April 21, 2020  |  

Capacity to utilize raffinose dictates pneumococcal disease phenotype.

Streptococcus pneumoniae is commonly carried asymptomatically in the human nasopharynx, but it also causes serious and invasive diseases such as pneumonia, bacteremia, and meningitis, as well as less serious but highly prevalent infections such as otitis media. We have previously shown that closely related pneumococci (of the same capsular serotype and multilocus sequence type [ST]) can display distinct pathogenic profiles in mice that correlate with clinical isolation site (e.g., blood versus ear), suggesting stable niche adaptation within a clonal lineage. This has provided an opportunity to identify determinants of disease tropism. Genomic analysis identified 17 and 27 single nucleotide polymorphisms (SNPs) or insertions/deletions in protein coding sequences between blood and ear isolates of serotype 14 ST15 and serotype 3 ST180, respectively. SNPs in raffinose uptake and utilization genes (rafR or rafK) were detected in both serotypes/lineages. Ear isolates were consistently defective in growth in media containing raffinose as the sole carbon source, as well as in expression of raffinose pathway genes aga, rafG, and rafK, relative to their serotype/ST-matched blood isolates. Similar differences were also seen between serotype 23F ST81 blood and ear isolates. Analysis of rafR allelic exchange mutants of the serotype 14 ST15 blood and ear isolates demonstrated that the SNP in rafR was entirely responsible for their distinct in vitro phenotypes and was also the determinant of differential tropism for the lungs versus ear and brain in a mouse intranasal challenge model. These data suggest that the ability of pneumococci to utilize raffinose determines the nature of disease.IMPORTANCES. pneumoniae is a component of the commensal nasopharyngeal microflora of humans, but from this reservoir, it can progress to localized or invasive disease with a frequency that translates into massive global morbidity and mortality. However, the factors that govern the switch from commensal to pathogen, as well as those that determine disease tropism, are poorly understood. Here we show that capacity to utilize raffinose can determine the nature of the disease caused by a given pneumococcal strain. Moreover, our findings provide an interesting example of convergent evolution, whereby pneumococci belonging to two unrelated serotypes/lineages exhibit SNPs in separate genes affecting raffinose uptake and utilization that correlate with distinct pathogenic profiles in vivo This further underscores the critical role of differential carbohydrate metabolism in the pathogenesis of localized versus invasive pneumococcal disease. Copyright © 2019 Minhas et al.

April 21, 2020  |  

Genomic characterization of Kerstersia gyiorum SWMUKG01, an isolate from a patient with respiratory infection in China.

The Gram-negative bacterium Kerstersia gyiorum, a potential etiological agent of clinical infections, was isolated from several human patients presenting clinical symptoms. Its significance as a possible pathogen has been previously overlooked as no disease has thus far been definitively associated with this bacterium. To better understand how the organism contributes to the infectious disease, we determined the complete genomic sequence of K. gyiorum SWMUKG01, the first clinical isolate from southwest China.The genomic data obtained displayed a single circular chromosome of 3, 945, 801 base pairs in length, which contains 3, 441 protein-coding genes, 55 tRNA genes and 9 rRNA genes. Analysis on the full spectrum of protein coding genes for cellular structures, two-component regulatory systems and iron uptake pathways that may be important for the success of the bacterial survival, colonization and establishment in the host conferred new insights into the virulence characteristics of K. gyiorum. Phylogenomic comparisons with Alcaligenaceae species indicated that K. gyiorum SWMUKG01 had a close evolutionary relationships with Alcaligenes aquatilis and Alcaligenes faecalis.The comprehensive analysis presented in this work determinates for the first time a complete genome sequence of K. gyiorum, which is expected to provide useful information for subsequent studies on pathogenesis of this species.

April 21, 2020  |  

Deciphering bacterial epigenomes using modern sequencing technologies.

Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Indeed, as the number of mapped bacterial methylomes approaches 2,000, increasing evidence supports roles for methylation in regulation of gene expression, virulence and pathogen-host interactions.

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