Detection of O25b-ST131 clone, CTX-M-1 and CTX-M-15 genes via real-time PCR in Escherichia coli strains in patients with UTIs obtained from a university hospital in Istanbul

Uropathogenic E. coli and Hybrid Pathotypes in Mexican Women with Urinary Tract Infections: A Comprehensive Molecular and Phenotypic Overview

Uropathogenic Escherichia coli (UPEC) is the main cause of urinary tract infections (UTIs) and carries virulence and resistance factors often found in mobilizable genetic elements, such as plasmids or pathogenicity islands (PAIs). UPEC is part of the extraintestinal pathogenic E. coli (ExPEC), but hybrid strains possessing both diarrheagenic E. coli (DEC) and ExPEC traits, termed "hypervirulent", present a significant health threat. This study assessed the prevalence of UPEC PAIs, ExPEC sequence types (ST), DEC genes, carbapenemase and extended-spectrum β-lactamase (ESBL) phenotypes, resistance genotypes, and plasmids in 40 clinical isolates of UPEC. Results showed that 72.5% of isolates had PAIs, mainly PAI IV536 (53%). ESBL phenotypes were found in 65% of β-lactam-resistant isolates, with 100% of carbapenem-resistant isolates producing carbapenemase. The predominant ESBL gene was blaCTX-M-2 (60%), and the most common resistance gene in fluoroquinolone and aminoglycoside-resistant isolates was aac(6')Ib (93%). Plasmids were present in 57% of isolates, and 70% belonged to the ST131 clonal group. Molecular markers for DEC pathotypes were detected in 20 isolates, with 60% classified as hybrid pathotypes. These findings indicate significant pathogenic potential and the presence of hybrid pathotypes in E. coli UTI clinical isolates in the Mexican population.

The Genotypic and Phenotypic Characteristics Contributing to Flomoxef Sensitivity in Clinical Isolates of ESBL-Producing E. coli Strains from Urinary Tract Infections

We carried out a molecular biological analysis of extended-spectrum β-lactamase (ESBL)-producing E. coli strains and their sensitivity to flomoxef (FMOX). Sequence type (ST) analysis by multilocus sequence typing (MLST) and classification of ESBL genotypes by multiplex PCR were performed on ESBL-producing E. coli strains isolated from urine samples collected from patients treated at our institution between 2008 and 2018. These sequences were compared with results for antimicrobial drug susceptibility determined using a micro-liquid dilution method. We also analyzed cases treated with FMOX at our institution to examine its clinical efficacy. Of the 911 E. coli strains identified, 158 (17.3%) were ESBL-producing. Of these, 67.7% (107/158) were strain ST-131 in ST analysis. Nearly all (154/158; 97.5%) were CTX-M genotypes, with M-14 and M-27 predominating. The isolated strains were sensitive to FMOX in drug susceptibility tests. Among the patient samples, 33 cases received FMOX, and of these, 5 had ESBL-producing E. coli. Among these five cases, three received FMOX for surgical prophylaxis as urinary carriers of ESBL-producing E. coli, and postoperative infections were prevented in all three patients. The other two patients received FMOX treatment for urinary tract infections. FMOX treatment was successful for one, and the other was switched to carbapenem. Our results suggest that FMOX has efficacy for perioperative prophylactic administration in urologic surgery involving carriers of ESBL-producing bacteria and for therapeutic administration for urinary tract infections. Use of FMOX avoids over-reliance on carbapenems or β-lactamase inhibitors and thus is an effective antimicrobial countermeasure.

Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification

Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.

