Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Case Reports
. 2019 Jul 24;19(1):660.
doi: 10.1186/s12879-019-4173-2.

Rapid diagnosis of Capnocytophaga canimorsus septic shock in an immunocompetent individual using real-time Nanopore sequencing: a case report

Seweryn Bialasiewicz  1   2 , Tania P S Duarte  3 , Son H Nguyen  3 , Vichitra Sukumaran  4 , Alexandra Stewart  4 , Sally Appleton  5 , Miranda E Pitt  3 , Arnold Bainomugisa  3 , Amy V Jennison  6 , Rikki Graham  6 , Lachlan J M Coin  3 , Krispin Hajkowicz  4   7
Affiliations
Case Reports

Rapid diagnosis of Capnocytophaga canimorsus septic shock in an immunocompetent individual using real-time Nanopore sequencing: a case report

Seweryn Bialasiewicz et al. BMC Infect Dis. .

Abstract

Background: Rapid diagnosis and appropriate treatment is imperative in bacterial sepsis due increasing risk of mortality with every hour without appropriate antibiotic therapy. Atypical infections with fastidious organisms may take more than 4 days to diagnose leading to calls for improved methods for rapidly diagnosing sepsis. Capnocytophaga canimorsus is a slow-growing, fastidious gram-negative bacillus which is a common commensal within the mouths of dogs, but rarely cause infections in humans. C. canimorsus sepsis risk factors include immunosuppression, alcoholism and elderly age. Here we report on the application of emerging nanopore sequencing methods to rapidly diagnose an atypical case of C. canimorsus septic shock.

Case presentation: A 62 year-old female patient was admitted to an intensive care unit with septic shock and multi-organ failure six days after a reported dog bite. Blood cultures were unable to detect a pathogen after 3 days despite observed intracellular bacilli on blood smears. Real-time nanopore sequencing was subsequently employed on whole blood to detect Capnocytophaga canimorsus in 19 h. The patient was not immunocompromised and did not have any other known risk factors. Whole-genome sequencing of clinical sample and of the offending dog's oral swabs showed near-identical C. canimorsus genomes. The patient responded to antibiotic treatment and was discharged from hospital 31 days after admission.

Conclusions: Use of real-time nanopore sequencing reduced the time-to-diagnosis of Capnocytophaga canimorsus in this case from 6.25 days to 19 h. Capnocytophaga canimorsus should be considered in cases of suspected sepsis involving cat or dog contact, irrespective of the patient's known risk factors.

Keywords: Capnocytophaga canimorsus; Diagnosis; Droplet digital PCR; Nanopore sequencing; Sepsis.

PubMed Disclaimer

Conflict of interest statement

SB, KH and LC hold a grant from the Queensland Government to explore MinION sequencing as a potential diagnostic tool. LC has received funding from Oxford Nanopore Technologies (ONT) to develop basecalling algorithms and to cover airfares and conference fees for an ONT community meeting. All other authors declare no competing interests. SB is a member of BMC Infectious Diseases Editorial Board.

Figures

Fig. 1
Fig. 1
Timeline of patient’s clinical management progression, including timing of diagnostic testing, bacterial loads (genome copies/mL of blood) of Capnocytophaga canimorsus (C.c) in whole blood as determined by bespoke droplet digital PCR, and antimicrobial therapy. ICU admission is used as the day 0 reference point
See this image and copyright information in PMC

References

    1. Verroken Alexia, Defourny Lydwine, le Polain de Waroux Olivier, Belkhir Leïla, Laterre Pierre-François, Delmée Michel, Glupczynski Youri. Clinical Impact of MALDI-TOF MS Identification and Rapid Susceptibility Testing on Adequate Antimicrobial Treatment in Sepsis with Positive Blood Cultures. PLOS ONE. 2016;11(5):e0156299. doi: 10.1371/journal.pone.0156299. - DOI - PMC - PubMed
    1. Yagupsky P. Diagnosing Kingella kingae infections in infants and young children. Expert Rev Anti-Infect Ther. 2017;15:925–934. doi: 10.1080/14787210.2017.1381557. - DOI - PubMed
    1. Brouqui P, Raoult D. Endocarditis due to rare and fastidious bacteria. Clin Microbiol Rev. 2001;14:177–207. doi: 10.1128/CMR.14.1.177-207.2001. - DOI - PMC - PubMed
    1. Greninger AL, Naccache SN, Federman S, et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 2015;7:99. doi: 10.1186/s13073-015-0220-9. - DOI - PMC - PubMed
    1. Charalampous T, Richardson H, Kay GL, et al. Rapid diagnosis of lower respiratory infection using Nanopore-based clinical metagenomics. bioRxiv 2018 [preprint]. August 9, 2018 [cited 2018 Oct 24]. Available from: 10.1101/387548

Publication types

MeSH terms

Substances