Rapid detection of Klebsiella pneumoniae carbapenemase genes in enterobacteriaceae directly from blood culture bottles by real-time PCR

Detection of blaKPC gene among carbapenemase producing Klebsiella pneumoniae isolated from different clinical specimens at tertiary care hospital of Nepal

BACKGROUND

Klebsiella pneumoniae infections have become a major cause of hospital acquired infection worldwide with the increased rate of acquisition of resistance to antibiotics. Carbapenem resistance mainly among Gram negative is an ongoing problem which causes serious outbreaks dramatically limiting treatment options. This prospective cross-sectional study was designed to detect blaKPC gene from carbapenem resistant K. pneumoniae.

MATERIALS AND METHODS

A totally of 1118 different clinical specimens were screened and confirmed for KPC producing K. pneumoniae phenotypically using Meropenem (10 μg) disc. The blaKPC gene was amplified from the isolates of K. pneumoniae to detect the presence of this gene.

RESULT

Of the total samples processed, 18.6% (n = 36) were K. pneumoniae and among 36 K. pneumoniae, 61.1% (n = 22/36) were meropenem resistant. This study demonstrated the higher level of MDR 91.7% (n = 33) and KPC production 47.2% (n = 17) among K. pneumoniae isolates. The blaKPC gene was detected in 8.3% (n = 3) of meropenem resistant isolates.

CONCLUSION

Since the study demonstrates the higher level of MDR and KPC producing K. pneumoniae isolates that has challenged the use of antimicrobial agents, continuous microbiology, and molecular surveillance to assist early detection and minimize the further dissemination of blaKPC should be initiated. We anticipate that the findings of this study will be useful in understanding the prevalence of KPC-producing K. pneumoniae in Nepal.

Microfluidic Chip for Detection of Drug Resistance at the Single-cell Level

Drug-resistant bacterial strains seriously threaten human health. Rapid screening of antibiotics is urgently required to improve clinical treatment. Conventional methods of antimicrobial susceptibility testing rely on turbidimetry that is evident only after several days of incubation. The lengthy time of the assay can delay clinical treatment. Here, we proposed a single-cell level rapid system based on a microfluidic chip. The detection period of 30 min to 2 h was significantly shorter than the conventional turbidity-based method. To promote detection efficiency, 16 independent channels were designed, permitting the simultaneous screening of 16 drugs in the microfluidic chip. Prepositioning of drugs in the chip permitted prolonged transportation and storage. This may allow for the widespread use of the novel system, particularly in the regions where medical facilities are scarce. The growth curves were reported rapidly through a custom code in Matlab after tracking and photographing the bacteria during microscopy examination. The capability of the proposed system was validated by antimicrobial susceptibility testing trials with standard strains. The system provides a potentially useful detection tool for drug-resistant bacteria.

Rapid Detection of Carbapenemase Production Directly from Blood Culture by Colorimetric Methods: Evaluation in a Routine Microbiology Laboratory

The aim of this study was to evaluate the two rapid colorimetric methods (CNPt-Direct and Blue-Carba) for the detection of carbapenemase production directly from blood culture in a routine microbiology laboratory. The methods were initially evaluated on spiked blood cultures with 61 carbapenemase-positive isolates. Afterwards, they were used in blood cultures (314 samples were evaluated) obtained from patients in a routine microbiology laboratory during a period of 6 months. The colorimetric methods were compared to the conventional culture of blood. The results of the spiked blood cultures indicated that both colorimetric methods presented positive results for the vast majority (95%) of the isolates harboring KPC, NDM, and IMP genes. However, the assay failed to detect many GES- and OXA-48-like-positive isolates (65% positive results). In the second part of the study, a total of 314 blood cultures from patients were evaluated, and 33 yielded Enterobacteriaceae isolates resistant to meropenem (30 isolates were positive for carbapenemases according to PCR). The colorimetric tests correctly detected 24 out of the 30 carbapenemase-positive isolates directly from the blood vial (80% positive results). Overall positive percent agreement and negative percent agreement were 80% and 100%, respectively. The colorimetric assays are simple and cost-effective methods that can be implemented in a routine microbiology laboratory, diminishing the time necessary to detect carbapenemase-producing isolates from 24 to 48 h to 3 to 5 h. Moreover, according to our results, the positive colorimetric test results do not need to be confirmed and can be immediately provided to the attending physician.

