scholarly journals Strains of Escherichia coli O157:H7 Differ Primarily by Insertions or Deletions, Not Single-Nucleotide Polymorphisms

2002 ◽  
Vol 184 (7) ◽  
pp. 1873-1879 ◽  
Author(s):  
Indira T. Kudva ◽  
Peter S. Evans ◽  
Nicole T. Perna ◽  
Timothy J. Barrett ◽  
Frederick M. Ausubel ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphisms ◽  
Epidemiological Surveillance ◽  
Escherichia Coli O157 ◽  
Nucleotide Polymorphisms ◽  
Strain Variation ◽  
Single Nucleotide ◽  
E Coli ◽  
K 12 ◽  
Genetic Events

ABSTRACT Escherichia coli O157:H7 (O157) strains demonstrate varied pulsed-field gel electrophoresis patterns following XbaI digestion, which enable epidemiological surveillance of this important human pathogen. The genetic events underlying PFGE differences between strains, however, are not defined. We investigated the mechanisms for strain variation in O157 by recovering and examining nucleotide sequences flanking each of the XbaI restriction enzyme sites in the genome. Our analysis demonstrated that differences between O157 strains were due to discrete insertions or deletions that contained the XbaI sites polymorphic between strains rather than single-nucleotide polymorphisms in the XbaI sites themselves. These insertions and deletions were found to be uniquely localized within the regions of the genome that are specific to O157 compared to E. coli K-12 (O islands), suggesting that strain-to-strain variation occurs in these O islands. These results may be utilized to devise novel strain-typing tools for this pathogen.

scholarly journals Genotypic analyses of uropathogenic Escherichia coli based on fimH single nucleotide polymorphisms (SNPs)

2007 ◽  
Vol 56 (10) ◽  
pp. 1363-1369 ◽  
Author(s):  
Sara Y. Tartof ◽  
Owen D. Solberg ◽  
Lee W. Riley
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphisms ◽  
Screening Test ◽  
Epidemiological Studies ◽  
Discriminatory Power ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Discriminatory Ability ◽  
E Coli

The application of genotyping techniques for subtyping uropathogenic Escherichia coli has contributed to better understanding of the epidemiology of community-acquired urinary tract infection (UTI). However, the current techniques are hampered by limited reproducibility, poor discriminatory power, labour-intensive performance or high cost. A screening test that is sequence-based would provide an inexpensive, reproducible way to subtype E. coli isolates. Such a test, if also discriminatory, would be highly useful for epidemiological studies. The discriminatory ability of 12 putative virulence genes (fimH, fliD, fliM, iha, motA, papA/H, kpsMTII, fepE, fimA, flgA, malG, purD) was evaluated based on single nucleotide polymorphisms (SNPs) in nine uropathogenic E. coli isolates, all previously found to belong to a single multilocus sequence type (MLST) complex (ST69). An additional 25 epidemiologically well-characterized E. coli isolates belonging to 12 distinct MLST clonal complexes were analysed for fimH SNP. None of the 12 genes except fimH were able to further discriminate the nine ST69-complex strains. Isolates belonging to the 12 non-ST69 MLST groups were separated into 10 fimH SNP subgroups. While fimH SNP analysis may not be an appropriate phylogenetic method, it offers discriminatory power similar to that of MLST and could be used as a simple, inexpensive screening test for epidemiological studies of uropathogenic E. coli.

scholarly journals Lineage and Genogroup-Defining Single Nucleotide Polymorphisms of Escherichia coli O157:H7

2013 ◽  
Vol 79 (22) ◽  
pp. 7036-7041 ◽  
Author(s):  
Woo Kyung Jung ◽  
James L. Bono ◽  
Michael L. Clawson ◽  
Shana R. Leopold ◽  
Smriti Shringi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Reservoir Host ◽  
Escherichia Coli O157 ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Biologically Relevant ◽  
E Coli

