scholarly journals First Indian report on Genome-wide Comparison of Multidrug-ResistantEscherichia colifrom Blood Stream Infections

2019 ◽  
Author(s):  
Naveen Kumar Devanga Ragupathi ◽  
Balaji Veeraraghavan ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
Shalini Anandan ◽  
Karthick Vasudevan ◽  
...  
Keyword(s):  
Virulence Gene ◽  
Carbapenem Resistance ◽  
Blood Stream ◽  
Genome Comparison ◽  
Whole Genome ◽  
Gene Profile ◽  
Aminoglycoside Resistance ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Genome Wide

AbstractBackgroundMultidrug-resistant (MDR)E. coliwith extended-spectrum β-lactamases (ESBLs) is becoming endemic in health care settings around the world. Baseline data on virulence and AMR of specific lineages ofE. colicirculating in developing countries like India is currently lacking.MethodsWhole-genome sequencing was performed for 60 MDRE. coliisolates. 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.ResultsGenome comparison revealed the presence of ST-131 global MDR and ST410 as emerging-MDR clades ofE. coli. AMR gene profile for cephalosporin and carbapenem resistance differed between the clades. GenotypesblaCTX-M-15andblaNDM-5were common among cephalosporinases and carbapenemases, respectively. For aminoglycoside resistance,rmtBwas 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 (blaNDMlineage) followed by ST405 (global clone ST131 equivalent) and ST410 (fast spreading high risk clone).ConclusionsThis is the first report on the whole genome analysis of MDRE. colilineages circulating in India. Data from this study will provide public health agencies a baseline portfolio of AMR and virulence in pathogenicE. coliin the region.

scholarly journals Comparative Whole Genome Analysis of Escherichia coli O157:H7 Isolates From Feedlot Cattle to Identify Genotypes Associated With the Presence and Absence of stx Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Mo Jia ◽  
Ifigenia Geornaras ◽  
Jennifer N. Martin ◽  
Keith E. Belk ◽  
Hua Yang
Keyword(s):  
Escherichia Coli ◽  
Metabolic Pathway ◽  
Genome Analysis ◽  
Feedlot Cattle ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Foodborne Outbreak ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Red Recombination

A comparative whole genome analysis was performed on three newly sequenced Escherichia coli O157:H7 strains with different stx profiles, previously isolated from feedlot cattle [C1-010 (stx1−, stx2c+), C1-057 (stx−), and C1-067 (stx1+, stx2a+)], as well as five foodborne outbreak strains and six stx-negative strains from NCBI. Phylogenomic analysis demonstrated that the stx2c-carrying C1-010 and stx-negative C1-057 strains were grouped with the six NCBI stx-negative E. coli O157:H7 strains in Cluster 1, whereas the stx2a-carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one stx2a-carrying strain, and the six NCBI stx-negative strains and identify their prophages at the stx insertion sites. All stx-carrying prophages contained both the three Red recombination genes (exo, bet, gam) and their repressor cI. On the other hand, the majority of the stx-negative prophages carried only the three Red recombination genes, but their repressor cI was absent. In the absence of the repressor cI, the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of stx genes. We further investigated each of the 10 selected E. coli O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two stx2a-carrying strains and one in the single stx2c-carrying and seven stx-negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in stx2a-carrying E. coli O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the stx2c-carrying and stx-negative E. coli O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic E. coli O157:H7 in livestock and downstream food production environments.

scholarly journals Genome-wide microsatellites and species specific markers in genus Phytophthora revealed through whole genome analysis

3 Biotech ◽  
2020 ◽  
Vol 10 (10) ◽  
Author(s):  
Deepu Mathew ◽  
P. S. Anju ◽  
Amala Tom ◽  
Neethu Johnson ◽  
M. Lidia George ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Genome Wide ◽  
Species Specific

scholarly journals Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India

2016 ◽  
Vol 60 (11) ◽  
pp. 6795-6805 ◽  
Author(s):  
Amit Ranjan ◽  
Sabiha Shaik ◽  
Agnismita Mondal ◽  
Nishant Nandanwar ◽  
Arif Hussain ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Effective Means ◽  
Genomic Analysis ◽  
Virulence Gene ◽  
Carbapenem Resistance ◽  
Control Measures ◽  
Large Sample Size ◽  
Gene Repertoire ◽  
Content Type ◽  
E Coli