Pathogenicity Islands in Uropathogenic Escherichia coli Clinical Isolate of the Globally Disseminated O25:H4-ST131 Pandemic Clonal Lineage: First Report from Egypt

Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). The pathogenesis of UTIs relies upon UPEC's acquisition of virulence determinants that are commonly inserted into large chromosomal blocks which are termed 'pathogenicity islands' (PAIs). In this study, we investigated the virulence-associated genes embedded in the chromosome of a UPEC Egyptian strain, EC14142. Additionally, we present a detailed characterization of the PAIs in the EGY_EC14142 chromosome. The isolate displayed a multidrug-resistant phenotype, and whole genome sequencing indicated that it belonged to the globally disseminated O25:H4-ST131 pandemic lineage and the H30-Rx clade. EGY_EC14142 carried genes that are responsible for resistance to aminoglycosides, fluoroquinolones, extended-spectrum β-lactams, macrolides, folate pathway antagonists, and tetracyclines. It encoded five PAIs with a high similarity to PAI II536, PAI IV536, PAI V536, PAI-536-icd, and PAIusp. The genome analysis of EGY_EC14142 with other closely related UPEC strains revealed that they have a high nucleotide sequence identity. The constructed maximum-likelihood phylogenetic tree showed the close clonality of EGY_EC14142 with the previously published ST131 UPEC international isolates, thus endorsing the broad geographical distribution of this clone. This is the first report characterizing PAIs in a UPEC Egyptian strain belonging to the globally disseminated pandemic clone O25:H4-ST131.

Filogenia y resistencia de cepas de Escherichia coli productoras de betalactamasas de espectro extendido a los antibióticos en pacientes con cáncer hospitalizados en Perú

Introducción. Las infecciones asociadas con la atención en salud constituyen un problema de salud pública porque aumentan la morbimortalidad de los pacientes, sobre todo de aquellos con factores de riesgo, como la inmunosupresión debida a enfermedades oncológicas. Es importante conocer la diversidad genética de losprincipales microorganimos causantes de infecciones hospitalarias mediante la vigilancia epidemiológica tradicional y la epidemiología molecular, para hacer un mejor seguimiento y detectar brotes tempranamente.Objetivo. Determinar el grupo filogenético y la resistencia a antibióticos de las cepas de Escherichia coli aisladas de pacientes con cáncer hospitalizados.Materiales y métodos. Se hizo un estudio de tipo transversal que incluyó 67 cepas de Escherichia coli productoras de betalactamasas de espectro extendido (BLEE). Se determinó el grupo filogenético, el perfil de resistencia a los antibióticos, los genes de resistencia a betalactámicos, el tipo de las muestras y los servicios de hospitalización de donde fueron recuperadas.Resultados. El grupo filogenético más frecuente fue el B2 (36 %). El 57 % de las cepas B2 fueron aisladas de muestras de orina y el 33 % provenía del servicio de urología. La resistencia a ciprofloxacino y gentamicina fue de 91 y 53 %, respectivamente, y el 79 % de las cepas tenía el gen blaCTX-M. Se encontró una relación significativa (p<0,05) entre los grupos filogenéticos y la resistencia a ciprofloxacina, así como a la edad del paciente.Conclusión. El filogrupo de E. coli predominante fue el B2. Se evidenció una gran resistencia a ciprofloxacina y gentamicina, una proporción elevada de cepas BLEE con el blaCTX-M, y una relación entre el grupo filogenético y la resistencia a ciprofloxacino.

Antibiotic resistance, phylogenetic typing, and virulence genes profile analysis of uropathogenic Escherichia coli isolated from patients in southern Iraq

Of the most common infectious diseases that occur mainly by uropathogenic Escherichia coli (UPEC) is urinary tract infections (UTIs). The purpose of this study was to investigate virulence factors, antibiotic resistance, and phylogenetic groups among UPEC strains isolated from patients with UTI in southern Iraq. A total of 100 UPEC isolates were collected from urine samples of UTI patients from various hospitals in southern Iraq, and confirmed by morphological and biochemical tests. Antimicrobial susceptibility testing on isolates was performed by disk diffusion method. Multiplex PCR techniques were used to evaluate the phylogenetic groups based on Clermont method and to detect the presence of six virulence factor genes. The majority of isolates belonged to the phylogenetic groups B2 (46%) and C (13%). The most prevalent virulence factors were fimH (96%), followed by aer (47%), papC (36%), cnf1 (17%), hly (15%), and afa (8%). Phenotypic testing showed that the isolates were most resistant to piperacillin, ticarcillin, amoxicillin/clavulanic acid (92%, 91%, and 88%, respectively) and most sensitive to amikacin and imipenem, respectively. The maximum antibiotic resistance and virulence factors were observed in the phylogenetic group B2. The results showed that the UPEC isolates had all six virulence factors with high frequency and the highest drug resistance. Besides, the results showed a direct relationship between virulence factors, gene diversity, phylogenetic background, and antimicrobial resistance in the UPEC isolates.

