Erratum to: Population structure of Drug-Susceptible,-Resistant and ESBL-producing Escherichia coli from community-acquired urinary tract infections

Antibiotic susceptibility and genomic analysis of ciprofloxacin-resistant and ESBLs-producing Escherichia coli in vegetables and their irrigation water and growing soil

The rise of antibiotic resistance in Escherichia coli has become a major global public health concern. While there is extensive research on antibiotic-resistant E. coli from human and animal sources, studies on vegetables and their environments are limited. This study investigated the prevalence and characteristics of ciprofloxacin-resistant (CIPR) E. coli in 13 types of edible raw vegetables, along with their irrigation water and soil in Shaanxi, China. Of 349 samples collected (157 vegetables, 59 water, and 133 soil), a total of 48 positive samples were detected, with one CIPRE. coli strain isolated from each sample being selected for further analyses. A striking observation was its high prevalence in irrigation water at 44.1 %, markedly exceeding that in vegetables (12.0 %) and soil (4.5 %). The susceptibility of Forty-eight CIPRE. coli isolates was evaluated using the disc diffusion method for 18 different antibiotics, all these isolates were not only resistant to the tested fluoroquinolones antibiotics (levofloxacin, nalidixic acid), but also displayed a multi-drug resistance (MDR) pattern. Twenty-eight (58.3 %) of 48 CIPRE. coli isolates exhibited extended spectrum β-lactamases (ESBLs) (CIPR-ESBLs) producing phenotype. Subsequently, whole-genome sequencing was performed on these 28 isolates. We identified 12 serotypes and STs each, with O101: H9 (35.7 %, 10/28) and ST10 (21.4 %, 6/28) being the most common. Further classification placed these isolates into five phylogenetic groups: A (57.1 %, 16/28), B1 (32.1 %, 9/28), D (3.6 %, 1/28), B2 (3.6 %,1/28), and F (3.6 %,1/28). Notelly, Identical ST types, serotypes and phylogroups were found in certain CIPR-ESBLs-producing E. coli from both vegetables and adjacent irrigation water. Genomic analysis of the 28 CIPR-ESBLs-producing E. coli isolates unveiled 73 resistance genes, associated with 13 amino acid mutations in resistance-determining regions (QRDRs) and resistance to 12 types of antibiotics. Each isolate was confirmed to carry both ESBLs and fluoroquinolone resistance genes, with the Ser83Ala mutation in GyrA (96.4 %, 27/28) being the most prevalent. A detailed analysis of Mobile Genetic Elements (MGEs) revealed that IncFIB and IncFII plasmid subtypes were most prevalent in 60.7 % and 67.9 % of isolates, respectively, with 75 % containing over 10 insertion sequences (IS) each. Furthermore, we observed that certain ESBL and PMQR genes were located on plasmids or in proximity to insertion sequences. In conclusion, our research highlights the widespread presence of CIPRE. coli in irrigation water and thoroughly examines the genetic characteristics of CIPR-ESBLs-producing E. coli strains, underlining the need for ongoing monitoring and management to reduce multidrug-resistant bacteria in vegetables and their environment.

Differential Afa/Dr Fimbriae Expression in the Multidrug-Resistant Escherichia coli ST131 Clone

Many antibiotic resistant uropathogenic Escherichia coli (UPEC) strains belong to clones defined by their multilocus sequence type (ST), with ST131 being the most dominant. Although we have a good understanding of resistance development to fluoroquinolones and third-generation cephalosporins by ST131, our understanding of the virulence repertoire that has contributed to its global dissemination is limited. Here we show that the genes encoding Afa/Dr fimbriae, a group of adhesins strongly associated with UPEC that cause gestational pyelonephritis and recurrent cystitis, are found in approximately one third of all ST131 strains. Sequence comparison of the AfaE adhesin protein revealed a unique allelic variant carried by 82.9% of afa-positive ST131 strains. We identify the afa regulatory region as a hotspot for the integration of insertion sequence (IS) elements, all but one of which alter afa transcription. Close investigation demonstrated that the integration of an IS1 element in the afa regulatory region leads to increased expression of Afa/Dr fimbriae, promoting enhanced adhesion to kidney epithelial cells and suggesting a mechanism for altered virulence. Finally, we provide evidence for a more widespread impact of IS1 on ST131 genome evolution, suggesting that IS dynamics contribute to strain level microevolution that impacts ST131 fitness. IMPORTANCE E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. Here, we utilized a large collection of ST131 isolates to investigate the prevalence, regulation, and function of Afa/Dr fimbriae, a well-characterized UPEC colonization and virulence factor. We show that the afa genes are found frequently in ST131 and demonstrate how the integration of IS elements in the afa regulatory region modulates Afa expression, presenting an example of altered virulence capacity. We also exploit a curated set of ST131 genomes to map the integration of the antibiotic resistance-associated IS1 element in the ST131 pangenome, providing evidence for its widespread impact on ST131 genome evolution.

