Association of Escherichia coli ST131 lineage with risk of urinary tract infection recurrence among young women

In vitro assays for clinical isolates of sequence type 131 Escherichia coli do not recapitulate in vivo infectivity using a murine model of urinary tract infection

Sequence type 131 isolates are a major cause of cystitis and pyelonephritis. Many studies rely solely on in vitro assays to screen for bacterial virulence factors associated with the pathogenicity of clinical isolates of Escherichia coli. Few studies have compared in vitro findings with in vivo infectivity of clinical isolates. The purpose of this study was to evaluate the correlation between in vitro assays with the ability to cause cystitis and pyelonephritis in a murine model of urinary tract infection. In vitro assays were conducted according to the published protocols and included motility assays, biofilm formation, epithelial cell adhesion and invasion, and curli production. Twenty-one uropathogenic E. coli (UPEC) isolates of E. coli ST131 and non-ST131 were used for both in vivo and in vitro studies. Six mice per isolate were inoculated via urethral catheterization. Colony forming units (CFUs) were determined from bladder and kidneys. In vitro and in vivo correlations were evaluated by multiple linear regression analysis. Pairwise linear regressions showed trendlines with weak positive correlations for motility, adhesion, and invasion and weak negative correlations for hemagglutination, biofilm, and curli production. The ability of E. coli ST131 and non-ST131 clinical isolates to cause cystitis and pyelonephritis varied among strains. The R2 Pearson correlation value was less than ±0.5 for any pair, indicating little to no statistical association between in vitro and in vivo findings. These data show that in vitro data are not predictive of the ability of ST131 E. coli to infect and/or cause disease in a mouse model.

IMPORTANCE

Urinary tract infections (UTIs) affect 150 million people annually, and E. coli ST131, a pandemic clone, has become responsible for a significant portion of those UTIs. How ST131 E. coli has become such a successful strain remains to be elucidated. When evaluating bacterial pathogenicity, it is customary to use in vitro assays to predict isolate virulence and fitness due to lower cost and ease of experimentation compared with in vivo models. It is common to use model organisms like pathogenic E. coli CFT073 or a non-pathogenic K12 lab strain as representatives for the entire species. However, our research has shown that model organisms differ from ST131 E. coli, and in vitro assays are poor predictors of ST131 isolate infectivity in a murine model of UTI. As such, research into the mechanisms of fitness/pathogenesis for ST131 infectivity needs to focus on these organisms rather than other types of UPEC.

Molecular determination of O25b/ST131 clone type among extended spectrum β-lactamases production Escherichia coli recovering from urinary tract infection isolates

Background

Escherichia coli (E. coli) O25b/ST131 clone causes urinary tract infection (UTI) and is associated with a broad spectrum of other infections, such as intra-abdominal and soft tissue infections, that can be affecting bloodstream infections. Therefore, since O25b/ST131 has been reported in several studies from Iran, in the current study, we have investigated the molecular characteristics, typing, and biofilm formation of O25b/ST131 clone type E. coli collected from UTI specimens.

Methods

A total of 173 E. coli isolates from UTI were collected. The susceptibility to all fourth generations of cephalosporins (cefazolin, cefuroxime, ceftriaxone, cefotaxime, ceftazidime, cefepime) and ampicillin, ampicillin-sulbactam and aztreonam was determined. Class A ESBLs, class D ESBL and the presence of pabB gene screenings to detect of O25b/ST131 clone type were performed by using of PCR. Biofilm formation was compared between O25b/ST131 isolates and non-O25b/ST131 isolates. Finally, ERIC-PCR was used for typing of ESBL positive isolates.

Results

Ninety-four ESBL positive were detected of which 79 of them were O25b/ST131. Antimicrobial susceptibility test data showed that most antibiotics had a higher rate of resistance in isolates of the O25b/ST131 clonal type. Biofilm formation showed that there was a weak association between O25b/ST131 clone type isolates and the level of the biofilm formation. ERIC-PCR results showed that E. coli isolates were genetically diverse and classified into 14 groups.

