National Institute of Cholera and Enteric Diseases

The concurrent presence of multiple New Delhi metallo-β-lactamase ( bla NDM ) variants within an isolate often goes undetected without next-generation sequencing. This study detects and characterizes dual bla NDM variants in Escherichia coli through Sanger and whole-genome sequencing. Additionally, a rapid identification method utilizing restriction digestion was designed for detecting bla NDM variants carrying M154L mutation. Antibiotic susceptibility, minimal inhibitory concentration for meropenem and ertapenem, PCR, and Sanger sequencing of bla NDM along with genome sequencing using Illumina and Nanopore technology were conducted. Transmissibility and replicon types of bla NDM -harboring plasmids were evaluated. Restriction digestion using restriction enzyme, BtsCI was developed to distinguish between bla NDM-1 and bla NDM variants possessing M154L mutation, such as bla NDM-5 , bla NDM-7 etc. Two isolates belonging to phylogroups A; ST167 and B1; ST101 and resistant to meropenem and ertapenem (≥16 mg/L) were recovered from the blood of a neonate and the rectal swab of a pregnant woman, respectively. bla NDM was detected by PCR, and Sanger sequences of bla NDM showed two peaks at 262 (G and T) and 460 (A and C) nucleotide positions indicative of more than one bla NDM variant. Hybrid assembly confirmed co-existence of bla NDM-1 and bla NDM-5 in each isolate. bla NDM-1 was located on IncY (ST167) and IncHI1A/HI1B (ST101), while bla NDM-5 was on IncFIA/FII (ST167) and IncC (ST101) plasmids in the two isolates. Digestion with BtsC1 could discriminate between bla NDM-1 and bla NDM-5 . The co-existence of multiple bla NDMs , bla NDM-1 , and bla NDM-5 in epidemic clones of E. coli is concerning. Restriction digestion method and Sanger sequencing can facilitate quick identification of dual bla NDM variants in a single isolate. IMPORTANCE The global dissemination of antimicrobial resistance genes is a serious concern. One such gene, bla NDM , has spread globally via plasmids. bla NDM confers resistance against all β-lactam antibiotics, except monobactams. Most of the earlier literature reported the presence of single bla NDM variant. However, this study reports the prevalence of dual bla NDM variants ( bla NDM-1 and bla NDM-5 ) located on two separate plasmids identified in two distinct Escherichia coli epidemic clones ST167 and ST101 isolated from a septicemic neonate and a pregnant mother, respectively. bla NDM-5 differs from bla NDM-1 due to the presence of two point mutations (i.e., V88L and M154L). This study detected dual bla NDM variants through Sanger sequences and further validated them through hybrid-genome assembly. Detection of multiple bla NDM variants in a single isolate remains difficult until genome sequencing or southern blotting is carried out. Hence, a simple restriction digestion method was devised to rapidly screen dual bla NDM variants containing M154L mutation.

The use of digital technologies in education play a crucial role in providing new and innovative forms of delivering education to teachers and students as well as broadening the learning process. The aim of this systematic review is to summarize existing evidence in order to evaluate the application of digitalization in undergraduate and postgraduate dental education. A literature review was completed using PubMed, SCOPUS and DOAJ search engines, following the search strategy using the PICO criteria, to identify English-language articles published between January 2013 and June 2023 that reported the use of digitalization in dental education. Following thorough research, 1721 articles were identified from e-databases. However, only 14 articles were added to this study after they were screened for eligibility. Quality assessment was performed by a checklist of important parameters using the National Institute of Health (NIH) assessment tool. Two studies focused on the knowledge regarding the utilization of digitalization in dental education, two studies examined the implementation of digitalization in dental education, two studies explored the user experience of utilizing digital dentistry, and eight studies investigated the perception and attitude towards digital dental education. The goal of incorporating digitalization in dental education should be to maximize the effectiveness of the many different digital technologies functioning together in patient care and dental education. The most significant advantage of understanding digital technology is its noteworthy benefits, which include compliance from patients, quick and prompt results and aesthetic outcomes.

