Comparison of BD Phoenix, Vitek 2, and MicroScan automated systems for detection and inference of mechanisms responsible for carbapenem resistance in Enterobacteriaceae

Carbapenem non-susceptibility overcalling by BD phoenix NMIC-500 panel

We aimed to assess the accuracy of BD Phoenix for determining carbapenem susceptibility because we observed a decline in carbapenem susceptibility rate from the biannual cumulative data, after we transitioned to the BD Phoenix form Vitek 2 system. Between October 2021 and May 2022, we collected 82 non-duplicated Enterobacterales showing non-susceptible to at least one of the three carbapenems by BD Phoenix. We performed the broth microdilution (BMD) and disk diffusion (DD) according to the CLSI guideline. Compared to BMD, the categorical agreements for ertapenem (ERT), imipenem (IPM) and meropenem (MEPM) was 58.8%, 56.8% and 91.5% for BD Phoenix and it was 85.4%, 89.0%, and 97.6%, respectively, for DD (p value; 0.0001 for ERT and IPM, p value; 0.17 for MEPM). The major errors/minor errors for ERT, IPM, and MEPM were 14.0%/31.7%, 2.94%/40.7%, and 2.56%/6.10%, respectively for BD Phoenix, compared to 0%/14.6%, 0%/9.8%, and 0%/2.5%, for DD. While errors in the BD Phoenix showed tendency towards resistance, those in DD displayed no tendency towards either resistance or susceptibility. With DD, 21 out of the 27 isolates showing susceptible/intermediate/susceptible pattern (ERT/IPM/MEPM) and 13 out of the 16 isolates showing intermediate/susceptible/susceptible pattern (ERT/IPM/MEPM), were correctly categorized by DD. However, for 22 isolates showing resistant/susceptible/susceptible pattern (ERT/IPM/MEPM), only 13 isolates were correctly categorized by DD. In conclusion, to mitigate the risk of overcalling carbapenem non-susceptibility with BD Phoenix, it will be helpful to perform a complementary test using DD and to provide comments on the DD results to clinicians.

Efficient Absorbance-Based Assay for Rapid Antibiotic Susceptibility Testing of Enterobacterales

It is increasingly important to rapidly receive information on the antimicrobial susceptibility of bacteria due to the rise in antimicrobial resistance worldwide. However, traditional phenotypic methods are time-consuming. Thus, the objective of this study was to develop a rapid assay that can detect antibiotic-resistant bacterial isolates phenotypically in less than 2 h. The microplate assay used in this study is based on absorbance measurements of pure bacterial isolates grown in liquid media with and without antibiotics. Absorbance was measured at the beginning of the assay and after 90 min of incubation at 37 °C. Susceptibility was calculated for bacterial isolates that, in the absence of antibiotics, exhibited more than a 50% growth increase by comparing the absorbance value of the culture in the presence of an antibiotic at 90 min with its initial value. Here, we show that it is possible to phenotypically screen the antibiotic susceptibility of Enterobacterales and Acinetobacter spp. isolates to three different antibiotics in 90 min. The test demonstrated an accuracy of 98.8%, sensitivity of 97.6%, and specificity of 99.6%. The false susceptibility rates were 0.2% and false resistance rates were 1.0%. This rapid and simple absorbance test has proven suitable for the screening of antibiotic susceptibility for a large number of strains with high accuracy and sensitivity. This method can be performed without specialized and costly materials and/or equipment, which makes it highly suitable for laboratories with limited resources.

β-lactam resistant phenotypes reported by VITEK®2 advanced expert systemTM (AES) compared to whole genome sequencing in Enterobacterales from North and Latin America

The VITEK®2 AES β-lactam phenotypes of 488 Enterobacterales from North and Latin America generated by the VITEK®2 were compared to the resistance genotypes provided by whole genome sequencing (WGS). The AES provided phenotypic reports for 447 (91.6 %) isolates, including isolates harbouring carbapenemases (195; 43.6 %), ESBLs (103; 23.0 %) and transferable AmpCs (tAmpC; 28; 6.3 %) genes, as well as wildtype isolates (WT; 121; 27.1 %). Overall, the AES report was accurate for 433/447 (96.9 %) isolates. The AES accurately reported carbapenemase, ESBL, and tAmpC phenotypes for 93.7 %, 93.7 %, and 98.4 % of isolates, respectively, and sensitivity/specificity rates were 96.4 %/91.7 %, 98.1 %/92.4 %, 82.1 %/99.5 %, and 100 %/98.8 %. 14 isolates carrying carbapenemase (7 total; 3 KPC, 2 MBL, 2 OXA-48-like), ESBL (2), and tAmpC-encoding genes (5) were not correctly identified by AES. The AES phenotypic report detected resistance mechanisms among Enterobacterales rapidly and could significantly aid future antimicrobial stewardship initiatives and patient care.

Reliability of a Screening Method Using Antibiotic Disks to Detect Carbapenemases in Glucose-Nonfermenting Gram-Negative Microorganisms From Clinical Samples of a Regional Hospital in Southeastern Spain

BACKGROUND

Infections by glucose-nonfermenting gram-negative bacilli (NFGNB) pose a major public health problem due to multiresistance to beta-lactam antibiotics, especially plasmid-borne carbapenemases. Their detection by microbiology laboratories is challenging, and there is a need for easy-to-use and reliable diagnostic techniques. Our objective was to evaluate an in-house screening method to presumptively detect carbapenemases in NFGNB in a simple and clinically useful manner.

METHODS

The study included 175 NFGNB isolates from urinary, respiratory, and rectal samples. In a triple assay, isolates were incubated at 37°C for 24 h on three solid-culture media: MacConkey II Agar, 5% Sheep Blood Columbia Agar and Mueller Hinton II Agar; meropenem (MEM) and cefepime (FEP) disks were employed for screening. Studies were then performed on the inhibition halo diameter, scanning effects, and the appearance of mutant colonies, which were compared with those observed using the colorimetric Neo-Rapid CARB Kit and immunochromatography (NG5-Test Carba and K-Set for OXA-23). Receiver operating characteristic curves were constructed for these data.

RESULTS

Carbapenemases were expressed by 79/175 (45.1%): 19 Pseudomonas aeruginosa and 60 Acinetobacter baumannii. Optimal inhibition halo diameter cutoffs to detect this resistance on 5% sheep blood agar were as follows: 6 mm (MEM) and 6.5 mm (FEP) for P. aeruginosa (in the absence of scanning effects and mutations) and 10.5 mm (MEM) and 16 mm (FEP) for A. baumannii (even in the presence of scanning effects).

CONCLUSION

The combined utilization of MEM and FEP antibiotic disks in 5% sheep blood agar, measuring their inhibition haloes, offers an effective method to predict the presence of carbapenemases as resistance mechanism in P. aeruginosa and A. baumannii.

Carbapenem-resistant Klebsiella pneumoniae: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge

INTRODUCTION

Klebsiella pneumoniae is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in K. pneumoniae has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant K. pneumoniae (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids.

AREAS COVERED

Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in K. pneumoniae.

EXPERT OPINION

CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.

