Use of Molecular Testing: “From Bench to Bedside”

Reviewed by David and Cindy

Fernandez-Pittol and colleagues conducted a multicenter, prospective analysis from January 2021 to June 2022, using a lateral flow immunoassay “BL-DetecTool” to evaluate for CTX-M enzymes (from 5 subfamilies) and carbapenemase enzymes (OXA-48, KPC, VIM, IMP and NDM) from urine, blood and rectal specimens identified to have Escherichia coli, Klebsiella pneumoniae complex, or Enterobacter species growth via culture.1  Processing time was approximately 5 minutes and results were read at 15 and 30 minutes.1  Resistance was confirmed with formal susceptibility testing or with PCR for gene presence.1  Prevalence of resistance varied by facility with CTX-M present in 5.9% to 28.5% of isolates and carbapenemases, 0 to 19.6%.1  The sensitivity of detection for CTX-M ranged from 90-100% in blood, 84-100% in urine and though did not perform as well with rectal samples (3.4 to 100% per rectal swab if direct sample, 75.8-100% if enriched with brain heart infusion).1  For carbapenemases, sensitivity ranged from 75 to 100% in blood, 42.8 to 100% in urine and 26 to 100% in rectal swabs without enrichment; 66 to 100% with enrichment.1  Thus resistance enzymes can be detected from clinical specimens with reasonable accuracy in blood and urine, with low cost and minimal technician time, raising the potential for improving early antibiotic selection and instituting timely isolation precautions to reduce risk of transmission to others.1 

Use of molecular testing may also be beneficial not only to determine resistance, but also helpful in more expedient diagnosis and subsequent selection of appropriate antimicrobial therapy. Markussen and colleagues explored the utility of syndromic PCR testing in patients who presented with community-acquired pneumonia to a single emergency department in Norway. The 2 primary outcomes were provision of pathogen-directed treatment based on a microbiological test result and the time to pathogen-directed treatment. There were 374 patients (59% male; median age, 72 years) included in the study, with 187 in each treatment arm. Analysis of primary outcomes showed that 66 patients (35.3%) in the intervention arm and 25 (13.4%) in the SOC arm received pathogen-directed treatment, corresponding to a reduction in absolute risk of 21.9 (95% CI, 13.5-30.3) percentage points and an odds ratio for the intervention arm of 3.53 (95% CI, 2.13-6.02; P < .001). The median time to pathogen-directed treatment within 48 hours was 34.5 (31.6-37.3) hours in the intervention arm and 43.8 (42.0-45.6) hours in the standard-of-care arm (mean difference, −9.4 hours; 95% CI, −12.7 to −6.0 hours; P < .001). The study was stopped early due to slow recruitment and “substantial” differences were shown between the two groups. The findings of the study are limited by external validity (eg internal guidance: benzylpenicillin was given as standard therapy for mild-moderate CAP) and early discontinuation of the study.


Fernandez-Pittol M, Bosch J, Ballesté-Delpierre C, et al. Multicenter study to assess the use of BL-DetecTool for the detection of CTX-M-type ESBLs and carbapenemases directly from clinical specimens. J Clin Microbiol. 2024;62(3):e0113623. doi: 10.1128/jcm.01136-23.

Markussen DL, Serigstad S, Ritz C, et al. Diagnostic Stewardship in Community-Acquired Pneumonia With Syndromic Molecular Testing: A Randomized Clinical Trial. JAMA Netw Open. 2024;7(3):e240830. doi:10.1001/jamanetworkopen.2024.0830

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