Assessment of public health laboratory preparedness and response in WHO South-East Asia region during the COVID-19 pandemic: lessons learned and future directions.

This Health Policy reviews the preparedness and response of public health laboratories in the WHO South-East Asia Region (SEAR) during the COVID-19 pandemic. Through a scoping review and in-depth interviews with key stakeholders, the study identifies successes, challenges, and lessons learned from available literature and the perspective of senior laboratory leaders. Key themes include human resources, health information systems, diagnostic capacity, public risk communication, biosafety, biosecurity, funding, and laboratory network coordination.

Strengthening pathogen genomic surveillance for health emergencies: insights from the World Health Organization's regional initiatives.

The onset of the COVID-19 pandemic triggered a rapid scale-up in the use of genomic surveillance as a pandemic preparedness and response tool. As a result, the number of countries with in-country SARS-CoV-2 genomic sequencing capability increased by 40% from February 2021 to July 2022. The Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022-2032 was launched by the World Health Organization (WHO) in March 2022 to bring greater coherence to ongoing work to strengthen genomic surveillance.

Transmission of SARS-CoV-2 in standardised first few X cases and household transmission investigations: A systematic review and meta-analysis.

We aimed to estimate the household secondary infection attack rate (hSAR) of SARS-CoV-2 in investigations aligned with the WHO Unity Studies Household Transmission Investigations (HHTI) protocol. We conducted a systematic review and meta-analysis according to PRISMA 2020 guidelines. We searched Medline, Embase, Web of Science, Scopus and medRxiv/bioRxiv for "Unity-aligned" First Few X cases (FFX) and HHTIs published 1 December 2019 to 26 July 2021.

External quality assessment of COVID-19 real time reverse transcription PCR laboratories in India.

Sudden emergence and rapid spread of COVID-19 created an inevitable need for expansion of the COVID-19 laboratory testing network across the world. The strategy to test-track-treat was advocated for quick detection and containment of the disease. Being the second most populous country in the world, India was challenged to make COVID-19 testing available and accessible in all parts of the country.

A second external quality assessment of isolation and identification of influenza viruses in cell culture in the Asia Pacific region highlights improved performance by participating laboratories.

Influenza viruses must be amplified in cell culture for detailed antigenic analysis and for phenotypic assays assessing susceptibility to antiviral drugs or for other assays. Following on from the first external quality assessment (EQA) for isolation and identification of influenza viruses using cell culture techniques in 2016, a follow up EQA was performed in 2019 for National Influenza Centres (NICs) in the World Health Organization (WHO) South East Asia and Western Pacific Regions. Nineteen WHO NICs performed influenza virus isolation and identification techniques on an EQA panel comprising 16 samples, containing influenza A or B viruses and negative control samples.

Pandemic influenza preparedness in the WHO South-East Asia Region: a model for planning regional preparedness for other priority high-threat pathogens.

Pandemic influenza preparedness has contributed significantly to building, strengthening and maintaining countries' core capacities to prepare for health emergencies. The Pandemic influenza preparedness framework for the sharing of influenza viruses and access to vaccines and other benefits (the PIP framework) was adopted by the World Health Assembly in 2011. The experiences and lessons learnt from the implementation of the PIP framework have provided insights that can be used to strengthen preparedness for epidemics of other priority high-threat pathogens in the World Health Organization (WHO) South-East Asia Region in line with obligations under the International Health Regulations, 2005 (IHR).

Insights to the diphtheria toxin encoding prophages amongst clinical isolates of from India.

Diphtheria is a dreadful disease caused by Corynebacterium diphtheriae. Lysogenised bacteriophages carrying toxin gene in C. diphtheriae can make the strain toxigenic.

Multiple mutations in lipid-A modification pathway & novel variants in colistin-resistant .

Aim: To investigate antimicrobial resistance mechanisms in a cluster of colistin-resistant .

Methods: Antimicrobial susceptibility was tested by disk diffusion and broth microdilution. Whole-genome sequencing and genome analysis were performed.

Multi locus sequence typing of Burkholderia pseudomallei isolates from India unveils molecular diversity and confers regional association in Southeast Asia.

Objectives: Burkholderia pseudomallei, the causative agent for melioidosis, has become a public health problem in India and across the world. Melioidosis can be difficult to diagnose because of the inconsistent clinical presentations of the disease. This study aims to determine the genetic diversity among the clinical isolates of B.

Whole genome shotgun sequences of Streptococcus pyogenes causing acute pharyngitis from India.

, belonging to group A streptococcus (GAS), causes over 600 million infections annually being a predominant human pathogen. Lack of genomic data on GAS from India is one limitation to understand its virulence and antimicrobial resistance determinants. The genome of GAS isolates from clinical samples collected at Navi Mumbai, India was sequenced and annotated.

Whole genome shotgun sequencing of Indian strains of .

Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS) isolates. Molecular data on clonality is lacking for GBS in India.

Whole-Genome Shotgun Sequencing of Cephalosporin-Resistant Serovar Typhi.

Typhoid is one of the leading causes of mortality in developing countries. Here, we report the draft genome sequences of four serovar Typhi strains isolated from bloodstream infections in a tertiary care hospital. The sequence data indicate genomes of ~4.

First Report on a Cluster of Colistin-Resistant Klebsiella pneumoniae Strains Isolated from a Tertiary Care Center in India: Whole-Genome Shotgun Sequencing.

Klebsiella pneumoniae is a nosocomial pathogen with clinical importance due to its increasing resistance to carbapenems and colistin. Here, we report the genome sequences of eight colistin-resistant K. pneumoniae strains which might help in understanding the molecular mechanism of the species.

Molecular Mechanisms of Colistin Resistance in Causing Bacteremia from India-A First Report.

Colistin has long been a reserve drug used for the treatment of carbapenem resistant . Carbapenem resistance in has been increasing and is as high as 44% in India. Although a reserve agent, with rise in rates of resistance to carbapenems, the usage of colistin has increased over the years leading to slow emergence of resistance.

Novel Observations in 11 Heteroresistant Vancomycin-Intermediate Methicillin-Resistant Staphylococcus aureus Strains from South India.

We report here the draft genome sequences of 11 heteroresistant vancomycin-intermediate Staphylococcus aureus (hVISA) strains from bloodstream infection. All strains harbor mutations in vraSR, graSR, walKR, and/or tcaRAB and are often implicated as the frequently mutated candidate genes in hVISA phenotypes.

Coexistence of Fosfomycin and Colistin Resistance in Klebsiella pneumoniae: Whole-Genome Shotgun Sequencing.

Resistance to colistin is a major threat that limits therapeutic choices for treating carbapenem-resistant Klebsiella pneumoniae infections. Herein, we report the draft genome sequences of two colistin-resistant K. pneumoniae isolates (BA41763 and B6753).

Whole-Genome Shotgun Sequencing of the First Observation of Neisseria meningitidis Sequence Type 6928 in India.

Neisseria meningitidis is one of the leading global causes of bacterial meningitis. Here, we discuss the draft genome sequences of two N. meningitidis strains, isolated from bloodstream infections in two pediatric patients at a tertiary care hospital in South India.