Evaluation of the BD Phoenix CPO Detect Panel for Detection and Classification of Carbapenemase Producing Enterobacterales

Carbapenem-resistant Enterobacterales (CRE) pose a serious public health threat due to their resistance to most antibiotics. Rapid and correct detection of carbapenemase producing organisms (CPOs) can help inform clinician decision making on antibiotic therapy. The BD Phoenix™ CPO detect panel, as part of antimicrobial susceptibility testing (AST), detects carbapenemase activity (P/N) and categorizes CPOs according to Ambler classes. We evaluated a CPO detect panel against 109 carbapenemase producing Enterobacterales (CPE) clinical isolates from Korea. The panel correctly detected carbapenemases production in 98.2% (n = 107/109) isolates and identified 78.8% (n = 26/33) class A, 65.9% (n = 29/44) class B, and 56.3% (n = 18/32) class D carbapenemase producers as harboring their corresponding Ambler classes. Specifically, the panel correctly classified 81.3% (n = 13/16) of K. pneumoniae KPC isolates to class A. However, the panel failed to classify 40.0% (n = 4/10) IMP and 63.6% (n = 7/11) VIM isolates to class B. Despite 27.5% (n = 30/109) CPE not being assigned Ambler classes, all of them tested carbapenemase positive. Our results demonstrate that the CPO detect panel is a sensitive test for detecting CPE and classifying KPC as class A, helping with antibiotics selection, but one-third of CPE remained unclassified for Ambler classes.

Carbapenem-Resistant enterobacterales in individuals with and without health care risk factors -Emerging infections program, United States, 2012-2015

BACKGROUND

Carbapenem-resistant Enterobacterales (CRE) are usually healthcare-associated but are also emerging in the community.

METHODS

Active, population-based surveillance was conducted to identify case-patients with cultures positive for Enterobacterales not susceptible to a carbapenem (excluding ertapenem) and resistant to all third-generation cephalosporins tested at 8 US sites from January 2012 to December 2015. Medical records were used to classify cases as health care-associated, or as community-associated (CA) if a patient had no known health care risk factors and a culture was collected <3 days after hospital admission. Enterobacterales isolates from selected cases were submitted to CDC for whole genome sequencing.

RESULTS

We identified 1499 CRE cases in 1194 case-patients; 149 cases (10%) in 139 case-patients were CA. The incidence of CRE cases per 100,000 population was 2.96 (95% CI: 2.81, 3.11) overall and 0.29 (95% CI: 0.25, 0.35) for CA-CRE. Most CA-CRE cases were in White persons (73%), females (84%) and identified from urine cultures (98%). Among the 12 sequenced CA-CRE isolates, 5 (42%) harbored a carbapenemase gene.

CONCLUSIONS

Ten percent of CRE cases were CA; some isolates from CA-CRE cases harbored carbapenemase genes. Continued CRE surveillance in the community is critical to monitor emergence outside of traditional health care settings.

Overprediction of Carbapenemase-Containing Isolates by an Automated AST Instrument's Computer Algorithm

BACKGROUND

The VITEK® 2 is generally accepted as a reliable method for predicting antibiotic resistance mechanisms including aminoglycoside phenotypes, beta lactam phenotypes, impermeability, and penicillinases. However, when it comes to predicting carbapenemases, the research that has been done is inconsistent in both methods and results.

METHODS

We compared the predictions of the VITEK 2 and Advanced Expert System™ (AES) with the results of the modified carbapenemase inactivation method in an academic medical center lab to evaluate the clinical reliability of the VITEK 2 and AES in routine workflow for the detection of carbapenemases.

RESULTS

Our findings show that the positive predictive value of carbapenemase detection on the VITEK2 and AES is 30.3% (91/300) in our patient population.

CONCLUSIONS

In light of these results, we propose that the VITEK 2 and AES be used as a screening tool for carbapenemase-containing organisms rather than as a definitive test.

Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected through CDC's Emerging Infections Program, United States, 2016-2018

The CDC's Emerging Infections Program (EIP) conducted population- and laboratory-based surveillance of US carbapenem-resistant Pseudomonas aeruginosa (CRPA) from 2016 through 2018. To characterize the pathotype, 1,019 isolates collected through this project underwent antimicrobial susceptibility testing and whole-genome sequencing. Sequenced genomes were classified using the seven-gene multilocus sequence typing (MLST) scheme and a core genome (cg)MLST scheme was used to determine phylogeny. Both chromosomal and horizontally transmitted mechanisms of carbapenem resistance were assessed. There were 336 sequence types (STs) among the 1,019 sequenced genomes, and the genomes varied by an average of 84.7% of the cgMLST alleles used. Mutations associated with dysfunction of the porin OprD were found in 888 (87.1%) of the genomes and were correlated with carbapenem resistance, and a machine learning model incorporating hundreds of genetic variations among the chromosomal mechanisms of resistance was able to classify resistant genomes. While only 7 (0.1%) isolates harbored carbapenemase genes, 66 (6.5%) had acquired non-carbapenemase β-lactamase genes, and these were more likely to have OprD dysfunction and be resistant to all carbapenems tested. The genetic diversity demonstrates that the pathotype includes a variety of strains, and clones previously identified as high-risk make up only a minority of CRPA strains in the United States. The increased carbapenem resistance in isolates with acquired non-carbapenemase β-lactamase genes suggests that horizontally transmitted mechanisms aside from carbapenemases themselves may be important drivers of the spread of carbapenem resistance in P. aeruginosa.

Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods

Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.

Antimicrobial resistance in Indian isolates of non typhoidal Salmonella of livestock, poultry and environmental origin from 1990 to 2017

A retrospective antimicrobial resistance study of nontyphoidal Salmonella enterica isolates from India during 1990-2017 was conducted to study the microbial susceptibility to antibiotics. A total of 271 Salmonella enterica isolates from poultry (n = 146), farm animals (n = 55) and environmental sources (n = 70) were tested for susceptibility using 15 antimicrobial drugs. The drug classes include aminoglycosides, phenicols, cephalosporins, penicillins, carbapenems, fluoroquinolones, and sulphonamide-trimethoprim. Study revealed that overall, 133 (49.08%) of 271 isolates were resistant to ≥ 1 antimicrobial drugs and 81 (29.89%) out of 271 isolates were multidrug resistant (resistance to ≥ 3 drugs). Majority (68.96%) of Typhimurium serovars (n = 87) were susceptible to all antibiotics tested, whereas only 5% Kentucky serovars (n = 40) were pan susceptible. All the drugs revealed decreasing trend of susceptibility from 1990 towards 2017 except cephalosporins and carbapenems. Statistical analysis of association between time period and antimicrobial resistance revealed a significance of < 0.05. Molecular detection of genetic determinants associated with antimicrobial resistance revealed the presence of genes like class I integrons, sul1, sul2, catIII, cmlA, dfrA, bla_TEM, bla_AmpC in the resistant isolates. Furthermore, plasmid mediated quinolone resistant determinants like qnrD and qnrS were also reported in the current study.

Evaluation of the BD Phoenix CPO detect panel for prediction of Ambler class carbapenemases

Rapid detection of carbapenemases as a cause of resistance is beneficial for infection control and antimicrobial therapy. The BD Phoenix NMIC-502 panel and CPO detect test identifies presence of carbapenemases in Enterobacterales such as Klebsiella pneumoniae and assigns them to Ambler classes. To evaluate the performance of the CPO detect panel, we employed a European collection of 1222 K. pneumoniae including carbapenem non-susceptible and susceptible clinical isolates from 26 countries, for which draft genomes were available after Illumina sequencing and the presence of carbapenemase genes had been identified by ARIBA gene calling. The CPO panel detected 488 out of 494 carbapenemase-encoding isolates as positive and six as negative. One-hundred and two isolates were tested positive for carbapenemase in the absence of any carbapenemase gene. The CPO panel identified 229 out of 230 KPC-positive isolates as carbapenemase producing and classified 62 of these as class A enzyme. Similarly, the CPO panel correctly specified 167 of 182 as class D. Regarding metallo-beta-lactamases, the CPO panel assigned 78 of 90 MBL positive isolates to class B enzymes. The sensitivity of the CPO panel in detecting carbapenemase activity was 99.5%, 97.7% and 98.3% for class A, B and D enzymes, respectively. The sensitivity in assignation to Ambler class A, B and D was 27%, 86% and 91%, respectively. An overall sensitivity of 98.8% and specificity of 86% in unclassified detection of carbapenemases was observed, with frequent false positive detection of carbapenemase producing organisms, thus rendering further confirmatory tests necessary.