Rapid detection of carbapenemase-producing Klebsiella pneumoniae strains derived from blood cultures by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS)

Background

Carbapenemase-producing Enterobacteriaceae (CPE), particularly carbapenemase-producing Klebsiella pneumoniae isolates, are important causative agents of nosocomial infections associated with significant mortality rates mostly in critical wards. The rapid detection and typing of these strains is critical either for surveillance purposes and to prevent outbreaks and optimize antibiotic therapy. In this study, the MALDI-TOF MS method was used to detect rapidly these isolates from blood cultures (BCs) and to obtain proteomic profiles enable to discriminate between carbapenemase-producing and non-carbapenemase-producing strains.

Results

Fifty-five K. pneumoniae strains were tested. Identification and carbapenemase-production detection assay using Ertapenem were performed both from bacterial pellets extracted directly from BCs flasks and from subcultures of these strains. For all isolates, a complete antimicrobial susceptibility testing and a genotypic characterization were performed.

We found 100% agreement between the carbapenemase-producing profile generated by MALDI TOF MS and that obtained using conventional methods. The assay detected and discriminated different carbapenemase-producing K. pneumoniae isolates within 30 min to 3 h after incubation with Ertapenem.

Conclusions

MALDI-TOF MS is a promising, rapid and economical method for the detection of carbapenemase-producing K. pneumoniae strains that could be successfully introduced into the routine diagnostic workflow of clinical microbiology laboratories.

Management of Pneumonia and Blood Stream Infections with New Antibiotic Adjuvant Entity (Ceftriaxone + Sulbactam + Disodium Edetate)- A Novel Way to Spare Carbapenems

INTRODUCTION

Nosocomial infections have been considered as a major health problem causing incremental morbidity, mortality and costs of therapy.

AIM

This retrospective study was initiated with aim to analyse the comparative efficacy of a novel Antibiotic Adjuvant Entity (AAE), a combination of ceftriaxone + sulbactam + disodium edetate and meropenem in combination with colistin, for the management of Multi Drug Resistant (MDR) nosocomial Gram-negative bacterial infections.

MATERIALS AND METHODS

Case history sheets of patients with documented MDR nosocomial Gram-negative infections who received either AAE or meropenem in combination with colistin for management of infections over a period of 3 years (November 2012 - October 2015) were included in the study. Data related to clinical management, demographics, vital signs and laboratory parameters along with prior antibiotic therapy, dose and clinical outcomes were evaluated thoroughly to analyse the clinical benefits of this new AAE+ colistin therapy for management of MDR nosocomial infections.

RESULTS

Out of 115 patients short listed for the study, 52 patients had received AAE + colistin therapy and 63 patients have received meropenem + colistin. AAE + colistin therapy resulted in significantly higher efficacy (86.53%) as compared to meropenem + colistin (63.49%). A rising trend in clinical cure rates was observed in AAE based combination therapy in contrast to the decreasing trend in meropenem based combination therapy. A progressive decline in clinical cure rates was observed in meropenem treated group over a period of 3 years due to rising carbapenemases and multiple resistance by pathogens, where as AAE maintained the same efficacy.

CONCLUSION

The AAE + colistin therapy has shown better bacteriological and clinical efficacy as compared to meropenem + colistin in the management of various nosocomial MDR Gram-negative infections. A significant number of meropenem failure patients responded to the AAE therapy highlighting the new hope to spare carbapenems.

