scholarly journals The Clonal Distribution and Diversity of Extraintestinal Escherichia coli Isolates Vary According to Patient Characteristics

2013 ◽  
Vol 57 (12) ◽  
pp. 5912-5917 ◽  
Author(s):  
Ritu Banerjee ◽  
Brian Johnston ◽  
Christine Lohse ◽  
Sujay Chattopadhyay ◽  
Veronika Tchesnokova ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Epidemiological Data ◽  
Patient Characteristics ◽  
The Elderly ◽  
Content Type ◽  
E Coli ◽  
Clonal Distribution ◽  
Midwest Region ◽  
Unselected Population ◽  
Sequence Types

ABSTRACTThe clonal distribution ofEscherichia coliacross an unselected population in the current era of widespread antimicrobial resistance is incompletely defined. In this study, we used a newly described clonal typing strategy based on sequencing offumCandfimH(i.e., CH typing) to infer multilocus sequence types (STs) for 299 consecutive, nonduplicate extraintestinalE. coliisolates from all cultures submitted to Olmsted County, MN, laboratories in February and March 2011 and then compared STs with epidemiological data. Forty-seven different STs were identified, most commonly ST131 (27%), ST95 (11%), ST73 (8%), ST127 (6%), and ST69 (5%). Isolates from these five STs comprised two-thirds of health care-associated (HA) isolates but only half of community-associated (CA) isolates. ST131 was represented overwhelmingly (88%) by a single recently expanded H30 subclone, which was the most extensively antimicrobial-resistant subclone overall and was especially predominant in HA infections and among adults >50 years old. In contrast, among patients 11 to 50 years old, ST69, -95, and -73 were more common. Because of the preponderance of the H30 subclone of ST131, ST diversity was lower among HA than CA isolates, and among antimicrobial-resistant than antimicrobial-susceptible isolates, which otherwise had similar ST distributions. In conclusion, in this U.S. Midwest region, the distribution and diversity of STs among extraintestinalE. coliclinical isolates vary by patient age, type of infection, and resistance phenotype. ST131 predominates among young children and the elderly, HA infections, and antimicrobial-resistant isolates, whereas other well-known pathogenic lineages are more common among adolescents and young adults, CA infections, and antimicrobial-susceptible isolates.

scholarly journals Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity

2021 ◽  
Vol 12 (1) ◽  
pp. 123-137
Author(s):  
Carolina Sabença ◽  
Gilberto Igrejas ◽  
Patrícia Poeta ◽  
Frédéric Robin ◽  
Richard Bonnet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Epidemiological Data ◽  
Generation Cephalosporin ◽  
Wild Animals ◽  
Variable Regions ◽  
E Coli ◽  
Wild Fauna ◽  
Long Read ◽  
Sequence Types ◽  
Animal Isolates

Objectives. Epidemiological data concerning third-generation cephalosporin (3GC) resistance in wild fauna are scarce. The aim of this study was to characterize the resistance genes, their genetic context, and clonal relatedness in 17 Escherichia coli resistant to 3GC isolated from wild animals. Methods. The isolates were characterized by short-read whole genome sequencing, and long-read sequencing was used for the hybrid assembly of plasmid sequences. Results. The 3GC resistance gene most identified in the isolates was the extended-spectrum β-lactamases (ESBL)-encoding gene blaCTX-M-1 (82.3%), followed by blaCTX-M-32 (5.9%), blaCTX-M-14 (5.9%), and blaSHV-12 (5.9%). E. coli isolates mainly belonged to the sequence types (STs) rarely reported from humans. The single nucleotide polymorphism (SNP)-based typing showed that most E. coli genomes from wild animals (wild boars, birds of prey, and buzzards) formed clonal clusters (<5 SNPs), showing a clonal dissemination crossing species boundaries. blaCTX-M-1-harboring IncI1-ST3 plasmid was the predominant ESBL-encoding plasmid (76.4%) in wild animal isolates. Plasmid comparison revealed a 110-kb self-transferable plasmid consisting of a conserved backbone and two variable regions involved in antimicrobial resistance and in interaction with recipient cells during conjugation. Conclusion. Our results highlighted the unexpected clonal dissemination of blaCTX-M-1-encoding clones and the complicity of IncI1-ST3 plasmid in the spread of blaCTX-M-1 within wild fauna.

