scholarly journals Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular-epidemiological study

2021 ◽  
Author(s):  
Elita Jauneikaite ◽  
Kate Honeyford ◽  
Oliver Blandy ◽  
Mia Mosavie ◽  
Max Pearson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Length Of Stay ◽  
Single Agent ◽  
Bloodstream Infections ◽  
Outcome Data ◽  
Sequence Type ◽  
Adverse Outcomes ◽  
Beta Lactam ◽  
E Coli ◽  
Sequence Types

Background Escherichia coli bloodstream infections have increased rapidly in the UK, for reasons that are unclear. The relevance of highly fit, or multi-drug resistant lineages such as ST131 to overall E. coli disease burden remains to be fully determined. We set out to characterise the prevalence of E. coli multi-locus sequence types (MLST) and determine if these were associated with adverse outcomes in an urban population of E. coli bacteraemia patients. Methods We undertook whole genome sequencing of E. coli blood isolates from all patients with diagnosed E. coli bacteraemia in north-west London from July 2015 to August 2016 and assigned multi-locus sequence types to all isolates. Isolate sequence types were linked to routinely collected antimicrobial susceptibility, patient demographic, and clinical outcome data to explore relationships between the E. coli sequence types, patient factors, and outcomes. Findings A total of 551 E. coli genomes were available for analysis. More than half of these cases were caused by four E. coli sequence types: ST131 (21%), ST73 (15%), ST69 (9%) and ST95 (8%). E. coli genotype ST131-C2 was associated with non-susceptibility to quinolones and third-generation cephalosporins, and also to amoxicillin, augmentin, gentamicin and trimethoprim. An association between the ST131-C2 lineage and longer length-of-stay was detected, although multivariable regression modelling did not demonstrate an association between E. coli sequence type and mortality. However, a number of unexpected associations were identified, including gentamicin non-susceptibility, ethnicity, and sex that might influence mortality and length-of-stay, requiring further research. Interpretation Although E. coli sequence type was associated with antimicrobial non-susceptibility patterns and length-of-stay, we did not find that E. coli sequence type was associated with increased mortality. Where ST131 is prevalent, caution is required when pairing beta-lactam agents with gentamicin or using single agent aminoglycosides.

scholarly journals Survey and Sequence Characterization of Bovine Mastitis-Associated Escherichia coli in Dairy Herds

2020 ◽  
Vol 7 ◽  
Author(s):  
John I. Alawneh ◽  
Ben Vezina ◽  
Hena R. Ramay ◽  
Hulayyil Al-Harbi ◽  
Ameh S. James ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Bovine Mastitis ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Sequence Type ◽  
Genotypic Differences ◽  
Beta Lactam ◽  
Sequence Characterization ◽  
E Coli

Escherichia coli is frequently associated with mastitis in cattle. “Pathogenic” and “commensal” isolates appear to be genetically similar. With a few exceptions, no notable genotypic differences have been found between commensal and mastitis-associated E. coli. In this study, 24 E. coli strains were isolated from dairy cows with clinical mastitis in three geographic regions of Australia (North Queensland, South Queensland, and Victoria), sequenced, then genomically surveyed. There was no observed relationship between sequence type (ST) and region (p = 0.51). The most common Multi Locus Sequence Type was ST10 (38%), then ST4429 (13%). Pangenomic analysis revealed a soft-core genome of 3,463 genes, including genes associated with antibiotic resistance, chemotaxis, motility, adhesion, biofilm formation, and pili. A total of 36 different plasmids were identified and generally found to have local distributions (p = 0.02). Only 2 plasmids contained antibiotic resistance genes, a p1303_5-like plasmid encoding multidrug-resistance (trimethoprim, quaternary ammonium, beta-lactam, streptomycin, sulfonamide, and kanamycin) from two North Queensland isolates on the same farm, while three Victorian isolates from the same farm contained a pCFSAN004177P_01-like plasmid encoding tetracycline-resistance. This pattern is consistent with a local spread of antibiotic resistance through plasmids of bovine mastitis cases. Notably, co-occurrence of plasmids containing virulence factors/antibiotic resistance with putative mobilization was rare, though the multidrug resistant p1303_5-like plasmid was predicted to be conjugative and is of some concern. This survey has provided greater understanding of antibiotic resistance within E. coli-associated bovine mastitis which will allow greater prediction and improved decision making in disease management.

scholarly journals Draft Genomic Sequences of Three Escherichia coli Sequence Type 131 Isolates (H45, H43ii, and H43iii) from Patients in Lagos, Nigeria

2020 ◽  
Vol 9 (17) ◽  
Author(s):  
Yishan Yang ◽  
Christopher H. Sommers ◽  
Eyitayo O. Adenipekun ◽  
Marina Ceruso ◽  
Charlene R. Jackson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Urine Samples ◽  
Genomic Sequences ◽  
Content Type ◽  
E Coli

