Evolution & adaptation in pathogenicity

“Nothing in biology makes sense except in the light of evolution” (T.Dobzhansky)

The host-pathogen interaction is no exception from this rule: while the pathogens adapt to the specific stresses and requirements inside their hosts, the hosts themselves are selected for best defense against damage done by these microorganisms. This evolutionary battle led to many astonishingly specific adaptations, from optimized nutrient uptake systems to our adaptive immunity.

We are interested in the mechanisms responsible for the adaptation of Candida albicans and C. glabrata, the two most important opportunistic pathogens among the Candida species, during the infection process. It is known for both species that they exhibit phenotypic and genotypic plasticity and can therefore react to changing environments by generating new phenotypes. For example, microevolution has clearly been demonstrated for the acquisition of high levels of antifungal drug resistance. In our laboratory, we used serial passage experiments to monitor the in vitro adaptation of fungi to macrophages, the “big eaters” of the immune system. We used two models: a wild type strain of C. glabrata and a hyphal-deficient C. albicans strain, which cannot escape from macrophages (as C. albicans normally does). In both cases we observed a striking change in the morphology of the strains after a series of co-culture passages. Usually, both strains grow as single cells, but during the microevolution experiment this growth form switched to a more filamentous form. Interestingly, the ability to form filaments is a well characterized virulence trait in wild type C. albicans, which was recreated here. We characterized the evolved strains in more detail using in vitro and in vivo experiments to investigate the impact of this phenotypic alteration on the pathogenicity of the strains. To determine the underlying genetic mechanisms, which cause the phenotypic alterations, we used different molecular techniques like microarrays, DNA and RNA sequencing. An in vivo adaptation experiment of C. albicans to the specific environment in the kidney complements our investigations into the adaptability of pathogenic yeasts in the host.

Basic laboratory evolution scheme -- the fungus is exposed to immune cells for 24 h, then re-isolated and confronted with fresh immune cells. This cycle is continued for months until the Candida species adapts to the immune cells. — Basic laboratory evolution scheme -- the fungus is exposed to immune cells for 24 h, then re-isolated and confronted with fresh immune cells. This cycle is continued for months until the *Candida* species adapts to the immune cells.

Result of an evolution experiment -- the mutant efg1∆/cph1∆ cannot form hyphae any more and is stuck in macrophages. After continuous co-incubation, hyphae formation re-appears and allows the mutant to kill the host cell like the non-mutated strain. Top, overall morphology of microcolonies; bottom, single cell morphologies. — Result of an evolution experiment -- the mutant *efg1*∆/*cph1*∆ cannot form hyphae any more and is stuck in macrophages. After continuous co-incubation, hyphae formation re-appears and allows the mutant to kill the host cell like the non-mutated strain. Top, overall morphology of microcolonies; bottom, single cell morphologies.

Publications

Arastehfar A, Boekhout T, Butler G, De Cesare GB, Dolk E, Gabaldón T, Hafez A, Hube B, Hagen F, Hovhannisyan H, Iracane E, Kostrzewa M, Lackner M, Lass-Flörl C, Llorens C, Mixão V, Munro C, Oliveira-Pacheco J, Pekmezovic M, Pérez-Hansen A, Sanchez AR, Sauer FM, Sparbier K, Stavrou AA, Vaneechoutte M, Vatanshenassan M (2019) Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 43(5), 517-547. Details PubMed

Bacher P, Hohnstein T, Beerbaum E, Röcker M, Blango MG, Kaufmann S, Röhmel J, Eschenhagen P, Grehn C, Seidel K, Rickerts V, Lozza L, Stervbo U, Nienen M, Babel N, Milleck J, Assenmacher M, Cornely OA, Ziegler M, Wisplinghoff H, Heine G, Worm M, Siegmund B, Maul J, Creutz P, Tabeling C, Ruwwe-Glösenkamp C, Sander LE, Knosalla C, Brunke S, Hube B, Kniemeyer O, Brakhage AA, Schwarz C, Scheffold A (2019) Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. Cell 176(6), 1340-1355.e15. Details PubMed

Domínguez-Andrés J, Novakovic B, Li Y, Scicluna BP, Gresnigt MS, Arts RJW, Oosting M, Moorlag SJCFM, Groh LA, Zwaag J, Koch RM, Ter Horst R, Joosten LAB, Wijmenga C, Michelucci A, van der Poll T, Kox M, Pickkers P, Kumar V, Stunnenberg H, Netea MG (2019) The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity. Cell Metab [Accepted] Details PubMed

