Molecular epidemiology of extended-spectrum β-lactamase-producing Escherichia coli in the community and hospital in Korea: emergence of ST131 producing CTX-M-15 (original) (raw)
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Journal of microbiology and biotechnology, 2016
The aims of this study were to characterize molecular epidemiological profiles of CTX-M-producing uropathogenic Escherichia coli isolates from a tertiary hospital in Daejeon, Korea, and to investigate the genetic diversity and compare the prevalence of sequence types (STs) in different areas. Extended spectrum β-lactamases (ESBL)-producing E. coli isolated from urine were analyzed for CTX-M, integrons, and insertion sequence common regions (ISCRs) by PCR and sequencing. Multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE), phylogenetic analysis, and rep-PCR were also used for molecular typing of the isolates. Of 80 CTX-M producers, 30 and 43 expressed CTX-M-15 and CTX-M-14, respectively. MLST analysis indicated that the most prevalent ST was ST131 (n = 31, 40.7%), followed by ST38 (n = 20, 26.3%), ST405 (n = 8, 10.5%), and ST69 (n = 5, 6.57%). Most CTX-M producers harbored class 1 integrons. ST131 strains belonged to phylogenetic group B2 and showed identical r...
Journal of Clinical Microbiology, 2013
We report the characteristics of 115 extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli clinical isolates, from 115 unique Danish patients, over a 1-year study interval (1 October 2008 to 30 September 2009). Forty-four (38%) of the ESBL isolates represented sequence type 131 (ST13)1, from phylogenetic group B2. The remaining 71 isolates were from phylogenetic groups D (27%), A (22%), B1 (10%), and B2 (3%). Serogroup O25 ST131 isolates (n ؍ 42; 95% of ST131) comprised 7 different K antigens, whereas two ST131 isolates were O16:K100:H5. Compared to non-ST131 isolates, ST131 isolates were associated positively with CTX-M-15 and negatively with CTX-M-1 and CTX-M-14. They also were associated positively with 11 virulence genes, including afa and dra (Dr family adhesins), the F10 papA allele (P fimbria variant), fimH (type 1 fimbriae), fyuA (yersiniabactin receptor), iha (adhesin siderophore), iutA (aerobactin receptor), kpsM II (group 2 capsules), malX (pathogenicity island marker), ompT (outer membrane protease), sat (secreted autotransporter toxin), and usp (uropathogenicity-specific protein) and negatively with hra (heat-resistant agglutinin) and iroN (salmochelin receptor). The consensus virulence gene profile (>90% prevalence) of the ST131 isolates included fimH, fyuA, malX, and usp (100% each), ompT and the F10 papA allele (95% each), and kpsM II and iutA (93% each). ST131 isolates were also positively associated with community acquisition, extraintestinal pathogenic E. coli (ExPEC) status, and the O25, K100, and H4 antigens. Thus, among ESBL E. coli isolates in Copenhagen, ST131 was the most prevalent clonal group, was community associated, and exhibited distinctive and comparatively extensive virulence profiles, plus a greater variety of capsular antigens than reported previously.
Background: Extended spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) constitute an emerging public-health concern. Consider that ESBL genes type CTX-M types has been increased significantly in most parts of the world. Few data are available on the CTX-M variants circulating in Sudan. Objective: This study used polymerase chain reaction (PCR) and bioinformatics tools to identify blaCTX-M and its variants for Extended-spectrum β-lactamase (ESBLs) producing clinical isolates of Escherichia coli (E. coli) obtained from hospitals in Khartoum-Sudan. Methods: A total of 216 nonrepetitive isolates were selected during 2007-2018. The phenotypic identification of ESBL production was confirmed according to CLSI guidelines. CTX-M genotype was analyzed by uniplex PCRs reactions subsequently sequences performed later sequences were analyzed using bioinformatics tools with nBLAST program, multiple alignments to determine CTX-M genotype variants. Nucleotide sequences were submitted to Gen Bank and accession numbers were obtained. Result: ESBL phenotype among 212 confirmed E.coli isolates was (34.9% of 212,n=74). (62.2% of 74, n=46) strains carried bla CTX-M genes, CTX-M genotype variants identified in this study as followed: blaCTX-M-15 gene was the most prevalent one (78.6%) followed by blaCTX 90 (14.3%) and CTX-M55 (7.1%), Conclusion: This study reveled high ESBL occurrence among E.coli isolates, with CTX-M 15 the predominant variants and highlights the incidence of CTX-M-55 for the first time from Sudan.
