Bacteriophage Resistance Mechanisms in the Fish Pathogen Flavobacterium psychrophilum: Linking Genomic Mutations to Changes in Bacterial Virulence Factors

Castillo, Daniel; Christiansen, Rói Hammershaimb; Dalsgaard, Inger; Madsen, Lone; Middelboe, Mathias

doi:10.1128/aem.03699-14

Cited by 79 publications

(93 citation statements)

References 64 publications

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“…Some repeat-spacer arrays remain relatively constant over millennia 41 , while in some cases no two identical CRISPR loci are found in cells living in close proximity 22 . A study on a closely related species, the fish pathogen Flavobacterium psychrophilum, identified only inactive CRISPR loci across multiple strains 42 . In F. columnare we report two dynamic CRISPR loci: C1, a type II-C system associated with a novel PAM and C2, a recently identified type VI-B system.…”

Section: Discussionmentioning

confidence: 99%

Long-term genomic coevolution of host-parasite interaction in the natural environment

Laanto

Hoikkala

Ravantti

et al. 2017

Preprint

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The antagonistic coevolution of parasite infectivity and host resistance alters the biological functionality of species, with effects spanning to communities and ecosystems. Still, studies describing long-term host-parasite coevolutionary dynamics in nature are largely missing.Furthermore, the role of host resistance mechanisms for parasite evolution is poorly understood, necessitating for the molecular and phenotypic characterization of both coevolving parasites and their hosts. We combined long-term field sampling (2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014), in vitro cross-infections and timeshift experiments with bacteriophage whole genome sequencing and bacterial (Flavobacterium columnare) CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) profiling to show the molecular details of the phage-bacterium arms race in the environment. Bacteria were generally resistant to phages from the past and susceptible to phages in the future. The bacterial resistance selected for increased phage infectivity and host range, correlating directly with the expansion of phage genome size by 2656 bp. In the bacterial host, two CRISPR loci were identified: a type II-C locus and an RNA-targeting type VI-B locus. While maintaining a core set of conserved spacers, phage-matching spacers appeared in the variable end of both CRISPR loci over time. The appearance of these CRISPR spacers in the bacterial host often corresponded with arms race -manner molecular changes in the protospacers of the coevolving phage population. However, the phenotypic data indicated that the relative role of constitutive defence may be more important in high phage pressure, highlighting the importance of our findings for understanding microbial community ecology and in the development of phage therapy applications.

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Section: Discussionmentioning

confidence: 99%

Long-term genomic coevolution of host-parasite interaction in the natural environment

Laanto

Hoikkala

Ravantti

et al. 2017

Preprint

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“…Evolution of phage resistance by bacterial pathogens is often associated with virulence trade-offs when surface structures are modified 19–21 , whereas similar trade-offs have not yet been reported in the literature for CRISPR-based resistance. We therefore hypothesised that the community context in which phage resistance evolves may have important knock-on effects for P. aeruginosa virulence.…”

Section: Figurementioning

confidence: 94%

Bacterial biodiversity drives the evolution of CRISPR-based phage resistance in Pseudomonas aeruginosa

Alseth

Pursey

et al. 2019

Preprint

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evolution of virulence; biodiversity 19 20 21Approximately half of all bacterial species encode CRISPR-Cas adaptive immune 22 systems 1 , which provide immunological memory by inserting short DNA sequences 23 from phage and other parasitic DNA elements into CRISPR loci on the host genome 2 . 24Whereas CRISPR loci evolve rapidly in natural environments 3 , bacterial species 25 typically evolve phage resistance by the mutation or loss of phage receptors under 26 laboratory conditions 4,5 . Here, we report how this discrepancy may in part be explained 27 by differences in the biotic complexity of in vitro and natural environments 6,7 . 28 Specifically, using the opportunistic pathogen Pseudomonas aeruginosa and its phage 29DMS3vir, we show that coexistence with other human pathogens amplifies the fitness 30 trade-offs associated with phage receptor mutation, and therefore tips the balance in 31 favour of CRISPR-based resistance evolution. We also demonstrate that this has 32 important knock-on effects for P. aeruginosa virulence, which became attenuated only if 33 the bacteria evolved surface-based resistance. Our data reveal that the biotic complexity 34 of microbial communities in natural environments is an important driver of the 35 evolution of CRISPR-Cas adaptive immunity, with key implications for bacterial fitness 36 and virulence. 37 38Pseudomonas aeruginosa is a widespread opportunistic human pathogen that thrives in a 39 range of different environments, including hospitals, where it is a common source of 40 nosocomial infections. In particular, it frequently colonises the lungs of cystic fibrosis 41 patients, in whom it is the leading cause of morbidity and mortality 8 . In part fuelled by a 42 renewed interest in the therapeutic use of bacteriophages as antimicrobials (phage 43 therapy) 9,10 , many studies have examined if and how P. aeruginosa evolves resistance to 44 phage (reviewed in ref. 11). The clinical isolate P. aeruginosa strain PA14 has been reported 45 to predominantly evolve resistance against its phage DMS3vir by the modification or 46 complete loss of the phage surface receptor 12 when grown in nutrient-rich medium 4 despite 47

