Biology subjects

Vasudevan, K.

Publications and source records attributed to Vasudevan, K..

4 recordsLinked to original sources

bioRxiv2019

First Indian report on Genome-wide Comparison of Multidrug-Resistant Escherichia coli from Blood Stream Infections

BackgroundMultidrug-resistant (MDR) E. coli with extended-spectrum {beta}-lactamases (ESBLs) is becoming endemic in health care settings around the world. Baseline data on virulence and AMR of specific lineages of E. coli circulating in developing countries like India is currently lacking.\n\nMethodsWhole-genome sequencing was performed for 60 MDR E. coli isolates. Genome-wide analysis was performed at single nucleotide polymorphism (SNP) level resolution to identify the relation between the isolates in context of time, virulence and AMR determinants possessed.\n\nResultsGenome comparison revealed the presence of ST-131 global MDR and ST410 as emerging-MDR clades of E. coli. AMR gene profile for cephalosporin and carbapenem resistance differed between the clades. Genotypes blaCTX-M-15 and blaNDM-5 were common among cephalosporinases and carbapenemases, respectively. For aminoglycoside resistance, rmtB was positive for 31.7% of the isolates, of which 30% were co-harboring carbapenemases. Further, the FimH types and virulence gene profile positively correlated with the SNP based phylogeny, which also revealed the evolution of MDR clones among the study population with temporal accumulation of SNPs. The predominant clone was ST167 (blaNDM lineage) followed by ST405 (global clone ST131 equivalent) and ST410 (fast spreading high risk clone).\n\nConclusionsThis is the first report on the whole genome analysis of MDR E. coli lineages circulating in India. Data from this study will provide public health agencies a baseline portfolio of AMR and virulence in pathogenic E. coli in the region.

genomics↗

bioRxiv2019

Environmental niche forecasts of globally threatened Yellow-throated Bulbul, Pycnonotus xantholaemus for conservation prospects in the Deccan peninsula, India

Yellow-throated Bulbul, Pycnonotus xantholaemus is an endemic, rare and threatened species with discontinuous distribution across Deccan peninsula. IUCN has enlisted surveys for newer populations as one of the conservation measures. We used maxent algorithm to generate environmental niche model for further surveys. We looked into climatic envelope at occurrence points and contrast it with background climatic envelope. We compared the model for current scenario and future scenario to assess change in extent of predicted niche over time. We used six variables: climatic, topographical and vegetation layers, and a final set of 102 verified presence locations to generate the model. Topographic ruggedness index and precipitation of wettest month (Bio13) were the strong predictors for Yellow-throated Bulbul niche. Model predicts highly discontinuous and small fragments totalling 7% area of peninsular India as suitable niche. Only 10 % of predicted niche falls within Indias protected area network. Loss of habitat due to granite quarrying and anthropogenic pressure will be a bigger threat than climate change.

ecology↗

bioRxiv2019

First hybrid complete genome of Aeromonas veronii reveals chromosome-mediated novel structural variant mcr-3.19 from human clinical specimen

BackgroundRecent findings substantiate the origin of plasmid-mediated colistin resistance gene mcr-3 from Aeromonads. The present study aimed to screen the plasmid-mediated colistin resistance among 30 clinical multidrug resistant (MDR) Aeromonas spp.\n\nResultsThe presence of mcr-1, mcr-2, mcr-3, and mcr-4 were screened by PCR, which revealed mcr-3 in a colistin susceptible isolate (FC951). All other isolates were negative for mcr genes. Sequencing of FC951 revealed that mcr-3 (mcr-3.19) identified was different from previously reported variants and had 95.62 and 95.28% nucleotide similarity with mcr-3.3 and mcr-3.10 gene. A hybrid assembly using IonTorrent and MinION reads revealed structural genetic information of mcr-3.19 with an insertion of ISAs18 within the gene. Due to this, mcr-3.19 was non-expressive which makes FC951 susceptible to colistin. Further, in silico sequence and protein structural analysis confirmed the new variant. To the best of our knowledge, this is the first report on novel mcr-3 variant (mcr-3.19).\n\nConclusionsThe significant role of mcr-like genes in different Aeromonas species remains unknown and needs additional investigation to understand the insights on colistin resistance mechanism.

microbiology↗

bioRxiv2019

Genetic diversity of clinical Bordetella pertussis ST2 strains in comparison with vaccine reference strains of India

Pertussis is a highly contagious disease of the respiratory tract caused by Bordetella pertussis, a bacteria that lives in the mouth, nose, and throat. Current study reports the highly accurate complete genomes of two clinical B. pertussis strains from India for the first time. The analysis revealed insertional elements flanked by IS481, which has been previously regarded as the important component for bacterial evolution. The two B. pertussis clinical strains exhibited diversity through genome degradation when compared to whole-cell pertussis vaccine reference strains of India. These isolates harboured multiple genetic virulence traits and toxin subunits, which belonged to sequence type ST2. The genome information of Indian clinical B. pertussis strains will serve as a baseline data to decipher more information on the genome evolution, virulence factors and their role in pathogenesis for effective vaccine strategies.

microbiology↗