Abstract

In healthcare, efficacy and speed are cardinal factors determining courses of analysis, diagnosis, and treatment. However, in infectious disease diagnostics, microbiological culture technology — a method dating back 160 years— is still the standard method for determining types and quantities of organisms. Next-generation sequencing (NGS) is a newer and more accurate method employed by MicroGen Vet (https://microgenvet.com) to generate accurate, life-changing—and often life-saving—results in a short timeframe to better suit patient outcomes.

Microbial culture technology is extensively used and known. However, despite its wide adoption and continued use, cultures may provide suboptimal results compared to NGS. Why might cultures fail or underperform compared to NGS? For issues like chronic infections, the root cause is often polymicrobial. Additionally, the culture that does grow might not represent the dominant organisms in a provided sample. If only a dominant or single organism is yielded, it may not lead to appropriate antimicrobial therapy and resolution of infection. Additional benefits of next-generation sequencing include:

• Ability to match microbes detected in samples to a database of 50,000 species
• Least expensive cost worldwide for qPCR+NGS testing
• Accepts the widest variety of sample/media types
• Faster turnaround times compared to cultures
• qPCR detection of 17 antimicrobial resistance genes for all major classes of antimicrobials

DNA-based diagnostics can effectively determine the microbes that are present in a biofilm. qPCR testing has been shown to be accurate and timelier than culturing, but has been limited by the diagnostic process. Specific panels are utilized to determine if a range of targeted pathogens are present in the sample (typically 8–15 per test). This means that veterinarians are hoping to confirm a suspected cause of the infection prior to the test, which may leave veterinarians with a trial-and-error approach to treatment. In conjunction with PCR, NGS has rapid turnaround times that range from three to five days, boasting 99% accuracy at identifying all bacteria and fungi in a sample, while detecting potential antimicrobial resistance genes. That level of effectiveness can help inform precise treatment that ends with patient relief and lowers overall treatment costs. Since its introduction into the healthcare field in the early 2000s, NGS has seen widespread use among clinicians in human and small animal practice and research of infectious diseases, microbiology, urology, wound care, and upper respiratory disease. It has been used for diagnostics in zoo and aquatic species such as lesser flamingos (Phoeniconaias minor), gorillas (Gorilla spp.), and California sea lions (Zalophus californianus) (unpub. data).

NGS proves the more effective process due to its ability to sequence up to millions of DNA strands, identifying all species of bacteria and fungi. DNA-based, next-generation testing takes all the benefits of qPCR to the next level by comparing all microbial DNA present in a sample against a comprehensive bioinformatics database containing over 50,000 known microbial DNA profiles. NGS provides the veterinarian with a comprehensive understanding of bacteria and fungi that are present in order to develop a targeted treatment protocol, resulting in vastly improved health outcomes for animal patients.

*Presenting author