Review of established and innovative detection methods for carbapenemase-producing Gram-negative bacteria

Abstract

SummaryThe minimal antibiotic options for carbapenemase-producing Gram-negative bacteria necessitate their rapid detection. A literature review of a variety of phenotypic and genotypic methods is presented. Advances in culture methods and screening media are still subject to long incubation hours. Biochemical methods have shorter turnaround times and higher sensitivities and specificities, but cannot differentiate between various types and variants. Spectrophotometric methods are cheap and efficient, but are uncommon in many clinical settings, while the MALDI-TOF MS is promising for species identification, typing and resistance gene determination. Although next generation sequencing (NGS) technologies provide a better platform to detect, type and characterize carbapenem-resistant bacteria, the different NGS platforms, the large computer memories and space needed to process and store genomic data and the nonuniformity in data analysis platforms are still a challenge. The sensitivities, specificities and turnaround times recorded in the various studies reviewed favours the use of the biochemical tests (Carba NP or Rapid Carb screen tests) for the detection of putative carbapenemaseproducing isolates. MALDI-TOF MS and/or molecular methods like microarray, loop-mediated isothermal amplification and real-time multiplex PCR assays could be used for further characterization in a reference laboratory. NGS may be used for advanced epidemiological and molecular studies.

Antibiotic resistance: What is so special about multidrug-resistant Gram-negative bacteria?

“…Examples for recent developments are the RAPIDEC ® CARBA NP assay for rapid detection of carbapenemases in Enterobacteriacea , P. aeruginosa and Acinetobacter spp., an immunochromatographic assay (the OXA-48 K-SeT assay) to detect OXA-48-like carbapenemase-producing Enterobacteriaceae from culture colonies, as well as a highly discriminatory universal blaSHV, blaTEM and blaCTX-M subtyping assay of clinically important ESBL genes, based on PCR and Sanger sequencing [51], [52], [53], [54]. …”

Carbapenem-Resistant Non-Glucose-Fermenting Gram-Negative Bacilli: the Missing Piece to the Puzzle

“…The Carba NP test II is similar to the Carba NP test but performs multiple reactions on each isolate. Amber class A, B, and D carbapenemases are identified by their inhibition in the presence of ␤-lactamase inhibitors, such as tazobactam, EDTA, and dipicolinic acid (DPA), as well as their ability to hydrolyze monobactams (58). Thus, carbapenemases can be correctly classified with clinical sensitivity and specificity comparable to those of molecular methods.…”

Genomic and phenotypic characterisation of fluoroquinolone resistance mechanisms in Enterobacteriaceae in Durban, South Africa

“…Contrary to β-lactams that are hydrolysed by β-lactamases to cause resistance [5–7], resistance to FQ is largely mediated by point mutations in the quinolone resistance determining regions (QRDR) of gyrA , gyrB , parC and parE [1,8]. In addition, extrusion by intrinsic efflux pumps and horizontal acquisition of the plasmid-mediated quinolone resistance (PMQR) genes such as qepA , qnr , oqxAB and aac(6’)-Ib-cr have been also implicated in low-level resistance to FQ [1,2,9].…”