Comparative Genomics Analyses Support the Reclassification of Bisgaard Taxon 40 as Mergibacter gen. nov., With Mergibacter septicus sp. nov. as Type Species: Novel Insights Into the Phylogeny and Virulence Factors of a Pasteurellaceae Family Member Associated With Mortality Events in Seabirds

Abstract

The Pasteurellaceae family has been associated with fatal diseases in numerous avian species. Several new taxa within this family, including Bisgaard taxon 40, have been recently described in wild birds, but their genomic characteristics and pathogenicity are not well understood. We isolated Bisgaard taxon 40 from four species of seabirds, including one sampled during a mass, multi-species mortality event in Florida, United States. Here, we present a comprehensive phenotypic and genetic characterization of Bisgaard taxon 40 and comparative genomic analysis with reference strains from the Pasteurellaceae family, aiming at determining its phylogenetic position, antimicrobial susceptibility profile, and identifying putative virulence factors. In silico multilocus sequence-based and whole-genome-based phylogenetic analysis clustered all Bisgaard taxon 40 strains together on a distinct branch separated from the other members of the Pasteurellaceae family, indicating that Bisgaard taxon 40 could represent a new genus. These findings were further supported by protein similarity analyses using the concatenation of 31 conserved proteins and other taxonomic approaches such as the percentage of conserved protein test. Additionally, several putative virulence factors were identified, including those associated with adhesion (capsule, ompA, ompH) and colonization (exbD, fur, galU, galE, lpxA, lpxC, and kdsA) of the host and a cytolethal distending toxin (cdt), which may have played a role in disease development leading to the mortality event. Considerably low minimum inhibitory concentrations (MICs) were found for all the drugs tested, in concordance with the absence of antimicrobial resistance genes in these genomes. The novel findings of this study highlight genomic and phenotypic characteristics of this bacterium, providing insights into genome evolution and pathogenicity. We propose a reclassification of these organisms within the Pasteurellaceae family, designated as Mergibacter gen. nov., with Mergibacter septicus sp. nov. as the type species. The type strain is Mergibacter septicus A25201T (=DSM 112696).

First Description of Mergibacter septicus Isolated from a Common Tern (Sterna hirundo) in Germany

“…septicus 19Y0039 grows aerobically on blood agar at 28 • C, 37 • C, and 42 • C with ßhaemolysis. Colonies are small, round, and shiny with a whitish-cream colony morphology, and Gram-negative rods can be seen under the microscope, in agreement with the findings of De Luca et al [11]. No growth was observed on MacConkey agar.…”

“…The antimicrobial resistance phenotype of M. septicus 19Y0039 was evaluated after incubation at 37 °C and 42 °C, respectively ( Supplementary Table S1 ). In contrast to the findings of De Luca et al (2021) [ 11 ] with regard to antibiotic susceptibility of the isolates used to describe the newly proposed genus and species Mergibacter septicus , the automated MICRONAUT-S system found M. septicus 19Y0039 to be resistant to colistin, cephalexin, clindamycin, oxacillin, and penicillin G. ETEST ® (BioMerieux GmbH) determined the Colistin MIC value to be at 2 µg/mL.…”

“…Putative virulence genes previously reported by De Luca et al [ 11 ] including a capsular gene, genes encoding for outer membrane proteins ( omp A, omp H), a superoxide dismutase ( sod A), a cytolethal distending toxin ( cdt ), as well as genes involved in lipooligosaccharide (LOS) synthesis ( gal U, gal E, lpx A, lpx C, and kds A) and iron metabolism ( fur and exb D) were searched for with BLASTN v 2.2.9 in M. septicus 19Y0039. The Fasta sequences of the putative virulence genes were kindly provided by Dr. De Luca and colleagues upon request.…”

“…Although little is known regarding its ecological habitat, transmission, and pathogenicity, it has been associated with multi-species mortality events in seabirds, including common and sandwich terns, as well as Rhinoceros Auklets ( Cerorhinca monocerata ) [ 9 , 10 ]. Affected birds presented with pneumonia, neurological signs, and septicaemia [ 9 , 10 , 11 ]. To date, reports on M. septicus have been sporadic and largely geographically confined to the USA (Florida; Washington) despite affecting migratory avian species.…”