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. This paper describes how WHO's tailored regional approaches contribute to expanding and further institutionalizing the use of genomic surveillance to guide pandemic preparedness and response measures as part of a harmonized global undertaking. Challenges to achieving this vision include difficulties obtaining sequencing equipment and supplies, shortages of skilled staff, and obstacles to maximizing the utility of genomic data to inform risk assessment and public health action. WHO is helping to overcome these challenges in collaboration with partners. Through its global headquarters, six regional offices, and 153 country offices, WHO is providing support for country-driven efforts to strengthen genomic surveillance in its 194 Member States, with activities reflecting regional specificities. WHO's regional offices serve as platforms for those countries in their respective regions to share resources and knowledge, engage stakeholders in ways that reflect national and regional priorities, and develop regionally aligned approaches to implementing and sustaining genomic surveillance within public health systems.

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

Diphtheria is a dreadful disease caused by Corynebacterium diphtheriae. Lysogenised bacteriophages carrying toxin gene in C. diphtheriae can make the strain toxigenic. However, such phage disseminates the toxin genes to other strains when it undergoes lytic phase. As little is known about the phage diversity in C. diphtheriae in India, the present study was undertaken to investigate the prophages integrated into the genome of 29 clinical isolates of C. diphtheriae using whole-genome shotgun sequencing. Amongst these isolates, 27 were toxigenic, while 2 were non-toxigenic strains. Of the 27 toxigenic strains, all harbored known phages carrying toxin gene and two other phages with unknown function. However, the two non-toxin strains did not harbour any of the phages in the genome. It is imperative to devise prevention strategies that hinder the dissemination of toxin by prophages, as it may increase the complications of diphtheria post-immunisation.

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

AIM: To investigate antimicrobial resistance mechanisms in a cluster of colistin-resistant Klebsiella pneumoniae. METHODS: Antimicrobial susceptibility was tested by disk diffusion and broth microdilution. Whole-genome sequencing and genome analysis were performed. RESULTS: The eight colistin-resistant K. pneumoniae isolates belonged to three different clones (ST11, 14 and 231). The eptA and arnT genes from lipid modification pathway had novel (R157S in arnT and Q319R in eptA) and rare mutations (V39L, R152H, S260L and A279G in eptA). Several substitutions were also identified in mgrB, pmrB, phoP and phoQ genes. The mcr genes were absent in all isolates. Isolates had variants from existing classes of fosA gene. CONCLUSION: Complex combination of mutations might have led to colistin resistance, which suggests that continuous surveillance of molecular mechanisms is required.

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

Streptococcus pyogenes, 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. Sequencing was performed on Ion Torrent PGM platform. The size of annotated S. pyogenes genomes ranged from ~1.69 to ~1.85 Mb with coverage of 38× to 189×. Most of the isolates had msr(D) and mef(A), and four isolates had erm(B) gene for macrolide resistance. The genome harboured multiple virulence factors including exotoxins in addition to phage elements in all GAS genomes. Four isolates belonged to sequence type ST28, 7 were identified as ST36 and 1 as ST55.

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. pseudomaelli from India in order to establish a molecular epidemiology and elucidate the Southeast Asian association. METHODS: Molecular typing using multi locus sequence typing was performed on thirty one archived B. pseudomallei clinical isolates, previously characterised from specimens obtained from patients admitted to the Christian Medical College & Hospital, Vellore from 2015 to 2016. Further investigations into the genetic heterogeneity and evolution at a regional and global level were performed using insilico tools. RESULTS: Multi locus sequence typing (MLST) of the isolates from systemic and localized forms of melioidosis, including blood, pus, tissue, and urine specimens, revealed twenty isolates with novel sequence types and eleven with previously reported sequence types. High genetic diversity was observed using MLST with a strong association within the Southeast Asian region. CONCLUSIONS: Molecular typing of B. pseudomallei clinical isolates using MLST revealed high genetic diversity and provided a baseline molecular epidemiology of the disease in India with a strong Southeast Asian association of the strains. Future studies should focus on whole genome based Single-Nucleotide-Polymorphism (SNP) which has the advantage of a high discriminatory power, to further understand the novel sequence types reported in this study.

Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae.

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. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative genome studies of GBS isolates at global level. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers NHPL00000000 - NHPO00000000.

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

Typhoid is one of the leading causes of mortality in developing countries. Here, we report the draft genome sequences of four Salmonella enterica serovar Typhi strains isolated from bloodstream infections in a tertiary care hospital. The sequence data indicate genomes of ~4.5 Mb for all isolates, with one plasmid in each.

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. The sequence data indicate genomes of ~5.2 to 5.4 Mb, along with several plasmids.

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). The sequence data indicate that BA41763 and B6753 contain genomes of ~5.9 and 5.7 Mb in size with several plasmids.

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. The sequence data indicate that strains VB13856 and VB15548 encode genomes of ~2.09 Mb in size with no plasmids.