Evolutionary dynamics of phage resistance in bacterial biofilms, bioRxiv, 2019-02-17

Interactions among bacteria and their viral predators, the bacteriophages, are likely among the most common ecological phenomena on Earth. The constant threat of phage infection to bacterial hosts, and the imperative of achieving infection on the part of phages, drives an evolutionary contest in which phage-resistant bacteria emerge, often followed by phages with new routes of infection. This process has received abundant theoretical and experimental attention for decades and forms an important basis for molecular genetics and theoretical ecology and evolution. However, at present, we know very little about the nature of phage-bacteria interaction -- and the evolution of phage resistance -- inside the surface-bound communities that microbes usually occupy in natural environments. These communities, termed biofilms, are encased in a matrix of secreted polymers produced by their microbial residents. Biofilms are spatially constrained such that interactions become limited to neighbors or near-neighbors; diffusion of solutes and particulates is reduced; and there is pronounced heterogeneity in nutrient access and therefore physiological state. These factors can dramatically impact the way phage infections proceed even in simple, single-strain biofilms, but we still know little of their effect on phage resistance evolutionary dynamics. Here we explore this problem using a computational simulation framework customized for implementing phage infection inside multi-strain biofilms. Our simulations predict that it is far easier for phage-susceptible and phage- resistant bacteria to coexist inside biofilms relative to planktonic culture, where phages and hosts are well-mixed. We characterize the negative frequency dependent selection that underlies this coexistence, and we then test and confirm this prediction using an experimental model of biofilm growth measured with confocal microscopy at single-cell and single-phage resolution.

biorxiv microbiology 0-100-users 2019

Cryptic inoviruses are pervasive in bacteria and archaea across Earth's biomes, bioRxiv, 2019-02-16

Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content, and infection cycle. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications such as phage display, or because of their impact on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a new machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like genomes from microbial genomes and metagenomes. Collectively, these represent six distinct proposed inovirus families infecting nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that these viruses may have occasionally transferred from bacterial to archaeal hosts. Finally, we identified an expansive diversity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere sparks new avenues for microbial manipulation approaches and innovative biotechnological applications.

biorxiv microbiology 100-200-users 2019

Cryptic inoviruses are pervasive in bacteria and archaea across Earth’s biomes, bioRxiv, 2019-02-16

AbstractBacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content, and infection cycle. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications such as phage display, or because of their impact on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a new machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like genomes from microbial genomes and metagenomes. Collectively, these represent six distinct proposed inovirus families infecting nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that these viruses may have occasionally transferred from bacterial to archaeal hosts. Finally, we identified an expansive diversity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere sparks new avenues for microbial manipulation approaches and innovative biotechnological applications.

biorxiv microbiology 100-200-users 2019

Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization, bioRxiv, 2019-02-16

Background E. faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim to describe the genome dynamics of this species. Results The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which entirely consisted of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalisation. We estimated the evolutionary rate of two clonal groups that colonized a single patient at 12.6 and 25.2 single nucleotide polymorphisms (SNPs)genomeyear. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of twelve different Insertion Sequence (IS) elements, with ISEfa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5 excision and insertion into the genome during gut colonization. Conclusions Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the patient gut. We observe considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.

biorxiv microbiology 0-100-users 2019

 

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