Heteroresistant Bacteria Detected by an Extended Raman-Based Antibiotic Susceptibility Test

Worldwide, multiresistant bacterial strains are emerging at unprecedented rates. This development seriously threatens the ability of humanity to treat even common infections, resulting in disability and death. Furthermore, this development endangers all medical achievements including cancer therapy or organ transplantations. Therefore, the World Health Organization has endorsed antimicrobial resistance as a great threat to humanity. To still allow effective treatment of patients, rapid, automated, and reliable antibiotic susceptibility testing (AST) of bacterial pathogens is essential. Thereby, speed and sensitivity of the AST results are crucial for improving patient care. Here, Raman spectroscopy as a nondestructive technique providing chemical-specific information is employed to monitor the deuterium uptake of metabolically active bacteria during antibiotic treatment, enabling fast and reliable AST. For this purpose, a bulk sample-preparation method was developed, allowing a high-throughput analysis of a significant number of cells. A protocol was developed for Gram-positive (Enterococcus faecalis) and Gram-negative (Escherichia coli) reference strains and was tested on 51 clinical isolates with well-characterized resistance phenotypes against ampicillin, ciprofloxacin, meropenem, and vancomycin. Borderline resistant and heteroresistant phenotypes were observed and further investigated. This is of critical importance as the sensitive detection of low-frequency heteroresistance in bacterial populations is a huge challenge. Such isolates seem susceptible but are resistant to treatment in vivo. Automatable analysis detects strong phenotypes within 3 h. On the basis of experimental and modeled data, heteroresistance is estimated to be detectable down to frequencies of 10^-6 and investigated on clinical isolates as a proof-of-concept study, but requiring longer incubation time.

Rapid qualitative antibiotic resistance characterization using VITEK MS

Development and standardization of simple, timely, and cost-effective antibiotic susceptibility assays are much needed to address the emergence of global resistance. The use of matrix-assisted laser desorption/ionization time of flight mass spectrometry is routine for bacterial identification. This study evaluated 2 assays using the VITEK MS for rapid detection and accurate differentiation of bacterial antibiotic susceptibility. We describe an extraction method and direct-on-target microdroplet growth assay (DOT-MGA). Non-susceptible and susceptible strains of Staphylococcus aureus, Enterococcus species, Escherichia coli, and Klebsiella pneumoniae were tested. The liquid extraction method and DOT-MGA proved to be reliable assays providing consistent differentiation between non-susceptible and susceptible strains. Results from this study support VITEK MS and these assays as rapid and accurate tools to augment traditional susceptibility testing. If implemented clinically, these assays can reduce the cost of patient care and the time to deliver critically needed treatment.

Carbapenem-Resistant Klebsiella pneumoniae: Microbiology Key Points for Clinical Practice

Carbapenemase–producing Klebsiella pneumoniae strains (Cp-Kpn) represent a challenge for clinical practitioners due to their increasing prevalence in hospital settings and antibiotic resistance. Clinical practitioners are often overwhelmed by the extensive list of publications regarding Cp-Kpn infections, treatment, characteristics, identification, and diagnosis. In this perspective article, we provide key points for clinical practitioners to consider for improved patient management including identification of risk factors and strategies for treatment. Additionally, we also discuss genetic underpinnings of antibiotic resistance, implementation of an antimicrobial stewardship program (ASP), and use of automated systems for detection of Cp-Kpn. Collectively, implementation of such key points would enhance clinical practices through providing practical knowledge to health professionals worldwide.

The Global Ascendency of OXA-48-Type Carbapenemases

Surveillance studies have shown that OXA-48-like carbapenemases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of nonendemicity, where they are responsible for nosocomial outbreaks. OXA-48, OXA-181, OXA-232, OXA-204, OXA-162, and OXA-244, in that order, are the most common enzymes identified among the OXA-48-like carbapenemase group. OXA-48 is associated with different Tn1999 variants on IncL plasmids and is endemic in North Africa and the Middle East. OXA-162 and OXA-244 are derivatives of OXA-48 and are present in Europe. OXA-181 and OXA-232 are associated with ISEcp1, Tn2013 on ColE2, and IncX3 types of plasmids and are endemic in the Indian subcontinent (e.g., India, Bangladesh, Pakistan, and Sri Lanka) and certain sub-Saharan African countries. Overall, clonal dissemination plays a minor role in the spread of OXA-48-like carbapenemases, but certain high-risk clones (e.g., Klebsiella pneumoniae sequence type 147 [ST147], ST307, ST15, and ST14 and Escherichia coli ST38 and ST410) have been associated with the global dispersion of OXA-48, OXA-181, OXA-232, and OXA-204. Chromosomal integration of bla _OXA-48 within Tn6237 occurred among E. coli ST38 isolates, especially in the United Kingdom. The detection of Enterobacterales with OXA-48-like enzymes using phenotypic methods has improved recently but remains challenging for clinical laboratories in regions of nonendemicity. Identification of the specific type of OXA-48-like enzyme requires sequencing of the corresponding genes. Bacteria (especially K. pneumoniae and E. coli) with bla _OXA-48, bla _OXA-181, and bla _OXA-232 are emerging in different parts of the world and are most likely underreported due to problems with the laboratory detection of these enzymes. The medical community should be aware of the looming threat that is posed by bacteria with OXA-48-like carbapenemases.

Rapid detection of antibiotic resistance in positive blood cultures by MALDI-TOF MS and an automated and optimized MBT-ASTRA protocol for Escherichia coli and Klebsiella pneumoniae

Introduction: For fast and effective antibiotic therapy of serious infections like sepsis, it is crucial with rapid information about antibiotic susceptibility, especially in a time when the number of infections caused by multi resistant bacteria has escalated in the world.Methods: Here, we have used a semi-quantitative MALDI-TOF-MS based method for antibiotic resistance detection, MBT-ASTRA™, which is based on the comparison of growth rate of the bacteria cultivated with and without antibiotics. We demonstrate a new protocol where several parameters have been optimized and automated leading to reduced hands-on time and improved capacity to simultaneously analyse multiple clinical samples and antibiotics.Results: Ninety minutes of incubation at 37 °C with agitation was sufficient to differentiate the susceptible and resistant strains of E. coli and K. pneumoniae, for the antibiotics cefotaxime, meropenem and ciprofloxacin. In total, 841 positive blood culture analyses of 14 reference strains were performed. The overall sensitivity was 99%, specificity 99% and the accuracy 97%. The assay gave no errors for cefotaxime (n = 263) or meropenem (n = 289) for sensitive and resistant strains, whilst ciprofloxacin (n = 289) gave six (0.7%) major errors (false resistance) and four (0.5%) very major errors (false susceptibility). The intermediate strains showed a larger variety compared to the E-test MIC values.Conclusions: The hands-on time and the analysis time to detect antibiotic resistance of clinical blood samples can be substantially reduced and the sample capacity can be increased by using automation and this improved protocol.

