Biology subjects

Vasudevan, K.

Publications and source records attributed to Vasudevan, K..

25 records · Page 2Linked to original sources

bioRxiv2020

Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance

BackgroundRecent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only sporadic cases of ceftriaxone resistant S. Typhi are reported. This study aimed at elucidating the phylogenetic evolutionary framework of ceftriaxone resistant S. Typhi isolates from India to predict their potential dissemination in endemic regions. MethodsFive ceftriaxone resistant S. Typhi isolates from three tertiary care hospitals in India were sequenced on an Ion Torrent Personal Genome Machine (PGM). A core genome single-nucleotide-polymorphism (SNP) based phylogeny of the isolates in comparison to the global collection of MDR and XDR S. Typhi isolates was built. Two of five isolates were additionally sequenced using Oxford Nanopore MinION to completely characterize the plasmid and understand its transmission dynamics within Enterobacteriaceae. ResultsComparative genomic analysis and detailed plasmid characterization indicate that while in Pakistan (4.3.1 lineage I) the XDR trait is associated with blaCTX-M-15 gene on IncY plasmid, in India (4.3.1 lineage II), the ceftriaxone resistance is due to short term adaptation of resistance plasmids such as IncX3 or IncN. ConclusionSince the bacterial acquisition of smaller resistance plasmids such as IncX3 or IncN from other Enterobacteriaceae can be much faster than the larger IncY plasmids, the rapid expansion of these genotypically novel XDR S. Typhi could potentially cause large outbreaks. Therefore, continuous monitoring of S. Typhi lineages carrying cephalosporin resistance on IncX3 or IncN plasmids is vital not just for India but globally. ImportanceGenomic analysis of cephalosporin resistant S. Typhi isolated from India indicates the potential of S. Typhi to develop cephalosporin resistance by acquiring diverse plasmids from other Enterobacteriaceae. We identified the occurrence of independent acquisition of drug-resistant plasmids such as IncX3 and IncN with genes encoding beta-lactamases in H58/4.3.1.2 lineage. A short term adaptation of drug-resistant plasmids in H58/4.3.1.2 lineage can be the reason for the sporadic cases cephalosporin resistant S. Typhi in India. However, the IncY plasmid acquired by isolates that belong to H58/4.3.1.1 lineage appeared to be well adapted as observed in XDR S. Typhi outbreak in Pakistan. Plasmid acquisition and maintenance of cephalosporin resistant S. Typhi appears to be specific to the phylogenetic lineage as lineages differ in compensating the initial cost imposed by the plasmid. The stable maintenance of these resistance plasmids without a fitness cost, are determinant in understanding the future spread of cephalosporin resistance in S. Typhi. Therefore, critical strategies in monitoring and control of cephalosporin resistant S. Typhi is needed to tackle further public health crisis.

genomics↗

bioRxiv2020

Origin and evolutionary dynamics of multi-drug resistant and highly virulent community-associated methicillin-resistant Staphylococcus aureus ST772-SCCmec V lineage

BackgroundCommunity-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are increasing in prevalence across the world. However, studies on the molecular epidemiology and the genomic investigation of MRSA are limited in India. ObjectivesTo understand the molecular epidemiology of MRSA and to reconstruct the origin and evolution of S. aureus belonged to the sequence type (ST772). MethodsA total of 233 non-repetitive MRSA isolates were screened for the presence staphylococcal cassette chromosome (SCCmec) types, multi-locus sequence types (MLST) and staphylococcal protein A (spa) types. Whole genome sequence data of ST772-SCCmec V (n=32) isolates were generated and analysed along with the publically available ST772-SCCmec V (n=273) genome. ResultsST772 (27%), ST22 (19%) and ST239 (16%) were found as the predominant STs. Analysis of the core SNPs using Bayesian time scaled phylogenetic analysis showed ST772-SCCmec V was emerged on the Indian subcontinent in 1960s. The acquisition of integrated resistance plasmid (IRP) in the ST772-SCCmec V lineage during 1990s, fixation of SCCmec V (5C2) and the double serine mutations (S84L, S80Y) appears to have played a key role in the successful expansion. The IRP carries the loci for multiple antibiotic resistant genes: beta-lactam (blaZ), aminoglycosides (aphA3-sat-aadE), macrolide (mphC), macrolide-lincosamide-streptogramin B (msrA) and bacitracin (bacA, bacB). ConclusionThe Panton Valentine Leukocidin (PVL) positive ST772 and ST22 MRSA lineages are observed in the hospital settings. ST772-SCCmec V has the multi-drug resistance trait of hospital-associated (HA) MRSA and the epidemiological characteristics of CA-MRSA. The antimicrobial use pattern may have driven the spread and survival of ST772 MRSA in hospitals.

microbiology↗

bioRxiv2020

Phylogenetic and evolutionary analysis reveals the recent dominance of ciprofloxacin resistant S. sonnei and local persistence of S. flexneri clones in India

Shigella is the second leading cause of bacterial diarrhea worldwide. Recently S. sonnei seems to be replacing S. flexneri in low and middle-income countries undergoing economic development. Despite this, studies focusing on these species at genomic level remain largely unexplored. Here we compared the genome sequences of S. flexneri and S. sonnei isolated from India with the publically available genomes of global strains. Our analysis provide evidence for the long term persistence of all PGs of S. flexneri and the recent dominance of ciprofloxacin-resistant S. sonnei lineage in India. Within S. flexneri PGs, majority of the study isolates belonged to PG3 within the predominance of serotype 2. For S. sonnei, the current pandemic involves globally distributed MDR clones that belong to Central Asia lineage III. The presence of such epidemiologically-dominant lineages in association with stable AMR determinants results in the successful survival in the community.

genomics↗

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↗