Conclusion

Our results demonstrated the importance and high prevalence of E. coli O25b/ST131 among UTI isolates with the ability to spread fast and disseminate antibiotic resistance genes.

Natural Bred ε2-Phages Have an Improved Host Range and Virulence against Uropathogenic Escherichia coli over Their Ancestor Phages

Alternative treatments for Escherichia coli infections are urgently needed, and phage therapy is a promising option where antibiotics fail, especially for urinary tract infections (UTI). We used wastewater-isolated phages to test their lytic activity against a panel of 47 E. coli strains reflecting the diversity of strains found in UTI, including sequence type 131, 73 and 69. The plaquing host range (PHR) was between 13 and 63%. In contrast, the kinetic host range (KHR), describing the percentage of strains for which growth in suspension was suppressed for 24 h, was between 0% and 19%, substantially lower than the PHR. To improve the phage host range and their efficacy, we bred the phages by mixing and propagating cocktails on a subset of E. coli strains. The bred phages, which we termed evolution-squared ε2-phages, of a mixture of Myoviridae have KHRs up to 23% broader compared to their ancestors. Furthermore, using constant phage concentrations, Myoviridae ε2-phages suppressed the growth of higher bacterial inocula than their ancestors did. Thus, the ε2-phages were more virulent compared to their ancestors. Analysis of the genetic sequences of the ε2-phages with the broadest host range reveals that they are mosaic intercrossings of 2-3 ancestor phages. The recombination sites are distributed over the whole length of the genome. All ε2-phages are devoid of genes conferring lysogeny, antibiotic resistance, or virulence. Overall, this study shows that ε2-phages are remarkably more suitable than the wild-type phages for phage therapy.

Temporal trends, risk factors and outcomes of infections due to extended-spectrum β-lactamase producing Enterobacterales in Swiss solid organ transplant recipients between 2012 and 2018

Background

The burden of antimicrobial resistance is high in solid organ transplant (SOT) recipients. Among Swiss SOT recipients, we assessed temporal trends of ESBL-producing Enterobacterales (ESBL-E), identified risk factors for ESBL-E, and assessed the impact of resistance on patient outcome.

Methods

Data from the Swiss Transplant Cohort Study (STCS), a nationwide prospective cohort of SOT-recipients, were analysed. Temporal trends were described for ESBL-detection among Escherichia coli and non-Escherichia coli. In a nested case–control study, cases with ESBL-E infection were 1:1 matched (by time since transplantation, organ transplant, pathogen) to controls infected with non-ESBL-E. Factors associated with resistance and with unfavourable 30-day outcome (death, infection relapse, graft loss) were assessed.

Results

From 2012 to 2018, we identified 1′212 infection episodes caused by Enterobacterales in 1′074 patients, thereof 11.4% (138/1′212) caused by ESBL-E. The proportion of ESBL-production among Escherichia coli remained stable over time (p = 0.93) but increased for non-E. coli (p = 0.02) Enterobacterales. In the case–control study (n = 102), antibiotic pre-treatment was independently associated with ESBL-production (aOR = 2.6, 95%-CI: 1.0–6.8, p = 0.046). Unfavourable outcome occurred in 24/51 (47%) cases and 9/51 (18%) controls (p = 0.003). Appropriate empiric antibiotic therapy was the only modifiable factor associated with unfavourable outcome.

Conclusions

In Swiss SOT-recipients, proportion of infections with ESBL-producing non-E. coli Enterobacterales increased in recent years. Antibiotic pre-treatment represents a risk factor for ESBL-E. Improving appropriateness of empiric antibiotic treatment might be an important measure to reduce unfavourable outcome, which was observed in almost half of SOT-recipients with ESBL-E infections.