Background Shigella spp. is one of the notable causes of global diarrheal morbidity and mortality, accounting for 13.2% of deaths in 2016. Antimicrobial resistance complicates shigellosis management. Understanding local disease epidemiology is crucial for developing effective preventive strategies, including vaccine use. Methods We investigated antimicrobial resistance, risk factors (socio-economic, behavioral, and water, sanitation and hygiene (WaSH), and clinical characteristics of Shigella diarrhea in Mukuru Informal settlement and surrounding villages in Nairobi, Kenya. Patients presenting with diarrhea, fever, or both in treatment centres had stool or rectal swab samples cultured and bacteria was identified through biochemical and serological tests. Results Shigella isolation among the 4,689 individuals presenting with diarrhea was 1.4% across all ages and with a similar isolation rate (1.5%) among children under 5 years of age. The majority (40, 59.7%) of the Shigella spp were Shigella flexneri, and the majority (34/40, 85%) of S. flexneri were resistant to trimethoprim/sulfamethoxazole, however, all were sensitive to amoxicillin-clavulanate, ceftazidime, ceftriaxone, and cefpodoxime. Multi-drug resistance was higher in S. sonnei (13, 48.1%) compared to S. flexneri (3, 7.5%). Shigella positivity was associated with bloody diarrhea, severe/moderate dehydration, coated tongue and high fever. Consumption of street food was also associated with Shigella diarrhea. Conclusion Despite low prevalence, shigellosis still poses a significant burden of diarrheal disease, warranting future incidence studies. First-line antibiotics against Shigella remain effective, but intermediate resistance to azithromycin and ciprofloxacin is a concerning trend. Improving household food preparation and handling could potentially reduce Shigella infections.

Introduction: Diarrhea is a leading contributor of mortality. Its disease burden can be assuaged using enhanced prognostics and therapeutics. A cross-sectional gut microbiome analysis of non-diarrheal and diarrheal fecal samples was conducted to meet the goals of the Global Action Plan for Pneumonia and Diarrhea. Hypothesis: Next-generation Sequencing as a tool for epidemiological surveillance helps in the comparison of structural diversity of the gut microbiome of diarrheal and non-diarrheal samples and can identify prognostic and therapeutic candidates. Aim: The pilot study was designed to identify taxa that are enriched in non-diarrheal samples and to predict gut microbial interactions. Methodology: 16SrRNA amplicon sequencing and analysis were deployed for taxonomic profiling and abundance interpretation of OTUs (Operational Taxonomic Units). Results: The findings suggested significant differences in structural composition between the two groups. Firmicutes was the most abundant phylum in most samples. B/F ratio was consistently <1 in all diarrheal samples. Proteobacteria was more abundant in diarrheal samples. Prevotellaceae was the most abundant family in non-diarrheal samples. Streptococcaceae was the most abundant family in 60% diarrheal samples.Where Streptococcaceae was suppressed, Bacteroideaceae and Nocardeaceae were the most abundant. In non-diarrheal samples where Bifidobacteriaceae was the most abundant other families were significantly low. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in non-diarrheal samples. Prevotella copri was the most abundant species in 70% non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples and were absent in diarrheal samples. Conclusion: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. This is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome. The study addressed gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics for protecting the endemic population from diarrhea and help in reaching Sustainable Development Goals 2 and 3.

We studied the relationship of frailty and acute lower respiratory infection (ALRI) among a multi-site cohort of community-dwelling older adults aged ≥60 years in India. During January 2019‒January 2020, participants completed the Edmonton Frail Scale (EFS) at baseline and every 3 months at four sites in India, with each participant completing a maximum of four surveys. Participants were categorized as non-frail (0–5 points), vulnerable (6–7 points), and frail (≥8 points) based on EFS score. Project nurses made weekly home visits to identify ALRI episodes with onset during past 7 days. We estimated adjusted hazard ratios (aHR) for having an ALRI episode within 90 days after EFS by frailty category. We also assessed risk of deterioration of frailty during 7–100 days after ALRI episode onset in terms of an increased EFS score by ≥1 point and change of frailty category. Among 5801 participants (median age 65 years, 41% males), 3568 (61·5%) were non-frail, 1507 (26%) vulnerable, and 726 (12·5%) frail at enrolment. Compared with non-frail participants, the hazard of an ALRI episode was higher among vulnerable (aHR: 1·6, (95%CI 1·3–2.0) and frail participants (aHR: 1·7, 95%CI 1·3–2·2). Participants having ALRI within the past 7–100 days were at increased risk of worsening frailty category (aOR: 1.9, 95%CI 1·3–2.8) compared to participants without an ALRI episode during the same period. The association between ALRIs and worsened frailty suggests prevention of ALRIs through vaccination and other strategies may have broad reaching health benefits for older adults.

