Olaya Rendueles

Institut Pasteur · Department of Genomes & Genetics

Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival rates in vivo upon exposure to stresses, like the host’s immune system or antibiotic therap...

Klebsiella variicola is an emergent human pathogen causing diverse infections, including in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like morphotype which is contin...

Bacterial evolution is affected by mobile genetic elements such as phages and conjugative plasmids, which may provide novel adaptive traits but also incur in fitness costs. Infection by these elements is affected by the bacterial capsule. Yet, its importance has been difficult to quantify and characterise because of the high diversity of bacterial...

Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival rates in vivo upon exposure to stresses, like the immune system of the host or antibiotic t...

Many bacterial genomes carry prophages whose induction can eliminate competitors. In response, bacteria may become resistant by modifying surface receptors, by lysogenization, or by other poorly known processes. All these mechanisms affect bacterial fitness and population dynamics. To understand the evolution of phage resistance, we co-cultivated a...

The extracellular capsule is a virulence factor present in many facultative pathogens, but its role in antimicrobial resistance remains controversial. To shed light on this debate, we tested six antibiotics on four Klebsiella pneumoniae species complex strains. Noncapsulated strains exhibited increased tolerance to polymyxins, but not to other anti...

Type VI secretion systems (T6SS), recently described in hypervirulent K. pneumoniae (hvKp) strains, are involved in bacterial warfare but their role in classical clinical strains (cKp) has been little investigated. In silico analysis indicated the presence of T6SS clusters (from zero to four), irrespective of the strains origin or virulence, with a...

Ecological causes of developmental evolution, for example from predation, remain much investigated, but the potential importance of latent phenotypes in eco-evo-devo has received little attention. Using the predatory bacterium Myxococcus xanthus, which undergoes aggregative fruiting body development upon starvation, we tested whether adaptation to...

The extracellular capsule is a major virulence factor, but its ubiquity in free-living bacteria with large environmental breadths suggests that it shapes adaptation to novel niches. Yet, how it does so, remains unexplored. Here, we evolve three Klebsiella strains and their capsule mutants in parallel. Their comparison reveals different phenotypic a...

Many bacterial species carry multiple phages, and despite the potential cost, which includes cell death upon phage induction, prophages can also provide the host multiple fitness advantages, including infection of direct competitors. However, the long-term efficiency of displacing conspecifics through prophage induction has received little attentio...

The extracellular capsule is a major virulence factor, but its ubiquity in free-living bacteria with large environmental breadths suggests that it shapes adaptation to novel niches. Yet, how it does so, remains unexplored. We evolved in parallel Klebsiella strains and their capsule mutants. Their comparison revealed different phenotypic and genoty...

While the major virulence factors for Vibrio cholerae, the cause of the devastating diarrheal disease cholera, have been extensively studied, the initial intestinal colonization of the bacterium is not well understood because non-human adult animals are refractory to its colonization. Recent studies suggest the involvement of an interbacterial kill...

Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that require a physical interaction with the cellular envelope. In the high-priority multi-drug-resistant nosocomial pathogens (ESKAPE), the first point of contact between the cell and virions or conjugative pili is the capsule. While the capsule can be a barri...

Ecological causes of developmental-system evolution, for example from predation, remain under intense investigation. An important open question is the role of latent phenotypes in eco-evo-devo. The predatory bacterium Myxococcus xanthus undergoes aggregative multicellular development upon starvation. Here we use M. xanthus to test whether evolution...

The fitness cost associated with the production of bacterial capsules is considered to be offset by the protection provided by these extracellular structures against biotic aggressions or abiotic stress. However, it is unknown if the capsule contributes to fitness in the absence of these. Here, we explored conditions favouring the maintenance of th...

Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that are affected by the cell envelope composition, notably the capsule. Here, we study the co-variation between the repertoire of capsule genes and MGEs in Klebsiella pneumoniae , a high-priority nosocomial enterobacteria. We show that capsules drive phage-med...

Background Evolution in one selective environment often latently generates phenotypic change that is manifested only later in different environments, but the complexity of behavior important to fitness in the original environment might influence the character of such latent-phenotype evolution. Using Myxococcus xanthus, a bacterium possessing two m...

The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish...

Klebsiella species are able to colonize a wide range of environments and include worrisome nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the...

Extracellular capsules protect the cell against both abiotic and biotic stresses such as bacteriophages and the host immune system. Yet, it is unclear if capsules contribute to fitness in the absence of external aggressions, in spite of the cost of production. Here, we enquire if there are conditions favouring the presence of the capsule in Klebsie...

The identification of commensal bacteria conferring resistance against pathogens is often hindered by the complexity of host microbial communities. We used germ-free, conventional and re-conventionalized zebrafish as a model to study the determinant of microbiota-associated colonization resistance against the fish pathogen Flavobacterium columnare....

Extracellular capsule polysaccharides increase the cellular fitness under abiotic stresses and during competition with other bacteria. They are best‐known for their role in virulence, particularly in human hosts. Specifically, capsules facilitate tissue invasion by enhancing bacterial evasion from phagocytosis and protect cells from biocidal molecu...

