[en] [en] AIMS: Understanding bacterial phage resistance mechanisms has implications for developing phage-based therapies. This study aimed to explore the development of phage resistance in Escherichia coli K1 isolates' to K1-ULINTec4, a K1-dependent bacteriophage.
METHODS AND RESULTS: Resistant colonies were isolated from two different strains (APEC 45 and C5), both previously exposed to K1-ULINTec4. Genome analysis and several parameters were assessed, including growth capacity, phage adsorption, phenotypic impact at capsular level, biofilm production and virulence in the in-vivo Galleria mellonella larvae model. One out of the 6 resistant isolates exhibited a significantly slower growth rate suggesting the presence of a resistance mechanism altering its fitness. Comparative genomic analysis revealed insertion sequences in the region 2 of the kps gene cluster involved in the capsule biosynthesis. In addition, an immunoassay targeting the K1 capsule showed a very low positive reaction compared to the control. Nevertheless, microscopic images of resistant strains revealed the presence of capsules with a clustered organization of bacterial cells and biofilm assessment showed an increased biofilm production compared to the sensitive strains. In the G. mellonella model, larvae infected with phage-resistant isolates showed better survival rates than larvae infected with phage-sensitive strains.
CONCLUSIONS: A phage resistance mechanism was identified at the genomic level and had a negative impact on the K1 capsule production. The resistant isolates showed an increased biofilm production, and a decreased virulence in vivo.
Disciplines :
Immunology & infectious disease
Author, co-author :
Antoine, Céline ; Université de Liège - ULiège > Fundamental and Applied Research for Animals and Health (FARAH)
Laforêt, Fanny ; Université de Liège - ULiège > Fundamental and Applied Research for Animals and Health (FARAH) > FARAH: Productions animales durables
Fall, Abdoulaye; FoodChain ID GENOMICS SA, Herstal, Belgium
Delcenserie, Véronique ✱; Université de Liège - ULiège > Département de sciences des denrées alimentaires (DDA) > Gestion de la qualité dans la chaîne alimentaire
Thiry, Damien ✱; Université de Liège - ULiège > Département des maladies infectieuses et parasitaires (DMI) > Bactériologie vétérinaire et maladies bactériennes animales
✱ These authors have contributed equally to this work.
Language :
English
Title :
K1 Capsule-dependent phage-driven evolution in Escherichia coli leading to phage resistance and biofilm production.
Alkeskas A, Ogrodzki P, Saad M et al. The molecular characterisation of Escherichia coli K1 isolated from neonatal nasogastric feeding tubes. BMC Infect Dis 2015;15:449. https://doi.org/10.1186/s128 79-015-1210-7.
Antoine C, Laforêt F, Blasdel B et al. In vitro characterization and in vivo efficacy assessment in Galleria mellonella larvae of newly isolated bacteriophages against Escherichia coli K1. Viruses 2021;13:2005.
Antoine C, Laforêt F, Goya-Jorge E et al. Phage targeting neonatal meningitis E. coli K1 in vitro in the intestinal microbiota of pregnant donors and impact on bacterial populations. Int J Mol Sci 2023;24:10580.
Azam AH, Tanji Y. Bacteriophage-host arm race: an update on the mechanism of phage resistance in bacteria and revenge of the phage with the perspective for phage therapy. Appl Microbiol Biotechnol 2019;103:2121–31.
Bull JJ, Vimr ER, Molineux IJ. A tale of tails: sialidase is key to success in a model of phage therapy against K1-capsulated Escherichia coli. Bone 2008;23:1–7.
Burmeister A, Fortier A, Roush C et al. Pleiotropy complicates a tradeoff between phage resistance and antibiotic resistance. Proc Natl Acad Sci USA 2020;117:11207–16.
Chapman-McQuiston E, Wu XL. Stochastic receptor expression allows sensitive bacteria to evade phage attack. Part I: experiments. Biophys J 2008;94:4525–36.
Dale AP, Woodford N. Extra-intestinal pathogenic Escherichia coli (ExPEC): disease, carriage and clones. J Infect 2015;71: 615–26.
Dy RL, Przybilski R, Semeijn K et al. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res 2014;42:4590–605.
Dziva F, Stevens MP. Colibacillosis in poultry: unravelling the molecular basis of virulence of avian pathogenic Escherichia coli in their natural hosts. Avian Pathol 2008;37:355–66.
Egido JE, Costa AR, Aparicio-Maldonado C et al. Mechanisms and clinical importance of bacteriophage resistance. FEMS Microbiol Rev 2022;46:fuab048.
Fernández L, Gutiérrez D, García P et al. Environmental pH is a key modulator of Staphylococcus aureus biofilm development under predation by the virulent phage phiIPLA-RODI. ISME J 2021;15:245–59.
