1
|
Wu Z, Yao Y, Li X, Cai H, Wang G, Yu W, Lou H, Chen Q, Zeng Z, Yu H, Xia J, Yu Y, Zhou H. Sensitive and rapid identification of pathogens by droplet digital PCR in a cohort of septic patients: a prospective diagnostic study. Infect Dis (Lond) 2024:1-12. [PMID: 38753988 DOI: 10.1080/23744235.2024.2354312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND There is a critical need for a rapid and sensitive pathogen detection method for septic patients. This study aimed to investigate the diagnostic efficacy of Digital droplet polymerase chain reaction (ddPCR) in identifying pathogens among suspected septic patients. METHODS We conducted a prospective pilot diagnostic study to clinically validate the multiplex ddPCR panel in diagnosing suspected septic patients. A total of 100 sepsis episodes of 89 patients were included in the study. RESULTS In comparison to blood culture, the ddPCR panel exhibited an overall sensitivity of 75.0% and a specificity of 69.7%, ddPCR yielded an additional detection rate of 17.0% for sepsis cases overall, with a turnaround time of 2.5 h. The sensitivity of ddPCR in the empirical antibiotic treatment and the non-empirical antibiotic treatment group were 78.6% versus 80.0% (p > 0.05). Antimicrobial resistance genes were identified in a total of 13 samples. Whenever ddPCR detected the genes beta-lactamase-Klebsiella pneumoniae carbapenemase (blaKPC) or beta-lactamase-New Delhi metallo (blaNDM), these findings corresponded to the cultivation of carbapenem-resistant gram-negative bacteria. Dynamic ddPCR monitoring revealed a consistent alignment between the quantitative ddPCR results and the trends observed in C-reactive protein and procalcitonin levels. CONCLUSIONS Compared to blood culture, ddPCR exhibited higher sensitivity for pathogen diagnosis in suspected septic patients, and it provided pathogen and drug resistance information in a shorter time. The quantitative results of ddPCR generally aligned with the trends seen in C-reactive protein and procalcitonin levels, indicating that ddPCR can serve as a dynamic monitoring tool for pathogen load in septic patients.
Collapse
Affiliation(s)
- Zhenping Wu
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hongliu Cai
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guobin Wang
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenqiao Yu
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhu Zeng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Yu
- Pilot Gene Technology (Hangzhou) Co., Ltd, Hangzhou, China
| | - Jiang Xia
- Pilot Gene Technology (Hangzhou) Co., Ltd, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
2
|
Ahsen A, Korsun P, Albahra F, Nair R, Tariq Z. Capnocytophaga canimorsus Infection in a 38-Year-Old Male after a Dog Bite. Case Rep Infect Dis 2023; 2023:9917898. [PMID: 37876860 PMCID: PMC10593545 DOI: 10.1155/2023/9917898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 09/06/2023] [Accepted: 09/23/2023] [Indexed: 10/26/2023] Open
Abstract
Here, we present a unique case of a 38-year-old male with a history of alcohol use disorder and multiple sexual partners, who presented with fulminant sepsis with shock, multiorgan failure, and livedo racemosa after a dog bite the week prior. The patient was intubated on arrival and was started on vasopressors and antibiotics. Eventually, the patient's clinical status improved, and he was transferred out of the intensive care unit. Blood cultures tested positive for oxidase-positive Gram-negative rods two days after collection, and species identification showed Capnocytophaga canimorsus.
Collapse
Affiliation(s)
- Ahmad Ahsen
- Department of Internal Medicine, Medical City Fort Worth, Fort Worth, TX, USA
| | - Philip Korsun
- Department of Internal Medicine, Medical City Fort Worth, Fort Worth, TX, USA
| | - Fadi Albahra
- Department of Internal Medicine, Medical City Fort Worth, Fort Worth, TX, USA
| | - Ranjit Nair
- Department of Critical Care, Medical City Fort Worth, Fort Worth, TX, USA
| | - Zain Tariq
- Department of Infectious Disease, Medical City Fort Worth, Fort Worth, TX, USA
| |
Collapse
|
3
|
Ring N, Low AS, Wee B, Paterson GK, Nuttall T, Gally D, Mellanby R, Fitzgerald JR. Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections. Microb Genom 2023; 9:mgen001066. [PMID: 37471128 PMCID: PMC10438823 DOI: 10.1099/mgen.0.001066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.
