Spread of pesticide resistance in the North Atlantic salmon lice population

Aims 

The following genetic study is a collaborative work between the IMR, the sea lice research center in the University of Bergen, and the Center for Integrative Genomics (CIGENE) at the Norwegian University of Life Science. Previous to this study, the only molecular markers available for salmon lice were a small number of microsatellites (between 10 and 20), which were insufficient to provide information about the whole genome, and evaluate genetic similarities between lice on different regions of the North Atlantic. The initial aim of the study was to develop a new set of 6000 Single Nucleotide Polymorphism (SNP) markers for salmon lice, and to use this new resource to answer questions related to the population structure of the lice. Incidentally, the study also revealed some genomic regions that seem to be involved in pesticide resistance.

Summary Since 1999, Emamectin benzoate, sold under the brand name SLICE, has been widely used as in-feed treatment to fight lice infestations in aquaculture. However, less than a decade after its introduction on the market, SLICE has started to lose efficiency due to probable development of genetic resistance in lice population. A recent article by Besnier and co-authors reports a genetic study of more than 500 individual lice sampled from 12 farms at different locations in the North Atlantic (see figure 1). This article reports important findings about the structure of lice population in the North Atlantic and about the genetic resistance to SLICE.

What is the structure of lice population and why is it important for managing infestations in aquaculture? The genetic study revealed that lice from distant places are very similar and that there is no such thing as a Norwegian, an Irish or a Canadian lice population. Instead we observe that lice in the North Atlantic belong to one large population where individuals can migrate over long distances. This has a direct impact on the management of lice infestation in aquaculture. Due to this interconnectivity, a genetic resistance that emerges in a given place (for example Norway) can very well spread across the whole ocean, and be found in Canada one or two years later. This means that dealing efficiently and durably with lice infestations and the problem of genetic resistance would require a coordinated response between all concerned regions.

What is making lice resistant to SLICE? We don’t know yet exactly what gene and what mutation is responsible for the resistance, but we have solid clues nevertheless. In the fish farm environment, lice are regularly exposed to pesticides. Lice that are not resistant to the treatment will quickly be eliminated, while resistant ones will survive, and potentially carry genes for resistance to their offspring. Resistance genes will spread in the population within a few generations. As a side effect of this process, genes located near the gene for resistance are also selected. This phenomenon, called selective sweep, means that all individuals that have the resistance also share an identical portion of DNA near the resistance gene. In the North Atlantic study, two such selective sweeps were detected – on lice chromosome 1 and 5. In the genomic regions of chromosome 1 and 5, six to eight genes are potentially responsible for resistance due to their function that is linked to drug resistance in other organisms. Further experiments will be needed to determine which, among those few genes, is/are responsible for the resistance to SLICE.

How could the resistance be caused by several genes? In some cases, drug resistance is due to only one mutation in one gene, however, in the case of resistance to SLICE, the picture looks a little different. With SLICE, it is likely that the resistance is obtained by the cumulative effect of several genes. This is referred to as complex, or polygenic resistance. Lice would become more resistant and tolerate higher doses of products as they cumulate a number of resistance genes.

Even if we get to know exactly which gene(s) make lice resistant, how will it help to deal with infestations in aquaculture? (What are the potential applications of the findings?) Knowing the genetic causes of pesticide resistance is powerful information that can be used to better manage genetic resistance and maintain the efficiency of pesticides for a longer period. With genetic markers that are diagnostic for drug resistance, one could for example implement routine controls to evaluate and monitor the frequency of resistance genes in the lice population at different geographical locations. This could help in decision making – for example choosing to switch from using pesticide A to pesticide B because the frequency of resistance to A is becoming too high. The results from the genetic study clearly indicate that the lice population is a dynamic entity that is capable of adapting very fast to new constraints such as a new chemical pesticide. In such conditions, knowing the genetic causes of pesticide resistance can help predict the short-term evolution of the lice population, and allow farmers be one step ahead of this evolution by selecting the chemical, or combination of chemicals, that will be most efficient for the next season.

Would we need such a complicated strategy if we find a new pesticide that kills lice efficiently? Given the present situation with lice infestations, there is an urgent need for new solutions to treat lice, either by introducing new chemical pesticides or by implementing new alternative methods. In the hypothesis of a new pesticide, the risk of it becoming inefficient due to resistance is very high. The results from the genetic study don’t let much room for optimism on that side. There is strong evidence that the mutation associated with SLICE resistance on chromosome 5 actually comes from one single individual. This means that circa 2005, one individual louse had a new mutation that provided a greater resistance to SLICE, and that five years later, this mutation was present in high frequency in many regions of the North Atlantic from Norway to Canada. This example reveals two very important pieces of information: a- When a genetic resistance emerges, even if it is only in one single individual, it only takes a few years before it colonizes most regions across the North Atlantic. b- The fact that a louse happened to have a mutation providing better resistance to SLICE should not be considered as a “bad luck” event that will probably not happen again. Given the huge number of lice in the ocean, even a very improbable event, such as a genetic mutation at the right place, is likely to happen sooner or later. Given points a and b, we expect that – even if a new efficient pesticide is commercialized tomorrow – if a genetic mutation can provide better resistance to the lice, this mutation will occur sooner or later, and it will spread very fast across the ocean, as it did for resistance to SLICE. This is the salmon lice version of Murphy’s law “Anything that can go wrong, will go wrong”. On chromosome 1, four sequences are present in high frequency (10 to 30% of the population) in several sites, indicating that the selected mutation was present in several lineages (at least four) before selection stated. On chromosome 5, only one sequence1 is present in all locations, indicating that the selected mutation appeared in one individual that transmitted the DNA sequence surrounding the mutation to its offspring. As we observe on Fig2.b the progeny of this individual can now be found in all regions of the North Atlantic. -1 In Fig2.b, the blue sequence is actually a close derivate of the red one. This suggests that the red sequence is the ancestral form and that the blue one derivates from the red after DNA recombination.

*Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis. Francois Besnier, Matthew Kent, Rasmus Skern-Mauritzen, Sigbjørn Lien, Ketil Malde, Rolf B Edvardsen, Simon Taylor, Lina ER Ljungfeldt, Frank Nilsen and Kevin A Glover BMC Genomics 2014, 15:937 doi:10.1186/1471-2164-15-937 The electronic version of this article is available at: http://www.biomedcentral.com/1471-2164/15/937