Comparison of Two Phenotypic Algorithms To Detect Carbapenemase-Producing Enterobacteriaceae

Phenotypic and genotypic detection methods for antimicrobial resistance in ESKAPE pathogens (Review)

Antimicrobial resistance (AMR) represents a growing public health problem worldwide. Infections with such bacteria lead to longer hospitalization times, higher healthcare costs and greater morbidity and mortality. Thus, there is a greater need for rapid detection methods in order to limit their spread. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) are a series of epidemiologically-important microorganisms of great concern due to their high levels of resistance. This review aimed to update the background information on the ESKAPE pathogens as well as to provide a summary of the numerous phenotypic and molecular methods used to detect their AMR mechanisms. While they are usually linked to hospital acquired infections, AMR is also spreading in the veterinary and the environmental sectors. Yet, the epidemiological loop closes with patients which, when infected with such pathogens, often lack therapeutic options. Thus, it was aimed to give the article a One Health perspective.

The Global Ascendency of OXA-48-Type Carbapenemases

Surveillance studies have shown that OXA-48-like carbapenemases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of nonendemicity, where they are responsible for nosocomial outbreaks. OXA-48, OXA-181, OXA-232, OXA-204, OXA-162, and OXA-244, in that order, are the most common enzymes identified among the OXA-48-like carbapenemase group. OXA-48 is associated with different Tn1999 variants on IncL plasmids and is endemic in North Africa and the Middle East. OXA-162 and OXA-244 are derivatives of OXA-48 and are present in Europe. OXA-181 and OXA-232 are associated with ISEcp1, Tn2013 on ColE2, and IncX3 types of plasmids and are endemic in the Indian subcontinent (e.g., India, Bangladesh, Pakistan, and Sri Lanka) and certain sub-Saharan African countries. Overall, clonal dissemination plays a minor role in the spread of OXA-48-like carbapenemases, but certain high-risk clones (e.g., Klebsiella pneumoniae sequence type 147 [ST147], ST307, ST15, and ST14 and Escherichia coli ST38 and ST410) have been associated with the global dispersion of OXA-48, OXA-181, OXA-232, and OXA-204. Chromosomal integration of bla _OXA-48 within Tn6237 occurred among E. coli ST38 isolates, especially in the United Kingdom. The detection of Enterobacterales with OXA-48-like enzymes using phenotypic methods has improved recently but remains challenging for clinical laboratories in regions of nonendemicity. Identification of the specific type of OXA-48-like enzyme requires sequencing of the corresponding genes. Bacteria (especially K. pneumoniae and E. coli) with bla _OXA-48, bla _OXA-181, and bla _OXA-232 are emerging in different parts of the world and are most likely underreported due to problems with the laboratory detection of these enzymes. The medical community should be aware of the looming threat that is posed by bacteria with OXA-48-like carbapenemases.

Evaluation of the Amplidiag CarbaR+VRE Kit for Accurate Detection of Carbapenemase-Producing Bacteria

As carbapenemase-producing Gram-negative bacilli (CP-GNB) (Enterobacteriaceae, Pseudomonadaceae, and Acinetobacter spp.) are becoming a major public health issue, there is an urgent need for accurate and fast diagnostic tests. The Amplidiag CarbaR+VRE assay is a multiplex nucleic acid-based in vitro diagnostic test intended for the detection of CP-GNB and vancomycin-resistant enterococci (VRE) from cultured colonies. We have evaluated its ability to detect carbapenemase genes in 100 well-characterized GNB and in 200 consecutive enterobacterial isolates with reduced susceptibility to carbapenems that were referred to the French National Reference Center for carbapenem resistance. The assay has been validated on purified DNA but also directly on colonies. The Amplidiag CarbaR+VRE assay could detect all KPC, NDM, VIM, IMP, and OXA-48-like variants tested and all acquired carbapenem-hydrolyzing oxacillinases from Acinetobacter baumannii (OXA-23, OXA-24/-40, and OXA-58) as well as the overexpressed chromosomally encoded OXA-51-like β-lactamase associated with an upstream inserted ISAba1 However, as claimed by the manufacturer, other carbapenemases such as GES-like carbapenemases (GES-2, GES-5, and GES-14), GIM-1, AIM-1, SPM-1, DIM-1, OXA-198 in Pseudomonas aeruginosa, or OXA-143-like in A. baumannii were not detected. Amplidiag CarbaR+VRE's performance values were high (100% sensitivity and 99% specificity) as it could detect the five major carbapenemases-NDM, VIM, IMP, KPC, and OXA-48-as well as OXA-type carbapenemases from Acinetobacter spp. that are currently emerging also among Proteus mirabilis and other enterobacterial isolates. It can provide a result directly from colonies growing on Mueller-Hinton (MH) agar or on selective screening medium in less than 2 h. Further evaluations are now necessary to determine the performance values directly on rectal swabs.

