Lab Med Online.  2022 Jul;12(3):175-182. 10.47429/lmo.2022.12.3.175.

Evaluation of the Xpert Carba-R Assay for Detection of Rectal Carbapenemase-producing Enterobacterales in a Korean Tertiary Hospital

• Han J
• Ha SI
• Shin DP
• Cha YJ
• Yoo IY
• Park YJ

• KMID: 2538602
• DOI: http://doi.org/10.47429/lmo.2022.12.3.175

Abstract

Background
Carbapenemase-producing Enterobacterales (CPE) have been highlighted as an urgent threat by international health authorities. Rapid detection of carbapenemase will allow implementation of infection control measures.
Methods
We assessed the performance of the Xpert Carba-R assay (Cepheid, USA) designed for rapid detection of five most common carbapenemases (bla_KPC, bla_NDM, bla_OXA-48, bla_VIM, and bla_IMP-1) from rectal swab specimens by comparing with the reference method, culture plus in-house PCR. A total of 26,178 specimens were collected from August 2018 to July 2020 and tested using the Xpert Carba-R assay and culture plus in-house PCR.
Results
Among the 26,178 specimens collected from 12,889 patients, 1,615 (6.2%) were detected using the Xpert Carba-R assay, whereas 1,525 specimens (5.8%) were detected using a reference method. The sensitivity, specificity, and positive and negative predictive values of the Xpert Carba-R assay compared to the results of the culture method were 97.4% (95% confidence interval [CI], 96.5% to 98.1%), 99.4% (95% CI, 99.3% to 99.5%), 91.8% (95% CI, 90.5% to 93.0%), and 99.8% (95% CI, 99.7% to 99.8%), respectively. The prevalence of CPE and carbapenem-resistant Enterobacteriaceae were 1.7% (220/12,889) and 5.4% (695/12,889), respectively. Klebsiella pneumoniae (108/220, 49.1%) was the most common species, followed by Escherichia coli (68/220, 30.9%) and Citrobacter freundii (17/220, 7.7%). blaKPC was the most common carbapenemase gene (123/220, 55.9%), followed by bla_NDM (56/220, 25.4%), bla_OXA-48 (27/220, 12.2%), and bla_NDM/OXA-48 (9/220, 4.1%).
Conclusions
Based on our results, we conclude that the Xpert Carba-R assay is a very useful tool for rapid identification of CPE rectal colonization.

Keyword

Carbapenemase; Carbapenemase-producing Enterobacterales; Xpert Carba-R assay; Surveillance; Infection control

Figure

• 

  Fig. 1 Comparison of median Ct value and interquartile range in (A) total true-positive (24.4, 20.4-28.8) and false-positive (35.1, 32.3-36.8) cases, (B) each true/false-positive carbapenemase type, KPC (24.7, 21.2-29.3), KPC* (29.9, 23.6-33.6), NDM (24.4, 20.6-29.2), NDM* (33.2, 30.7-34.4), OXA-48 (22.7, 19.1-26.9), OXA-48* (35.0, 32.1-37.0), VIM (25.1, 21.9-32.1), VIM* (34.2, 34.1-36.1), IMP (33.2, 28.1-35.9), and IMP* (35.4, 33.9-36.8). Each boxplot represents the range from the 25th to the 75th percentiles of each group. *carbapenemase genes with/without the star symbol indicate false/true-positive cases as observed in the Xpert Carba-R assay. Abbreviations: TP, true-positive; FP, false-positive.

• 

  Fig. 2 Distribution of genotypes of CPE for two periods: (A) August, 2018-July, 2019 and (B) August, 2019-July, 2020. Abbreviations: KPN, K. pneumoniae; ECO, E. coli; CFR, C. freundii; KOX, K. oxytoca; ECL, E. cloacae.

Reference

1. Albiger B, Glasner C, Albiger B, Glasner C, Struelens MJ, Grundmann H, et al. 2015; the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) working group. Carbapenemase-producing Enterobacteriaceae in Europe: assessment by national experts from 38 countries, May 2015. Euro Surveill. 20:30062. DOI: 10.2807/1560-7917.ES.2015.20.45.30062. PMID: 26675038.

2. Tokatlidou D, Tsivitanidou M, Pournaras S, Ikonomidis A, Tsakris A, Sofianou D. 2008; Outbreak caused by a multidrug-resistant Klebsiella pneumoniae clone carrying bla_VIM-12 in a university hospital. J Clin Microbiol. 46:1005–8. DOI: 10.1128/JCM.01573-07. PMID: 18199780. PMCID: PMC2268336.

3. Korea Centers of Disease Control, Prevention. Incidence of carbapenem-resistant enterobacteriae in Korea, 2018-2020. https://www.kdca.go.kr/board/board.es?mid=a20602010000&bid=0034&act=view&list_no=717046.

4. Centers for Disease Control, Prevention. 2015. Facility guidance for control of carbapenem-resistant Enterobacteriaceae (CRE): November 2015 update - CRE toolkit 2015. https://www.cdc.gov/hai/pdfs/cre/CRE-guidance-508.pdf. Updated on Nov 2015.

5. Viau R, Frank KM, Jacobs MR, Wilson B, Kaye K, Donskey CJ, et al. 2016; Intestinal carriage of carbapenemase-producing organisms: current status of surveillance methods. Clinical Microbiol Rev. 29:1–27. DOI: 10.1128/CMR.00108-14. PMID: 26511484. PMCID: PMC4771221.

