Sequence Type 131 Clone Research Articles

Prevalence of O25b-ST131 Escherichia coli Clone: Fecal Carriage of Extended-Spectrum β-Lactamase and Carbapenemase-Producing Isolates in Healthy Adults in Tehran, Iran.

Fecal carriage of multidrug-resistant Escherichia coli, particularly sequence type 131 (ST131), is becoming a global concern. This study aimed at determining the prevalence rate and molecular epidemiology of extended-spectrum β-lactamase-producing E. coli (ESBL-Ec), carbapenemase-producing E. coli (CPEc), ceftazidime/avibactam (CAZ/AVI)-resistant E. coli, and ST131 isolates in healthy fecal carriers in Tehran, Iran. Among 540 samples studied, 233 (43.1%) carried ESBL-Ec, with the majority (93.9%) harboring the blaCTX-M. The carriage rate of CPEc was 2.5% (n = 14/540), and blaNDM gene was the predominant carbapenemase gene. Most CPEc isolates (n = 11/14) was shown to be resistant to CAZ/AVI. Among ESBL-Ec/CPEc, 7.3% (n = 17/233) belonged to E. coli ST131 clone, which was identified by polymerase chain reaction and confirmed by multilocus sequence typing. The ST131 isolates genetically typed by pulsed-field gel electrophoresis were heterogeneous and four different plasmids were detected by plasmid typing, with the IncFIA/FIB being the major type. Our findings disclose that the presence of carbapenem-resistant ST131 isolates, which are also resistant to CAZ/AVI, contributes to the spread of resistant strains in the community. Therefore, screening and monitoring of such resistant clone in healthy people is necessary.

Seven-year surveillance of the prevalence of antimicrobial-resistant Escherichia coli isolates, with a focus on ST131 clones, among healthy people in Osaka, Japan

ObjectivesEscherichia coli (E. coli) is an indicator of antimicrobial resistance, and some strains of E. coli cause infectious diseases. E. coli sequence type 131 (ST131) – a global antimicrobial-resistant pandemic E. coli clone – is frequently detected in clinical specimens. Antimicrobial-resistant bacteria are monitored via national surveillance in clinical settings; however, monitoring information in non-clinical settings is limited. This study elucidated antimicrobial resistance trends of E. coli and dissemination of ST131 among healthy people in non-clinical settings. MethodsThis study collected 517 E. coli isolates from healthy people in Osaka, Japan, between 2013 and 2019. It analysed antimicrobial susceptibility of the isolates and detected the bla and mcr genes in ampicillin-resistant and colistin-resistant isolates, respectively, and the ST131 clone. ResultsAntimicrobial resistance rates of the bacteria isolated from healthy people in non-clinical settings were lower than for those in clinical settings. The resistance of the isolates to cefotaxime (4.4%) and ciprofloxacin (13.5%) gradually increased during the study period. In 23 cefotaxime-resistant isolates, the most frequent bla genes belonged to the blaCTX-M-9 group, followed by blaCTX-M-1 goup, blaTEM and blaCMY-2. One mcr-1-harbouring colistin-resistant isolate was detected in 2016. The incidence of the E. coli O25b-ST131 clone was approximately 5% until 2015 and 10% after 2016. ConclusionBoth ciprofloxacin resistance and O25b-ST131 clone frequency increased during the study period. Antimicrobial-resistant bacteria gradually spread in healthy people in non-clinical settings; one reason behind this spread was dissemination of global antimicrobial-resistant pandemic clones.

