Distribution of β-lactamase genes among carbapenem-resistant Klebsiella pneumoniae strains isolated from patients in Turkey

Characterization of resistance genes and replicon typing in Carbapenem-resistant Klebsiella pneumoniae strains

OBJECTIVE

In our study, K. pneumoniae strains (non-susceptible to carbapenem) (n = 60) were obtained from various clinical samples from Rize State Hospital between 2015 and 2017 and it is aimed to identify antibiotic resistance genes and replicon typing.

METHODS

Antibiotic susceptibility tests of the strains were performed with Kirby-Bauer disk diffusion test and the Vitek-2 automated system (BioMerieux, France). Antibiotic resistance genes and replicon typing was characterized by PCR method.

RESULTS

It was determined that K. pneumaniae isolates were mostly isolated from the samples of the intensive care unit. All of the K. pneumoniae strains examined in this study were found to be ampicillin/sulbactam and ertapenem resistant but colistin susceptible. Amoxacillin/clavulonic acid resistance was detected at 98.14% of strains. The blaOXA-48 gene was mostly detected in isolates. The most common type of plasmid was I1 and 3 different plasmid types were found in five different strains together.

CONCLUSION

This study also shows that the distribution of NDM-1 and OXA-48 carbapenemases has increased since the first co-display in Türkiye and that IncHI1 is the first record in our country. This study provides an overview of the major plasmid families occurring in multiple antibiotic-resistant strains of K. pneumoniae. To our knowledge, this study represents the first report of IncHI1 record in Türkiye.

Effect of N-acetyl cysteine, rifampicin, and ozone on biofilm formation in pan-resistant Klebsiella pneumoniae: an experimental study

BACKGROUND

To the best of our knowledge, this is the first study to evaluate the effectiveness of specific concentrations of antibiofilm agents, such as N-acetyl cysteine (NAC), rifampicin, and ozone, for the treatment of pan-resistant Klebsiella pneumoniae (PRKp).

OBJECTIVES

We evaluated the effectiveness of antibiofilm agents, such as NAC, rifampicin, and ozone, on biofilm formation in PRKp at 2, 6, 24, and 72 h.

DESIGN AND SETTING

This single-center experimental study was conducted on June 15, 2017, and July 15, 2018, at Istanbul Faculty of Medicine, Istanbul University, Turkey.

METHODS

Biofilm formation and the efficacy of these agents on the biofilm layer were demonstrated using colony counting and laser-screened confocal microscopy.

RESULTS

NAC at a final concentration of 2 μg/mL was administered to bacteria that formed biofilms (24 h), and no significant decrease was detected in the bacterial counts of all isolates (all P > 0.05). Rifampicin with a final concentration of 0.1 μg/mL was administered to bacteria that formed biofilm (24 h), and no significant decrease was detected in bacterial count (all P > 0.05). Notably, ozonated water of even 4.78 mg/L concentration for 72 h decreased the bacterial count by ≥ 2 log10.

CONCLUSION

Different approaches are needed for treating PRKp isolates. We demonstrate that PRKp isolates can be successfully treated with higher concentrations of ozone.

Outbreak and control of Achromobacter denitrificans at an academic hospital in Pretoria, South Africa

OBJECTIVE

In this study, we sought to determine the source of an outbreak of Achromobacter denitrificans infections in patients at a tertiary-care academic hospital.

DESIGN

Outbreak report study with intervention. The study period extended from February 2018 to December 2018.

SETTING

The study was conducted at a tertiary-care academic hospital in Pretoria, South Africa.

PATIENTS AND PARTICIPANTS

All patients who cultured A. denitrificans from any site were included in this study. During the study period, 43 patients met this criterion.

INTERVENTIONS

Once an outbreak was confirmed, the microbiology laboratory compiled a list of affected patients. A common agent, chlorhexidine-and-water solution, was used as a disinfectant-antiseptic for all affected patients. The laboratory proceeded to culture this solution. Environmental and surface swabs were also cultured from the hospital pharmacy area where this solution was prepared. Repetitive-element, sequence-based, polymerase chain reaction (rep-PCR) was performed on the initial clinical isolates to confirm the relatedness of the isolates.