Carbapenemases in Enterobacteriaceae: Detection and Antimicrobial Therapy

Carbapenem-resistant Enterobacteriaceae (CRE) have spread rapidly around the world in the past few years, posing great challenges to human health. The plasmid-mediated horizontal transmission of carbapenem-resistance genes is the main cause of the surge in the prevalence of CRE. Therefore, the timely and accurate detection of CRE, especially carbapenemase-producing Enterobacteriaceae, is very important for the clinical prevention and treatment of these infections. A variety of methods for the rapid detection of CRE phenotypes and genotypes have been developed for use in clinical microbiology laboratories. To overcome the lack of efficient antibiotics, CRE infections are often treated with combination therapies. Moreover, novel drugs and emerging strategies appeared successively and in various stages of development. In this article, we summarized the global distribution of various carbapenemases. And we focused on summarizing and comparing the advantages and limitations of the detection methods and the therapeutic strategies of CRE primarily.

Evaluation of Modified Hodge Test as a Non-molecular Assay for Accurate Detection of KPC-producing Klebsiella pneumoniae

Klebsiella pneumoniae carbapenemase (KPC) have become a major therapeutic challenge because of its increasingly fast dissemination throughout the world. Accurate detection of KPC is essential for optimal treatment. The Clinical and Laboratory Standards Institutes (CLSI) for fast detection of KPC producers currently recommend Modified Hodge Test (MHT) and Carba NP test. MHT can directly detect carbapenemase production in Enterobacteriaceae isolates. The current study was conducted to evaluate the capacity of MHT with two carbapenem disks for accurate detection of KPC. MHT was performed according to guidelines of CLSI to identify isolates with carbapenem resistance. In doing so, two substrates of MHT were assigned into two groups for examination: meropenem and ertapenem groups. A total of 96 non-repetitive clinical isolates of Klebsiella pneumoniae were tested. The presence of the bla KPC gene in each MHT-positive isolate was examined by PCR. A total of 54 isolates exhibited reduced susceptibility or resistance to carbapenems. Sensitivity of MHT with two carbapenem disks was similar. Specificity of the MHT with meropenem disk was 64% and with ertapenem disk was 53%. Detection of KPC by MHT with meropenem disk was found to be more effective than with ertapenem disk. Based on our results, the presence of KPC does not in itself influence the categorization of resistance. Therefore, the use of MHT with ertapenem disk for the rapid detection of KPC among K. pneumoniae for infection control should not be recommended.

Emergence of OXA-48 Carbapenemase Producing Klebsiella pneumoniae in a Neonatal Intensive Care Unit in Marrakech, Morocco

Goal:

This work aims to describe and explore the circumstances of appearance of Klebsiella pneumoniae producing OXA-48 carbapenemase, which has occurred in a neonatal intensive care service at the Mohammed VI University Hospital of Marrakech.

Results:

During February 2015, the alert was triggered by the isolation of 6 isolates of K pneumoniae with the same antibiotic susceptibility profile in the neonatal intensive care service, suggesting a possible outbreak. Blood cultures represented the main site of isolation of these isolates. The phenotypic study of the isolates made it possible to identify a strain of K pneumoniae susceptible to third-generation cephalosporins, ciprofloxacin, and aminoglycosides, and resistant to ertapenem, β-lactamases inhibitors (ticarcillin-clavulanate, piperacillin-tazobactam; amoxicillin-clavulanic acid), and cotrimoxazole. The genotypic study of the epidemic isolate revealed the presence of the bla_OXA-48 gene. The action to be taken was the establishment of corrective measures to stop this epidemic to a multi-resistant germ transmitted by hand transmission. The reinforcement of hygiene measures and the awareness of the staff made it possible to put an end to the epidemic at March 30, 2015, without closing the service. The outcome of 6 infected newborns was fatal due to the fragile terrain and the inappropriate probabilistic antibiotic therapy.

Conclusion:

The production of carbapenemase in K pneumoniae is an emerging resistance mechanism that must be suspected and identified to offer targeted therapy and to limit its spread. The implementation of a local policy to control multidrug-resistant germs is essential to limit their dissemination in hospitals.

Rapid antibiotic susceptibility testing on blood cultures using MALDI-TOF MS

Antibiotic resistance is a major public health problem requiring the early optimization of antibiotic prescriptions. Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS) has been shown to accurately identify bacteria from positive blood culture. Here, we developed a rapid detection of Escherichia coli resistance to amoxicillin (AMX) and cefotaxime (CTX) from positive blood culture based on MALDI-TOF MS. Potential sparing of broad-spectrum antibiotics was also evaluated. We tested 103 E. coli-positive blood cultures. Blood cultures were subculture 1-hour in antibiotic-free rich liquid media before further incubation with and without AMX for 2.5 h or CTX for 2 h. Protein extracts associated with an internal control were spotted on a MALDI-TOF target and spectra were analyzed with the MBT-ASTRA prototype software (Bruker Daltonik GmbH, Bremen, Germany). Bacterial growth ratio was calculated from the AUC spectra obtained in the presence and absence of the antibiotic and compared to a threshold which classified E. coli as susceptible or resistant. Results were interpreted with MICs determined using agar dilution method as reference technique. MBT-ASTRA recognized 95% and 84% of the AMX- and CTX-susceptible isolates, respectively. Overall, quantitative analysis of mass spectra allows susceptibility testing within 4 hours after the positivity of blood culture with E. coli. At the first report of positive blood culture, MALDI-TOF MS would then provide the prescribers with the bacterial identification and the susceptibility to AMX and CTX, thus limiting the use of broad-spectrum compounds.

The emergence of carbapenem-resistant Klebsiella pneumoniae isolates producing OXA-48 and NDM in the Southern (Asir) province, Saudi Arabia

OBJECTIVES

To identify the prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) and the most common types of cabapenemases among CRKP in the Southern (Asir) province hospitals, Saudi Arabia. Methods: The cross-sectional study was conducted between late April and September in 2015. A total of 54 Klebsiella pneumoniae (K. pneumoniae) isolates with reduced sensitivity to carbapenems were obtained from various clinical specimens of the 2 largest hospitals in the Southern province. Minimum inhibitory concentrations (MICs) of carbapenems were confirmed using E-test. Molecular detection of the most common carbapenemase genes (blaIMP, bla-carbapenem-hydrolyzing oxacillinase [OXA-48], blaVIM, bla-New Delhi metallo-ß-lactamas [NDM], and blaKPC) was performed using multiplex-polymerase chain reaction. Results: The current study found that increasing age and intensive care unit admission were associated with CRKP isolation. The major type of carbapenemases was OXA-48 with 81.5% (n=44) and it seems to reach an endemic level. New Delhi metallo-ß-lactamas (NDM) was the second most frequent carbapenemase by 7.4% (n=4) of isolates while Verona integron-encoded metallo-ß-lactamase (VIM) was reported only in one isolate. Conclusion: Saudi Arabia receives large numbers of visitors and migrant workers from OXA-48 and NDM endemic countries such as Turkey, India, and Pakistan every year.

Prospective evaluation of the OKN K-SeT assay, a new multiplex immunochromatographic test for the rapid detection of OXA-48-like, KPC and NDM carbapenemases

Objectives: There is an urgent need for accurate and fast diagnostic tests capable of identifying carbapenemase producers. Here, we assessed the performance of a new multiplex lateral flow assay (OKN K-SeT) for the rapid detection of OXA-48-like, KPC and NDM carbapenemase-producing Enterobacteriaceae from culture colonies.

Methods: Two hundred collection isolates with characterized β-lactamase content and 183 non-duplicate consecutive isolates referred to two National Reference Centres over a 2 month period in 2016 were used to evaluate the OKN K-SeT assay.