Clonal diversity, virulence genes content and subclone status of Escherichia coli sequence type 131: comparative analysis of E. coli ST131 and non-ST131 isolates from Iran

BackgroundThe Escherichia coli sequence type 131 (ST131) is a well established clone causing significant extraintestinal infections worldwide. However, no studies have been reported the phenotypic and molecular traits of ST131 isolates in comparison to other clones of E. coli from Iran. So, we determined the differences between 69 ST131 strains collected during a one year surveillance study and 84 non-ST131 isolates, including 56 clinical fluoroquinolone resistant and 28 broiler colibacillosis isolates in terms of clonality and genetic background.ResultsST131 isolates were associated with phylogroup B2 (68 out of 69 isolates, 98.4%), while clinical non-ST131 and fluoroquinolone resistant broiler isolates mainly belonged to phylogroup A. The highest virulence score was observed in ST131 clone, while they showed less diversity in virulence profiles than other clinical isolates. Almost all of the ST131 isolates (95.6%) were ExPEC and had the highest virulence scores, but their resistance scores were less than clinical non-ST131 isolates. Broiler isolates showed higher prevalence of ExPEC-associated virulence genes and CTX-M-G1/G9 resistance determinants as compared to clinical non-ST131 isolates. While blaOXA-48/NDM carbapenemases were mostly found in ST131 clone, resistance rate against ertapenem was higher among clinical non-ST131 strains. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, followed by non-ST131 and broiler isolates.ConclusionsST131 isolates possess the ability to make a balance between clonality and extent of resistance/virulence genes content, so this phenomenon gives a fitness advantage over other E. coli clones. The broilers E. coli population poses a potential zoonotic risk which could be transmitted to the community through the food chain. A number of factors are involved in the dissemination of and infections due to ST131 clone.

Risk factors and molecular features of sequence type (ST) 131 extended-Spectrum-\u03b2-lactamase-producing Escherichia coli in community-onset female genital tract infections

BackgroundEscherichia coli (E. coli) is known to cause urinary tract infection (UTI) and meningitis in neonates, as well as existing as a commensal flora of the human gut. Extended-spectrum β-lactamase (ESBL)-producing E. coli has increased in the community with the spread of CTX-M type ESBL-producing sequence type 131 (ST131)-O25-H30Rx E. coli clone. The role of ESBL-producing E. coli in female genital tract infection has not been elucidated. The clinical and molecular features of E. coli isolated from community-onset female genital tract infections were evaluated to elucidate the current burden in the community, focusing on the highly virulent and multidrug-resistant ST131 clone.MethodsWe collected and sequenced 91 non-duplicated E. coli isolates from the female genital tract of 514 patients with community-onset vaginitis. ESBL genotypes were identified by PCR and confirmed to be ESBL-producers by sequencing methods. ST131 clones were screened by PCR for O16-ST131 and O25b-ST131. Pulsed-field gel electrophoresis (PFGE) and PCR-based replicon typing (PBRT) were conducted in ESBL producers. Independent clinical risk factors associated with acquiring ESBL-producing E. coli and ST131 clone were analyzed using multivariate logistic regression analysis.ResultsOf the 514 consecutive specimens obtained from the infected female genital tract, 17.7% (91/514) had E. coli infection, of which 19.8% (18/91) were ESBL producers. CTX-M-15 was the most common type (n = 15). O25b-ST131 and O16-ST131 clones accounted for 15.4% (14/91) and 6.6% (6/91), respectively. In plasmid analysis, ten isolates succeeded in conjugation and plasmid types were IncFII (n = 4), IncFI (n = 3), IncI1-Iγ (n = 3) with one non-typable case. Compared to ESBL-nonproducing E. coli, ESBL-producing E. coli acquisition was strongly associated with recurrent vaginitis (OR 40.130; 95% CI 9.980–161.366), UTI (OR 18.915; 95% CI 5.469–65.411), and antibiotics treatment (OR 68.390; 95% CI 14.870–314.531).ConclusionA dominant clone of CTX-M type ESBL-producing E. coli in conjugative plasmids seems to be circulating in the community and considerable number of ST131 E. coli in the genital tract of Korean women was noted. Sustained monitoring of molecular epidemiology and control of the high-risk group is needed to prevent ESBL-producing E. coli from spreading throughout the community.