Escherichia coli sequence type 131 (ST131) has recently emerged as a leading multidrug-resistant pathogen that causes urinary tract and bloodstream infections in humans. Here, we report the draft genomic sequences of three E. coli ST131 isolates, H45, H43ii, and H43iii, from urine samples of patients in Lagos, Nigeria.

scholarly journals Three cases of mcr-1-positive colistin-resistant Escherichia coli bloodstream infections in Italy, August 2016 to January 2017

2017 ◽  
Vol 22 (16) ◽  
Author(s):  
Marta Corbella ◽  
Bianca Mariani ◽  
Carolina Ferrari ◽  
Francesco Comandatore ◽  
Erika Scaltriti ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Bloodstream Infections ◽  
Tertiary Hospital ◽  
Whole Genome ◽  
E Coli ◽  
Sequence Types

We describe three cases of bloodstream infection caused by colistin-resistant Escherichia coli in patients in a tertiary hospital in Italy, between August 2016 and January 2017. Whole genome sequencing detected the mcr-1 gene in three isolated strains belonging to different sequence types (STs). This occurrence of three cases with mcr-1-positive E. coli belonging to different STs in six months suggests a widespread problem in settings where high multidrug resistance is endemic such as in Italy.

scholarly journals High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli

2017 ◽  
Vol 61 (6) ◽  
Author(s):  
Lucas B. Harrison ◽  
Nancy D. Hanson
Keyword(s):  
Escherichia Coli ◽  
Principal Component Analysis ◽  
High Resolution ◽  
High Resolution Melting ◽  
Principal Component ◽  
Cost Effective ◽  
Sequence Type ◽  
Content Type ◽  
E Coli ◽  
Sequence Types

ABSTRACT Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification.

scholarly journals Epidemic Emergence in the United States of Escherichia coli Sequence Type 131-H30 (ST131-H30), 2000 to 2009

2017 ◽  
Vol 61 (8) ◽  
Author(s):  
James R. Johnson ◽  
Stephen Porter ◽  
Paul Thuras ◽  
Mariana Castanheira
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Single Agent ◽  
Temporal Trends ◽  
Virulence Gene ◽  
The United States ◽  
Sequence Type ◽  
Content Type ◽  
E Coli ◽  
Recent Emergence

ABSTRACT The H30 subclone of Escherichia coli sequence type 131 (ST131-H30) has become the leading antimicrobial resistance E. coli lineage in the United States and often exhibits resistance to one or both of the two key antimicrobial classes for treating Gram-negative infections, extended-spectrum cephalosporins (ESCs) and fluoroquinolones (FQs). However, the timing of and reasons for its recent emergence are inadequately defined. Accordingly, from E. coli clinical isolates collected systematically across the United States by the SENTRY Antimicrobial Surveillance Program in 2000, 2003, 2006, and 2009, 234 isolates were selected randomly, stratified by year, within three resistance categories: (i) ESC-reduced susceptibility, regardless of FQ phenotype (ESC-RS); (ii) FQ resistance, ESC susceptible (FQ-R); and (iii) FQ susceptible, ESC susceptible (FQ-S). Susceptibility profiles, phylogroup, ST, ST131 subclone, and virulence genotypes were determined, and temporal trends and between-variable associations were assessed statistically. From 2000 to 2006, concurrently with the emergence of ESC-RS and FQ-R strains, the prevalence of (virulence-associated) phylogroup B2 among such strains also rose dramatically, due entirely to rapid emergence of ST131, especially H30. By 2009, H30 was the dominant E. coli lineage overall (22%), accounting for a median of 43% of all single-agent and multidrug resistance (68% for ciprofloxacin). H30's emergence increased the net virulence gene content of resistant (especially FQ-R) isolates, giving stable overall virulence gene scores despite an approximately 4-fold expansion of the historically less virulent resistant population. These findings define more precisely the timing and tempo of H30's emergence in the United States, identify possible reasons for it, and suggest potential consequences, including more frequent and/or aggressive antimicrobial-resistant infections.

scholarly journals Multiresistant Uropathogenic Escherichia coli from a Region in India Where Urinary Tract Infections Are Endemic: Genotypic and Phenotypic Characteristics of Sequence Type 131 Isolates of the CTX-M-15 Extended-Spectrum-β-Lactamase-Producing Lineage

2012 ◽  
Vol 56 (12) ◽  
pp. 6358-6365 ◽  
Author(s):  
Arif Hussain ◽  
Christa Ewers ◽  
Nishant Nandanwar ◽  
Sebastian Guenther ◽  
Savita Jadhav ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Sequence Type ◽  
Health Concern ◽  
Beta Lactam ◽  
Content Type ◽  
E Coli ◽  
Extended Spectrum ◽  
Tract Infections

