Dataset Information

Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar.

ABSTRACT: We report here the draft genome sequence of a Chryseobacterium indologenes strain, isolated from a blood culture of a 2.2-year-old child admitted to the hospital for vomiting and coughing. The genome was composed of 5,063,674?bp and had 37.04% GC content. We detected 4,796 genes with predicted protein-coding functions, including those associated with antibiotic resistance.

SUBMITTER: Rabenandrasana MAN

PROVIDER: S-EPMC6715870 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar.

Rabenandrasana Mamitina Alain Noah MAN Rafetrarivony Lala Fanomezantsoa LF Rivoarilala Lalainasoa Odile LO Enouf Vincent V Robinson Annick Lalaina AL Rakotozanany Ando A Vanhomwegen Jessica J Caro Valérie V Von Platen Cassandre C Manuguerra Jean-Claude JC Collard Jean-Marc JM

Microbiology resource announcements 20190829 35

We report here the draft genome sequence of a <i>Chryseobacterium indologenes</i> strain, isolated from a blood culture of a 2.2-year-old child admitted to the hospital for vomiting and coughing. The genome was composed of 5,063,674 bp and had 37.04% GC content. We detected 4,796 genes with predicted protein-coding functions, including those associated with antibiotic resistance. ...[more]

PMID: 31467100

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Project description:Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (bla IND-13, bla CIA-3, bla TEM-116, bla OXA-209, bla VEB-15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.

Dataset Information

Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar.

Publications

Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar.

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