Advances in the detection of carbapenemase among Enterobacterales

doi:10.19871/j.cnki.xfcrbzz.2024.03.017

Abstract

Abstract: In recent years, bacterial drug resistance has become a major challenge to public health, with carbapenem-resistant Enterobacteriaceae (CRE) being particularly resistant to antibiotics. The main resistance mechanism of CRE is the production of carbapenemases, which are carried differently by different strains and encode different resistance genes; therefore, early detection of carbapenemases and resistance genes plays an important role in controlling the spread of drug-resistant bacteria. The current phenotypic assays for carbapenemases are the modified Hodge assay, the carbapenem inactivation assay, the Carba NP assay, the immunological assay, and mass spectrometry. For the detection of genotypes, there are real-time fluorescence quantitative PCR assay microarray technology, isothermal amplification assay and sequencing technology, all of which are widely used in the detection of carbapenemases. Understanding the advantages and disadvantages of each detection technology is very important for the selection of the most appropriate detection method in practical applications, this paper focuses on the research progress of CRE carbapenemase detection methods and the advantages and disadvantages of each method are reviewed, to provide data support for the detection and prevention of CRE as well as the control of nosocomial infections.

Key words: Carbapenem resistant Enterobacteriaceae, Carbapenemase, Diagnosis, Detection

CLC Number:

R517.9

Hua Shaowei, Zhao Zijin, Zhao Meng, Shen Xinxin, Feng Zhishan. Advances in the detection of carbapenemase among Enterobacterales[J]. Electronic Journal of Emerging Infectious Diseases, 2024, 9(3): 78-85.

