Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen

Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study, we investigate two factors that are predicted to influence the mutation rate: ecology and genome size. We conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact that ecology can have on the adaptive potential of bacterial pathogens.     

Physiological aspects of multiple blood feeding in the malaria vector Anopheles tessellatus

The malaria vector Anopheles tessellatus is able to take several blood meals in a gonotrophic cycle. The fecundity is largely dependent on the first blood meal and is not generally increased by subsequent blood meals during a gonotrophic cycle. Larval rearing densities influenced adult body size. There is an inverse relationship between wing length and larval rearing densities. Smaller mosquitoes produced from larvae reared at higher densities had reduced body reserves of protein, lipid and carbohydrates. At emergence, ovarian development in An. tessellatus is in the previtellogenic stage and it remained at this stage until the intake of a blood meal. The number of ovarian follicles is related to wing length and, irrespective of adult body size, An. tessellatus developed oocytes to maturity with a single blood meal. This is attributed to the availability of metabolic reserves above the threshold level required for further development of oocytes. Mosquitoes that took more than one blood meal had largely digested their previous blood meal and had ongoing vitellogenesis. Blood meals subsequent to the first one apparently contribute mainly to increasing metabolic reserves. The stimulus for a second and third blood meal in An. tessellatus appears to be completion of the digestion of the previous blood meal. There was no evidence that multiple blood meals taken in the first gonotrophic cycle influenced fecundity significantly in the second cycle.     

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.