Collapse
Affiliation(s)
- Natalie Ring
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Alison S. Low
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bryan Wee
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gavin K. Paterson
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Tim Nuttall
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Richard Mellanby
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
4
|
Sardo S, Pes C, Corona A, Laconi G, Crociani C, Caddori P, Luisa Boi M, Finco G. The Great pretender: the first case of septic shock due to Capnocytophaga canimorsus in Sardinia. A Case report and review of the literature. J Public Health Res 2022; 11:22799036221133234. [PMID: 36451937 PMCID: PMC9703562 DOI: 10.1177/22799036221133234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/29/2022] [Indexed: 10/04/2023] Open
Abstract
Capnocytophaga canimorsus (C. canimorsus) is an emerging pathogen in critical care. C. canimorsus is a Gram-negative bacillus, commonly isolated as a commensal microorganism of the oral flora of healthy dogs and cats. A 63-year-old woman came to the emergency department with fever, chills, and malaise 2 days after a minor dog bite. After admission to the medicine ward, she developed respiratory failure and livedo reticularis. In the intensive care unit (ICU), she presented full-blown septic shock with thrombocytopenia, coagulopathy, severe acute kidney injury, and liver injury. We describe the first case of septic shock with Multiple Organ Dysfunction Syndrome related to Capnocytophaga canimorsus infection in Sardinia and its treatment in a tertiary hospital ICU. We also review recent literature on the relevance of C. canimorsus in human disease and critical illness.
Collapse
Affiliation(s)
- Salvatore Sardo
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato, Italy
| | - Claudia Pes
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato, Italy
| | - Andrea Corona
- Kantonsspital Graubünden, 7000 Chur, Department ANIR, Intensivmedizin, Switzerland
| | - Giulia Laconi
- Anesthesia and Intensive Care Service, Emergency Department, Azienda Ospedaliero Universitaria di Ferrara, Cona FE, Italy
| | - Claudia Crociani
- Azienda Ospedaliera Brotzu, San Michele Hospital, Microbiology, Piazzale Alessandro Ricchi, Cagliari, Italy
| | - Pietro Caddori
- Azienda Ospedaliera Brotzu, San Michele Hospital, Intensive Care Unit, Piazzale Alessandro Ricchi, Cagliari, Italy
| | - Maria Luisa Boi
- Azienda Ospedaliera Brotzu, San Michele Hospital, Intensive Care Unit, Piazzale Alessandro Ricchi, Cagliari, Italy
| | - Gabriele Finco
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato, Italy
| |
Collapse
|
5
|
Fernández Vecilla D, Aspichueta Vivanco C, Angulo López I, Baraia-Etxaburu Artetxe JM, Renzi F, Díaz de Tuesta del Arco JL. A case of septic arthritis caused by Capnocytophaga canimorsus in an HIV patient. Access Microbiol 2022; 4:acmi000368. [PMID: 36004364 PMCID: PMC9394666 DOI: 10.1099/acmi.0.000368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
Invasive infections caused by Capnocytophaga canimorsus, a Gram-negative rod found in the oral cavity of healthy dogs and cats, are rare but they are increasing worldwide. We report a case of septic arthritis in a native knee joint due to this micro-organism. A 57-year-old man, with a well-controlled chronic HIV infection, attended the Emergency Department because of left knee pain and shivering without measured fever. A knee arthrocentesis and a computed tomography scan were performed, revealing septic arthritis with collections in the left leg posterior musculature. He was admitted to the Infectious Diseases Department for antibiotic treatment. Initial synovial fluid was inoculated in blood culture bottles, and the anaerobic one was positive after 63 h. Gram stain revealed fusiform Gram-negative rods, identified as C. canimorsus by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) directly from the bottle. Identification was confirmed by 16S rRNA sequencing and serotyping was performed by PCR, with serovar A as the outcome. Due to an unfavourable clinical course, the patient required two surgical cleanings and after appropriate antibiotic treatment he was discharged 2 months later.