ABSTRACTEscherichia colisequence type 131 (O25b:H4), associated with the CTX-M-15 extended-spectrum beta-lactamases (ESBLs) and linked predominantly to the community-onset antimicrobial-resistant infections, has globally emerged as a public health concern. However, scant attention is given to the understanding of the molecular epidemiology of these strains in high-burden countries such as India. Of the 100 clinicalE. coliisolates obtained by us from a setting where urinary tract infections are endemic, 16 ST131E. coliisolates were identified by multilocus sequence typing (MLST). Further, genotyping and phenotyping methods were employed to characterize their virulence and drug resistance patterns. All the 16 ST131 isolates harbored the CTX-M-15 gene, and half of them also carried TEM-1; 11 of these were positive forblaOXAgroups 1 and 12 foraac(6′)-Ib-cr. At least 12 isolates were refractory to four non-beta-lactam antibiotics: ciprofloxacin, gentamicin, sulfamethoxazole-trimethoprim, and tetracycline. Nine isolates carried the class 1 integron. Plasmid analysis indicated a large pool of up to six plasmids per strain with a mean of approximately three plasmids. Conjugation and PCR-based replicon typing (PBRT) revealed that the spread of resistance was associated with the FIA incompatibility group of plasmids. Pulsed-field gel electrophoresis (PFGE) and genotyping of the virulence genes showed a low level of diversity among these strains. The association of ESBL-encoding plasmid with virulence was demonstrated in transconjugants by serum assay. None of the 16 ST131 ESBL-producingE. colistrains were known to synthesize carbapenemase enzymes. In conclusion, our study reports a snapshot of the highly virulent/multiresistant clone ST131 of uropathogenicE. colifrom India. This study suggests that the ST131 genotypes from this region are clonally evolved and are strongly associated with the CTX-M-15 enzyme, carry a high antibiotic resistance background, and have emerged as an important cause of community-acquired urinary tract infections.

scholarly journals 1054. Biofilm Formation Among Escherichia coli Bloodstream Infection Isolates Is Associated With Source of Bacteremia and Bacterial Sequence Type

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S315-S315
Author(s):  
Carolyn Chang ◽  
Felicia Ruffin ◽  
Vance G Fowler ◽  
Joshua T Thaden
Keyword(s):  
Escherichia Coli ◽  
Biofilm Formation ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Clinical Impact ◽  
Sequence Type ◽  
Apache Ii Score ◽  
E Coli ◽  
Biofilm Production ◽  
Bacterial Sequence

Abstract Background The clinical impact of Escherichia coli biofilm formation is unknown. Methods Adults with E. coli bloodstream infections (BSI) were prospectively enrolled from 2002 to 2015. All E. coli isolates were genotyped using Multilocus sequence typing (MLST) and underwent crystal violet biofilm formation assay quantified by absorbance at 540 nm (OD540) in triplicate. Associations between biofilm formation and patient/bacterial characteristics were characterized by t-tests and ANOVA tests. Results Ninety-eight percent (186) of the 189 isolates formed detectable biofilms. Bacterial sequence type (ST) was associated with biofilm formation (P < 0.001), as ST73 (average OD540 = 0.017) and ST393 (average OD540 = 0.016) had higher average biofilm formation while ST69 (average OD540 = 0.007) and ST405 (average OD540 = 0.002) had lower biofilm formation. E. coli isolates with non-multidrug-resistant (non-MDR) phenotype were associated with increased biofilm formation (MDR: average OD540 = 0.006; average non-MDR: OD540 = 0.01; P = 0.003). BSI isolates arising from pneumonia or urine/pyelonephritis were associated with the highest biofilm production (P = 0.04). No associations were identified between biofilm formation and route of infection, APACHE-II score, mortality, or complications of BSI. Conclusion In this prospective study of E. coli BSI isolates, biofilm formation was associated with ST, non-MDR phenotype, and BSI source. Disclosures All authors: No reported disclosures.

scholarly journals Large Fecal Reservoir of Escherichia coli Sequence Type 131-H30 Subclone Strains That Are Shared Within Households and Resemble Clinical ST131-H30 Isolates

2019 ◽  
Vol 221 (10) ◽  
pp. 1659-1668
Author(s):  
Muhanad Mohamed ◽  
Connie Clabots ◽  
Stephen B Porter ◽  
Tricia Bender ◽  
Paul Thuras ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
The Elderly ◽  
Sequence Type ◽  
Clinical Isolates ◽  
Intestinal Colonization ◽  
E Coli ◽  
Household Transmission ◽  
Household Members ◽  
Sequence Types

