Genomic analysis reveals high intra-species diversity of Shewanella algae

Abstract

Shewanella algae is widely distributed in marine and freshwater habitats, and has been proved to be an emerging marine zoonotic and human pathogen. However, the genomic characteristics and pathogenicity of Shewanella algae are unclear. Here, the whole-genome features of 55 S . algae strains isolated from different sources were described. Pan-genome analysis yielded 2863 (19.4 %) genes shared among all strains. Functional annotation of the core genome showed that the main functions are focused on basic lifestyle such as metabolism and energy production. Meanwhile, the phylogenetic tree of the single nucleotide polymorphisms (SNPs) of core genome divided the 55 strains into three clades, with the majority of strains from China falling into the first two clades. As for the accessory genome, 167 genomic islands (GIs) and 65 phage-related elements were detected. The CRISPR-Cas system with a high degree of confidence was predicted in 23 strains. The GIs carried a suite of virulence genes and mobile genetic elements, while prophages contained several transposases and integrases. Horizontal genes transfer based on homology analysis indicated that these GIs and prophages were parts of major drivers for the evolution and the environmental adaptation of S. algae . In addition, a rich putative virulence-associated gene pool was found. Eight classes of antibiotic-associated resistance genes were detected, and the carriage rate of β-lactam resistance genes was 100 %. In conclusion, S. algae exhibits a high intra-species diversity in the aspects of population structure, virulence-associated genes and potential drug resistance, which is helpful for its evolution in pathogenesis and environmental adaptability.

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

“…3389/fmicb.2023.1124225 variants in Shewanella spp. from CG1, which is consistent with previous reports (Araújo et al, 2021;Huang et al, 2022). The fact that some Shewanella spp.…”

“…(Sharma and Kalawat, 2010;Yousfi et al, 2017;Ng et al, 2022). Although most infection-related species were identified as Shewanella algae and Shewanella putrefaciens, in the last years the employment of molecular based-methods improved the identification of other pathogenic species, such as S. xiamenensis (Parmeciano Di Noto et al, 2016;Thorell et al, 2019;Huang et al, 2022). Furthermore, some Shewanella species can also cause infections in aquatic animals (e.g., S. algae) or coexist as symbionts or epibionts (e.g., Shewanella pealeana and Shewanella woodyi) (Hau and Gralnick, 2007;Janda and Abbott, 2014); while other species have shown to be important dissimilatory metal-reducing bacteria (Zhong et al, 2018).…”

“…Previous studies with few isolates showed that this genus is capable of acquiring a wide variety of mobile elements, such as plasmids, prophages, group II (GII) introns, integrons, and integrative and conjugative elements (ICEs) (Pembroke and Piterina, 2006;Larouche and Roy, 2009;Quiroga and Centrón, 2009;Ramírez et al, 2010;Carattoli, 2013;Parmeciano Di Noto et al, 2016;Fang et al, 2018;Parmeciano Di Noto et al, 2019;Thorell et al, 2019;Huang et al, 2022). Recently, a comprehensive analysis of integron integrases reported that multiple horizontal genetic transfer (HGT) events were implicated in the emergence and spread of novel mobile integrons (Nuñez et al, 2022).…”

“…isolated from clinical samples (Ramírez et al, 2010;Di Noto et al, 2016;Almuzara et al, 2017). Few studies are limited and focused on the analysis of the accessory genome of Shewanella spp., particularly on the mobilome, resistome, and virulome of S. algae isolates (Deng et al, 2019;Wang et al, 2020;Huang et al, 2022), which encode beneficial genetic traits that contribute to its survival. Recently, Zhong et al (2018) suggested that Shewanella spp.…”

Shewanella algae, an Emerging Human Pathogen: A Series of Four Cases From a Portuguese Hospital

“…Notably, antibiotic resistance to S. algae is increasing (namely among carbapenems, cephalosporins, and fluoroquinolones [ 6 , 7 , 11 ]), and multiple determinants of antibiotic resistance have been detected in the genes [ 15 ]. A recent whole-genome analysis of S. algae found eight classes of antibiotic-associated resistance genes, including β-lactam resistance genes, in 100 % of the isolates [ 16 ]. To date, the European Committee on Antimicrobial Susceptibility Testing has not defined clinical breakpoints for susceptibility testing, indicating the reason the microbiology laboratory did not perform susceptibility tests on S. algae isolates from the patients in this report.…”