Viruses are intracellular obligate parasites that heavily rely on host machinery to undergo replication and survival. They activate and block almost all known types of programmed cell death. These modulate viral pathogenesis and host antiviral immunity to a great extent. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had resulted in a recent global pandemic that caused millions of deaths worldwide. Similar to other viral infections, it has also been reported that SARS-CoV-2 induces cell death in infected cells. This leads to severe inflammation, contributing to viral pathogenicity and poor prognosis. Biopsy samples from postmortem patients indicate the occurrence of cell death. But, the connection between SARS-CoV-2 and mechanisms of cell death is yet to be elucidated. Among the cell death pathways, apoptosis, necroptosis, pyroptosis, and ferroptosis majorly contribute to disease pathogenesis. So, this chapter will focus on current evidence and research progress in the modulation of cell death due to SARS-CoV-2 infection. This will aid in uncovering novel therapeutic strategies in treating COVID-19 patients.

Activation of the innate immune system triggers inflammatory cell death in response to microbial infections or disruptions in cellular homeostasis. PANoptosis represents a novel and distinct inflammatory programmed cell death pathway governed by complex PANoptosome assemblies and emphasizes the substantial interplay and cross-talk among pyroptosis (P), apoptosis (A), or necroptosis (N). This study briefly overviews the basic processes underlying apoptosis, pyroptosis, and necroptosis, along with their extensive cross-talk events within PANoptosis. The PANoptosis concept and the PANoptosome complex’s assembly process, which triggers cell death, will be explained. It emphasizes the notable contribution of PANoptosis to a range of cancer types, such as digestive cancers, breast cancers, and gliomas, illustrating its impact on tumor development and patient prognosis. Furthermore, the study discusses recent advancements in cancer treatment, highlighting the promise of targeting PANoptosis to enhance anti-tumor immune responses and diverse approaches for modulating PANoptosis pathways to achieve therapeutic benefits. In the future, continued research on PANoptosis will deepen our understanding of the core mechanisms governing cell death and contribute crucial scientific insights to cancer research.

Shigella infection poses a significant public health challenge in the developing world. However, lack of a widely available mouse model that replicates human shigellosis creates a major bottleneck to better understanding of disease pathogenesis and development of newer drugs and vaccines. BALB/c mice pre-treated with streptomycin and iron (FeCl3) plus desferrioxamine intraperitoneally followed by oral infection with virulent Shigella flexneri 2a resulted in diarrhea, loss of body weight, bacterial colonization and progressive colitis characterized by disruption of epithelial lining, loss of crypt architecture with goblet cell depletion, increased polymorphonuclear infiltration into the mucosa, submucosal swelling (edema), and raised proinflammatory cytokines and chemokines in the large intestine. To evaluate the usefulness of the model for vaccine efficacy studies, mice were immunized intranasally with a recombinant protein vaccine containing Shigella invasion protein invasion plasmid antigen B (IpaB). Vaccinated mice conferred protection against Shigella, indicating that the model is suitable for testing of vaccine candidates. To protect both Shigella and Salmonella, a chimeric recombinant vaccine (rIpaB–T2544) was developed by fusing IpaB with Salmonella outer membrane protein T2544. Vaccinated mice developed antigen-specific serum IgG and IgA antibodies and a balanced Th1/Th2 response and were protected against oral challenge with Shigella (S. flexneri 2a, Shigella dysenteriae, and Shigella sonnei) using our present mouse model and Salmonella (Salmonella Typhi and Paratyphi) using an iron overload mouse model. We describe here the development of an oral Shigella infection model in wild-type mouse. This model was successfully used to demonstrate the immunogenicity and protective efficacy of a candidate protein subunit vaccine against Shigella.

Campylobacter species are the most common pathogens responsible for foodborne gastroenteritis worldwide. India is a region with frequent diarrheal infections and a high level of Campylobacter infection incidence, but the detailed genomic information is limited. This study aimed to characterize 112 isolates of Campylobacter from diarrhea patients at two hospitals in Kolkata, West Bengal, by whole genome analysis. The Campylobacter isolates consisted of 90 C. jejuni, 20 C. coli, and 2 C. lari isolates. Multilocus sequence typing analysis revealed that the largest sequence type (ST) populations were ST-2131 in C. jejuni and ST-830 in C. coli and seven novel STs were found in C. jejuni and one in C. coli. Notably, ST-2131, which is rarely seen elsewhere, was positive for a sialylated LOS-related gene (wlaN +neuA + cstIII) associated with Guillain-Barré syndrome. Antibiotic resistance factors predicted from the genome sequence included blaOXA variants (58.9%), tet(O) (54.5%), tet(W) (0.9%), ant(6)-Ia (0.9%), mutation in GyrA (T86I, T86I+D90N, T86I+P104S, T86I+D90N+P104S) (79.5%), and mutation in 23S rRNA (A2075G) (12.5%). In addition to the high drug resistance of Campylobacter in Kolkata, Campylobacter pathogens were circulating that may be associated with Guillain-Barré syndrome. This study indicates the importance of genomic analysis in the surveillance of pathogens, which provides genomic information on genetic diversity, virulence mechanisms, and determinants of antimicrobial resistance.

