Rapid Detection and Monitoring of Flavobacterium psychrophilum in Water by Using a Handheld, Field‐Portable Quantitative PCR System

Abstract

Advances in technology are making it easier for rapid field detection of microbes in aquaculture. Specifically, real-time quantitative PCR (qPCR) analysis, which has traditionally been confined to laboratory-based protocols, is now available in a handheld, field-portable system. The feasibility of using the Biomeme handheld qPCR system for rapid (<50 min) on-site detection and monitoring of Flavobacterium psychrophilum from filtered water samples was evaluated. Paired water samples were collected over a 23-d period from microcosm tanks that housed fish injected with known levels of F. psychrophilum. Water samples were filtered through 0.45-μm nitrocellulose filters and were analyzed with both the Biomeme qPCR platform and a traditional bench qPCR protocol. The two methods identified similar fluctuations in F. psychrophilum DNA throughout the study. Standard curves relating quantification cycles to the number of F. psychrophilum colonyforming units (CFU) were constructed and analyzed; results indicated that CFU increased rapidly between days 6 and 8 of the trial and then progressively decreased during the remaining 15 d. Average calculated log 10 (CFU/mL) values were significantly correlated between the two platforms. Rapid, field-based qPCR can be incorporated into daily water quality monitoring protocols to help detect and monitor microbes in aquaculture systems.In aquaculture, the health status of farmed stocks is often directly linked to the microbe composition within the aquatic environment (Bentzon-Tilia et al. 2016).

Disease in Central Valley Salmon: Status and Lessons from Other Systems

“…River water samples can be used to map the spatial and temporal distribution of infectious agents and potential exposure landscapes of salmon to diseases in a watershed (Hallett and Bartholomew 2006;Richey et al 2018). Advancements in environmental DNA (eDNA) technology are allowing researchers to rapidly determine the presence and abundance (e.g., cells L -1 ) of multiple agents in a single sample in near-real time (Nguyen et al 2018). As costs fall and sensitivity increases, it will become easier to pinpoint hot spots of infectious agents and associate them with environmental variables and/or identify sources.…”

Updating PCR

“…The two methods identified similar fluctuations in F. psychrophilum DNA throughout the study. This research demonstrated the proof of concept that rapid field qPCR testing can be used to detect and monitor for aquatic microbes, with results comparable to those from laboratory-based qPCR analysis under ideal laboratory testing conditions [5]. …”

Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food?

“…However, all the above methods are lab-based and time consuming, so that the development of rapid and portable devices with more routine throughput screening methods are likely to continue into the immediate future. Recent research related to on-site detection of GM crops include; loop-mediated isothermal amplification (LAMP) (Hardinge et al, 2018;Singh et al, 2019;Loo et al, 2019), LAMP and a lateral flow biosensor (Cheng et al, 2017), PCR and a lateral flow biosensor (Gao et al, 2019), handheld field-portable qPCR systems (Nguyen et al, 2018;Russell et al, 2018), and nanopore sequencing (Fraiture et al, 2018;Russell et al, 2018).…”