Genetic and Virulence Characteristics of a Hybrid Atypical Enteropathogenic and Uropathogenic Escherichia coli (aEPEC/UPEC) Strain

Hybrid strains of Escherichia coli combine virulence traits of diarrheagenic (DEC) and extraintestinal pathogenic E. coli (ExPEC), but it is poorly understood whether these combined features improve the virulence potential of such strains. We have previously identified a uropathogenic E. coli (UPEC) strain (UPEC 252) harboring the eae gene that encodes the adhesin intimin and is located in the locus of enterocyte effacement (LEE) pathogenicity island. The LEE-encoded proteins allow enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) to form attaching and effacing (A/E) lesions in enterocytes. We sought to characterize UPEC 252 through whole-genome sequencing and phenotypic virulence assays. Genome analysis unveiled that this strain harbors a complete LEE region, with more than 97% of identity comparing to E2348/69 (EPEC) and O157:H7 Sakai (EHEC) prototype strains, which was functional, since UPEC 252 expressed the LEE-encoded proteins EspB and intimin and induced actin accumulation foci in HeLa cells. Phylogenetic analysis performed comparing 1,000 single-copy shared genes clustered UPEC 252 with atypical EPEC strains that belong to the sequence type 10, phylogroup A. Additionally, UPEC 252 was resistant to the bactericidal power of human serum and colonized cells of the urinary (T24 and HEK293-T) and intestinal (Caco-2 and LS174T) tracts. Our findings suggest that UPEC 252 is an atypical EPEC strain that emerges as a hybrid strain (aEPEC/UPEC), which could colonize new niches and potentially cause intestinal and extraintestinal infections.

Molecular Characterization of Multidrug Resistant Uropathogenic E. Coli Isolates from Jordanian Patients

Background

Emergence of multi-drug resistant uropathogenic E. coli strains is an increasing problem to empirical treatment of urinary tract infections in many countries. This study investigated the magnitude of this problem in Jordan.

Methods

A total of 262 E. coli isolates were recovered from urine samples of Jordanian patients which were suspected to have urinary tract infections (UTIs). All isolates were primarily identified by routine biochemical tests and tested for antimicrobial susceptibility by disc diffusion method. Fifty representative Multidrug Resistance (MDR) E. coli isolates to 3 or more antibiotic classes were tested for the presence of resistance genes of blaCTX-M- 1, 9 and 15, carbapenemase (blaIMP, blaVIM, blaNDM-1, blaOXA-48), fluoroquinolones mutated genes (parC and gyrA) and clone of ST131 type using PCR methods.

Results

A total of 150/262 (57.3%) of E. coli isolates were MDR. Urine samples of hospitalized patients showed significantly more MDR isolates than outpatients. Fifty representative MDR E. coli isolates indicated the following molecular characteristics: All were positive for mutated parC gene and gyrA and for ST131 clone, and 78% were positive for genes of CTX-M-15, 76% for CTX-M-I and for 8% CTX-M-9, respectively. Additionally, all 50 MDR E. coli isolates were negative for carbapenemase genes (blaIMP, blaVIM, blaNDM-1, blaOXA-48), except of one isolate was positive for blaKPC-2 .

Conclusion

This study indicates alarming high rates recovery of MDR uropathogenic E. coli from Jordanian patients associated with high rates of positive ST131 clone, fluoroquinolone resistant and important types of blaCTX-M.