Prevalence and characteristics of ST131 clone among unselected clinical Escherichia coli in a Chinese university hospital

BackgroundEscherichia coli clinical sequence type 131 (ST131) has emerged as an extensively antimicrobial resistant E. coli clonal group in recent years throughout the world. The aim of this study was to investigate the prevalence and molecular characteristics of ST131 among unselected E. coli clinical isolates in a Chinese university hospital.MethodsSeven hundred consecutive E. coli isolates were collected at a Chinese university hospital between 2014 and 2015. Isolates belonging to ST131 were identified by PCR and multilocus sequence typing (MLST), and then characterized for antibiotic resistance, CTX-M-type extended-spectrum β-lactamase genes, fluoroquinolone resistance genes, O types, phylogenetic groups, virulence factors and PFGE patterns.ResultsOverall, 83 (11.6%) isolates were identified as ST131 group. The H30 lineage accounted for 53 (63.9%) of the ST131 isolates, including 13 H30-Rx and 40 H30 non-Rx. The remaining 30 isolates belonged to H41 lineage. Two O types were identified in this study: O25b (66.3%) and O16 (33.7%). Compared with O25b-B2-ST131 isolates, O16-B2-ST131 isolates harbored less virulence factors of adhesins. ST131 H30 Rx isolates had significantly higher virulence score than those of other isolates. O16-B2-ST131 isolates were shown to have a lower resistance to quinolones than O25b-B2-ST131 isolates. 5 nonsynonymous mutations (GyrA S83 L, D87N, ParC S80I, E84V and ParE I529L) were strongly associated with ST131 H30 and O25b isolates. Results of PFGE demonstrated that these isolates were classified into 68 pulsotypes and these subtypes were grouped into 23 different PFGE clusters using 70% similarity cut-off value.ConclusionsThis is the first study to reveal the prevalence and molecular characteristic of ST131 clonal group among consecutive clinical E. coli isolates in China. Our findings demonstrated that ST131 lineage accounts for a small proportion of clinical E. coli isolates in China, which included two major groups: O25b-B2-ST131 and O16-B2-ST131. Our results implies that O16-B2-ST131 subclone may be an important type of E. coli ST 131 in China, which suggests that future studies should not ignore such clone in this country.

First Report of Prevalence of CTX-M-15-Producing Escherichia coli O25b/ST131 from Iran.

The emergence of Escherichia coli sequence type 131 (ST131) as a multidrug-resistant and virulent pathogen represents a major challenge to public health globally. Recently, the O25b/ST131 E. coli producing CTX-M-15 with high virulence potential has been reported worldwide, but has received little attention in Iran. This study is the first in Iran to specifically determine the spread of the O25b/ST131 clone producing CTX-M-15 among E. coli isolates belonging to the B2 phylogenetic group. ST131 clone in phylogenetic group B2 was detected based on PCR detection of ST131-specific single-nucleotide polymorphisms in mdh and gyrB. O25b/ST131 E. coli clone was confirmed utilizing O25b/ST131 clone allele-specific PCR for the pabB gene. All group B2 E. coli isolates were characterized based on antibiotic susceptibility, extended-spectrum β-lactamase (ESBL) enzymes, and virulence traits. Our results demonstrated that 38 out of the 154 B2 group isolates (24.7%) were identified as belonging to the ST131 clone. Furthermore, of these, 28 isolates (73.6%) were detected as O25b/ST131 clone. Antibiotic resistance of ST131 E. coli isolates to ciprofloxacin, gentamicin, cefotaxime, and aztreonam was significantly higher than non-ST131 isolates. Almost all of the O25b/ST131 isolates with the ability for ESBL production were reported as CTX-M-15 producing (95.5%). Our results showed that the most prevalent virulence trait in ST131 clone was ompT (94.7%). This study is the first to report the prevalence of the CTX-M-15-producing O25b/ST131 E. coli in Iran. Our findings reinforce the surveillance of dissemination of ST131 E. coli clone as a major drug-resistant pathogen and an important new public health threat.

