posted on 2021-07-21, 15:48authored byMark A. Borchardt, Alexandria B. Boehm, Marc Salit, Susan K. Spencer, Krista R. Wigginton, Rachel T. Noble
Real-time quantitative
polymerase chain reaction (qPCR) and digital
PCR (dPCR) methods have revolutionized environmental microbiology,
yielding quantitative organism-specific data of nucleic acid targets
in the environment. Such data are essential for characterizing interactions
and processes of microbial communities, assessing microbial contaminants
in the environment (water, air, fomites), and developing interventions
(water treatment, surface disinfection, air purification) to curb
infectious disease transmission. However, our review of recent qPCR
and dPCR literature in our field of health-related environmental microbiology
showed that many researchers are not reporting necessary and sufficient
controls and methods, which would serve to strengthen their study
results and conclusions. Here, we describe the application, utility,
and interpretation of the suite of controls needed to make high quality
qPCR and dPCR measurements of microorganisms in the environment. Our
presentation is organized by the discrete steps and operations typical
of this measurement process. We propose systematic terminology to
minimize ambiguity and aid comparisons among studies. Example schemes
for batching and combining controls for efficient work flow are demonstrated.
We describe critical reporting elements for enhancing data credibility,
and we provide an element checklist in the Supporting Information.
Additionally, we present several key principles in metrology as context
for laboratories to devise their own quality assurance and quality
control reporting framework. Following the EMMI guidelines will improve
comparability and reproducibility among qPCR and dPCR studies in environmental
microbiology, better inform engineering and public health actions
for preventing disease transmission through environmental pathways,
and for the most pressing issues in the discipline, focus the weight
of evidence in the direction toward solutions.