6. Nijhuis R, Samuelsen Ø, Savelkoul P, van Zwet A. 2013; Evaluation of a new real-time PCR assay (Check-Direct CPE) for rapid detection of KPC, OXA-48, VIM, and NDM carbapenemases using spiked rectal swabs. Diagn Microbiol Infect Dis. 77:316–20. DOI: 10.1016/j.diagmicrobio.2013.09.007. PMID: 24135412.

7. Braun SD, Monecke S, Thürmer A, Ruppelt A, Makarewicz O, Pletz M, et al. 2014; Rapid identification of carbapenemase genes in gram-negative bacteria with an oligonucleotide microarray-based assay. PLoS One. 9:e107079. DOI: 10.1371/journal.pone.0107079. PMCID: PMC4152334.

8. Lolans K, Calvert K, Won S, Clark J, Hayden MK. 2010; Direct ertapenem disk screening method for identification of KPC-producing Klebsiella pneumoniae and Escherichia coli in surveillance swab specimens. J Clin Microbiol. 48:836–41. DOI: 10.1128/JCM.01988-09. PMID: 20071553. PMCID: PMC2832415.

9. Poirel L, Walsh TR, Cuvillier V, Nordmann P1. 2011; Multiplex PCR for detection of acquired carbapenemase genes. Diagn Microbiol Infect Dis. 70:119–23. DOI: 10.1016/j.diagmicrobio.2010.12.002. PMID: 21398074.

10. Bradford PA, Bratu S, Urban C, Visalli M, Mariano N, Landman D, et al. 2004; Emergence of carbapenem-resistant Klebsiella species possessing the class A carbapenem-hydrolyzing KPC-2 and inhibitor-resistant TEM-30 beta-lactamases in New York City. Clin Infect Dis. 39:55–60. DOI: 10.1086/421495. PMID: 15206053.

11. Clark RB, Sharp SB. 2009. Cumitech 31A: Verification and validation of procedures in the clinical microbiology laboratory. Washington, DC: American Society for Microbiology.

12. Park SH, Kim JS, Kim HS, Yu JK, Han SH, Kang MJ, et al. 2020; Prevalence of carbapenem-resistant Enterobacteriaceae in Seoul, Korea. J Bacteriol Virol. 50:107–16. DOI: 10.4167/jbv.2020.50.2.107.

13. Tato M, Ruiz-Garbajosa P, Traczewski M, Dodgson A, McEwan A, Humphries R, et al. 2016; Multisite evaluation of Cepheid Xpert Carba-R assay for detection of carbapenemase-producing organisms in rectal swabs. J Clin Microbiol. 54:1814–9. DOI: 10.1128/JCM.00341-16. PMID: 27122379. PMCID: PMC4922077.

14. Moore NM, Cantón R, Carretto E, Peterson LR, Sautter RL, Traczewski MM. Carba-R Study Team. 2017; Rapid identification of five classes of carbapenem resistance genes directly from rectal swabs by use of the Xpert Carba-R assay. J Clin Microbiol. 55:2268–75. DOI: 10.1128/JCM.00137-17. PMID: 28515213. PMCID: PMC5483930.

15. Logan LK, Weinstein RA. 2017; The epidemiology of carbapenem-resistant Enterobacteriaceae: the impact and evolution of a global menace. J Infect Dis. 215:S28–36. DOI: 10.1093/infdis/jiw282. PMID: 28375512. PMCID: PMC5853342.

16. Tenny S, Hoffman MR. Prevalence. https://www.ncbi.nlm.nih.gov/books/NBK430867/. Updated on May 2021.

17. Pham HP, Staley EM, Raju D, Marin MJ, Kim CH. 2020; Laboratory assay evaluation demystified: a review of key factors in˝uencing interpretation of test results using different assays for SARS-CoV-2 infection diagnosis. Lab Med. 51:e66–70. DOI: 10.1093/labmed/lmaa045. PMID: 32634229. PMCID: PMC7454829.

18. Byun J-H, Kim YA, Kim M, Kim B, Choi JY, Park YS, et al. 2020; Evaluation of Xpert Carba-R assay v.2 to detect carbapenemase genes in two hospitals in Korea. Ann Lab Med. 40:209–15. DOI: 10.3343/alm.2020.40.3.209. PMID: 31858760. PMCID: PMC6933065.

19. Hong DJ, Bae IK, Jang IH, Jeong SH, Kang HK, Lee K. 2015; Epidemiology and characteristics of metallo-β-lactamase-producing Pseudomonas aeruginosa. Infect Chemother. 47:81–97. DOI: 10.3947/ic.2015.47.2.81. PMID: 26157586. PMCID: PMC4495280.

20. van Duin D, Doi Y. 2017; The global epidemiology of carbapenemase-producing Enterobacteriaceae. Virulence. 8:460–9. DOI: 10.1080/21505594.2016.1222343. PMID: 27593176. PMCID: PMC5477705.

21. Jeong SH, Lee KM, Lee J, Bae IK, Kim JS, Kim HS, et al. 2015; Clonal and horizontal spread of the bla_OXA-232 gene among Enterobacteriaceae in a Korean hospital. Diagn Microbiol Infect Dis. 82:70–2. DOI: 10.1016/j.diagmicrobio.2015.02.001. PMID: 25702524.