scholarly journals Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

2021 ◽  
Author(s):  
Timothy J Davies ◽  
Jeremy Swann ◽  
Anna E Sheppard ◽  
Hayleah Pickford ◽  
Samuel Lipworth ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Random Sequence ◽  
Real Life ◽  
Poor Performance ◽  
Real Data ◽  
Clinical Settings ◽  
Large Set ◽  
Gene Variants ◽  
E Coli ◽  
Gene Profiles

Several bioinformatics genotyping algorithms are now commonly used to characterise antimicrobial resistance (AMR) gene profiles in whole genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking. Here, we used both simulated datasets and a large set of real E. coli WGS data (n=1818 isolates) to systematically investigate genotyping methods in greater detail. Simulated constructs and real sequences were processed using four different bioinformatic programs (ABRicate, ARIBA, KmerResistance, and SRST2, run with the ResFinder database) and their outputs compared. For simulations tests where 3,092 AMR gene variants were inserted into random sequence constructs, KmerResistance was correct for all 3,092 simulations, ABRicate for 3,082 (99.7%), ARIBA for 2,927 (94.7%) and SRST2 for 2,120 (68.6%). For simulations tests where two closely related gene variants were inserted into random sequence constructs, ABRicate identified the correct alleles in 11,382/46,279 (25%) of simulations, ARIBA in 2494/46,279 (5%), SRST in 2539/46,279 (5%) and KmerResistance in 38,826/46,279 (84%). In real data, across all methods, 1392/1818 (76%) isolates had discrepant allele calls for at least one gene. Our evaluations revealed poor performance in scenarios that would be expected to be challenging (e.g. identification of AMR genes at <10x coverage, discriminating between closely related AMR gene sequences), but also identified systematic sequence classification (i.e. naming) errors even in straightforward circumstances, which contributed to 1081/3092 (35%) errors in our most simple simulations and at least 2530/4321 (59%) discrepancies in real data. Further, many of the remaining discrepancies were likely artefactual, with reporting cut-off differences accounted for at least 1430/4321 (33%) discrepants. Comparing outputs generated by running multiple algorithms on the same dataset can help identify and resolve these artefacts, but ideally new and more robust genotyping algorithms are needed.

Polyester Cloth–Based Hybridization Array System for Identification of Enterohemorrhagic Escherichia coli Serogroups O26, O45, O103, O111, O121, O145, and O157

2012 ◽  
Vol 75 (9) ◽  
pp. 1691-1697 ◽  
Author(s):  
BURTON W. BLAIS ◽  
MARTINE GAUTHIER ◽  
MYLÈNE DESCHÊNES ◽  
GEORGE HUSZCZYNSKI
Keyword(s):  
Escherichia Coli ◽  
Marker Gene ◽  
Enterohemorrhagic Escherichia Coli ◽  
Oligonucleotide Probes ◽  
E Coli ◽  
Polyester Cloth ◽  
Gene Profiles ◽  
Pcr Products ◽  
Different Strains ◽  
Immunoenzymatic Assay

A cloth-based hybridization array system (CHAS) was developed for the identification of foodborne colony isolates of seven priority enterohemorrhagic Escherichia coli (EHEC-7) serogroups targeted by U.S. food inspection programs. Gene sequences associated with intimin; Shiga-like toxins 1 and 2; and the antigenic markers O26, O45, O103, O111, O121, O145, and O157 were amplified in a multiplex PCR incorporating a digoxigenin label, and detected by hybridization of the PCR products with an array of specific oligonucleotide probes immobilized on a polyester cloth support, with subsequent immunoenzymatic assay of the captured amplicons. The EHEC-7 CHAS exhibited 100% inclusivity and 100% exclusivity characteristics with respect to detection of the various markers among 89 different E. coli strains, with various marker gene profiles and 15 different strains of non–E. coli bacteria.

scholarly journals Clinical and Molecular Correlates of Escherichia coli Bloodstream Infection from Two Geographically Diverse Centers in Rochester, Minnesota, and Singapore

2018 ◽  
Vol 62 (10) ◽  
Author(s):  
Shehara M. Mendis ◽  
Shawn Vasoo ◽  
Brian D. Johnston ◽  
Stephen B. Porter ◽  
Scott A. Cunningham ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Odds Ratio ◽  
Virulence Gene ◽  
Fluoroquinolone Resistance ◽  
Content Type ◽  
E Coli ◽  
Gene Profiles ◽  
Clonal Distribution ◽  
To Receive ◽  
Community Onset