Drummond RA, Swamydas M, Oikonomou V, Zhai B, Dambuza IM, Schaefer BC, Bohrer AC, Mayer-Barber KD, Lira SA, Iwakura Y, Filler SG, Brown GD, Hube B, Naglik JR, Hohl TM, Lionakis MS (2019) CARD9+ microglia promote antifungal immunity via IL-1β- and CXCL1-mediated neutrophil recruitment. Nat Immunol 20(5), 559-570. Details PubMed

Fischer D, Gessner G, Fill TP, Barnett R, Tron K, Dornblut K, Kloss F, Stallforth P, Hube B, Heinemann SH, Hertweck C, Scherlach K, Brunke S (2019) Disruption of membrane integrity by the bacteria-derived antifungal jagaricin. Antimicrob Agents Chemother 63(9), pii: e00707-19. Details PubMed

Gimeno-Valiente F, Riffo-Campos ÁL, Vallet-Sánchez A, Siscar-Lewin S, Gambardella V, Tarazona N, Cervantes A, Franco L, Castillo J, López-Rodas G (2019) ZNF518B gene up-regulation promotes dissemination of tumour cells and is governed by epigenetic mechanisms in colorectal cancer. Sci Rep 9(1), 9339. Details PubMed

Grondman I, Arts RJW, Koch RM, Leijte GP, Gerretsen J, Bruse N, Kempkes RWM, Ter Horst R, Kox M, Pickkers P, Netea MG, Gresnigt MS (2019) Frontline Science: Endotoxin-induced immunotolerance is associated with loss of monocyte metabolic plasticity and reduction of oxidative burst. J Leukoc Biol [Accepted] Details PubMed

Ho J, Yang X, Nikou SA, Kichik N, Donkin A, Ponde NO, Richardson JP, Gratacap RL, Archambault LS, Zwirner CP, Murciano C, Henley-Smith R, Thavaraj S, Tynan CJ, Gaffen SL, Hube B, Wheeler RT, Moyes DL, Naglik JR (2019) Candidalysin activates innate epithelial immune responses via epidermal growth factor receptor. Nat Commun 10(1), 2297. Details PubMed

Ikonomova SP, Moghaddam-Taaheri P, Wang Y, Doolin MT, Stroka KM, Hube B, Karlsson AJ (2019) Effects of histatin 5 modifications on antifungal activity and kinetics of proteolysis. Protein Sci , Details PubMed

Ishchuk OP, Ahmad KM, Koruza K, Bojanovič K, Sprenger M, Kasper L, Brunke S, Hube B, Säll T, Hellmark T, Gullstrand B, Brion C, Freel K, Schacherer J, Regenberg B, Knecht W, Piškur J (2019) RNAi as a Tool to Study Virulence in the Pathogenic Yeast Candida glabrata. Front Microbiol 10, 1679. Details PubMed

Jaeger M, Matzaraki V, Aguirre-Gamboa R, Gresnigt MS, Chu X, Johnson MD, Oosting M, Smeekens SP, Withoff S, Jonkers I, Perfect JR, van de Veerdonk FL, Kullberg BJ, Joosten LAB, Li Y, Wijmenga C, Netea MG, Kumar V (2019) A Genome-Wide Functional Genomics Approach Identifies Susceptibility Pathways to Fungal Bloodstream Infection in Humans. J Infect Dis [Accepted] Details PubMed

Jaeger M, Pinelli M, Borghi M, Constantini C, Dindo M, van Emst L, Puccetti M, Pariano M, Ricaño-Ponce I, Büll C, Gresnigt MS, Wang X, Gutierrez Achury J, Jacobs CWM, Xu N, Oosting M, Arts P, Joosten LAB, van de Veerdonk FL, Veltman JA, Ten Oever J, Kullberg BJ, Feng M, Adema GJ, Wijmenga C, Kumar V, Sobel J, Gilissen C, Romani L, Netea MG (2019) A systems genomics approach identifies SIGLEC15 as a susceptibility factor in recurrent vulvovaginal candidiasis. Sci Transl Med [Accepted] Details PubMed

Naglik JR, Gaffen SL, Hube B (2019) Candidalysin: discovery and function in Candida albicans infections. Curr Opin Microbiol 52, 100-109. Details PubMed

Pekmezovic M, Mogavero S, Naglik JR, Hube B (2019) Host-Pathogen Interactions during Female Genital Tract Infections. Trends Microbiol , pii: S0966-842X(19)30190-8. (Review) Details PubMed

Siscar-Lewin S, Hube B, Brunke S (2019) Antivirulence and avirulence genes in human pathogenic fungi. Virulence 10(1), 935-947. Details PubMed

Swidergall M, Khalaji M, Solis N, Moyes D, Drummond R, Hube B, Lionakis M, Murdoch C, Filler S, Naglik J (2019) Candidalysin is required for neutrophil recruitment and virulence during systemic Candida albicans infection. J Infect Dis 220(9), 1477-1488. Details PubMed

