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 the implementation of these strategies in clinical practice.

Keywords:

• 16S rDNA PCR
• antimicrobial stewardship
• culture-negative infections
• mass spectrometry
• multiplex PCR
• PCR/ESI-MS

Acknowledgements

The authors are supported by the National Institutes of Health and VISN 10 Veterans Affairs Research Initiative Program.

Financial & competing interests disclosure

R Sampath is a salaried employee of Ibis Biosciences, an Abbott Company. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Key issues

• 16S rDNA PCR and PCR/ESI-MS have both evolved from environmental scientific research tools to novel clinical applications.

• 16S rDNA PCR and PCR/ESI-MS share the advantage that knowledge of a predetermined target is not necessary for pathogen detection.

• Both 16S rDNA PCR and PCR/ESI-MS provide opportunities to adjust antimicrobial treatment, avoiding the pitfalls associated with widespread use of overly broad empiric antimicrobial treatment.

• The premise of salvage microbiology is that species-specific diagnostic information derived from patients who have cultures submitted following initiation of antimicrobial treatment is valuable for the management of individual cases of infection and for institutional efforts to optimize antimicrobial prescribing practices.

• 16S rDNA PCR and PCR/ESI-MS have shown the capacity to detect clinically relevant pathogens from specimens obtained from 30 to 60% of patients who have cultures submitted following initiation of antimicrobial treatment. Unlike 16S rDNA PCR, PCR/ESI-MS is capable of distinguishing all pathogens in a polymicrobial infection without additional testing.

• Unlike 16S rDNA PCR, PCR/ESI-MS provides a single platform for diagnostic testing of clinical specimens for yeast, invasive fungi and viral pathogens.

• Head-to-head comparisons of 16S rDNA PCR versus PCR/ESI-MS are lacking.

• Exploration of the most appropriate role of 16S rDNA PCR versus PCR/ESI-MS with various clinical samples (sterile body fluids, surgical specimens, blood, nonsterile specimens such as respiratory samples) and subsequent optimization are needed.

• Implementation of systematic institutional programs to capitalize on the potential outcome and cost-saving opportunities these technologies offer will require close collaboration across multiple disciplines.

• More clinical studies of these new technologies designed to compare outcomes for specific patient populations are required before these platforms can be incorporated into ‘real-world’ quality improvement initiatives.