Field evaluation of a simple and rapid diagnostic test, RLDT to detect Shigella and enterotoxigenic E. coli in Indian children.

The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected additional 12% Shigella and 13% ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.

Prevalence and changing antimicrobial resistance profiles of Shigella spp. isolated from diarrheal patients in Kolkata during 2011-2019.

BACKGROUND: The primary aim of this study was to investigate the occurrence, characteristics, and antimicrobial resistance patterns of various Shigella serogroups isolated from patients with acute diarrhea of the Infectious Diseases Hospital in Kolkata from 2011-2019. PRINCIPAL FINDINGS: During the study period, Shigella isolates were tested for their serogroups, antibiotic resistance pattern and virulence gene profiles. A total of 5.8% of Shigella spp. were isolated, among which S. flexneri (76.1%) was the highest, followed by S. sonnei (18.7%), S. boydii (3.4%), and S. dysenteriae (1.8%). Antimicrobial resistance against nalidixic acid was higher in almost all the Shigella isolates, while the resistance to ß-lactamases, fluoroquinolones, tetracycline, and chloramphenicol diverged. The occurrence of multidrug resistance was found to be linked with various genes encoding drug-resistance, multiple mutations in the topoisomerase genes, and mobile genetic elements. All the isolates were positive for the invasion plasmid antigen H gene (ipaH). Dendrogram analysis of the plasmid and pulsed-field electrophoresis (PFGE) profiles revealed 70-80% clonal similarity among each Shigella serotype. CONCLUSION: This comprehensive long-term surveillance report highlights the clonal diversity of clinical Shigella strains circulating in Kolkata, India, and shows alarming resistance trends towards recommended antibiotics. The elucidation of this study's outcome is helpful not only in identifying emerging antimicrobial resistance patterns of Shigella spp. but also in developing treatment guidelines appropriate for this region.

Field evaluation of a simple and rapid diagnostic test, RLDT to detect Shigella and enterotoxigenic E. coli in Indian children.

The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected 12% more Shigella and 13% more ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.

Epidemiology of major entero-pathogenic viruses and genetic characterization of Group A rotaviruses among children (≤5 years) with acute gastroenteritis in eastern India, 2018-2020.

AIMS: This study was carried out from January 2018 to March 2020 in Kolkata, eastern India to determine the prevalence rates and epidemiological patterns associated with the major viral agents of gastroenteritis among children ≤5 years of age. Molecular characterization of GARV, the predominant agent of viral gastroenteritis, was done to understand their genotype diversity. METHODS AND RESULTS: 1284 of 3157 stool samples (~40%) from children (≤5 years) with acute gastroenteritis tested positive for one or more enteric viruses with positivity rates 25.11%, 8.74%, 6.62% and 6.11% for GARV, HAdV-F, AstV and NoV respectively. Co-infection was observed in 5.31% of cases. Associated clinical/meteorological variables like age, sex, symptoms, temperature and precipitation were assessed to find any correlation between these and enteric virus infection rates. >70% of viral gastroenteritis cases were observed in 6-24 months' age group. GARV and AstV infection occurred mostly during cooler months while HAdV-F infection mostly occurred during warmer periods. No definite seasonality was observed for NoV infections. Clinical severity associated with GARV infection was higher compared to other enteric viruses. Genotyping of rotavirus positive samples revealed G3P[8] was the predominantly circulating GARV genotype throughout the study period. CONCLUSIONS: GARV remained the predominant viral agent of acute gastroenteritis among children though its prevalence rates in this region declined significantly compared to the previous years (2010-2016). The prevalence of other enteric viruses was below 10%. SIGNIFICANCE AND IMPACT OF STUDY: This study provides valuable insights regarding the current burden of viral gastroenteritis in Eastern India. The 2-year study in children will provide the baseline data for future surveillance studies in evaluating the impact of the introduced GARV vaccine on the overall prevalence of viral gastroenteritis.

Characterization of diarrhoeagenic Escherichia coli with special reference to antimicrobial resistance isolated from hospitalized diarrhoeal patients in Kolkata (2012-2019), India.

AIMS: This study analyses the prevalence and antimicrobial resistance (AMR) of major diarrhoeagenic Escherichia coli (DEC) pathotypes detected in hospitalized diarrhoeal patients in Kolkata, India, during 2012-2019. METHODS AND RESULTS: A total of 8891 stool samples were collected from the Infectious Diseases Hospital, Kolkata and screened for the presence of enteric pathogens. Multiplex PCR identified the presence of DEC in 7.8% of the samples, in which ETEC was most common (47.7%) followed by EAEC (38.4%) and EPEC (13.9%). About 54% cases were due to sole DEC infections. Majority of the mixed DEC infections were caused by the Vibrio spp. (19.1%) followed by Rotavirus (14.1%) and Campylobacter spp. (8.4%). ETEC and EAEC were associated significantly with diarrhoea in children <5 years of age, whereas EPEC and also ETEC were prevalent in patients aged between 5 and 14 years. AMR profile showed high prevalence of multidrug resistance (MDR) among DEC (56.9%) in which 9% were resistant to antibiotics of six different antimicrobial classes. Screening of the AMR conferring genes of DEC showed the presence of blaCTX-M3 (30.2%) in highest number followed by blaTEM (27.5%), tetB (18%), sul2 (12.6%), strA (11.8%), aadA1 (9.8%), blaOXA-1 (9%), dfrA1 (1.6%) and blaSHV (1.2%). CONCLUSIONS: These findings highlighted the high prevalence of MDR in major DEC pathotypes that could be considered as the leading aetiological bacterial agent responsible for diarrhoea and suggests a significant public health threat. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study can help to improve the understanding of the epidemiology of DEC infections in patients with diarrhoea. Monitoring of AMR surveillance needs special attention because the DEC isolates were highly resistant to commonly used antimicrobials in the treatment of diarrhoea.

