scholarly journals CleanRecomb, a quick tool for recombination detection in SNP based cluster analysis

2018 ◽  
Author(s):  
Mark Østerlund ◽  
Kristoffer Kiil
Keyword(s):  
Cluster Analysis ◽  
Genome Sequences ◽  
E Coli ◽  
Recombination Detection

AbstractWe present CleanRecomb, a tool to quickly filter a SNP matrix for likely recombination events.MethodThe method evaluates segments with identical SNP profiles over the genome, based on the assumption that SNPs in the absense of recombination events are uniformly distributed across the genome. The method is evaluated on a set of 9 ST200 E. coli genome sequences.ResultsThe detected recombination events coincide with regions of elevated SNP density.

Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments

2008 ◽  
Vol 58 (3) ◽  
pp. 537-547 ◽  
Author(s):  
B. R. Mohapatra ◽  
A. Mazumder
Keyword(s):  
Cluster Analysis ◽  
Disease Transmission ◽  
Management Practices ◽  
Gastrointestinal Disease ◽  
Function Analysis ◽  
Average Rate ◽  
Aquatic Environments ◽  
Correct Classification ◽  
Comparative Efficacy ◽  
E Coli

Development of efficient techniques to discriminate the sources of E. coli in aquatic environments is essential to improve the surveillance of fecal pollution indicators, to develop strategies to identify the sources of fecal contamination, and to implement appropriate management practices to minimize gastrointestinal disease transmission. In this study the robustness of five different rep-PCR methods, such as REP-PCR, ERIC-PCR, ERIC2-PCR, BOX-PCR and (GTG)5-PCR were evaluated to discriminate 271 E. coli strains isolated from two watersheds (Lakelse Lake and Okanagan Lake) located in British Columbia, Canada. Cluster analysis of (GTG)5-PCR, BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR profiles of 271 E. coli revealed 43 clusters, 35 clusters, 28 clusters, 23 clusters and 14 clusters, respectively. The discriminant analysis of rep-PCR genomic fingerprints of 271 E. coli isolates yielded an average rate of correct classification (watershed-specific) of 86.8%, 82.3%, 78.4%, 72.6% and 55.8% for (GTG)5-PCR, BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR, respectively. Based on the results of cluster analysis and discriminant function analysis, (GTG)5-PCR was found to be the most robust molecular tool for differentiation of E. coli populations in aquatic environments.

scholarly journals Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity

2017 ◽  
Vol 5 (50) ◽  
Author(s):  
Jayanthi Gangiredla ◽  
Mark K. Mammel ◽  
Tammy J. Barnaba ◽  
Carmen Tartera ◽  
Solomon T. Gebru ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Human Health ◽  
Potential Risk ◽  
Phylogenetic Relationships ◽  
Genomic Diversity ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli

ABSTRACT Pathogenic and nonpathogenic Escherichia coli strains present a vast genomic diversity. We report the genome sequences of 2,244 E. coli isolates from multiple animal and environmental sources. Their phylogenetic relationships and potential risk to human health were examined.

scholarly journals Whole-Genome Draft Sequences of Nine Asymptomatic Escherichia coli Bacteriuria Isolates from Diabetic Patients

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Christoph Stork ◽  
Beáta Kovács ◽  
Eva Trost ◽  
Tamás Kovács ◽  
György Schneider ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract Infection ◽  
Asymptomatic Bacteriuria ◽  
Diabetic Patients ◽  
Whole Genome ◽  
Genome Sequences ◽  
Disease Response ◽  
Symptomatic Urinary Tract Infection ◽  
E Coli ◽  
Genome Draft

ABSTRACT Escherichia coli can colonize the urinary bladder without causing a disease response in the host. This asymptomatic bacteriuria (ABU) can protect against recurrent symptomatic urinary tract infection by virulent bacteria. Here, we report the whole-genome sequences of nine E. coli ABU isolates from diabetic patients.

Cluster analysis of coronavirus sequences using computational sequence descriptors: With applications to SARS, MERS and SARS-CoV-2 (CoVID-19)

2021 ◽  
Vol 17 ◽  
Author(s):  
Marjan Vračko ◽  
Subhash C. Basak ◽  
Tathagata Dey ◽  
Ashesh Nandy
Keyword(s):  
Cluster Analysis ◽  
Virus Type ◽  
Genome Sequences ◽  
Alignment Free ◽  
The World

Background: Study of 573 genome sequences belonging to SARS, MERS and SARS-CoV-2 (CoVID-19) viruses. Objective: To compare the virus sequences, which originate from different places around the world. Methods: Alignment free methods for representation of sequences and chemometrical methods for analyzing of clusters. Results: Majority of genome sequences are clustered with respect on virus type, but some of them are outliers. Conclusion: We indicate 71 sequences, which tend to belong to more than cluster.