References

[1] NORDMANN P, POIREL L.Epidemiology and Diagnostics of Carbapenem Resistance in Gram-negative Bacteria[J]. Clin Infect Dis, 2019, 69(Suppl 7): S521-s528.
[2] WANG Q, WANG X, WANG J, et al.Phenotypic and Genotypic Characterization of Carbapenem-resistant Enterobacteriaceae: Data From a Longitudinal Large-scale CRE Study in China (2012-2016)[J]. Clin Infect Dis, 2018, 67(suppl_2): S196-s205.
[3] GAO H, LIU Y, WANG R, et al.The transferability and evolution of NDM-1 and KPC-2 co-producing Klebsiella pneumoniae from clinical settings[J]. EBio Medicine, 2020, 51: 102599.
[4] 陈刚, 杨勇, 罗安静, 等. 亚胺培南用药现状及其与常见革兰氏阴性菌耐药性的相关性分析[J/CD]. 新发传染病电子杂志, 2021, 6(3): 225-229.
[5] JEAN SS, LEE WS, LAM C, et al.Carbapenemase-producing Gram-negative bacteria: current epidemics, antimicrobial susceptibility and treatment options[J].Future Microbiol, 2015, 10(3): 407-25.
[6] HUNG WT, CHENG MF, TSENG FC, et al.Bloodstream infection with extended-spectrum beta-lactamase-producing Escherichia coli: The role of virulence genes[J]. J Microbiol Immunol Infect, 2019, 52(6): 947-955.
[7] LOGAN LK, WEINSTEIN RA.The Epidemiology of Carbapenem-Resistant Enterobacteriaceae: The Impact and Evolution of a Global Menace[J].J Infect Dis, 2017, 215(suppl_1): S28-s36.
[8] LEE YL, CHEN HM, HII IM, et al.Carbapenemase-producing Enterobacterales infections: recent advances in diagnosis and treatment[J]. Int J Antimicrob Agents, 2022, 59(2): 106528.
[9] LUTGRING JD, LIMBAGO BM.The Problem of Carbapenemase-Producing-Carbapenem-Resistant-Enterobacteriaceae Detection[J]. J Clin Microbiol,2016, 54(3): 529-534.
[10] PIERCE VM, SIMNER PJ, LONSWAY DR, et al.Modified Carbapenem Inactivation Method for Phenotypic Detection of Carbapenemase Production among Enterobacteriaceae[J]. J Clin Microbiol, 2017, 55(8): 2321-2333.
[11] HOWARD JC, CREIGHTON J, IKRAM R, et al.Comparison of the performance of three variations of the Carbapenem Inactivation Method (CIM, modified CIM [mCIM] and in-house method (iCIM)) for the detection of carbapenemase-producing Enterobacterales and non-fermenters[J]. J Glob Antimicrob Resist, 2020, 21: 78-82.
[12] PAPAGIANNITSIS CC, ŠTUDENTOVÁ V, IZDEBSKI R, et al.Matrix-assisted laser desorption ionization-time of flight mass spectrometry meropenem hydrolysis assay with NH4HCO3, a reliable tool for direct detection of carbapenemase activity[J]. J Clin Microbiol, 2015, 53(5): 1731-1735.
[13] NORDMANN P, SADEK M, DEMORD A, et al.NitroSpeed-Carba NP Test for Rapid Detection and Differentiation between Different Classes of Carbapenemases in Enterobacterales[J]. J Clin Microbiol, 2020, 58(9): e00932-20.
[14] HOPKINS KL, MEUNIER D, NAAS T, et al.Evaluation of the NG-Test CARBA 5 multiplex immunochromatographic assay for the detection of KPC, OXA-48-like, NDM, VIM and IMP carbapenemases[J]. J Antimicrob Chemother, 2018, 73(12): 3523-3526.
[15] RICCOBONO E, ANTONELLI A, PECILE P, et al.Evaluation of the KPC K-SeT® immunochromatographic assay for the rapid detection of KPC carbapenemase producers from positive blood cultures[J]. J Antimicrob Chemother, 2018, 73(2): 539-540.
[16] WAREHAM DW, PHEE LM, ABDUL MOMIN MHF.Direct detection of carbapenem resistance determinants in clinical specimens using immunochromatographic lateral flow devices[J]. J Antimicrob Chemother, 2018, 73(7): 1997-1998.
[17] 李静, 耿志军, 郑晶, 等. 胶体金免疫层析法快速检测CRE碳青霉烯酶的效果评价[J]. 蚌埠医学院学报, 2021, 46(8):1089-1092.
[18] DORTET L, TANDÉ D, DE BRIEL D, et al.MALDI-TOF for the rapid detection of carbapenemase-producing Enterobacteriaceae: comparison of the commercialized MBT STAR®-Carba IVD Kit with two in-house MALDI-TOF techniques and the RAPIDEC® CARBA NP[J]. J Antimicrob Chemother, 2018, 73(9):2352-2359.
