New Developments in Clinical Bacteriology Laboratories

Abstract

There are a number of changes underway in modern clinical bacteriology laboratories. Panel-based molecular diagnostics are now available for numerous applications, including, but not limited to, detection of bacteria and select antibacterial resistance markers in positive blood culture bottles, detection of acute gastroenteritis pathogens in stool, and detection of selected causes of acute meningitis and encephalitis in the cerebrospinal fluid. Today, rapid point-of-care nucleic acid amplification tests are bringing the accuracy of sophisticated molecular diagnostics closer to patients. A proteomic technology, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, is enabling rapid, accurate, and cost-effective identification of bacteria, as well as fungi, recovered in cultures. Laboratory automation, common in chemistry laboratories, is now available for clinical bacteriology laboratories. Finally, there are several technologies under development, such as rapid phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis for the detection of bacteria in clinical specimens. It is helpful for clinicians to be aware of the pace of new development in their bacteriology laboratory to enable appropriate test ordering, to enable test interpretation, and to work with their laboratories and antimicrobial stewardship programs to ensure that new technology is implemented to optimally improve patient care.

Figure 1. Test ordering guidance for infectious diarrhea

A general guide to laboratory testing for infectious causes of diarrhea is shown. Note that culture is necessitated in cases where antimicrobial susceptibility testing is required, and can be tailored to isolation of the organism(s) detected by the molecular panel (i.e., reflexive culture). The same approach can be used if isolates are needed by public health departments [i.e., stool testing positive by a multiplex GI panel can be submitted to a public health department where culture can be performed to isolate the organism(s) detected.]

Figure 2

A bacterial or fungal colony (typically single) is “picked” from a culture plate to a “spot” on a MALDI-TOF MS target plate (a reusable or disposable plate with a number of test spots) using a wooden or plastic stick, pipette tip, or loop. One or many isolates may be tested at a time. Cells may be treated with formic acid on the target plate. The spot is then overlain with matrix. Following a short drying period, the plate is placed in the mass spectrometer for analysis. A mass spectrum is generated and automatically compared against a database of mass spectra by the software, resulting in identification of the organism (Morganella morganii in position A4 in the example). (Adapted from Communiqué article, January 2013. Theel ES. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of bacterial and yeast isolates. www.mayomedicallaboratories.com/articles/communique/2013/01-maldi-tof-mass-spectrometry.)