RESULTS

In total, 43 isolates of A. denitrificans were cultured from patient specimens during the outbreak. The laboratory cultured A. denitrificans from all bottles of chlorhexidine-and-water solutions sampled from the wards and the pharmacy. The culture of the dispenser device used to prepare this solution also grew A. denitrificans. The rep-PCR confirmed the clonality of the clinical isolates with 2 genotypes dominating.

CONCLUSIONS

Contaminated chlorhexidine-and-water solutions prepared at the hospital pharmacy was determined to be the source of the outbreak. Once this item was removed from the hospital, the laboratory did not culture any further A. denitrificans isolates from patient specimens.

Characteristics in the whole-genome sequence of Klebsiella pneumoniae ST147 from Turkey

The study aimed to analyze antibiotic resistance determinants in a carbapenem-resistant Klebsiella pneumoniae by whole-genome sequencing (WGS). K. pneumoniae was isolated from a urine sample and it was characterized by 16S rDNA sequencing in Turkey. This strain was named as Kpn Rize-53-TR. Antimicrobial susceptibility testing was performed for seventeen antibiotics by VITEK-2 and the result was confirmed by MIC. The whole genome of isolate was sequenced by Illumina and was analysed by bioinformatic tools for MLST, replicon types, and antimicrobial resistance genes. The whole genome data was submitted to NCBI. The isolate was found to be resistant to all tested β-lactam antibiotics and the highest MIC values were found for piperacillin, piperacillin/tazobactam (≥128). No resistance to colistin and moderate susceptibility to amikacin and tetracycline was observed. The isolate carried 12 resistance genes belonging to 10 resistance classes; ere(A), fosA, oqxB, cmlA1, aac(a)-IIa, bla KPC-2, bla TEM-1A, bla SHV-67, bla CTX-M-15, bla OXA-1-2-9. Mutations were detected in gyrA (83Y) and parC (80I) genes. Clonal subtype of the isolate was ST147, and it had wzi420 and wzc38 alleles. Its serotype was O3/O3a. The bla KPC-2 was firstly found in both ST147 clonal group in Turkey and in serotype O3/O3a in the world. By plasmid replicon typing, five plasmids IncFII(K), Col(BS512), IncR, IncFIA(HI1) and IncFIB(pQil) were determined in Kpn Rize-53-TR and bla KPC-2 was located on IncFII(K) plasmid. The presence of bla KPC-2 on the plasmid with other resistance genes accelerates its own spread together with other resistance genes.

Epidemiology and high incidence of metallo-β-lactamase and AmpC-β-lactamases in nosocomial Pseudomonas aeruginosa

OBJECTIVES

Isolates producing metallo-β-lactamase (MBL) have a significant impact on therapeutic and diagnostic layouts, plus their increased frequency has been reported globally. Determination of incidence of clinical isolates of Pseudomonas aeruginosa that are capable of producing MBL and AmpC-β-lactamases making them resistant to imipenem and cefoxitin.

MATERIALS AND METHODS

Out of 1159 collected samples of urine, wound swabs, blood, tissue, and pus, the isolation rate of P. aeruginosa in the period of March 2020 to February 2021 was 22.0% (255/1159). Bacterial strains that were resistant towards imipenem were further processed for detecting the β-lactamase group of genes followed by statistical analysis of risk factors done based on clinical sample, gender, plus department of sample collection.

RESULTS

The percentage of resistance against imipenem was found to be 53%. Out of 135 strains, phenotypic tests revealed MBLs incidence to be 61.5% by combination disc test and 81.5% by Modified Hodge test (MHT). Frequencies of blaIMP-1, blaVIM, blaSHV, blaTEM, and blaOXA genes were calculated to be 13%, 15%, 32%, 43%, and 21%, respectively. Co-expressions of blaMBLs (blaVIM and blaIMP-1) plus blaESBL (blaSHV, blaOXA, blaTEM) were detected using simplex and multiplex PCR. blaTEM, blaSHV, and blaOXA co-existed in 7.5% of clinical isolates. 5.5% of the isolates exhibited simultaneous expression of MBL/ESBL genes. 15% of the isolates resistant to cefoxitin were positive for the blaAmpC gene (17/114).

CONCLUSION

This is a pioneer report from Pakistan that concomitantly presents expression of blaVIM and blaIMP-1 with blaTEM, blaOXA, blaSHV, and blaAmpC in isolates of P. aeruginosa.