Escherichia coli Resistance to Fluoroquinolones in Community-Acquired Uncomplicated Urinary Tract Infection in Women: a Systematic Review

Antibiotic resistance is a threat to public health, and uncomplicated urinary tract infections (uUTIs) are an example of this concern. This systematic review (International Prospective Register of Systematic Reviews [PROSPERO] ID: CRD42020156674) is the first to determine the prevalence of Escherichia coli resistance to fluoroquinolones in women with community-acquired uUTI. PubMed and Embase searches were conducted; 38 studies fulfilled eligibility criteria and were included in the systematic review. Within Europe, ciprofloxacin resistance in E. coli isolates varied between countries and increased in some from 2006 to 2008 and 2014 to 2016, specifically in the United Kingdom (0.5% to 15.3%), Germany (8.7% to 15.1%), and Spain (22.9% to 30.8%), although methodologies and settings were often not comparable. In Asia, there was a substantial increase in ciprofloxacin resistance during 2008 to 2014 from 25% to more than 40%. In North America, resistance to ciprofloxacin also increased between 2008 and 2017, from 4% to 12%. Data exploring different age groups did not show a consistent relationship with resistance, whereas two studies found that fluoroquinolone resistance was higher in postmenopausal women than premenopausal women. One study indicated a link between fluoroquinolone resistance and uUTI recurrence. These findings may have implications for the empirical treatment of uUTI with fluoroquinolones globally, but more data are needed to fully understand regional situations and impact patient management.

Cranberry Polyphenols and Prevention against Urinary Tract Infections: Relevant Considerations

Cranberry (Vaccinium macrocarpon) is a distinctive source of polyphenols as flavonoids and phenolic acids that has been described to display beneficial effects against urinary tract infections (UTIs), the second most common type of infections worldwide. UTIs can lead to significant morbidity, especially in healthy females due to high rates of recurrence and antibiotic resistance. Strategies and therapeutic alternatives to antibiotics for prophylaxis and treatment against UTIs are continuously being sought after. Different to cranberry, which have been widely recommended in traditional medicine for UTIs prophylaxis, probiotics have emerged as a new alternative to the use of antibiotics against these infections and are the subject of new research in this area. Besides uropathogenic Escherichia coli (UPEC), the most common bacteria causing uncomplicated UTIs, other etiological agents, such as Klebsiellapneumoniae or Gram-positive bacteria of Enterococcus and Staphylococcus genera, seem to be more widespread than previously appreciated. Considerable current effort is also devoted to the still-unraveled mechanisms that are behind the UTI-protective effects of cranberry, probiotics and their new combined formulations. All these current topics in the understanding of the protective effects of cranberry against UTIs are reviewed in this paper. Further progresses expected in the coming years in these fields are also discussed.

Distribution of Pathogenicity Island Markers and H-Antigen Types of Escherichia coli O25b/ST131 Isolates from Patients with Urinary Tract Infection in Iran

Escherichia coli serogroup O25b-sequence type 131 (E. coli O25b/ST131) is known as a multidrug-resistant organism with high virulence potential and has received attention internationally. We aim to investigate the prevalence of O25b/ST131 and the distribution of bla_CTX-M-15, pathogenicity island (PAI) markers, phylogenetic groups, and H-antigen typing in the E. coli O25b/ST131 isolated from patients with urinary tract infection (UTI) in Tehran, the capital of Iran. Seventy (26.9%) E. coli isolates were identified as O25b/ST131. There was also a significant difference in the prevalence of virulence genes, including papA, sfa, sat, cnf1, iutA, kpMII, traT, and usp, in the O25b/ST131 isolates rather than non-O25b/ST131 ones (p ≤ 0.05). Furthermore, 78% of the O25b/ST131 isolates carried four to seven PAIs, while 71% of non-O25b/ST131 isolates carried two to four PAI markers (p ≤ 0.05). Our study showed that in addition to H4, other H-antigens may play a role in the O25b/ST131 virulence potential. Besides, a significant association was found between the history of previous UTIs and infection among the O25b/ST131 clone isolates. Pulsed-field gel electrophoresis revealed circulating of O25b:H4-ST131/PST43 clone in both hospital and community. Approximately one in every three uropathogenic E. coli isolates was the O25b/ST131 clone, representing a significant public health threat. Practical investigation on O25b/ST131 can be helpful in better understanding of ST131 evolution and controlling UTI in hospitals.