ABSTRACTEscherichia coliO157:H7 is a zoonotic human pathogen for which cattle are an important reservoir host. Using both previously published and new sequencing data, a 48-locus single nucleotide polymorphism (SNP)-based typing panel was developed that redundantly identified 11 genogroups that span six of the eight lineages recently described forE. coliO157:H7 (J. L. Bono, T. P. Smith, J. E. Keen, G. P. Harhay, T. G. McDaneld, R. E. Mandrell, W. K. Jung, T. E. Besser, P. Gerner-Smidt, M. Bielaszewska, H. Karch, M. L. Clawson, Mol. Biol. Evol. 29:2047–2062, 2012) and additionally defined subgroups within four of those lineages. This assay was applied to 530 isolates from human and bovine sources. The SNP-based lineage groups were concordant with previously identifiedE. coliO157:H7 genotypes identified by other methods and were strongly associated with carriage of specific Stx genes. Two SNP lineages (Ia and Vb) were disproportionately represented among cattle isolates, and three others (IIa, Ib, and IIb) were disproportionately represented among human clinical isolates. This 48-plex SNP assay efficiently and economically identifies biologically relevant lineages withinE. coliO157:H7.

scholarly journals A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
Veronika Tchesnokova ◽  
Hovhannes Avagyan ◽  
Mariya Billig ◽  
Sujay Chattopadhyay ◽  
Pavel Aprikian ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Susceptibility ◽  
Clinical Diagnostics ◽  
Resolving Power ◽  
Nucleotide Polymorphisms ◽  
Typing Method ◽  
Single Nucleotide ◽  
E Coli ◽  
Specificity And Sensitivity ◽  
Urine Specimens

Abstract Background.  Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods.  We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results.  Fifty-four unique SNP combinations (“septatypes”) were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 102 colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusions.  7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy.

scholarly journals Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0131967 ◽  
Author(s):  
Sean M. Griffing ◽  
Duncan R. MacCannell ◽  
Amber J. Schmidtke ◽  
Molly M. Freeman ◽  
Eija Hyytiä-Trees ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Resolution ◽  
Single Nucleotide Polymorphisms ◽  
Shiga Toxin ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Evolution of Enterohemorrhagic Escherichia coli O26 Based on Single-Nucleotide Polymorphisms

2013 ◽  
Vol 5 (10) ◽  
pp. 1807-1816 ◽  
Author(s):  
Stefan Bletz ◽  
Martina Bielaszewska ◽  
Shana R. Leopold ◽  
Robin Köck ◽  
Anika Witten ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphisms ◽  
Enterohemorrhagic Escherichia Coli ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Genome-Based Analyses of Fitness Effects and Compensatory Changes Associated with Acquisition of blaCMY-, blaCTX-M-, and blaOXA-48/VIM-1-Containing Plasmids in Escherichia coli

Antibiotics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 90
Author(s):  
Michael Pietsch ◽  
Yvonne Pfeifer ◽  
Stephan Fuchs ◽  
Guido Werner
Keyword(s):  
Escherichia Coli ◽  
Growth Rates ◽  
Beta Lactamase ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genomic Changes ◽  
E Coli ◽  
Fitness Effects ◽  
Growth Differences

(1) Background: Resistance plasmids are under selective conditions beneficial for the bacterial host, but in the absence of selective pressure, this carriage may cause fitness costs. Compensation of this fitness burden is important to obtain competitive ability under antibiotic-free conditions. In this study, we investigated fitness effects after a conjugative transfer of plasmids containing various beta-lactamase genes transferred into Escherichia coli. (2) Methods: Fourteen beta-lactamase-encoding plasmids were transferred from clinical donor strains to E. coli J53. Growth rates were compared for all transconjugants and the recipient. Selected transconjugants were challenged in long-term growth experiments. Growth rates were assessed at different time points during growth for 500 generations. Whole-genome sequencing (WGS) of initial and evolved transconjugants was determined. Results: Most plasmid acquisitions resulted in growth differences, ranging from −4.5% to 7.2%. Transfer of a single blaCMY-16-carrying plasmid resulted in a growth burden and a growth benefit in independent mating. Long-term growth led to a compensation of fitness burdens and benefits. Analyzing WGS revealed genomic changes caused by Single Nucleotide Polymorphisms (SNPs) and insertion sequences over time. Conclusions: Fitness effects associated with plasmid acquisitions were variable. Potential compensatory mutations identified in transconjugants’ genomes after 500 generations give interesting insights into aspects of plasmid–host adaptations.

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