Molecular Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Isolates Producing blaVIM, blaNDM, and blaIMP in Clinical Centers in Isfahan, Iran

Background: The emergence and spread of metallo-beta-lactamase (MBL)-producing Klebsiella pneumoniae are growing global public health concerns. One of the most common mechanisms of carbapenem resistance is the production of MBLs, including Verona integron-encoded metallo-beta-lactamase (VIM), New Delhi metallo-beta-lactamase (NDM) and imipenemase (IMP). Objectives: This study aimed to investigate MBLs production among K. pneumoniae isolates. Methods: In this study, 240 K. pneumoniae isolates were collected from clinical samples in three clinical centers of Isfahan, Iran, during February 2017 and November 2018. All isolates were identified using biochemical, microbiological, and molecular methods, and then antimicrobial susceptibility tests were performed to find MBL-producing isolates via phenotypic and genotypic detection methods. Moreover, the minimum inhibitory concentration (MIC) of antibiotics against MBL-positive strains was determined by E-test. Eventually, the clonal relatedness of the MBL-positive strains was analyzed using both multilocus sequence typing (MLST) and rep-PCR. Results: Overall, 33.7% (81/240) of the isolates were resistant to carbapenems, among which 25 (30.8%) were considered MBL-positive. Among 81 strains resistant to carbapenems, genes encoding FimH, rmpA, and mrkD were detected in 87.6% (71/81), 11.1% (9/81), and 67.9% (55/81) of the isolates, respectively. Besides, TEM and SHV as antibiotic resistance genes were detected in 49.3% (40/81) and 80.2% (65/81) of the isolates. But, magA was not detected in any of the tested isolates. The PCR results revealed that blaVIM-1 was the most prevalent gene (13.6%; 11/81), while both blaIMP-1 and blaNDM-1 were only detected in two isolates. Multilocus sequence typing demonstrated that 15 MBL producers belonged to three sequence types (ST): 11 to ST23, two to ST1147, and two to ST15. Finally, rep-PCR typing showed similar fingerprints with MLST, except for ST23, such that ST23 was discriminated in two clonal groups, suggesting the greater discriminatory power of rep-PCR. Conclusions: Here, we reported the emergence of MBL-producing K. pneumoniae in clinical centers of Isfahan, Iran. The findings are alarming and represent the urgent need for the application of infection control programs.

Cefoperazone/sulbactam: New composites against multiresistant gram negative bacteria?

Sulbactam, a class A β-lactamase inhibitor, added to cefoperazone either at a fixed 8 mg/L level of sulbactam or at a level of fixed cefoperazone: sulbactam ratio (2:1) would constitute a combination form of cefoperazone/sulbactam, which has better activities against Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii than cefoperazone alone. Cefoperazone/sulbactam (1:1 or 1:2) has greater in-vitro activity against most multidrug-resistant organisms (ESBL- and AmpC-producing Enterobacteriaceae and carbapenem-resistant A. baumannii except for carbapenem-resistant P. aeruginosa) than a 2:1 ratio. However, increased sulbactam concentration may induce AmpC production. Besides, sulbactam concentration might not be readily achievable in serum if the susceptibility rates were defined by the breakpoints of higher sulbactam composites, such as ≤16/16 (1:1) or 16/32 (1:2) mg/L. Carbapenemases (KPC-, OXA-type enzymes and metallo-β-lactamases) can't be inhibited by sulbactam. Some in-vitro studies showed that increasing sulbactam composites of cefoperazone/sulbactam had no effect on carbapenem-resistant P. aeruginosa, suggesting the presence of carbapenemases or AmpC overproduction that could not be overcome by increasing sulbactam levels to recover cefoperazone activity. Sulbactam alone has good intrinsic activity against carbapenem-resistant Acinetobacter strains sometimes even in the presence of carbapenemase genes, suggesting unsteady levels of carbapenemases. In conclusion, appropriate composites of cefoperazone and β-lactamase inhibitor sulbactam may expand the clinical use if the pharmacokinetic optimization could be achieved in the human serum.

Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio's SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both blaOXA-48 and blaNDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.

Detection of carbapenem-resistant Klebsiella pneumoniae strains harboring carbapenemase, beta-lactamase and quinolone resistance genes in intensive care unit patients

Aim: Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) strains are important nosocomial pathogens worldwide. In this study, we aimed to reveal the antibiotic resistance of clinical CR-Kp strains and determine the presence of KPC, OXA-48, VIM and IMP carbapenemase genes. CTX-M-1, TEM-1, SHV-1 extended-spectrum beta-lactamase (ESBL) genes, qnrA, qnrB, qnrS plasmid-mediated quinolone resistance genes and sul1 and sul2 sulfonamide resistance genes provided molecular epidemiological data.

