Genetic approach toward linkage of Iran 2012-2016 cholera outbreaks with 7th pandemic Vibrio cholerae.

Vibrio cholerae, as a natural inhabitant of the marine environment is among the world-leading causes of diarrheal diseases. The present study aimed to investigate the genetic relatedness of Iran 2012-2016 V. cholerae outbreaks with 7th pandemic cholera and to further characterize the non-ST69/non-ST75 sequence types strains by whole-genome sequencing (WGS).Twenty V. cholerae isolates related to 2012, 2013, 2015 and 2016 cholera outbreaks were studied by two genotyping methods - Pulsed-field Gel Electrophoresis (PFGE) and Multi-locus Sequence Typing (MLST)-and by antimicrobial susceptibility testing. Seven sequence types (STs) and sixteen pulsotypes were detected. Sequence type 69 was the most abundant ST confirming that most (65%, 13/20) of the studied isolates collected in Iran between 2012 and 2016 belonged to the 7th pandemic clone. All these ST69 isolates (except two) exhibited similar pulsotypes. ST75 was the second most abundant ST. It was identified in 2015 and 2016. ST438, ST178, ST579 and STs of 983 and 984 (as newfound STs) each were only detected in one isolate. All strains collected in 2016 appeared as distinct STs and pulsotypes indicative of probable different originations. All ST69 strains were resistant to nalidixic acid. Moreover, resistance to nalidixic acid, trimethoprim-sulfamethoxazole and tetracycline was only observed in strains of ST69. These properties propose the ST69 as a unique genotype derived from a separate lineage with distinct resistance properties. The circulation of V. cholerae ST69 and its traits in recent years in Iran proposes the 7th pandemic strains as the ongoing causes of cholera outbreaks in this country, although the role of ST75 as the probable upcoming dominant ST should not be ignored.Genomic analysis of non-ST69/non-ST75 strains in this study showed ST579 is the most similar ST type to 7th pandemic sequence types, due to the presence of wild type-El Tor sequences of tcpA and VC-1319, VC-1320, VC-1577, VC-1578 genes (responsible for polymyxin resistance in El Tor biotype), the traits of rstC of RS1 phage in one strain of this ST type and the presence of VPI-1 and VSP-I islands in ST579 and ST178 strains. In silico analysis showed no significant presence of resistance genes/cassettes/plasmids within non-ST69/non-ST75 strains genomes. Overall, these data indicate the higher susceptibility of V. cholerae non-ST69/non-ST75 strains in comparison with more ubiquitous and more circulating ST69 and ST75 strains.In conclusion, the occurrence of small outbreaks and sporadic cholera cases due to V. cholerae ST69 in recent years in Iran shows the 7th pandemic strains as the persistent causes of cholera outbreaks in this country, although the role of ST75 as the second most contributed ST should not be ignored. The occurrence of non-ST69/non-ST75 sequence types with some virulence factors characteristics in border provinces in recent years is noteworthy, and further studies together with surveillance efforts are expected to determine their likely route of transport.

Prevalence of Brucella melitensis and Brucella abortus tetracyclines resistance: A systematic review and meta-analysis.

INTRODUCTION: Brucellosis is a zoonotic disease that can be transmitted from animals to humans. Brucellosis is caused by bacteria of the genus Brucella, which are typically transmitted through contact with infected animals, unpasteurized dairy products, or airborne pathogens. Tetracyclines (tetracycline and doxycycline) are antibiotics commonly used to treat brucellosis; however, antibiotic resistance has become a major concern. This study assessed the worldwide prevalence of tetracycline-resistant Brucella isolates. METHODS: A systematic search was conducted in Scopus, PubMed, Web of Science, and EMBASE using relevant keywords and Medical Subject Headings (MeSH) terms until August 13, 2022, to identify relevant studies for meta-analysis. A random effects model was used to estimate the proportion of resistance. Meta-regression analysis, subgroup analysis, and examination of outliers and influential studies were also performed. RESULTS: The prevalence rates of resistance to tetracycline and doxycycline were estimated to be 0.017 (95% confidence interval [CI], 0.009-0.035) and 0.017 (95%CI, 0.011-0.026), respectively, based on 51 studies conducted from 1983 to 2020. Both drugs showed increasing resistance over time (tetracycline: r = 0.077, P = 0.012; doxycycline: r = 0.059, P = 0.026). CONCLUSION: The prevalence of tetracycline and doxycycline resistance in Brucella was low (1.7%) but increased over time. This increase in tetracycline and doxycycline resistance highlights the need for further research to understand resistance mechanisms and develop more effective treatments.

Prevalence of colistin resistance of Klebsiella pneumoniae isolates in Iran: a systematic review and meta-analysis.

