Resultados de investigación

Supplemental information: Document S1. Figures S1–S7 and Table S5. Table S1. General features of the 46 isolated bacteriophages. Phage ID, phylogenetic classification in 13 groups, genome size and circularity, sequencing depth, GC %, CDS, putative lysogeny genes, taxonomic family, subfamily, and genus according to IGS values with the closest phage are provided. Additionally, concentration of phages for the spot assay, formation of plaque haloes, susceptible CLTs, RBP system and number of depolymerase domains (Dpos) are also shown. REP: transcription repressor/regulator, PAR: parAB genes, REC: recombinases. TSP: Tail spike protein. CBM: carbohydrate-binding module. Taxonomy ranks marked with a star can be reclassified based on relationships showed in this study. CLTs marked with a star indicate that bacteria were acapsular. Dpos marked with a star indicate putative soluble Dpos. Table S2. General features of the 138 Klebsiella clinical strains. The strain, sequencing details, virulence and antibiotic resistance scores, wzi allele, CLT and OLT inference, number of prophages, CRISPR loci, and presence of defense systems and secondary receptors are provided. The presence of a capsule was determined by visual inspection of colonies using light microscopy. Table S3. Phage-bacteria positive combinations. The strain used for phage isolation is indicated. Spotting: positive by the spot-assay. Virulent: positive by the killing planktonic or progeny assay. Table S4. Clustering of phage RBDs with putative depolymerase activity from this work and the literature. RBDs are identified by the phage name followed by the phage protein in which the domain was detected, and the positions considered after the removal of the anchor domain. Document S2. Article plus supplemental information., Peer reviewed

Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences., Peer reviewed

Table S1: Sampling information of the Salmonella enterica isolates included in this study. Table S2: Summary of sequence read quality. Table S3: Summary of assembly results. Table S4: Serotypes and STs. Table S5: Isolates included in HSC and their features. Figure S1: Sequence and structure of the contig containing the mcr-1 gene with the Incx4 plasmid., Peer reviewed

Figure S1: PCA of genomic signatures based on hexamer frequencies of the reference bacteria; Figure S2: k4freq-based distances of the bacterial genera to the reference phages; Figure S3: ROC curves for k4freq and k14exact; Figure S4: Statistical error analysis for different k-mer options; Figure S5: k14exact-based distances of the bacterial genera to the reference phages; Figure S6: Distances of 75 Klebsiella strains to 41 Klebsiella phages; Table S1: Bacterial genomes in the reference set; Table S2: Phage genomes in the reference set; Table S3: Plasmids in the reference set; Table S4: Summary of statistical comparisons of genomic distances; Table S5: Lysogenic activity of K. pneumoniae phages; Table S6: Bacterial single-cells and phages detected in their assemblies., Peer reviewed

The 16S rRNA gene sequence of strain P4.10XT have been deposited in GenBank under the accession number MZ994596. The genomic assembly of strain P4.10XT has been deposited under the GenBank accession number ASM2156869v1., Peer reviewed

Table S1. Absolute frequencies of Hemiptera: Aphididae by sampling area and year. Table S2: Absolute frequencies of Hymenoptera: Braconidae: Aphidiinae by sampling area and year. In parentheses, the total number of tillers examined. Table S3: Absolute frequencies of hyperparasitoids by sampling area and year. In parentheses, the total number of tillers examined., Peer reviewed

Dataset of the Sensbio applications. The CSV file is used as a database of the known TF-ligand interactions. The txt file describes the headers of the csv., Peer reviewed

Cartela tallada en madera en el frontal del sagrario de la Iglesia de Santa María con la fecha de ejecución (1551)., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Inscripción en una cruz de piedra incrustada en el muro de una casa situada en la calle de San Millán. La inscripción contiene el lema "INRI" y la fecha., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed

Inscripción en los sillares del dintel de la puerta de la capilla de la Dolorosa. Contiene una serie de símbolos , entre ellos una corona y pequeños corazones, los anagramas de Jesús y María y la datación., CSIC. Proyecto intramural: “Epigrafía latina inédita de los siglos XV al XVIII en monumentos civiles y eclesiásticos de la provincia de Cuenca (2006-2007). Referencia: 2006 | 0| 011., Peer reviewed