Post-monsoon waterlogging-associated upsurge of cholera cases in and around Kolkata metropolis, 2015.

The Infectious Diseases and Beliaghata General Hospital, Kolkata, India witnessed a sudden increase in admissions of diarrhoea cases during the first 2 weeks of August 2015 following heavy rainfall. This prompted us to investigate the event. Cases were recruited through hospital-based surveillance along with the collection of socio-demographic characteristics and clinical profile using a structured questionnaire. Stool specimens were tested at bacteriological laboratory of the National Institute of Cholera and Enteric Diseases (NICED), Kolkata. Admission of 3003 diarrhoea cases, clearly indicated occurrence of outbreak in Kolkata municipal area as it was more than two standard deviation of the mean number (911; s.d. = 111) of diarrhoea admissions during the same period in previous 7 years. Out of 164 recruited cases, 25% were under-5 children. Organisms were isolated from 80 (49%) stool specimens. Vibrio cholerae O1 was isolated from 50 patients. Twenty-eight patients had this organism as the sole pathogen. Among 14 infants, five had cholera. All V. cholerae O1 isolates were resistant to nalidixic acid, followed by co-trimoxazole (96%), streptomycin (92%), but sensitive to fluroquinolones. We confirmed the occurrence of a cholera outbreak in Kolkata during August 2015 due to V. cholerae O1 infection, where infants were affected.

Upsurge and spread of G3 rotaviruses in Eastern India (2014-2016): Full genome analyses reveals heterogeneity within Wa-like genomic constellation.

Advent of new strains and shift in predominantly circulating genotypes are characteristics of group- A rotavirus (RVA), one of the major causes of childhood gastroenteritis. During diarrheal disease surveillance at Kolkata, India (2014-2016), a shift in circulating RVA strains from G1P[8] to G3P[8] was seen. Stool samples from children (n = 3048) with acute gastroenteritis were tested of which 38.7% were RVA positive. G1 was the predominant strain (65.3%) in 2014-2015 whereas in late 2015 and 2016, G3 became the preponderant strain (44.6%). In the past decade G3 strains were not observed in this region, we conducted whole genome sequencing of representative strains to gain insight into the phenomenon of emergence and genetic constellation of these circulating human G3 strains. The analyses revealed intergenogroup reassortment in G3P[4] strains (among Wa and DS-1-like genogroup) whereas G3P[8] strains were authentic Wa-like. Phylogenetic analysis revealed Kolkata G3 strains as polymorphic and thus they formed two sub-clusters due to antigenic differences in their VP7 protein. One of the sub-clusters had the wild-type threonine at 87 amino acid position while another sub-cluster had an isoleucine mutation. Presence of additional N-linked glycosylation site at amino acid 283 of VP7 glycoprotein suggests that the major neutralizing epitope on the VP7 (G3) of RotaTeq vaccine differs from the currently circulating G3 strains. The study is important as efficiency of rotavirus vaccine depends on the circulating heterogeneous genotype constellations. Continuous monitoring of circulating RVA strains in endemic settings like India is therefore important in pre- and post-vaccination period to monitor the emergence of new reassortant genotypes in addition to assessing vaccine efficacy.

A case control study investigating factors associated with high infant death in Saiha district of Mizoram, India bordering Myanmar.

