Correlation of RAPD-PCR Profiles with ESBL Production in Clinical Isolates of Klebsiella pneumoniae in Tehran

Comparative Assessment of Different PCR-Based Typing Methods of Pseudomonas aeruginosa Isolates

Introduction

Pseudomonas aeruginosa is one of the important causes of nosocomial infections. Analyzing the diversity of these isolates is important to control the diseases caused by them. Studies of molecular epidemiology depend on the application of typing methods.

Purpose

This study aims to assess the performance of PCR- based typing techniques (RAPD, ribotyping, tDNA, and ERIC) in determining the genetic diversity of 44 P. aeruginosa urinary isolates.

Methods

Performance parameters were analyzed for each of the tested methods. The banding pattern was assessed by calculating polymorphism, genotypic gene diversity and the effective multiplex ratio. Moreover, strain diversity, typeability, and discriminatory power were used to measure the efficiency of typing methods. The congruence among typing methods was calculated by Rand’s and Wallace coefficients.

Results

P-640 among RAPD primers and Ribo-2 among ribotyping primers were more informative as they gave high strain diversity, the highest number of clusters, and highest discriminatory power (ISD=70.45%, 29 clusters at 70% cutoff, DI=0.97 and ISD=75%, 25 clusters at 70% cutoff DI=0.969, respectively). Comparison of typing methods showed that RAPD-PCR gave the highest mean percent polymorphism per assay (76.85%) followed by ERIC-PCR. ERIC-PCR outperformed in most marker parameters; highest mean number of alleles, number of monomorphic bands per assay unit, mean genotypic gene diversity, effective multiplex ratio, and assay efficiency index. Calculated congruence revealed that individual methods demonstrate moderate to poor predictive power. Interestingly, this power increased by combining data obtained from another method.

Conclusion

RAPD primer (P-640) had more discrimination power followed by ribo-2 and ERIC. The performance and predictive power of typing methods can be improved by combining data obtained from different methods as ERIC+OPA-02 and ERIC+P-640 combinations gave complete typeability and discrimination of isolates. ERIC, ERIC+OPA-02, and ERIC+P-640 combinations can provide finer discrimination and classification of P. aeruginosa strains than the other tested methods.

Carbapenem-Resistant Klebsiella Pneumoniae in Iran: a Systematic Review and Meta-Analysis

The global emergence and dissemination of carbapenem-resistant (CR)-Klebsiella pneumoniae is an important healthcare concern owing to the limited therapeutic options that are available. The aim of the present study was to evaluate the prevalence of CR K. pneumoniae in different parts of Iran. A comprehensive literature search was performed in national and international databases. After applying predefined inclusion and exclusion criteria, 36 articles reporting prevalence of CR K. pneumoniae were collected. The pooled prevalence of CR K. pneumoniae was estimated to be 11.3% (95% CI: 0.084-0.15). The highest and lowest prevalence rates of CR K. pneumoniae were in Isfahan 58% (95% CI: 0.48-0.67) and Tehran 0.004 (95% CI: 0.00-0.05), respectively. The highest and lowest resistance rates were seen against aztreonam (55%, 95% CI: 0.48-0.62) and amikacin (23%, (95% CI: 0.17-0.29), respectively. The findings of the present study revealed that the prevalence of CR K. pneumoniae is alarmingly high in the majority of Iranian hospitals.

RAPD PCR Profile, Antibiotic Resistance, Prevalence of armA Gene, and Detection of KPC Enzyme in Klebsiella pneumoniae Isolates

The increasing prevalence of multidrug-resistant Klebsiella pneumoniae strains isolated from hospitals shows the limitation of recent antibiotics used for bacterial eradication. In this study, 81 K. pneumoniae isolates were collected from three hospitals in Tehran. Antibiotic susceptibility test showed the highest rates of resistance to cefotaxim (85.5%) and ceftazidime (78.3%), and the lowest rates of resistance were detected for colistin (16.9%), streptomycin (16.8%), and chloroamphenicol (21.7%). Eleven different resistance patterns were observed. Sixty-six out of 81 isolates (81.5%) were found to be multidrug resistant (MDR), and 35.8% of them belonged to A3 resistance pattern. 7.4% and 66.7% were KPC enzyme and armA gene positive, respectively. RAPD PCR assay of these bacteria showed 5 clusters, 16 single types, and 14 common types, and there was not any correlation between genetic patterns of the isolates and presence of resistance agents. Simultaneous detection of resistance-creating agents could be an important challenge for combination therapy of MDR K. pneumoniae-caused infections.

