Phylogenetic group, antibiotic resistance, virulence gene, and genetic diversity of Escherichia coli causing bloodstream infections in Iran.

Escherichia coli is one of the most important pathogens causing bloodstream infections (BSIs) throughout the world. We sought to characterize the phylogroup classification, major human sequence types (STs), antimicrobial resistance, presence of selected antimicrobial resistance and virulence genes, and genetic diversity of E. coli isolated from patients with BSIs at the University Hospital in Iran. A total of 100 E. coli bloodstream isolates were collected between December 2020 and June 2022. This study used PCR to investigate phylogenetic groups (A, B1, B2, C, D, E, and F), four major STs (ST69, ST73, ST95, and ST131), antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), and pathogenicity islands (PAIs). Antimicrobial susceptibility testing was done by disk diffusion method. Genetic diversity was analyzed by repetitive element sequence-based PCR (REP-PCR). The phylogenetic group B2 (32%) predominated, followed by phylogenetic group E (25%). ST131 (28%) was the most prevalent ST and the majority of these isolates (89.3%) were of serotype O25b. Most of E. coli isolates (75%) were categorized as multidrug resistant (MDR) with high rates of resistance (>55%) to ampicillin, trimethoprim-sulfamethoxazole, ciprofloxacin, cefazolin, and ceftriaxone. The most frequent ARGs were bla TEM (66%), sul1 (57%), and sul2 (51%). The most prevalent VAGs and PAIs were fimH (type 1 fimbriae adhesin; 85%), aer (iucC) (aerobactin; 79%), traT (serum resistance; 77%), iutA (aerobactin siderophore receptor; 69%), and PAI IV536 (75%), respectively. The highest rate of ARGs and VAGs was observed in the ST131 isolates. REP-PCR analysis showed high diversity among the studied isolates. The high prevalence of MDR septicemic E. coli with different types of ARGs, VAGs and genotypes is an extremely worrisome sign of BSIs treatment and poses a major threat for hospitalized patients. Active surveillance, stringent prescribing policies, increasing the awareness of ARGs among clinicians and re-defining the infection control measures are essential to curb the dissemination of these strains.

Phenotypic and genotypic evaluation of aminoglycoside resistance in Escherichia coli isolated from patients with blood stream infections in Tehran, Iran.

Background and Objectives: Escherichia coli is a significant causative agent of bloodstream infections (BSIs). Aminoglycoside antibiotics play a crucial role in treating severe infections such as sepsis and pneumonia. However, resistance to these antibiotics often occurs due to the production of aminoglycoside-modifying enzymes (AMEs). This study was conducted to assess antimicrobial susceptibility patterns against various aminoglycosides and to determine the prevalence of common AME genes in E. coli strains isolated from BSIs. Materials and Methods: Sixty-five E. coli isolates were obtained from blood samples in a referral hospital in Tehran, Iran. The susceptibility patterns of aminoglycosides were determined using disk diffusion method and AMEs genes were investigated using PCR assay. Results: Resistance to aminoglycosides was observed in 64.6% (42/65) of the isolates. The most frequent resistance rate was found for kanamycin (44.6%) and gentamicin (38.5%), followed by tobramycin (29.2%) and amikacin (4.6%). The most frequent AME gene was aac(3)-IVa, which detected in 49.2% isolates, followed by aac(6)-Ib (40%), aac(3)-IIa (32.3%), and ant(2)-Ia (30.8%), respectively. Conclusion: Athough the findings of this survey are based on specimens collected from a single hospital, our study shows that the high prevalence of aminoglycoside resistance is primarily attributed to the presence of the aac(3)-Iva, aac(6)-Ib and aac(3)-IIa genes. The low rate of resistance to amikacin makes this antibiotic a good candidate for treatment of BSIs due to E. coli.

In Vitro antibiotic combinations of Colistin, Meropenem, Amikacin, and Amoxicillin/clavulanate against multidrug-resistant Klebsiella pneumonia isolated from patients with ventilator-associated pneumonia.

