Implications of bacterial viruses on pathogenic bacteria : from natural microbial communities to therapeutic applications

Bacterial viruses (i.e. phages) are ubiquitous intracellular parasites of bacteria, that along with protist grazers account for majority of bacterial mortality in nature. Phages impose strong selection for bacterial phage-resistance, which is often coupled with fitness costs on bacterial traits such as growth ability, virulence or motility. Traditionally phage-host interactions have been studied with two species systems in the laboratory, neglecting the complex web of interactions present in natural communities. The ability of phages to selectively kill bacteria has ignited an interest on phages as alternative antibacterials. However, in order to develop phage therapy, understanding of phage-host interactions in the eco-evolutionary context is essential. In this thesis I studied the implications of lytic phages on opportunistic pathogenic bacteria, as opportunists often have the ability reproduce and reside in outside-host environments, where they are predisposed to a variety of selection pressures. The role of phages in top-down control of bacterial biomass and the evolution of bacterial phage-resistance were studied in the presence of protist predators with differing feeding modes, in low-resource systems mimicking natural pond environment. Hypothesis of coincidental evolution suggests that virulence is a by-product of selection for traits that maximize bacterial fitness in environmental reservoirs. Yet, disease outbreaks by opportunists are relatively rare, suggesting that something constrains the selection for virulence. To assess the role of lytic phages on the evolution of virulence, bacteria were cultured in low-resource environment, accompanied with changes in temperature regime or changes in composition of the community of interacting bacterial enemy species, and the virulence of bacteria was measured in vivo. To study whether the potential phage-resistant bacteria surviving phage therapy would be coupled with lowered virulence, due to costs associated with phage-resistance, a clinical bacterial isolate was exposed to phage cocktails and the virulence of the phage-resistant bacteria was measured in vivo. given the strong selection for phage- resistance, the prospects of phage therapy depend a great deal on whether new phages infecting pathogenic bacteria can be readily isolated from environment. To address this, an attempt was made to isolate phages against clinical bacterial isolates harboring resistance genes to multiple antibiotics. A single lytic phage was shown to be a non- efficient top-down regulator of bacterial biomass. Rapidly emerging phage-resistant bacteria took over the bacterial populations after initial lysis by phages and protist grazers accounted for most of the long-term negative trophic effects on bacterial biomass. The presence of protist predators selected for bacteria that were less susceptible to infection by lytic phages, which suggests an overlap in the bacterial defense against a parasite and predatory protists. In general, the presence of lytic phages selected for lowered virulence in bacteria. High temperature selected for more virulent and more motile bacteria, but this was constrained by the presence of a lytic phage. In the multispecies communities the presence of all bacterial enemies led to decreased virulence in vivo. Altogether, these results contrast the hypothesis of coincidental evolution, and suggest that the presence of phages in natural reservoirs constrains the evolution of virulence, most likely through fitness costs associated with phage-resistance. Exposure to phage cocktails was also shown to be associated with decreased bacterial virulence in the phage-resistant bacteria. However, exposure to some individual phages resulted in more virulent bacteria, suggesting that the outcome of therapy could depend on the identity of the phage cocktail. Finally, a phage cocktail lysing a wide range of clinical strains was isolated from sewage. This, along with geographical patterns of phage infections suggest that new phages are available in environmental reservoirs for therapy, and the emergence of phage-resistance should not hinder the prospects of phage therapy in the global perspective.Bakteerivirukset (faagit) ovat bakteerien solunsisäisiä loisia, jotka yhdessä alkueliösaalistajien kanssa aiheuttavat suurimman osan bakteerien kuolleisuudesta luonnossa. Faagit luovat voimakkaan valintapaineen faagivastustuskyvylle ja vastustuskyvystä seuraa usein kustannus esimerkiksi bakteerin kasvu-, taudinaiheuttamis- tai liikkumiskyvylle. Perinteisesti faagin ja isännän välisiä vuorovaikutuksia on tutkittu kahden lajin kokeissa laboratoriossa, mutta lähestymistapa jättää huomiotta luonnollisissa yhteisöissä vallitsevien vuorovaikutusten kirjon. Koska faagit tappavat kohdennetusti tiettyjä bakteereita, on ehdotettu, että faageja voitaisiin käyttää antibiootteina. Faagiterapian kehittäminen vaatii kuitenkin faagi-isäntä vuorovaikutusten tuntemusta niin ekologisesta kuin evolutiivisestakin näkökulmasta. Tässä väitöskirjassa olen tutkinut lyyttisten bakteerivirusten vaikutuksia opportunistisiin taudinaiheuttajabakteereihin. Osa opportunistisista bakteereista kykenee elämään ja lisääntymään isäntänsä ulkopuolisissa ympäristöissä, missä ne altistuvat lukuisille erilaisille valintapaineille. Tutkin faagien merkitystä bakteeribiomassan vähentäjinä, sekä bakteerien faagivastustuskyvyn evoluutiota matalaravinteisissa lampea muistuttavassa ympäristössä, joissa oli faagien lisäksi läsnä ravinnonhankintatavoiltaan toisistaan poikkeavia alkueliöitä. Sattumanvaraisen evoluution hypoteesin (coincidental evolution hypothesis) mukaan taudinaiheuttamiskyky on seurausta sellaisiin elinkiertopiirteisiin kohdistuvasta valinnasta, jotka parantavat kelpoisuutta isännän ulkopuolisissa ympäristöissä. Opportunistien aiheuttamat tautiepidemiat ovat kuitenkin verraten harvinaisia, mikä viittaa siihen että jokin tekijä ympäristössä toimii vastavoimana taudinaiheuttamiskykyyn kohdistuvalle valinnalle. Faagien vaikutuksia opportunistibakteerien taudinaiheuttamiskyvyn evoluutioon tutkittiin niinikään matalaravinteisessa ympäristössä, joissa vaihtelevina ympäristötekijöinä olivat joko lämpötila tai bakteereja ravinnokseen käyttävien vihollisten eri yhdistelmät. Kokeiden päätteeksi taudinaiheuttamiskyky mitattiin hyönteisissä. Kliinistä taudinaiheuttajabakteerikantaa altistettiin faagi-koktaileille (phage cocktails) kokeessa, jonka tarkoituksena oli selvittää onko faageille vastustuskykyisten bakteerin taudinaiheuttamiskyky alentunut faagipuolustuksen aiheuttamien kustannusten seurauksena, ja mahdolliset muutokset taudinaiheuttamiskyvyssä mitattiin hyönteisissä. Faagivastustuskykyyn kohdistuvan voimakkaan valintapaineen huomioonottaen faagiterapian onnistumisen kannalta on merkittävää, voidaanko uusia faageja tarvittaessa eristää ympäristöstä. Tavoitteeksi asetettiin eristää uusia faageja, jotka estävät kliinisten antibiooteille vastustuskykyisten bakteereiden kasvua. Yksittäinen faagityyppi osoittautui tehottomaksi säätelemään bakteeribiomassan määrää pitkällä aikavälillä ja faageille vastustuskykyiset bakteerit palauttivat populaatiot nopeasti lähes kontrollitasolle. Alkueläimet näin ollen vastasivat pitkällä aikavälillä käytännössä kaikesta bakteeribiomassan vähentymisestä. Alkueliöt vaikuttivat myös bakteerien faagivastustuskyvyn evoluutioon: alkueliöille altistuneet bakteerit olivat vähemmän alttiita faagi-infektioille. Korkea lämpötila johti taudinaiheuttamiskykyvyn nousuun bakteereissa, mutta ilmiö kumoutui faagien vaikutuksesta. Monilajisissa yhteisöissä kaikkien bakteeripetojen läsnäolo taas alensi bakteerien taudinaiheuttamiskykyä. Nämä tulokset puhuvat sattumanvaraisen evoluution hypoteesia vastaan ja faagit näyttäisivät sen sijaan luovan valintapaineen vähemmän taudinaiheuttamiskykyisille bakteereille. Myös faagikoktailit aiheuttivat taudinaiheuttamiskyvyn laskua bakteereissa. Jotkut yksittäiset virukset näyttivät kuitenkin nostavan bakteerien taudinaiheuttamiskykyä vastustuskykyisissä bakteereissa, minkä vuoksi tuleekin noudattaa erityistä varovaisuutta valittaessa faageja koktaileihin ja faagiterapiaan. Jätevedestä onnistuttiin eristämään kokoelma faageja, jotka estivät kasvua laajassa joukossa kliinisiä antibiooteille vastustuskykyisiä bakteerikantoja. Tämä tulos yhdessä faagi-infektioiden maantiedettä koskevien havaintojen kanssa antaa olettaa, että uusia faageja on eristettävissä ympäristövarannoista ja että laaja-alaisen faagivastustuskyvyn syntyminen ei ole este faagiterapian kehittämiselle tulevaisuudessa

Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases

Peer reviewe

Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages

Background: Consumer-resource interactions constitute one of the most common types of interspecific antagonistic interaction. In natural communities, complex species interactions are likely to affect the outcomes of reciprocal co-evolution between consumers and their resource species. Individuals face multiple enemies simultaneously, and consequently they need to adapt to several different types of enemy pressures. In this study, we assessed how protist predation affects the susceptibility of bacterial populations to infection by viral parasites, and whether there is an associated cost of defence on the competitive ability of the bacteria. As a study system we used Serratia marcescens and its lytic bacteriophage, along with two bacteriovorous protists with distinct feeding modes: Tetrahymena thermophila (particle feeder) and Acanthamoeba castellanii (surface feeder). The results were further confirmed with another study system with Pseudomonas and Tetrahymena thermophila. Results: We found that selection by protist predators lowered the susceptibility to infections by lytic phages in Serratia and Pseudomonas. In Serratia, concurrent selection by phages and protists led to lowered susceptibility to phage infections and this effect was independent from whether the bacteria shared a co-evolutionary history with the phage population or not. Bacteria that had evolved with phages were overall more susceptible to phage infection (compared to bacteria with history with multiple enemies) but they were less vulnerable to the phages they had co-evolved with than ancestral phages. Selection by bacterial enemies was costly in general and was seen as a lowered fitness in absence of phages, measured as a biomass yield. Conclusions: Our results show the significance of multiple species interactions on pairwise consumer-resource interaction, and suggest potential overlap in defending against predatory and parasitic enemies in microbial consumer-resource communities. Ultimately, our results could have larger scale effects on eco-evolutionary community dynamics.Peer reviewe