OBJECTIVE: Klebsiella pneumoniae is a gram-negative pathogen common cause of nosocomial infections. Colistin is a last resort antibiotic to treat infections caused by K. pneumoniae. In recent years, the resistance rate to colistin has increased in K. pneumoniae. This study evaluated the prevalence of colistin resistance of K. pneumoniae isolates in Iran using a systematic review and meta-analysis. METHOD: A systematic search was performed for relevant articles until August 2021 in the following database: PubMed, Scopus, SID and Google Scholar. The pooled prevalence of colistin resistance in clinical K. pneumoniae isolates analyzed using Comprehensive Meta-Analysis Software (CMA). RESULTS: Finally, 19 articles with appropriate criteria were included in the meta-analysis. Our results showed 6.9% of the pooled prevalence of colistin resistance in clinical K. pneumoniae isolates in Iran. The results of subgroup analysis demonstrated increase resistance of colistin from 4.8%; (95% CI 1.5-13.9%) in 2013-2018 to 8.2%; (95% CI 3.4-18.6%), in 2019-2021. Also, the results of our study showed a strong association between the carbapenem producing K. pneumoniae and increased resistance to colistin. CONCLUSIONS: This study showed a high prevalence of colistin resistance in K. pneumoniae isolates. It is recommended that regular evaluation be performed to control colistin resistance.

Prevalence of Brucella melitensis and Brucella abortus Fluoroquinolones Resistant Isolates: A Systematic Review and Meta-Analysis.

Background: Brucellosis impact both animals and humans worldwide. However, using antibiotics for brucellosis remains controversial despite decades of research. Relapse can complicate treatment in this area. Since the mid-1980s, microbiologists, and physicians have studied fluoroquinolones' use for treating human brucellosis. The principal advantages of fluoroquinolones are their intracellular antimicrobial activity, low nephrotoxicity, good pharmacokinetics, and the lack of drug-level monitoring. Fluoroquinolones inhibit disease recurrence. In vitro and clinical data were used to study the prevalence of Brucella melitensis and Brucella abortus fluoroquinolone-resistant isolates. Methods: The PubMed, Scopus, Embase, and Web of Science databases were carefully searched until August 6, 2022, for relevant papers. The number of resistant isolates and sample size were used to estimate the proportion of resistant isolates, fitting a model with random effects, and DerSimonian-Laird estimated heterogeneity. Furthermore, meta-regression and subgroup analyses were used to assess the moderators to identify the sources of heterogeneity. Meta-analysis was performed using R software. Results: Forty-seven studies evaluated fluoroquinolone resistance in Brucella spp. Isolates. Fluoroquinolones have shown high in vitro efficacy against Brucella spp. The resistance rates to ofloxacin, sparfloxacin, fleroxacin, pefloxacin, and lomefloxacin were 2%, 1.6%, and 4.6%, respectively. Conclusion: Clinical in vitro tests demonstrated that fluoroquinolones can eradicate Brucella spp. Owing to first-line medication resistance, recurrence, and toxicity, it is essential to standardize the Brucella antimicrobial susceptibility test method for a more precise screening of resistance status. Fluoroquinolones are less resistant to fluoroquinolone-based treatments in modern clinical practice as alternatives to standard therapy for patients with brucellosis relapse after treatment with another regimen and in patients who have developed toxicity from older agents.

Prevalence of antibiotic resistance in clinical isolates of Mycobacterium kansasii: a systematic review and meta-analysis.

INTRODUCTION: The prevalence of diseases caused by non-tuberculous mycobacteria (NTM), including M. kansasii, is increasing, necessitating further information to guide prevention, control, and treatment strategies. AREAS COVERED: A comprehensive analysis of articles published until February 2023 was conducted on PubMed, Web of Science, and Scopus databases to investigate antibiotic resistance in M. kansasii species. Stata software version 17 was employed for all analyses. EXPERT OPINION: A total of 1647 articles were obtained through database search. After removing duplicates and unrelated studies, 17 cross-sectional studies that examined the breakpoints proposed by CLSI were included. The rates of resistance of M. kansasii to various antibiotics were as follows: clarithromycin (0%), rifampin (1%), amikacin (0%), ciprofloxacin (14%), linezolid (0%), moxifloxacin (0%), rifabutin (1%), doxycycline (96%), and SXT (49%). Our findings underscore the importance of managing and monitoring the use of these antibiotics, as well as the need for further studies to elucidate the exact mechanism of M. kansasii resistance to these antibiotics.

Prevalence of Brucella melitensis and Brucella abortus aminoglycoside-resistant isolates: a systematic review and meta-analysis.

