Biology subjects

Govindan, V.

Publications and source records attributed to Govindan, V..

5 recordsLinked to original sources

bioRxiv2022

Large retrospective WGS study describes three major sequence types of S. aureus in India and reveals two novel multi-drug resistant sub-lineages of S. aureus Clonal Complex 22

BackgroundS. aureus is a major pathogen in India, causing nosocomial infections, but little is known about its molecular epidemiology and mechanisms of resistance in hospital settings. Here, we use WGS to characterize 508 S. aureus clinical isolates collected across India and analyze them in a global context. MethodsWhole-genome sequencing was performed on 508 clinical isolates of S. aureus collected from 17 sentinel sites across India between 2014 and 2019 with the Illumina platform. AMR genotypes were predicted using Staphopia. Isolates carrying novel SCCmec cassettes were further characterized using long-read sequencing. A temporal analysis of clonal complex (CC) 22 global isolates from 14 different studies was performed using BactDating. ResultsSequencing results confirmed 478 isolates as S. aureus. ST22, ST772 & ST239 were the major clones identified. An in-depth analysis of the 175 CC22 Indian isolates identifies two novel ST22 MRSA clones, PVL+ and one harboring the tsst-1 gene. Temporal analysis showed that these two ST22 clusters shared a common ancestor in the 1980s and they became widespread after the year 2000 in India. Analyzing these in a global context, we found evidence of transmission of the two Indian clones to other parts of the world. ConclusionOur study describes a large retrospective S. aureus sampled from India. By comparing the Indian isolates globally we show the evidence of the international transmission of ST22 Indian isolates. Even though the two of the major dominant clones (ST772 and ST239) using WGS have been reported, this is the first study that describes the third dominant clone (ST22) in India. Impact statementStaphylococcus aureus is an opportunistic pathogen listed as a high-priority pathogen by WHO. It is a leading cause of nosocomial infections in India and worldwide. Our study is the first study to describe the epidemiology of S. aureus in India with a large sample set of 478. Here we describe a collection of 478 S. aureus genomes, isolated from 17 sentinel sites in India, between 2014 and 2019. With the focus on understanding sequence types, AMR profiles, SCCmec types, and spa types and discuss these in the context of previous molecular studies on S. aureus conducted in India. We also conducted an in-depth analysis of the Clonal Complex 22 Indian isolates and we identified two novel ST22 MRSA clones, both PVL+ and one harboring the tsst-1 gene. Temporal analysis shows that these two ST22 clusters originated around 2010 in India. Analyzing these in a global context, we found evidence of transmission of the two Indian clones in other parts of the world. Analysis of a cluster of 33 isolates belonging to ST239 from a single hospital in Bangalore indicates an outbreak that persisted over the period of three years from a single contamination source. The novel SCCmec types identified in our study are characterized using long reads to understand their genetic structure. Data SummaryO_LIIllumina read files of the strains used in the study have been deposited in European Nucleotide Archive, BioProject PRJEB29740 (https://www.ebi.ac.uk/ena/browser/view/PRJEB29740?show=reads). A full list of accession numbers for all sequence read files is provided in Supplementary table 2. C_LIO_LINanopore reads are submitted to ENA under the BioProject PRJEB50484. C_LIO_LIMetadata and other related information on the strains are provided in the microreact project with different views in this link microreact.org/s.aureus_ghru_analysis. C_LIO_LIStrain information for the ST22 samples used from other studies is provided in microreact at this link: https://microreact.org/project/2xDvKQhriNveJ4kiVYsmSQ-s-aureus-wgs-study. The authors confirm all supporting data, code and protocols have been provided within the article or the supporting data repository. C_LI

genomics↗

bioRxiv2022

Allele mining, evolutionary genetic analysis of TaHKT1;5 gene and evaluation of salinity stress in selected lines of wheat.