Rotavirus (RV) accounts for 19.11% of global diarrheal deaths. Though GAVI assisted vaccine introduction has curtailed RV induced mortality, factors like RV strain diversity, differential infantile gut microbiome, malnutrition, interference from maternal antibodies and other administered vaccines, etc. often compromise vaccine efficacy. Herein emerges the need of antivirals which can be administered adjunct to vaccination to curb the socio-economic burden stemming from frequent RV infection. Cognisance of pathogen-perturbed host cellular physiology has revolutionized translational research and aided precision-based therapy, particularly for viruses, with no metabolic machinery of their own. To date there has been limited exploration of the host cellular metabolome in context of RV infection. In this study, we explored the endometabolomic landscape of human intestinal epithelial cells (HT-29) on RV-SA11 infection. Significant alteration of host cellular metabolic pathways like the nucleotide biosynthesis pathway, alanine, aspartate and glutamate metabolism pathway, the host citric acid cycle was observed in RV-SA11 infection scenario. Detailed study further revealed that RV replication is exclusively dependent on glutamine metabolism for their propagation in host cells. Glutamine metabolism generates glutamate, aspartate, and asparagine which facilitates virus infection. Abrogation of aspartate biogenesis from glutamine by use of Aminooxyacetic acid (AOAA), significantly curbed RV-SA11 infection in-vitro and in-vivo. Overall, the study improves our understanding of host-rotavirus interactome and recognizes host glutamine metabolism pathway as a suitable target for effective therapeutic intervention against RV infection.

Introduction : Direct-acting antivirals (DAAs) are highly effective in treating HCV infection, but a small subset of patients may fail to achieve SVR12 and require further intervention. In resource-limited settings where second-line DAAs (such as SOF/VEL/VOX) may be unavailable, optimizing first-line treatments is essential. This study evaluated the efficacy (SVR12) of re-treatment regimen based on first-line DAAs (SOF/VEL) with ribavirin. Method: This retrospective study screened all viremic patients who attended the apex treatment center (ATC) between January 2019 and December 2023 and received DAAs as per the national Viral Hepatitis control program (NVHCP) guidelines. Patients who failed to achieve SVR12 were subsequently retreated with the available first-line regimen (SOF/VEL plus ribavirin). Results: A total of 1,814 viremic patients attended the apex treatment center (ATC). 1262 patients completed therapy. 1198 (94.9%) patients achieved SVR 12 and 64 patients (5.1%) failed to achieve SVR 12. Additionally, 41 patients with DAA failure were referred from treatment center (TC) and model treatment center (MTC) for evaluation. After further exclusions, 36 patients were enrolled, and 30 of them were offered retreatment. The majority of patients were male (64.5%) with a median age of 45 years (IQR; 19-68). Five patients were cirrhotic, while the remainder was non-cirrhotic. Baseline HCV RNA levels before the retreatment regimen was 87,882 IU/ml (IQR; 9,870-484,902). Most patients (96.6%) had genotype 3 HCV infection. Prior to retreatment, 27 patients had received a 12-week regimen of Sofosbuvir and Daclatasvir, while only three had been treated with the Sofosbuvir-Velpatasvir regimen. After retreatment with Sofosbuvir, Velpatasvir, and Ribavirin, 22 patients (73%) achieved SVR12. None of the patients experienced any adverse event. Conclusion: First-line DAAs are highly effective to treat naïve patients. In the absence of second-line options, retreatment with first-line DAAs (SOF/VEL plus ribavirin) is a viable alternative.

Anti-microbial stewardship program (AMSP) is practiced only in tertiary hospitals in India, though, the lower tier hospitals remain the first point of contact in patient care. This study was conducted in lower tier hospitals to calculate antibiotic and multiple antibiotic prescription rate (APR, MPR) for common infections and finding existing strength of health system for optimizing antibiotic prescription. We conducted a cross sectional convergent parallel mix-method study in eight lower tier hospitals of three districts of West Bengal, India. Six hundred OPD prescriptions of UTI, ARI, AUFI, ADD were evaluated. Qualitative data collected through in-depth interviews of medical officers/officers in administrative positions, infection control nurses were analyzed using content analysis method. APR was 63.8% in primary tier hospitals and 60.8% in secondary tier hospitals. The MPR was higher in secondary tier hospital (23.8%). Presence of infection control committee, designated nursing staff, initiation of prescription audit, increased monitoring were identified as few facilitators for future implementation of AMSP in lower tier hospitals. The routine infection control activities of lower tier hospitals are currently delinked from AMR containment measures and thus, customized AMSP needs to be established in these hospitals catering two third of the population of India.

