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Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis.

ABSTRACT: Because of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-time (SMRT) analysis. Protein-coding genes, rRNAs and tRNAs were predicted. Functional annotations of the genome using different databases revealed several genes related to pathogenicity including antibiotic resistance genes and prophages. Our work demonstrates that whole genome sequencing can enhance the resolution of clinical investigations and our data can be used as a reference genome during the rapid diagnosis of C. kerstersii infections in the future.

SUBMITTER: Jiang X

PROVIDER: S-EPMC6219407 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis.

Jiang Xiawei X Liu Wenhong W Zheng Beiwen B

Scientific data 20181106

Because of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-ti ...[more]

PMID: 30398469

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Project description:RationaleComamonas kerstersii mainly causes intra-abdominal infections with favorable outcomes due to high antibiotic susceptibility. We report the first case of pneumonia caused by C Kerstersii, which promoted patient death, and a second urinary tract infection by C Kerstersii with extensive drug resistance.Patient concernsA 46-year-old male (Case 1) with craniocerebral injury underwent emergency decompressive craniectomy, but his condition deteriorated further and presented with discontinuous fever, small moist rales on both lungs, and respiratory failure. Retrospective average nucleotide identity (ANI) analysis of the genomic sequence of the sputum isolate identified it as C Kerstersii 12322-1, antimicrobial susceptibility testing (AST) revealed that it was sensitive to 18 of 21 tested antibiotics.An 82-year-old male (Case 2) with hypertrophic prostate experienced gradual obstruction during urination, and a urine test revealed WBC ++. Retrospective ANI analysis of the urine isolate identified it as C Kerstersii 121606, which was resistant to 18 of 21 tested antibiotics.DiagnosesCase 1 was diagnosed empirically as pneumonia caused by C Kerstersii strain 12322-1 secondary to craniocerebral injury and confirmed by retrospective ANI analysis; case 2 was diagnosed empirically as urinary infection secondary to prostate hyperplasia caused by C Kerstersii strain 121606 confirmed by the retrospective ANI analysis.InterventionsCase 1 was administered cefoxitin, cefodizime, imipenem-cilastatin sodium, and underwent comprehensive salvage management. Case 2 was administered doxycycline alone.OutcomesCase 1 died partially because of untimely identification of the responsible bacteria-12322-1. Case 2 was cured even 121606 exhibited an extensive drug resistance feature.LessonsExcept for intra-abdominal infections with good prognosis, we verified that C Kerstersii could also cause extra-abdominal infections, such as the first pneumonia case and urinary infection. It could promote patient death; actual infections were underestimated due to identification difficulties, posing a health threat due to the presence of extensive drug resistance.

Dataset Information

Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis.

Publications

Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis.

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