Results: The assay correctly detected all 42 OXA-48-like-, 27 KPC- and 30 NDM-producing isolates from the collection panel, including 7 isolates that co-produced NDM and OXA-181 carbapenemases. No cross-reactivity was observed with non-targeted carbapenemases (n = 41) or with non-carbapenemase producers (n = 60). Prospectively, all OXA-48-like (n = 69), KPC (n = 9) and NDM (n = 19) carbapenemase-producing Enterobacteriaceae isolates were correctly detected, while 11 carbapenemase producers not targeted by the assay went undetected [VIM (n = 8) and OXA-23/OXA-58-like (n = 3)]. Overall, the sensitivity and specificity of the assay were 100%.

Conclusions: The OKN assay is efficient, rapid and easy to implement in the workflow of a clinical microbiology laboratory for the confirmation of OXA-48, NDM and KPC carbapenemases. This test represents a powerful diagnostic tool as it enables the rapid detection of the most clinically important carbapenemases without the need for more costly and less frequently available molecular assays.

Comparation of Phenotypic and Genotypic Profile of Carbapenemase Producing Escherichia coli

Carbapenemase-producing Escherichia coli (E. coli) has caused trouble in therapeutic antibiotic selection. Carbapenemase screening procedure in laboratories is usually based on inacurate semi-automatic system. Confirmation and classification of carbapenemases according to Ambler can be done with combination of phenotypic methods, i.e., Modified Hodge Test (MHT), Sodium Mercaptoacetic Acid (SMA), and 3-Aminophenylboronic Acid (PBA). This study aimed to compare profiles of carbapenemase-producing E. coli which were confirmed and classified phenotypically with the genotypic profiles. E. coli isolates from urine specimens which were potential as carbapenemase-producers according to semi-automatic system BD Phoenix were phenotypically tested with MHT, SMA, and PBA. Isolates were grouped as carbapenemase-producers and non carbapenemase-producers. Phenotypic carbapenemase-producer isolates were classified based on Ambler criteria. All isolates were then tested with Polymerase Chain Reaction (PCR) for the presence of OXA-48, IMP1, IMP2, GES, VIM, NDM, KPC genes. Out of 30 isolates, 6 isolates (20.0%) were MHT positive, and 25 isolates (83.3%) were SMA positive, which indicated that most isolates produced were carbapenemase Ambler B. PCR confirmed 12 isolates (40.0%) had VIM gene which were classified as carbapenemase Ambler B. Phenotypic confirmatory test had 100% sensitivity and 22.2% specificity. Classification with phenotypic confirmatory test had 91.7% match with PCR. Phenotypic confirmatory test detected more carbapenemase than PCR. This low specificity may be caused by inappropriate use of diagnostic gold standard. PCR should not be used for routine carbapenemase confirmation because of vast diversity of carbapenemases. Phenotypic confirmatory test can classify carbapenemase according to Ambler classification.

Phenotypic and Molecular Characterization of Multidrug Resistant Klebsiella pneumoniae Isolated from Different Clinical Sources in Al-Najaf Province-Iraq

BACKGROUND AND OBJECTIVE

Burns infections and urinary tract infections are the most important prevalent diseases in Asian countries, such as Iraq. Klebsiella pneumoniae is one of the most important bacteria cause this type of infections especially in hospitals. Therefore, the aim of this study was to investigate the prevalence of multi-drug resistance K. pneumoniae and extended-spectrum beta-lactamases producing K. pneumoniae isolates from inpatients with urinary tract infection and burns infections in Al-Kufa hospital in Al-Najaf province, Iraq.

MATERIALS AND METHODS

A total of 285 clinical samples were collected from in-patients infected with urinary tract infection (141 urine samples) and burns infections (144 burns swabs). Fourteen different antibiotics were used by disc diffusion method and 13 antimicrobials resistance genes were used by PCR technique.

RESULTS

A total of 43 K. pneumoniae strains were isolated. The highest resistance rate was observed for amoxicillin 25 μg and amoxicillin+clavulanic acid 20+10 μg (97.67%) while the lowest resistance rate was observed for imipenem 10 μg (9.30%). The most common resistance associated-genes were blaSHV (86.04%) and at lower prevalence were IMP (9.30%).

CONCLUSION

Klebsiella pneumoniae strains isolated from burns infections were more virulent than those isolated from urinary tract infections.

Performance evaluation of BD Phoenix™, an automated microbiology system, for the screening of IMP-producing Enterobacteriaceae

BD Phoenix™ is an automated bacterial identification and susceptibility testing system. Here, its performance in screening IMP-producing Enterobacteriaceae was evaluated. The system identified 97.8% of IMP producers as being nonsusceptible to imipenem or meropenem, which was higher than that identified by the broth microdilution method (91.3%, imipenem; 41.3%, meropenem).

High Prevalence of Multidrug-Resistant Bacteria in Libyan War Casualties Admitted to a Tertiary Care Hospital, Germany

The ongoing Libyan conflict constantly causes victims among the military and civilian population. Cross-border transfer of patients represents a high risk of introducing multidrug-resistant organisms (MDROs), for example, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci, and carbapenem-resistant gram-negative organisms (CROs), into the country of destination. This study assessed the MDRO status in Libyan war casualties (n = 67) admitted to Northwest Medical Centre in Frankfurt/Main, Germany, from August 2016 till January 2017. Identified multidrug-resistant nonfermenters and Enterobacteriaceae were subjected to molecular detection of β-lactamases and further mechanisms of resistance. All isolates were typed by enzymatic macrorestriction and subsequent pulsed-field gel electrophoresis. MDROs were found in 40 (60%) patients, including 25 (37%) positive for at least one CRO and 11 (16%) patients with MRSA. A total of 37 isolates of Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli, Enterobacter cloacae, and Serratia marcescens produced carbapenemases: NDM (n = 17), OXA-48 (n = 15), and OXA-23 (n = 9) in addition to other β-lactamases (with bla_{CTX-M-group-1} being most frequent) and plasmid-mediated quinolone resistance genes (qnrB, aac(6')Ib-cr). Bacterial strain typing revealed the presence of various clones. This high MDRO rate in Libyan war casualties demands awareness, appropriate screening, and containment measures for medical institutions involved in medical care to avoid patient-to-patient transmission.

Rapid Identification of OXA-48 and OXA-163 Subfamilies in Carbapenem-Resistant Gram-Negative Bacilli with a Novel Immunochromatographic Lateral Flow Assay

We assessed a novel immunochromatographic lateral flow assay for direct identification of OXA-48-like carbapenemases and accurate differentiation of allele variants with distinct substrate profiles (OXA-48 or OXA-163 subfamilies). The assay allowed rapid (less than 4 min) and reliable direct confirmation of OXA-163- and/or OXA-48-like enzymes (with 100% sensitivity and 100% specificity) from cultured colonies that were recovered from both solid medium and spiked blood culture bottles.

Carbapenem resistant Pseudomonas aeruginosa and Acinetobacter baumannii at Mulago Hospital in Kampala, Uganda (2007-2009)

Background

Multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii are common causes of health care associated infections worldwide. Carbapenems are effective against infections caused by multidrug resistant Gram-negative bacteria including Pseudomonas and Acinetobacter species. However, their use is threatened by the emergence of carbapenemase-producing strains. The aim of this study was to determine the prevalence of carbapenem-resistant P. aeruginosa and A. baumannii at Mulago Hospital in Kampala Uganda, and to establish whether the hospital environment harbors carbapenem-resistant Gram-negative rods.