The growing prevalence of antimicrobial resistance (AMR) necessitates the development of new treatment methods to combat diseases like cholera. Lytic bacteriophages are viruses that specifically target and lyse bacteria upon infection, making them a possible treatment option for multi-drug-resistant pathogens. The current study investigated the potential role of bacteriophages isolated from clinical stool and sewage water samples in treating multi-drug-resistant Vibrio cholerae infection, finding that over 95% of the strains were susceptible. Whole-genome sequencing (WGS) analysis revealed that both Vibrio phage 4141 (4141) and Vibrio phage MJW (MJW) contain double-stranded DNA genomes consisting of 38,498 bp (43% GC) and 49,880 bp (42.5% GC) with 46 and 64 open reading frames (ORFs), respectively. Transmission electron microscope (TEM) and WGS analysis of Vibrio phage 4141 and Vibrio phage MJW validated that they are classified under the family Autographiviridae and Zobellviridae, respectively. Furthermore, both the phages showed highly significant biofilm degradation properties. The characterization of the phages and their strict host range, high spectrum of lytic ability, high efficiency of biofilm degradation, and close genetic similarity to the therapeutic phages indicates that these phages may be useful for therapeutic purposes for treating MDR V. cholerae infection in the future.

Influenza viruses (types A, B, C, and D) belong to the family orthomyxoviridae. Out of all the influenza types, influenza A virus (IAV) causes human pandemic outbreaks. Its pandemic potential is predominantly attributed to the genetic reassortment favored by a broad spectrum of host species that could lead to an antigenic shift along with a high rate of mutations in its genome, presenting a possibility of subtypes with heightened pathogenesis and virulence in humans (antigenic drift). In addition to antigenic shift and drift, there are several other inherent properties of its viral RNA species (vRNA, vmRNA, and cRNA) that significantly contribute to the success of specific stages of viral infection. In this review, we compile the key features of IAV RNA, such as sequence motifs and secondary structures, their functional significance in the infection cycle, and their overall impact on the virus's adaptive and evolutionary fitness. Because many of these motifs and folds are conserved, we also assess the existing antiviral approaches focused on targeting IAV RNA. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease

We present a novel report of abundance of halophilic Vibrio alginolyticus with thermotolerant and enterotoxigenic characteristics from community water system of an inland-focus of India causing diarrheal outbreak as an index pathogen. Though, Vibrio alginolyticus causing diarrhea after exposure to marine water and consumption of seafood was reported globally, its existence in non-saline drinking-water sources with pathogenic viability was unknown. A 'matched-pair-case–control' study identified the primary source of V. alginolyticus infection as ‘tap-water’ distributed by the municipality, used for drinking (MOR: 8.33; 95% CI 2.51–27.6) and household chores (MOR: 3.75; 95% CI 1.24–11.3). Cardinal toxin gene ‘tdh’ and other pathogenicity markers viz.tlh, vppC, toxR, VPI, T3SS1 and sxt were detected in V. alginolyticus isolates. Expression potential of the hemolytic genes are demonstrated by hemolysis assay and transcriptome analysis. Altogether 30.55% of isolates exhibited strong hemolytic potential in vitro. RT-PCR revealed uninterrupted virulence gene expression in outbreak strains under heat stress. Surprisingly, ~ 100% of V. alginolyticus from the outbreak focus were sensitive/partially sensitive to all group of antibiotics except β-lactums, carbapenem and quinolones. High drug-sensitivity suggested lack of previous human gut exposure and indicated a fresh dissemination from the environmental niche to the community domain. The maximum likelihood phylogeny depicted multiple clades in V. alginolyticus strains from Pan India sources. Isolated outbreak strains shared common ancestry with the strains from nearby riverine system, a source of ‘drinking water’ supplied to the affected community, confirming its environmental origin. V. alginolyticus, traditionally a fish-pathogen, is steadily gaining an emerging epidemiological relevance alongside other waterborne diarrheagenic bacteria and its ‘thermotolerant’ attribute poses additional threat under the canvas of climate change.