Evaluation of the Carbapenem Detection Set™ for the detection and characterization of carbapenemase-producing Enterobacteriaceae

The objective of this study was to assess the performance of the Carbapenemase Detection Set™ (CDS; Mast Diagnostics) in association with i) the EUCAST meropenem screening cut-off and ii) the faropenem-temocillin algorithm (FTa) for the screening of carbapenemase-producing Enterobacteriaceae (CPE). A total of 200 well-characterized enterobacterial isolates with reduced susceptibility to at least one carbapenem including 63 non-CPEs and 137 CPEs belonging to different Ambler classes were initially screened for CPEs using i) the EUCAST meropenem cut-off (diameter <25 mm) and ii) the FTa. Highly suspected CPEs underwent further testing using the CDS, which is based on the inhibition zone diameters determination of combined disks (A: meropenem, B: meropenem + dipicolinic acid, C: meropenem + cloxacillin, and D: meropenem + boronic acid). With the FTa, 66.7% of the non-CPE isolates were correctly identified. Most OXA-48-like producers (90.5%) were detected with 98.6% specificity. The FTa discriminates CPE from non-CPE with 100% sensitivity, but complementary tests were still needed for 59 % (118/200) of the strains. The EUCAST cut-off led to 3 false-negative results (2 OXA-181 and 1 NMC-A producer) resulting in a sensitivity of 97.8% for the discrimination between CPE and non-CPE, and 75.5% (151/200) of the strains still required complementary test. The CDS reduced the number of isolates requiring additional tests from 59% to 22%, and from 75.5% to 38% for FTa and EUCAST cut-off, respectively. FTa possesses very good specificities for the detection and classification of Ambler class A and most class B carbapenemase-producers, except for IMP producers, which were almost not detected (10/11). In conclusion, the association of the CDS with the FTa presented only 22% of inconclusive results, while this number was 38% with the EUCAST meropenem CPE screening cut-off.

Evaluation of the CRE and ESBL ELITe MGB® kits for the accurate detection of carbapenemase- or CTX-M-producing bacteria

As carbapenemase-producing Enterobacteriaceae (CPE) and extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are becoming a major public health issue, there is an urgent need for accurate and fast diagnostic tests. The ELITe InGenius is a fully automated sample-to-result system designed for the extraction and detection by multiplex real-time polymerase chain reaction of carbapenemases KPC, NDM, VIM, IMP, and OXA-48-like variants and CTX-M group 1 and 9-producers from diverse sample matrices such as colonies, positive blood cultures, and rectal swabs. CRE and ESBL ELITe MGB® kits were evaluated on 153 cultured colonies of enterobacterial isolates with characterized β-lactamase content, on 30 spiked blood cultures, and the CRE kit was also evaluated on 53 clinical rectal swabs collected prospectively during a 3-month period and 10 spiked rectal swabs. CRE ELITe MGB® kit's performances reached 100% sensitivity and 100% specificity, while for the ESBL ELITe kit, 100% sensitivity and 96.6% specificity were observed, with a sample to result of less than 3 h and a total percentage of agreement with expected results of 99.6% (255/256).