Results

Between February 2007 and September 2009, a total of 869 clinical specimens were processed for culture and sensitivity testing yielding 42 (5 %) P. aeruginosa and 29 (3 %) A. baumannii isolates, of which 24 % (10/42) P. aeruginosa and 31 % (9/29) A. baumannii were carbapenem-resistant. Additionally, 80 samples from the hospital environment were randomly collected and similarly processed yielding 58 % (46/80) P. aeruginosa and 14 % (11/80) A. baumannii, of which 33 % (15/46) P. aeruginosa and 55 % (6/11) A. baumannii were carbapenem-resistant. The total number of isolates studied was 128. Carbapenemase genes detected were bla_IMP-like (36 %, 9/25), bla_VIM-like (32 %, 8/25), bla_SPM-like (16 %, 4/25); bla_NDM-1-like (4 %, 1/25) in carbapenem-resistant P. aeruginosa, and bla_OXA-23-like (60 %, 9/15), bla_OXA-24-like (7 %, 1/15), bla_OXA-58-like (13 %, 2/15), and bla_VIM-like (13 %, 2/15) in carbapenem-resistant A. baumannii. Furthermore, class 1 integrons were detected in 38 % (48/128) of P. aeruginosa and Acinetobacter, 37 % (26/71) of which were in clinical isolates and 39 % (22/57) in environment isolates. Gene cassettes were found in 25 % (12/48) of integron-positive isolates. These were aminoglycoside adenylyltransferase ant(4′)-IIb (3 isolates); trimethoprim-resistant dihydrofolate reductase dfrA (2 isolates); adenyltransferase aadAB (3 isolates); QacE delta1 multidrug exporter (2 isolates); quinolone resistance pentapeptide repeat protein qnr (1 isolate); and metallo-β-lactamase genes bla_VIM-4-like, bla_IMP-19-like, and bla_IMP-26-like (1 isolate each). Gene cassettes were missing in 75 % (36/48) of the integron-positive isolates.

Conclusions

The prevalence of carbapenem-resistant P. aeruginosa and Acinetobacter among hospitalized patients at Mulago Hospital is low compared to rates from South-East Asia. However, it is high among isolates and in the environment, which is of concern given that the hospital environment is a potential source of infection for hospitalized patients and health care workers.

Electronic supplementary material

The online version of this article (doi:10.1186/s40064-016-2986-7) contains supplementary material, which is available to authorized users.

Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods

Carbapenemases have become a significant mechanism for broad-spectrum β-lactam resistance in Enterobacteriaceae and other Gram-negative bacteria such as Pseudomonas and Acinetobacter spp. Intestinal carriage of carbapenemase-producing organisms (CPOs) is an important source of transmission. Isolation of carriers is one strategy that can be used to limit the spread of these bacteria. In this review, we critically examine the clinical performance, advantages, and disadvantages of methods available for the detection of intestinal carriage of CPOs. Culture-based methods (Centers for Disease Control and Prevention [CDC] protocols, chromogenic media, specialized agars, and double-disk synergy tests) for detecting carriage of CPOs are convenient due to their ready availability and low cost, but their limited sensitivity and long turnaround time may not always be optimal for infection control practices. Contemporary nucleic acid amplification techniques (NAATs) such as real-time PCR, hybridization assays, loop-mediated isothermal amplification (LAMP), or a combined culture and NAAT approach may provide fast results and/or added sensitivity and specificity compared with culture-based methods. Infection control practitioners and clinical microbiologists should be aware of the strengths and limitations of available methods to determine the most suitable approach for their medical facility to fit their infection control needs.

Performance evaluation of three automated identification systems in detecting carbapenem-resistant Enterobacteriaceae

Background

Carbapenem-resistant Enterobacteriaceae (CRE) is prevalent around the world. Rapid and accurate detection of CRE is urgently needed to provide effective treatment. Automated identification systems have been widely used in clinical microbiology laboratories for rapid and high-efficient identification of pathogenic bacteria. However, critical evaluation and comparison are needed to determine the specificity and accuracy of different systems. The aim of this study was to evaluate the performance of three commonly used automated identification systems on the detection of CRE.

Methods

A total of 81 non-repetitive clinical CRE isolates were collected from August 2011 to August 2012 in a Chinese university hospital, and all the isolates were confirmed to be resistant to carbapenems by the agar dilution method. The potential presence of carbapenemase genotypes of the 81 isolates was detected by PCR and sequencing. Using 81 clinical CRE isolates, we evaluated and compared the performance of three automated identification systems, MicroScan WalkAway 96 Plus, Phoenix 100, and Vitek 2 Compact, which are commonly used in China. To identify CRE, the comparator methodology was agar dilution method, while the PCR and sequencing was the comparator one to identify CPE.

Results

PCR and sequencing analysis showed that 48 of the 81 CRE isolates carried carbapenemase genes, including 23 (28.4 %) IMP-4, 14 (17.3 %) IMP-8, 5 (6.2 %) NDM-1, and 8 (9.9 %) KPC-2. Notably, one Klebsiella pneumoniae isolate produced both IMP-4 and NDM-1. One Klebsiellaoxytoca isolate produced both KPC-2 and IMP-8. Of the 81 clinical CRE isolates, 56 (69.1 %), 33 (40.7 %) and 77 (95.1 %) were identified as CRE by MicroScan WalkAway 96 Plus, Phoenix 100, and Vitek 2 Compact, respectively. The sensitivities/specificities of MicroScan WalkAway, Phoenix 100 and Vitek 2 were 93.8/42.4 %, 54.2/66.7 %, and 75.0/36.4 %, respectively.

Conclusions

The MicroScan WalkAway and Viteck2 systems are more reliable in clinical identification of CRE, whereas additional tests are required for the Pheonix 100 system. Our study provides a useful guideline for using automated identification systems for CRE identification.

Frequency, Antimicrobial Resistance and Genetic Diversity of Klebsiella pneumoniae in Food Samples

This study aimed to assess the frequency of Klebsiella pneumoniae in food samples and to detect antibiotic resistance phenotypes, antimicrobial resistance genes and the molecular subtypes of the recovered isolates. A total of 998 food samples were collected, and 99 (9.9%) K. pneumoniae strains were isolated; the frequencies were 8.2% (4/49) in fresh raw seafood, 13.8% (26/188) in fresh raw chicken, 11.4% (34/297) in frozen raw food and 7.5% (35/464) in cooked food samples. Antimicrobial resistance was observed against 16 antimicrobials. The highest resistance rate was observed for ampicillin (92.3%), followed by tetracycline (31.3%), trimethoprim-sulfamethoxazole (18.2%), and chloramphenicol (10.1%). Two K. pneumoniae strains were identified as extended-spectrum β-lactamase (ESBL)–one strain had three beta-lactamases genes (bla_SHV, bla_CTX-M-1, and bla_CTX-M-10) and one had only the bla_SHV gene. Nineteen multidrug-resistant (MDR) strains were detected; the percentage of MDR strains in fresh raw chicken samples was significantly higher than in other sample types (P<0.05). Six of the 18 trimethoprim-sulfamethoxazole-resistant strains carried the folate pathway inhibitor gene (dhfr). Four isolates were screened by PCR for quinolone resistance genes; aac(6’)-Ib-cr, qnrB, qnrA and qnrS were detected. In addition, gyrA gene mutations such as T247A (Ser83Ile), C248T (Ser83Phe), and A260C (Asp87Ala) and a parC C240T (Ser80Ile) mutation were identified. Five isolates were screened for aminoglycosides resistance genes; aacA4, aacC2, and aadA1 were detected. Pulsed-field gel electrophoresis-based subtyping identified 91 different patterns. Our results indicate that food, especially fresh raw chicken, is a reservoir of antimicrobial-resistant K. pneumoniae, and the potential health risks posed by such strains should not be underestimated. Our results demonstrated high prevalence, antibiotic resistance rate and genetic diversity of K. pneumoniae in food in China. Improved control and prevention strategies are urgently needed.

