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Year : 2016  |  Volume : 34  |  Issue : 2  |  Page : 216--218

An Xpert screen to identify carbapenemases

Mubin Kazi, Chaitali Nikam, Anjali Shetty, Camilla Rodrigues 
 Department of Microbiology, P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, Maharashtra, India

Correspondence Address:
Camilla Rodrigues
Department of Microbiology, P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, Maharashtra


To prevent the spread of carbapenemases-producing Enterobacteriaceae (CPE) active surveillance, contact isolation and cohorting infected patients should be practiced. Rectal swabs for the Xpert MDRO-assay of 32 patients were included. 71.85% were positive for targets incorporated into the MDRO-assay; whereas 28% were phenotypically not CRE and Xpert negative (9.37% had different mechanism [bla OXA]). The assay identified 59.3%, 9.37% and 3.1% as bla NDM, bla NDM+VIM and bla VIM, respectively. The assay is a screening test that identifies CPE harbouring organism within an hour and can be installed at tertiary-care facilities to screen colonized patients.

How to cite this article:
Kazi M, Nikam C, Shetty A, Rodrigues C. An Xpert screen to identify carbapenemases.Indian J Med Microbiol 2016;34:216-218

How to cite this URL:
Kazi M, Nikam C, Shetty A, Rodrigues C. An Xpert screen to identify carbapenemases. Indian J Med Microbiol [serial online] 2016 [cited 2020 Jul 2 ];34:216-218
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During past several years, the presence of carbapenemase-producing Enterobacteriaceae (CPE) has become a major health-care concern. The occurrence of CPE harbouring strains makes the situation worrisome, as treatment of such cases becomes challenging often leading to therapeutic failure. [1] If the mechanism of resistance is plasmid-mediated the spread of such resistance is rapid; requiring judicious and rapid screening of patients admitted to tertiary - care facilities. Screening of patients for CPE allows Health-care-workers to put into practice strict contact isolation protocols, thus preventing its further spread. Early screening by implementing an assay that is rapid, sensitive and non-laborious to identify CPE -harbouring strains is essential. The following study was performed: (a) To evaluate GeneXpert MDRO-assay (bla NDM , bla VIM , bla KPC) directly on to the rectal swabs. (b) To compare GeneXpert MDRO-assay results with an in-house developed multiplex-polymerase chain reaction (MPCR).

 Materials and Methods

For this, during May 2013-August 2013, we conducted an IRB approved study by collecting two rectal swabs from 32 patients. The patients enrolled in the study were pre-identified with carbapenem-resistant Enterobacteriaceae (CRE) in clinical samples such as blood and tracheal secretion. An informed consent was obtained from each of the participating patient or their relatives. Swab no 1 was processed for phenotypic analysis (Mac Conkeys agar with a meropenem disk and an enrichment method). For Swab no 2, ~2 ml of sample reagent (provided by manufacture) was added to 15 ml tarson's tube, the lower end of the swab was placed in sample reagent, the tube was capped and vortexed for 10-30 s and using a transfer pipette, the sample was loaded into the sample port of MDRO-assay cartridge. The assay cartridge was further loaded on to GeneXpert module and run by selecting the assay programme - MDRO_Alpha 1 assay. The turn-around-time for the assay was 50 min.

 Results and Discussion

Of the 32 rectal samples collected, 25 were CRE (meropenem resistant), whereas seven were culture negative. Among the 25 CRE culture positive, 88% (n = 22) were positive for the target gene incorporated in the MDRO cartridge, where as 12% (n = 3) had a different resistant mechanism (bla OXA) (in house-multiplex PCR). [2] The concordance between the phenotypic and Xpert MDRO-assay was 100% for the target genes incorporated in the MDRO cartridge. The assay rapidly identified CPE-harbouring strains directly from rectal swabs. Furthermore, in case of 10 culture negative samples (culture negative [n = 7] + target gene not incorporated in the cartridge [n = 3]), 90% (n = 9) were Xpert negative and one sample was Xpert positive.

bla NDM is the most prevalent CPE in the subcontinent. [3] The presence of bla NDM alone confers resistance to most of the clinically treatable antibiotics. The present study highlights the fact that among the patients infected with CRE, 62.5% (20/32) cases carried bla NDM alone, 9.3% (3/32) had both bla NDM and bla VIM and 3.1% (1/32) had bla VIM as the mechanism of resistance whereas 25% (8/32) [Table 1] had none of the targeted carbapenemases. Moreover, there are reports of co-existence of OXA-181 and NDM-1. [4] In addition, an in-house multiplex PCR was performed on the bacterial isolates showed 31.8% (7/22) harbored both bla OXA181/48 and bla NDM-1. In order to resolve the discrepancies (26% [6/23]) between GeneXpert MDRO-assay performed on rectal swab and in-house MPCR on isolates; GeneXpert MDRO-assay was performed on specific (discrepant) isolates no 1, 6, 7, 14, 19 and 27. The results of discrepant isolates are listed in [Table 2]. The current need is early screening, active surveillance, good hand hygiene, cohorting infected patients from the uninfected ones and judicious use of antibiotics. [5] This necessitates implementation of assays that are rapid, sensitive and nonlaborious in identifying CPE-harbouring strain.{Table 1}{Table 2}


The GeneXpert assay is a rapid screening test for identification of CPE. In addition to the above targets (NDM, VIM, KPC), the newer assays can detect OXA and IMP variants.


We thank Dr. Fred Tenover for providing us MDRO-assay cartridges. We also thank the National Health and Education Society, P. D. Hinduja National Hospital and Medical Research Centre for funding this study. We also thank the hospital staff of the Department of Laboratory Medicine for their support and co-operation.

Financial support and sponsorship

This study was funded by the National Health and Education Society, P. D. Hinduja National Hospital and Medical Research Centre.

Conflicts of interest

There are no conflicts of interest.


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