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

PCR Techniques and Their Clinical Applications

Kary B. Mullis developed a revolutionary method name polymerase chain reaction (PCR) in 1983, which can synthesize new strand of DNA complementary to the template strand of DNA and produce billions of copies of a DNA fragment only in few hours. Denaturation, annealing, and extension are the three primary steps involved in the PCR process, which generally requires thermocyclers, DNA template, a pair of primers, Taq polymerase, nucleotides, buffers, etc. With the development of PCR, from traditional PCR, quantitative PCR, to next digital PCR, PCR has become a powerful tool in life sciences and medicine. Applications of PCR techniques for infectious diseases include specific or broad-spectrum pathogen detection, assessment and surveillance of emerging infections, early detection of biological threat agents, and antimicrobial resistance analysis. Applications of PCR techniques for genetic diseases include prenatal diagnosis and screening of neonatal genetic diseases. Applications of PCR techniques for cancer research include tumor-related gene detection. This chapter aimed to discuss about the different types of PCR techniques, including traditional PCR, quantitative PCR, digital PCR, etc., and their applications for rapid detection, mutation screen or diagnosis in infectious diseases, inherited diseases, cancer, and other diseases.

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00520-8.

Biofilm and Gene Expression Characteristics of the Carbapenem-Resistant Enterobacterales, Escherichia coli IMP, and Klebsiella pneumoniae NDM-1 Associated with Common Bacterial Infections

In light of the limited therapeutic options with Carbapenem-Resistant Enterobacterales (CRE) infections, understanding the bacterial risk factors, such as biofilm formation and related gene expression of CRE, is vital. This study investigates the biofilm formation and biofilm-related gene expression of two enteric Enterobacterales with major CR determinants Escherichia coli IMP and Klebsiella pneumoniae NDM-1, which were seen in high prevalence in most common bacterial infections over the past few years. To our knowledge, this is the first study that demonstrated the relationship between biofilm formation and the related gene expression, to understand the potential molecular mechanisms during the biofilm formation in CRE. Biofilms were quantified by tissue culture plate assay at the stages of the biofilm development: initial attachment (6 h), microcolony formation (12 h), maturation (24 h), and dispersion (48 h). In a dispersion, event bacteria detach without any mechanical means and colonise another area. To investigate the influence of different growth conditions on biofilm formation, biofilms were quantified under different growth conditions. In parallel, quantitative real-time PCR (qPCR) assessed the biofilm-related gene expression of a cluster of genes, including biofilm maturation, quorum sensing, stress survival, and antibiotic resistance. Structural changes during biofilm development were assessed via confocal laser scanning microscopy (CLSM). We observed that the biofilm formation of CRE is correlated with the biofilm development stages, with maximum biofilm observed at 24 h at the maturation stage. Our data also showed that biofilm growth, under the condition tested, is the major factor influencing the variability of biofilm gene expression quantification assays. qPCR analyses have demonstrated that the expression of biofilm-related genes is highly correlated with phenotypic biofilm development, and these findings can be further expanded to understand the variation in regulation of such genes in these significant CRE pathogens. Our study demonstrated that both CRE strains, E. coli IMP and K. pneumoniae NDM-1, are high biofilm formers, and genes involved in biofilm development are upregulated during biofilm growth. The characteristic of the increased biofilm formation with the upregulation of antibiotic-resistant and biofilm-related genes indicates the successful pathogenic role of biofilms of these selected CRE and is attributed to their multi-drug resistance ability and successful dissemination of CRE in common bacterial infections.

Antibiotic resistance and random amplified polymorphic DNA typing of Klebsiella pneumoniae isolated from clinical and water samples

The study aimed to screen for the presence of multidrug-resistant Klebsiella pneumoniae from diarrheal stool and environmental water samples and to check the epidemiological link between the two categories. Isolates obtained after culturing on different media were tested for antibiotic resistance and extended-spectrum beta-lactamase (ESBL) production. Polymerase chain reaction (PCR) analysis was done for important β-lactamase encoding genes. Random amplified polymorphic DNA (RAPD) typing was done using two primers. Results showed a high prevalence of K. pneumoniae from fish market effluents compared with stool and well water. Stool isolates showed high resistance to ceftazidime (80.0%) and cefepime (80.0%), fish market effluent isolates to cefoperazone-sulbactam (92.1%), and erythromycin (78.9%), while well water isolates to erythromycin (72.7%) and cefuroxime (54.4%). The ESBL genes bla_CTX , bla_SHV , and bla_TEM were detected in 22.85%, 14.28%, and 42.85% of K. pneumoniae isolates, respectively. The results of RAPD-PCR showed high genetic similarities between the isolates from different sources. PRACTITIONER POINTS: Detection of multi-drug resistant Klebsiella strains in hospital wastewater and drinking water sources has progressively increased since its emerging resistance to third-generation cephalosporins and carbapenems. Detection of beta-lactamase encoding genes by molecular techniques and typing by random amplified polymorphic DNA (RAPD) can be useful in identifying the genetic fingerprints for epidemiological study. Implementation of effective antimicrobial stewardship program and infection control policy thereby helps assess the risk factors associated with infections.

