Detection of Antimicrobial Resistance in Veterinary Bacterial Pathogens

Abstract

For decades, antimicrobial resistance (AMR) in bacteria is detected using standardized phenotypic methods like disc diffusion and broth dilution. World Health Organization categorized molecular tests for AMR into four classes, viz., sequence-based, hybridization-based, amplification-based, and immunoassays. Sequence-based assays include whole genome sequencing and nanopore in which genome sequences are evaluated to find out the resistant genes. Hybridization-based tests involve the use of hybridized nucleic acid probes that target gene sequences for their specific detection. In amplification-based tests like polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP), target gene sequence is amplified into multiple copies permitting detection. The basis for immunoassays such as lateral flow immunoassay and nucleic acid-based lateral flow assay is the capacity of the antibody to bind to the target genes as well as their products to allow detection. However, novel resistance mechanisms cannot be detected absolutely by these molecular methods, since a clear understanding of the responsible DNA sequences is essential. To examine and anticipate the resistance of bacterial isolates from sequence data, various high-throughput bioinformatics tools are available. Recent studies are centered on the development of novel tools that recognize genes associated with AMR and the single nucleotide polymorphisms (SNPs) directly from short reads and produce comprehensive and customizable output. As far as the detection of degree of resistance in a particular setting and the mechanisms of resistance are concerned, molecular and phenotypic AMR diagnostics complement each other.