Phenotypic and molecular detection of the bla KPC gene in clinical isolates from inpatients at hospitals in São Luis, MA, Brazil

Background

Bacteria that produce Klebsiella pneumoniae carbapenemases (KPCs) are resistant to broad-spectrum β-lactam antibiotics. The objective of this study was to phenotypically and genotypically characterize the antibiotic susceptibility to carbapenems of 297 isolates recovered from clinical samples obtained from inpatients at 16 hospitals in São Luis (Maranhão, Brazil).

Methods

The study was conducted using phenotypic tests and molecular methods, including polymerase chain reaction (PCR), sequencing and enterobacterial repetitive intergenic consensus (ERIC)-PCR. The nonparametric chi-square test of independence was used to evaluate the associations between the bacterial bla_KPC gene and the modified Hodge test, and the chi-square adherence test was used to assess the frequency of carbapenemases and their association with the bla_KPC gene.

Results

The most frequently isolated species were Acinetobacter baumannii (n = 128; 43.0%), K. pneumoniae (n = 75; 25.2%), and Pseudomonas aeruginosa (n = 42; 14.1%). Susceptibility assays showed that polymixin B was active against 89.3% of the bacterial isolates. The Acinetobacter spp. and K. pneumoniae strains were susceptible to amikacin and tigecycline, and Pseudomonas spp. were sensitive to gentamicin and amikacin. Among the 297 isolates, 100 (33.7%) were positive for the bla_KPC gene, including non-fermentative bacteria (A. baumannii) and Enterobacteriaceae species. Among the isolates positive for the bla_KPC gene, K. pneumoniae isolates had the highest positivity rate of 60.0%. The bla_KPC gene variants detected included KPC-2, which was found in all isolates belonging to species of the Enterobacteriaceae family. KPC-2 and KPC-3 were observed in A. baumannii isolates. Importantly, the bla_KPC gene was also detected in three Raoultella isolates and one isolate of the Pantoea genus. ERIC-PCR patterns showed a high level of genetic diversity among the bacterial isolates; it was capable of distinguishing 34 clones among 100 strains that were positive for bla_KPC and were circulating in 11 of the surveyed hospitals.

Conclusions

The high frequency of the bla_KPC gene and the high degree of clonal diversity among microorganisms isolated from patients from different hospitals in São Luis suggest the need to improve the quality of health care to reduce the incidence of infections and the emergence of carbapenem resistance in these bacteria as well as other Gram-negative pathogens.

Diagnostics and Resistance Profiling of Bacterial Pathogens

Worldwide infectious disease is one of the leading causes of death. Despite improvements in technology and healthcare services, morbidity and mortality due to infections have remained unchanged over the past few decades. The high and increasing rate of antibiotic resistance is further aggravating the situation. Growing resistance hampers the use of conventional antibiotics, and substantial higher mortality rates are reported in patients given ineffective empiric therapy mainly due to resistance to the agents used. These infections cause suffering, incapacity, and death and impose an enormous financial burden on both healthcare systems and on society in general. The accelerating development of multidrug resistance is one of the greatest diagnostic and therapeutic challenges to modern medicine. The lack of new antibiotic options underscores the need for optimization of current diagnostics, therapies, and prevention of the spread of multidrug-resistant organisms. The so-called -omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have yielded large-scale datasets that advanced the search for biomarkers of infectious diseases in the last decade. One can imagine that in the future the implementation of biomarker-driven molecular test systems will transform diagnostics of infectious diseases and will significantly accelerate the identification of the bacterial pathogens at the infected host site. Furthermore, molecular tests based on the identification of markers of antibiotic resistance will dramatically change resistance profiling. The replacement of culturing methods by molecular test systems for early diagnosis will provide the basis not only for a prompt and targeted therapy, but also for a much more effective stewardship of antibiotic agents and a reduction of the spread of multidrug resistance as well as the appearance of new antibiotic resistances.