Methods: A total of 175 K. pneumoniae strains were isolated from clinical samples of patients hospitalised in an intensive care unit (ICU) betweent April and October 2017. The strains were identified with conventional methods, with VITEK 2 (BioMerieux, France) and MALDI-TOF MS (Bruker, USA). Antimicrobial susceptibilities were tested using the disc-diffusion method and E-test (BioMerieux, France). Antimicrobial resistance genes were investigated via real-time PCR in strains identified as CR-Kp.

Results: High frequencies of bla_TEM-1 (86.36%), bla_SHV-1 (86.36%), and bla_CTX-M-1 (95.45%) genes were found in CR-Kp strains. Morever, all three ESBL genes coexisted in 77.3% of all strains. bla_KPC was detected in 12 (54.55%) of the strains, and 4 of them which had an MIC> 16 μg/mL to imipenem showed bla_OXA-48 positivity as well. The qnrS gene determinant (86.36%) had the highest frequency, and strains carrying qnrA showed higher MICs for ciprofloxacin.

Conclusion: CR-Kp strains are able to develop different antimicrobial resistance patterns according to regional changes in antimicrobial therapeutic policies. Thus, it is important to monitor the regional molecular epidemiological data for efficient treatment.

Systematic surveillance and meta-analysis on the prevalence of metallo-β-lactamase producers among carbapenem resistant clinical isolates in Pakistan

BACKGROUND

Emergence of carbapenem resistance (CR) is a health concern of pertinent importance. Epidemiological surveillance of CR at global and indigenous level (Pakistan) can help to improve infection control and establish pharmacovigilance programs. This study evaluates the prevalence of clinically significant CR isolates, and its genetic variant distribution among geographical regions of Pakistan.

METHODS

A meta-analysis was conducted to present the current rate of CR infections and prevalence of Metallo-β-lactamases (MBLs). The proposed subject was researched using electronic databases to identify the available literature. Thereafter, relevant data was extracted and statistical analysis was performed using STATA version 14.

RESULTS

A total of 110 relevant studies were identified with 19 meeting the inclusion criteria for the meta-analysis of CR, while 22 for MBLs. Pooled rate for carbapenem resistance was determined to be 0.28 (95% CI: 0.26-0.31) with overall significant heterogeneity (I²=99.61%, P<0.001) and significant estimated score ES=0 (Z=22.65, P<0.001). In Pakistan, the pooled proportion of MBL producers was 0.34 (95% CI: 0.29-0.39) with overall heterogeneity significance (I²=99.62%, P<0.001) and significant ES=0 (Z=13.17, P<0.001).

CONCLUSION

Conclusively, diverse variants of carbapenemases (VIM, IMP, NDM, KPC, GIM) along with other β-lactamase variants (OXA, TEM, SHV, CTX-M) have been reported across the country. However, New Delhi Metallo-β-lactamase (NDM)-variants were reported in predominant literature. The prevalence of CR isolates in Pakistan is alarming, associated with MBL production primarily evident from the studies. The study emphasizes the need for regular surveillance, pharmacovigilance and antibiotic stewardship programs to ensure the availability of data to the authorities for preemptive measures of infection control.

Rising Threat of OXA-48 and other Carbapenemase Encoding Genes among Carbapenem Resistant Enterobacteriaceae in India