Molecular Epidemiology of Multidrug-Resistant Uropathogenic Escherichia coli O25b Strains Associated with Complicated Urinary Tract Infection in Children

Background: Uropathogenic Escherichia coli (UPEC) has increased the incidence of urinary tract infection (UTI). It is the cause of more than 80% of community-acquired cystitis cases and more than 70% of uncomplicated acute pyelonephritis cases. Aim: The present study describes the molecular epidemiology of UPEC O25b clinical strains based on their resistance profiles, virulence genes, and genetic diversity. Methods: Resistance profiles were identified using the Kirby–Bauer method, including the phenotypic production of extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs). The UPEC serogroups, phylogenetic groups, virulence genes, and integrons were determined via multiplex PCR. Genetic diversity was established using pulsed-field gel electrophoresis (PFGE), and sequence type (ST) was determined via multilocus sequence typing (MLST). Results: UPEC strains (n = 126) from hospitalized children with complicated UTIs (cUTIs) were identified as O25b, of which 41.27% were multidrug resistant (MDR) and 15.87% were extensively drug resistant (XDR). The O25b strains harbored the fimH (95.23%), csgA (91.26%), papGII (80.95%), chuA (95.23%), iutD (88.09%), satA (84.92%), and intl1 (47.61%) genes. Moreover, 64.28% were producers of ESBLs and had high genetic diversity. ST131 (63.63%) was associated primarily with phylogenetic group B2, and ST69 (100%) was associated primarily with phylogenetic group D. Conclusion: UPEC O25b/ST131 harbors a wide genetic diversity of virulence and resistance genes, which contribute to cUTIs in pediatrics.

Comparative Study of CTX-M-15 Producing Escherichia coli ST131 Clone Isolated from Urinary Tract Infections and Acute Diarrhoea

Background and Purpose

The alarming increase in the prevalence of CTX-M-15 extended-spectrum β-lactamase (ESBL) producing E. coli has been significantly linked to the clonal expansion of emerging sequence type (ST131). This study aimed to screen for the O16/O25-ST131 clones among different phylogenetic types of E. coli strains isolated from urinary and diarrhoeal samples.

Methods

A total of 205 E. coli strains isolated from patients with UTI and acute diarrhoea were investigated by phenotypic and genotypic methods for ESBL identification. Molecular methods were used for identification of O25/O16-ST131 clone and phylogenetic typing of E. coli isolates.

Results

O25-ST131 clone was detected in 89/105 (84.8%) and 47/100 (47%) of urinary and intestinal E. coli isolates, respectively, with a significant difference (P-value<0.001). There was a significant high rate of occurrence of ESBLs, MDR, and antibiotic resistance to most antibiotic classes among O25-ST131 than non-O25-ST131 isolates. CTX-M-15 gene was detected in 64/71 (90%) of ESBLs producing intestinal isolates and 54/79 (68.4%) of urinary ESBLs producing isolates. The O25-ST131 clone was reported among all phylogenetic groups. The O16-ST131 clone serotype was not detected in the study isolates.

Conclusion

High prevalence of the O25-ST131 clone was reported among extraintestinal and intestinal E. coli isolates. First detection of the O25-ST131 clone among phylogenetic groups other than group B2 draws attention of the ability of this clone to transfer among commensal groups. An increasing in the prevalence of CTX-M-15 among E. coli strains especially of intestinal origin is alarming as the intestine is the main reservoir for ExPEC strains causing UTI.