Antibacterial effects of Octenicept, and benzalkonium chloride on Acinetobacter baumannii strains isolated from clinical samples and determination of genetic diversity of isolates by RAPD-PCR method

BACKGROUND

Acinetobacter baumannii (A. baumannii) is among the important causes of nosocomial infections. Due to the emergence of antibiotic resistance, many problems have been raised in the successful treatment of patients infected by this bacterium with the subsequent mortality. Therefore, the present study was performed to evaluate the antibacterial effect of Octenicept (OCT), and Benzalkonium chloride (BZK) against A. baumannii strains isolated from clinical samples, and to determine the genetic diversity of strains by RAPD-PCR method.

METHODS

A total of 119 A. baumannii isolates were collected and confirmed by conventional culture and biochemical tests and PCR assay. Susceptibility of the isolates to antibiotics was evaluated by standard antibiotic susceptibility testing (AST). For antiseptics OCT and BZK, Minimum inhibitory concentration (MIC) was assessed by broth microdilution method. The prevalence of qacE and qacΔE1 genes related to antiseptics was estimated by PCR assay. Finally, genetic diversity of strains was determined by using RAPD-PCR.

RESULTS

All 119 suspected isolates were confirmed as A. baumannii using conventional microbiologic tests and PCR assay. The isolates were mostly originated from blood samples. In AST, the lowest resistance was seen for ciprofloxacin and gentamicin. For antiseptics, the MIC values were reported as 15.26 μg/ml for OCT and 640 μg/ml for BZK. The antiseptic genes of qacE and qacΔE1 were found to be present in 56 (47.05%) and 59 (49.57%) of isolates respectively. RAPD typing revealed great diversity among A. baumannii isolates, with 37 clusters in isolates from ICU, of which 32 clusters were single and 5 were multiple.

CONCLUSIONS

Considering the increase of resistance to antiseptics, it is of importance to monitor the susceptibility of A. baumannii to antiseptics and to promote antiseptic stewardship in hospitals. Furthermore, in this study great diversity was observed among A. baumannii isolates, which is important in understanding the molecular epidemiology of the outbreaks caused by this organism in the hospitals.

High frequency of multidrug-resistant (MDR) Klebsiella pneumoniae harboring several β-lactamase and integron genes collected from several hospitals in the north of Iran

Background

Klebsiella pneumoniae is one of the leading causes of hospital outbreaks worldwide. Also, antibiotic-resistant K. pneumoniae is progressively being involved in invasive infections with high morbidity and mortality. The aim of the current study was to determine antimicrobial susceptibility patterns and the incidence of resistance genes (integron types and β-lactamase-encoded genes) among clinical isolates of K. pneumoniae.

Methods

In this cross-sectional study, a total of 100 clinical samples were obtained from hospitalized patients in three teaching hospitals in the north of Iran, from November 2018 and October 2019. Antimicrobial susceptibility testing was performed using disk agar diffusion test in line with CLSI recommendations. For colistin, minimum inhibitory concentration (MIC) was determined using broth microdilution. Based on antibiogram, multi-drug resistant (MDR) and extensive-drug resistant (XDR) strains were detected. Finally, integron types and β-lactamase resistance genes were identified using polymerase chain reaction technique.

Results

The most and least clinical samples were related to the urine and bronchoalveolar lavage, respectively. Based on the antibiogram results, amikacin and gentamicin exhibited good activity against K. pneumoniae strains in vitro. The high resistance rate (93%) to ampicillin/sulbactam predicts the limited efficacy of this antibiotic, in the hospitals studied. Among all the 100 isolates, the frequency of MDR and XDR phenotypes were 58% and 13%, respectively, while no pan-drug resistant (PDR) strains were found. In the MDR K. pneumoniae strains, the prevalence of bla_SHV, bla_TEM, bla_CTX-M-15, bla_KPC, bla_OXA-48, bla_NDM β-lactamase genes were 91.4%, 82.7%, 79.3%, 29.3%, 36.2% and 6.9%, respectively, however 91.4% of the isolates were carrying intI gene. Class II and III integrons were not detected in any isolates.