BACKGROUND: Hospital infections such as ventilator-associated pneumonia (VAP) due to multidrug-resistant Klebsiella pneumoniae (MDR-KP) strains have increased worldwide. In addition, biofilm production by these resistant isolates has confronted clinicians with higher treatment failure and infection recurrence. Given the paucity of new agents and limited data on combination therapy for MDR-KPs, the present study sought to evaluate the in vitro activity of several antibiotic combinations against planktonic and biofilm MDR-KPs isolated from patients with VAP. RESULTS: All 10 carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates demonstrated multidrug resistance against the tested antibiotics. At planktonic mode, combinations of colistin-meropenem and amoxicillin/clavulanate in combination with meropenem, colistin, or amikacin showed synergism against 60-70% isolates. On the other hand, in the biofilm state, colistin-based combinations exhibited synergism against 50-70% isolates and the most effective combination was colistin-amikacin with 70% synergy. CONCLUSIONS: The results revealed that combinations of amoxicillin/clavulanate with colistin, meropenem, or amikacin in the planktonic mode and colistin with amoxicillin/clavulanate, meropenem, or amikacin in the biofilm mode could effectively inhibit CRKP isolates, and thus could be further explored for the treatment of CRKPs.

HVHC-ESD-Induced Oxygen Vacancies: An Insight into the Phenomena of Interfacial Interactions of Nanostructure Oxygen Vacancy Sites with Oxygen Ion-Containing Organic Compounds.

The challenging environmental chemical and microbial pollution has always caused issues for human life. This article investigates the detailed mechanism of photodegradation and antimicrobial activity of oxide semiconductors and realizes the interface phenomena of nanostructures with toxins and bacteria. We demonstrate how oxygen vacancies in nanostructures affect photodegradation and antimicrobial behavior. Additionally, a novel method with a simple, tunable, and cost-effective synthesis of nanostructures for such applications is introduced to resolve environmental issues. The high-voltage, high-current electrical switching discharge (HVHC-ESD) system is a novel method that allows on-the-spot sub-second synthesis of nanostructures on top and in the water for wastewater decontamination. Experiments are done on rhodamine B as a common dye in wastewater to understand its photocatalytic degradation mechanism. Moreover, the antimicrobial mechanism of oxide semiconductors synthesized by the HVHC-ESD method with oxygen vacancies is realized on methicillin- and vancomycin-resistant Staphylococcus aureus strains. The results yield new insights into how oxygen ions in dyes and bacterial walls interact with the surface of ZnO with high oxygen vacancy, which results in breaking of the chemical structure of dyes and bacterial walls. This interaction leads to degradation of organic dyes and bacterial inactivation.

Determining effects of nitrate, arginine, and ferrous on antibiotic recalcitrance of clinical strains of Pseudomonas aeruginosa in biofilm-inspired alginate encapsulates.

BACKGROUND: Biofilms play a role in recalcitrance and treatability of bacterial infections, but majority of known antibiotic resistance mechanisms are biofilm-independent. Biofilms of Pseudomonas aeruginosa, especially in cystic fibrosis patients infected with the alginate producing strains in their lungs, are hard to treat. Changes in growth-related bacterial metabolism in biofilm affect their antibiotic recalcitrance which could be considered for new therapies designed based on these changes. In this study, effects of nitrate, arginine, and ferrous were investigated on antibiotic recalcitrance in alginate-encapsulated P. aeruginosa strains isolated from cystic fibrosis patients in the presence of amikacin, tobramycin, and ciprofloxacin. Also, expression of an efflux pump gene, mexY, was analyzed in selected strains in the presence of amikacin and ferrous. METHODS: Clinical P. aeruginosa strains were isolated from cystic fibrosis patients and minimum inhibitory concentration of amikacin, tobramycin, and ciprofloxacin was determined against all the strains. For each antibiotic, a susceptible and a resistant or an intermediate-resistant strain were selected, encapsulated into alginate beads, and subjected to minimal biofilm eradication concentration (MBEC) test. After determining MBECs, sub-MBEC concentrations (antibiotics at concentrations one level below the determined MBEC) for each antibiotic were selected and used to study the effects of nitrate, arginine, and ferrous on antibiotic recalcitrance of encapsulated strains. Effects of ferrous and amikacin on expression of the efflux pump gene, mexY, was studied on amikacin sensitive and intermediate-resistant strains. One-way ANOVA and t test were used as the statistical tests. RESULTS: According to the results, the supplements had a dose-related effect on decreasing the number of viable cells; maximal effect was noted with ferrous, as ferrous supplementation significantly increased biofilm susceptibility to both ciprofloxacin and amikacin in all strains, and to tobramycin in a resistant strain. Also, treating an amikacin-intermediate strain with amikacin increased the expression of mexY gene, which has a role in P. aeruginosa antibiotic recalcitrance, while treating the same strain with ferrous and amikacin significantly decreased the expression of mexY gene, which was a promising result. CONCLUSIONS: Our results support the possibility of using ferrous and arginine as an adjuvant to enhance the efficacy of conventional antimicrobial therapy of P. aeruginosa infections.

