The Phylogenetic Relatedness of bla NDM-1 Harboring Extended-Spectrum β-Lactamase Producing Uropathogenic Escherichia coli and Klebsiella pneumoniae in the North of Iran

Engineered phage enzymes against drug-resistant pathogens: a review on advances and applications

In recent decades, the expansion of multi and extensively drug-resistant (MDR and XDR) bacteria has reached an alarming rate, causing serious health concerns. Infections caused by drug-resistant bacteria have been associated with morbidity and mortality, making tackling bacterial resistance an urgent and unmet challenge that needs to be addressed properly. Endolysins are phage-encoded enzymes that can specifically degrade the bacterial cell wall and lead to bacterial death. There is remarkable evidence that corroborates the unique ability of endolysins to rapidly digest the peptidoglycan particular bonds externally without the assistance of phage. Thus, their modulation in therapeutic approaches has opened new options for therapeutic applications in the fight against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology areas. The use of genetically engineered phage enzymes (EPE) promises to generate endolysin variants with unique properties for prophylactic and therapeutic applications. These approaches have gained momentum to accelerate basic as well as translational phage research and the potential development of therapeutics in the near future. This review will focus on the novel knowledge into EPE and demonstrate that EPE has far better performance than natural endolysins and phages in dealing with antibiotic-resistant infections. Therefore, it provides essential information for clinical trials involving EPE.

Prevalence and epidemiological investigation of mgrB-dependent colistin resistance in extensively drug resistant Klebsiella pneumoniae in Iran

Carbapenemases-producing K. pneumoniae are challenging antimicrobial therapy of hospitalised patients, which is further complicated by colistin resistance. The aim of this study was to investigate the molecular epidemiological insights into carbapenemases-producing and colistin-resistant clinical K. pneumoniaeA total of 162 colistin resistant clinical strains of K. pneumoniae were collected during 2017-2019. Antimicrobial susceptibility and the colistin minimum inhibitory concentration were determined. Using PCR assay, the prevalence of resistance-associated genes including blaKPC, blaIMP, blaVIM, blaOXA-48, blaNDM-1 and mcr-1 to -9 was examined. Additionally, a PCR assay was used to examine the mgrB gene in colistin-resistant bacteria. 94.4% of the tested strains were resistant to imipenem and 96.3% were resistant to meropenem. Colistin resistance (MIC > 4 µg/L) was observed in 161 isolates (99.4%) by Colistin Broth Disk Elution method. The KPC enzyme was the most common carbapenemase and was identified in 95 strains (58.6%), followed by the IMP, VIM and OXA-48 detected in 47 (29%), 23 (14.2%) and 12 (7.4%) isolates, respectively. However, no NDM-1 gene was detected. Additionally, none of the studied isolates harbored mcr variants, while mgrB gene was observed in 152 (92.6%) isolates. Colistin resistance of K. pneumoniae isolates may be associated with mgrB gene mutation. To stop the spread of resistant K. pneumoniae, surveillance must be improved, infection prevention protocols must be followed, and antibiotic stewardship must be practised.

The emergence of plasmid-encoded oxacillinase and carbapenemase among uropathogenic Escherichia coli (UPEC) isolated from hospitalized patients in the North of Iran

Carbapenemase enzyme production is responsible for resistance to carbapenem among Gram-negative bacteria. This study aimed to detect common carbapenemase and oxacilinase genes among uropathogenic E. coli (UPEC) isolated from hospitalized patients in Rasht, north of Iran. In the present study, from 2000 urine samples, 263 UPEC strains were isolated from inpatients with urinary tract infections (UTI) in 2020. The Kirby-Bauer disk diffusion susceptibility test was used to determine the sensitivity or resistance of isolates to antimicrobial compounds. The double-disk test confirmed extended-spectrum β lactamase (ESBL) production phenotypically, and the presence and distribution of genes encoding carbapenemase and oxacilinase were investigated using polymerase chain reaction (PCR). Based on the findings, 13/263 isolates (8 ESBL and five non-ESBL) showed a non-susceptible phenotype to at least one of the studied carbapenem group antibiotics, and 121 (46%) isolates were ESBL-producers. PCR for oxacilinase and carbapenemase genes was done on all 126 isolates, including ESBL-positive and carbapenem-resistant strains, in which 10 (7.9%) and 25 (19.8%) isolates harbored OXA-1 and IMP genes, respectively. Also, OXA-2, OXA-10, OXA-48, VIM, and NDM genes were not found in any studied isolates. IMP and OXA-1 genes among carbapenemase-producing isolates indicate the possible spread of antibiotic-resistant strains. Hence, identification and control of ESBL and carbapenemase-producing strains, although with almost low frequency due to plasmid genes encoding carbapenemase, is essential for infection control.