[19] CALDERARO A, BUTTRINI M, PIERGIANNI M, et al.Evaluation of a modified meropenem hydrolysis assay on a large cohort of KPC and VIM carbapenemase-producing Enterobacteriaceae[J]. PLoS One, 2017, 12(4): e0174908.
[20] AL-ZAHRANI IA.Routine detection of carbapenem-resistant gram-negative bacilli in clinical laboratories. A review of current challenge[J]. Saudi Med J, 2018, 39(9): 861-872.
[21] YOSHIOKA N, HAGIYA H, DEGUCHI M, et al.Multiplex Real-Time PCR Assay for Six Major Carbapenemase Genes[J]. Pathogens, 2021, 10(3):276
[22] SCHMIDT K, STANLEY KK, HALE R, et al.Evaluation of multiplex tandem PCR (MT-PCR) assays for the detection of bacterial resistance genes among Enterobacteriaceae in clinical urines[J]. J Ant Chem, 2019, 74(2): 349-356.
[23] SALIMNIA H, FAIRFAX MR, LEPHART PR, et al.Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial[J]. J Clin Microbiol, 2016, 54(3): 687-698.
[24] ALTUN O, ALMUHAYAWI M, ULLBERG M, et al.Clinical evaluation of the FilmArray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles[J]. J Clin Microbiol, 2013, 51(12):4130-4136.
[25] BLASCHKE AJ, HEYREND C, BYINGTON CL, et al.Rapid identification of pathogens from positive blood cultures by multiplex polymerase chain reaction using the FilmArray system[J]. Diagn Microbiol Infect Dis, 2012, 74(4):349-355.
[26] SULLIVAN KV, DEBURGER B, ROUNDTREE SS, et al.Pediatric multicenter evaluation of the Verigene gram-negative blood culture test for rapid detection of inpatient bacteremia involving gram-negative organisms, extended-spectrum beta-lactamases, and carbapenemases[J]. J Clin Microbiol,2014, 52(7): 2416-2421.
[27] LEDEBOER NA, LOPANSRI BK, DHIMAN N, et al.Identification of Gram-Negative Bacteria and Genetic Resistance Determinants from Positive Blood Culture Broths by Use of the Verigene Gram-Negative Blood Culture Multiplex Microarray-Based Molecular Assay[J]. J Clin Microbiol,,2015, 53(8): 2460-2472.
[28] MOORE NM, CANTÓN R, CARRETTO E, et al. Rapid Identification of Five Classes of Carbapenem Resistance Genes Directly from Rectal Swabs by Use of the Xpert Carba-R Assay[J]. J Clin Microbiol, 2017, 55(7):2268-2275.
[29] TATO M, RUIZ-GARBAJOSA P, TRACZEWSKI M, et al.Multisite Evaluation of Cepheid Xpert Carba-R Assay for Detection of Carbapenemase-Producing Organisms in Rectal Swabs[J]. J Clin Microbiol, 2016, 54(7):1814-1819.
[30] SONG Y, DOU F, HE S, et al.Laboratory and Clinical Evaluation of DNA Microarray for the Detection of Carbapenemase Genes in Gram-Negative Bacteria from Hospitalized Patients[J]. Biomed Res Int, 2019, 2019: 8219748.
[31] TORRES FINK I, TORMO PALOP N, BORRÁS SALVADOR R, et al. Evaluation of the DNA microarray "AMR Direct Flow Chip Kit" for detection of antimicrobial resistance genes from Gram-positive and Gram-negative bacterial isolated colonies[J]. Enferm Infecc Microbiol Clin (Engl Ed), 2019, 37(7): 454-457.
[32] HRABÁK J, CHUDÁKOVÁ E, PAPAGIANNITSIS CC. Detection of carbapenemases in Enterobacteriaceae: a challenge for diagnostic microbiological laboratories[J]. Clin Microbiol Infect, 2014, 20(9): 839-853.
[33] XU H, TANG H, LI R, et al.A New Method Based on LAMP-CRISPR-Cas12a-Lateral Flow Immunochromatographic Strip for Detection[J]. Infect Drug Resist, 2022, 15: 685-696.
[34] LIANG M, XIAO B, CHEN L, et al.Rapid Detection of blaKPC in Carbapenem-Resistant Enterobacterales Based on CRISPR/Cas13a[J]. Curr Microbiol. 2023, 80(11):352.
[35] FENG ZS, LI JY, ZHANG JY, et al.Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus[J]. J Microbiol Methods, 2022, 193: 106404.
[36] ZHANG W, FENG Y, ZHAO H, et al.A Recombinase Aided Amplification Assay for Rapid Detection of the Klebsiella pneumoniae Carbapenemase Gene and Its Characteristics in Klebsiella pneumoniae[J]. Front Cell Infect Microbiol, 2021, 11: 746325.
[37] FENG Y, XUE G, FENG J, et al.Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children[J]. Front Microbiol, 2021, 12: 691289.
