Analytical Performance of Multiplexed Screening Test for 10 Antibiotic Resistance Genes from Perianal Swab Samples

Abstract

BACKGROUND Multiantibiotic-resistant bacteria pose a threat to patients and place an economic burden on health care systems. Carbapenem-resistant bacilli and extended-spectrum β-lactamase (ESBL) producers drive the need to screen infected and colonized patients for patient management and infection control. METHODS We describe a multiplex microfluidic PCR test for perianal swab samples (Acuitas® MDRO Gene Test, OpGen) that detects the vancomycin-resistance gene vanA plus hundreds of gene subtypes from the carbapenemase and ESBL families Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), Verona integron-mediated metallo-β-lactamase (VIM), imipenemase metallo-β-lactamase (IMP), OXA-23, OXA-48, OXA-51, CTX-M-1, and CTX-M-2, regardless of the bacterial species harboring the antibiotic resistance. RESULTS Analytical test sensitivity per perianal swab is 11–250 CFU of bacteria harboring the antibiotic resistance genes. Test throughput is 182 samples per test run (1820 antibiotic resistance gene family results). We demonstrate reproducible test performance and 100% gene specificity for 265 clinical bacterial organisms harboring a variety of antibiotic resistance genes. CONCLUSIONS The Acuitas MDRO Gene Test is a sensitive, specific, and high-throughput test to screen colonized patients and diagnose infections for several antibiotic resistance genes directly from perianal swab samples, regardless of the bacterial species harboring the resistance genes.

Carbapenemases in Enterobacteriaceae: Detection and Antimicrobial Therapy

“…As well as the methods described above, several other molecular methods are used to detect CPE. For example, Walker et al (2016) combined nested PCR, real-time PCR, and microfluidics to identify the common carbapenemases genes. A PCR-based method in a cartridge format developed to detect CPE in rectal swabs, which is run on the GeneXpert platform, displayed high sensitivity (96.6%) and specificity (98.6%) within a short time (32–48 min) (Tato et al, 2016).…”

The rapid spread of carbapenem-resistant Enterobacteriaceae

“…A multiplex PCR assay using peptide nucleic acid probes reported high sensitivity and specificity (both above 99.0%) in identifying bla KPC , bla OXA-48 , bla GES , bla IMP , bla VIM , and bla NDM from a mixture of Enterobacteriaceae isolates [Jeong 2015]. One assay combined nested PCR, rtPCR, and microfluidics to obtain class level identification of carbapenemases ( bla KPC , bla VIM , bla OXA-23 , bla OXA-48 , bla OXA-51 ) and ESBLs for rapid detection of diverse multidrug resistant organisms including CRE [Walker 2016]. A PCR-based assay for rectal swabs had high sensitivity (96.6%) and specificity (98.6%) at identifying bla KPC , bla NDM , bla VIM , bla OXA-48 , and bla IMP-1 on a rapid time-scale (32–48 minutes) [Tato 2016].…”

Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review

“…Walker and colleagues have employed a multiplexed nested PCR technique where the 2nd step of the nested PCR was performed on Biomark TM System. An Integrated Fluidic Circuit (Fluidigm) dynamic array capable of analyzing 192 samples against 24 separate PCR assays was used to evaluate 10 antibiotic resistance genes in perianal swab samples collected from patients [83].…”