Distribution and expression of virulence genes (hlyA, sat) and genotyping of Escherichia coli O25b/ST131 by multi-locus variable number tandem repeat analysis in Tehran, Iran

Escherichia coli ST131 is a pandemic clone with high antibiotic resistance, and it is a major causative agent of urinary tract infection (UTI) and bloodstream infections. This study evaluated the distribution and expression of virulence genes and genotyping of E. coli O25b/ST131 by Multi-locus variable number tandem repeat analysis (MLVA) method among UTI in patients at Tehran hospitals, Iran.A total of 107 E. coli isolates were collected from UTI patients. Polymerase chain reaction (PCR) amplification of the pabB gene was used to identify E. coli O25b/ST131 and the prevalence of sat and hlyA virulence genes was also analyzed. The microtiter method quantified biofilm formation ability in E. coli O25b/ST131. The Real-Time PCR (qRT-PCR) was performed to evaluate the expression of sat and hlyA genes. Finally, MLVA was performed for E. coli O25b/ST131 genotyping by targeting seven tandem repeats. SPSS-16 software was used for statistical analysis. Molecular study showed that 71% of isolates carried the pabB gene and were considered E. coli O25b/ST131 strains. Also, 45.8% and 17.8% of isolates carried sat and hlyA genes, respectively. The 57.9% isolates had biofilm formation ability. Expression of the studied virulence genes showed an increase in strong biofilm producing E. coli O25b/ST131 strains. A total of 76 (100%) E. coli O25b/ST131 strains were typed by the MLVA method.High prevalence of E. coli O25b/ST131 isolates in UTI patients can be a serious warning to the treatment due to the high antibiotic resistance rate, expression of virulence genes, and biofilm formation.

High frequency of carbapenem-resistant Enterobacteriaceae fecal carriage among ICU hospitalized patients from Southern Iran

Objectives

The worldwide emergence of carbapenem-resistant Enterobacteriaceae (CRE) has become a major therapeutic concern to medical institutions. To date, no study has determined the frequency and risk factors of inpatients with CRE fecal carriage in Southern Iran. We studied the features of carbapenemase-producing Enterobacteriaceae (CPE) collected from the central ICU of a university hospital.

Materials and Methods

Totally, 173 samples, including 124 stool samples from 46 ICU inpatients on admission and different follow-ups, 9 ICU staff, and 40 environmental samples were included. CRE was identified using microbiological methods. Antimicrobial susceptibility was investigated by using the disk diffusion method and E-test. Carbapenemase producers were detected using the mCIM method. Seven carbapenemase genes were characterized. The genetic relationship among 20 CPE was elucidated by PFGE.

Results

The overall fecal carriage rate was 28.2%, while CRE acquisition was 6.1%. CRE were classified as Klebsiella pneumoniae (71.4%), Escherichia coli (23.8%), and Enterobacter aerogenes (4.8%). From 21 CRE, 20 (95.2%) produced carbapenemases, of which 10, 15, 10, 25, 5, and 65% were blaKPC, blaSME, blaIMP, blaVIM, blaNDM and blaOXA-48-positive, respectively. Out of 20 CPE, 14 different PFGE patterns were observed, categorized into six clusters, suggestive of non-clonal spread. No difference between the examined risk factors with CRE carriage was shown.

Conclusion

The data indicate a high CRE fecal carriage rate among inpatients. Our findings implicate the widespread of OXA-48 carbapenemase together with heterogeneity among CRE with great concern for dissemination and therapeutic threat. Early diagnosis and monitoring of CRE among inpatients are urgent.