This study reports the novel allelic diversity in HKT 1;5 gene (High Affinity Potassium Transporter) in bread wheat and its phylogenetic relationship among the paralogs/orthologs of in Triticum aestivum and its wild relatives. HKT 1;5 gene is a known and pivotal gene associated with the salinity tolerance in plants upon the discrimination of K+ over Na+ in leaves without change in Na+ concentration in root. This gene was sequenced in a diverse collection of bread wheat, durum wheat, wild relatives, and ditelosomic lines. Sequence analysis in bread wheat led to the identification of four alleles, which could be distinguished by number of SNPs. Sequence comparison between monocot bread wheat and dicot Arabidopsis thaliana revealed that the HKT1;5 gene is conserved at level of exonic regions; however, the presence of transposable elements especially in intronic regions is further intriguing towards evolutionary relatedness. Two paralogous or major alleles observed in Triticum monoccum and Aegilops tauschii were further categorized as sub-alleles based on their SNPs comparison. This gene was absent in T. urartu in accordance with existing evidence, while it was found in A. speltoides (an allelic variant) with a few base pairs insertion in the exon1 region causing a frameshift mutation with an altered amino acids and genomic database mining unveiled additional alleles in this species. Ditelosomic lines with 4DL and 4DS chromosomes revealed a higher similarity with bread and durum wheat respectively. Phylogenetic studies of HKT1;5 orthologs from different Poaceae species revealed the occurrence of five different ortholog groups with taxonomic consistency. Phenotyping based salinity stress experiment distinguished the unknown lines for salinity tolerance and sensitiveness in comparison with known reference lines and possible allelic comparison was made. The salinity stress analysis further revealed that some known drought/heat tolerance lines showed slightly better salinity tolerance with mean values and variability of traits than known saline tolerant wheat line at controlled ambient.

genetics↗

bioRxiv2022

Gene editing for accelerated breeding in wheat

Diseases adversely affect grain yield of crop plants. Leaf rust is a major disease of wheat. As race-specific resistance breaks down, introduction of newer sources of resistance often from older accessions is necessary. Linkage drag from the donor accessions adversely impacts grain yield. As a result, CIMMYT breeding effort has shifted to using durable resistance, also referred to as race non-specific host resistance, which allows slow rusting but maintains grain yield. One of the key genes for durable resistance is Lr67 and the resistant form of this gene is absent in CIMMYT elite lines. Hence, we have initiated efforts to convert the susceptible copy of Lr67 into its resistant form directly in these elite lines using gene editing. This would eliminate backcrossing and thus save time as well as eliminate linkage drag that would accompany the resistant copy of the gene if it were to be introgressed from an older accession. As first steps, we have isolated and sequenced the genomic copies from each of the A, B, and D genome of the Lr67 gene from three elite lines and an experimental line. Identification of more than 50 single nucleotide polymorphisms (SNPs) in the open reading frames (ORF) among these lines would be useful in designing the guide RNA molecules with precision. Further, we have streamlined genetic transformation of these elite lines, a prerequisite step for gene editing.

molecular biology↗

bioRxiv2021

Molecular dissection of Carbapenem-resistant Acinetobacter baumannii circulating in Indian hospitals usingWhole Genome Sequencing

ObjectivesCarbapenem-resistant Acinetobacter baumannii (CRAB) has acquired worldwide recognition as a serious nosocomial infection. It poses a concern to hospitalized patients because of the limited therapeutic options available. Thus, we investigated the molecular epidemiology and antibiotic resistance profiles of A. baumannii isolates in India. Materials and MethodsWe characterized 306 retrospective A. baumannii clinical isolates collected from 18 centers across 10 states and 1 Union Territory of India between 2015 and 2019. Molecular epidemiology, and carbapenem resistance were studied by Whole Genome Sequencing. ResultsA total of 105 different Sequence Types (STs) were identified including 48 reported STs and 57 Novel STs. 99 isolates were classified into Clonal Complex 451 (CC451) among which ST848 and ST1956 were the common STs. Carbapenemase resistance was confirmed in all the isolates with the presence of intrinsic blaOXA-51-like genes, and the acquired blaOXA-23 and blaNDM-1 genes. ConclusionMost of the isolates were grouped under clonal complex 451. ST1053 caused an outbreak in Northern India during 2018 and 2019. Novel MLST alleles and STs were also detected, underlining an evolutionary divergence in India. The carbapenem-resistance was dominated by OXA-type carbapenemases and further surveillance of these carbapenem-resistant A. baumannii and antimicrobial stewardship should be strengthened.

genomics↗

bioRxiv2021

High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

summaryWe report insights into genome sequences of Indian K. pneumoniae isolates, highlighting the presence of high-risk international clones and genetic pools different from those predominating in other regions. Identification of multidrug-resistant and hypervirulent K. pneumoniae elicits public health concerns. BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India due to 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 MethodsWe 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, MLST, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism (SNP) phylogeny were inferred from their whole genome sequences. ResultsPhylogenetic analysis of the 325 Klebsiella isolates that passed QC revealed 3 groups: K. pneumoniae sensu stricto (n=307), K. quasipneumoniae (n=17), and K. varicolla (n=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%). ConclusionOur 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 virulent and transmissible lineages. FundingThis work was supported by Official Development Assistance (ODA) funding from the National Institute of Health Research [grant number 16_136_111]. This research was commissioned by the National Institute of Health Research using Official Development Assistance (ODA) funding. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research or the Department of Health. Conflict of InterestThe authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest.

genomics↗