Multiple broad-spectrum Beta-lactamase targets for comprehensive surveillance

An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes

Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant bla_CTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments.

Extended-spectrum β-lactamase (ESBL) polymerase chain reaction assay on rectal swabs and enrichment broth for detection of ESBL carriage

BACKGROUND

Extended-spectrum β-lactamase (ESBL) screening and contact precautions on patients at high risk for ESBL carriage are considered important infection control measures. Since contact precautions are costly and may negatively impact patient care, rapid exclusion of ESBL carriage and therefore earlier discontinuation of contact precautions are desired.

AIM

In the present study, the performance of an ESBL polymerase chain reaction (PCR) targeting blaCTX-M genes was evaluated as a screening assay for ESBL carriage.

METHODS

Two methods were assessed: PCR performed directly on rectal swabs and PCR on enrichment broth after incubation overnight. The reference standard was culture of ESBL-producing Enterobacteriaceae on selective agar after overnight enrichment and confirmation by the combination disc diffusion method. Microarray was used for discrepancy analysis. A secondary analysis was performed to evaluate the added value of including a blaSHV target in the PCR.

FINDINGS

A total of 551 rectal swabs from 385 patients were included, of which 28 (5%) were ESBL positive in culture. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 86%, 98%, 67%, and 99%, respectively, for PCR directly on swabs, and 96%, 98%, 75%, and 100%, respectively, for PCR on enrichment broth. Adding a blaSHV target to the assay resulted in a lower PPV without increasing the sensitivity and NPV.

CONCLUSION

Screening for ESBL by PCR directly on rectal swabs has a high negative predictive value, is up to 48h faster than traditional culture and therefore facilitates earlier discontinuation of contact precautions, thereby improving patient care and saving valuable resources in the hospital.

Evaluation of Genotypic and Phenotypic Methods to Detect Carbapenemase Production in Gram-Negative Bacilli

BACKGROUND

Carbapenemase-producing gram-negative bacteria (CP-GNB) are an urgent and expanding public health threat. Rapid and accurate identification of these organisms facilitates infection prevention efforts in healthcare facilities. The objective of our study was to evaluate methods to detect and identify CP-GNB.

METHODS

We examined 189 carbapenem-resistant GNB(CR-GNB), including Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii complex, using 3 different methods: 2 methods to screen isolates of GNB for carbapenemase production [the carbapenem inactivation method (CIM) and 2 chromogenic agars] and a molecular method (Cepheid GeneXpert Carba-R) to identify the mechanism of carbapenem resistance and the associated resistance genes (bla_KPC, bla_NDM, bla_IMP, bla_OXA-48-like, and bla_VIM).

RESULTS

The CIM was a simple and inexpensive phenotypic screen to differentiate between CR-GNB and CP-GNB, with improved analytical performance characteristics and inter-reader correlation compared to the modified Hodge test. Both chromogenic agars evaluated (HardyCHROM CRE and chromID CARBA) were able to support growth of most of the organisms tested, including isolates possessing the bla_OXA-48-like gene. However, these media had a low analytical specificity for carbapenemase production, with breakthrough of CR-GNB that did not produce a carbapenemase. The Xpert Carba-R assay was rapid and easy to perform, and demonstrated 100% positive and negative agreement for characterization of genetic determinants of carbapenem resistance.

CONCLUSIONS

Screening by CIM followed by the Xpert Carba-R PCR is an accurate method for detecting and characterizing CP-GNB, including Enterobacteriaceae, P. aeruginosa, and A. baumannii complex.

Comparison of chromogenic media for recovery of carbapenemase-producing enterobacteriaceae (CPE) and evaluation of CPE prevalence at a tertiary care academic medical center

We evaluated the performance characteristics of chromID CARBA and HardyCHROM Carbapenemase for the detection of carbapenemase-producing Enterobacteriaceae (CPE). A CPE prevalence study was conducted using chromID CARBA; this demonstrated that in low-prevalence settings, CPE screening agars may lack specificity, and confirmation of putative isolates is necessary.

Sensitivity of surveillance testing for multidrug-resistant Gram-negative bacteria in the intensive care unit

We tested intensive care unit patients for colonization with multidrug-resistant Gram-negative bacilli (MDR GNB) and compared the results with those of concurrent clinical cultures. The sensitivity of the surveillance test for detecting MDR GNB was 58.8% (95% confidence interval, 48.6 to 68.5%). Among 133 patients with positive surveillance tests, 61% had no prior clinical culture with MDR GNB.