Emergence and Spread of Cephalosporinases in Wildlife: A Review

Simple Summary

Antimicrobial resistance (AMR) is one of the global public health challenges nowadays. AMR threatens the effective prevention and treatment of an ever-increasing range of infections, being present in healthcare settings but also detected across the whole ecosystem, including wildlife. This work compiles the available information about an important resistance mechanism that gives bacteria the ability to inactivate cephalosporin antibiotics, the cephalosporinases (extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase), in wildlife. Through a rigorous systematic literature review in the Web of Science database, the available publications on this topic in the wildlife sphere were analysed. The emergence and spread of cephalosporinases in wildlife has been reported in 46 countries from all continents (52% in Europe), with descriptions mainly in birds and mammals. The most widely disseminated cephalosporinases in human-related settings (e.g. CTX-M-1, CTX-M-14, CTX-M-15 and CMY-2) are also the most reported in wildlife, suggesting that anthropogenic pressure upon natural environments have a strong impact on antimicrobial resistance spread, including the dissemination of genes encoding these enzymes. Our work highlights the urgence and importance of public and ecosystem health policies, including improved surveillance and control strategies that breakdown AMR transmission chains across wildlife, as part of an integrated strategy of the One Health approach.

Abstract

In the last decade, detection of antibiotic resistant bacteria from wildlife has received increasing interest, due to the potential risk posed by those bacteria to wild animals, livestock or humans at the interface with wildlife, and due to the ensuing contamination of the environment. According to World Health Organization, cephalosporins are critically important antibiotics to human health. However, acquired resistance to β-lactams is widely distributed and is mainly mediated by extended-spectrum beta-lactamase and AmpC beta-lactamases, such as cephalosporinases. This work thus aimed to compile and analyse the information available on the emergence and dissemination of cephalosporinases in wildlife worldwide. Results suggest a serious scenario, with reporting of cephalosporinases in 46 countries from all continents (52% in Europe), across 188 host species, mainly birds and mammals, especially gulls and ungulates. The most widely reported cephalosporinases, CTX-M-1, CTX-M-14, CTX-M-15 and CMY-2, were also the most common in wild animals, in agreement with their ubiquity in human settings, including their association to high-risk clones of Escherichia coli (E. coli), such as the worldwide distributed CTX-M-15/ST131 E. coli. Altogether, our findings show that anthropogenic activities affect the whole ecosystem and that public policies promoting animal and environmental surveillance, as well as mitigation measures to avoid antimicrobial misuse and AMR spread, are urgently needed to be out in practise.

Antimicrobial Resistance and Extended-Spectrum Beta-Lactamase (ESBL) Genes in E. coli Isolated from Equine Fecal Samples in Turkey

The extensive use of antibacterial agents used for treatment in human and veterinary clinics to increase yield in livestock and aquaculture in developing countries causes the detection and spread of multidrug-resistant (MDR) strains in different sources. The presence of Escherichia coli strains is very common in racehorses and it's a serious problem on horse farms. Extended-spectrum beta-lactamase (ESBL) production is an important source of MDR development in Gram-negative strains such as E.coli. This study aimed to detect the presence of ESBL genes in E. coli strains isolated from horse farms in eastern Turkey. A total of 200 equine fecal samples were collected from 16 horse farms (70 Thoroughbred and 130 Arabian horses) in the Adana and Şanlıurfa provinces of Turkey. The presence of ESBL genes, such as blaCTX-M, blaTEM, blaSHV, blaOXA-48, and blaKPC in the E. coli strains was investigated using real-time PCR. According to the real-time PCR results, 107 (53.5%) out of 200 E. coli strains were positive for at least one gene. BlaCTX-M, blaSHV, and blaTEM were detected in 11, 6, and 4 strains respectively. blaCTX-M+blaSHV coexisted in 16 strains, blaCTX-M+blaTEM in 11 strains, blaSHV+blaOXA-48 in 8 strains, blaTEM+blaSHV in 8 strains, blaCTX+blaSHV+ blaOXA-48 coexistent in 3 strains, blaCTX-M+blaTEM+blaSHV+blaOXA-48 in 7 strains, blaCTX-M+ blaTEM+blaSHV+blaKPC in 2 strains, and finally, blaCTX-M+blaTEM+blaSHV+blaOXA-48+blaKPC in 3 strains. In a summary, ESBL-producing E. coli strains were frequently seen in the racehorses from eastern Turkey. The excessive misuse of antibiotics has led to the evolution of MDR strains such as ESBL-producing E. coli that cause serious health problems and are difficult to treat. Routine molecular epidemiology studies are warranted to closely monitor these resistant strains.

