Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines

Rebecca J Barnewall; Ian B Marsh; Jane C Quinn

doi:10.3389/fmolb.2022.902401

Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines

Front Mol Biosci. 2022 Jul 18:9:902401. doi: 10.3389/fmolb.2022.902401. eCollection 2022.

Authors

Rebecca J Barnewall^{1

2}, Ian B Marsh³, Jane C Quinn^{1

2}

Affiliations

¹ School of Agricultural, Environmental and Veterinary Science, Charles Sturt University, Wagga Wagga, NSW, Australia.
² Gulbali Institute, Wagga Wagga, NSW, Australia.
³ NSW DPI, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia.

Abstract

Qualitative and quantitative PCR-based tests are widely used in both diagnostics and research to assess the prevalence of disease-causing pathogens in veterinary medicine. The efficacy of these tests, usually measured in terms of sensitivity and specificity, is critical in confirming or excluding a clinical diagnosis. We undertook a meta-analysis to assess the inherent value of published PCR diagnostic approaches used to confirm and quantify bacteria and viruses associated with bovine respiratory disease (BRD) in cattle. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A thorough search of nine electronic databases (Web of Science, EBSCOhost, Cambridge journals online, ProQuest, PubMed, Sage journals online, ScienceDirect, Wiley online library and MEDLINE) was undertaken to find studies that had reported on the use of PCR and/or qPCR for the detection and/or quantification of BRD associated organisms. All studies meeting the inclusion criteria for reporting quantitative PCR for identification of BRD associated microorganisms were included in the analysis. Studies were then assessed on the applications of the Minimum Information for Publication of Quantitative Real-Time PCR Experiment (MIQE) and PCR primer/probe sequences were extracted and tested for in silico specificity using a high level of stringency. Fourteen full-text articles were included in this study. Of these, 79% of the analysed articles did not report the application of the MIQE guidelines in their study. High stringency in silico testing of 144 previously published PCR primer/probe sequences found many to have questionable specificity. This review identified a high occurrence of primer/probe sequences with a variable in silico specificity such that this may have implications for the accuracy of reporting. Although this analysis was only applied to one specific disease state, identification of animals suspected to be suffering from bovine respiratory disease, there appears to be more broadly a need for veterinary diagnostic studies to adopt international best practice for reporting of quantitative PCR diagnostic data to be both accurate and comparable between studies and methodologies.

Keywords: BRDC; MIQE; PCR; bovine respiratory disease; cattle; molecular diagnostics; qPCR; quantification.