The blp Locus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx

Genomic Sequence of Streptococcus salivarius MDI13 and Latilactobacillus sakei MEI5: Two Promising Probiotic Strains Isolated from European Hakes (Merluccius merluccius, L.)

Frequently, diseases in aquaculture have been fought indiscriminately with the use of antibiotics, which has led to the development and dissemination of (multiple) antibiotic resistances in bacteria. Consequently, it is necessary to look for alternative and complementary approaches to chemotheraphy that are safe for humans, animals, and the environment, such as the use of probiotics in fish farming. The objective of this work was the Whole-Genome Sequencing (WGS) and bioinformatic and functional analyses of S. salivarius MDI13 and L. sakei MEI5, two LAB strains isolated from the gut of commercial European hakes (M. merluccius, L.) caught in the Northeast Atlantic Ocean. The WGS and bioinformatic and functional analyses confirmed the lack of transferable antibiotic resistance genes, the lack of virulence and pathogenicity issues, and their potentially probiotic characteristics. Specifically, genes involved in adhesion and aggregation, vitamin biosynthesis, and amino acid metabolism were detected in both strains. In addition, genes related to lactic acid production, active metabolism, and/or adaptation to stress and adverse conditions in the host gastrointestinal tract were detected in L. sakei MEI5. Moreover, a gene cluster encoding three bacteriocins (SlvV, BlpK, and BlpE) was identified in the genome of S. salivarius MDI13. The in vitro-synthesized bacteriocin BlpK showed antimicrobial activity against the ichthyopathogens Lc. garvieae and S. parauberis. Altogether, our results suggest that S. salivarius MDI13 and L. sakei MEI5 have a strong potential as probiotics to prevent fish diseases in aquaculture as an appropriate alternative/complementary strategy to the use of antibiotics.

BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection

Successful colonization of a host requires bacterial adaptation through genetic and population changes that are incompletely defined. Using chromosomal barcoding and high-throughput sequencing, we investigate the population dynamics of Streptococcus pneumoniae during infant mouse colonization. Within 1 day post inoculation, diversity was reduced >35-fold with expansion of a single clonal lineage. This loss of diversity was not due to immune factors, microbiota, or exclusive genetic drift. Rather, bacteriocins induced by the BlpC-quorum sensing pheromone resulted in predation of kin cells. In this intra-strain competition, the subpopulation reaching a quorum likely eliminates others that have yet to activate the blp locus. Additionally, this reduced diversity restricts the number of unique clones that establish colonization during transmission between hosts. Genetic variation in the blp locus was also associated with altered transmissibility in a human population, further underscoring the importance of BlpC in clonal selection and its role as a selfish element.

Epidemiological dynamics of bacteriocin competition and antibiotic resistance

Bacteriocins, toxic peptides involved in the competition between bacterial strains, are extremely diverse. Previous work on bacteriocin dynamics has highlighted the role of non-transitive 'rock-paper-scissors' competition in maintaining the coexistence of different bacteriocin profiles. The focus to date has primarily been on bacteriocin interactions at the within-host scale (i.e. within a single bacterial population). Yet in species such as Streptococcus pneumoniae, with relatively short periods of colonization and limited within-host diversity, ecological outcomes are also shaped by processes at the epidemiological (between-host) scale. Here, we first investigate bacteriocin dynamics and diversity in epidemiological models. We find that in these models, bacteriocin diversity is more readily maintained than in within-host models, and with more possible combinations of coexisting bacteriocin profiles. Indeed, maintenance of diversity in epidemiological models does not require rock-paper-scissors dynamics; it can also occur through a competition-colonization trade-off. Second, we investigate the link between bacteriocin diversity and diversity at antibiotic resistance loci. Previous work has proposed that bacterial duration of colonization modulates the fitness of antibiotic resistance. Due to their inhibitory effects, bacteriocins are a plausible candidate for playing a role in the duration of colonization episodes. We extend the epidemiological model of bacteriocin dynamics to incorporate an antibiotic resistance locus and demonstrate that bacteriocin diversity can indeed maintain the coexistence of antibiotic-sensitive and -resistant strains.

Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms

Streptococcus pneumoniae (the 'pneumococcus') is a significant cause of morbidity and mortality worldwide, causing life-threatening diseases such as pneumonia, bacteraemia, and meningitis, with an annual death burden of over one million. Discovered over a century ago, pneumococcal serotype 1 (S1) is a significant cause of these life-threatening diseases. Our understanding of the epidemiology and biology of pneumococcal S1 has significantly improved over the past two decades, informing the development of preventative and surveillance strategies. However, many questions remain unanswered. Here, we review the current state of knowledge of pneumococcal S1, with a special emphasis on clinical epidemiology, genomics, and disease mechanisms.

Gene Expression Regulation in Airway Pathogens: Importance for Otitis Media

Otitis media (OM) is an inflammatory disorder in the middle ear. It is mainly caused by viruses or bacteria associated with the airways. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are the three main pathogens in infection-related OM, especially in younger children. In this review, we will focus upon the multifaceted gene regulation mechanisms that are well-orchestrated in S. pneumoniae, H. influenzae, and M. catarrhalis during the course of infection in the middle ear either in experimental OM or in clinical settings. The sophisticated findings from the past 10 years on how the othopathogens govern their virulence phenotypes for survival and host adaptation via phase variation- and quorum sensing-dependent gene regulation, will be systematically discussed. Comprehensive understanding of gene expression regulation mechanisms employed by pathogens during the onset of OM may provide new insights for the design of a new generation of antimicrobial agents in the fight against bacterial pathogens while combating the serious emergence of antimicrobial resistance.

Intra-Species Interactions in Streptococcus pneumoniae Biofilms

Streptococcus pneumoniae is a human pathogen responsible for high morbidity and mortality worldwide. Disease is incidental and is preceded by asymptomatic nasopharyngeal colonization in the form of biofilms. Simultaneous colonization by multiple pneumococcal strains is frequent but remains poorly characterized. Previous studies, using mostly laboratory strains, showed that pneumococcal strains can reciprocally affect each other's colonization ability. Here, we aimed at developing a strategy to investigate pneumococcal intra-species interactions occurring in biofilms. A 72h abiotic biofilm model mimicking long-term colonization was applied to study eight pneumococcal strains encompassing 6 capsular types and 7 multilocus sequence types. Strains were labeled with GFP or RFP, generating two fluorescent variants for each. Intra-species interactions were evaluated in dual-strain biofilms (1:1 ratio) using flow cytometry. Confocal microscopy was used to image representative biofilms. Twenty-eight dual-strain combinations were tested. Interactions of commensalism, competition, amensalism and neutralism were identified. The outcome of an interaction was independent of the capsular and sequence type of the strains involved. Confocal imaging of biofilms confirmed the positive, negative and neutral effects that pneumococci can exert on each other. In conclusion, we developed an experimental approach that successfully discriminates pneumococcal strains growing in mixed biofilms, which enables the identification of intra-species interactions. Several types of interactions occur among pneumococci. These observations are a starting point to study the mechanisms underlying those interactions.

Bacteriocin Production by Beta-Hemolytic Streptococci

Beta-hemolytic streptococci cause a variety of infectious diseases associated with high morbidity and mortality. A key factor for successful infection is host colonization, which can be difficult in a multispecies environment. Secreting bacteriocins can be beneficial during this process. Bacteriocins are small, ribosomally produced, antimicrobial peptides produced by bacteria to inhibit the growth of other, typically closely related, bacteria. In this systematic review, bacteriocin production and regulation of beta-hemolytic streptococci was surveyed. While Streptococcus pyogenes produces eight different bacteriocins (Streptococcin A-FF22/A-M49, Streptin, Salivaricin A, SpbMN, Blp1, Blp2, Streptococcin A-M57), only one bacteriocin of Streptococcus agalactiae (Agalacticin = Nisin P) and one of Streptococcus dysgalactiae subsp. equisimilis (Dysgalacticin) has been described. Expression of class I bacteriocins is regulated by a two-component system, typically with autoinduction by the bacteriocin itself. In contrast, a separate quorum sensing system regulates expression of class II bacteriocins. Both identified class III bacteriocins are plasmid-encoded and regulation has not been elucidated.