Collapse
Affiliation(s)
| | | | - Itziar Angulo López
- Basurto University Hospital, Avenida Montevideo n°18, 48013, Bilbao (Vizcaya), Spain
| | | | - Francesco Renzi
- Namur Research Institute for Life Sciences, Research Unit in Biology of Microorganisms, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | | |
Collapse
|
6
|
Fernández Vecilla D, Calvo Muro FE, Renzi F, Díaz de Tuesta Del Arco JL. [Sepsis caused by Capnocytophaga canimorsus in an immunocompetent patient]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2022; 35:304-306. [PMID: 35468716 PMCID: PMC9134879 DOI: 10.37201/req/006.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/26/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022]
Affiliation(s)
- D Fernández Vecilla
- Domingo Fernández Vecilla, Basurto University Hospital. 18 Avenida Montevideo, 48013, Bilbao (Vizcaya). Spain.
| | | | | | | |
Collapse
|
7
|
Merino I, de la Fuente A, Domínguez-Gil M, Eiros JM, Tedim AP, Bermejo-Martín JF. Digital PCR applications for the diagnosis and management of infection in critical care medicine. Crit Care 2022; 26:63. [PMID: 35313934 PMCID: PMC8935253 DOI: 10.1186/s13054-022-03948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10–25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.
Collapse
Affiliation(s)
- Irene Merino
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José María Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain. .,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| |
Collapse
|
8
|
Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
Collapse
Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
| |
Collapse
|
9
|
Irwin AD, Coin LJM, Harris PNA, Cotta MO, Bauer MJ, Buckley C, Balch R, Kruger P, Meyer J, Shekar K, Brady K, Fourie C, Sharp N, Vlad L, Whiley D, Beatson SA, Forde BM, Paterson D, Clark J, Hajkowicz K, Raman S, Bialasiewicz S, Lipman J, Schlapbach LJ, Roberts JA. Optimising Treatment Outcomes for Children and Adults Through Rapid Genome Sequencing of Sepsis Pathogens. A Study Protocol for a Prospective, Multi-Centre Trial (DIRECT). Front Cell Infect Microbiol 2021; 11:667680. [PMID: 34249774 PMCID: PMC8261237 DOI: 10.3389/fcimb.2021.667680] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/20/2021] [Indexed: 11/23/2022] Open
Abstract
Background Sepsis contributes significantly to morbidity and mortality globally. In Australia, 20,000 develop sepsis every year, resulting in 5,000 deaths, and more than AUD$846 million in expenditure. Prompt, appropriate antibiotic therapy is effective in improving outcomes in sepsis. Conventional culture-based methods to identify appropriate therapy have limited yield and take days to complete. Recently, nanopore technology has enabled rapid sequencing with real-time analysis of pathogen DNA. We set out to demonstrate the feasibility and diagnostic accuracy of pathogen sequencing direct from clinical samples, and estimate the impact of this approach on time to effective therapy when integrated with personalised software-guided antimicrobial dosing in children and adults on ICU with sepsis. Methods The DIRECT study is a pilot prospective, non-randomized multicentre trial of an integrated diagnostic and therapeutic algorithm combining rapid direct pathogen sequencing and software-guided, personalised antibiotic dosing in children and adults with sepsis on ICU. Participants and interventions DIRECT will collect microbiological and pharmacokinetic samples from approximately 200 children and adults with sepsis admitted to one of four ICUs in Brisbane. In Phase 1, we will evaluate Oxford Nanopore Technologies MinION sequencing direct from blood in 50 blood culture-proven sepsis patients recruited from consecutive patients with suspected sepsis. In Phase 2, a further 50 consecutive patients with suspected sepsis will be recruited in whom MinION sequencing will be combined with Bayesian software-guided (ID-ODS) personalised antimicrobial dosing. Outcome measures The primary outcome is time to effective antimicrobial therapy, defined as trough drug concentrations above the MIC of the pathogen. Secondary outcomes are diagnostic accuracy of MinION sequencing from whole blood, time to pathogen identification and susceptibility testing using sequencing direct from whole blood and from positive blood culture broth. Discussion Rapid pathogen sequencing coupled with antimicrobial dosing software has great potential to overcome the limitations of conventional diagnostics which often result in prolonged inappropriate antimicrobial therapy. Reduced time to optimal antimicrobial therapy may reduce sepsis mortality and ICU length of stay. This pilot study will yield key feasibility data to inform further, urgently needed sepsis studies. Phase 2 of the trial protocol is registered with the ANZCTR (ACTRN12620001122943). Trial registration Registered with the Australia New Zealand Clinical Trials Registry Number ACTRN12620001122943