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.

Spreading of extended-spectrum β-lactamase-producing Escherichia coli ST131 and Klebsiella pneumoniae ST11 in patients with pneumonia: a molecular epidemiological study

Supplemental Digital Content is available in the text

Background:

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are the important pathogens causing pneumonia. This study aimed to investigate the clinical characteristics and molecular epidemiology of ESBL-producing E. coli and K. pneumoniae causing pneumonia at a large teaching hospital in China.

Methods:

We collected patient's clinical data and ESBL-producing E. coli and K. pneumoniae strains causing pneumonia (from December 2015 to June 2016) at a hospital in Wuhan. The susceptibilities, multi-locus sequence typing, homologous analysis, ESBL genes by polymerase chain reaction and sequencing were determined.

Results:

A total of 59 ESBL-producing strains (31 E. coli and 28 K. pneumoniae) isolated from patients with pneumonia were analyzed. The majority of strains were isolated from patients were with hospital-acquired pneumonia (37/59, 62.7%), followed by community-acquired pneumonia (13/59, 22.0%), and ventilator-related pneumonia (9/59, 15.3%). The E. coli ST131 (9 isolates, 29.0%) and K. pneumoniae ST11 (5 isolates, 17.9%) were the predominant sub-types. The most prevalent ESBL gene was CTX-M-14, followed by SHV-77, CTX-M-3, SHV-11, and CTX-M-27. At least 33 (55.9%) of the ESBL-producing strains carried two or more ESBL genes. The ISEcp1 and IS26 were found upstream of all blaCTX-M (CTX-Ms) and of most blaSHV (SHVs) (57.6%), respectively. Moreover, three ESBL-producing K. pneumoniae ST11 strains which were resistant to carbapenems carried the bla_NDM-1 and bla_KPC-2, two of which also bearing bla_OXA-48 were resistant to all antibiotics (including Tigecycline).

Conclusions:

Hospital-acquired pneumonia is more likely correlated with ESBL-producing E. coli and K. pneumoniae. ESBL-producing E. coli ST131 and multi-drug resistance ESBL-producing, as well as New Delhi metallo-β-lactamase-1 (NDM-1) and Klebsiella pneumoniae carbapenemases-2 (KPC-2) bearing K. pneumoniae ST11 are spreading in patients with pneumonia in hospital.

BacTag - a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing

BACKGROUND

Bacteria carry a wide array of genes, some of which have multiple alleles. These different alleles are often responsible for distinct types of virulence and can determine the classification at the subspecies levels (e.g., housekeeping genes for Multi Locus Sequence Typing, MLST). Therefore, it is important to rapidly detect not only the gene of interest, but also the relevant allele. Current sequencing-based methods are limited to mapping reads to each of the known allele reference, which is a time-consuming procedure.

RESULTS

To address this limitation, we developed BacTag - a pipeline that rapidly and accurately detects which genes are present in a sequencing dataset and reports the allele of each of the identified genes. We exploit the fact that different alleles of the same gene have a high similarity. Instead of mapping the reads to each of the allele reference sequences, we preprocess the database prior to the analysis, which makes the subsequent gene and allele identification efficient. During the preprocessing, we determine a representative reference sequence for each gene and store the differences between all alleles and this chosen reference. Throughout the analysis we estimate whether the gene is present in the sequencing data by mapping the reads to this reference sequence; if the gene is found, we compare the variants to those in the preprocessed database. This allows to detect which specific allele is present in the sequencing data. Our pipeline was successfully tested on artificial WGS E. coli, S. pseudintermedius, P. gingivalis, M. bovis, Borrelia spp. and Streptomyces spp. data and real WGS E. coli and K. pneumoniae data in order to report alleles of MLST house-keeping genes.

CONCLUSIONS

We developed a new pipeline for fast and accurate gene and allele recognition based on database preprocessing and parallel computing and performed better or comparable to the current popular tools. We believe that our approach can be useful for a wide range of projects, including bacterial subspecies classification, clinical diagnostics of bacterial infections, and epidemiological studies.