Evaluation of an Immunochromatographic Lateral Flow Assay (OXA-48 K-SeT) for Rapid Detection of OXA-48-Like Carbapenemases in Enterobacteriaceae

We evaluated an immunochromatographic lateral flow assay to detect OXA-48-like carbapenemases (OXA-48 K-SeT) in Enterobacteriaceae (n = 82). One hundred percent sensitivity and specificity were observed using bacteria recovered from both solid medium and spiked blood culture bottles, and the results were obtained in <10 min.

An 11,000-isolate same plate/same day comparison of the 3 most widely used platforms for analyzing multidrug-resistant clinical pathogens

Stewardship of the dwindling number of effective antibiotics relies on accurate phenotyping. We sought to conduct the first large-scale, same plate and day comparison of the 3 most widely used bacterial analyzers. A total of 11,020 multidrug-resistant clinical isolates corresponding to more than 485,000 data points were used to compare the 3 major identification and antibiotic susceptibility testing (AST) platforms. Bacterial suspensions, prepared from a single plate, were simultaneously tested on all platforms in the same laboratory. Discrepancies were derived from MIC values using 2014 interpretive guidelines. Molecular methods and manual microbroth dilution were reference standards. Most discrepancies were due to drug-organism-AST platform combination instead of individual factors. MicroScan misidentified Acinetobacter baumannii (P<0.001) and underestimated carbapenem susceptibility in Klebsiella pneumoniae. Vitek-2 and Phoenix had higher discrepancies for blaKPC-containing Enterobacteriaceae (P<0.05) and reported false susceptibilities more often. While all platforms performed according to standards, each had strengths and weaknesses for organism identification, assaying specific drug-organism combinations and inferring carbapenemase production.

Accuracy of in vitro susceptibility tests for carbapenemase-producing Gram-negative bacteria

Accurate susceptibility results on antibiotic-resistant bacteria are essential for proper treatment of infections. In this study, 100 metallo-β-lactamase (MBL)-producing strains and 95 isolates with Klebsiella pneumoniae carbapenemase (KPC) were tested for carbapenem susceptibility using two automated platforms, the Phoenix and Vitek-2 systems, and a manual Etest. Phoenix showed higher categorical agreements (97% for imipenem and 94% for meropenem) compared with those from Vitek-2 (92 and 74%) and Etest (89 and 96%), respectively, when testing MBL strains. Categorical agreement for imipenem tests with KPC-producing strains was 88.4% with the Phoenix system, 83.2% with the Vitek 2 system and 90.5% with the Etest. Categorical agreement was 100% for all tests with ertapenem. In conclusion, the Phoenix system demonstrated a higher accuracy than Vitek-2 in testing carbapenemase-producing strains, particularly in MBL strains.

Carbapenemases: A worldwide threat to antimicrobial therapy

Carbapenems are potent β-lactams with activity against extended-spectrum cephalosporinases and β-lactamases. These antibiotics, derived from thienamycn, a carbapenem produced by the environmental bacterium Streptomyces cattleya, were initially used as last-resort treatments for severe Gram-negative bacterial infections presenting resistance to most β-lactams but have become an empirical option in countries with high prevalence of Extended Spectrum β-lactamase-producing bacterial infections. Imipenem, the first commercially available carbapenem, was approved for clinical use in 1985. Since then, a wide variety of carbapenem-resistant bacteria has appeared, primarily Enterobacteriaceae such as Escherichia coli or Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa and Acinetobacter baumannii, presenting different resistance mechanisms. The most relevant mechanism is the production of carbapenem-hydrolyzing β-lactamases, also known as carbapenemases. These enzymes also inactivate all known β-lactams, and some of these enzymes can be acquired through horizontal gene transfer. Moreover, plasmids, transposons and integrons harboring these genes typically carry other resistance determinants, rendering the recipient bacteria resistant to almost all currently used antimicrobials, as is the case for K. pneumoniae carbapenemase - or New Delhi metallo-β-lactamases-type enzymes. The recent advent of these enzymes in the health landscape presents a serious challenge. First, the emergence of carbapenemases limits the currently available treatment options; second, these enzymes pose a risk to patients, as some studies have demonstrated high mortality associated with carbapenemase-producing bacterial infections; and third, these circumstances require an extra cost to sanitary systems, which are particularly cumbersome in developing countries. Therefore, emphasis should be placed on the early detection of these enzymes, the prevention of the spread of carbapenemase-producing bacteria and the development of new drugs resistant to carbapenemase hydrolysis.

Challenges to accurate susceptibility testing and interpretation of quinolone resistance in Enterobacteriaceae: results of a Spanish multicentre study

OBJECTIVES

The objective of this study was to evaluate the proficiency of Spanish laboratories with respect to accurate susceptibility testing and the detection and interpretation of quinolone resistance phenotypes in Enterobacteriaceae.

METHODS

Thirteen strains of Enterobacteriaceae were sent to 62 participating centres throughout Spain; strains harboured GyrA/ParC modifications, reduced permeability and/or plasmid-mediated quinolone resistance genes. The centres were requested to evaluate nalidixic acid and five quinolones, provide raw/interpreted clinical categories and to detect/infer resistance mechanisms. Consensus results from reference centres were used to assign minor, major and very major errors (mEs, MEs and VMEs, respectively).

RESULTS

Susceptibility testing in the participating centres was frequently performed using the MicroScan WalkAway, Vitek 2 and Wider systems (48%, 30% and 8%, respectively). CLSI/EUCAST breakpoints were used in 71%/29% of the determinations. The percentage of VMEs for all quinolones was well below 2%. Only ofloxacin and moxifloxacin showed higher values for raw VMEs (6.6%), which decreased to 0% and 2.9%, respectively, in the interpreted VMEs. These errors were particularly associated with the CC-03 strain [qnrS2 + aac(6')-Ib-cr]. For MEs, percentages were always <10%, except in the case of ofloxacin and nalidixic acid. There was a significantly higher percentage of all types of errors for strains whose MICs were at the border of clinical breakpoints.

CONCLUSIONS

The use of different breakpoints and methods, the complexity of mutation-driven and transferable resistance mechanisms and the absence of specific tests for detecting low-level resistance lead to high variability and represent a challenge to accuracy in susceptibility testing, particularly in strains with MICs on the border of clinical breakpoints.

Screening rectal swabs for carbapenemase genes

In an outbreak setting, we screened 16,296 samples from 3,644 patients by PCR for the presence of blaOXA-48, blaVIM, blaIMP, blaNDM, and blaKPC. The blaOXA-48 gene was found in samples from 43 patients infected with 9 different species of Enterobacteriaceae. Five patients had Pseudomonas aeruginosa isolates containing blaVIM. The negative predictive value of screening was 100%, and the positive predictive value was 86%.

The spread of carbapenemase-producing bacteria in Africa: a systematic review

BACKGROUND

Carbapenems are the last line of defence against ever more prevalent MDR Gram-negative bacteria, but their efficacy is threatened worldwide by bacteria that produce carbapenemase enzymes. The epidemiology of bacteria producing carbapenemases has been described in considerable detail in Europe, North America and Asia; however, little is known about their spread and clinical relevance in Africa.

