Salvage microbiology: opportunities and challenges in the detection of bacterial pathogens following initiation of antimicrobial treatment

Abstract

Broad-range 16S ribosomal RNA gene PCR coupled with Sanger sequencing was originally employed by soil scientists and was subsequently adapted for clinical applications. PCR coupled with electrospray ionization mass spectrometry has also progressed from initial applications in the detection of organisms from environmental samples into the clinical realm and has demonstrated promise in detection of pathogens in clinical specimens obtained from patients with suspected infection but negative cultures. We review studies of multiplex PCR, 16S ribosomal RNA gene PCR and sequencing and PCR coupled with electrospray ionization mass spectrometry for detection of bacteria in specimens that were obtained from patients during or after administration of antibiotic treatment, and examine the role of each for assisting in antimicrobial treatment and stewardship efforts. Following an exploration of the available data in this field we discuss the opportunities that the preliminary investigations reveal, as well as the challenges faced with implementation of these strategies in clinical practice.

Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis

“…All of these confirmed true positives were from patients who were previously exposed to antibiotic therapy which is consistent with previous findings in patients with sepsis demonstrating that BC sensitivity is reduced by approximately 50% after the initiation of antimicrobial therapy (Cheng et al, 2019). It also suggests the T2Bacteria Panel performance may have limited interference from empirical antimicrobial treatment, which continues to be an issue with culture‐based diagnostics (Farrell et al, 2015).…”

Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study

“…This is a general characteristic of molecular nucleic acid amplification-based techniques such as PCR and is not specific to UNGS [16,17]. The most probable cause of this discrepancy is that in infections, including those occurring in immunocompromised adults, the load of viable bacteria (if any in the context of antimicrobial therapy) is several orders of magnitude lower than genome copy number [17,18]. Indeed, the microbial load in infections of immunocompromised individuals is generally low.…”

Identification of bacterial species by untargeted NMR spectroscopy of the exo-metabolome

“…Nevertheless, technological developments have given birth to automated systems (Vitek2, bioMérieux; BD Phoenix, Becton Dickinson). 2,3 Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has evolved into a rapid and highly reliable analytical tool for the characterization of micro-organisms in clinical laboratories, 4 and other emerging novel diagnostic approaches have been applied to bacteria studies like genomic analysis, 5,6 biochemical sensors, [7][8][9][10] optical scattering technology, 3 mass spectrometry, 11 or infrared 12 and Raman [13][14][15] spectroscopies. Likewise, NMR spectroscopy has been proposed to study bacteria.…”