Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019-2020

BACKGROUND: External quality assessments (EQAs) for the molecular detection of human respiratory syncytial virus (RSV) are necessary to ensure the standardisation of reliable results. The Phase II, 2019-2020 World Health Organization (WHO) RSV EQA included 28 laboratories in 26 countries. The EQA panel evaluated performance in the molecular detection and subtyping of RSV-A and RSV-B. This manuscript describes the preparation, distribution, and analysis of the 2019-2020 WHO RSV EQA. METHODS: Panel isolates underwent whole genome sequencing and in silico primer matching. The final panel included nine contemporary, one historical virus and two negative controls. The EQA panel was manufactured and distributed by the UK National External Quality Assessment Service (UK NEQAS). National laboratories used WHO reference assays developed by the United States Centers for Disease Control and Prevention, an RSV subtyping assay developed by the Victorian Infectious Diseases Reference Laboratory (Australia), or other in-house or commercial assays already in use at their laboratories. RESULTS: An in silico analysis of isolates showed a good match to assay primer/probes. The panel was distributed to 28 laboratories. Isolates were correctly identified in 98% of samples for detection and 99.6% for subtyping. CONCLUSIONS: The WHO RSV EQA 2019-2020 showed that laboratories performed at high standards. Updating the composition of RSV molecular EQAs with contemporary strains to ensure representation of circulating strains, and ensuring primer matching with EQA panel viruses, is advantageous in assessing diagnostic competencies of laboratories. Ongoing EQAs are recommended because of continued evolution of mismatches between current circulating strains and existing primer sets

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 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

Epidemiological investigation and successful management of a Burkholderia cepacia outbreak in a neurotrauma intensive care unit

Objective: The detailed epidemiological and molecular characterization of an outbreak of Burkholderia cepacia at a neurotrauma intensive care unit of a level 1 trauma centre is described. The stringent infection control interventions taken to successfully curb this outbreak are emphasized. Methods: The clinical and microbiological data for those patients who had more than one blood culture that grew B. cepacia were reviewed. Bacterial identification and antimicrobial susceptibility testing was done using automated Vitek 2 systems. Prospective surveillance, environmental sampling, and multilocus sequence typing (MLST) were performed for extensive source tracking. Intensive infection control measures were taken to further control the hospital spread. Results: Out of a total 48 patients with B. cepacia bacteraemia, 15 (31%) had central line-associated blood stream infections. Two hundred and thirty-one environmental samples were collected and screened, and only two water samples grew B. cepacia with similar phenotypic characteristics. The clinical strains characterized by MLST typing were clonal. However, isolates from the water represented a novel strain type (ST-1289). Intensive terminal cleaning, disinfection of the water supply, and the augmentation of infection control activities were done to curb the outbreak. A subsequent reduction in bacteraemia cases was observed. Conclusion: Early diagnosis and appropriate therapy, along with the rigorous implementation of essential hospital infection control practices is required for successful containment of this pathogen and to curb such an outbreak. Keywords: Burkholderia cepacia, Outbreak, Neurotrauma unit, MLST typing, Novel ST typ

Details of the study isolates identifiers and corresponding year of isolation, type of infection, geographical location, and the sequence type information.

<p>Details of the study isolates identifiers and corresponding year of isolation, type of infection, geographical location, and the sequence type information.</p

Comparison between the nucleotide diversity of MLST housekeeping genes of the study isolates.

<p>Comparison between the nucleotide diversity of MLST housekeeping genes of the study isolates.</p

Epidemiological year of isolation of the STs identified in the study isolates from different South Asian countries.

<p>Epidemiological year of isolation of the STs identified in the study isolates from different South Asian countries.</p

Populations structure analysis.

<p><b>(A)</b> goeBURST analysis of 1643 STs present in the PubMLST database. Each dot represents the single ST. Groups are formed by linking the STs that are double locus variants (DLV) and called as clonal complex (CC). The largest clonal complex 300 has the other STs leaving 1634, 1632, 1636, 1639 as singletons (<b>B</b>) Snapshot of the clonal complex 300.</p

Distribution and association of the study ST’s with the ST’s from Southeast Asian region retrieved from the PubMLST database (10).

<p>Light Green–ST1364 (Kerala & Sri Lanka); Dark Green ST375 (Tamilnadu & Thailand); Black—ST1552 (Tamilnadu and Pondicherry); Red—ST51 (Tamilnadu, Singapore, China, Thailand, Malaysia and Burma); Purple—ST228 (West Bengal, Thailand &Vietnam); Blue–ST1099 (Jharkhand & China); Brown–ST56 (West Bengal Bangladesh, Cambodia & Vietnam); Orange—ST300 (West Bengal and Thailand); Yellow–ST99 (Bangladesh, Philippines, Thailand and Malaysia). The figure was recreated using open source-<a href="https://commons.wikimedia.org/wiki/Atlas_of_the_world" target="_blank">https://commons.wikimedia.org/wiki/Atlas_of_the_world</a>.</p