Draft Genome of Multidrug-Resistant Klebsiella pneumoniae 223/14 Carrying KPC-6, Isolated from a General Hospital in Malaysia

We performed whole genome sequencing on a clinical multidrug-resistant Klebsiella pneumoniae strain 223/14. Investigation into its draft genome revealed the presence of KPC-6 variant, suggesting carbapenemase is present in this isolate. We found a plasmid-borne KPC gene (882 bp) inserted between two transposase genes in the genome of K. pneumoniae 223/14.

Molecular detection of antibiotic resistance genes from positive blood cultures

Rapid detection of the bacterial causative agent causing sepsis must be coupled with rapid identification of the antibiotic resistant mechanism that the pathogen might possess. Real-time PCR (qPCR)-based assays have been extensively utilized in the clinical microbiology field as diagnostic tools for the rapid detection of specific nucleic acid (NA) targets. In this chapter, we will discuss the technical aspects of using an internally controlled qPCR assay for the rapid detection of Klebsiella pneumoniae carbapenemase gene (bla KPC) in positive Bactec blood culture bottles. The multiplex qPCR (bla KPC/RNase P) utilizes specific primers and probes for the detection of the bacterial carbapenem resistance mechanism, bla KPC gene, and the internal control RNase P. The internal control of the qPCR assay is vital for detecting any inhibitors that are well known to be present in the blood culture bottles. Rapid detection of the antibiotic resistant mechanism present in the bacterial pathogen causing sepsis can help in better managing patients' infection.

Population Structure of Klebsiella pneumoniae Causing Bloodstream Infections at a New York City Tertiary Care Hospital: Diversification of Multidrug-Resistant Isolates

Despite the growing importance of carbapenem-resistant Klebsiella pneumoniae (CRKP), the clonal relationships between CRKP and antibiotic-susceptible isolates remain unclear. We compared the genetic diversity and clinical features of CRKP, third-generation and/or fourth-generation cephalosporin-resistant (Ceph-R) K. pneumoniae, and susceptible K. pneumoniae isolates causing bloodstream infections at a tertiary care hospital in New York City between January 2012 and July 2013. Drug susceptibilities were determined with the Vitek 2 system. Isolates underwent multilocus sequence typing and PCR sequencing of the wzi and blaKPC genes. Clinical and microbiological data were extracted from patient records and correlated with molecular data. Among 223 patients, we identified 272 isolates. Of these, 194 were susceptible, 30 Ceph-R, and 48 CRKP, belonging to 144 sequence types (STs). Susceptible (127 STs) and Ceph-R (20 STs) isolates were highly diverse. ST258 dominated CRKP strains (12 STs, with 63% ST258). There was minimal overlap in STs between resistance groups. The blaKPC-3 gene (30%) was restricted to ST258/wzi154, whereas blaKPC-2 (70%) was observed for several wzi allele types. CRKP infections occurred more frequently among solid organ transplant (31%) and dialysis (17%) patients. Mortality rates were high overall (28%) and highest among CRKP-infected patients (59%). In multivariable analyses, advanced age, comorbidities, and disease severity were significant predictors of 30-day mortality rates, whereas the K. pneumoniae susceptibility phenotype was not. Among CRKP infections, we observed a borderline significant association of increased mortality rates with ST258 and the wzi154 allele. Although the clonal spread of ST258 continues to contribute substantially to the dissemination of CRKP, non-ST258 strains appear to be evolving. Further investigations into the mechanisms promoting CRKP diversification and the effects of clonal backgrounds on outcomes are warranted.

