Abstract
The CRISPR–Cas are adaptive immune systems found in archaea and bacteria, responsible for providing sequence-specific resistance against foreign DNA. Strains of Pseudomonas aeruginosa may carry CRISPR/Cas system types I-F, I-E and/or I-C; however, several aspects related to the epidemiology and functionality of these systems have not yet been revealed. Here, we report 13 genomes of clinical strains of P. aeruginosa from Brazil that were positive for CRISPR/Cas system types I-F and I-E, a rare feature in this species. The phylogenetic tree, which was constructed with 161 other publicly available genomes, suggested no direct relationship between positive strains, and the various types of CRISPR/Cas systems were spread throughout the tree. Comparative analysis of the genetic locations of type I-F and a specific orphan CRISPR array (without cas genes), named the LES locus, showed sequence similarities between this orphan locus and type I-F, but these LES loci were inserted in a different genomic location. We also report the presence of prophages, the presence of anti-CRISPR genes, and possibly the presence of self-targeting spacers. Here, we conclude that CRISPR/Cas is highly associated with certain lineages and is spread throughout the phylogenetic tree, showing no clear pattern of evolutionary distribution. Moreover, the LES locus might be a CRISPR1 locus related to type I-F that may have been misplaced and maintained over time. Furthermore, strains carrying I-F and I-E are rare, and not all of them are closely related. Further functional work is needed to better comprehend if aspects reported in this study are functional, including the LES locus, self-targeting spacers, anti-CRISPR protection, and I-F/I-E-carrying lineages.
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Acknowledgments
The authors thank the Núcleo de Plataformas Tecnológicas (NPT) from the Aggeu Magalhães Institute for the use of its sequencing platform.
Funding
This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico [Grant Number 404016/2016–2]; Fundação Oswaldo Cruz/ Conselho Nacional de Desenvolvimento Científico e Tecnológico [Grant Number: 400781/2019–0]; and Programa Inova Fiocruz – Geração de Conhecimento [Grant Number: VPPCB-007-FIO-18–2-99].
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Ana Carolina de Oliveira Luz: Conceptualization, methodology, investigation, data curation, writing (original draft), and writing (review and editing). Wilson José da Silva Junior: Methodology, software, and formal analysis. José Bandeira do Nascimento Junior: Methodology, software, and formal analysis. Julia Mariana Assis da Silva: Methodology and investigation. Valdir de Queiroz Balbino: Writing (review and editing) and supervision. Tereza Cristina Leal-Balbino: Conceptualization, writing (original draft), writing (review and editing), supervision, project administration, and funding acquisition.
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Not applicable. The present work did not involve humans, human specimens, or tissues. Bacteria were obtained purified from the hospitals per request.
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de Oliveira Luz, A.C., da Silva Junior, W.J., do Nascimento Junior, J.B. et al. Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems. Curr Genet 67, 663–672 (2021). https://doi.org/10.1007/s00294-021-01173-4
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DOI: https://doi.org/10.1007/s00294-021-01173-4