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 Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

2019 ◽  
Vol 32 (3) ◽  
Author(s):  
Amee R. Manges ◽  
Hyun Min Geum ◽  
Alice Guo ◽  
Thaddeus J. Edens ◽  
Chad D. Fibke ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Surveillance Systems ◽  
Inclusion Criteria ◽  
Prevention Strategies ◽  
Content Type ◽  
E Coli ◽  
Treatment And Prevention ◽  
Pathogenic Escherichia Coli ◽  
Sequence Types ◽  
Study Inclusion

SUMMARY Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.

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 Molecular Diversity and Plasmid Analysis of KPC-Producing Escherichia coli

2016 ◽  
Vol 60 (7) ◽  
pp. 4073-4081 ◽  
Author(s):  
Kalyan D. Chavda ◽  
Liang Chen ◽  
Michael R. Jacobs ◽  
Robert A. Bonomo ◽  
Barry N. Kreiswirth
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Rapid Evolution ◽  
The United States ◽  
Content Type ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Plasmid Analysis ◽  
Replication Gene ◽  
Sequence Types

ABSTRACTThe emergence and spread ofKlebsiella pneumoniaecarbapenemase (KPC) amongEnterobacteriaceaepresents a major public health threat to the world. Although not as common as inK. pneumoniae, KPC is also found inEscherichia colistrains. Here, we genetically characterized 9 carbapenem-resistantE. colistrains isolated from six hospitals in the United States and completely sequenced theirblaKPC-harboring plasmids. The nine strains were isolated from different geographical locations and belonged to 8 differentE. colisequence types. SevenblaKPC-harboring plasmids belonged to four different known incompatibility groups (IncN, -FIA, -FIIK2, and -FIIK1) and ranged in size from ∼16 kb to ∼241 kb. In this analysis, we also identified two plasmids that have novel replicons: (i) pBK28610, which is similar to p34978-3 with an insertion of Tn4401b, and (ii) pBK31611, which does not have an apparent homologue in the GenBank database. Moreover, we report the emergence of a pKP048-like plasmid, pBK34397, inE. coliin the United States. Meanwhile, we also found examples of interspecies spread ofblaKPCplasmids, as pBK34592 is identical to pBK30683, isolated fromK. pneumoniae. In addition, we discovered examples of acquisition (pBK32602 acquired an ∼46-kb fragment including a novel replication gene, along with Tn4401band other resistance genes) and/or loss (pKpQIL-Ec has a 14.5-kb deletion compared to pKpQIL-10 and pBK33689) of DNA, demonstrating the plasticity of these plasmids and their rapid evolution in the clinic. Overall, our study shows that the spread ofblaKPC-producingE. coliis largely due to horizontal transfer ofblaKPC-harboring plasmids and related mobile elements into diverse genetic backgrounds.

scholarly journals Limited Transmission ofblaCTX-M-9-Type-Positive Escherichia coli between Humans and Poultry in Vietnam

2015 ◽  
Vol 59 (6) ◽  
pp. 3574-3577 ◽  
Author(s):  
Shuhei Ueda ◽  
Bui Thi Kim Ngan ◽  
Bui Thi Mai Huong ◽  
Itaru Hirai ◽  
Le Danh Tuyen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antibiotic Resistance Genes ◽  
Phylogenetic Group ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Vietnamese Community ◽  
Group Compositions ◽  
Sequence Types

ABSTRACTWe examined whetherEscherichia coliisolates that produce CTX-M-9-type extended-spectrum β-lactamases (ESBL) are transferred between humans and chickens in a Vietnamese community. The phylogenetic group compositions, sequence types, antimicrobial resistance profiles, the prevalence of plasmid antibiotic resistance genes, and the plasmid replicon types generally differed between the human and chickenE. coliisolates. Our results suggest that transmission of theblaCTX-M-9-positiveE. colibetween humans and poultry was limited.

scholarly journals Clinical Epidemiology and Molecular Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli in Nepal: Characteristics of Sequence Types 131 and 648

2015 ◽  
Vol 59 (6) ◽  
pp. 3424-3432 ◽  
Author(s):  
Jatan Bahadur Sherchan ◽  
Kayoko Hayakawa ◽  
Tohru Miyoshi-Akiyama ◽  
Norio Ohmagari ◽  
Teruo Kirikae ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Clinical Epidemiology ◽  
University Teaching ◽  
Drug Resistant ◽  
Content Type ◽  
Acquired Drug Resistance ◽  
E Coli ◽  
Extended Spectrum ◽  
Sequence Types