ABSTRACT Escherichia coli bacteremia is caused mainly by sequence type complex 131 (STc131) and two clades within its fluoroquinolone-resistance-associated H30 subclone, H30R1 and H30Rx. We examined clinical and molecular correlates of E. coli bacteremia in two geographically distinct centers. We retrospectively studied 251 unique E. coli bloodstream isolates from 246 patients (48 from the Mayo Clinic, Rochester, MN [MN], and 198 from Tan Tock Seng Hospital, Singapore [SG]), from October 2013 through March 2014. Isolates underwent PCR for phylogroup, STc, blaCTX-M type, and virulence gene profiles, and medical records were reviewed. Although STc131 accounted for 25 to 27% of all E. coli bacteremia isolates at each site, its extended-spectrum-β-lactamase (ESBL)-associated H30Rx clade was more prominent in SG than in MN (15% versus 4%; P = 0.04). In SG only, patients with STc131 (versus other E. coli STc isolates) were more likely to receive inactive initial antibiotics (odds ratio, 2.8; P = 0.005); this was true specifically for patients with H30Rx (odds ratio, 7.0; P = 0.005). H30Rx comprised 16% of community-onset bacteremia episodes in SG but none in MN. In SG, virulence scores were higher for H30Rx than for H30R1, non-H30 STc131, and non-STc131 isolates (P < 0.02 for all comparisons). At neither site did mortality differ by clonal status. The ESBL-associated H30Rx clade was more prevalent and more often of community onset in SG, where it predicted inactive empirical treatment. The clonal distribution varies geographically and has potentially important clinical implications. Rapid susceptibility testing and clonal diagnostics for H30/H30Rx might facilitate earlier prescribing of active therapy.

scholarly journals Improvement of Antibiotics Susceptibility of Escherichia coli in a Tertiary Hospital in Japan

2019 ◽  
pp. 1-5
Author(s):  
Yuji Watanabe ◽  
Masafumi Seki
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Tertiary Hospital ◽  
Clinical Settings ◽  
Infection Control Team ◽  
Beta Lactamases ◽  
E Coli ◽  
Control Team ◽  
Extended Spectrum Beta Lactamases ◽  
Antibiotics Susceptibility

Antimicrobial stewardship team (AST) and Infection Control Team (ICT) have recently been linked Infectious diseases (ID) physicians, and implemented in clinical settings in Japan. The microbiological effects of an AST and ICT, in addition to Diagnostic stewardship team (DST) supported by ID physicians in our tertiary hospital were shown in significant reduction of antibiotic resistance of Escherichia coli (E coli) including extended spectrum beta-lactamases (ESBL)-producing E coli.

scholarly journals Comparison of Virulence Gene Profiles of Escherichia coli Strains Isolated from Healthy and Diarrheic Swine

2006 ◽  
Vol 72 (7) ◽  
pp. 4782-4795 ◽  
Author(s):  
Toni A. Chapman ◽  
Xi-Yang Wu ◽  
Idris Barchia ◽  
Karl A. Bettelheim ◽  
Steven Driesen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dimensional Space ◽  
Virulence Gene ◽  
Clinical Isolates ◽  
Algorithm Analysis ◽  
E Coli ◽  
Gene Profiles ◽  
Extraintestinal Disease ◽  
Highly Correlated ◽  
Postweaning Diarrhea

ABSTRACT A combination of uni- and multiplex PCR assays targeting 58 virulence genes (VGs) associated with Escherichia coli strains causing intestinal and extraintestinal disease in humans and other mammals was used to analyze the VG repertoire of 23 commensal E. coli isolates from healthy pigs and 52 clinical isolates associated with porcine neonatal diarrhea (ND) and postweaning diarrhea (PWD). The relationship between the presence and absence of VGs was interrogated using three statistical methods. According to the generalized linear model, 17 of 58 VGs were found to be significant (P < 0.05) in distinguishing between commensal and clinical isolates. Nine of the 17 genes represented by iha, hlyA, aidA, east1, aah, fimH, iroNE. coli , traT, and saa have not been previously identified as important VGs in clinical porcine isolates in Australia. The remaining eight VGs code for fimbriae (F4, F5, F18, and F41) and toxins (STa, STb, LT, and Stx2), normally associated with porcine enterotoxigenic E. coli. Agglomerative hierarchical algorithm analysis grouped E. coli strains into subclusters based primarily on their serogroup. Multivariate analyses of clonal relationships based on the 17 VGs were collapsed into two-dimensional space by principal coordinate analysis. PWD clones were distributed in two quadrants, separated from ND and commensal clones, which tended to cluster within one quadrant. Clonal subclusters within quadrants were highly correlated with serogroups. These methods of analysis provide different perspectives in our attempts to understand how commensal and clinical porcine enterotoxigenic E. coli strains have evolved and are engaged in the dynamic process of losing or acquiring VGs within the pig population.