Assendorp EL, Gresnigt MS, Sprenkeler EGG, Meis JF, Dors N, van der Linden JWM, Henriet SSV (2018) Adjunctive interferon-γ immunotherapy in a pediatric case of Aspergillus terreus infection. Eur J Clin Microbiol Infect Dis [Accepted] Details PubMed

Gerwien F, Skrahina V, Kasper L, Hube B, Brunke S (2018) Metals in fungal virulence. FEMS Microbiol Rev 42(1), (Review) Details PubMed Open Access

Guerrero QW, Fan L, Brunke S, Milkowski A, Rosado-Mendez IM, Hall TJ (2018) Power Spectrum Consistency among Systems and Transducers. Ultrasound Med Biol [Accepted] Details PubMed

Wolf T, Kämmer P, Brunke S, Linde J (2018) Two's company: studying interspecies relationships with dual RNA-seq. Curr Opin Microbiol 42, 7-12. (Review) Details PubMed Open Access

Hsieh SH, Brunke S, Brock M (2017) Encapsulation of antifungals in micelles protects Candida albicans during gall-bladder infection. Front Microbiol 8, 117. Details PubMed Open Access

Böttcher B, Pöllath C, Staib P, Hube B, Brunke S (2016) Candida species rewired hyphae developmental programs for chlamydospore formation. Front Microbiol 7, 1697. Details PubMed Open Access

Naranjo-Ortíz MA, Brock M, Brunke S, Hube B, Marcet-Houben M, Gabaldón T (2016) Widespread inter- and intra-Ddmain horizontal gene transfer of d-amino acid metabolism enzymes in eukaryotes. Front Microbiol 7, 2001. Details PubMed Open Access

Böttcher B, Palige K, Jacobsen ID, Hube B, Brunke S (2015) Csr1/Zap1 maintains zinc homeostasis and influences virulence in Candida dubliniensis but is not coupled to morphogenesis. Eukaryot Cell 14(7), 661-670. Details PubMed Open Access PDF

Brunke S, Quintin J, Kasper L, Jacobsen ID, Richter ME, Hiller E, Schwarzmüller T, d'Enfert C, Kuchler K, Rupp S, Hube B, Ferrandon D (2015) Of mice, flies - and men? Comparing fungal infection models for large-scale screening efforts. Dis Model Mech (8), 473-486. Details PubMed Open Access PDF

Brunke S, Hube B (2014) Adaptive prediction as a strategy in microbial infections. PLOS Pathog 10(10), e1004356. Details PubMed Open Access

Brunke S, Seider K, Fischer D, Jacobsen ID, Kasper L, Jablonowski N, Wartenberg A, Bader O, Enache-Angoulvant A, Schaller M, d’Enfert C, Hube B (2014) One small step for a yeast - Microevolution within macrophages renders Candida glabrata hypervirulent due to a single point mutation. PLOS Pathog 10(10), e1004478. Details PubMed Open Access

Fischer D, Hube B, Brunke S (2014) Fine-scale chromosomal changes in fungal fitness. J Curr Fungal Infect Rep Vol. 8(2), 171-178. (Review) Details

Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K (2014) Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial Mucorales (Mucoromycotina). PLOS Genetics 10(8), e1004496. Details PubMed Open Access

Wartenberg A, Linde J, Martin R, Schreiner M, Horn F, Jacobsen ID, Jenull S, Wolf T, Kuchler K, Guthke R, Kurzai O, Forche A, d'Enfert C, Brunke S, Hube B (2014) Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLOS Genet 10(12), e1004824. Details PubMed Open Access

Brunke S, Hube B (2013) Two unlike cousins: Candida albicans and C. glabrata infection strategies. Cell Microbiol 15(5), 701-708. (Review) Details PubMed Open Access

Lüttich A, Brunke S, Hube B, Jacobsen ID (2013) Serial passaging of Candida albicans in systemic murine infection suggests that the wild type strain SC5314 is well adapted to the murine kidney. PLOS One 8(5), e64482. Details PubMed Open Access

Staff

Dr. Sascha Brunke

Phone: +49 3641 532-1222 Email: sascha.brunke@leibniz-hki.de

Daniel Fischer

Phone: +49 3641 532-1488 Email: daniel.fischer@leibniz-hki.de

Franziska Pieper

Phone: +49 3641 532-1220 Email: franziska.pieper@leibniz-hki.de

Theresa Rothe

Email: theresa.rothe@leibniz-hki.de

Sofia Siscar Lewin

Phone: +49 3641 532-1518 Email: sofia.lewin@leibniz-hki.de