Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism

Abstract

The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g., cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but nonidentical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins, and the selenocysteinyl tRNA.

Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591

“…Noteworthy in C. avium is the absence of the selenocysteinyl tRNA and genes encoding selenium-associated proteins, e.g., selenocysteine insertion proteins, selenoproteins, and selenoprotein-associated chaperones. The absence of selenium metabolism was reported previously for Campylobacter lanienae and related taxa ( 7 ). An ortholog of the C. jejuni fibronectin-binding protein CadF is also not encoded by C. avium .…”

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“…El método se conoce como el "Cape Town Protocol" CTP (por sus siglas en inglés) e inicialmente se desarrolló para el aislamiento de Campylobacter a partir de muestras de heces humanas (Lastovica & Le Roux, 2000). Diversos estudios han adaptado esta metodología de filtración por membrana para el aislamiento de múltiples miembros de la familia Campylobacteraceae en muestras de pollo crudos, así como en muestras ambientales ( Quiñones et al, 2007;Speegle et al, 2009;Miller et al, 2014;Miller et al, 2017). El presente estudio, utilizó un tamaño de poro de membrana de 0.65 µm, porque se ha demostrado su eficacia en la recuperación de Campylobacter en muestras de líquido de pollo crudo empaquetado (Quiñones et al, 2007;Speegle et al, 2009;Miller et al, 2014;Berrang et al, 2017).…”

“…The method is known as the "Cape Town Protocol" and was initially developed for the isolation of campylobacters from human stool samples (Lastovica & Le Roux, 2000). In subsequent studies, this membrane filtration methodology was then adapted for the isolation of multiple members of the Campylobacteraceae family from raw chicken carcasses as well as environmental samples (Quiñones et al, 2007;Speegle et al, 2009;Miller et al, 2014;Miller et al, 2017). In the present study, a membrane pore size of 0.65 µm was selected, as previously shown for its efficacy in the recovery of campylobacters from package liquid from raw chicken carcasses (Quiñones et al, 2007;Speegle et al, 2009;Miller et al, 2014;Berrang et al, 2017).…”

“…Para aumentar la eficiencia en el aislamiento y la detección de Campylobacter en alimentos y/o muestras ambientales, las metodologías han empleado una variedad de medios de enriquecimiento adicionados con antibióticos para disminuir la flora microbiana presente en la muestra y promover el crecimiento y aislamiento de Campylobacter cuando están presentes en cantidades bajas (Man, 2011;Kaakoush et al, 2015). Tomando en cuenta la movilidad de las campilobacterias, los protocolos de filtración por membrana han demostrado ser eficientes en la recuperación de las campilobacterias provenientes de muestras clínicas, ambientales y de alimentos ( Lastovica & Le Roux, 2000;Quiñones et al, 2007;Speegle et al, 2009;Miller et al, 2014;Miller et al, 2017).…”

“…For the effective isolation and detection of Campylobacter from food or environmental samples, methodologies employ the use of a variety of enrichment media in conjunction with the incorporation of antibiotics to reduce microbial flora and promote the growth and isolation of campylobacters when present in low numbers (Man, 2011;Kaakoush et al, 2015). By taking advantage of the increased motility of campylobacteria, the use of a membrane filtration protocol has proven to effectively recover campylobacteria from clinical, environmental and food samples (Lastovica & Le Roux, 2000;Quiñones et al, 2007;Speegle et al, 2009;Miller et al, 2014;Miller et al, 2017).…”