Characteristics of fosA-carrying plasmids in E. coli and Klebsiella spp. isolates originating from food and environmental samples

2021 ◽  
Author(s):  
Michael Biggel ◽  
Katrin Zurfluh ◽  
Andrea Treier ◽  
Magdalena Nüesch-Inderbinen ◽  
Roger Stephan
Keyword(s):  
High Susceptibility ◽  
Genome Sequences ◽  
E Coli ◽  
Short Read Sequencing ◽  
Fosfomycin Resistance ◽  
Enterobacteriaceae Infections ◽  
High Level ◽  
Resistance Rates ◽  
Klebsiella Spp ◽  
Genetic Context

Abstract Objectives Fosfomycin is an important antibiotic for the treatment of MDR Enterobacteriaceae infections. High susceptibility rates are, however, threatened by the spread of plasmids encoding fosfomycin-modifying enzymes. In this study, we sought to characterize the genetic context of fosA in plasmids from Escherichia coli and Klebsiella spp. isolates recovered from food, wastewater and surface water in Switzerland. Methods E. coli and Klebsiella spp. isolates collected between 2012 and 2019 in Switzerland were screened for fosfomycin resistance. Presence of fosA was verified by PCR and sodium phosphonoformate (PPF) disc potentiation testing, and transferability was tested using conjugation assays. Whole-genome sequences including complete fosA-containing plasmids were determined using long- and short-read sequencing. Results In 11 E. coli and two Klebsiella spp. isolates, high-level fosfomycin resistance was mediated by plasmids containing fosA3 (n = 12) or fosA8 (n = 1). Four isolates harboured a near-identical 45 kb IncN plasmid with fosA3, while replicon types varied in the remaining plasmids. The fosA genes were typically embedded in IS26-bounded transposition units and frequently located in the proximity of blaCTX-M transposition units. Conclusions Although fosfomycin resistance rates are currently low, the presence of fosA-encoding plasmids circulating in the Enterobacteriaceae population suggests that fosfomycin resistance may rapidly spread upon increased selection pressure. Transposition mobility of fosA and co-location on plasmids with other resistance genes may further promote its dissemination.

scholarly journals Autotransporters of Escherichia coli: a sequence-based characterization

Microbiology ◽  
2010 ◽  
Vol 156 (8) ◽  
pp. 2459-2469 ◽  
Author(s):  
Timothy J. Wells ◽  
Makrina Totsika ◽  
Mark A. Schembri
Keyword(s):  
Escherichia Coli ◽  
Biofilm Formation ◽  
Domain Architecture ◽  
Bioinformatic Analysis ◽  
Tissue Tropism ◽  
Genome Sequences ◽  
E Coli ◽  
Disease Outcomes ◽  
High Degree ◽  
Encoding Genes

Autotransporter (AT) proteins are found in all Escherichia coli pathotypes and are often associated with virulence. In this study we took advantage of the large number of available E. coli genome sequences to perform an in-depth bioinformatic analysis of AT-encoding genes. Twenty-eight E. coli genome sequences were probed using an iterative approach, which revealed a total of 215 AT-encoding sequences that represented three major groups of distinct domain architecture: (i) serine protease AT proteins, (ii) trimeric AT adhesins and (iii) AIDA-I-type AT proteins. A number of subgroups were identified within each broad category, and most subgroups contained at least one characterized AT protein; however, seven subgroups contained no previously described proteins. The AIDA-I-type AT proteins represented the largest and most diverse group, with up to 16 subgroups identified from sequence-based comparisons. Nine of the AIDA-I-type AT protein subgroups contained at least one protein that possessed functional properties associated with aggregation and/or biofilm formation, suggesting a high degree of redundancy for this phenotype. The Ag43, YfaL/EhaC, EhaB/UpaC and UpaG subgroups were found in nearly all E. coli strains. Among the remaining subgroups, there was a tendency for AT proteins to be associated with individual E. coli pathotypes, suggesting that they contribute to tissue tropism or symptoms specific to different disease outcomes.

scholarly journals Initial Assessment of the Molecular Epidemiology ofblaNDM-1in Colombia