BACKGROUND: Infant mortality has dropped considerably in India over the last 5 years. A sharp contrast to this decline in national average of infant mortality is the rate recorded during 2014-2015 from the southernmost district of Saiha, Mizoram having a common international border with Myanmar. As this district specific rate (113 per 1000 live births) is 3 times higher compared to the national and state average, the present investigation was carried out to identify associated factors. METHODS: We examined secondary data made available by the national health mission, consulted with local community members and generated primary data through interviews. A case-control study design was followed. Mothers, who delivered a child during 2013-2015 and subsequently lost them due to infant death, formed the case group and controls were selected from same neighborhood as with case-mothers. The mother and child tracking system maintained by the district specific national health mission office was used for recruiting cases and controls. A total of 195 mothers were interviewed; 66 of them belonged to 'cases' and 129 were 'controls'. RESULTS: The mean age of the respondents was 27 years (median 27; SD ± 5; minimum 17 & maximum 44). In uni-variate analyses 'child delivery at home', 'low birth weight', 'non-attendance of school by mothers', 'completed standard of school education by mothers', 'both parents working', 'mothers receiving blood transfusion during last pregnancy', and 'fourth or more birth order during last pregnancy' were associated with infant deaths. Intriguingly, the number of daily kuhva (raw areca nut) intake during last pregnancy was significantly higher among case-mothers compared to controls. In conditional logistic regression, 'low birth weight' (adjusted OR (AOR) 14.7; 95% CI 2.1-101.8; p = 0.006), and 'consumption of 4 or more kuhva per day' (AOR 8; 95% CI 1.9-34.3; p = 0.005) were independently associated with infant-death-experiences. CONCLUSION: The present investigation merits due attention from policy makers and health planners for immediate improvement in peri-natal and neonatal care services in the remote district of Saiha. Need for further research exploring socio-behavioural issues around areca nut consumption and effects of interventions to reduce areca nut intake on maternal and children health are underscored.

Impact of climate change on health and strategies for mitigation and adaptation.

Climate change and its negative impacts on health are now globally recognized. A wide variety of diseases and health conditions - ranging from heat and radiation-related illnesses to water and vector-borne diseases, under-nutrition, respiratory and cardiac problems, drowning, injuries and mental stress arising from extreme and sudden weather events and their resultant population displacements - all have been associated with various components of changing climate. However, the exact nature and extent of such impacts are yet to be firmly established since many other non-climate factors also produce or affect similar outcomes. This calls for more research specially from the underdeveloped countries, where such impacts are disproportionately more but reliable data are remarkably less. Recognizing the importance of human influences on global warming, almost all countries in the world have undertaken some kind of policies and measures to mitigate adverse climatic changes. Unfortunately, even without further addition of greenhouse gases (GHGs) in our climate, the amount of GHGs already released has the potential to continue the damages for many more decades to come. Thus, all countries should also place priorities in assessing their own vulnerabilities from climate change and take adaptive measures accordingly. As climate change exerts its impact simultaneously in many non-health sectors as well, this would require strong intersectoral cooperation at various levels.

The malaria and typhoid fever burden in the slums of Kolkata, India: data from a prospective community-based study.

Recent research has indicated that the malaria burden in Asia may have been vastly underestimated. We conducted a prospective community-based study in an impoverished urban site in Kolkata, India, to estimate the burden of malaria and typhoid fever and to identify risk factors for these diseases. In a population of 60452 people, 3605 fever episodes were detected over a 12-month period. The blood films of 93 febrile patients contained Plasmodium (90 P. vivax, 2 P. falciparum and 1 P. malariae). Blood cultures from 95 patients grew Salmonella enterica serotype Typhi. Malaria patients were found to be significantly older (mean age 29 years) compared with patients with typhoid fever (15 years; P<0.001) but had similar clinical features on presentation. Having a household member with malaria, illiteracy, low household income and living in a structure not built of bricks were associated with an increased risk for malaria. Having a household member with typhoid fever and poor hygiene were associated with typhoid fever. A geographic analysis of the spatial distribution of malaria and typhoid fever cases detected high-risk neighbourhoods for each disease. Focal interventions to minimise human-vector contact and improved personal hygiene and targeted vaccination campaigns could help to prevent malaria and typhoid fever in this site.

Factors associated with reported diarrhoea episodes and treatment-seeking in an urban slum of Kolkata, India.

In an urban slum in eastern Kolkata, India, reported diarrhoea rates, healthcare-use patterns, and factors associated with reported diarrhoea episodes were studied as a part of a diarrhoea-surveillance project. Data were collected through a structured interview during a census and healthcare-use survey of an urban slum population in Kolkata. Several variables were analyzed, including (a) individual demographics, such as age and educational level, (b) household characteristics, such as number of household members, religious affiliation of the household head, building material, expenditure, water supply and sanitation, and (c) behaviour, such as hand-washing after defecation and healthcare use. Of 57,099 study subjects, 428 (0.7%) reported a diarrhoea episode sometime during the four weeks preceding the interview. The strongest independent factors for reporting a history of diarrhoea were having another household member with diarrhoea (adjusted odds ratio [OR]=3.8; 95% confidence interval [CI] 3.3-4.4) and age less than 60 months (adjusted OR=3.7; 95% CI 3.0-4.7). The first choice of treatment by the 428 subjects was as follows: 151 (35%) had self- or parent-treatment, 150 (35%) consulted a private allopathic practitioner, 70 (16%) went directly to a pharmacy, 29 (7%) visited a hospital, 14 (3%) a homoeopathic practitioner, 2 (0.5%) an ayurvedic practitioner, and 12 (3%) other traditional healers. The choices varied significantly with the age of patients and their religion. The findings increase the understanding of the factors and healthcare-use patterns associated with diarrhoea episodes and may assist in developing public-health messages and infrastructure in Kolkata.