Microbial Drug Resistance, 2011
In Egypt, little is known about the genetic background of Escherichia coli isolates harboring extended-spectrum b-lactamase (ESBL). Five hundred twenty Enterobacteriaceae were prospectively collected (May 2007-August 2008) at the Theodor Bilharz Research Institute (Cairo). Among the collected Enterobacteriaceae, 56% (n ¼ 291) were E. coli and 32% (n ¼ 165) Klebsiella pneumoniae. A total of 16% (n ¼ 83) of all isolates were ESBL, 19% (n ¼ 55) of the E. coli and 14% (n ¼ 23) of the K. pneumoniae. The proportion of E. coli ESBL producers did not differ significantly between in and outpatients (20% vs. 17%) but was significantly different for nonE. coli ESBL producers (18.5% vs. 1.2%: p ¼ 0.0001). The majority of E. coli ESBL producers (75%) was isolated from urine. All the ESBL-producing Enterobacteriaceae available for molecular study (n ¼ 74) produced CTX-M-15. Among the CTX-M-15-producing E. coli isolates; 40% belonged to phylogenetic group A, 32% to D, and 26% to B2. ERIC-2 PCR profiles were obtained for all these E. coli isolates and multilocus sequence typing for those belonging to group B2. Genotyping analyses showed strain diversity; however, some clusters had profiles indistinguishable from that of previously published clones. Multilocus sequence typing showed that 75% of E. coli group B2 belonged to clone ST131. This indicates that a new country in Africa is adversely affected by clones of E. coliproducing CTX-M-15.
Journal of Biomedicine and Biotechnology, 2009
The emergence of Escherichia coli that produce extended spectrum beta-lactamases (ESBLs) and are multidrug resistant (MDR) poses antibiotic management problems. Forty-seven E. coli isolates from various public hospitals in Malaysia were studied. All isolates were sensitive to imipenem whereas 36 were MDR (resistant to 2 or more classes of antibiotics). PCR detection using gene-specific primers showed that 87.5% of the ESBL-producing E. coli harbored the blaTEM gene. Other ESBL-encoding genes detected were bla(OXA), bla(SHV), and bla(CTX-M). Integron-encoded integrases were detected in 55.3% of isolates, with class 1 integron-encoded intI1 integrase being the majority. Amplification and sequence analysis of the 5'CS region of the integrons showed known antibiotic resistance-encoding gene cassettes of various sizes that were inserted within the respective integrons. Conjugation and transformation experiments indicated that some of the antibiotic resistance genes were likely plasmid-encoded and transmissible. All 47 isolates were subtyped by PFGE and PCR-based fingerprinting using random amplified polymorphic DNA (RAPD), repetitive extragenic palindromes (REPs), and enterobacterial repetitive intergenic consensus (ERIC). These isolates were very diverse and heterogeneous. PFGE, ERIC, and REP-PCR methods were more discriminative than RAPD in subtyping the E. coli isolates. Copyright (C) 2009 King-Ting Lim et al.
Frontiers in Cellular and Infection Microbiology, 2020
The present study was carried out to evaluate the prevalence of sequence type 131 (ST131) among 188 extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) collected in 2015 in Lucus Augusti University hospital (Lugo, Spain) and AP-HP Beaujon hospital (Clichy, France) with regard to other STs and to characterize, the types of ESBL produced, serotypes, virulence factor (VF)-encoding genes and the ST131 clades and subclades. ST131 was detected in 33 (39.1%) and 46 (47.9%) of the isolates in Lucus Augusti and Beaujon, respectively. The 109 remaining isolates displayed 57 other STs, the following STs being displayed by at least three isolates: ST10 (8 isolates), ST23 (3), ST38 (4), ST58 (3), ST88 (5), ST95 (4), ST167 (3), ST354 (5), ST361 (3), ST410 (6), ST648 (4), ST744 (3), and ST1615 (6). ST354, ST410, and ST1615 were significantly (P < 0.05) more frequent in Lucus Augusti (5.4%, 6.5%, and 6.5%) than in Beaujon (0% for the three STs). The new globally emerging clone ST1193 among extraintestinal clinical ESBL-EC was identified in one isolate from France and one from Spain. CTX-M-15 was the commonest ESBL detected in the two hospitals (44.6% in Lucus Augusti and 50.0% in Beaujon). CTX-M-14 was significantly (P = 0.0003) more frequent in Lucus Augusti (31.5%) than in Beaujon (10.4%), whereas CTX-M-1 (20.8 vs. 7.6%; P = 0.008) and CTX-M-27 (15.6 vs. 6.5%; P = 0.0389) were more frequent in Beaujon than in Lucus Augusti. The ST131 isolates showed a higher virulence score (mean 13.367) compared with the non-ST131 isolates (mean 7.661) (P < 0.001). Among the 79 ST131 isolates, most of them (52; 65.8%) belonged to subclade C2 (also known as subclone Flament-Simon et al. Clones and Virulence Genes of ESBL-EC H30Rx) followed by those belonging to subclade C1 (cluster C1-M27: 16 isolates, 20.3%; cluster non-C1-M27: 6 isolates, 7.6%) and clade A (4 isolates; 5.1%). The C2 subclade isolates showed a higher VF-encoding gene score (mean 14.250) compared with the C1-M27 cluster isolates (mean 10.875) (P < 0.001). In conclusion, this study highlights the epidemiological differences between the ESBL-EC isolated from two hospitals of France and Spain obtain in 2015 and reports, for the first time, the presence of clone ST1193 in Spain.
