An insight into whole genome sequencing data of methicillin-resistant Staphylococcus aureus circulating in a teaching hospital in North India.

PURPOSE: To provide an insight into the Whole-genome sequencing (WGS) data of MRSA strains circulating in a teaching hospital in north India. METHODS: An exploratory study was conducted in which fifty non-repetitive MRSA isolates obtained from pus samples of inpatients from July 2018 to February 2019 were subjected to preliminary identification (ID) and antibiotic susceptibility testing (AST) at our centre. These isolates were later sent to Central Research Laboratory, India for further testing using the VITEK-2 compact system followed by WGS. Only eighteen isolates were eventually considered for final analysis and the rest (n â€‹= â€‹32) were excluded due to various technical reasons. RESULTS: The WGS confirmed MRSA isolates predominantly belonged to CC22 (56.25%) and CC30 (31.25%). The CC22 MRSA strains carried SCCmec types IVa (77.8%) & IVc (22.2%) and belonged to spa types t005 (44.4%), t4584 (22.2%), t11808 (11.1%), t1328 (11.1%) and t309 (11.1%), respectively. The MRSA isolates of CC30 carried SCCmec types IVa (60%), IVg (20%) & V (20%) and belonged to spa types t021 (80%) & t2575 (20%), respectively. One MRSA isolate carried a novel SCCmec type V. The luk-PV and tsst-1 genes were present in 93.75% and 33.33% of MRSA isolates, respectively. The concordance between the phenotypic and genotypic AST results was 100% for Beta-lactams, Fluoroquinolones, Tetracyclines & Lipoglycopeptides, respectively. CONCLUSIONS: Through this study, we intend to embark upon a relatively newer avenue of clinical-genomic surveillance of nosocomial bacterial isolates like MRSA, which would help us improve the existing infection control and antibiotic stewardship practices in our hospital.

Molecular characterisation of carbapenem-resistant Klebsiella pneumoniae clinical isolates: preliminary experience from a tertiary care teaching hospital in the Himalayas.

BACKGROUND: There is a lack of whole-genome sequencing (WGS) data on multidrug-resistant (MDR) bacteria from the Uttarakhand region of India. The aim of this study was to generate WGS data of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates recovered from patients in Uttarakhand's tertiary care centre. METHODS: A cross-sectional study included 29 MDR K. pneumoniae test isolates obtained from various clinical samples submitted to the bacteriology laboratory for culture and sensitivity testing from July 2018 to August 2019. After preliminary identification and antibiotic susceptibility testing, these isolates were subjected to WGS. RESULTS: A total of 27 of 29 isolates were CRKP. ST14 was the most common sequence type (n=8 [29.6%]). Carbapenem resistance was mainly encoded by OXA-48-like genes (21/27 [77.8%]). All isolates had a varied arsenal of resistance genes to different antibiotic classes. KL2 (9/27 [33.3%]) and KL51 (8/27 [29.6%]) were dominant K loci types. O1 and O2 together accounted for 88.9% (n=27) of CRKP isolates. Genes encoding yersiniabactin (ybt) and aerobactin (iuc) were identified in 88.9% (24/27) and 29.6% (8/27) of isolates. The predominant plasmid replicons present were ColKP3 (55.5%), IncFII(K) (51.8%) and IncFIB(pQil) (44.4%). CONCLUSIONS: This study emphasises the need for continued genomic surveillance of MDR bacteria that could be instrumental in developing treatment guidelines based on integrating phenotypic and molecular methods.

Circulation of Third-Generation Cephalosporin Resistant Salmonella Typhi in Mumbai, India.

We report the persistent circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, linked to the acquisition and maintenance of a previously characterized IncX3 plasmid carrying the ESBL gene blaSHV-12 and the fluoroquinolone resistance gene qnrB7 in the genetic context of a triple mutant also associated with fluoroquinolone resistance.