Global prevalence and antibiotic resistance in clinical isolates of Stenotrophomonas maltophilia: a systematic review and meta-analysis.

Introduction: Stenotrophomonas maltophilia is a little-known environmental opportunistic bacterium that can cause broad-spectrum infections. Despite the importance of this bacterium as an emerging drug-resistant opportunistic pathogen, a comprehensive analysis of its prevalence and resistance to antibiotics has not yet been conducted. Methods: A systematic search was performed using four electronic databases (MEDLINE via PubMed, Embase, Scopus, and Web of Science) up to October 2019. Out of 6,770 records, 179 were documented in the current meta-analysis according to our inclusion and exclusion criteria, and 95 studies were enrolled in the meta-analysis. Results: Present analysis revealed that the global pooled prevalence of S. maltophilia was 5.3 % [95% CI, 4.1-6.7%], with a higher prevalence in the Western Pacific Region [10.5%; 95% CI, 5.7-18.6%] and a lower prevalence in the American regions [4.3%; 95% CI, 3.2-5.7%]. Based on our meta-analysis, the highest antibiotic resistance rate was against cefuroxime [99.1%; 95% CI, 97.3-99.7%], while the lowest resistance was correlated with minocycline [4·8%; 95% CI, 2.6-8.8%]. Discussion: The results of this study indicated that the prevalence of S. maltophilia infections has been increasing over time. A comparison of the antibiotic resistance of S. maltophilia before and after 2010 suggested there was an increasing trend in the resistance to some antibiotics, such as tigecycline and ticarcillin-clavulanic acid. However, trimethoprim-sulfamethoxazole is still considered an effective antibiotic for treating S. maltophilia infections.

Molecular Characteristics of Staphylococcus aureus Strains Isolated from Nasal Cavity and Wound Infections Among Diabetic Patients.

Staphylococcus aureus is the most common pathogen contributing to diabetic foot infections (DFI). Nasal transmission of S. aureus potentially increases the risk of endogenous infection. The aim of this study was to determine the genetic diversity and antibiotic resistance profile of S. aureus isolates in nasal and wound samples from diabetic patients. A cross-sectional study was conducted from July 2018 to September 2019. S. aureus was isolated from the anterior nares and wounds of diabetic patients. All S. aureus isolates were characterized by detection of resistance and virulence genes (mecA, ermA, ermC, hla, hlb, hlg, sea, lukDE, pvl), staphylococcal cassette chromosome mec (SCCmec)-typing and staphylococcal protein A (spa)-typing. A total of 34 S. aureus were isolated from the wounds of 115 diabetic patients with DFI. Twenty-four S. aureus isolates were collected from the anterior nares of patients, and thirteen patients had concurrent S. aureus in nasal and wound specimens. The prevalence of methicillin-resistant S. aureus (MRSA) in nasal specimens was noticeable (41.7%), and the most common spa-type in nasal and wound specimens was t14870. Nearly half of the patients with concurrent S. aureus in wound and nasal specimens had similar isolates from both sites. Our data suggest that detection and screening of S. aureus colonization in the nasal cavity may prevent subsequent endogenous infections, particularly with MRSA strains.

Antimicrobial resistance pattern, virulence determinants and molecular analysis of carbapenem-resistant Klebsiella pneumoniae isolated from clinical samples in Iran.