Klebsiella species are able to colonize a wide range of environments and include daunting nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the...

Capsules allow bacteria to colonize novel environments, to withstand numerous stresses, and to resist antibiotics. Yet, even though genetic exchanges with other cells should be adaptive under such circumstances, it has been suggested that capsules lower the rates of homologous recombination and horizontal gene transfer. We analysed over one hundred...

Species recombination in function of capsule and competence for natural transformation. A. Co-occurrence between the presence of capsule and competence system in our species database. Dashed line indicates the ratio of species encoding at least one capsule system in the database (51%). Pearson's χ2 test with Yates' continuity correction. N.S. = not...

Capsules encoded in plasmids. Distribution of capsules in the chromosome and plasmids. Dashed line indicates the average across the whole dataset (~4%). (DOCX)

Percentage of sequence similarity for the 5% percentile of the core genome. (DOCX)

Statistic details for rates of genetic exchange and genetic richness. We performed a logistic regression to control for genome size and other associated variables to the response trait. (DOCX)

Phylogenetic analysis of the distribution of MGEs and capsule systems. We estimated the phylogenetic inertia of the presence of capsules and MGE in genomes using Pagel’s λ included in the phytools package and a 16SrRNA phylogenetic tree. The null hypothesis (λ = 0, no inertia) was always rejected. (DOCX)

List of capsule systems found in prophages. (DOCX)

Gene exchange in bacterial species is higher in species coding for capsules as calculated with the rarefied sets (five randomly chosen genomes per species). A. Percentage of genes for which the null hypothesis of no homologous recombination was rejected by the PhiPack program as measured by the tests: CHI, PHI, and NSS * P < 0.05, GLM. B. Number of...

Co-occurrence between capsule systems and CRISPR-Cas systems. CRISPR-Cas were identified as described in [96]. N.S. = not significant, Pearson’s χ2 test. (DOCX)

Summary statistics of capsule systems detected in the database. A. Number of systems of each capsule type detected in the dataset of 5576 genomes. Numbers on top of bars indicate percentage of each capsule type. B. Distribution of genomes encoding a capsule (Cg+) in each bacterial species for which we dispose of more than 4 genomes. We discarded sp...

List of plasmids with capsule systems. (DOCX)

Controls for the analyses of recombination. (DOCX)

Cladogram of analysed bacterial species. The tree was built using the 16S rRNA sequences of 122 bacterial species. From the inside to the outside: squares indicate the presence (full) or absence (empty) of capsule systems in all genomes of each species; rectangles represent the core (orange) and pan-genome (red) size, the number of homologous recom...

Core genome size of species with (Csp+) and without capsule(Csp-). Core genome size is expressed as the number of gene families present in all genomes of a given species (N = 127, ** P < 0.01, logistic regression controlled by genome size, S1 Table). (DOCX)

Gene exchange in bacterial species calculated using only species with all genomes belonging to Csp- or Csp+. This resulted in a reduced dataset with 110 species, of which 59 were Csp- and 51 Csp+. A. Percentage of genes for which the null hypothesis of no homologous recombination was rejected by the PhiPack program as measured by the tests: CHI, PH...

Increased amount of foreign DNA in genomes coding for capsules. Cumulative size of all prophages (A) and plasmids (B) per genome, log10-scale. Statistical test corresponds to a logistic regression controlled by genome size *** P <0.001 (DOCX)

Phylogenetic inertia of gene transfer exchanges and capsule systems. We estimated the phylogenetic inertia of several genetic transfer measures using Pagel’s λ included in the phytools package and a 16SrRNA phylogenetic tree. The null hypothesis is λ = 0 (no phylogenetic effect). (DOCX)

Phylogenetic corrections for association between MGEs and capsule systems. To test for the co-occurrence of MGE and capsule in a genome, we used BayesTraitsv3 (see methods) to calculate the Bayes factor. Bayes Factors can be interpreted as follows: <2 weak evidence, >2 positive evidence, 5–10 strong evidence, and >10 very strong evidence. The lower...

Average number of mobile genetic elements per genome. Only genomes with at least one MGE were taken into account. P-values corresponds to the test of difference between the mean number of MGEs in Cg+ and in Cg- (all corrected for genome size and phylogeny, see S3 Table for details). (DOCX)

Controls for phylogenetic inertia. (DOCX)

Heatmap representing the correlations between the different measures of recombination used in this study. All correlations are statistically significant, P < 0.001. (DOCX)

Orthologous proteins and identity between the Salmonella enterica prophages. A. Number of orthologous proteins between the prophages in Salmonella bearing a capsule operon. Threshold for orthologous genes was set to 80% similarity. B. Identity (lower triangle) was calculated for the 59 proteins common to all prophages for all pairwise comparison us...

Raw data used in this study. A. Species data. This file corresponds to the data represented in Fig 1 and describes the average genome size, core and pan-genome sizes, recombination events and horizontal gene transfer events for each of the 127 species. The number of genomes, the percentage of capsulated genomes as well as their clade is indicated....

Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer‐membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer‐membrane pro...

In social organisms, cheaters that gain a fitness advantage by defecting from the costs of cooperation reduce the average level of cooperation in a population. Such cheating load can be severe enough to cause local extinction events when cooperation is necessary for survival, but can also mediate group-level selection against cheaters across spatia...

Extracellular capsules constitute the outermost layer of many bacteria, are major virulence factors, and affect antimicrobial therapies. They have been used as epidemiological markers and recently became vaccination targets. Despite the efforts to biochemically serotype capsules in a few model pathogens, little is known of their taxonomic and envir...

List of identified false positives and false negatives. (PDF)

Correlation between genome size and capsule complexity. The length of the capsule system (i.e. number of genes in the system) is used as a proxy for capsule complexity. Genome size was log10-transformed before analysis. We used Spearman’s rank association (rho) as a measure of correlation. (PDF)

Presence of selected pathogens in metagenomes. Numbers and color shading represent the percentage of metagenomes per sub-environment in which each species is present (from white to blue, 0 to 100% respectively). (PDF)

Genomes with more than five capsule systems detected. (PDF)

Statistics for the dependent evolution between pairs of capsule types. This was first calculated by the analysis of contingency tables of co-occurrence (using χ2). In complement, for each capsule pair, we made the analysis to account for phylogenetic dependence using the fitPagel function. We then computed the likelihood ratio and the corresponding...

Cumulative density of the number of genes (system length). The graph shows the cumulative density function of the number of genes of each capsule group. There are significant differences in the number of genes (system length) per capsule group and subgroup as measured by the test: Kruskal-Wallis, df = 7, P < 0.0001. The post hoc Tukey HSD was signi...

Correlation between capsule systems and life style traits. Cladogram based on the 16S rRNA sequence of species. For species with more than one sequenced genome in our database, the 16S rRNA sequence was randomly chosen. Squares on the outer part of the tree indicate, from inner circle to outer circle, whether species (i) have a capsule system, (ii)...

P-value distribution after application of phylogenetic controls. To test for the dependence between presence of capsule and bacterial lifestyle, the fitPagel function was performed on 100 trees obtained by bootstrap experiments on the multiple alignment. We plot the distribution of the corresponding P values (log-scale) in the graphs. Blue dashed l...

Distribution of bacterial species in our database in function of the type of ecological interaction with hosts (A) and type of host (B). NA indicates that information was lacking or ambiguous. (TIF)

List of HMM profiles used in this study. (PDF)

Environmental distribution and abundance of species in relation to the presence of capsule system in their genomes. A. Relative abundance of Csp+ and Csp- across environments. Y-axis is in log scale. Statistics reflect significant differences in the relative abundance between Csp+ and Csp-, non-parametric Wilcoxon test and Benjamini & Hochberg post...

Detection of false positives and false negatives. (PDF)

Results of the validation of our model. (PDF)

Number of times each capsule type co-occurs in a genome. The diagonal represents the number of genomes in which the same capsule group co-occurs. (PDF)

Details of the genomes used to generate the Enterobacteria core genome. (PDF)

Stepwise multiple regression. Results of the controls for other variables (Z) when building a linear model where presence or absence of the capsule is the dependent variable (Y) and the focal variable is the independent variable (X). The complete linear model is Y~X+Z. The analysis was done using a stepwise multiple regression (forward using the mi...

Summary of metagenomic data. (PDF)

Association between the presence of capsules and pathogenic traits. A. Frequency of Csp+ and Csp- in function of their growth class ** P < 0.01 for significant dependent evolution between growth class and presence of capsule. B. Average infection dose values (ID50) expressed in the log scale. C-D. Frequency of Csp+ and Csp- in function of the motil...

Distribution of distances between two capsule systems of the same group within a replicon. Log-scaled X-axis represents distance in kilobase pairs. (TIF)

Datasets used in this study: (i) list of prokaryotic genomes analysed, (ii) list of capsule systems identified, (iii) bacterial lifestyle, (iv) metagenomes analysed. (XLSX)

An atypically large outbreak of Elizabethkingia anophelis infections occurred in Wisconsin. Here we show that it was caused by a single strain with thirteen characteristic genomic regions. Strikingly, the outbreak isolates show an accelerated evolutionary rate and an aty-pical mutational spectrum. Six phylogenetic sub-clusters with distinctive temp...

Single nucleotide polymorphisms (SNP) observed among outbreak isolates

: BEAST input file using SNP data.

Outbreak isolates and comparative strains included in the study

Antimicrobial susceptibility values.

Supplementary Figures, Supplementary Tables, Supplementary Methods and Supplementary References.

Genomic features and annotations associated with the Wisconsin outbreak specific regions and deletion in 4 outbreak strains

Antimicrobial resistance features of the outbreak strain detected using ResFams

Virulence-associated features of the outbreak strain detected using the VFDB database.

SNP tree with node names.