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. 2024 Oct 21:57:111050.
doi: 10.1016/j.dib.2024.111050. eCollection 2024 Dec.

Whole genome sequencing data of Klebsiella pneumoniae Ch1-39 isolated from chili powder

Mayra Paola Mena Navarro  1 , Merle Ariadna Espinosa Bernal  1 , Ana Laura Vega Rodríguez  1 , Daniel Alejandro Ferrusca Bernal  1 , Juan Enrique de Jesús López  2 , Maria Carlota García Gutiérrez  2 , Karla Isabel Lira De León  1 , Bertha Isabel Carvajal Gaimez  3 , David Gustavo García Gutiérrez  1 , Alma Delia Bertadillo Jilote  1 , Miguel Angel Ramos Lopez  1 , José Luis Hernández Flores  4 , Juan Campos Guillén  1
Affiliations

Whole genome sequencing data of Klebsiella pneumoniae Ch1-39 isolated from chili powder

Mayra Paola Mena Navarro et al. Data Brief. .

Abstract

Klebsiella pneumoniae Ch1-39 was isolated from chili powder elaborated at San Luis Potosí, México. This microorganism can be found in diverse ecological niches as water, soil, air, plants and hospital setting, it is considered as a relevant opportunistic pathogen causing several diseases and showing increasingly multi-resistance to antibiotics. The genome was sequenced on the Illumina NovaSeq platform and bioinformatic analyses were made at the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). The genome consisted of 72 contigs with a total size of 5,410,125 bp, 5,361 protein coding sequences (CDS), a total of 6 rRNA and 76 tRNA with an average G + C content of 57.22 %. The genome data was deposited at National Center for Biotechnology Information (NCBI) under accession number Bioproject ID PRJNA1062060, Bio Sample ID SAMN40269967. The genome accession number was JBAWUH000000000.

Keywords: Antibiotic Resistance genes (ARGs); Chili powder; Complete genome; Klebsiella pneumoniae Ch1-39; Virulence factor genes.

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Figures

Fig 1
Fig. 1
Circular genomic map and subsystems information for K. pneumoniae Ch1-39. From the outside to the center are the assembled contigs, ORF, CDS in the front strand, CDS on the reverse strand, RNA genes, CDS with similarity to known antibiotic resistance genes, CDS with similarity to virulence factors, GC content and GC skew. Distribution of the subsystems are displayed in the figure below. In subsystems coverage, 42 % indicates a total of 2619 genes and 58 % represent those not indicated in subsystem average with a total 2824 genes.
Fig 2
Fig. 2
Genes predicting antibiotic resistance were grouped into ten mechanisms of action. (1) antibiotic activation enzyme, (2) antibiotic inactivation enzyme, (3) antibiotic resistance gene cluster, cassette or operon, (4) antibiotic target in susceptible species, (5) antibiotic target protection protein, (6) efflux pump conferring antibiotic resistance, (7) gene conferring resistance via absence, (8) protein altering cell wall charge conferring antibiotic resistance, (9) protein modulating permeability to antibiotic and (10) regulator modulating expression of antibiotic resistance genes. Created using Biorender.
Fig 3
Fig. 3
Phylogenetic tree including clinical and environmental strains of K. pneumoniae Ch1-39. The Codon Tree pipeline of BV-BRC was used to generate bacterial phylogenetic trees with Klebsiella genus strains. The following strains were included: K. pneumoniae MJH599 (573.64640), K. pneumoniae KPHDC1 (573.57106), K. pneumoniae IR5017 (573.56497), K. pneumoniae strain E5 (573.14977), K. pneumoniae strain 5422 (573.1345), K. pneumoniae 9459 (573.56896), K. pneumoniae strain CCI2 (573.34158), K. pneumoniae LR53-19KP (573.51887), K. pneumoniae 61,575_sr (573.64625), K. pneumoniae KP24 (573.54327), K. pneumoniae strain ST15-OXA48 (573.29101), K. pneumoniae UPMP 1783 (573.43879), K. pneumoniae DS-1 (573.53759), K. pneumoniae WP2-S17-ESBL-02 (573.32411), K. pneumoniae strain CVUAS 5452.2 (573.39775), K. pneumoniae 14,652 (573.63146), K. pneumoniae 14,660 (573.56900), K. pneumoniae strain 06 (573.32125). The color and figure of the node represent country and year collection for each insolated strain.
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