Virulence Factors of <i>E. coli</i> ST131 and Its H30 and H30Rx Subclones Among Extended-Spectrum Beta-Lactamase Producing Isolates

<i>Escherichia coli</i> sequence type 131 (ST131) is a pandemic clone causing predominantly community and hospital-onset antimicrobial-resistant infections. Recently, H30-Rx subclone of <i>E. coli</i> has been disseminated among ST131 strains in combination with beta lactamase subtype CTX-15that may play a role in the prevalence of antibiotic resistance among <i>E. coli</i> strains that cause extra-intestinal infections. This study has been done to investigate the virulence factors of ST131 with their subclones: H30-Rx and non H30-Rx strains. A hundred <i>E. coli</i> isolates which were isolated from different clinical samples were collected from K.R hospital, Mysore. Polymerase chain reaction (PCR) method was used to investigate 19 of the virulence factors among <i>E. coli</i> stains. Out of 100 <i>E. coli</i> strains, 87 of the isolates belonged to ST131, 24 isolates belonged to H30 subclone, and 22/24 (91.7%) belonged to H30-Rx subcolne. ST131 strains harbored high virulence factors more than non ST131 strains and the differences between them were significant for <i>papC</i>, <i>papEF</i> and <i>fyuA</i> genes. All H30-Rx strains were positive for <i>iutA</i> and <i>fimH</i>, however, 95.5% and 81.8% of H30-Rx strains were positive for <i>fyuA</i> and <i>kpsMII</i> respectively and the differences between H30-Rx and non H30-Rx strains were significant for those genes. There are no more reports about H30 and H30-Rx subclones of ST131 <i>E. coli</i> in India. Further studies should be done to investigate the prevalence of ST131 in different places in India and to highlight the other virulence factors to control the dissemination of ST131 clone.

Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone.

ABSTRACTEscherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome of E. coli EC958, the most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081 methylated adenines in the genome of EC958 discovered three m6A methylation motifs that have not been described previously. Subsequent SMRT sequencing of isogenic knockout mutants identified the two type I methyltransferases (MTases) and one type IIG MTase responsible for m6A methylation of novel recognition sites. Although both type I sites were rare, the type IIG sites accounted for more than 12% of all methylated adenines in EC958. Analysis of the distribution of MTase genes across 95 ST131 genomes revealed their prevalence is highly conserved within the ST131 lineage, with most variation due to the presence or absence of mobile genetic elements on which individual MTase genes are located.

Clinical Features and Treatment Outcomes of Bloodstream Infections Caused by Extended-Spectrum β-Lactamase-Producing Escherichia coli Sequence Type 131.

Despite the remarkable emergence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli sequence type 131 (ST131), the clinical features and outcomes of infections caused by ST131 remain poorly described. From 2011 to 2012, we collected ESBL-producing E. coli isolates from patients with bloodstream infections in 13 hospitals in Korea and compared clinical characteristics and outcomes between ST131 and non-ST131 clones. Of the 110 ESBL-producing isolates, the most common ST was ST131 (30.9%). Multivariate analysis showed that recent operation was the only variable associated with the ST131 clone; other comorbid conditions and clinical features were similar between ST131 and non-ST131 clones. CTX-M-14 and CTX-M-15 were the predominant types of ESBLs, and CTX-M-15 was significantly associated with ST131. The rate of nonsusceptibility to ciprofloxacin was higher in ST131 than in non-ST131 clones (94.1% vs. 75.0%). No significant differences in 30-day mortality rates were found between ST131 and non-ST131 clones. Multivariate analysis revealed that older age (odds ratio [OR]=5.39, 95% confidence interval [CI] 1.22-23.89; p=0.027), nosocomial infection (OR=4.81, 95% CI 1.15-20.15; p=0.032), and higher Pitt bacteremia score (OR=7.26, 95% CI 1.41-37.42; p=0.018) were independent risk factors for 30-day mortality. The ESBL-producing E. coli ST131 clone has emerged and disseminated in Korea. Our findings reveal similarities in clinical and demographic characteristics between ST131 and non-ST131 clones. Although a more resistant profile has been detected in ST131, patients with the ST131 clone did not exhibit a higher mortality rate.

