Phylogenetic analysis, biofilm formation, antimicrobial resistance and relationship between these characteristics in Uropathogenic Escherichia coli.

BACKGROUND: In the present study, we examine the prevalence of phylogenetic groups, O-serogroups, adhesin genes, antimicrobial resistance, the level of gene expression associated with biofilm formation, and the presence of extended-spectrum beta-lactamase (ESBL) in UPEC strains isolated from both pediatric and adult patients. METHODS: In this cross-sectional study, 156 UPEC isolates were collected from UTI patients. ESBL-producing isolates were detected using the double-disc synergy (DDS) method, and biofilm formation was assessed through a microplate assay. The presence of O-serogroups, adhesion factors and resistance genes, including ESBLs and PMQR genes, was detected by PCR, and isolates were categorized into phylogenetic groups using multiplex PCR. Additionally, the quantitative real-time PCR method was also used to determine the expression level of genes related to biofilm. RESULTS: During the study period, 50.6% (79/156) of the samples were obtained from children, and 49.4% (77/156) were from adults. The highest rate of resistance was to NA (91.7%), while FM (10.9%) had the lowest rate of antibiotic resistance. In addition, 67.9% (106/156) of UPEC isolates were ESBL producers. Most of UPEC isolates belonged to phylogenetic group B2 (37.1%). This study revealed that blaCTX-M and qnrS are widely distributed among UPEC isolates. The mean expression levels of fimA genes were significantly higher in non-biofilm producers than in biofilm producers (p < 0.01). CONCLUSIONS: The high antibiotic resistance rates in this study highlight the significance of local resistance monitoring and investigating underlying mechanisms. Our findings indicate the dominance of phylogroup B2 and group D as the prevailing phylogenetic groups. Consequently, it is imperative to investigate the epidemiological aspects and characterize UPEC isolates across diverse regions and time frames.

Worldwide prevalence of extended-spectrum ß-lactamases-producing uropathogenic Escherichia coli isolates among kidney transplant patients: a systematic review and meta-analysis.

A significant proportion of urinary tract infections (UTIs), typically affecting kidney transplant patients (KTPs), is attributed to the presence of extended-spectrum ß-lactamases (ESBLs) and multi-drug resistance (MDR) in Escherichia coli strains. For this reason, the current meta-analysis was conducted to summarize the frequency of ESBL-producing UPEC among KTPs. A systematic search was conducted to identify studies in the Web of Science, PubMed, Embase, and Scopus electronic databases between 2000 and 2021. Finally, 16 articles were selected for data extraction, and meta-analysis was performed using the metaprop command in the STATA (version 11) software. From those studies, the pooled prevalence of ESBL-producing uropathogenic E. coli (UPEC) isolates was 40%. The subcategory analysis results based on continent indicated that Asian countries had the highest rate of ESBL-producing isolates with 45%, followed by 40%, 28%, and 16% in Europe, South America and North America, respectively. Uncomfortably, high level of UPEC isolates in the current investigation was ESBL-producing isolates. These isolates pose a high serious threat to public health because they can contribute to the spread of antimicrobial resistance in the local population and hasten the ineffectiveness of the majority of commonly prescribed antibiotics for the treatment of UTI in KTPs and other patients.

Expression Assessment of the Helicobacter pyloribabA and sabA Genes in Patients with Peptic Ulcer, Duodenal Ulcer and Gastric Cancer.

Helicobacter pylori as a common gastrointestinal (GI) pathogen must possess certain virulence characteristics to colonize the stomach, evade host immune responses, and subsequently induce GI diseases. This research aimed to investigate the expression level of two important genes, the sialic acid-binding adherence (SabA) and the blood group antigen-binding adhesion (BabA) in H. pylori strains isolated from adult patients living in the northern part of Iran, and their association with peptic ulcer disease (PUD) and gastric cancer (GC). This cross-sectional study was carried out on adult patients referring to the GI clinic of the hospitals affiliated to Babol University of Medical Sciences, Iran. New cases diagnosed with gastritis, peptic ulcer or gastric cancer were included. Endoscopic-guided gastric biopsies were examined and H. pylori positive colonies were analyzed to determine the expression of babA and sabA genes, utilizing specific primers and the SYBR Green dye. Among 175 patients with mean age of 51.6±15.6 years, 101 (57.7%) of the individuals tested positive for H. pylori infection. Statistical analysis revealed a significant correlation between sabA (P=0.003) and babA (P=0.002) gene expression and development of PUD and GC. Smoking (P=0.052), gender (P=0.004) and positive babA gene expression (P=0.009) had the greatest association with occurrence of PUD or GC in H. pylori positive patients.  In summary, the presence of the sabA gene in people infected with H. pylori increased the risk of GC compared to gastritis, while, the presence of the babA gene was significantly increased in gastric ulcer patients. Considering the diversity of H. pylori isolates and the varying results observed in different geographical regions, further comprehensive studies are required to evaluate the function of these genes in H. pylori pathogenesis and their relationship with clinical outcomes.

