Complete Genome Sequences of Bordetella flabilis, Bordetella bronchialis, and "Bordetella pseudohinzii"

A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies

The genus Bordetella includes bacteria that are found in the environment and/or associated with humans and other animals. A few closely related species, including Bordetella pertussis, are human pathogens that cause diseases such as whooping cough. Here, we present a large database of Bordetella isolates and genomes and develop genotyping systems for the genus and for the B. pertussis clade. To generate the database, we merge previously existing databases from Oxford University and Institut Pasteur, import genomes from public repositories, and add 83 newly sequenced B. bronchiseptica genomes. The public database currently includes 2582 Bordetella isolates and their provenance data, and 2085 genomes ( https://bigsdb.pasteur.fr/bordetella/ ). We use core-genome multilocus sequence typing (cgMLST) to develop genotyping systems for the whole genus and for B. pertussis, as well as specific schemes to define antigenic, virulence and macrolide resistance profiles. Phylogenetic analyses allow us to redefine evolutionary relationships among known Bordetella species, and to propose potential new species. Our database provides an expandable resource for genotyping of environmental and clinical Bordetella isolates, thus facilitating evolutionary and epidemiological research on whooping cough and other Bordetella infections.

Contribution of a Novel Pertussis Toxin-Like Factor in Mediating Persistent Otitis Media

Chronic otitis media (COM) is the long-term infection and inflammation of the middle ears typically caused by upper respiratory tract pathogens that are able to ascend the Eustachian tube. Our understanding of contributing factors is limited because human otopathogens cannot naturally colonize or persist in the middle ears of mice. We recently described a natural COM in mice caused by Bordetella pseudohinzii and proposed this as an experimental system to study bacterial mechanisms of immune evasion that allow persistent infection of the middle ear. Here we describe a novel pertussis toxin (PTx)-like factor unique to B. pseudohinzii, apparently acquired horizontally, that is associated with its particularly efficient persistence and pathogenesis. The catalytic subunit of this toxin, PsxA, has conserved catalytic sites and substantial predicted structural homology to pertussis toxin catalytic subunit PtxA. Deletion of the gene predicted to encode the catalytic subunit, psxA, resulted in a significant decrease in persistence in the middle ears. The defect was not observed in mice lacking T cells, indicating that PsxA is necessary for persistence only when T cells are present. These results demonstrate the role of a novel putative toxin in the persistence of B. pseudohinzii and its generation of COM. This PsxA-mediated immune evasion strategy may similarly be utilized by human otopathogens, via other PTx-like toxins or alternative mechanisms to disrupt critical T cell functions necessary to clear bacteria from the middle ear. This work demonstrates that this experimental system can allow for the detailed study of general strategies and specific mechanisms that otopathogens use to evade host immune responses to persist in the middle ear to cause COM.

Outbreak of Burkholderia contaminans endophthalmitis traced to a clinic ventilation system

We describe the follow-up investigation of an outbreak of endophthalmitis due to Burkholderia contaminans following cataract surgery in a single clinic. Whole-genome sequence analysis of bacteria recovered from affected patients and the clinic identified the clinic's ventilation system as the source of infection.

Genotypic and phenotypic adaptation of pathogens: lesson from the genus Bordetella

PURPOSE OF REVIEW

To relate genomic changes to phenotypic adaptation and evolution from environmental bacteria to obligate human pathogens, focusing on the examples within Bordetella species.

RECENT FINDINGS

Recent studies showed that animal-pathogenic and human-pathogenic Bordetella species evolved from environmental ancestors in soil. The animal-pathogenic Bordetella bronchiseptica can hijack the life cycle of the soil-living amoeba Dictyostelium discoideum, surviving inside single-celled trophozoites, translocating to the fruiting bodies and disseminating along with amoeba spores. The association with amoeba may have been a 'training ground' for bacteria during the evolution to pathogens. Adaptation to an animal-associated life style was characterized by decreasing metabolic versatility and genome size and by acquisition of 'virulence factors' mediating the interaction with the new animal hosts. Subsequent emergence of human-specific pathogens, such as Bordetella pertussis from zoonoses of broader host range progenitors, was accompanied by a dramatic reduction in genome size, marked by the loss of hundreds of genes.

SUMMARY

The evolution of Bordetella from environmental microbes to animal-adapted and obligate human pathogens was accompanied by significant genome reduction with large-scale gene loss during divergence.

Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

Several species of the Gram-negative genus Bordetella are the cause of respiratory infections in mammals and birds, including whooping cough (pertussis) in humans. Very recently, a novel atypical species, Bordetella pseudohinzii, was isolated from laboratory mice. These mice presented no obvious clinical symptoms but elevated numbers of neutrophils in bronchoalveolar lavage fluid and inflammatory signs in histopathology. We noted that this species can occur at high prevalence in a mouse facility despite regular pathogen testing according to the FELASA-recommendations. Affected C57BL/6 J mice had, in addition to the reported pulmonary alterations, tracheal inflammation with reduced numbers of ciliated cells, slower ciliary beat frequency, and largely (>50%) compromised cilia-driven particle transport speed on the mucosal surface, a primary innate defence mechanism. In an in vitro-model, Bordetella pseudohinzii attached to respiratory kinocilia, impaired ciliary function within 4 h and caused epithelial damage within 24 h. Regular testing for this ciliotropic Bordetella species and excluding it from colonies that provide mice for lung research shall be recommended. On the other hand, controlled colonization and infection with Bordetella pseudohinzii may serve as an experimental model to investigate mechanisms of mucociliary clearance and microbial strategies to escape from this primary innate defence response.

Cystic Fibrosis Mice Develop Spontaneous Chronic Bordetella Airway Infections

Chronic pulmonary disease and infection is the primary cause of morbidity and mortality in people with cystic fibrosis (CF). Though Pseudomonas aeruginosa, is most commonly found in the airways of individuals with CF, there is increasing appreciation for the diversity of the CF microbiome, including other taxa such as Bordetella. Here we describe the identification and impact of Bordetella pseudohinzii infection in CF mice, which previously have not been thought to develop spontaneous airway infections. We determined that CF mice are more susceptible to the B. pseudohinzii infections, and less able to resolve the infection than non-CF mice. Moreover, in both CF and non-CF mice, B. pseudohinzii infections lead to markedly reduced respiratory rates and a CF-specific immune response. These results establish the CF mouse model as an important tool for the study of CF-relevant infection and highlight the potential contribution of Bordetella to CF clinical pathology.

Draft genome of Bordetella pseudohinzii BH370 isolated from trachea and lung tissues of a laboratory mouse

In this study, we present the draft genome sequence of B. pseudohinzii BH370 recovered from the trachea and lung tissues of an ICR mouse in Malaysia. The genome consists of 4,474,040 bp with a GC content of 66.4%. Annotation using RAST algorithm displayed 5119 protein encoding and 52 RNA genes. The CRISPR-cas genomic sequences previously reported in B. pseudohinzii were identified. The nucleotide sequences of BH370 was deposited into the European Nucleotide Archive under the genome assembly accession number FPJN01000000.