Members of Enterobacteriaceae family are responsible for both community and hospital acquired infections. Because of development of antimicrobial resistance carbapenem has remained as last resort of drug for treatment of infections caused by these bacteria.Mechanism for development of this resistance in carbapenem resistant Enterobacteriaceae (CRE) may due to production of carbapenemases, efflux mechanism or loss of outer membrane porins.The most common carbapenemase enzymes are Class A – KPC, Class B – NDM, VIM and IMP and Class D oxacillinase(OXA-48 like enzymes).In India, most prevalent carbapenemase encoding gene is NDM-1but there is rising threat of OXA-48 prevalence. Unlike the phenotypic methods, the genotypic methods are useful to discriminate the type of carbapenemase enzyme, specifically for OXA-48 like enzymes. Total 170 CRE isolates were subjected for multiplex PCR study for their molecular characterization. Of the 170 CRE isolates,68.2 % (n=116) were positive for NDM-1 gene while 44.1 % (n= 75) of the isolates showed presence of OXA-48 gene. VIM (2.3%), KPC (1.7 %) were responsible for carbapenemase production while none of the isolates showed presence of IMP gene. NDM-1 and OXA-48 coexisted in 21.2 % (n=36) of the total isolates. OXA-48 causes weak hydrolysis of carbapenem because of which it is under reported with routine diagnostic methods. Early detection of OXA-48 and other carbapenemase encoding genes, helps for contact precautions and effective therapy which prevents further escalation and horizontal spread of CRE.

Multidrug-resistant Klebsiella pneumoniae in hospital-acquired infections: Concomitant analysis of antimicrobial resistant strains

BACKGROUND

Hospital-acquired infections caused by K pneumoniae are difficult to eradicate since K pneumoniae carries resistance genes for many antimicrobials, including carbapenems. The study aimed to determine the prevalence of hospital-acquired infections caused by multiple drug-resistant K pneumoniae and identify carbapenem and fluoroquinolone resistance by phenotypic and genotypic methods amongst hospitalised patients.

METHODS

Two hundred and fifty samples from patients with hospital-acquired infections were included. Identification and susceptibility testing for K pneumoniae isolates was performed by standard methods. The detection of carbapenemase resistance (bla_KPC , bla_VIM-1 and bla_OXA-48 ) and plasmid-mediated quinolone resistance (PMQR; qnrA, qnrB and qnrS) genes was performed using PCR assay.

RESULTS

Out of 250 samples, 42 (16.8%) were multiple drug-resistant K pneumoniae, and the frequency of K Pneumoniae isolation was higher in urine samples, in the age group (<10 years), in ICU and in patients with longer hospital stay. Twenty-four (57%) of the isolates were resistant to Meropenem, 13 (31%) were resistant to Imipenem and 35 (83.3%) were resistant to Ciprofloxacin. bla_OXA-48 gene was detected in 9 (21.4%) of isolates, and bla_VIM-1 gene was detected in 6 (14.3%) of isolates. However, no isolate harboured bla_KPC gene. PMQR genes were detected in 100% of ciprofloxacin resistant isolates, and qnrS was the dominant.

CONCLUSION

Multidrug-resistant K pneumoniae isolates harbouring bla_OXA-48, bla_VIM-1 and PMQR genes are emerging in hospitals particularly with long hospital stays.

Characterization of Klebsiella pneumoniae Coproducing KPC and NDM-1 Carbapenemases from Turkey

Aims: The emergence of multidrug-resistant and carbapenem-resistant Klebsiella pneumoniae has became a major public health threat. In this study, we describe the characteristics of isolates coproducing KPC and NDM-1 carbapenemases from patients hospitalized at an emergency unit in Ankara, Turkey, between January and August 2018. The isolates were characterized by antibiogram susceptibility, carbapenemase and extended-spectrum beta-lactamase production, plasmid-mediated colistin (COL) resistance, and high-level aminoglycoside resistance. Pulsed field gel electrophoresis (PFGE), sequencing, wzi typing, multilocus sequence typing, and plasmid analysis were used to investigate the epidemiological relationship between the isolates. Results: All isolates were found to be resistant to amoxicillin-clavulanic acid, piperacillin-tazobactam, cefotaxime, cefoxitin, cefuroxime, ceftazidime, cefepime, imipenem, meropenem, ertapenem, amikacin, gentamicin, ciprofloxacin, levofloxacin, and trimethoprim-sulfamethoxazole. The minimum inhibitory concentration values for imipenem, meropenem, and ertapenem were >32 μg/mL, and >256 μg/mL for amikacin and gentamicin, and two isolates were found to be susceptible to both tigecycline and COL. All strains were positive for SHV, CTX-M, and rmtC, and negative for mcr-1 genes. A/C and FIIA_S plasmids were found in all isolates. All isolates had the same PFGE pattern: wzi type 93 and ST15. Conclusion: Here, we have documented the characteristics of KPC- and NDM-1-coproducing isolates that harbored SHV, CTX-M, and rmtC and were typed as wzi 93 and ST15. We conclude that continuous monitoring of carbapenemases for unusual carbapenemase production is crucial to prevent the spread of these powerful isolates.

Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach

In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.

Next-generation sequencing of plasmid carrying blaOXA-48 in Klebsiella pneumoniae from Turkey

A carbapenem-resistant Klebsiella pneumoniae strain was isolated in Turkey in 2012 and bla_NDM-1 and bla_OXA-48 genes were observed in this strain. The aim of this study was to investigate transferability of plasmid bearing bla_OXA-48 in K. pneumoniae and to use whole-genome sequencing in order to understand the genetic context of plasmid. K. pneumoniae strain was used as donor in conjugation experiments. Antibiotic susceptibility profile of selected transconjugant was determined. Plasmid was isolated from transconjugant colony and was named as pKPT. Complete sequencing of the pKPT was conducted using a next-generation sequencing. Annotation of the contigs was performed using the Geneious R9, followed by finding open reading frames (ORFs) with selected web-based tools. BLAST analysis was performed at the NCBI BLAST server to determine genes showing more than 90% similarity with these ORFs. Results of antibiotic susceptibility test showed that transconjugant colony was resistant to ampicillin/sulbactam, piperacillin, and piperacillin/tazobactam. The pKPT plasmid had a length of 45,217 bp and an average G + C content of 49%. Blast analysis revealed that pKPT was included in the IncL/M incompatibility group. The pKPT was found to contain bla_OXA-48 within Tn1999.2 transposon without any other antibiotic resistance gene.

Identification, molecular characterization, and structural analysis of the blaNDM-1 gene/enzyme from NDM-1-producing Klebsiella pneumoniae isolates

NDM-1 comprises a carbapenemase that was first detected in 2008 in New Delhi, India. Since then, NDM-1-producing Klebsiella pneumoniae strains have been reported in many countries and usually associated with intra and inter-hospital dissemination, along with travel-related epidemiological links. In South America, Brazil represents the largest reservoir of NMD-1-producing K. pneumoniae. Here, we focused on the detection and molecular/structural characterization of the bla_NDM-1 resistance gene/enzyme from 24 K. pneumoniae clinical isolates in the Midwest region of Brazil. Antimicrobial susceptibility assays showed that all isolates are resistant to carbapenems. Molecular typing of the isolates revealed seven clonal groups among the K. pneumoniae isolates, which may indicate intra or inter-hospital dissemination. Moreover, the bla_NDM-1 gene was detected in all 24 K. pneumoniae isolates and the full bla_NDM-1 gene was cloned. Bioinformatics analysis showed that the NDM-1 enzyme sequence found in our isolates is highly conserved when compared to other NDM-1 enzymes. In addition, molecular docking studies indicate that the NDM-1 identified binds to different carbapenems through hydrogen and zinc coordination bonds. In summary, we present the molecular characterization of NDM-1-producing K. pneumoniae strains isolated from different hospitals, also providing atomic level insights into molecular complexes NDM-1/carbapenem antibiotics.

High frequency and molecular epidemiology of metallo-β-lactamase-producing gram-negative bacilli in a tertiary care hospital in Lahore, Pakistan

Background

Metallo-β-lactamase (MBL)-producing isolates have a strong impact on diagnostic and therapeutic decisions. A high frequency of MBL-producing gram-negative bacilli has been reported worldwide. The current study was based on determining the incidence of MBL-producing imipenem-resistant clinical isolates and investigating the β-lactamase gene variants in strains conferring resistance to a carbapenem drug (imipenem).

Methods

A total of 924 gram negative isolates were recovered from a tertiary care hospital in Lahore, Pakistan, during a two-year period (July 2015 to February 2017). The initial selection of bacterial isolates was based on antibiotic susceptibility testing. Strains resistant to imipenem were processed for the molecular screening of β-lactamase genes. Statistical analysis for risk factor determination was based on age, gender, clinical specimen and type of infection.

Results

The rate of imipenem resistance was calculated to be 56.51%. Among the 142 strains processed, the phenotypic tests revealed that the incidence of MBLs was 63.38% and 86.61% based on the combination disc test and the modified Hodge test, respectively. The frequencies of bla_TEM, bla_SHV,bla_OXA,bla_IMP-1, and bla_VIM genes were calculated to be 46%, 34%, 24%, 12.5% and 7%, respectively. The co-expression of bla_MBL (bla_IMP and bla_VIM) and bla_ESBL (bla_TEM, bla_SHV,bla_OXA) was also detected through multiplex and singleplex PCR. bla_OXA, bla_TEM and bla_SHV coexisted in 82% of the isolates. Co-expression of ESBL and MBL genes was found in 7% of the isolates.

