Evolution of copper resistance in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids

Abstract

Lateral gene transfer can precipitate rapid evolutionary change. In 2010 the global pandemic of kiwifruit canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) reached New Zealand. At the time of introduction, the single clone responsible for the outbreak was sensitive to copper, however, analysis of a sample of isolates taken in 2015 and 2016 showed that a quarter were copper resistant. Genome sequences of seven strains showed that copper resistance (comprising czc/cusABC and copABCD systems) along with resistance to arsenic and cadmium, was acquired via uptake of integrative conjugative elements (ICEs), but also plasmids. Comparative analysis showed ICEs to have a mosaic structure, with one being a tripartite arrangement of two different ICEs and a plasmid that were isolated in 1921 (USA), 1968 (NZ) and 1988 (Japan), from P. syringae pathogens of millet, wheat and kiwifruit, respectively. Two of the Psa ICEs were nearly identical to two ICEs isolated from kiwifruit leaf colonists prior to the introduction of Psa into NZ. Additionally, we show ICE transfer in vitro and in planta, analyze fitness consequences of ICE carriage, capture the de novo formation of novel recombinant ICEs, and explore ICE host-range.

Genetic diversity ofPseudomonas syringaepv.actinidiae, pathogen of kiwifruit bacterial canker

“…In addition, it is feared that because Psa has a high degree of genome plasticity, adaptive mutations may occur in destination countries, which may make the damage more severe. The many mobile genetic elements, such as genomic islands including IME and ICE, prophages, transposons and plasmids, which are present on the genomes of Psa could bring new features to Psa, leading to the introduction of environmental adaptability, such as drug resistance, and the acceleration of changes in pathogenicity/virulence (Sawada et al ., , ; Genka et al ., ; Butler et al ., ; McCann et al ., , ; Fujikawa & Sawada, , ; Bardaji et al ., ; Colombi et al ., ; Vanneste, ). Each biovar has high homogeneity within the core genome, but when the information from the accessory genome is included in the phylogenomic analysis, a large diversity appears in each biovar, suggesting that Psa has been continuously accumulating insertion/deletion and mutation events.…”

“… Numerous integrative and conjugative elements (ICEs) have been detected so far from biovar 3 strains (Butler et al ., ; McCann et al ., ; Butler & Poulter, ; Colombi et al ., ). Among them, three major ICEs that are often detected from pandemic strains of biovar 3 are shown in this table. …”

The ecological genetics of Pseudomonas syringae from kiwifruit leaves

“…Different fertilizer and spray regimes (copper, antibiotics, Actigard TM and biological agents) are employed by growers to prevent or manage Psa infection throughout the growing season (http://www.kvh.org.nz/vdb/document/99346). These practices may have selected for copper and streptomycin resistance in Psa and kiwifruit epiphytes in NZ and elsewhere (Han et al, 2003;Colombi et al, 2017;Petriccione et al, 2017).…”

“…On the leaf surface, Psa is likely to encounter and interact with a diverse range of plant-colonising bacteria (Hirano and Upper, 2000;Lindow and Brandl, 2003). Physical proximity increases the likelihood of competitive interactions affecting disease outcomes (Lindow and Brandl, 2003;Hibbing et al, 2010) and increases the probability of horizontal gene transfer (Sawada et al, 1999;Polz et al, 2013;Colombi et al, 2017).…”

Horizontal gene transfer gone wild: promiscuity in a kiwifruit pathogen leads to resistance to chemical control

“…In an alarming finding reported in a recent issue of environmental microbiology, Colombi et al . () describe how the epidemic Psa strain circulating in New Zealand since 2010 was able to acquire genes conferring resistance to copper bactericides within 4 years of its introduction. Detailed molecular investigation on several strains isolated after its first appearance, however, has provided a fascinating story of the apparent promiscuity of Psa and the myriad of different ways in which copper resistance has evolved in this pathogen, occurring from horizontal gene transfer mediated by acquisition of both plasmids and integrative conjugative elements (ICEs).…”