2016 ◽  
Vol 60 (7) ◽  
pp. 4346-4350 ◽  
Author(s):  
Laura J. Rojas ◽  
Meredith S. Wright ◽  
Elsa De La Cadena ◽  
Gabriel Motoa ◽  
Kristine M. Hujer ◽  
...  
Keyword(s):  
Hot Spot ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Initial Assessment ◽  
Genome Sequences ◽  
Gram Negative ◽  
Content Type ◽  
E Coli ◽  
Resistance Determinants ◽  
Novel Complex

ABSTRACTWe report complete genome sequences of fourblaNDM-1-harboring Gram-negative multidrug-resistant (MDR) isolates from Colombia. TheblaNDM-1genes were located on 193-kb Inc FIA, 178-kb Inc A/C2, and 47-kb (unknown Inc type) plasmids. Multilocus sequence typing (MLST) revealed that these isolates belong to sequence type 10 (ST10) (Escherichia coli), ST392 (Klebsiella pneumoniae), and ST322 and ST464 (Acinetobacter baumanniiandAcinetobacter nosocomialis, respectively). Our analysis identified that the Inc A/C2 plasmid inE. colicontained a novel complex transposon (Tn125and Tn5393with three copies ofblaNDM-1) and a recombination “hot spot” for the acquisition of new resistance determinants.

scholarly journals Complete Annotated Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains and One Atypical Enteropathogenic E. coli Strain, Isolated from Naturally Colonized Cattle of German Origin

2017 ◽  
Vol 5 (19) ◽  
Author(s):  
Lutz Geue ◽  
Christian Menge ◽  
Christian Berens ◽  
Stefanie A. Barth
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Coli Strain ◽  
Enteric Pathogens ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli ◽  
German Origin ◽  
Cattle Herds ◽  
German Cattle

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) are important zoonotic enteric pathogens with the main reservoir in cattle. Here, we present the genomes of two STEC strains and one atypical enteropathogenic E. coli strain from cattle origin, obtained during a longitudinal study in German cattle herds.

scholarly journals RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning

2020 ◽  
Author(s):  
Linda van der Graaf van Bloois ◽  
Jaap A. Wagenaar ◽  
Aldert L. Zomer
Keyword(s):  
Bacterial Species ◽  
Draft Genome ◽  
Single Copy ◽  
Chromosomal Marker ◽  
Web Interface ◽  
Large Single Copy ◽  
Genome Sequences ◽  
Multiple Features ◽  
E Coli ◽  
Marker Proteins

AbstractAntimicrobial resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. However, draft whole genome sequences are fragmented, making it difficult to discriminate plasmid and chromosomal contigs. Current methods that predict plasmid sequences from draft genome sequences rely on single features, like k-mer composition, circularity of the DNA molecule, copy number or sequence identity to plasmid replication genes, all of which have their drawbacks, especially when faced with large single copy plasmids, which often carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict if the likely source of a contig is plasmid or chromosomal. The tool RFPlasmid supports models for 17 different bacterial species, including Campylobacter, E. coli, and Salmonella, and has a species agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as standalone tool and via web interface.

scholarly journals Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes

2020 ◽  
Author(s):  
Jacob Stanley Iramiot ◽  
Henry Kajumbula ◽  
Joel Bazira ◽  
Etienne P. de Villiers ◽  
Benon B. Asiimwe
Keyword(s):  
Escherichia Coli ◽  
Efflux Pump ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Drug Resistant ◽  
Genome Sequences ◽  
E Coli ◽  
Resistant Genes ◽  
Pastoralist Community ◽  
Western Uganda

AbstractBackgroundThe crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes.MethodsThis was a laboratory based cross sectional study. Bacterial isolates analyzed in this study were 42 multidrug resistant E. coli isolated from stool samples from both humans and cattle in pastoralist communities collected between January 2018-March 2019. Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant) and 21/42 isolates were ESBL producers; 13/42 from human and 8/42 from cattle. Whole Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant genes.ResultsThe genomes of the human E. coli generally clustered together and away from those of cattle origin. The E. coli isolates were assigned to eight different phylogroups: A, B1, B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes was higher from the E. coli population from humans than those from cattle. Among these were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235: Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone; qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2, sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump.A high variation of virulence genes was registered among the E. coli genomes from humans than those of cattle origin.ConclusionThe E. coli of human and cattle origin are largely independent with different ancestral origins. Limited sharing of strains and resistance genes presents a challenge to the hypothesis that AMR in humans is as a result of antibiotic misuse on the farm.

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