Conclusion

The MDR K. pneumoniae is becoming a serious problem in hospitals, with many strains developing resistance to most available antimicrobials. Our results indicate co-presence of a series of β-lactamase and integron types on the MDR strains recovered from hospitalized patients. The increasing rate of these isolates emphasizes the importance of choosing an appropriate antimicrobial regimen based on antibiotic susceptibility pattern.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-021-00476-1.

Co-existence of NDM-1 and OXA-48 genes in Carbapenem Resistant Klebsiella pneumoniae clinical isolates in Kafrelsheikh, Egypt

Background

The noteworthy spread of carbapenem-resistant K. pneumoniae (CR-KP) isolates represents a significant safety threat.

Objective

Determination of the carbapenemase genes incidence among CR-KP clinical isolates in Kafrelsheikh, Egypt.

Methods

A total of 230 K. pneumoniae isolates were recovered from four hospitals in Kafrelsheikh, Egypt. Susceptibility testing was conducted using Kirby-Bauer method and automated-Vitek2 system. CR-KP isolates were tested using modified Hodge test (MHT) and combined disk synergy test. PCR and DNA sequencing were conducted for CR-KP isolates to recognize the included carbapenemase-genes.

Results

Out of 230 K. pneumoniae isolates, 50 isolates presented resistance to carbapenem (meropenem). All 50 CR-KP isolates were multidrug-resistant (MDR). Genes like blaNDM-1 and blaOXA-48 were the only detected genes among CR-KP with an incidence of 70.0% and 52.0%, respectively. Up to 74.0% of the tested isolates carried at least one of the two recorded genes, among them 48.0% co-harbored both blaNDM-1 and blaOXA-48 genes. The accession-numbers of sequenced blaNDM-1 and blaOXA-48 genes were MG594615 and MG594616, respectively.

Conclusion

This study reported a high incidence of MDR profile with the emergence of blaNDM-1 and blaOXA-48 genes co-existence in CR-KP isolates in Kafrelsheikh, Egypt. Hence, more restrictions should be applied against the spread of such serious pathogens.

Spread of NDM-producing Klebsiella pneumoniae in a tertiary Greek hospital

Bacterial carbapenem resistance, especially when mediated by transferable carbapenemases, is of important public health concern. An increased number of metallo-β-lactamase (MBL)-producing Klebsiella pneumoniae strains isolated in a tertiary hospital in Thessaloniki, Greece, called for further genetic investigation.The study included 29 non-repetitive carbapenem resistant K. pneumoniae isolates phenotypically characterized as MBL-producers collected in a tertiary hospital in Greece. The isolates were screened for the detection of carbapenemase genes (K. pneumoniae carbapenemase (blaKPC), Verona-integron-encoded MBL-1 (blaVIM-1), imipenemase (blaIMP), oxacillinase-48 (blaOXA-48) and New Delhi MBL (blaNDM)). The genetic relationship of the isolates was determined by Random Amplified Polymorphic DNA (RAPD) analysis. The whole genome sequences (WGS) from two NDM-positive K. pneumoniae isolates were further characterized.The presence of New Delhi MBL (blaNDM) gene was confirmed in all K. pneumoniae isolates, while blaKPC and blaVIM-1 genes were co-detected in one and two isolates, respectively. The RAPD analysis showed that the isolates were clustered into two groups. The whole genome sequence analysis of two K. pneumoniae isolates revealed that they belonged to the sequence type 11, they carried the blaNDM-1 gene, and exhibited differences in the number and type of the plasmids and the resistant genes.All MBL-producing K. pneumoniae isolates of the study harbored a blaNDM gene, while WGS analysis revealed genetic diversity in resistance genes. Continuous surveillance is needed to detect the emergence of new clones in a hospital setting, while application of antimicrobial stewardship is the only way to reduce the spread of multi-resistant bacteria.

