Use of the Xpert CarbaR assay for direct detection of carbapenemase genes from blood cultures and urine samples

Xpert Carba-R Assay on Flagged Blood Culture Samples: Clinical Utility in Intensive Care Unit Patients with Bacteremia Caused by Enterobacteriaceae

Introduction and background

Rapid molecular diagnostics to predict carbapenem resistance well before the availability of routine drug sensitivity testing (DST) can serve as an antimicrobial stewardship tool in the context of high rates of Carbapenem-resistant Enterobacteriaceae (CRE).

Materials and methods

A retrospective observational study of patients more than 18 years of age on whom Xpert Carba-R (FDA approved for rectal swab specimen) was done on gram-negative bacteria (GNB) flagged blood culture samples, in an Indian intensive care unit between January 2015 and November 2018. We analyzed the performance of Xpert Carba-R in comparison with routine DST.

Results

A total of 164 GNBs were isolated from 160 patients. Klebsiella pneumoniae and Escherichia coli were the predominant isolates. Carba-R was positive in 35.36% of samples and 45.34% were carbapenem-resistant (CR) on routine DST. The distribution of the CR gene was: Oxacillinase (OXA) (50%), NDM (32.7%) followed by OXA and NDM co-expression (15.51%). The sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, positive predictive value, and negative predictive value of Carba-R were 90.74, 93.15, 13.25, 0.10, 83.58 and 96.31% for Enterobacteriaceae. The median time to obtain the Carba-R report was 30 hours 34 minutes vs 74 hours and 20 minutes for routine DST. Based on the Carba-R report, 9.72% of patients had escalation and 27.08% had de-escalation of antibiotics.

Conclusion

Xpert Carba-R serves as a rapid diagnostic tool for predicting carbapenem resistance in intensive care unit patients with bacteremia caused by Enterobacteriaceae.

How to cite this article

Rajendran S, Gopalakrishnan R, Tarigopula A, Kumar DS, Nambi PS, Sethuraman N, et al. Xpert Carba-R Assay on Flagged Blood Culture Samples: Clinical Utility in Intensive Care Unit Patients with Bacteremia Caused by Enterobacteriaceae. Indian J Crit Care Med 2023;27(9):655-662.

A Rapid Carbapenemase Genes Detection Method with Xpert Carba-R from Positive Blood Cultures Compared with NG-Test Carba 5 and Sequencing

Objective

The objective of the current study was to evaluate the performance of Xpert Carba-R for the direct detection and identification of carbapenemase genes from positive blood cultures.

Methods

Pathogens which extracted from positive blood cultures and identified using MALDI-TOF MS as Enterobacterales were included in this study. Xpert Carba-R was used for the rapid detection of carbapenemase genes from positive blood cultures. NG-Test CARBA 5 and polymerase-chain reaction (PCR) sequencing were used for the detection of carbapenemases and carbapenemase genes in positive blood culture isolates, respectively. Finally, antibiotic susceptibility tests were conducted using the VITEK-2 Compact system.

Results

A total of 133 positive blood cultures of Enterobacterales were collected and 27 of them were detected to carry carbapenemase genes using Xpert Carba-R. In comparison with PCR sequencing results, the sensitivity and specificity of Xpert Carba-R and NG-Test CARBA 5 were calculated as 100%. Additionally, Xpert Carba-R could significantly shorten the turnaround time by directly detecting positive blood cultures comparing with NG-Test CARBA 5. For 27 carbapenem-producing strains, the resistance rates of carbapenems and aztreonam were 96.3% and 92.6%, respectively. Strains carrying the blaKPC gene were all sensitive to ceftazidime-avibactam. All strains were sensitive to tigecycline and colistin.

Conclusion

Xpert Carba-R is suitable for the rapid detection of main carbapenemase genes from positive blood cultures with high sensitivity and specificity. In comparison with NG-Test CARBA 5 and PCR sequencing methods, the timely and convenient method can be a useful test to guide optimal therapy and infection control.

Molecular Detection of Carbapenemase Enzymes Directly from Positive Blood Cultures Using Xpert Carba-R

Objective  The performance of Xpert Carba-R assay for the direct identification of carbapenemases directly from positive blood culture vials was evaluated.

Materials and Methods  In total, 176 positively flagged blood culture vials, yielding carbapenem-resistant GNB (CR-GNB), were enrolled for the detection and differentiation of blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP using Xpert Carba-R.

Results   Klebsiella pneumoniae (76/176, 43.1%), Acinetobacter baumannii complex (67/176, 38%), and Escherichia coli (29/176,16.4%) were the predominant isolates. Overall, NDM production was the commonest (61/176, 34.6%), followed by the co-production of NDM + OXA-48 and the absence of any CR gene (44/176, 25%), followed by OXA-48 (27/176, 15.3%). In CR K. pneumoniae , the co-production of NDM + OXA-48 was most frequent (34/76, 44.7%), whereas in the A. baumannii complex , no CR gene was detected in the majority of isolates (38/67, 56.7%). bla NDM was the commonest gene in E. coli (18/29, 62%) and A. baumannii complex (26/67, 38.8%).

Conclusion  Xpert Carba-R can identify the molecular mechanism of CR within hours after a blood culture turns positive and, thus, has the potential for optimization of antimicrobial therapy, choosing appropriate novel β-lactam combination agents, as well as infection control interventions.

Rapid Carbapenemase Detection With Xpert Carba-R V2 Directly On Positive Blood Vials

The rapid detection of carbapenemase allows implementation of infection control measures and adaptation of antibiotic therapy. We evaluated the performances of the Xpert Carba-R V2^® assay for the direct detection and identification of carbapenemase on positive blood cultures. We focused our evaluation on its detection capacity and on the risks of interference due to the patient’s blood. Isolates of several variants of OXA-48-like (n=10), KPC (n=10), NDM (n=11), VIM (n=7), IMP-1 (n=1) carbapenemases and 14 non carbapenemase-producing Enterobacteriaceae were tested. For each isolate (n=53), an aerobic vial was seeded, and incubated in Bactec Fx (Becton Dickinson^®) automate. When positive, the Xpert^® Carba-R-V2 assay was assessed for carbapenemase detection using 40 µl aliquot. Reproducibility tests were performed on a subset of 23 isolates using aerobic and anaerobic vials. Longer incubation time was also evaluated on 6 isolates. A complementary prospective study in real-time testing of patient-derived clinical samples on 20 additional positive blood vials with Gram negative bacilli on direct examination was performed. Perfect sensitivity and specificity (100%) were observed regardless of the carbapenemase type, the blood vials used and the time of incubation. Xpert^® Carba-R-V2 assay is suitable for the rapid detection of the main carbapenemase genes directly on positive blood vials. Its performances and rapid time analysis allow its use in routine to guide therapeutic choices and to implement infection control measures.