Sivertsen, A. | Search bioRxiv

bioRxiv2025

Reassessing taxonomy and virulence in the Fusobacterium nucleatum group - Rebuttal of Fusobacterium animalis clades "Fna C1" and "Fna C2", genome announcement for Fusobacterium watanabei and description of Fusobacterium paranimalis sp. nov.

There is a considerable interest in the association between Fusobacterium animalis and colorectal cancer (CRC). Recently, it was suggested that this association is valid only for a distinct clade of F. animalis (Fna C2) and that F. animalis strains belonging to another clade (Fna C1) are only associated with the oral cavity. It was further suggested that this made Fna C1 a natural comparator when looking for candidate genes associated with the pathogenicity of Fna C2. Based on such comparisons, three candidate operons enriched in CRC were suggested to explain the strong colorectal tumor association of F. animalis. In the present paper we show that major taxonomic errors invalidate the existence of two distinct clades of F. animalis and that Fna C1 is simply a rediscovery and misclassification of Fusobacterium watanabei. We further reassess the phylogenetic structure of the entire Fusobacterium nucleatum group encompassing F. animalis and all known closely related species and confirm the current taxonomy using contemporary phylogenetic principles. We also describe a novel Fusobacterium species more closely related to F. animalis than any other known species, for which we propose the name Fusobacterium paranimalis sp. nov.. We further searched for the three proposed candidate virulence operons of F. animalis across the entire F. nucleatum group and show that some or all of these are present in all other species except F. watanabei. We also observe considerable variability of Type 5 secretion systems (T5SS) by subtype and abundance across the F. nucleatum group. ImportanceIt is known that Fusobacterium animalis is able to survive within colorectal tumors. Recently, it was proposed that only one "clade" of Fusobacterium animalis could be found in colorectal tumors, and that another "clade" within the same species was instead only found in the oral cavity, and that differences in gene content could explain the habitat difference. We here show that these "clades" are two separate species by sequencing the type strain of the oral cavity-associated species, which is Fusobacterium watanabei. We also revisit other related species within the "Fusobacterium nucleatum group" to confirm that they are separate species, exemplified by presenting a new species, F. paranimalis sp.nov., which genetically is more related to F. animalis than any other known species including F. watanabei. We look at gene content of the entire group, and conclude that known virulence genes cannot fully explain F. animalis cancer association.

genomics↗

bioRxiv2023

Comprehensive contact tracing during an outbreak of alpha-variant SARS-CoV-2 in a rural community reveals less viral genomic diversity and higher household secondary attack rates than expected

Sequencing of SARS-CoV-2 genomes throughout the COVID-19 pandemic has generated a wealth of data on viral evolution across populations, but only a few studies have so far explored SARS-CoV-2 evolution across transmission networks of tens to hundreds of persons. Here, we couple data from SARS-CoV-2 sequencing with contact tracing data from an outbreak with a single origin in a rural Norwegian community where samples from all exposed persons were collected prospectively. A total of 134 nasopharyngeal samples were positive by PCR. Among the 121 retrievable genomes, 81 were identical to the genome of the introductor, thus demonstrating that genomics offers limited additional value to manual contact-tracing. In the cases where mutations were discovered, five small genetic clusters were identified. We observed a household secondary attack rate of 67%, with 92% of household members infected among households with secondary transmission, suggesting that SARS-CoV-2 introduction into large families are likely to affect all household members. ImportanceIn outbreak investigations, obtaining a full overview of infected individuals within a population is seldom acheived. We here present an example of just that, where a single introduction of B1.1.7 SARS-CoV-2 within a rural community allowed for tracing of the virus, from an introductor via dissemination through larger gatherings, into households. The outbreak occurred before widespread vaccination, allowing for a "natural" outbreak development with community lock-down. We show through sequencing that the virus can infect up to five consecutive persons without gaining mutations, thereby showing that contact tracing seems more important than sequencing for local outbreak investigations. We also show how families with small children are less likely to contain spread to all family members if SARS-CoV-2 enters the household either by a child or a caregiver, as isolation of the primary infected is difficult in such scenarios.

microbiology↗