ABSTRACT
BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India because of its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India. MATERIALS AND METHODS: We characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013-2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, multilocus sequence type, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism phylogeny were inferred from their whole genome sequences. RESULTS: Phylogenetic analysis of the 325 Klebsiella isolates that passed quality control revealed 3 groups: K. pneumoniae sensu stricto (nâ =â 307), K. quasipneumoniae (nâ =â 17), and K. variicola (nâ =â 1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates, respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%) and Col group (35.0%). CONCLUSION: Our study documents for the first time the genetic diversity of K and O antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these transmissible lineages.
Subject(s)
Klebsiella Infections , Klebsiella pneumoniae , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Bacterial Proteins/genetics , Carbapenems/pharmacology , Carbapenems/therapeutic use , Genomics , Humans , Klebsiella Infections/drug therapy , Klebsiella Infections/epidemiology , Microbial Sensitivity Tests , Multilocus Sequence Typing , Phylogeny , Retrospective Studies , beta-Lactamases/geneticsABSTRACT
BackgroundMedical professionals and researchers have been urging the need for wide and rapid testing of citizens in order to plan measures that can contain the spread of the virus. Antibody tests play an important role throughout the patient care pathway and are vital for the management and surveillance of the virus. Although RT-PCR is considered as the gold standard, serological tests based on antibodies are helpful for on-time detection. We performed one to one assessment of point-of-care lateral flow assay (POCTs), enzyme immunoassay (EIAs), electrochemiluminescence immunoassay (CLIA), to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG antibody. Materials and Methods611 healthcare workers were recruited between November and December 2020 at Central Research Laboratory, KIMS. Collected serum samples were analysed according to manufacturers protocol. The Standard Q IgG/IgM combo assay, Anti-SARS CoV-2 Human IgG ELISA, and the Elecsys(R) to measure the IgG titer of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ResultsThe kits displayed a sensitivity of 61.2%,79.5%, 91.8% and specificity of 61.7%,64.1%,80.2% for the Standard Q IgG/IgM combo assay, Anti-SARS CoV-2 Human IgG ELISA, and the Elecsys(R) in order. ConclusionOur results indicate high sensitivity and specificity for the Elecsys(R) assay compared to Anti-SARS CoV-2 Human IgG ELISA, the Standard Q IgG/IgM combo assay.