Abstract Background Emerging antimicrobial-resistant Escherichia coli represent mainly the nested (fluoroquinolone-resistant [FQR]) H30R and H30Rx subclones within sequence type 131 (ST131). Intestinal colonization and within-household transmission may underlie H30R’s emergence. Methods We screened fecal samples from 741 volunteers (383 veterans, 358 household members, including pets) for ST131 and FQR E. coli (FQREC) and used molecular profiling to resolve unique strains. Selected strains underwent PCR-based detection of phylogroups, sequence types (STs), H30, H30Rx, and 53 virulence genes (VGs). Within-household strain sharing was compared with household, host, and bacterial characteristics. Fecal isolates were compared with clinical isolates. Results Colonization prevalence was 5.1% for H30R, 8% for ST131 (67% FQREC), and 10% for FQREC (52% ST131). ST131 isolates exhibited more VGs than non-ST131 isolates. Strain sharing (27% of multisubject households, 18% of corresponding subjects) was associated with the elderly, FQREC, H30R, H30Rx, ST73, and specific VGs. Fecal ST131 and FQREC isolates resembled contemporaneous and historical clinical isolates according to all studied traits. Conclusions Veterans and their human household members commonly carry and extensively share FQREC, predominantly H30R, thereby likely facilitating the ST131 pandemic. Strain sharing corresponds with multiple bacterial characteristics, including FQ resistance and specific VGs, which may promote intestinal colonization and/or host-to-host transmission.

Characterization of Extended-Spectrum β-Lactamase–Producing Escherichia coli Isolates from Pigs and Farm Workers

2016 ◽  
Vol 79 (9) ◽  
pp. 1630-1634 ◽  
Author(s):  
HONGNA ZHANG ◽  
ZHENZHEN ZHAI ◽  
QING LI ◽  
LINGHONG LIU ◽  
SHUYUAN GUO ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Type ◽  
Farm Workers ◽  
Enterobacterial Repetitive Intergenic Consensus ◽  
E Coli ◽  
Extended Spectrum ◽  
Rectal Swabs ◽  
Pig Farm ◽  
Sequence Types

ABSTRACT Food-producing animals can serve as reservoirs for extended-spectrum β-lactamase (ESBL)–producing Escherichia coli. The present study aimed to characterize and compare ESBL-carrying E. coli isolates from both pigs and farm workers. Rectal swabs were obtained from 60 pigs on four pig-fattening farms (15 samples per farm), and rectal swabs were taken from 40 farm workers on these farms (10 samples per farm). ESBL-carrying E. coli isolates from the workers and pigs were characterized by ESBL genotype, antibiotic susceptibility, enterobacterial repetitive intergenic consensus type, and multilocus sequence type. ESBL-producing E. coli was detected in 34 (56.7%) of 60 pigs, and 20.0% (8 of 40) of the farm workers were positive for ESBL-producing E. coli. More importantly, ESBL-producing E. coli isolates with the same β-lactamase genes, antibiotic resistance profiles, enterobacterial repetitive intergenic consensus types, and multilocus sequence types were detected in both pigs and workers on the same pig farm. These findings were suggestive for transfer of ESBL-producing E. coli between animals and humans.

scholarly journals Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections driven by multiple resistance mechanisms across diverse sequence types

2020 ◽  
Author(s):  
Thomas Edwards ◽  
Eva Heinz ◽  
Jon van Aartsen ◽  
Alex Howard ◽  
Paul Roberts ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bloodstream Infections ◽  
Tertiary Hospital ◽  
Resistance Mechanisms ◽  
Clinical Isolates ◽  
Multiple Resistance ◽  
E Coli ◽  
Or Gene ◽  
First Time ◽  
Sequence Types

AbstractResistance to piperacillin/tazobactam in Escherichia coli is usually mediated by mechanisms providing resistance to 3rd generation cephalosporins, such as extended-spectrum β-lactamases and carbapenemases. Recent reports have identified E. coli strains with resistance to piperacillin/tazobactam but susceptibility to 3rd generation cephalosporins, achieved through hyperproduction of penicillinases, but the genetic diversity of this phenotype and the diversity of resistance mechanisms are unknown. We analysed the genomes of 63 clinical isolates of E. coli with this phenotype, isolated between 2014-2017 at a single tertiary hospital in Liverpool, UK. The phenotype was displayed in a broad range of sequence types which, after comparison with a UK-wide collection, reflected the overall diversity of E. coli clinical isolates. Resistance mechanisms were also diverse, and included predicted hyperproduction of penicillinases, either via strong promoters or gene amplification, carriage of inhibitor resistant β-lactamases, and an S133G blaCTX-M-15 mutation detected for the first time in clinical isolates.

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