Collapse
Affiliation(s)
- Adam D Irwin
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Patrick N A Harris
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Menino Osbert Cotta
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Michelle J Bauer
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Cameron Buckley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Ross Balch
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Peter Kruger
- Intensive Care Unit, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Jason Meyer
- Intensive Care Unit, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Kiran Shekar
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Adult Intensive Care Services and Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Kara Brady
- Adult Intensive Care Services and Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Cheryl Fourie
- Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, Brisbane, QLD, Australia
| | - Natalie Sharp
- Paediatric Intensive Care Unit, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia
| | - Luminita Vlad
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - David Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Brian M Forde
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - David Paterson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Julia Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Krispin Hajkowicz
- Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, Brisbane, QLD, Australia
| | - Sainath Raman
- Paediatric Intensive Care Unit, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia
| | - Seweryn Bialasiewicz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jeffrey Lipman
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Luregn J Schlapbach
- Paediatric Intensive Care Unit, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia.,Department of Pediatric and Neonatal Intensive Care, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jason A Roberts
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
10
|
Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform 2021; 22:6109725. [PMID: 33483726 DOI: 10.1093/bib/bbaa403] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.
Collapse
Affiliation(s)
- Dropen Sheka
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary
| |
Collapse
|
11
|
Tsunoda H, Nomi H, Okada K, Kenzaka T. Clinical course of Capnocytophaga canimorsus bacteremia from acute onset to life crisis. Clin Case Rep 2021; 9:266-268. [PMID: 33489170 PMCID: PMC7813053 DOI: 10.1002/ccr3.3511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 08/17/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Capnocytophaga canimorsus bacteremia can present without signs of sepsis just after onset. For patients with fever, discerning the history of an animal bite is crucial. If it is positive for a dog bite, antibiotic treatment should be started.
Collapse
Affiliation(s)
- Hideki Tsunoda
- Department of Family MedicineShiga University of Medical ScienceOtsuJapan
| | - Hidetomo Nomi
- Department of CardiologySaku Central Hospital Advanced Care CenterSakuJapan
| | - Kunihiko Okada
- Department of Emergency MedicineSaku Central Hospital Advanced Care CenterSakuJapan
| | - Tsuneaki Kenzaka
- Department of Internal MedicineHyogo Prefectural Tamba Medical CenterTambaJapan
- Division of Community Medicine and Career DevelopmentKobe University Graduate School of MedicineKobeJapan
| |
Collapse
|
12
|
Lamb HJ, Hayes BJ, Nguyen LT, Ross EM. The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock. Genes (Basel) 2020; 11:E1478. [PMID: 33317066 PMCID: PMC7763041 DOI: 10.3390/genes11121478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: 'crush-side genotyping' for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.
Collapse
Affiliation(s)
- Harrison J. Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4067, Australia; (B.J.H.); (L.T.N.); (E.M.R.)
| | | | | | | |
Collapse
|