ABSTRACTThe global dissemination and increasing incidence of carbapenem-resistant, Gram-negative organisms have resulted in acute public health concerns. Here, we present a retrospective multicenter study on molecular characterization of metallo-β-lactamase (MBL)-producing clinicalEscherichia coliisolates recovered from extraintestinal infections in two hospitals in Pune, India. We screened a large sample size of 510E. coliisolates for MBL production wherein we profiled their molecular determinants, antimicrobial resistance phenotypes, functional virulence properties, genomic features, and transmission dynamics. Approximately 8% of these isolates were MBL producers, the majority of which were of the NDM-1 (69%) type, followed by NDM-5 (19%), NDM-4 (5.5%), and NDM-7 (5.5%). MBL producers were resistant to all antibiotics tested except for colistin, fosfomycin, and chloramphenicol, which were effective to various extents. Plasmids were found to be an effective means of dissemination of NDM genes and other resistance traits. All MBL producers adhered to and invaded bladder epithelial (T24) cells and demonstrated significant serum resistance. Genomic analysis of MBL-producingE. coliisolates revealed higher resistance but a moderate virulence gene repertoire. A subset of NDM-1-positiveE. coliisolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. A majority of MBL-producingE. colistrains revealed unique genotypes, suggesting that they were clonally unrelated. Overall, the coexistence of virulence and carbapenem resistance in clinicalE. coliisolates is of serious concern. Moreover, the emergence of NDM-1 among the globally dominantE. coliST101 isolates warrants stringent surveillance and control measures.

scholarly journals Patents and Genome-Wide DNA Sequence Analysis: Is it Safe to Go into the Human Genome?

2014 ◽  
Vol 42 (S1) ◽  
pp. 42-50 ◽  
Author(s):  
Robert Cook-Deegan ◽  
Subhashini Chandrasekharan
Keyword(s):  
Clinical Applications ◽  
Patent Infringement ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Business Decisions ◽  
Gene Patents ◽  
Clinical Laboratories ◽  
Genome Wide ◽  
Human Genes ◽  
Genome Analyses

Whether, and to what degree, do patents granted on human genes cast a shadow of uncertainty over genomics and its applications? Will owners of patents on individual genes or clusters of genes sue those performing whole-genome analyses on human samples for patent infringement? These are related questions that have haunted molecular diagnostics companies and services, coloring scientific, clinical, and business decisions. Can the profusion of whole-genome analysis methods proceed without fear of patent infringement liability?Whole-genome sequencing (WGS) is proceeding apace. Academic centers have been performing whole-genome and -exome sequencing (WES) in research for at least five years, and academic clinical laboratories with national reach have been doing sequencing for clinical applications for almost as long. Companies have also been offering WGS and WES as a clinical service for a few years now. So far as we know, no one has been sued for infringement of “gene patents” for performing WGS.

scholarly journals Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Indiana C629, a Carbapenem-Resistant Bacterium Isolated from Chicken Carcass in China

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Wei Wang ◽  
Feng Liu ◽  
Zixin Peng ◽  
Fengqin Li ◽  
Aiguo Ma
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
Carbapenem Resistance ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Carbapenem Resistant ◽  
Chicken Carcass ◽  
Plasmid Genes

The carbapenem-resistant Salmonella enterica subsp. enterica serovar Indiana strain C629 was isolated from a chicken carcass collected from a slaughterhouse in Qingdao, China. The complete genome sequence of C629 contains a circular 4,791,723-bp chromosome and a circular 210,106-bp plasmid. Genes involved in carbapenem resistance of this bacterium were identified by whole-genome analysis.

scholarly journals Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies potential targets of allele-specific immunity to clinical malaria