Association between Virulence Factors and Extended Spectrum Beta-Lactamase Producing Klebsiella pneumoniae Compared to Nonproducing Isolates

Klebsiella pneumoniae is considered an important opportunistic multidrug-resistant pathogen. Extended spectrum β-lactamases (ESBLs) and expression of a multitude of virulence factors may work in a harmony resulting in treatment failure. This study was undertaken to compare the virulence characteristics and genetic relatedness between ESBL and non-ESBL producing K. pneumoniae. Methods. Antibiotic sensitivity test of all isolates was determined by disc diffusion assay. Phenotypic and genotypic detection of ESBL were done. Various virulence factors and some virulence factor-associated genes were screened. Random amplified polymorphic DNA (RAPD) was employed to investigate the genetic fingerprints of ESBL from non-ESBL producing K. pneumoniae. Results. 50% of isolates were ESBL producers. A significant association was observed between ESBL production and biofilm (strong and moderate), serum resistance, and iss gene. Moreover, significant association between non-ESBL producers and hypermucoviscosity was identified. Dendogram analysis of RAPD profile classified K. pneumoniae isolates into four clusters (a, b, c, and d). Seventy-six percent of ESBL producers belonged to cluster a. In conclusion, this study suggests a correlation between ESBL production and some virulence factors. Therefore, success of treatment depends mainly on increased clinicians awareness and enhanced testing by laboratories to reduce the spread of these isolates.

Detection of a CTX-M group 2 beta-lactamase gene in a Klebsiella pneumoniae isolate from a tertiary care hospital, Trinidad and Tobago

Background

Identification of the prevalence and spread of ESBL-mediated antibiotic resistance is essential especially in the hospital setting. It is for this reason, more and more studies are highlighting the importance of complementing phenotypic ESBL-detection techniques with molecular techniques in order to understand the basis and extent of this form of resistance among clinically evolved bacterial populations, especially those belonging to the Enterobacteriaceae family. However, in Trinidad and Tobago and other Caribbean countries, very little is known regarding ESBL detection rates and/or the prevalence of genes conferring ESBL resistance.

Methodology

Sixty-six Klebsiella pneumoniae isolates from clinical specimens phenotypically identified by the Microscan Walkaway-96 System as potential ESBL-producers were analysed in this study. Screening and confirmation of these isolates as ESBL producers was done by the Clinical and Laboratory Standards Institute (CLSI) approved methods. Polymerase chain reaction amplification of beta-lactamase genes bla_TEM, bla_SHV, bla_CTX-M1, bla_CTX-M2 and bla_AmpC was performed to identify mechanisms of β-lactam resistance.

Results

ESBL-producing K. pneumoniae was confirmed in 78.8% (41/52) from isolates collected from a variety of sources during the period, April–July 2015. bla_SHV (84.8%) and bla_CTX-M (46.9%) were the predominant β-lactamase genes identified. A single K. pneumoniae isolate possessed a bla_CTX-M group 2 beta-lactamase gene. RAPD analysis identified a number of epidemiologically related isolates. However, current isolates were unrelated to isolates from previous years.

Conclusion

This study revealed that among K. pneumoniae isolates exhibiting extended spectrum β-lactam resistance, there was a high prevalence of bla_SHV and bla_CTX-M genes. This result highlights the need for a reliable epidemiological apparatus that involves the molecular characterisation of ESBL resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12941-017-0209-x) contains supplementary material, which is available to authorized users.