Rapid detection and identification of strains carrying carbapenemases directly from positive blood cultures using MALDI-TOF MS

MALDI-TOF MS has been evaluated to detect carbapenemases activity and pathogen identification directly from positive blood cultures. 21 non-carbapenemase producers and 19 carbapenemase producers Enterobacteriaceae and Pseudomonas aeruginosa strains were included in the study. This technique is simple and detects carbapenemases in 4.5h with high sensitivity and specificity.

blaKPC gene Detection in Clinical Isolates of Carbapenem Resistant Enterobacteriaceae in a Tertiary Care Hospital

INTRODUCTION

Carbapenem resistance among Enterobacteriaceae, especially in Klebsiella pneumoniae and Escherichia coli, is an emerging problem worldwide. A common mechanism of carbapenem resistance is the production of class-A, Klebsiella pneumoniae carbapenemase (KPC).

AIMS AND OBJECTIVES

The present study focused on determining the antibiotic resistance pattern and prevalence of bla KPC gene coding for KPC in carbapenem resistant Enterobacteriaceae.

METHODOLOGY

Forty six carbapenem resistant isolates belonging to the family Enterobacteriaceae were tested for antibiotic sensitivity pattern. Modified Hodge Test (MHT) and PCR for bla KPC gene detection were performed on these isolates. Of these, 22 were Klebsiella pneumoniae, 21 were Escherichia coli, 2 were Citrobacter species and 1 was Proteus mirabilis Results: Forty three (93.4%) out of the 46 isolates were resistant to Meropenem, 34 (73.9%) were resistant to Imipenem and 30 (65.2%) were resistant to both Imipenem and Meropenem. Modified Hodge Test was positive in 38 (82.6%) out of 46 isolates and blaKPC gene was detected in 31 (67.4%) isolates. bla KPC gene was detected in 28 out of the 38 MHT positive isolates.

Rapid detection of carbapenemase-producing Enterobacteriaceae from blood cultures

The biochemical-based Carba NP test has been evaluated to detect carbapenemase-producing Enterobacteriaceae (n = 193) directly from spiked blood cultures. It was able to rapidly detect KPC (n = 50), IMP (n = 27), VIM (n = 37), NDM (n = 33) and OXA-48-like producers (n = 46) with sensitivity and specificity of 97.9% and 100%, respectively. This cost-effective technique may be implemented in any microbiology laboratory and offers a reliable test for an early identification of carbapenemase-producing Enterobacteriaceae directly from blood culture that could be useful for the management of infected patients.

Rapid detection of carbapenemase activity through monitoring ertapenem hydrolysis in Enterobacteriaceae with LC-MS/MS

BACKGROUND

Bacteria are increasingly resistant to antibiotics used to treat life-threatening infections in critically ill patients. The carbapenems represent the last line of defense against Gram-negative rods that are increasingly resistant to all other classes of β-lactam antibiotics used to treat life-threatening infections in critically ill patients. Carbapenem resistance in Gram-negative rods is most commonly caused by expression of carbapenemases, enzymes that hydrolyze the β-lactam ring of carbapenem antibiotics rendering them inactive. All of the available diagnostic tests rely on bacterial growth rendering them time consuming; therefore, rapid diagnostic tests are needed to identify multidrug (including carbapenem)-resistant bacteria.

RESULTS

We report the development of a novel LC-MS/MS method that detects carbapenemase activity from bacterial isolates. Incubation of a bacterial suspension with physiological levels of ertapenem leads to carbapenemase-mediated drug hydrolysis that produces a specific metabolite with an 18 Da increase in m/z within 1 h. Using the ratio of metabolite:parent, detected by LC-MS/MS from the culture, the sensitivity, specificity and a threshold cutoff for carbapenemase production (interpretive criteria) have been determined.

CONCLUSION

A 100% correlation of our LC-MS/MS assay with the modified Hodge test (functional test for carbapenemase production) and PCR emphasizes the robust nature of this assay. The assay requires minimal hands-on time and a straightforward protocol allowing convenient implementation into clinical laboratories. Inclusion of stable isotope-labeled standard will further increase the robustness of the assay. This assay offers several advantages over other similar assays that use MALDI-TOF MS analysis.