2020 ◽  
Author(s):  
Zalak Shah ◽  
Myo T Naung ◽  
Kara A Moser ◽  
Matthew Adams ◽  
Andrea G Buchwald ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Clinical Malaria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Multiple Alleles ◽  
Vaccine Candidates ◽  
Genome Wide ◽  
Allele Specific

Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. This immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode likely targets of naturally acquired immunity and that should be further characterized for their potential as vaccine candidates.

scholarly journals Association of Genetically Related Escherichia coli Strains with Ulcerative Colitis - A Preliminary Study

2011 ◽  
Vol 2 (2) ◽  
pp. 93-96
Author(s):  
Ritu Agarwal ◽  
Chaman Deep ◽  
Saurabh K Patel ◽  
Ashok K Jain ◽  
Gopal Nath
Keyword(s):  
Escherichia Coli ◽  
Ulcerative Colitis ◽  
Genetic Relatedness ◽  
Bacterial Species ◽  
Rectal Mucosa ◽  
Whole Genome ◽  
Medical Sciences ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Major Cluster

Objective: To explore the genetic relatedness among the Escherichia coli isolates recovered from rectal mucosa of patients with Ulcerative Colitis(UC) as well as from non specific diarrhoea patients by using ERIC PCR (whole genome analysis). Material & Methods: A total of 44 strains of E coli, each from patients suffering from UC with exacerbation while on maintenance therapy, were isolated to see if there is any association with specific genotype of E coli with the clini-cal condition. For comparison, 20 strains of E coli were also isolated from patients suffering from non specific diarrhoea. These isolates were subjected to ERIC PCR for analysing similarity/ dissimilarity with each other based on the distribution of ERIC sequences in the whole genome of the bacterial species. Results: The dendrogram prepared on the basis of banding pattern showed that majority of UC patients (39/44, 88.6%) grouped in to one major cluster while second major cluster comprised mostly strains isolated from patients with non specific diarrhoea i.e. controls (17/18, 94.4%). Moreover, in the cluster representing UC patients, a total of 11 strains were observed to be genotypically similar followed by 8 strains by ERIC PCR. Conclusion: Our results strongly indicate that specific Escherichia coli strains may be involved/ associated with UC and its relapse. Key Words: Ulcerative colitis; Escherichia coli; ERIC; PCR DOI: http://dx.doi.org/10.3126/ajms.v2i2.4769Asian Journal of Medical Sciences 2 (2011) 93-96

scholarly journals Dominance of ST131Escherichia colicarryingblaCTX-Min patients with bloodstream infections caused by cephalosporin-resistant strains in Australia, New Zealand and Singapore: whole genome analysis of isolates from a randomised trial

2017 ◽  
Author(s):  
Patrick N. A. Harris ◽  
Nouri L. Ben Zakour ◽  
Leah W. Roberts ◽  
Alexander M. Wailan ◽  
Hosam M. Zowawi ◽  
...  
Keyword(s):  
New Zealand ◽  
Resistance Genes ◽  
Controlled Trial ◽  
Randomised Trial ◽  
Significant Proportion ◽  
Antibiotic Resistance Genes ◽  
Bloodstream Infections ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
E Coli