Gencay YE, Sørensen MCH, Wenzel CQ et al. Phase variable expression of a single phage receptor in Campylobacter jejuni NCTC12662 influences sensitivity toward several diverse CPS-dependent phages. Front Microbiol 2018;9: 82. https://www.frontiersin.org/ articles/10.3389/fmicb.2018.00082
Goldfarb T, Sberro H, Weinstock E et al. BREX is a novel phage resistance system widespread in microbial genomes. EMBO J 2015;34:169–83.
Hosseinidoust Z, Tufenkji N, van de Ven TGM. Formation of biofilms under phage predation: considerations concerning a biofilm increase. Biofouling 2013;29:457–68
KIM K. Human meningitis-associated Escherichia Coli. Physiol Behav 2017;176:139–48.
Kim MS, Kim YD, Hong SS et al. Phage-encoded colanic acid-degrading enzyme permits lytic phage infection of a capsule-forming resistant mutant Escherichia coli strain. Appl Environ Microb 2015;81:900–9.
King JE, Aal Owaif H, Jia J et al. Phenotypic heterogeneity in expression of the K1 polysaccharide capsule of uropathogenic Escherichia coli and downregulation of the capsule genes during growth in urine. Infect Immun 2015;83:2605–13.
Lacqua A, Wanner O, Colangelo T et al. Emergence of biofilm-forming subpopulations upon exposure of Escherichia coli to environmental bacteriophages. Appl Environ Microb 2006;72:956–59.
Leiman PG, Battisti AJ, Bowman VD et al. The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. J Mol Biol 2007;371:836–49.
Maneval WE. Staining bacteria and yeasts with acid dyes. Stain Technol 1941;16-1:13–19. https://www.tandfonline.com/doi/abs/10.3 109/10520294109106189
McCarthy AJ, Birchenough GMH, Taylor PW. Loss of trefoil factor 2 sensitizes rat pups to systemic infection with the neonatal pathogen Escherichia coli K1. Infect Immun 2019;87/5:e00878–18.
McCarthy AJ, Negus D, Martin P et al. Pathoadaptive mutations of Escherichia coli K1 in experimental neonatal systemic infection. PLoS One 2016;11:1–16
Millen AM, Horvath P, Boyaval P et al. Mobile CRISPR/Casmediated bacteriophage resistance in Lactococcus lactis. PLoS One 2012;7:e51663.
Møller-Olsen C, Ho SFS, Shukla RD et al. Engineered K1F bacteriophages kill intracellular Escherichia coli K1 in human epithelial cells. Sci Rep 2018;8:17559.
Mora A, Viso S, López C et al. Poultry as reservoir for extraintestinal pathogenic Escherichia coli O45:K1:H7-B2-ST95 in humans. Vet Microbiol 2013;167:506–12
Moulin-Schouleur M, Schouler C, Tailliez P et al. Common virulence factors and genetic relationships between O18:K1:H7 Escherichia coli isolates of human and avian origin. J Clin Microbiol 2006;44:3484–92.
Mushtaq N, Redpath M, Luzio JP et al. Prevention and cure of systemic Escherichia coli K1 infection by modification of the bacterial phenotype. Antimicrob Agents Chemother 2004;48:1503–8.
Ofir G, Melamed S, Sberro H et al. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat Microbiol 2018;3:90–98
Oliveira PH, Touchon M, Rocha EPC. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res 2014;42:10618–31
Sarowska J, Futoma-Koloch B, Jama-Kmiecik A et al. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut Pathogens 2019;11/1:1–16.
Schneider G, Szentes N, Horváth M et al. Kinetics of targeted phage rescue in a mouse model of systemic Escherichia coli K1. Biomed Res Int 2019;2018:2018.
Scholl D, Rogers S, Adhya S et al. Bacteriophage K1-5 encodes two different tail fiber proteins, allowing it to infect and replicate on both K1 and K5 strains of Escherichia coli. J Virol 2001;75:2509–15.
Seed KD, Faruque SM, Mekalanos JJ et al. Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1. PLoS Pathog 2012;8:e1002917.
Sharma G, Sharma S, Sharma P et al. Escherichia coli biofilm: development and therapeutic strategies. J Appl Microbiol 2016;121:309–19.
Smith HW, Huggins MB. Successful treatment of experimental Escherichia coli infections in mice using phage: its general superiority over antibiotics. Microbiology 1982;128:307–18.
Styles K, Locke RK., Cowley LA et al. Transposable element insertions into the Escherichia coli polysialic acid gene cluster result in resistance to the K1F bacteriophage. Microbiol Spectr 2022;10:e02112–21.
Valle J, Da Re S, Henry N et al. Broad-spectrum biofilm inhibition by a secreted bacterial polysaccharide. Proc Natl Acad Sci USA 2006;103:12558–63.
Wu J, Yang J, Cho WC et al. Argonaute proteins: structural features, functions and emerging roles. J Adv Res 2020;24:317–24.