METHODS

We systematically searched in PubMed, EBSCOhost, Web of Science, Scopus, Elsevier Masson Consulte and African Journals Online, international conference proceedings, published theses and dissertations for studies reporting on carbapenemase-producing bacteria in Africa. We included articles published in English or French up to 28 February 2014. We calculated the prevalence of carbapenemase producers only including studies where the total number of isolates tested was at least 30.

RESULTS

Eighty-three studies were included and analysed. Most studies were conducted in North Africa (74%, 61/83), followed by Southern Africa (12%, 10/83), especially South Africa (90%, 9/10), West Africa (8%, 7/83) and East Africa (6%, 6/83). Carbapenemase-producing bacteria were isolated from humans, the hospital environment and community environmental water samples, but not from animals. The prevalence of carbapenemase-producing isolates in hospital settings ranged from 2.3% to 67.7% in North Africa and from 9% to 60% in sub-Saharan Africa.

CONCLUSIONS

Carbapenemase-producing bacteria have been described in many African countries; however, their prevalence is poorly defined and has not been systematically studied. Antibiotic stewardship and surveillance systems, including molecular detection and genotyping of resistant isolates, should be implemented to monitor and reduce the spread of carbapenemase-producing bacteria.

Quantitative matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid resistance detection

Antibiotic resistance in Gram-negative microorganisms is an increasing health care problem. The rapid detection of such resistance is crucial for starting an early specific therapy and to enable initiation of the required hygiene measures. With continued emphasis on reducing the cost of laboratory testing, only economical/low-cost approaches have a chance of being implemented. During recent years, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been developed to be a standard method in microbiology laboratories for the rapid and cost-efficient identification of microorganisms. Extending the usage of MALDI-TOF MS in the clinical microbiology laboratory to the area of resistance testing is an attractive option. Quantitative MALDI-TOF MS using an internal standard facilitates the measurement of the quantity of peptides and small proteins within a spectrum. These quantities correlate to the number of microorganisms and therefore to the growth of a microorganism. The comparison of growth in the presence or absence of an antibiotic allows for analysis of the susceptibility behavior of a strain. Here, we describe a novel method and its application in the analysis of 108 Klebsiella sp. isolates. After 1 h of incubation at a meropenem concentration of 8 μg/ml, a sensitivity of 97.3% and a specificity of 93.5% were achieved (compared to Etest results).

Phenotypic and molecular characteristics of carbapenem-resistant Enterobacteriaceae in a health care system in Los Angeles, California, from 2011 to 2013

Carbapenem-resistant Enterobacteriaceae (CRE) are a concern for health care in the United States but remain relatively uncommon in California. We describe the phenotype, clonality, and carbapenemase-encoding genes present in CRE isolated from patients at a Californian tertiary health care system. CRE for this study were identified by evaluating the antibiograms of Enterobacteriaceae isolated in the UCLA Health System from 2011 to 2013 for isolates that were not susceptible to meropenem and/or imipenem. The identification of these isolates was subsequently confirmed by matrix-associated laser desorption ionization-time of flight, and broth microdilution tests were repeated to confirm the CRE phenotype. Real-time PCR for bla(KPC), bla(SME), bla(IMP), bla(NDM-1), bla(VIM), and bla(OXA-48) was performed. Clonality was assessed by repetitive sequence-based PCR (repPCR) and multilocus sequence typing (MLST). Of 15,839 nonduplicate clinical Enterobacteriaceae isolates, 115 (0.73%) met the study definition for CRE. This number increased from 0.5% (44/8165) in the first half of the study to 0.9% (71/7674) in the second (P = 0.004). The most common CRE species were Klebsiella pneumoniae, Enterobacter aerogenes, and Escherichia coli. A carbapenemase-encoding gene was found in 81.7% (94/115) of CRE and included bla(KPC) (78.3%), bla(NDM-1) (0.9%), and bla(SME) (2.6%). The majority of bla(KPC) genes were in K. pneumoniae isolates, which fell into 14 clonal groups on typing. bla(KPC) was identified in more than one species of CRE cultured from the same patient in four cases. Three bla(SME)-carrying Serratia marcescens isolates and one bla(NDM-1) carrying Providencia rettgeri isolate were detected. CRE are increasing in California, and carbapenemases, particularly KPC, are a common mechanism for carbapenem resistance in this region.

Rising rates of carbapenem-resistant enterobacteriaceae in community hospitals: a mixed-methods review of epidemiology and microbiology practices in a network of community hospitals in the southeastern United States

OBJECTIVE

Describe the epidemiology of carbapenem-resistant Enterobacteriaceae (CRE) and examine the effect of lower carbapenem breakpoints on CRE detection.

DESIGN

Retrospective cohort.

SETTING

Inpatient care at community hospitals.

PATIENTS

All patients with CRE-positive cultures were included.

METHODS

CRE isolated from 25 community hospitals were prospectively entered into a centralized database from January 2008 through December 2012. Microbiology laboratory practices were assessed using questionnaires.

RESULTS

A total of 305 CRE isolates were detected at 16 hospitals (64%). Patients with CRE had symptomatic infection in 180 cases (59%) and asymptomatic colonization in the remainder (125 cases; 41%). Klebsiella pneumoniae (277 isolates; 91%) was the most prevalent species. The majority of cases were healthcare associated (288 cases; 94%). The rate of CRE detection increased more than fivefold from 2008 (0.26 cases per 100,000 patient-days) to 2012 (1.4 cases per 100,000 patient-days; incidence rate ratio (IRR), 5.3 [95% confidence interval (CI), 1.22-22.7]; P = .01). Only 5 hospitals (20%) had adopted the 2010 Clinical and Laboratory Standards Institute (CLSI) carbapenem breakpoints. The 5 hospitals that adopted the lower carbapenem breakpoints were more likely to detect CRE after implementation of breakpoints than before (4.1 vs 0.5 cases per 100,000 patient-days; P < .001; IRR, 8.1 [95% CI, 2.7-24.6]). Hospitals that implemented the lower carbapenem breakpoints were more likely to detect CRE than were hospitals that did not (3.3 vs 1.1 cases per 100,000 patient-days; P = .01).

CONCLUSIONS

The rate of CRE detection increased fivefold in community hospitals in the southeastern United States from 2008 to 2012. Despite this, our estimates are likely underestimates of the true rate of CRE detection, given the low adoption of the carbapenem breakpoints recommended in the 2010 CLSI guidelines.

Investigation of the first outbreak of OXA-48-producing Klebsiella pneumoniae in Ireland

BACKGROUND

Carbapenemase-producing Enterobacteriaceae (CPE) strains are encountered with increasing frequency in Europe. In November 2010 the European Centre for Disease Control (ECDC) graded Ireland as only having sporadic occurrence of CPE.

AIM

To describe the epidemiological and molecular typing analysis of the first outbreak of OXA-48-producing Klebsiella pneumoniae in an Irish tertiary care referral centre.

METHODS

Sixteen OXA-48-producing K. pneumoniae isolates were detected, from both clinical and screening specimens, and analysed by pulsed-field gel electrophoresis and by multi-locus sequence typing.

FINDINGS

Typing analysis revealed that two outbreak strains were circulating in the hospital, one among surgical patients and one among medical patients. The 'medical strain' ST13 had already been identified as an internationally disseminated clone, whereas the 'surgical strain' ST221 had not previously been reported as an OXA-48-carrying strain.

CONCLUSION

Although the outbreak on surgical wards was successfully controlled by implementing strict infection control measures, intermittent detection of individual patients carrying the 'medical strain' of OXA-48 K. pneumoniae has persisted since then. The experience from this outbreak suggests that OXA-48 K. pneumoniae is endemic at low level in the healthcare setting in the Dublin region.