Genetic Diversity, Carbapenem Resistance Genes, and Biofilm Formation in UPEC Isolated from Patients with Catheter-Associated Urinary Tract Infection in North of Iran.

Background: Infections due to carbapenem-resistant Enterobacteriaceae (CRE) are associated in patients with urinary catheters alarming rate of emergency status. The aim of this study is to investigate the molecular causes of carbapenem resistance among UPEC as well as antimicrobial resistance trends. Additionally, the potential of isolates to produce biofilms, in addition to their clonal and genetic diversity, was investigated. Material and Methods. A cross-sectional study was accomplished on a collection of 76 non-duplicate UPEC isolates obtained from CAUTIs from May 2021 to September 2021. The modified carbapenem inactivation method (mCIM) and EDTA-modified carbapenem inactivation method (eCIM) test was performed for the detection of carbapenemase and metallo-beta-lactamase activity. Also, the presence of carbapenemase genes was determined using PCR assays. In 96-well microtiter plates, biofilm development was evaluated. ERIC-PCR was used to investigate the clonal and genetic variety of isolates. Results: A total of 76 confirmed UPEC isolates were obtained from patients mentioned to teaching hospitals in Babol, Iran. The results of antibiotic susceptibility testing revealed a high rate of antibiotic resistance against nalidixic acid (81.6%) and trimethoprim-sulfamethoxazole (80.3%). Among UPEC isolates, 63.2% and 13.2% of UPEC isolates were positive for MBL production. The frequencies of the studied genes are in order of bla NDM (14.5%), bla OXA-23 (2.6%), and bla OXA-48 (2.6%). Forty-two isolates (55.3%) were positive for biofilm formation. ERIC-PCR revealed that UPEC isolates could be categorized into nine clusters A-I and five isolates were categorized as a singleton. Conclusion: The high prevalence of MDR and carbapenemase-producing isolates among the UPEC strain in this investigation is concerning. Moreover, the bla NDM was the most frequent cause of producing metallo-beta-lactamase and carbapenemase. Also, analysis revealed a partial genetic similarity among the studied isolates, indicating that the same UPEC clones may have spread to other hospital units.

Phylogenetic Group Distribution of Uropathogenic Escherichia coli and Related Antimicrobial Resistance Pattern: A Meta-Analysis and Systematic Review.

The phylogenetic classification of Escherichia coli isolates is of great importance not only for understanding the populations of E. coli but also for clarifying the relationship between strains and diseases. The present study aimed to evaluate the prevalence of phylogenetic groups, antibiotic susceptibility pattern, and virulence genes among uropathogenic E. coli (UPEC) isolated from different parts of Iran through a systematic review and meta-analysis. Several international electronic sources, including Web of Science, PubMed, Scopus, and Embase, were searched (2000-2020) in order to identify the studies compatible with our inclusion criteria. The meta-analysis was performed using the metaprop program in the STATA (version 11) software. Based on our comprehensive search, 28 studies meeting the eligibility criteria were included in the meta-analysis. The pooled prevalence of phylogroups B2, D, B1, and A was 39%, 26%, 18%, and 8%, respectively. In addition, there was a significant heterogeneity among different phylogroups. However, according to the results of Begg's and Egger's tests, there were no significant publication bias in phylogroups B2, D, B1, and A. This research provided the first comprehensive study on phylogroups of UPEC isolated in Iran. Our findings indicated that phylogroup B2 and group D were the most predominant phylogenetic groups among UPEC isolates in various regions of Iran. In addition, we observed that certain phylogenetic groups are more antibiotic resistant than the others. It was also observed that the dissemination of virulent phylogroup B2 and D should be controlled via comprehensive infection control measures. Additionally, certain strategies should be developed for monitoring the antibiotic therapy.

Integron and its role in antimicrobial resistance: A literature review on some bacterial pathogens.

In recent years, different acquired resistance mechanisms, including transposons, bacteriophages, plasmids, and integrons have been identified as involved in the spread of resistance genes in bacteria. The role of integrons as mobile genetic elements playing a central role in antibiotic resistance has been well studied and documented. Integrons are the ancient structures that mediate the evolution of bacteria by acquiring, storing, disposing, and resorting to the reading frameworks in gene cassettes. The term integron describes a large family of genetic elements, all of which are able to capture gene cassettes. Integrons were classified into three important classes based on integrase intI gene sequence. Integrons can carry and spread the antibiotic resistance genes among bacteria and are among the most significant routes of distribution of resistance genes via horizontal transfer. All integrons have three essential core features. The first feature is intI, the second one is an integron-associated recombination site, attI, and an integron-associated promoter, Pc, is the last feature. Among them, the class 1 integron is a major player in the dissemination of antibiotic resistance genes across pathogens and commensals. Various classes of integrons possessing a wide variety of gene cassettes are distributed in bacteria throughout the world. This review thus focuses on the distribution of integrons among important bacteria.

