-valent pneumococcal conjugate vaccine (PCV20) offers expanded serotype coverage and the potential to simplify adult vaccination strategies. Methods: A multidisciplinary expert panel convened to develop evidence-informed expert opinions on PCV20 use in adults. A narrative literature review (2010–2025), a structured pre-meeting web-based survey, and structured discussions using the Nominal Group Technique were conducted. Expert opinions were refined, reviewed, and approved by all panel members. Results: Based on the available evidence and expert deliberations, the panel supported single-dose PCV20 for adults aged ≥50 years and at-risk individuals aged 18–49 years. The panel also provided specialty-specific recommendations to facilitate the implementation of PCV20 in routine clinical practice across diverse adult populations in India. Conclusions: These multidisciplinary expert opinions provide practical guidance for PCV20 use in Indian adults and are intended to complement, not replace, the formal national recommendations and to support informed clinical decision-making for adult pneumococcal vaccination in India, while acknowledging remaining uncertainty regarding effectiveness, implementation, affordability, and the need for further India-specific evidence.

Introduction: Streptococcus pneumoniae remains a major cause of severe, life-threatening disease across all age groups. Effective surveillance of serotype distribution is crucial for informing nationwide vaccine policy, particularly in high-burden countries such as India. While the traditional Quellung reaction is the gold standard for pneumococcal serotyping, its implementation is limited by high costs, labor intensity, and restricted accessibility. Whole genome sequencing (WGS)-based approaches have emerged as scalable alternatives, promising greater efficiency. Methods: Six leading WGS-based pneumococcal serotyping tools - SeroBA, Pneumo-Typer, PneumoKITy, PfaSTer, SeroCall, and PneumoCaT - were evaluated using a large collection of Streptococcus pneumoniae isolates obtained from publicly available datasets (supplementary table S1). Serotype level and serogroup level concordance with reference phenotypic serotyping methods was calculated as proportions with 95% confidence intervals (CIs) using the Wilson score method. Results: A total of 1,629 Streptococcus pneumoniae genomes were analyzed, of which 1,595 met assembly-level quality control (QC) criteria. The remaining 34 QC-failed genomes were retained for downstream analysis, as WGS-based serotyping tools continued to generate consistent and reliable serogroup-level assignments despite reduced assembly quality. Overall, Pneumo-Typer (93.86%) and SeroBA (91.16%) achieved the highest concordance with reference phenotypic serotyping methods identifying major serotypes. However, despite its strong concordance rate, Pneumo-Typer exhibited reduced performance in species-level discrimination. Conclusions: WGS-based serotyping represents a robust, scalable alternative to antisera-based classification for pneumococcal surveillance, with particular relevance for high-burden settings where conventional typing methods remain inaccessible. SeroBA provided the overall balance between serotype concordance, serogroup concordance, species-level discrimination, and computational performance. Integrating WGS-driven surveillance with global genomic datasets will strengthen epidemiological understanding of serotype dynamics, track vaccine-driven serotype replacement, and underpin evidence-based pneumococcal vaccine policy for high-burden countries.