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as an important global threat in recent years. The objective of the present study was to characterize the molecular characteristics, antibiotic resistance pattern and the distribution of virulence factors in CRKP isolated from different clinical specimens. A total of 60 clinical CRKP isolates were collected from clinical samples. Based on Clinical Laboratory Standards Institute guidelines, antimicrobial susceptibility testing was assessed by the disk diffusion method. Carbapenem and aminoglycoside resistance determinants in addition to virulence genes were inspected by PCR. Molecular characteristics of CRKP isolates were analyzed by random amplified polymorphic DNA (RAPD) PCR and enterobacterial repetitive intergenic consensus (ERIC) PCR. All isolates were resistant to imipenem, meropenem, cefoxitin, levofloxacin, cefotaxime, ceftazidime and ciprofloxacin. Resistance to tetracycline, gentamicin and kanamycin were detected in 53%, 75% and 72% of isolates, respectively. The most common carbapenem resistance genes were OXA-48 (28.5%) and NDM (22%). The most common aminoglycosides resistance genes were aac6´Ib (57%) and aac(3)-IVa (28%). The most prevalent virulence genes were mrkD (82%), entB (62%) and ybts (58%). ERIC and RAPD analyses revealed 55 and 53 different patterns of CRKP isolates, respectively. We conclude that CRKP infections have been associated with different genotypes and that the carbapenemase type (OXA-48) and AME gene (aac6´-Ib) were widely distributed in CRKP isolates in our hospital. Continued compliance with existing phenotypes and genotypes, and strict enforcement of infection control guidelines, are recommended approaches for the prevention and dissemination of these strains.

Multiplex detection of five common respiratory pathogens from bronchoalveolar lavages using high resolution melting curve analysis.

BACKGROUND: The study describes the application of the multiplex high-resolution melting curve (MHRM) assay for the simultaneous detection of five common bacterial pathogens (Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii and Escherichia coli) directly from bronchoalveolar lavage samples. RESULTS: Our MHRM assay successfully identified all five respiratory pathogens in less than 5 h, with five separate melting curves with specific melt peak temperatures (Tm). The different Tm were characterized by peaks of 78.1 ± 0.4 °C for S. aureus, 83.3 ± 0.1 °C for A. baumannii, 86.7 ± 0.2 °C for E. coli, 90.5 ± 0.1 °C for K. pneumoniae, 94.5 ± 0.2 °C for P. aeruginosa. The overall sensitivity and specificity of MHRM were 100% and 88.8-100%, respectively. CONCLUSIONS: Our MHRM assay offers a simple and fast alternative to culture approach for simultaneous detection of five major bacterial lower respiratory tract infection pathogens. Utilization of this assay can help clinicians initiate prompt and appropriate antimicrobial treatment, towards reducing the morbidity and mortality of severe respiratory infections.

Multiple-locus variable-number tandem repeat analysis for genotyping of erythromycin-resistant group B streptococci in Iran.

BACKGROUND: Group B Streptococcus (GBS or S. agalactiae) is an important pathogen causing severe invasive diseases in neonates, pregnant women, and adults with underlying medical conditions. METHODS: To investigate the incidence of resistance to macrolide, lincosamide and streptogramin type B (MLSB) antibiotics, macrolide and tetracycline resistance determinants and genetic relationships, a total of 146 clinical isolates of GBS were collected from Tehran, Iran. The genetic relationships between erythromycin-resistant strains were determined by multilocus variable tandem repeat analysis (MLVA). RESULTS: All isolates were susceptible to penicillin, vancomycin, linezolid, and quinupristin-dalfopristin, but were resistant to tetracycline (96.6%, 141/146), erythromycin (28.1%, 41/146) and clindamycin (16.4%, 24/146). Among the 41 erythromycin-resistant GBS (ERGBS), the most common antimicrobial resistance gene was tetM detected in 92.7% (38/41) of the isolates followed by ermTR and ermB found in 65.8% (27/41) and 29.3% (12/41) of isolates, respectively. Of the 41 ERGBS, 95% (39/41) exhibited the constitutive MLSB phenotype, 2.4% (1/41) displayed inducible MLSB and 2.4% (1/41) had M phenotype. The erm methylase genes were widely related to MLSB phenotype isolates, while the mefA gene was associated with M phenotype. MLVA analysis performed on the 41 ERGBS revealed that 34 MLVA types (MTs). MLVA analysis showed that infections due to ERGBS have been caused by a variety of genotypes, suggesting that ERGBS were clonally unrelated and dissemination of these isolates was not due to a clonal outbreak. CONCLUSION: Careful usage of macrolide antibiotics in therapy, continued surveillance of resistance rate and appropriate infection control measures can help to reduce spreading of resistance isolates.