Class I integrons among multidrug resistant Enterobacter spp. isolates from hospitalized patients in Babol, North of Iran.

BACKGROUND: Multidrug resistance (MDR) in Enterobacter spp. has created therapeutic challenges all over the world. The present study was conducted for evaluating the prevalence of class I integron, determining the gene cassettes and antimicrobial resistance profile of Enterobacter spp. isolates from clinical samples in Babol, North of Iran. METHODS: During a 13-month period, 30 Enterobacter spp. isolates were collected from Ayatollah Rouhani Hospital, Babol, Iran. Various types of antimicrobial agents were used to determine the resistance pattern. Class I integron and associated gene cassettes were detected by PCR assay. RESULTS: The resistance rates to AP, CPM, CTX, TM, NI, IMI, AK, CIP and GM antimicrobials were 100%, 93.3%, 33.3%, 33.3%, 30%, 20%, 20%, 20% and 13.3%, respectively. The distribution results of int genes showed that 63.3% of isolates carried the intI genes. Also, the prevalence of aadB, dfrA1, bla OXA30 and bla PSE1 genes were estimated at 36.6%%, 33.3%, 6.6% and 0%, respectively. CONCLUSION: Our results showed that class I integrons have a widespread distribution among the Enterobacter spp. isolates and have clinical relevance to MDR isolates. The results confirmed the necessity for uninterrupted monitoring to prevent distribution of multidrug resistance among Enterobacter spp. strains in Iran.

No Evidence for an Association between JC Polyomavirus Infection and Gastroduodenal Diseases.

BACKGROUND: Helicobacter pylori (HP) infection is one of the hypothesized infectious etiologies of gastric cancer (GC) and other gastroduodenal diseases. It was suggested that other infectious agents, including oncogenic viruses, may increase the risk of gastroduodenal diseases. A number of reports regarding JC polyomavirus (JCPyV) have shown that JCPyV could be implicated in colorectal cancer and gastrointestinal carcinogenesis. OBJECTIVE: The current investigation aimed to investigate whether JCPyV could have any association with the pathogenesis of gastroduodenal diseases either alone or together with HP. METHODS: A total of 237 fresh or formalin-fixed and paraffin-embedded gastroduodenal samples were examined by quantitative real-time polymerase chain reaction targeting the JCPyV large tumor antigen (LTag) oncogene, and viral load was determined as viral copy number/cell. RESULTS: In total, 2 out of 237 samples (0.8%) were positive for JCPyV LTag DNA. One positive sample derived from diffuse-type gastric adenocarcinoma (6.8 × 10-3 copies/cell) and other JCPyV-positive sample obtained from a patient with gastritis (2.5 × 10-3 copies/cell) were recorded. Both JCPyV-positive samples were negative for HP infection. CONCLUSION: This study suggests no association between JCPyV infection and GC or other gastroduodenal diseases. The very low frequency of JCPyV LTag sequences in GC is an important aspect that weakens the hypothesis of the pathogenic role of JCPyV in gastric tumor induction.

Molecular characterization of Staphylococcus aureus strains isolated among hospital staff nasal carriers of Babol, Iran.

BACKGROUND: Staphylococcus aureus (s. aureus) nasal carriers, particularly the healthcare staff can be considered as a potential source for the spread of resistant strains. The aim of this study was to determine the molecular characterization of S. aureus strains isolated among the staff nasal carriers in one of the teaching hospitals in Babol. METHODS: A total of 120 nasal swabs were taken from the staff of Ayatollah Rouhani Hospital Babol during 2016. The antibiotic resistance pattern was performed by disc diffusion method for 13 antibiotics, including cefoxitin, cephalothin, teicoplanin, vancomycin, daptomycin, oxacillin, amoxicillin, amikacin, linezolid, ciprofloxacin, levofloxacin, erythromycin, rifampin, according to the CLSI 2015. Polymerase chain reaction (PCR) was used to detect mecA and pvl genes. Finally, the different SCCmec types were determined by multiplex- PCR method. RESULTS: Among the 120 collected specimens, 40(33.3%) S. aureus isolates were approved. 28(70%) of strains were identified as methicillin-resistant Staphylococcus aureus (MRSA) and the frequency of pvl gene was confirmed 2(5%). Based on the multiplex PCR assay, four different SCCmec types were detected as 35.7% type I, 14.2% type III, 7.1% type II and 3.5% type IV. By a disc diffusion method, no resistance pattern was observed to vancomycin, while 100% of strains were resistant to amoxicillin. CONCLUSION: Consequently our results illustrated that isolated S. aureus strains among the staff nasal carriers via mentioned molecular characterization may lead to increase the nosocomial persistent infections in hospitalized patients and also health care workers.