Vestrheim, D. F. | Search bioRxiv

bioRxiv2021

Spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis

Competitive interactions between pathogen strains drive infection risk. Vaccines are thought to perturb strain diversity through shifts in immune pressures, however, this has rarely been measured due to inadequate data and analytical tools. Bordetella pertussis (B. pertussis), responsible for 160,000 deaths annually1, provides a rare natural experiment as many countries have switched from whole cell vaccines to acellular vaccines, which have very different immunogenic properties2,3. Here we use 3,344 sequences from 23 countries and build phylogenetic models to reveal that B. pertussis has substantial diversity within communities, with the relative fitness of local genotypes changing in response to switches in vaccine policy. We demonstrate that the number of transmission chains circulating within subnational regions is strongly associated with host population size. It takes 5-10 years for individual lineages to be homogeneously distributed throughout Europe or the United States. Increased fitness of pertactin-deficient strains following implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These findings highlight the role of national vaccine policies in shifting local diversity of a pathogen that still poses a large burden on global public health.

genetics↗

bioRxiv2019

Impact of narrow spectrum Penicillin V on the oral and fecal resistome in a young child treated for otitis media

BackgroundAntibiotic overuse has led to a global emergence of resistant bacteria, and children are among the frequent users. Most studies with broad-spectrum antibiotics show severe impact on the resistome development of patients. Although narrow-spectrum antibiotics are believed to have less side-effects, their impact on the microbiome and resistome is mostly unknown. The aim of this study was to investigate the impact of the narrow-spectrum antibiotic phenoxymethylpenicillin (Penicillin V) on the microbiome and resistome of a child treated for acute otitis media (OM).\n\nMethodsOral and fecal samples were collected from a one-year child before (day 0) and after (day 5 and 30) receiving Penicillin V against OM. Metagenomic sequencing data was analysed to determine taxonomic profiling, using Kraken and Bracken software, and resistance profiling, using KMA in combination with the ResFinder database.\n\nResultsIn the oral samples, 11 antimicrobial resistance genes (ARGs), belonging to four classes, were identified at baseline. At day 5, the abundance of some ARGs was increased, some remained unchanged, while others disappeared. At day 30, most ARGs had returned to baseline levels, or lower. In the fecal samples we observed seven ARGs at baseline and five at day 5, with only one gene observed at day 5 being present at baseline. At day 30 the number of ARGs increased to 21 ARGs from 7 different classes.\n\nConclusionsPenicillin V had a remarkable impact on the fecal resistome indicating that even narrow-pectrum antibiotics may have important consequences in selecting for a more resistant microbiome.

microbiology↗