Dataset Information

Hospital-based sentinel surveillance for Streptococcus pneumoniae and other invasive bacterial diseases in India (HBSSPIBD): design and methodology.

ABSTRACT: INTRODUCTION:Streptococcus pneumoniae is one of the frequently isolated organisms and an important aetiological agent of invasive bacterial diseases (IBD) like pneumonia, meningitis and sepsis. As a measure to control the burden of IBD, the Government of India introduced Pneumoccocal Conjugate Vaccine-13 (PCV-13) in the Universal Immunization Program in high burden districts of five states in a phased manner from 2017 onwards. It is essential to understand the trend of circulating pneumococcal serotypes associated with IBD in the prevaccination and postvaccination scenarios to decide on the expansion of vaccination programmes and PCV reformulation. This manuscript describes the protocol for hospital-based sentinel surveillance for S. pneumoniae and other organisms causing IBD across various geographical regions in India. METHODS AND ANALYSIS:Hospital-based surveillance is established in selected hospitals to recruit children aged 1-59 months with symptoms of pneumonia and other IBD. Diagnostic criteria were adapted from standard WHO case definitions. Case Report Forms (CRFs) are used to collect data from the enrolled children. Blood, cerebrospinal fluid (CSF) and other normally sterile body fluids are collected and subjected to microscopy, cytology, latex agglutination, biochemistry, bacteriological culture and real-time PCR as applicable. Pneumococcal isolates are serotyped and tested for assessing antimicrobial resistance patterns. Data will be analysed by simple descriptive statistics to estimate the proportion of pneumonia and other IBD due to S. pneumoniae, Hemophilus influenzae type b and Neisseria meningitidis. Prevalence of bacterial infection, circulating pneumococcal serotypes, antibiotic resistance patterns, serotype variability across seasons and regions will be described in terms of percentage with 95% confidence interval. ETHICS AND DISSEMINATION:The institutional review boards of the coordinating centre, all sentinel sites, regional and national reference laboratories approved the project. The results will be published in peer-reviewed journals and shared with stakeholders for deciding on revising vaccination strategy appropriately.

SUBMITTER: Rajkumar P

PROVIDER: S-EPMC7245370 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Hospital-based sentinel surveillance for <i>Streptococcus pneumoniae</i> and other invasive bacterial diseases in India (HBSSPIBD): design and methodology.

Rajkumar Prabu P Bharathy Sukumar S Girish Kumar C P CP Veeraraghavan Balaji B Verghese Valsan V Gupta Nivedita N Kangusamy Boopathi B Ravi Muthusamy M Jayaraman Yuvaraj Y

BMJ open 20200408 4

<h4>Introduction</h4><i>Streptococcus pneumoniae</i> is one of the frequently isolated organisms and an important aetiological agent of invasive bacterial diseases (IBD) like pneumonia, meningitis and sepsis. As a measure to control the burden of IBD, the Government of India introduced Pneumoccocal Conjugate Vaccine-13 (PCV-13) in the Universal Immunization Program in high burden districts of five states in a phased manner from 2017 onwards. It is essential to understand the trend of circulating ...[more]

PMID: 32273315

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Project description:The novel coronavirus 2019 (COVID-19) global pandemic has drastically affected the world economy, raised public anxiety, and placed a substantial psychological burden on the governments and healthcare professionals by affecting over 4.7 million people worldwide. As a preventive measure to minimise the risk of community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in India, a nationwide lockdown was imposed initially for 21 days to limit the movement of 1.3 billion people. These restrictions continue in most areas, with a conditional relaxation occurring in a few Indian states. In an attempt to assess the emerging mutants of SARS-CoV-2 and determine their spread in India, we analysed 112 complete genomes of SARS-CoV-2 in a time-lapse manner. We found 72 distinct SARS-CoV-2 haplotypes, defined by 143 polymorphic sites and high haplotype diversity, suggesting that this virus possesses a high evolutionary potential. We also demonstrated that early introduction of SARS-CoV-2 into India was from China, Italy and Iran and observed signs of community spread of the virus following its rapid demographic expansion since its first outbreak in the country. Additionally, we identified 18 mutations in the SARS-CoV-2 spike glycoprotein and a few selected mutations showed to increase stability, binding affinity, and molecular flexibility in the overall tertiary structure of the protein that may facilitate interaction between the receptor binding domain (RBD) of spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor. The study provides a pragmatic view of haplotype-dependent spread of SARS-CoV-2 in India which could be important in tailoring the pharmacologic treatments to be more effective for those infected with the most common haplotypes. The findings based on the time-lapse sentinel surveillance of SARS-CoV-2 will aid in the development of a real-time practical framework to tackle the ongoing, fast-evolving epidemic challenges in the country.

Project description:BackgroundGlobally, over 800 000 children under five die each year from infectious diseases caused by Streptococcus pneumoniae. To understand genetic relatedness between isolates, study transmission routes, assess the impact of human interventions e.g. vaccines, and determine infection sources, genotyping methods are required. The 'gold standard' genotyping method, Multi-Locus Sequence Typing (MLST), is useful for long-term and global studies. Another genotyping method, Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA), has emerged as a more discriminatory, inexpensive and faster technique; however there is no universally accepted method and it is currently suitable for short-term and localised epidemiology studies. Currently Australia has no national MLST database, nor has it adopted any MLVA method for short-term or localised studies. This study aims to improve S. pneumoniae genotyping methods by modifying the existing MLVA techniques to be more discriminatory, faster, cheaper and technically less demanding than previously published MLVA methods and MLST.MethodsFour different MLVA protocols, including a modified method, were applied to 317 isolates of serotyped invasive S. pneumoniae isolated from sterile body sites of Queensland children under 15 years from 2007-2012. MLST was applied to 202 isolates for comparison.ResultsThe modified MLVA4 is significantly more discriminatory than the 'gold standard' MLST method. MLVA4 has similar discrimination compared to other MLVA techniques in this study). The failure to amplify particular loci in previous MLVA methods were minimised in MLVA4. Failure to amplify BOX-13 and Spneu19 were found to be serotype specific.ConclusionWe have modified a highly discriminatory MLVA technique for genotyping Queensland invasive S. pneumoniae. MLVA4 has the ability to enhance our understanding of the pneumococcal epidemiology and the changing genetics of the pneumococcus in localised and short-term studies.

Dataset Information

Hospital-based sentinel surveillance for Streptococcus pneumoniae and other invasive bacterial diseases in India (HBSSPIBD): design and methodology.

Publications

Hospital-based sentinel surveillance for <i>Streptococcus pneumoniae</i> and other invasive bacterial diseases in India (HBSSPIBD): design and methodology.

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