Prevalence of antimicrobial resistant Escherichia coli from patients with suspected urinary tract infection in primary care, Denmark

BACKGROUND

Escherichia coli is the most common pathogen causing Urinary Tract Infections (UTI). Data from the current National Surveillance program in Denmark (DANMAP) may not accurately represent the prevalence of resistant E. coli in primary care, because only urine samples from complicated cases may be forwarded to the microbiological departments at hospitals for diagnostic examination. The aim of this study was to assess the prevalence of resistant E. coli to the most commonly used antimicrobial agents in primary care in a consecutive sample of patients from general practice.

METHODS

Observational study carried out from December 2014 to December 2015. Thirty-nine general practices from The Capital Region of Denmark included adult patients with urinary tract symptoms and suspected UTI. All urine samples were sent to the central laboratory Statens Serum Institut (SSI). Significant bacteriuria was interpreted according to the European Urinalysis Standards. Susceptibility testing was performed and interpreted according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) standards.

RESULTS

From the 39 general practices 505 patients were recruited. Completed data were obtained from 485 (96%) patients. According to the European Urinalysis Standards, 261 (54%) patients had positive bacteriuria. The most common uropathogen in patients with uncomplicated (uUTI) and complicated (cUTI) urinary tract infection was E. coli 105 (69%) and 76 (70%), respectively. Eighty-two (45%) of 181 E. coli isolates were resistant to at least one of the tested antibiotics and 50 out of 82 isolates were resistant to two or more antimicrobial agents. The highest resistance-rate was found against ampicillin 34% (95% CI 24;42) in uUTI and 36% (24;46) in cUTI. There were no differences in the distribution of resistance between uncomplicated and complicated cases. The prevalence of resistance was similar to the one reported in DANMAP 2014.

CONCLUSION

In E. coli from uUTI there is high resistance rates to antimicrobial agents commonly used in primary care. There was no difference in the distribution of resistant E. coli in suspected uUTI vs cUTI. In Denmark, data from the National Surveillance program DANMAP can guide the decision for choice of antibiotic in patients with suspected UTI seeking care in primary care.

TRIAL REGISTRATION

ClinicalTrials.gov NCT02249273 .

Evaluation of MLVA for epidemiological typing and outbreak detection of ESBL-producing Escherichia coli in Sweden

BACKGROUND

To identify the spread of nosocomial infections and halt outbreak development caused by Escherichia coli that carry multiple antibiotic resistance factors, such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases, is becoming demanding challenges due to the rapid global increase and constant and increasing influx of these bacteria from the community to the hospital setting. Our aim was to assess a reliable and rapid typing protocol for ESBL-E. coli, with the primary focus to screen for possible clonal relatedness between isolates. All clinical ESBL-E. coli isolates, collected from hospitals (n = 63) and the community (n = 41), within a single geographical region over a 6 months period, were included, as well as clinical isolates from a polyclonal outbreak (ST131, n = 9, and ST1444, n = 3). The sporadic cases represented 36 STs, of which eight STs dominated i.e. ST131 (n = 33 isolates), ST648 (n = 10), ST38 (n = 9), ST12 and 69 (each n = 4), ST 167, 405 and 372 (each n = 3). The efficacy of multiple-locus variable number tandem repeat analysis (MLVA) was evaluated using three, seven or ten loci, in comparison with that of pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST).

RESULTS

MLVA detected 39, 55 and 60 distinct types, respectively, using three (GECM-3), seven (GECM-7) or ten (GECM-10) loci. For GECM-7 and -10, 26 STs included one type and eleven STs each included several types, the corresponding numbers for GECM-3 were 29 and 8. The highest numbers were seen for ST131 (7,7 and 8 types, respectively), ST38 (5,5,8) and ST648 (4,5,5). Good concordance was observed with PFGE and GECM-7 and -10, despite fewer types being identified with MLVA; 78 as compared to 55 and 60 types. The lower discriminatory power of MLVA was primarily seen within the O25b-ST131 lineage (n = 34) and its H30-Rx subclone (n = 21). Epidemiologically unrelated O25b-ST131 isolates were clustered with O25b-ST131 outbreak isolates by MLVA, whereas the ST1444 outbreak isolates were accurately distinguished from unrelated isolates.

CONCLUSION

MLVA, even when using only three loci, represents an easy initial typing tool for epidemiological screening of ESBL-E. coli. For the ST131-O25b linage, complementary methods may be needed to obtain sufficient resolution.