Characterization of virulence factors and antibacterial activity of curcumin in hypervirulent Klebsiella pneumoniae

Aim: Klebsiella pneumoniae is a threat to human health due to its carbapenem-resistance and hypervirulent phenotype. Curcumin is a well-known antimicrobial agent. Hence, it is important to investigate the antivirulence activity of curcumin against hypervirulent K. pneumoniae isolates. Materials & methods: Carbapenemase presence and prevalence of hypervirulent isolates were determined. Inhibition of biofilm formation and expression of virulence genes were analyzed by colorimetry and real-time PCR tests. Results: Sixteen hypervirulent K. pneumoniae isolates were identified. The optimum activity of curcumin was detected at 1/2 minimum inhibitory concentration. Curcumin possessed appropriate antibiofilm, anti-efflux and anticapsule activities. Conclusion: According to the crucial role of biofilm, capsule and efflux systems in the pathogenesis of hypervirulent K. pneumoniae, curcumin may be used to improve anti-Klebsiella treatment.

Virulence characterization and clonal analysis of uropathogenic Escherichia coli metallo-beta-lactamase-producing isolates

Background

Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract infection (UTI); however, treatment of UTI has been challenging due to increased antimicrobial resistance (AMR). One of the most important types of AMR is carbapenem resistance (CR). CR bacteria are known as an important threat to global public health today. Class B metallo-beta-lactamases (MBLs) are one of the major factors for resistance against carbapenems. We aimed to investigate the characteristics of UPEC isolates producing MBL.

Methods

A cross-sectional study was conducted from October 2018 to December 2019 in Ahvaz; Iran. UPEC isolates were identified by biochemical and molecular methods. Metallo-beta-lactamase-producing isolates were detected using modified carbapenem inactivation method (mCIM) and EDTA-CIM (eCIM) tests. MBL genes, phylogenetic group, and virulence genes profile of carbapenem resistant isolates were determined. Conjugation assay and plasmid profiling were conducted to evaluate the ability of transferring of CR to other E. coli isolates. Clonal similarity of isolates were assessed using Enterobacterial intergenic repetitive element sequence (ERIC)-PCR.

Results

Among 406 UPEC isolates, 12 (2.95%) carbapenem-resistant were detected of which 11 were phenotypically MBL-producing strains. Four isolates were resistant to all investigated antimicrobial agents and were considered possible pandrug-resistant (PDR). bla_NDM, bla_OXA-48, bla_IMP-1, and bla_IMP-2 genes were found in 9, 5, 1, and 1 isolates, respectively. Among 30 virulence genes investigated, the traT, fyuA followed by fimH, and iutA with the frequency of 8 (66.7%), 8 (66.7%), 7 (58.3%), and 7 (58.3%) were the most identified genes, respectively. Siderophore production was the main virulence trait among carbapenem-resistant UPEC isolates. Except for two, all other isolates showed weak to moderate virulence index. In all recovered isolates, CR was readily transmitted via plasmids to other isolates during conjugation experiments.

Conclusion

MBL and carbapenemase genes, especially bla_NDM and bla_OXA-48 are spreading rapidly among bacteria, which can be a threat to global public health. Therefore monitoring the emergence and dissemination of new AMR is necessary to continuously refine guidelines for empiric antimicrobial therapy. Understanding the mechanisms of resistance and virulence in this group of bacteria can play an effective role in providing new therapeutic methods.

Prevalence of Transferable OXA-1 β-Lactamase Associated with Carbapenem-Resistant Klebsiella pneumoniae Isolates in Iraq

This study was designed to explore the incidence of blaOXA-1 amongst Klebsiella pneumoniae isolates with resistant to carbapenem. Between December 2014 and April 2015, one hundred samples were taken from two hospitals: Babylon Teaching Hospital for Maternity and Pediatric / Babylon Province (clinical, umbilical infections, n= 40; environmental, n=20) and Karbala Hospital for Pediatric / Karbala Province (40 stool samples). All patients were hospitalized or attended these hospitals, all under 1 year of age. Seventeenth (17%) isolates were identified as Klebsiella pneumoniae. The antibiotic resistance profile of isolates was tested using disk diffusion method. High-level of resistance was recorded with ampicillin (94.1%) and piperacillin (88.2%) antibiotics. Resistance to carbapenem was reported in two K.pneumoniae isolates, these were investigated for the existence of OXA-1β-lactamase using Polymerase Chain Reaction (PCR) technique. Two (100%) isolates gave positive result. Transference of this gene was studied by conjugation experiment. The blaOXA-1 gene conjugated successfully in 1 (50%) isolate only.