scholarly journals Evolution of diarrheagenic Escherichia coli pathotypes in India

2019 ◽  
Vol 11 (04) ◽  
pp. 346-351
Author(s):  
Pankaj Singh ◽  
Sharda C. Metgud ◽  
Subarna Roy ◽  
Shashank Purwar
Keyword(s):  
Escherichia Coli ◽  
Cross Sectional Study ◽  
Clinical Settings ◽  
Accurate Identification ◽  
Cross Sectional ◽  
E Coli ◽  
Medical College ◽  
Diarrheagenic Escherichia Coli ◽  
Proper Management ◽  
Heat Stable

Abstract CONTEXT: Diarrheagenic Escherichia coli (DEC) is the leading cause of infectious diarrhea in developing countries. On the basis of virulence and phenotypic characteristics, the DEC is categorized into multiple pathotypes. Each pathotype has different pathogenesis and geographical distribution. Thus, the proper management of disease relies on rapid and accurate identification of DEC pathotypes. AIMS: The aim of the study was to determine the prevalence of DEC pathotypes in India. MATERIALS AND METHODS: A cross-sectional study was carried out between January 2008 and December 2012 at Jawaharlal Nehru Medical College and KLES Dr. Prabhakar Kore Hospital and Medical Research Center, Belgaum (Karnataka), India. A total of 300 stool samples were collected from diarrhea patients with age >3 months. The DEC was identified by both conventional and molecular methods. RESULTS: Of 300 samples, E. coli were detected in 198 (66%) and 170 (56.6%) samples by culture and polymerase chain reaction, respectively. Among DEC (n = 198) isolates, eae gene (59.5%) was the most prevalent followed by stx (27.7%), east (27.2%), elt (12.6%), est (10.6%), ipaH (5.5%), and eagg (1.5%) genes. On the basis of virulence genes, enteropathogenic E. coli (33.8%) was the most common pathotype followed by Shiga toxin-producing E. coli (STEC, 23.2%), enterotoxigenic E. coli (ETEC, 13.6%), enteroinvasive E. coli (5.5%), enteroaggregative heat-stable enterotoxin 1-harboring E. coli (EAST1EC, 4.5%), STEC/ETEC (3.5%), STEC/enteroaggregative E. coli (STEC/EAEC, 1.0%), and EAEC (0.05%). CONCLUSIONS: The hybrid DEC is potentially more virulent than basic pathotypes. The pathotyping should be included in clinical settings for the proper management of DEC-associated diarrhea.

scholarly journals Intestine and Environment of the Chicken as Reservoirs for Extraintestinal Pathogenic Escherichia coli Strains with Zoonotic Potential

2008 ◽  
Vol 75 (1) ◽  
pp. 184-192 ◽  
Author(s):  
Christa Ewers ◽  
Esther-Maria Ant�o ◽  
Ines Diehl ◽  
Hans-C. Philipp ◽  
Lothar H. Wieler
Keyword(s):  
Escherichia Coli ◽  
Virulence Gene ◽  
Infection Model ◽  
E Coli ◽  
Gene Profiles ◽  
Pathogenic Escherichia Coli ◽  
Zoonotic Risk ◽  
Resistant Strains ◽  
Genetic Pool

ABSTRACT Although research has increasingly focused on the pathogenesis of avian pathogenic Escherichia coli (APEC) infections and the “APEC pathotype” itself, little is known about the reservoirs of these bacteria. We therefore compared outbreak strains isolated from diseased chickens (n = 121) with nonoutbreak strains, including fecal E. coli strains from clinically healthy chickens (n = 211) and strains from their environment (n = 35) by determining their virulence gene profiles, phylogenetic backgrounds, responses to chicken serum, and in vivo pathogenicities in a chicken infection model. In general, by examining 46 different virulence-associated genes we were able to distinguish the three groups of avian strains, but some specific fecal and environmental isolates had a virulence gene profile that was indistinguishable from that determined for outbreak strains. In addition, a substantial number of phylogenetic EcoR group B2 strains, which are known to include potent human and animal extraintestinal pathogenic E. coli (ExPEC) strains, were identified among the APEC strains (44.5%) as well as among the fecal E. coli strains from clinically healthy chickens (23.2%). Comparably high percentages (79.2 to 89.3%) of serum-resistant strains were identified for all three groups of strains tested, bringing into question the usefulness of this phenotype as a principal marker for extraintestinal virulence. Intratracheal infection of 5-week-old chickens corroborated the pathogenicity of a number of nonoutbreak strains. Multilocus sequence typing data revealed that most strains that were virulent in chicken infection experiments belonged to sequence types that are almost exclusively associated with extraintestinal diseases not only in birds but also in humans, like septicemia, urinary tract infection, and newborn meningitis, supporting the hypothesis that not the ecohabitat but the phylogeny of E. coli strains determines virulence. These data provide strong evidence for an avian intestinal reservoir hypothesis which could be used to develop intestinal intervention strategies. These strains pose a zoonotic risk because either they could be transferred directly from birds to humans or they could serve as a genetic pool for ExPEC strains.

