Prophage-driven genomic structural changes promote Bartonella vertical evolution

Abstract

Bartonella is a genetically diverse group of vector-borne bacteria. Over 40 species have been characterized to date, mainly from mammalian reservoirs and arthropod vectors. Rodent reservoirs harbor one of the largest Bartonella diversity described to date, and novel species and genetic variants are continuously identified from these hosts. Yet, it is still unknown if this significant genetic diversity stems from adaptation to different niches or from intrinsic high mutation rates. Here, we explored the vertical occurrence of spontaneous genomic alterations in 18 lines derived from two rodent-associated Bartonella elizabethae-like strains, evolved in nonselective agar plates under conditions mimicking their vector- and mammalian-associated temperatures, and the transmission cycles between them (i.e., 26 °C, 37 °C, and alterations between the two), using mutation accumulation experiments. After ∼1,000 generations, evolved genomes revealed few point mutations (average of one-point mutation per line), evidencing conserved single-nucleotide mutation rates. Interestingly, three large structural genomic changes (two large deletions and an inversion) were identified over all lines, associated with prophages and surface adhesin genes. Particularly, a prophage, deleted during constant propagation at 37 °C, was associated with an increased autonomous replication at 26 °C (the flea-associated temperature). Complementary molecular analyses of wild strains, isolated from desert rodents and their fleas, further supported the occurrence of structural genomic variations and prophage-associated deletions in nature. Our findings suggest that structural genomic changes represent an effective intrinsic mechanism to generate diversity in slow-growing bacteria and emphasize the role of prophages as promoters of diversity in nature.

Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov., two novel species closely related to the zoonotic Bartonella elizabethae, isolated from black rats and wild desert rodent-fleas

“…Recently, using multi-locus sequence analysis (MLSA) on 448 isolates of members of the genus Bartonella from G. pyramidum and G. andersoni and their S. cleopatrae associated fleas, 18 different sequence types of the OE 1-1 strain were identified and were proposed to represent a single species [22]. Additionally, this strain has been used as a model for several in vivo and in vitro ecological and evolutionary studies [9,30,32,33].…”

Deciphering active prophages from metagenomes

“…Three model systems for which sequencing data was publicly available were identified for use as positive controls. All experiments and sequencing were performed elsewhere (Hertel et al 2015; Gutiérrez et al 2018; Ho et al 2016) ( Supplemental Table S1 ). Each system, since they represent isolate bacteria, have a much higher read coverage compared to a typical metagenome assembled genome.…”

Bartonellagene transfer agent: Evolution, function, and proposed role in host adaptation

“…Such a dual role represents an asset for Bartonella , considering the adverse host(s) environments they are facing and the repeated alternation between transmission bottlenecks and rapid expansion phases within different niches (Chomel et al, ; Gutierrez et al, ). Remarkably, an in‐vitro evolution experiment performed by repetitive single‐colony passaging of two rodent‐associated Bartonella strains revealed low‐level accumulation of single nucleotide variations (in the range of 1 per 1,000 generations; Gutierrez et al, ). This experiment reproduces the larger prophage‐driven genomic reorganisations that are commonly seen in natural isolates (Gutierrez, Markus, et al, ).…”

“…Remarkably, an in‐vitro evolution experiment performed by repetitive single‐colony passaging of two rodent‐associated Bartonella strains revealed low‐level accumulation of single nucleotide variations (in the range of 1 per 1,000 generations; Gutierrez et al, ). This experiment reproduces the larger prophage‐driven genomic reorganisations that are commonly seen in natural isolates (Gutierrez, Markus, et al, ). However, it poorly reflects the genetic diversity observed at the nucleotide level for rodent‐associated Bartonella species sampled from wild animals and their flea hosts (Bai, Kosoy, Lerdthusnee, Peruski, & Richardson, ; Gutierrez et al, ; Inoue et al, ; D. M. Li et al, ).…”

“…They thus could also contribute to genome diversification by recombination. Prophages have been directly implicated in Bartonella genome dynamics, notably by lineage‐specific genomic expansion and reduction or by large genomic rearrangements, even at the species level (Berglund et al, ; Berglund et al, ; Engel & Dehio, ; Gutierrez, Markus, et al, ; Guy et al, ; Harms, Segers, et al, ; Lindroos et al, ). Of note, the nature and occurrence of Bartonella prophages is very heterogeneous, none of them is conserved throughout the Bartonellae or even within sublineages, and strain‐specific variations are observed.…”