MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

Abstract

Background Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. Results Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici ( Pst ), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. Conclusions MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats. Electronic supplementary material The online version of this article (10.1186/s12915-019-0684-y) contains supplementary material, which is available to authorized users.

Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus

“…Population genetic information drives the selection of isolates for activities as diverse as basic mechanistic research and plant germplasm screening for disease resistance. It also helps to pinpoint the origin of pandemic strains and the evolutionary potential of different pathogen populations [7][8][9][10][11][12]. A thorough understanding of the global population structure is essential for any surveillance program that aims at rapidly detecting pathogen incursions into new geographical areas.…”

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

“…Population genetic information drives the selection of isolates for activities as diverse as basic mechanistic research and plant germplasm screening for disease resistance. It also helps to pinpoint the origin of pandemic strains and the evolutionary potential of different pathogen populations [7][8][9][10][11][12] . A thorough understanding of the global population structure is essential for any surveillance program that aims at rapidly detecting pathogen incursions into new geographical areas.…”

Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

“…Using this approach, they were able to identify respiratory pathogens in human samples. An alternative to sophisticated DNA extraction methodology is amplicon sequencing (Kilianski et al , 2015; Radhakrishnan et al , 2019). This latter approach was assessed in order to overcome the low throughput of the flowcells and to set up a more reliable and sensitive method, based on the amplification of two housekeeping genes followed by Nanopore sequencing.…”