scholarly journals Virulence gene profiles of avian pathogenic Escherichia coli isolated from chickens with colibacillosis in Bulawayo, Zimbabwe

2015 ◽  
Vol 82 (1) ◽  
Author(s):  
Joshua Mbanga ◽  
Yvonne O. Nyararai
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Virulence Gene ◽  
Economic Losses ◽  
Avian Pathogenic Escherichia Coli ◽  
Pcr Assay ◽  
E Coli ◽  
Gene Profiles ◽  
Pathogenic Escherichia Coli ◽  
Polymerase Chain

Colibacillosis, a disease caused by avian pathogenic Escherichia coli (APEC), is one of the main causes of economic losses in the poultry industry worldwide. This study was carried out in order to determine the APEC-associated virulence genes contained by E. coli isolates causing colibacillosis in chickens. A total of 45 E. coli isolates were obtained from the diagnostics and research branch of the Central Veterinary Laboratories, Bulawayo, Zimbabwe. These isolates were obtained from chickens with confirmed cases of colibacillosis after postmortem examination. The presence of the iutA, hlyF, ompT, frz, sitD, fimH, kpsM, sitA, sopB, uvrY, pstB and vat genes were investigated by multiplex polymerase chain reaction (PCR) assay. Of the 45 isolates, 93% were positive for the presence of at least one virulence gene. The three most prevalent virulence genes were iutA (80%), fimH (33.3%) and hlyF (24.4%). The kpsM, pstB and ompT genes had the lowest prevalence, having been detected in only 2.2% of the isolates. All 12 virulence genes studied were detected in the 45 APEC isolates. Virulence gene profiles were constructed for each APEC isolate from the multiplex data. The APEC isolates were profiled as 62.2% fitting profile A, 31.1% profile B and 6.7% profile C. None of the isolates had more than seven virulence genes. Virulence profiles of Zimbabwean APEC isolates are different from those previously reported. Zimbabwean APEC isolates appear to be less pathogenic and may rely on environmental factors and stress in hosts to establish infection.

scholarly journals Effects of alphamune G on the performance, serum and haematological parameters of Escherichia coli challenged turkey poults

2020 ◽  
Vol 40 (2) ◽  
pp. 112-121
Author(s):  
S. A. Bolu ◽  
M. T. Adelakun
Keyword(s):  
Escherichia Coli ◽  
Poor Performance ◽  
Positive Control ◽  
Negative Control ◽  
E Coli ◽  
Turkey Poults ◽  
Randomized Design ◽  
Completely Randomized Design ◽  
Improved Performance ◽  
Haematological Indices

A study was conducted to determine the response of Turkey poults to graded levels of Alphamune G (0.00+, 0.03, 0.04, 0.05, 0.06 and 0.00 %-) when challenged with Escherichia coli orally for 7 days. The graded levels were the treatments viz 0.00%+ (positive control), Alphamune G at 0.03, 0.04, 0.05, 0.06% and 0.00%- (negative control; infected without Alphamune G supplementation). Each treatment was allotted 3 replicates of 6 poults. The experiment which was conducted for 56 days employed a completely randomized design. E. coli was isolated from the intestinal digesta of a colisepticaemic chicken. 108 turkey poults were used in this study. Poults were infected with E.coli for 7 days through the drinking water and given the treatment. The performance parameters of Alphamune G supplementation were significantly affected. The cumulative weight, Feed intake and weight gain were highest for turkey poults fed 0.06% Alphamune G supplementation. These values were also directly proportional to the supplementation levels of Alphamune G. The birds given the negative treatment (0.00 %-) had relatively poor performance compared to the other treatments. The specific enzymes studied were significantly affected (p<0.05) by the treatments. ALT and AST were significantly highest for turkey poults fed the negative control. Enzyme values became optimum at 0.05% Alphamune G supplementation. At 0.06% of Alphamune G supplementation, cellular mitigations of the effects of E. coli was measurable. Urea and creatinine were not significantly (p>0.05) influenced by the treatments. Haematological indices such as WBC and specific differential counts (lymphocytes and neutrophils) were affected significantly (P<0.05) by supplemental levels of Alphamune G The Inclusion of Alphamune G at 0.06% in the diets improved performance of turkey poults when challenged with Escherichia coli.