[38] 何安娜, 张梦怡, 李逢钰, 等. 人乳头瘤病毒6型和11型通用型含内源性内参的重组酶介导的等温扩增技术检测方法的建立[J/CD]. 新发传染病电子杂志, 2022, 7(2): 25-29.
[39] MA X.Isothermal Amplification Technology for Diagnosis of COVID-19: Current Status and Future Prospects[J]. Zoonoses, 2022, 243:123388.
[40] FAN G, ZHANG R, HE X, et al.RAP: A Novel Approach to the Rapid and Highly Sensitive Detection of Respiratory Viruses[J]. Front Bioeng Biotechnol,2021, 9: 766411.
[41] ZHANG R, OU X, SUN X, et al.Multiplex LNA probe-based RAP assay for rapid and highly sensitive detection of rifampicin-resistant Mycobacterium tuberculosis[J]. Front Microbiol, 2023, 14: 1141424.
[42] TIAN F, JIN C, JI S, et al.A Rapid and Sensitive Detection of HIV-1 with a One-Pot Two-Stage Reverse Transcription Recombinase Aided Real-Time PCR Assay[J]. Trop Med Infect Dis, 2023, 8(2): 105.
[43] ZHAO S, TYSON GH, CHEN Y, et al.Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp[J]. Appl Environ Microbiol, 2016, 82(2): 459-66.
[44] 胥诗琴, 石晓路, 陆慧群, 等. 创伤弧菌基于基因组学的毒力因子及耐药基因的研究进展[J/CD]. 新发传染病电子杂志, 2023, 8(1): 74-81.
[45] AL-FARSI HM, CAMPOREALE A, ININBERGS K, et al.Clinical and molecular characteristics of carbapenem non-susceptible Escherichia coli: A nationwide survey from Oman[J]. PLoS One, 2020, 15(10): e0239924.
[46] AL FADHLI A, JAMAL W, ROTIMI VO.Molecular characterization of rectal isolates of carbapenemase-negative carbapenem-resistant enterobacterales obtained from ICU patients in Kuwait by whole-genome sequencing[J]. J Med Microbiol, 2021, 70(9):1-10.
[47] MOUSSA J, NASSOUR E, TAHAN E, et al.Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon[J].J Infect Public Health, 2023, 16(12): 1947-1953.
[48] MARIN J, CLERMONT O, ROYER G, et al.The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France[J]. Appl Environ Microbiol, 2022, 88(15):e0066422.
[49] BOUTIN S, SCHERRER M, SPÄTH I, et al. Cross-contamination of carbapenem-resistant Gram-negative bacteria between patients and hospital environment in the first year of a newly built surgical ward[J]. J Hosp Infect, 2024, 144:118-127.
[50] WANG K, LI P, LIN Y, et al.Metagenomic Diagnosis for a Culture-Negative Sample From a Patient With Severe Pneumonia by Nanopore and Next-Generation Sequencing[J]. Front Cell Infect Microbiol, 2020, 10:182
[51] Guo Y, Li Z, Li L, et al.A dual-process of targeted and unbiased Nanopore sequencing enables accurate and rapid diagnosis of lower respiratory infections[J]. EBio Medicine, 2023, 98:104858.
[52] TAMMA PD, OPENE BN, GLUCK A, et al.Comparison of 11 Phenotypic Assays for Accurate Detection of Carbapenemase-Producing Enterobacteriaceae[J]. J Clin Microbiol,2017, 55(4): 1046-1055.
[53] SARVA K, MARIMUTHU RAGAVAN R, TADI LJ, et al.Performance of Carbapenemase Nordmann-Poirel, Modified Carbapenem Inactivation, and EDTA Carbapenem Inactivation Methods for Detecting Carbapenem-Resistant Klebsiella pneumoniae Isolates[J]. Microb Drug Resist, 2023, 29(11): 504-509.
[54] LITERACKA E, HERDA M, BARANIAK A, et al.Evaluation of the Carba NP test for carbapenemase detection in Enterobacteriaceae, Pseudomonas spp. and Acinetobacter spp., and its practical use in the routine work of a national reference laboratory for susceptibility testing[J]. Eur J Clin Microbiol Infect Dis, 2017, 36(11): 2281-2287.
[55] TAMMA PD, SIMNER PJ.Phenotypic Detection of Carbapenemase-Producing Organisms from Clinical Isolates[J]. J Clin Microbiol, 2018, 56(11): e01140-18.
[56] YENGUI M, TRABELSI R, KHANNOUS L, et al.Rapid Detection of Beta-Lactamases Genes among Enterobacterales in Urine Samples by Using Real-Time PCR[J]. Biomed Res Int, 2022, 2022: 8612933.
[57] CHEN N, LI G, SI Y, et al.Evaluation of LAMP assay using phenotypic tests and PCR for detection of blaKPC gene among clinical samples[J]. J Clin Lab Anal, 2022, 36(4): e24310.