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Spencer E, Peters T, Eline Y, Saucedo L, Linzan K, Paull K, Miller C, Van Leuven J. Bacteriophage resistance evolution in a honey bee pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602782. [PMID: 39026776 PMCID: PMC11257554 DOI: 10.1101/2024.07.09.602782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Honey bee (Apis mellifera) larvae are susceptible to the bacterial pathogen Paenibacillus larvae, which causes severe damage to bee colonies. Antibiotic treatment requires veterinary supervision in the United States, is not used in many parts of the world, perpetuates problems associated with antibiotic resistance, and can necessitate residual testing in bee products. There is interest in using bacteriophages to treat infected colonies (bacteriophage therapy) and several trials are promising. Nevertheless, the safety of using biological agents in the environment must be scrutinized. In this study we analyzed the ability of P. larvae to evolve resistance to several different bacteriophages. We found that bacteriophage resistance is rapidly developed in culture but often results in growth defects. Mutations in the bacteriophage-resistant isolates are concentrated in genes encoding potential surface receptors. Testing one of these isolates in bee larvae, we found it to have reduced virulence compared to the parental P. larvae strain. We also found that bacteriophages are likely able to counteract resistance evolution. This work suggests that while bacteriophage-resistance may arise, its impact will likely be mitigated by reduced pathogenicity and secondary bacteriophage mutations that overcome resistance.
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Affiliation(s)
- Emma Spencer
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Tracey Peters
- Department of Biological Sciences, University of Idaho, Moscow, ID
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID
| | - Yva Eline
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID
| | - Lauren Saucedo
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | | | - Keera Paull
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Craig Miller
- Department of Biological Sciences, University of Idaho, Moscow, ID
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID
| | - James Van Leuven
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID
- Department of Animal Veterinary and Food Sciences, University of Idaho, Moscow, ID
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Dion MB, Shah SA, Deng L, Thorsen J, Stokholm J, Krogfelt KA, Schjørring S, Horvath P, Allard A, Nielsen DS, Petit MA, Moineau S. Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages. THE ISME JOURNAL 2024; 18:wrae005. [PMID: 38366192 PMCID: PMC10910852 DOI: 10.1093/ismejo/wrae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/18/2024]
Abstract
CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Ling Deng
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
| | - Philippe Horvath
- IFF Danisco, Health & Biosciences, Dangé-Saint-Romain 86220, France
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dennis S Nielsen
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Micalis, Jouy-en-Josas 78350, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
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Kok DN, Zhou D, Tsourkas PK, Hendrickson HL. Paenibacillus larvae and their phages; a community science approach to discovery and initial testing of prophylactic phage cocktails against American Foulbrood in New Zealand. MICROBIOME RESEARCH REPORTS 2023; 2:30. [PMID: 38045927 PMCID: PMC10688787 DOI: 10.20517/mrr.2023.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/05/2023] [Accepted: 07/15/2023] [Indexed: 12/05/2023]
Abstract
Background: American foulbrood (AFB) is a devastating disease of the European honey bee (Apis mellifera) and is found throughout the world. AFB is caused by the bacterium Paenibacillus larvae (P. larvae). Treatment with antibiotics is strictly forbidden in many regions, including New Zealand. Safe and natural prophylactic solutions to protect honey bees from AFB are needed. Bacteriophages are a well-studied alternative to antibiotics and have been shown to be effective against P. larvae in other countries. Methods: We employed a community science approach to obtaining samples from around New Zealand to discover novel bacteriophages. Standard isolation approaches were employed for both bacteria and bacteriophages. Host range testing was performed by agar overlay spot tests, and cocktail formulation and in vitro testing were performed in 96-well plate assays, followed by sub-sampling and CFU visualization on agar plates. Results: Herein, we describe the discovery and isolation of eight P. larvae bacterial isolates and 26 P. larvae bacteriophages that are novel and native to New Zealand. The phage genomes were sequenced and annotated, and their genomes were compared to extant sequenced P. larvae phage genomes. We test the host ranges of the bacteriophages and formulate cocktails to undertake in vitro testing on a set of representative bacterial strains. These results form the basis of a promising solution for protecting honey bees in New Zealand from AFB.
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Affiliation(s)
- Danielle N. Kok
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Diana Zhou
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Philippos K. Tsourkas
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53792, USA
| | - Heather L. Hendrickson
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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Kok DN, Turnbull J, Takeuchi N, Tsourkas PK, Hendrickson HL. In Vitro Evolution to Increase the Titers of Difficult Bacteriophages: RAMP-UP Protocol. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:68-81. [PMID: 37350994 PMCID: PMC10282794 DOI: 10.1089/phage.2023.0005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Background Bacteriophages are becoming increasingly important in the race to find alternatives to antibiotics. Unfortunately, bacteriophages that might otherwise be useful are sometimes discarded due to low titers making them unsuitable for downstream applications. Methods Here, we present two distinct approaches used to experimentally evolve novel New Zealand Paenibacillus larvae bacteriophages. The first approach uses the traditional agar-overlay method, whereas the other was a 96-well plate liquid infection protocol that improved phage titers in as little as four days. We also used a mathematical model to probe the parameters and limits of the RAMP-UP approach to rapidly select mutants that improve bacteriophage titers. Results Both experimental approaches resulted in an increase in plaque-forming units (PFU/mL). The liquid infection approach developed here, which we call RAMP-UP for Rapid Adaptive Mutation of Phage - UP, was significantly faster and simpler, and allowed us to evolve high titer bacteriophages in as little as four days. Titers were increased from 100-100,000-fold relative to their ancestors. The resultant titers were sufficient to extract and sequence DNA from these bacteriophages. An analysis of these phage genomes is provided. Conclusion The RAMP-UP protocol is an effective method for experimentally evolving previously intractable bacteriophages in a high-throughput and expeditious manner.
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Affiliation(s)
- Danielle N. Kok
- School of Natural Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Joanne Turnbull
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Nobuto Takeuchi
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Philippos K. Tsourkas
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Heather L. Hendrickson
- School of Natural Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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