Searching for putative virulence factors in the genomes of Shewanella indica and Shewanella algae

Prevalence and pathogenic potential of Shewanella species in oysters and seawater collected from the Chesapeake Bay and Maryland Coastal Bays

Shewanella is a genus of Gram-negative marine bacteria with some species associated with human and shellfish illnesses. This study evaluated the abundance of Shewanella species in oysters and seawater from the Chesapeake and Maryland Coastal Bays at four sites between 2019 and 2021. Physicochemical parameters such as temperature, salinity, dissolved oxygen, turbidity, pH, chlorophyll-a, rainfall within the last 48 h, total dissolved solids, and atmospheric pressure were also recorded to evaluate if there was a correlation between environmental parameters and the level of Shewanella. The highest total Shewanella counts were 1.8 × 107 CFU/g in oysters and 4.0 × 102 CFU/mL in seawater. 16S rRNA sequencing was performed on 1,344 representative isolates of which 890 (713 oyster, 177 seawater) were confirmed as Shewanella within 16 species. The top four species isolated from oysters and seawater were S. khirikhana a known shrimp pathogen (49%), S. marisflavi (19%), S. loihica (11%), and S. algae (8%). Testing for alpha and beta hemolysis were performed on all confirmed Shewanella isolates. Beta hemolysis was observed in 405 (46%) of the isolates of which 313 were in oysters and 92 in seawater. In oysters, beta-hemolysis was most prevalent in S. khirikhana (233 of 344 isolates, 68%), while in seawater 64 of 92 isolates (70%) were beta-hemolytic strains. Beta-hemolysis suggests that these could be potentially pathogenic strains. Correlations were performed between physicochemical attributes of the seawater and Shewanella counts. Only seawater temperature and dissolved oxygen correlated with Shewanella counts (r = 0.45 and - 0.41), respectively. No correlations were observed between the physicochemical parameters and Shewanella abundances in oysters. Results suggest that virulent strains of Shewanella may be present in oysters and seawater from the Chesapeake and Maryland Coastal Bays, perhaps as a consequence of rising seawater temperatures.

Emergence of mcr-4.3 genes in a novel Shewanella specie isolated from the Arctic environment

Mobile colistin resistance (mcr) genes are pivotal contributors to last-line of antimicrobial resistance in human infections. Shewanella, historically recognized as a natural environmental bacterium with metal reduction capabilities, recently has been observed in clinical settings. However, limited knowledge has been explored on genetic differences between strains from non-clinical and clinical strains. In this study, we conducted the whole genome sequencing on six Arctic strains, illustrated the phylogenetic relationships on published 393 Shewanella strains that categorized the genus into four lineages (L1 to L4). Over 86.4% of clinical strain group (CG) strains belonged to L1 and L4, carrying mcr-4 genes and a complete metal-reduction pathways gene cluster. Remarkably, a novel Arctic Shewanella strain in L3, exhibits similar genetic characteristics with CG strains that carried both mcr-4 genes and a complete metal reduction pathway gene cluster. It raised concerns about the transmission ability from environment to clinic setting causing in the potential infections, and emphasized the need for monitoring the emerging strains with human infections.

Physiochemical and biological characteristics of fouling on landfill leachate treatment systems surface

Fouling of landfill leachate, a biofilm formation process on the surface of the collection system, migration pipeline and treatment system causes low efficiency of leachate transportation and treatment and increases cost for maintenance of those facilities. In addition, landfill leachate fouling might accumulate pathogens and antibiotic resistance genes (ARGs), posing threats to the environment. Characterization of the landfill leachate fouling and its associated environmental behavior is essential for the management of fouling. In this study, physicochemical and biological properties of landfill leachate fouling and the possible accumulation capacity of pathogens and ARGs were investigated in nitrification (aerobic condition) and denitrification (anaerobic condition) process during landfill leachate biological treatment, respectively. Results show that microbial (bacterial, archaeal, eukaryotic, and viral) community structure and function (carbon fixation, methanogenesis, nitrification and denitrification) differed in fouling under aerobic and anaerobic conditions, driven by the supplemental leachate water quality. Aerobic fouling had a higher abundance of nitrification and denitrification functional genes, while anaerobic fouling harbored a higher abundance of carbon fixation and methanogenesis genes. Both forms of leachate fouling had a higher abundance of pathogens and ARGs than the associated leachate, suggesting the accumulation capacity of fouling on biotic pollutants. Specifically, aerobic fouling harbored three orders of magnitude higher multidrug resistance genes mexD than its associated leachate. This finding provides fundamental knowledge on the biological properties of leachate fouling and suggests that leachate fouling might harbor significant pathogens and ARGs.

Robinsoniella peoriensis: an emerging pathogen with few virulence factors

Robinsoniella peoriensis is a Gram-positive bacterium which is anaerobic, spore-forming, and non-motile. It was initially isolated and characterized from feces and swine manure. Strains of this species have since been identified from different mammalian and non-mammalian gastrointestinal tracts. Strains have also been isolated from a variety of human infections, such as bacteremia, bone infections, and skin structures. R. peoriensis has recently been reported as causative for pyometra, which could result in death in the absence of sufficient antimicrobial treatment. However, to the author's knowledge, there has not been a single virulence factor identified. A major challenge of modern medicine is the failure of conventional procedures to characterize the capability of an emerging pathogen to cause disease. The goal of this study is to initially characterize the pathogenicity of this bacterium using a pathogenomics approach.

Shewanella infection in humans: Epidemiology, clinical features and pathogenicity

The genus Shewanella consists of Gram-negative proteobacteria that are ubiquitously distributed in environment. As the members of this genus have rapidly increased within the past decade, several species have become emerging pathogens worldwide, attracting the attention of the medical community. These species are also associated with severe community- and hospital-acquired infections. Patients infected with Shewanella spp. had experiences of occupational or recreational exposure; meanwhile, the process of infection is complex and the pathogenicity is influenced by a variety of factors. Here, an exhaustive internet-based literature search was carried out in PUBMED using terms “Achromobacter putrefaciens,” “Pseudomonas putrefaciens,” “Alteromonas putrefaciens” and “Shewanella” to search literatures published between 1978 and June 2022. We provided a comprehensive review on the epidemiology, clinical features and pathogenicity of Shewanella, which will contribute a better understanding of its clinical aetiology, and facilitate the timely diagnosis and effective treatment of Shewanella infection for clinicians and public health professionals.

The Fulminating Course of Infection Caused by Shewanella algae: A Case Report

Shewanella algae, a Gram-negative bacillus found in warm saltwater environments, has been increasingly recognized as a human pathogen that can cause infection of the skin and soft tissue, ear, blood, and intra-abdominal. In this case, we report a Shewanella algae infection that caused sepsis, renal insufficiency, cardiac dysfunction, fistula and massive pleural effusion after surgery in a 73-year-old man with cancer of the esophagus and cardia.

Genomic analysis reveals high intra-species diversity of Shewanella algae

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.

Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae

We report the complete genome sequence and base modification analysis of the Shewanella algae type strain CECT 5071 (= OK-1 = ATCC 51192 = DSM 9167 = IAM 14159). The genome is composed of a single chromosome of 4,924,764 bp, with a GC content of 53.10%.