Genotyping and Virulence Analysis of Drug Resistant Clinical Klebsiella pneumoniae Isolates in Egypt

Klebsiella pneumoniae is a highly drug-resistant human pathogen responsible for a variety of serious infections. Integrons, mobile genetic elements capable of integrating antibiotic resistance genes, and the capsule are important virulence factors that increase bacteria resistance to phagocytosis and antimicrobial agents. Molecular typing is an effective tool for identifying the likely etiology of infection. This study aimed to investigate the presence of the rmpA, wcaG, intI1, intI2, and intI3 virulence genes in clinical Klebsiella pneumoniae isolates, and explore their molecular genotypes by using ERIC-PCR. Fifty Klebsiella pneumoniae strains were isolated from various specimens. Antimicrobial resistance was evaluated by using the disc diffusion method. Five genes were amplified by conventional PCR. Genotyping was performed molecularly by using ERIC-PCR. Forty-seven isolates were multi-drug resistant. In all, 18%, 36%, and 98% of the 50 K. pneumoniae isolates were positive for rmpA, wcaG, and intI1 genes, respectively; however, all isolates were negative for intI2 and intI3 genes. Dendogram analysis of the ERIC-PCR results showed 49 distinct patterns, arranged in five clusters. Our study demonstrates high levels of antibiotic resistance and virulence among clinical isolates of K. pneumoniae. Such resistance reflects a growing problem for public health. Further, the presence of integrons increases the horizontal spread of antibiotic resistance and virulence genes among bacterial isolates. The ERIC-PCR technique is an effective method for molecular typing and epidemiological studies of hospital-acquired infections.

Involvement of the AcrAB Efflux Pump in Ciprofloxacin Resistance in Clinical Klebsiella Pneumoniae Isolates

BACKGROUND

Increasing prevalence of multiple antibiotic resistance in Klebsiella pneumoniae strains confines the therapeutic options used to treat bacterial infections.

OBJECTIVE

We aimed in this study to investigate the role of AcrAB and qepA efflux pumps and AAC(6')-Ib-cr enzyme in ciprofloxacin resistance and to detect the RAPD-PCR fingerprint of K. pneumoniae isolates.

METHODS

A total of , 117 K. pneumoniae isolates were collected from hospitalized patients in three hospitals in Tehran, Iran, from August 2013 to March 2014. Antimicrobial susceptibility tests were performed by the disk diffusion method. Molecular identification and expression level of encoding quinolone resistance genes, acrA, acrB, qepA, and aac(6')-Ib-cr, were performed by PCR and real-- time PCR assays, respectively. All the K. pneumoniae isolates containing the mentioned genes were used simultaneously for RAPD-PCR typing.

RESULTS

Colistin and carbapenems were the most efficient antibiotics against the clinical isolates of K. pneumoniae. PCR assay demonstrated that among the 117 isolates, 110 (94%) and 102 (87%) were positive for acrA and acrB gene and 5 (4%) and 100 (85%) isolates showed to have qepA and aac(6')-Ib-cr genes, respectively. Determination for AcrAB pump expression in 21% of strains demonstrated an increased expression, and the mean increase expression for acrB genes was 0.5-81. The results of RAPD-PCR reflected that in 95% CI, all isolates belonged to a clone.

CONCLUSION

A high prevalence of genes encoding quinolone resistance in K. pneumoniae was detected in clinical samples. Therefore, the control of infection and prevention of drug-resistant bacteria spread need careful management of medication and identification of resistant isolates.

The threat of carbapenem-resistant gram-negative bacteria in a Middle East region

Data on the status of carbapenem-resistant microorganisms in the Middle East countries are scarce. The aim of this review was to collect available data regarding resistance to carbapenems in a Middle East region. Available data regarding carbapenem-resistant isolates were considered for evaluation in this review. Biomedical electronic databases were systematically searched to find related articles. The key terms used were "carbapenem-resistant, resistant gram-negative bacilli, Enterobacteriaceae, fermenting and non-fermenting gram-negative bacilli, Pseudomonas, Acinetobacter, Klebsiella and Iran". After primary screening, 275 relevant articles were selected to be assessed thoroughly. Resistance rate to carbapenems was reported between 1% and 86% during years 2006-2018. Most of the carbapenem-resistant microorganisms were isolated from burn patients. Modified Hodge test was a commonly used phenotypic test. Only in few studies, genotypic assays were considered. Pattern of antibiotic use can affect emergence of resistant microorganisms. Rational use of drugs, and specifically, antibiotics is a challenging issue in developing countries. Mean number of drugs per prescription in these countries was higher than the World Health Organization standards. Overuse of antibiotics, especially injectable ones, and easy access to antibiotics without prescription is a warning alarm for future antibiotic resistance in developing countries. Establishing antimicrobial stewardship's programs is new in the hospitals. Unfortunately, rules and regulatory issues to restrict antibiotic access in community pharmacies and prescription by general physicians are limited.