European Journal of Clinical Microbiology & Infectious Diseases, 2012
The objective of this investigation was to analyse the carriage rate of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in faecal samples of healthy humans in Tunisia and to characterise the recovered isolates. One hundred and fifty samples were inoculated on MacConkey agar plates supplemented with cefotaxime (2 μg/ml) for ESBL-positive E. coli recovery. The characterisation of ESBL genes and their genetic environments, detection of associated resistance genes, multilocus sequence typing (MLST) and phylogroup typing were performed by polymerase chain reaction (PCR) and sequencing. The presence and characterisation of integrons and virulence factors were studied by PCR and sequencing. ESBL-positive E. coli isolates were detected in 11 of 150 faecal samples (7.3%) and one isolate/sample was further characterised. These isolates contained the bla CTX-M-1 (ten isolates) and bla TEM-52c genes (one isolate). The ISEcp1 (truncated by IS10 in four strains) and orf477 sequences were found upstream and downstream, respectively, of all bla CTX-M-1 genes. Seven different sequence types (STs) and three phylogroups were identified among CTX-M-1-producing isolates [ST/phylogroup (number of isolates)]: ST58/B1 (3), ST57/D (2), ST165/A (1), ST155/B1 (1), ST10/A (1), ST398/A (1) and ST48/B1 (1). The TEM-52-producing isolate was typed as ST219 and phylogroup B2. Six ESBL isolates contained class 1 integrons with the gene cassettes dfrA17-aadA5 (five isolates) and dfrA1-aadA1 (one). Healthy humans in the studied country could be a reservoir of CTX-M-1-producing E. coli.
PLoS ONE, 2013
Extended-spectrum b-lactamase producing Escherichia coli (ESBL-E. coli) were isolated from infants hospitalized in a neonatal, post-surgery ward during a four-month-long nosocomial outbreak and six-month follow-up period. A multi-locus variable number tandem repeat analysis (MLVA), using 10 loci (GECM-10), for 'generic' (i.e., non-STEC) E. coli was applied for sub-species-level (i.e., sub-typing) delineation and characterization of the bacterial isolates. Ten distinct GECM-10 types were detected among 50 isolates, correlating with the types defined by pulsed-field gel electrophoresis (PFGE), which is recognized to be the 'gold-standard' method for clinical epidemiological analyses. Multi-locus sequence typing (MLST), multiplex PCR genotyping of bla CTX-M , bla TEM , bla OXA and bla SHV genes and antibiotic resistance profiling, as well as a PCR assay specific for detecting isolates of the pandemic O25b-ST131 strain, further characterized the outbreak isolates. Two clusters of isolates with distinct GECM-10 types (G06-04 and G07-02), corresponding to two major PFGE types and the MLSTbased sequence types (STs) 131 and 1444, respectively, were confirmed to be responsible for the outbreak. The application of GECM-10 sub-typing provided reliable, rapid and cost-effective epidemiological characterizations of the ESBL-producing isolates from a nosocomial outbreak that correlated with and may be used to replace the laborious PFGE protocol for analyzing generic E. coli.
Epidemiology and Infection, 2010
To monitor the changing trend of extended-spectrum beta-lactamase (ESBL)-producing bacteria, a 7-year continuous study was launched in 2001 at the largest tertiary hospital in Taiwan. A significant increase over the study period was evident for ESBL-producing isolates of Escherichia coli (4.8-10.0%) and Klebsiella pneumoniae (15.0-23.4%). Molecular investigation conducted in three separate periods revealed the prevalent ESBL types and their genetic relatedness. CTX-M-producing isolates (73.8%) were more prevalent than SHV-type ESBLs (37.0%), the most frequent being CTX-M-14 (34.3%), CTX-M-3 (25.9%), and SHV-12 (25.7%). However, a marked increase of CTX-M-15-producing isolates from 2.1% in 2002 to 29.6% in 2007 was also noted. The increase of ESBL-producing isolates in both species may be mainly due to the horizontal transmission of resistance plasmids, while clonal expansion of some epidemic strains further added to the dispersion of ESBL-producing K. pneumoniae.