Eavesdropping and crosstalk between secreted quorum sensing peptide signals that regulate bacteriocin production in Streptococcus pneumoniae

Quorum sensing (QS), where bacteria secrete and respond to chemical signals to coordinate population-wide behaviors, has revealed that bacteria are highly social. Here, we investigate how diversity in QS signals and receptors can modify social interactions controlled by the QS system regulating bacteriocin secretion in Streptococcus pneumoniae, encoded by the blp operon (bacteriocin-like peptide). Analysis of 4096 pneumococcal genomes detected nine blp QS signals (BlpC) and five QS receptor groups (BlpH). Imperfect concordance between signals and receptors suggested widespread social interactions between cells, specifically eavesdropping (where cells respond to signals that they do not produce) and crosstalk (where cells produce signals that non-clones detect). This was confirmed in vitro by measuring the response of reporter strains containing six different blp QS receptors to cognate and non-cognate peptides. Assays between pneumococcal colonies grown adjacent to one another provided further evidence that crosstalk and eavesdropping occur at endogenous levels of signal secretion. Finally, simulations of QS strains producing bacteriocins revealed that eavesdropping can be evolutionarily beneficial even when the affinity for non-cognate signals is very weak. Our results highlight that social interactions can mediate intraspecific competition among bacteria and reveal that competitive interactions can be modified by polymorphic QS systems.

Competitive Dominance within Biofilm Consortia Regulates the Relative Distribution of Pneumococcal Nasopharyngeal Density

Streptococcus pneumoniae is a main cause of child mortality worldwide, but strains also asymptomatically colonize the upper airways of most children and form biofilms. Recent studies have demonstrated that ∼50% of colonized children carry at least two different serotypes (i.e., strains) in the nasopharynx; however, studies of how strains coexist are limited. In this work, we investigated the physiological, genetic, and ecological requirements for the relative distribution of densities, and spatial localization, of pneumococcal strains within biofilm consortia. Biofilm consortia were prepared with vaccine type strains (i.e., serotype 6B [S6B], S19F, or S23F) and strain TIGR4 (S4). Experiments first revealed that the relative densities of S6B and S23F were similar in biofilm consortia. The density of S19F strains, however, was reduced to ∼10% in biofilm consortia, including either S6B, S23F, or TIGR4, in comparison to S19F monostrain biofilms. Reduction of S19F density within biofilm consortia was also observed in a simulated nasopharyngeal environment. Reduction of relative density was not related to growth rates, since the Malthusian parameter demonstrated similar rates of change of density for most strains. To investigate whether quorum sensing (QS) regulates relative densities in biofilm consortia, two different mutants were prepared: a TIGR4ΔluxS mutant and a TIGR4ΔcomC mutant. The density of S19F strains, however, was similarly reduced when consortia included TIGR4, TIGR4ΔluxS, or TIGR4ΔcomC Moreover, production of a different competence-stimulating peptide (CSP), CSP1 or CSP2, was not a factor that affected dominance. Finally, a mathematical model, confocal experiments, and experiments using Transwell devices demonstrated physical contact-mediated control of pneumococcal density within biofilm consortia.IMPORTANCEStreptococcus pneumoniae kills nearly half a million children every year, but it also produces nasopharyngeal biofilm consortia in a proportion of asymptomatic children, and these biofilms often contain two strains (i.e., serotypes). In our study, we investigated how strains coexist within pneumococcal consortia produced by vaccine serotypes S4, S6B, S19F, and S23F. Whereas S6B and S23F shared the biofilm consortium, our studies demonstrated reduction of the relative density of S19F strains, to ∼10% of what it would otherwise be if alone, in consortial biofilms formed with S4, S6B, or S23F. This dominance was not related to increased fitness when competing for nutrients, nor was it regulated by quorum-sensing LuxS/AI-2 or Com systems. It was demonstrated, however, to be enhanced by physical contact rather than by a product(s) secreted into the supernatant, as would naturally occur in the semidry nasopharyngeal environment. Competitive interactions within pneumococcal biofilm consortia regulate nasopharyngeal density, a risk factor for pneumococcal disease.

Interbacterial predation as a strategy for DNA acquisition in naturally competent bacteria

Natural competence enables bacteria to take up exogenous DNA. The evolutionary function of natural competence remains controversial, as imported DNA can act as a source of substrates or can be integrated into the genome. Exogenous homologous DNA can also be used for genome repair. In this Opinion article, we propose that predation of non-related neighbouring bacteria coupled with competence regulation might function as an active strategy for DNA acquisition. Competence-dependent kin-discriminated killing has been observed in the unrelated bacteria Vibrio cholerae and Streptococcus pneumoniae. Importantly, both the regulatory networks and the mode of action of neighbour predation differ between these organisms, with V. cholerae using a type VI secretion system and S. pneumoniae secreting bacteriocins. We argue that the forced release of DNA from killed bacteria and the transfer of non-clonal genetic material have important roles in bacterial evolution.