The environmental microbiology minimum information (EMMI) Guidelines: qPCR and dPCR quality and reporting for environmental microbiology

Authors: BORCHARDT, MARK; BOEHM, ALEXANDRIA - STANFORD UNIVERSITY; SALIT, MARC - STANFORD UNIVERSITY; SPENCER, SUSAN; WIGGINTON, KRISTA - UNIVERSITY OF MICHIGAN; NOBLE, RACHEL - UNIVERSITY OF NORTH CAROLINA

Submitted to: Environmental Science and Technology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2021
Publication Date: 7/21/2021
Citation: Borchardt, M.A., Boehm, A.B., Salit, M., Spencer, S.K., Wigginton, K.R., Noble, R.T. 2021. The environmental microbiology minimum information (EMMI) Guidelines: qPCR and dPCR quality and reporting for environmental microbiology. Environmental Science and Technology. https://doi.org/10.1021/acs.est.1c01767.
DOI: https://doi.org/10.1021/acs.est.1c01767

Interpretive Summary: Genetic methods for detecting microbial genes in the environment are now common practice, for example, measuring microbial contaminants in drinking water or recreational water. The methods yield rapid and sensitive results and are not difficult to learn. However, without appropriate checks on method performance, the resulting data may have significant errors, which may lead to incorrect conclusions and difficulty in making comparisons with other studies. In this paper we provide guidance on the appropriate checks, using positive and negative controls, for producing high quality measurements of microorganisms in the environment. We propose terminology to reduce confusion among scientists using the methods, and we show how various types of controls can be carried-out in an efficient fashion in the laboratory. In addition, we discuss key principles in the science of measurement and standards to assist laboratories with their own plan for checking the performance of their methods. Following the guidelines in this paper will help researchers produce trustworthy data and impactful studies.

Technical Abstract: Quantitative measurements of microbial contaminants in the environment (water, air, fomites) are essential for understanding the role of the environment in the transmission of infectious disease, and developing interventions (water treatment, surface disinfection, air purification) to curb transmission. Methods that focus on quantification of organism-specific, nucleic-acid targets are revolutionizing quantitative biology, and our understanding of the role of the environment in infectious disease. However, based on our review of recent literature, we found 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 necessary and sufficient controls needed to make high quality, quantitative measurements of microorganisms in the environment. 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, and we provide clear guidance on reporting of method and analysis details. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance/quality control reporting framework. Following the guidelines in this paper will lend credence to measurements published by researchers, while advancing our understanding of the role of the environment in human health.