scholarly journals Virulence Factor Gene Profiles of Escherichia coli Isolates from Clinically Healthy Pigs

2006 ◽  
Vol 72 (10) ◽  
pp. 6680-6686 ◽  
Author(s):  
Peter Schierack ◽  
Hartmut Steinrück ◽  
Sylvia Kleta ◽  
Wilfried Vahjen
Keyword(s):  
Escherichia Coli ◽  
Virulence Factor ◽  
Virulence Genes ◽  
Clinical Signs ◽  
Virulence Gene ◽  
Bacterial Populations ◽  
Factor Gene ◽  
E Coli ◽  
Gene Profiles ◽  
Virulence Factor Gene

ABSTRACT Nonpathogenic, intestinal Escherichia coli (commensal E. coli) supports the physiological intestinal balance of the host, whereas pathogenic E. coli with typical virulence factor gene profiles can cause severe outbreaks of diarrhea. In many reports, E. coli isolates from diarrheic animals were classified as putative pathogens. Here we describe a broad variety of virulence gene-positive E. coli isolates from swine with no clinical signs of intestinal disease. The isolation of E. coli from 34 pigs from the same population and the testing of 331 isolates for genes encoding heat-stable enterotoxins I and II, heat-labile enterotoxin I, Shiga toxin 2e, and F4, F5, F6, F18, and F41 fimbriae revealed that 68.6% of the isolates were positive for at least one virulence gene, with a total of 24 different virulence factor gene profiles, implying high rates of horizontal gene transfer in this E. coli population. Additionally, we traced the occurrence of hemolytic E. coli over a period of 1 year in this same pig population. Hemolytic isolates were differentiated into seven clones; only three were found to harbor virulence genes. Hemolytic E. coli isolates without virulence genes or with only the fedA gene were found to be nontypeable by slide agglutination tests with OK antisera intended for screening live cultures against common pathogenic E. coli serogroups. The results appear to indicate that virulence gene-carrying E. coli strains are a normal part of intestinal bacterial populations and that high numbers of E. coli cells harboring virulence genes and/or with hemolytic activity do not necessarily correlate with disease.

scholarly journals Different Escherichia coli B2-ST131 clades (B and C) producing extended-spectrum β-lactamases (ESBL) colonizing residents of Portuguese nursing homes

2017 ◽  
Vol 145 (15) ◽  
pp. 3303-3306 ◽  
Author(s):  
C. RODRIGUES ◽  
E. MACHADO ◽  
S. FERNANDES ◽  
L. PEIXE ◽  
Â. NOVAIS
Keyword(s):  
Escherichia Coli ◽  
Pilot Study ◽  
Clinical Settings ◽  
Clonal Structure ◽  
Carriage Rate ◽  
E Coli ◽  
The North ◽  
Faecal Samples ◽  
M 14

SUMMARYESBL-producing Enterobacteriaceae and particularly Escherichia coli ST131 isolates producing CTX-M enzymes are commonly found colonizing the intestine of nursing home (NH) residents, but ST131 subclonal structure has been scarcely explored in this vulnerable population. Our goal was to perform a pilot study to assess the faecal carriage rate and epidemiological features of ESBL- and/or carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE, respectively) among NH residents. For this purpose, faecal samples from residents at 4 different NHs in the North of Portugal (representing 9·5% of the residents’ population, July 2014) were screened for ESBL-E and/or CPE by phenotypic and genotypic methods. Clonal structure and plasmid typing of ESBL-producing E. coli (ESBL-Ec) was performed by PCR and sequencing. Four ESBL-Ec isolates (2 CTX-M-15/2 CTX-M-14) were found in 20% of the samples, all belonging to the pandemic clonal lineage B2-ST131-O25b:H4. Two different clades were identified, the C2/H30-Rx-virotype C producing CTX-M-15 and an atypical B/H22-like-virotype D5 (producing CTX-M-14 and fluoroquinolone-resistant), firstly described in Portugal. This pilot study highlights the role of NH residents as a source of different ST131 clades, besides emphasizing the importance of E. coli B2-ST131 subtyping in different clinical settings, and understanding the transmission dynamics of the different variants.

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