Synopsis/AbstractObjectivesTo characterise multi-drug resistantEscherichia coliisolated from patients in Australia, New Zealand and Singapore with bloodstream infection (BSI).MethodsWe prospectively collected third-generation cephalosporin resistant (3GC-R)E. colifrom blood cultures obtained from patients enrolled in a randomised controlled trial. Whole genome sequencing was used to characterise antibiotic resistance genes, sequence types (STs), plasmids and phylogenetic relationships. Antibiotic susceptibility was determined using disk diffusion and Etest.ResultsA total of 70E. coliwere included, of which the majority were ST131 (61.4%). BSI was most frequently from a urinary source (69.6%), community-associated (62.9%) and in older patients (median age 71 years [IQR 64-81]). The median Pitt bacteraemia score at presentation was 1 (IQR 0-2, range 0-3) and ICU admission was infrequent (3.1%). ST131 possessed significantly more acquired resistance genes than non-ST131 (p=0.003). Clade C1/C2 ST131 predominated (30.2% and 53.5% of all ST131 respectively) and these were all resistant to ciprofloxacin. All clade A ST131 were community-associated. The predominant ESBL types wereblaCTX-M(78.6% of isolates) and were strongly associated with ST131, with the majorityblaCTX-M-15. Clade C1 was associated withblaCTX-M-14andblaCTX-M-27, whereasblaCTX-M-15predominated in clade C2. Plasmid-mediated AmpC (p-AmpC) genes (mainlyblaCMY-2) were also frequent (17.1%) but were more common with non-ST131 strains (p< 0.001). The majority of plasmid replicon types were IncF.ConclusionsIn a prospective collection of 3GC-RE. colicausing BSI in the Australasian region, community-associated Clade C1/C2 ST131 predominate in association withblaCTX-MESBLs, although a significant proportion of non-ST131 strains carriedblaCMY-2.

scholarly journals RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

2020 ◽  
Vol 6 ◽  
pp. e251 ◽  
Author(s):  
Zhaodong Hao ◽  
Dekang Lv ◽  
Ying Ge ◽  
Jisen Shi ◽  
Dolf Weijers ◽  
...  
Keyword(s):  
Gc Content ◽  
R Package ◽  
Whole Genome ◽  
Data Mapping ◽  
Data Types ◽  
Model Species ◽  
Chromosomal Distribution ◽  
Whole Genome Analysis ◽  
Genome Wide ◽  
Genome Wide Data

Background Owing to the rapid advances in DNA sequencing technologies, whole genome from more and more species are becoming available at increasing pace. For whole-genome analysis, idiograms provide a very popular, intuitive and effective way to map and visualize the genome-wide information, such as GC content, gene and repeat density, DNA methylation distribution, genomic synteny, etc. However, most available software programs and web servers are available only for a few model species, such as human, mouse and fly, or have limited application scenarios. As more and more non-model species are sequenced with chromosome-level assembly being available, tools that can generate idiograms for a broad range of species and be capable of visualizing more data types are needed to help better understanding fundamental genome characteristics. Results The R package RIdeogram allows users to build high-quality idiograms of any species of interest. It can map continuous and discrete genome-wide data on the idiograms and visualize them in a heat map and track labels, respectively. Conclusion The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics.

scholarly journals Prevalence, serodiversity and antibiogram of enterotoxigenic Escherichia coli (ETEC) in diarrhoeic calves and lambs of Kashmir valley (J&K), India

2015 ◽  
Vol 7 (1) ◽  
pp. 477-481 ◽  
Author(s):  
Rusheeba Manzoor ◽  
Mohammad Irfan Shah ◽  
Asma- Ul-husna ◽  
Shakil Ahmad Wani ◽  
Farhat Pandit ◽  
...  
Keyword(s):  
Prevalence Rate ◽  
Differential Susceptibility ◽  
Virulence Gene ◽  
Enterotoxigenic Escherichia Coli ◽  
Kashmir Valley ◽  
Gene Profile ◽  
E Coli ◽  
Virulent Gene ◽  
First Time

Enterotoxigenic E. coli (ETEC) is the major cause of diarrhoea in neonatal animals. This study determined the prevalence, serological diversity, virulence gene profile and in-vitro antibiogram of ETEC isolates from diarrhoeic faeces of calves and lambs. The prevalence rate of ETEC in lambs was recorded 18.46 % with O8 as predominant serotype. However, in calves the prevalence rate was recorded 8.57 % with O15 and O26 as predominant serotypes. The antibiogram screening showed differential susceptibility pattern among ETEC isolates with highest resistance to ampicillin and highest sensitivity to enrofloxacin. In the present study, for the first time it was reported that the diarrhoea in calves and lambs occur due to virulent gene est not due to elt gene, which was absent in all the isolates.

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