Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Abstract

Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.

Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance

“…In this article, we provided a detailed description of pan-genome characteristics of S. xiamenensis . Although there are previous works focusing on Shewanella spp., our results demonstrated a clear shift in antibiotic resistance for S. xiamenensis recently [ 7 , 40 ]. Mobile genetic elements and macromolecular secretion systems may aid in this process.…”

“…Mobile genetic elements, including genome islands, prophage, ISs and integrons, are important vectors for DNA transfer, expanding the gene pool [ 53 ]. A total of 2,423 ISs were identified, with an average of 48.46 in each genome, which were significantly more than the average number of 4–12 ISs per genome reported before [ 7 ]. The origins of ISs were from Shewanella , Salmonella and Aeromonas , indicating that HGT between bacteria in aquatic environments may occur.…”

“…Therefore, a total of 50 genome sequences were selected for pan-genome analysis, including ten genomes involved in previous study [ 7 ]. The AAI and TETRA values of 49 genomes against S. xiamenensis reference strain HD6416 were all high than 97.48% and 0.99, respectively (Supplemental Table S 3 and S 4 ).…”

“…S. xiamenensis has been identified as an important carrier of antibiotic resistance genes, as it is considered as the source of bla OXA−48 [ 6 ]. Although multiple studies focused on Shewanella genus, the strains used were mostly isolated before 2019 [ 7 ]. At present, significant changes in the antibiotic resistance of S. xiamenensis have been unraveled.…”

Prevalence and molecular characteristics of Shewanella infection in diarrhea patients in Beijing, China 2017–2019

“… Cerbino et al (2023) performed virulome analysis on Shewanella spp. They put forward that there is a correlation between the VAS T6SS and the S. algae lineage.…”