Prevalence of E. coli ST131 among Uropathogenic E. coli Isolates from Iraqi Patients in Wasit Province, Iraq

The emergence of Escherichia coli sequence type 131 (E. coli ST131) clone represents a major challenge to public health globally, since this clone is reported as highly virulent and multidrug-resistant, thus making it successfully disseminated worldwide. In Iraq, there is no previous study dealing with this important clone, so this project was suggested to investigate its presence within uropathogenic E. coli (UPEC) from Iraqi patients in Wasit Province. A total of 112 UPEC isolates from cases of acute urinary tract infection (UTI) were analysed for phylogenetic groups by quadruplex PCR; then, these isolates were investigated for E. coli ST131 clone by both conventional and real-time PCR procedures. The antibiotic susceptibility test was performed by the disk diffusion method. The results revealed that, out of 112 UPEC isolates, 38 (33.9%) belonged to phylogroup B2. For conventional PCR, 92.1% (35/38) of B2 E. coli isolates were positive for E. coli ST131, of which 34 were O25b-ST131 strain and 1 was O16-ST131 strain. However, serogroups O25b and O16 represented 17.1% and 2.8%, respectively. By RT-PCR assay, 15.1% (17/112) and 44.7% (17/38) of total and B2 E. coli isolates were confirmed as being E. coli ST131, respectively. The highest resistance rates of E. coli ST131 isolates were against the β-lactams, while low resistance rates were against amikacin, nitrofurantoin, and gentamicin. Fortunately, all isolates were susceptible to carbapenems. Moreover, 52.9% (9 out of 17) of E. coli ST131 isolates were MDR. In conclusion, the presence of E. coli ST131 among UPEC isolates from Iraqi patients is confirmed with high resistance to most antimicrobials included in this study.

Emergence of Escherichia coli ST131 Causing Urinary Tract Infection in Western Asia: A Systematic Review and Meta-Analysis

Escherichia coli sequence type (ST) 131 is considered a high-risk pandemic clone and frequently extended-spectrum β-lactamase (ESBL)-producing clone that is strongly associated with the global dissemination of CTX-M-15 type. The emergence of ST131 has become a public health threat because this clonal group typically exhibits multiple virulence factors and antimicrobial resistance. Therefore, this study aimed to analyze the literature published on the estimation of the prevalence of clone ST131 among E. coli strains isolated from patients with urinary tract infections in western Asia. A systematic search was carried out to identify eligible articles in the Web of Science, PubMed, Scopus, Embase, and Google Scholar electronic databases from January 2010 to December 2018. Next, 13 articles meeting the inclusion criteria were selected for data extraction and analysis by Comprehensive Meta-Analysis Software. The included studies were conducted in Iran, Jordan, Kuwait, Pakistan, Saudi Arabia, Turkey, and Yemen. In all studies, the pooled prevalence of ST131 was 24.6% (95% CI: 13.5%-40.4%) in wild type isolates, 42.7% (95% CI: 32.5%-53.5%) among ESBLs-producing isolates, and 64.8% (95% CI: 36%-85.5%) among multiple-drug resistant (MDR) isolates. Moreover, the prevalence of ST131 isolates carrying CTX-M-15 type was 68% (95% CI: 48.4%-82.8%). Our study indicated the high prevalence of broadly disseminated ST131 clone among MDR and ESBLs isolates in western Asia. Moreover, O25b was the predominant ST131 clone type, which was mostly associated with CTX-M-15 type.