Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen

Abstract

Genome sequencing has been useful to gain an understanding of bacterial evolution. It has been used for studying the phylogeography and/or the impact of mutation and recombination on bacterial populations. However, it has rarely been used to study gene turnover at microevolutionary scales. Here, we sequenced Mexican strains of the human pathogen Acinetobacter baumannii sampled from the same locale over a 3 year period to obtain insights into the microevolutionary dynamics of gene content variability. We found that the Mexican A. baumannii population was recently founded and has been emerging due to a rapid clonal expansion. Furthermore, we noticed that on average the Mexican strains differed from each other by over 300 genes and, notably, this gene content variation has accrued more frequently and faster than the accumulation of mutations. Moreover, due to its rapid pace, gene content variation reflects the phylogeny only at very short periods of time. Additionally, we found that the external branches of the phylogeny had almost 100 more genes than the internal branches. All in all, these results show that rapid gene turnover has been of paramount importance in producing genetic variation within this population and demonstrate the utility of genome sequencing to study alternative forms of genetic variation.

The Genomic Context for the Evolution and Transmission of Community-Associated Staphylococcus aureus ST59 Through the Food Chain

“…Given that the SNP-based analysis was focused on the core genes of these isolates, we also constructed a dendrogram according to the presence and absence of accessory genes. Importantly, the distribution of isolates between the different clades did not fully align with their presentation in the SNP-based phylogenetic tree; although other groups have reported similar discrepancies (Orsi et al, 2011;Anastasi et al, 2016;Graña-Miraglia et al, 2017;Henri et al, 2017). Several reasons may account for this observation, such as natural factors including horizontal gene transfer and recombination, and technical factors including gaps in the draft genomes and inaccurate parameters for the pan-genome estimation (Orsi et al, 2011;Rouli et al, 2015).…”

“…The output of Prokka was used to construct the pan-genome using Roary v3.11.2, with a BLASTP identity cutoff of 90% . A profile of absence (0) or presence (1) of all genes was generated according to the pangenome distribution of all samples, and a hierarchically clustered heatmap was created with this matrix by using the Pearson correlation function in R (Graña-Miraglia et al, 2017).…”

Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus

“…We want to highlight that the biology of the species under consideration could have a very important effect on the number of orthologous genes found. For instance, highly recombinogenic species, such as Neisseria gonorrhoeae ( Ezewudo et al, 2015 ) and Acinetobacter baumannii ( Grana-Miraglia et al, 2017 ), would have fewer orthologous genes than more clonal species. Nonetheless, the strategy employed by us should work even in these species, although the number of potential orthologous genes should be much less.…”

Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade

“…Several are the studies where has been demonstrated by NGS analysis the high degree of variation in A . baumannii clinical isolates, including single nucleotide polymorphisms (SNPs) and large DNA fragment variations in the resistance island (RI) regions, the type VI secretion system (T6SS) and the bacteriophages 27 , 28 . One of the key determinants of the size, composition, structure and development of a microbial community is the predation pressure exerted by bacteriophages 29 .…”