INTRODUCTION: Aminoglycosides are vital antibiotics for treating Brucella infections, because they interfere with bacterial protein production and are often combined with other antibiotics. They are cost-effective, have fewer side effects, and can penetrate biofilms. The prevalence of brucellosis has increased in recent years, increasing the need for effective treatments. In addition, the emergence of multidrug-resistant Brucella strains has highlighted the need for an updated and comprehensive understanding of aminoglycoside resistance. This systematic review aimed to provide a comprehensive overview of the global prevalence of aminoglycoside resistance in B. melitensis and B. abortus. METHODS: A systematic search of online databases was conducted and eligible studies met certain criteria and were published in English. Quality assessment was performed using the JBI Checklist. A random-effects model was fitted to the data, and meta-regression, subgroup, and outlier/influential analyses were performed. The analysis was performed using R and the metafor package. RESULTS: The results of this systematic review and meta-analysis suggested that the average prevalence rates of streptomycin, gentamicin, and amikacin resistance were 0.027 (95% confidence interval [CI], 0.015-0.049), 0.023 (95% CI, 0.017-0.032), and 0.008 (95% CI, 0.002-0.039), respectively. The prevalence of streptomycin resistance was higher in the unidentified Brucella group than in the B. abortus and B. melitensis groups (0.234, 0.046, and 0.017, respectively; p < 0.02). The prevalence of gentamicin resistance increased over time (r = 0.064; 95% CI, 0.018 to 0.111; p = 0.007). The prevalence of resistance did not correlate with the quality score for any antibiotic. Funnel plots showed a potential asymmetry for streptomycin and gentamicin. These results suggest a low prevalence of antibiotic resistance in the studied populations. CONCLUSION: The prevalence of aminoglycoside resistance in B. melitensis and B. abortus was low. However, gentamicin resistance has increased in recent years. This review provides a comprehensive and updated understanding of aminoglycoside resistance in B. melitensis and B. abortus.

Prevalence of Mycobacterium kansasii in clinical and environmental isolates, a systematic review and meta-analysis.

Background: Mycobacterium kansasii infection is one of the most common causes of non-tuberculosis mycobacterial (NTM) disease worldwide. However, accurate information on the global prevalence of this bacterium is lacking. Therefore, this study was conducted to investigate the prevalence of M. kansasii in clinical and environmental isolates. Methods: Databases, including PubMed, Scopus, and the Web of Science, were utilized to gather articles on the prevalence of M. kansasii in clinical and environmental isolates. The collected data were analyzed using Comprehensive Meta-Analysis software. Results: A total of 118 and 16 studies met the inclusion criteria and were used to analyze the prevalence of M. kansasii in clinical and environmental isolates, respectively. The prevalence of M. kansasii in NTM and environmental isolates were 9.4 and 5.8%, respectively. Subsequent analysis showed an increasing prevalence of M. kansasii over the years. Additionally, the results indicated a significant difference in the prevalence of this bacteria among different regions. Conclusion: The relatively high prevalence of M. kansasii among NTM isolates suggests the need for further implementation of infection control strategies. It is also important to establish appropriate diagnostic criteria and management guidelines for screening this microorganism in environmental samples in order to prevent its spread, given its high prevalence in environmental isolates.

Anti-biofilm Activity of a Lytic Phage Against Vancomycin-Resistant Enterococcus faecalis.

Background & Objective: This study aims to isolate a lytic bacteriophage against planktonic Enterococcus faecalis V583 culture and evaluate its ability to disrupt and inhibit biofilm. Methods: An anti-E. faecalis phage was isolated from sewage and visualized by electron microscopy, the vB_EfsS_V583 (V583) host range was determined by spot test on 13 E. faecalis clinical strains. Inhibition and degradation experiments were designed to investigate the effect of phage on biofilm. In the inhibition and degradation assay, biofilms were formed in the presence and absence of phage, respectively. Finally, crystal violet method tested the effect of phage on biofilm. Results: Phage V583 belongs to the Siphoviridae family and can infect all E. faecalis strains. Antibacterial activity has been shown to degrade and inhibit biofilm produced by V583. The study results showed that phage v583 is more efficient in biofilm inhibition than biofilm degradation. In both assays, phage-treated wells' absorption is less than untreated wells. These results were confirmed by Colony-forming unit reduction in the treated biofilm. Conclusion: The anti-biofilm activity showed that phage therapy using phage V583 might be an alternative tool to remove E. faecalis biofilms.

Biological characteristics and anti-biofilm activity of a lytic phage against vancomycin-resistant Enterococcus faecium.

BACKGROUND AND OBJECTIVES: An important leading cause of the emergence of vancomycin-resistant enterococci, especially Enterococcus faecium, is the inefficiency of antibiotics in the elimination of drug-resistant pathogens. Consequently, the need for alternative treatments is more necessary than ever. MATERIALS AND METHODS: A highly effective bacteriophage against vancomycin-resistant E. faecium called vB-EfmS-S2 was isolated from hospital sewage. The biological properties of phage S2 and its effect on biofilm structures were determined. RESULTS: Phage S2 was specifically capable of lysing a wide range of clinical E. faecium isolates. According to Electron microscopy observations, the phage S2 belonged to the Siphoviridea family. Suitable pH spectra for phage survival was 5-11, at which the phage showed 100% activity. The optimal temperature for phage growth was 30-45°C, with the highest growth at 37°C. Based on one-step growth curve results, the latent period of phage S2 was 14 min with a burst size of 200 PFU/ml. The phage S2 was also able to tolerate bile at concentrations of 1 and 2% and required Mg2+ for an effective infection cycle. Biofilms were significantly inhibited and disrupted in the presence of the phage. CONCLUSION: According to the results, phage S2 could potentially be an alternative for the elimination and control of vancomycin-resistant E. faecium biofilm.