Conclusion

To our knowledge, this is the first report from Pakistan presenting the concomitant expression of bla_OXA, bla_TEM and bla_SHV with bla_IMP-1 and bla_VIM in MBL-producing gram-negative bacilli.

Identification of carbapenemase-mediated resistance among Enterobacteriaceae bloodstream isolates: A molecular study from India

Acquired resistance in carbapenem-resistant Enterobacteriaceae (CRE) conferred by carbapenemases is a major concern worldwide. Consecutive, non-duplicate isolates of Escherichia coli (EC) and Klebsiella pneumoniae from clinically diagnosed bloodstream infections were screened for the presence of carbapenem resistance by standard disk-diffusion method and minimum inhibitory concentration breakpoints using the Clinical and Laboratory Standards Institute guidelines. Carbapenemase-encoding genes were amplified by polymerase chain reaction. Of 387 isolates (214 K. pneumoniae, 173 EC) tested, 93 (24.03%) were found to be CRE. Of these, 71 (76.3%) were positive for at least one tested carbapenemase gene. The frequency of carbapenemase genes was New Delhi metallo-β-lactamse-1 (65.6%), oxacillinase (OXA)-48 (24.7%), OXA-181 (23.6%), Verona integron-encoded metallo-β-lactamase (6.4%) and K. pneumoniae carbapenemase (2.1%). Our study identified presence of carbapenemases in a large proportion of CRE isolates. Delineation of resistance mechanisms is important in view of future therapeutics concerned with the treatment of CRE and for aiding control efforts by surveillance and infection control interventions.

Polymyxins: Antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes

Polymyxins are well-established antibiotics that have recently regained significant interest as a consequence of the increasing incidence of infections due to multidrug-resistant Gram-negative bacteria. Colistin and polymyxin B are being seriously reconsidered as last-resort antibiotics in many areas where multidrug resistance is observed in clinical medicine. In parallel, the heavy use of polymyxins in veterinary medicine is currently being reconsidered due to increased reports of polymyxin-resistant bacteria. Susceptibility testing is challenging with polymyxins, and currently available techniques are presented here. Genotypic and phenotypic methods that provide relevant information for diagnostic laboratories are presented. This review also presents recent works in relation to recently identified mechanisms of polymyxin resistance, including chromosomally encoded resistance traits as well as the recently identified plasmid-encoded polymyxin resistance determinant MCR-1. Epidemiological features summarizing the current knowledge in that field are presented.

Molecular detection of β-lactamase and integron genes in clinical strains of Klebsiella pneumoniae by multiplex polymerase chain reaction

INTRODUCTION:

Infections caused by β-lactamase-producing gram-negative bacteria, such as Klebsiella pneumoniae, are increasing globally with high morbidity and mortality. The aim of the current study was to determine antimicrobial susceptibility patterns and the prevalence of antibiotic resistance genes (β-lactamase and integron genes) using multiplex PCR.

METHODS

One-hundred K. pneumoniae isolates were collected from different clinical samples. Antibiotic susceptibility testing was performed with thirteen different antibiotics. Multiplex-PCR was used to detect β-lactamase (bla TEM, bla CTX-M, bla SHV , bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC) and integron genes (int I, int II, and int III).

RESULTS:

The highest and lowest rate of resistance was exhibited against amikacin (93%) and imipenem (8%), respectively. The frequency of β-lactamase-positive K. pneumoniae was 37%, and the prevalence of the bla TEM, bla CTX-M, bla SHV , bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC genes was 38%, 24%, 19%, 12%, 6%, 11%, 33%, 0%, 28%, and 23%, respectively. Of the 100 isolates, eight (8%) were positive for class I integrons; however, class II and III integrons were not detected in any of the strains.

CONCLUSIONS:

These results indicate co-carriage of a number of β-lactamase genes and antibiotic resistance integrons on the same plasmids harboring multi-drug resistance genes. It seems that these properties help to decrease treatment complications due to resistant bacterial infections by rapid detection, infection-control programs and prevention of transmission of drug resistance.