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“…In the family Flavobacteriaceae , the CRISPR-Cas systems in Flavobacterium columnare were shown to play a role in host-phage interactions, which drives long-term genome coevolution through arms-race-like mechanisms between the host and phages (79), serving as an example of genome stability. On the other hand, the CRISPR-Cas machinery appeared not to play a role as a resistance mechanism against phages in fish pathogenic Flavobacterium psychrophilum (80). Availability of the E. anophelis strains that possess CRISPR-Cas with and without ICEs enables further studies on co-evolution of mobile elements and host defense systems in the bacteria.…”

Section: Resultsmentioning

confidence: 99%

In SilicoIdentification of Three Types of Integrative and Conjugative Elements (ICEs) inElizabethkingia anophelisStrains Isolated from Around the World

Pei

Nicholson

et al. 2018

Preprint

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27Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. 28 We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis 29 derived from various environmental settings and human infections from different geographic 30 regions around the world over past decades from 1950s. Thirty-one of these 36 strains harbor 31 integrative and conjugative elements (ICEs). A total of 52 ICEs were identified, and 32 categorized into three ICE types based on the architecture of signature genes in the 33 conjugation module. The type II and III ICEs were found to integrate into regions adjacent to 34 tRNA genes, while type I ICEs used a variety of integration sites, inserting into intergenic 35 regions or even directly into a gene, sometimes disrupting gene function. Integrases such as 36 tyrosine recombinases, serine recombinases and DDE transposases were found in most ICEs. 37 The ICEs carry various cargo genes including transcription regulators and those involved in 38 antibiotic resistance. The CRISPR-Cas system was found in nine strains, including four 39 strains in which CRISPR-Cas machinery and ICEs co-exist. ICE distribution in the strains 40 showed no geographic or temporal patterns. The ICEs in E. anophelis differ in gene structure 41 and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. This is the 42 first set of ICEs identified in the family Flavobacteriaceae. As a prevalent type of mobile 43 genetic elements in various strains of E. anophelis around the world, the categorization of 44 ICEs will facilitate further investigations such as virulence, genome epidemiology and 45 adaptation genomics of E. anophelis. 46 Importance 47Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity 48 between strains from around the world becomes apparent as more genomes are sequenced. 49The Integrative Conjugative Element (ICE), found in many bacterial species, contains genes 50 3 for transfer via conjugation and integration into the chromosome, along with various cargo 51 genes. ICEs are identified in 31 of 36 strains and categorized into three types based on 52 architecture of modular genes, integrases, and integration sites. ICE distribution in different 53 strains displays no spatial and temporal patterns. Several ICE-containing strains also 54 possessed CRISPR-Cas units, considered to be the bacterial adaptive immune system 55 providing protection against phage and predatory mobile genetic elements. This co-existence 56 suggests that ICEs are beneficial or at least not harmful to the bacterial cells they inhabit. 57ICEs as a component of the mobile genetic repertoire enable recipients to resist antibiotics, 58 survive disinfecting agents, and adapt to various ecological niches.

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Bacteriophage Resistance Mechanisms in the Fish Pathogen Flavobacterium psychrophilum: Linking Genomic Mutations to Changes in Bacterial Virulence Factors

Cited by 79 publications

References 64 publications

Long-term genomic coevolution of host-parasite interaction in the natural environment

Long-term genomic coevolution of host-parasite interaction in the natural environment

Bacterial biodiversity drives the evolution of CRISPR-based phage resistance in Pseudomonas aeruginosa

In SilicoIdentification of Three Types of Integrative and Conjugative Elements (ICEs) inElizabethkingia anophelisStrains Isolated from Around the World

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