A Sensitive and Accurate Recombinase Polymerase Amplification Assay for Detection of the Primary Bacterial Pathogens Causing Bovine Respiratory Disease

Cheyenne C Conrad; Rana K Daher; Kim Stanford; Kingsley K Amoako; Maurice Boissinot; Michel G Bergeron; Trevor Alexander; Shaun Cook; Brenda Ralston; Rahat Zaheer; Yan D Niu; Tim McAllister

doi:10.3389/fvets.2020.00208

A Sensitive and Accurate Recombinase Polymerase Amplification Assay for Detection of the Primary Bacterial Pathogens Causing Bovine Respiratory Disease

Front Vet Sci. 2020 Apr 22:7:208. doi: 10.3389/fvets.2020.00208. eCollection 2020.

Authors

Affiliations

¹ Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada.
² Centre de Recherche en Infectiologie de l'Université Laval, Québec City, QC, Canada.
³ Alberta Agriculture and Forestry, Lethbridge, AB, Canada.
⁴ National Centre for Animal Disease, Canadian Food Inspection Agency, Lethbridge, AB, Canada.
⁵ Alberta Agriculture and Forestry, Airdrie, AB, Canada.
⁶ Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.

Abstract

Rapid and accurate diagnosis of bovine respiratory disease (BRD) presents a substantial challenge to the North American cattle industry. Here we utilize recombinase polymerase amplification (RPA), a fast and sensitive isothermal DNA-based technology for the detection of four BRD pathogens (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, Mycoplasma bovis), genes coding antimicrobial resistance (AMR) and integrative conjugative elements (ICE) which can harbor AMR genes. Eleven RPA assays were designed and validated including: a) one conventional species-specific multiplex assay targeting the 4 BRD pathogens, b) two species-specific real-time multiplex RPA assays targeting M. haemolytica/M. bovis and P. multocida/H. somni, respectively with a novel competitive internal amplification control, c) seven conventional assays targeting AMR genes (tetH, tetR, msrE, mphE, sul2, floR, erm42), and d) one real-time assay targeting ICE. Each real-time RPA assay was tested on 100 deep nasopharyngeal swabs (DNPS) collected from feedlot cattle previously assessed for targets using either culture methods and/or polymerase chain reaction (PCR) verification (TC-PCR). The developed RPA assays enabled sensitive and accurate identification of BRD agents and AMR/ICE genes directly from DNPS, in a shorter period than TC-PCR, showing considerable promise as a tool for point-of-care identification of BRD pathogens and antimicrobial resistance genes.

Keywords: antimicrobial resistance; bovine respiratory disease; competitive internal amplification; integrative conjugative element; recombinase polymerase amplification.