ABSTRACTRecently, CTX-M-type extended-spectrum-β-lactamase (ESBL)-producingEscherichia colistrains have emerged worldwide. In particular,E. coliwith O antigen type 25 (O25) and sequence type 131 (ST131), which is often associated with the CTX-M-15 ESBL, has been increasingly reported globally; however, epidemiology reports on ESBL-producingE. coliin Asia are limited. Patients with clinical isolates of ESBL-producingE. coliin the Tribhuvan University teaching hospital in Kathmandu, Nepal, were included in this study. Whole-genome sequencing of the isolates was conducted to analyze multilocus sequence types, phylotypes, virulence genotypes, O25b-ST131 clones, and distribution of acquired drug resistance genes. During the study period, 105 patients with ESBL-producingE. coliisolation were identified, and the majority (90%) of these isolates were CTX-M-15 positive. The most dominant ST was ST131 (n= 54; 51.4%), followed by ST648 (n= 15; 14.3%). All ST131 isolates were identified as O25b-ST131 clones, subclone H30-Rx. Three ST groups (ST131, ST648, and non-ST131/648) were compared in further analyses. ST648 isolates had a proportionally higher resistance to non-β-lactam antibiotics and featured drug-resistant genes more frequently than ST131 or non-ST131/648 isolates. ST131 possessed the most virulence genes, followed by ST648. The clinical characteristics were similar among groups. More than 38% of ESBL-producingE. coliisolates were from the outpatient clinic, and pregnant patients comprised 24% of ESBL-producingE. colicases. We revealed that the high resistance of ESBL-producingE. colito multiple classes of antibiotics in Nepal is driven mainly by CTX-M-producing ST131 and ST648. Their immense prevalence in the communities is a matter of great concern.

scholarly journals The cnf1 gene is associated to an expanding Escherichia coli ST131 H30Rx/C2 sublineage and confers a competitive advantage for host colonization

2021 ◽  
Author(s):  
Landry Laure TSOUMTSA MEDA ◽  
Luce LANDRAUD ◽  
Serena PETRACCHINI ◽  
Stéphane DESCORPS-DECLERE ◽  
Emeline PERTHAME ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gastrointestinal Tract ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Clinical Strain ◽  
Host Colonization ◽  
E Coli ◽  
Clonal Distribution ◽  
Cytotoxic Necrotizing Factor 1 ◽  
Sequence Types

Epidemiological projections point to acquisition of ever-expanding multidrug resistance (MDR) by Escherichia coli, a commensal of the digestive tract acting as a source of urinary tract pathogens. We performed a high-throughput genetic screening of predominantly clinical E. coli isolates from wide geographical origins. This revealed a preferential distribution of the Cytotoxic Necrotizing Factor 1 (CNF1)-toxin encoding gene, cnf1, in four sequence types encompassing the pandemic E. coli MDR lineage ST131. This lineage is responsible for a majority of extraintestinal infections that escape first-line antibiotic treatment and has known enhanced capacities to colonize the gastrointestinal tract (GIT). Statistical modeling uncovered a dominant global expansion of cnf1-positive strains within multidrug-resistant ST131 subclade H30Rx/C2. Despite the absence of phylogeographical signals, cnf1-positive isolates adopted a clonal distribution into clusters on the ST131-H30Rx/C2 phylogeny, sharing a similar profile of virulence factors and the same cnf1 allele. Functional analysis of the cnf1-positive clinical strain EC131GY ST131-H30Rx/C2, established that a cnf1-deleted EC131GY is outcompeted by the wildtype strain in a mouse model of competitive infection of the bladder while both strains behave similarly during monoinfections. This points for positive selection of cnf1 during UTI rather than urovirulence. Wildtype EC131GY also outcompeted the mutant when concurrently inoculated into the gastrointestinal tract, arguing for selection within the gut. Whatever the site of selection, these findings support that the benefit of cnf1 enhancing host colonization by ST131-H30Rx/C2 in turn drives a worldwide dissemination of the cnf1 gene together with extended spectrum of antibiotic resistance genes.

scholarly journals Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population

2021 ◽  
Vol 7 (5) ◽  
Author(s):  
Frédéric Auvray ◽  
Alexandre Perrat ◽  
Yoko Arimizu ◽  
Camille V. Chagneau ◽  
Nadège Bossuet-Greif ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Whole Genome Sequence ◽  
Active Metabolites ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Sequence Types ◽  
Trna Locus ◽  
Integrative And Conjugative Element

The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E. coli isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the E. coli population, while preserving its functionality.

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.

Sign in / Sign up

Export Citation Format

Share Document