Complete Sequence of a KPC-Producing IncN Multidrug-Resistant Plasmid from an Epidemic Escherichia coli Sequence Type 131 Strain in China

We report here the nucleotide sequence of a novel blaKPC-2-harboring incompatibility group N (IncN) plasmid, pECN580, from a multidrug-resistant Escherichia coli sequence type 131 (ST131) isolate recovered from Beijing, China. pECN580 harbors β-lactam resistance genes blaKPC-2, blaCTX-M-3, and blaTEM-1; aminoglycoside acetyltransferase gene aac(6')-Ib-cr; quinolone resistance gene qnrS1; rifampin resistance gene arr-3; and trimethoprim resistance gene dfrA14. The emergence of a blaKPC-2-harboring multidrug-resistant plasmid in an epidemic E. coli ST131 clone poses a significant potential threat in community and hospital settings.

The Epidemic of Extended-Spectrum-β-Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H 30-Rx

ABSTRACTThe Escherichia coli sequence type 131 (ST131) clone is notorious for extraintestinal infections, fluoroquinolone resistance, and extended-spectrum beta-lactamase (ESBL) production, attributable to a CTX-M-15-encoding mobile element. Here, we applied pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing to reconstruct the evolutionary history of the ST131 clone. PFGE-based cluster analyses suggested that both fluoroquinolone resistance and ESBL production had been acquired by multiple ST131 sublineages through independent genetic events. In contrast, the more robust whole-genome-sequence-based phylogenomic analysis revealed that fluoroquinolone resistance was confined almost entirely to a single, rapidly expanding ST131 subclone, designated H30-R. Strikingly, 91% of the CTX-M-15-producing isolates also belonged to a single, well-defined clade nested within H30-R, which was named H30-Rx due to its more extensive resistance. Despite its tight clonal relationship with H30Rx, the CTX-M-15 mobile element was inserted variably in plasmid and chromosomal locations within the H30-Rx genome. Screening of a large collection of recent clinical E. coli isolates both confirmed the global clonal expansion of H30-Rx and revealed its disproportionate association with sepsis (relative risk, 7.5; P < 0.001). Together, these results suggest that the high prevalence of CTX-M-15 production among ST131 isolates is due primarily to the expansion of a single, highly virulent subclone, H30-Rx.

Escherichia coli Bloodstream Infection After Transrectal Ultrasound-Guided Prostate Biopsy: Implications of Fluoroquinolone-Resistant Sequence Type 131 as a Major Causative Pathogen

Transrectal ultrasound-guided (TRUS) prostate biopsy is a commonly performed procedure, and fluoroquinolones are the most frequently given prophylactic antimicrobials. In the context of increasing fluoroquinolone resistance, and the international emergence of fluoroquinolone-resistant sequence type 131 (ST131) Escherichia coli, we describe a large series of E. coli bacteremia after TRUS biopsy. All male patients admitted with community-onset (CO) E. coli bacteremia from January 2006 through December 2010 were included. Patient characteristics, treatment outcomes, and rates of antimicrobial resistance were compared between patients with TRUS biopsy-related bacteremia and other male patients with CO E. coli bacteremia. Molecular typing was performed on E. coli isolates to determine phylogenetic group. A total of 258 male patients were admitted with CO E. coli bacteremia. Of these, 47 patients (18%) were admitted after TRUS biopsy. Patients who had undergone TRUS biopsy were twice as likely to require intensive care admission (25% vs 12%) and had significantly higher rates of resistance to gentamicin (43%), trimethoprim-sulphamethoxazole (60%), and ciprofloxacin (62%) as well as all 3 agents in combination (19%). Thirty-six percent of post-TRUS biopsy patients did not receive active empirical antibiotic therapy. The ST131 clone accounted for 41% of all E. coli isolates after TRUS biopsy. E. coli bacteremia can be a life-threatening complication of TRUS biopsy. Infecting strains are frequently multidrug-resistant and resistant to common empirical antibiotic agents. E. coli ST131 is an important cause of sepsis after TRUS biopsy. Further studies should evaluate colonization with fluoroquinolone-resistant E. coli as a risk factor for postbiopsy sepsis.

