Icts of Interest: The authors declare no conflict of interest. The
Icts of Interest: The authors declare no conflict of interest. The funders had no role within the design and style of your study, inside the collection, analyses, or interpretation of information, or inside the writing in the manuscript; nonetheless, NordGen authorized publishing of the outcomes.
microorganismsArticleGenomic Evaluation of Prophages from Klebsiella pneumoniae Clinical IsolatesAndreia T. Marques 1, , Lu Tanoeiro 1 , Aida Duarte 2,three , Luisa Gon lves 4 , Jorge M. B. V or 1 and Filipa F. Vale 1, Pathogen Genome Bioinformatics and Computational Biology, SBP-3264 custom synthesis Analysis Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; [email protected] (L.T.); [email protected] (J.M.B.V.) Faculty of Pharmacy, Universidade de Lisboa, Av. Gama Pinto, 1649-003 Lisboa, Portugal; [email protected] Centro de Investiga o Interdisciplinar Egas Moniz, Instituto Universit io Egas Moniz, 2829-511 Monte da Caparica, Portugal Clinical Pathology Unit, Hospital SAMS, Cidade de Gabela, 1849-017 Lisboa, Portugal; [email protected] Correspondence: [email protected] (A.T.M.); [email protected] or [email protected] (F.F.V.)Citation: Marques, A.T.; Tanoeiro, L.; Duarte, A.; Gon lves, L.; V or, J.M.B.; Vale, F.F. Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates. Microorganisms 2021, 9, 2252. https://doi.org/10.3390/ microorganisms9112252 Academic Editor: Igor V. Babkin Received: 15 September 2021 Accepted: 25 October 2021 Published: 28 OctoberAbstract: Klebsiella pneumoniae is definitely an rising threat to public wellness and represents one of one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic components which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion internet sites and phylogenetic evaluation of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored a minimum of a single prophage and we identified 104 intact prophages (69.three ). The prophage size ranges from 29.7 to 50.6 kbp, coding in between 32 and 78 putative genes. The prophage GC content material is 51.two , reduce than the typical GC content of 57.1 in K. pneumoniae. Comprehensive prophages have been classified into 3 households inside the order Caudolovirales: Myoviridae (59.six ), Siphoviridae (38.five ) and Podoviridae (1.9 ). Also, an alignment and phylogenetic analysis revealed nine distinct clusters. Proof of recombination was detected inside the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) have been maintained. These benefits help the knowledge that prophages are diverse and broadly disseminated in K. pneumoniae YTX-465 site genomes, contributing towards the evolution of this species and conferring extra phenotypes. Additionally, we identified K. pneumoniae prophages within a set of endolysin genes, which were located to code for proteins with lysozyme activity, cleaving the -1,four linkages between N-acetylmuramic acid and N-acetyl-Dglucosamine residues in the peptidoglycan network and as a result representing genes together with the possible for lysin phage therapy. Search phrases: K. pneumoniae genomes; prophages; bacteriophage; bioinformatics; genomic analysis; comparative genomics; phylogeny; sequence annotation and comparison; phage endolysinsPublisher’s Note: MDPI stays.