Data from: Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases

Lytic bacteriophages and protozoan predators are the major causes of bacterial mortality in natural microbial communities, which also makes them potential candidates for biological control of bacterial pathogens. However, little is known about the relative impact of bacteriophages and protozoa on the dynamics of bacterial biomass in aqueous and biofilm phases. Here, we studied the temporal and spatial dynamics of bacterial biomass in a microcosm experiment where opportunistic pathogenic bacteria Serratia marcescens was exposed to particle-feeding ciliates, surface-feeding amoebas, and lytic bacteriophages for 8 weeks, ca. 1300 generations. We found that ciliates were the most efficient enemy type in reducing bacterial biomass in the open water, but least efficient in reducing the biofilm biomass. Biofilm was rather resistant against bacterivores, but amoebae had a significant long-term negative effect on bacterial biomass both in the open-water phase and biofilm. Bacteriophages had only a minor long-term effect on bacterial biomass in open-water and biofilm phases. However, separate short-term experiments with the ancestral bacteriophages and bacteria revealed that bacteriophages crash the bacterial biomass dramatically in the open-water phase within the first 24 h. Thereafter, the bacteria evolve phage-resistance that largely prevents top-down effects. The combination of all three enemy types was most effective in reducing biofilm biomass, whereas in the open-water phase the ciliates dominated the trophic effects. Our results highlight the importance of enemy feeding mode on determining the spatial distribution and abundance of bacterial biomass. Moreover, the enemy type can be crucially important predictor of whether the rapid defense evolution can significantly affect top-down regulation of bacteria

Biomass dynamics in free water and biofilm

Biomass dynamics in free water and biofil

Systematic Comparison of Epidemic and Non-Epidemic Carbapenem Resistant Klebsiella pneumoniae Strains

Over the past few decades, extensively drug resistant (XDR) resistant Klebsiella pneumoniae has become a notable burden to healthcare all over the world. Especially carbapenemase-producing strains are problematic due to their capability to withstand even last resort antibiotics. Some sequence types (STs) of K. pneumoniae are significantly more prevalent in hospital settings in comparison to other equally resistant strains. This provokes the question whether or not there are phenotypic characteristics that may render certain K. pneumoniae more suitable for epidemic dispersal between patients, hospitals, and different environments. In this study, we selected seven epidemic and non-epidemic carbapenem resistant K. pneumoniae isolates for extensive systematic characterization for phenotypic and genotypic qualities in order to identify potential factors that precede or emerge from epidemic successfulness. Studied characteristics include growth rates and densities in different conditions (media, temperature, pH, resource levels), tolerance to alcohol and drought, inhibition between strains, ability to compensate pH, as well as various genomic features. Overall, there are clear differences between isolates, yet, only drought tolerance was found to notably associate with non-epidemic K. pneumoniae strains. We further report a preliminary study on the potential to control K. pneumoniae ST11 with an antimicrobial component produced by a non-epidemic K. pneumoniae. This component initially restricts bacterial growth, but stable resistance develops rapidly in vitro.peerReviewe

Eigenvectors describing dimensions of multivariate evolution under different kind of enemies (loadings, i.e. correlations, of original variables to new composite variable, based on MANOVA.

<p>Eigenvectors describing dimensions of multivariate evolution under different kind of enemies (loadings, i.e. correlations, of original variables to new composite variable, based on MANOVA.</p

Growth rate (panel A), yield (panel B) and biofilm forming ability (panel C) differences between ancestral clones and clones that have evolved alone (B) or in different combinations of bacterial enemies.

<p>Anc.: ancestral bacterial strain DB 11; B: bacteria; A: amoebae; C: ciliate; P: phage. Letters indicate if treatment means are considered statistically similar (p>0.05) after Bonferroni correction for multiple comparisons. Tests are based on the post hoc comparisons of estimated marginal means for treatments of ANOVA testing the effects of treatment and population identity on these traits. Bars correspond to measurements of 6 clones from 8 replicate populations, in ancestor n = 16).</p

Growth rate with amoebae (panel A), yield with amoebae (panel B) and yield with ciliate (panel C) differences between ancestral clones and clones that have evolved alone or in different combinations of bacterial enemies.

<p>Anc.: ancestral bacterial strain DB 11; B: bacteria; A: amoebae; C: ciliate; P: phage. Letters indicate if treatment means are considered statistically similar after Bonferroni correction for multiple comparisons. Tests are based on the post hoc comparisons of estimated marginal means for treatments of ANOVA testing the effects of treatment and population identity on these traits. Bars correspond to measurements of 6 clones from 8 replicate populations, in ancestor n = 16).</p