Bacteremia Caused by Extended-Spectrum-β-Lactamase-Producing Escherichia coli Sequence Type ST131 and Non-ST131 Clones: Comparison of Demographic Data, Clinical Features, and Mortality

Escherichia coli producing the highly virulent, multidrug-resistant, CTX-M-15 extended-spectrum β-lactamase (ESBL), sequence type 131 (ST131), has emerged on three continents since the late 2000s. We described the molecular epidemiology, clinical features, and outcome of ESBL-producing E. coli bacteremia in Taiwan from 2005 to 2010. This study aims to determine whether the risk factors, clinical features, and outcomes of the ST131 isolate differ from those of non-ST131 isolates. From 2005 to 2010, we collected 122 nonduplicated, consecutive, ESBL-producing E. coli isolates from bloodstream infections in a 1,200-bed hospital in Taiwan. Isolates were characterized using multilocus sequence typing. Demographic data, clinical features, and outcomes were collected from medical chart records. Thirty-six (29.5%) patients with bacteremia with ESBL-producing E. coli ST131 were identified. Patients with clone ST131 were more likely to have secondary bacteremia and noncatheterized urinary tract infections (P < 0.05). Secondary bacteremia (odds ratio [OR], 5.05; 95% confidence interval [CI], 1.08 to 23.56) and urinary catheter nonuse (OR, 3.77; 95% CI, 1.17 to 12.18) were independent risk factors for the ST131 clone after adjustment. Mortality rates at day 28 were similar in ST131 and non-ST131 populations. Independent risk factors predicting mortality at day 28 included malignancy, shock, and hospital-acquired bacteremia. In ESBL-producing E. coli bloodstream infections, the ST131 clone was not associated with health-care-associated risk factors, such as urinary catheter use or antibiotic exposure. Although highly virulent and multidrug resistant, the ST131 clone was not associated with higher mortality than non-ST131 clones.

Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain

Escherichia coli sequence type 131 (ST131) is a worldwide pandemic clone, causing predominantly community-onset antimicrobial-resistant infection. Its pandemic spread was identified in 2008 by utilizing multilocus sequence typing (MLST) of CTX-M-15 extended-spectrum β-lactamase-producing E. coli from three continents. Subsequent research has confirmed the worldwide prevalence of ST131 harbouring a broad range of virulence and resistance genes on a transferable plasmid. A high prevalence of the clone (∼30%-60%) has been identified amongst fluoroquinolone-resistant E. coli. In addition, it potentially harbours a variety of β-lactamase genes; most often, these include CTX-M family β-lactamases, and, less frequently, TEM, SHV and CMY β-lactamases. Our knowledge of ST131's geographical distribution is incomplete. A broad distribution has been demonstrated amongst antimicrobial-resistant E. coli from human infection in Europe (particularly the UK), North America, Canada, Japan and Korea. High rates are suggested from limited data in Asia, the Middle East and Africa. The clone has also been detected in companion animals, non-companion animals and foods. The clinical spectrum of disease described is similar to that for other E. coli, with urinary tract infection predominant. This can range from cystitis to life-threatening sepsis. Infection occurs in humans of all ages. Therapy must be tailored to the antimicrobial resistance phenotype of the infecting isolate and the site of infection. Phenotypic detection of the ST131 clone is not possible and DNA-based techniques, including MLST and PCR, are described.