Salmonella enterica serovar Enteritidis is a leading cause of invasive non-typhoidal Salmonella (iNTS) disease globally, particularly in sub-Saharan Africa. In contrast, the epidemiology and population structure of invasive S . Enteritidis in South Asia remain poorly characterized. This study investigates the clinical presentation, phylogenetic relationships and genomic characteristics of S . Enteritidis bloodstream infections (BSIs) in India. Clinical data were collected from 101 patients with S . Enteritidis BSI between 2012 and 2022. Whole-genome sequencing was performed on representative bloodstream isolates together with isolates from non-blood clinical specimens and poultry sources. Comparative genomic analyses included phylogenetic reconstruction, invasiveness index prediction, and prophage characterization. Infants and immunosuppressed individuals were disproportionately affected by iNTS disease. Phylogenetic analysis identified four major lineages of S . Enteritidis. Most BSI isolates clustered in a previously unrecognized lineage, designated the Global Intermediate Clade, which occupied a phylogenetic position between the Global outlier and Global epidemic clades. Bayesian inference dated its most recent common ancestor to around 1789 AD (95% HPD: 1692–1941), with global circulation confirmed by European and Asian isolates. The Global Intermediate clade exhibited the second-highest invasiveness index (median 0.221, SD 0.013) after the West African clade; however, this index reflects genomic signatures associated with invasiveness and should not be interpreted as a direct measure of virulence. Poultry isolates clustered separately from the dominant bloodstream-associated lineage. Pan-genome analysis identified a lineage-specific mosaic prophage composed of modules homologous to prophages found in diverse Enterobacterales. This study provides the first detailed genomic insight into invasive S . Enteritidis in India and identifies a previously unrecognized Global Intermediate Clade associated with bloodstream infection. The distinct phylogenetic placement and genomic features of this lineage, including a lineage-specific mosaic prophage, warrant further investigation and support the need for expanded One Health genomic surveillance.

Introduction: Pneumococcal disease, caused by Streptococcus pneumoniae , is a major public health burden with high morbidity and mortality across all age groups in India. Limited adult pneumococcal vaccination policies, evolving serotype patterns, and delayed herd protection from paediatric immunization continue to challenge effective prevention of pneumococcal disease in adults. Methods: This retrospective laboratory surveillance study includes Streptococcus pneumoniae isolates from adults (>18 years) collected between January 2018 and May 2025 at Christian Medical College, Vellore and were serotyped using the Quellung and co-agglutination method. Percentage of serotype coverage for PCV20, PCV21, and PPSV23 was analysed. Results: Among 1,065 adult pneumococcal isolates, PCV20 covers 66.5% of invasive pneumococcal disease (IPD) serotypes, including emerging serotypes such as 15B and 11A, while PCV21 aligns poorly with the local epidemiology, covering only 46.5% of adult IPD serotypes. PPSV23 offers limited additional relevant serotype coverage beyond PCV20 and is limited by lower immunogenicity and hyporesponsiveness to multiple doses. Discussion: Our findings highlight significant gaps between the circulating serotypes in adults in India and those covered by current vaccines. PCV20 shows promise for broader adult protection; however, further multi-centre studies, cost-effectiveness analyses, and enhanced surveillance are needed to inform policy and optimize immunization strategies in resource-limited settings.

Aims: The convergence of multidrug resistance and hypervirulence in Klebsiella pneumoniae (MDR-HvKp) has narrowed treatment options. Despite growing interest in phage-antibiotic synergy, this study evaluates the underexplored combinatorial effects of phage and antibiotics, including drug-specific interactions and sequence dependency, against the biofilm-forming MDR-HvKp clinical strain. Methods and results: A T5-like Klebsiella bacteriophage, Round, within the genus Webervirus, was therapeutically and genomically characterized. A biofilm-forming clinical strain, Kleb_134, was used to evaluate in vitro phage-antibiotic interactions with meropenem, colistin, and tigecycline in planktonic and biofilm models. In planktonic assays, phage combinations with meropenem and colistin resulted in a multi-log CFU reduction compared to monotherapies, whereas reduced efficacy was observed with tigecycline. In biofilm assays, pre-phage treatment followed by antibiotic exposure demonstrated the strongest biofilm reduction. Drug-specific and sequence-dependent effects were evident. Meropenem-phage combinations reduced biofilm biomass by 2.85-fold (high phage titre) and 3.8-fold (low phage titre), while colistin-phage combinations achieved reductions of 8.4-fold (high phage titre) and 2.8-fold (low phage titre). Conclusions: Sequential phage-antibiotic treatment was effective against MDR-HvKp biofilms, with pre-phage exposure enhancing antibiotic access through biofilm disruption. The bacteriostatic nature of tigecycline reduced efficacy by affecting phage replication. These findings highlight the importance of treatment sequence and antibiotic selection, and extend existing knowledge in optimizing therapeutic outcomes in MDR-HvKp infections.