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Li MN, Wang T, Wang N, Han Q, You XM, Zhang S, Zhang CC, Shi YQ, Qiao PZ, Man CL, Feng T, Li YY, Zhu Z, Quan KJ, Xu TL, Zhang GF. A detailed analysis of 16S rRNA gene sequencing and conventional PCR-based testing for the diagnosis of bacterial pathogens and discovery of novel bacteria. Antonie Van Leeuwenhoek 2024; 117:102. [PMID: 39012584 DOI: 10.1007/s10482-024-01999-1] [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: 01/18/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024]
Abstract
This study represents the first analysis of the bacterial community in chickens affected by swollen head syndrome, utilizing 16S rRNA gene sequencing. Samples were obtained from clinical laying chickens and were examined for the presence of Avibacterium paragallinarum (APG) and Ornithobacterium rhinotracheale (ORT) using conventional polymerase chain reaction (PCR). From the samples, five APG-positive (APG) and APG-negative (N-APG) samples were chosen, along with five specific pathogen-free chickens, for 16S rRNA gene sequencing. Results showed that APG and ORT were widely detected in the chicken samples with swollen head syndrome (SHS, 9/10), while APG was detected in all five specific pathogen-free (SPF) samples. In contrast, conventional PCR sensitivity was found to be inadequate for diagnosis, with only 35.7% (5/14) and 11.1% (1/9) sensitivity for APG and ORT, respectively, based on 16S rRNA gene sequencing data. Furthermore, 16S rRNA gene sequencing was able to quantify the bacteria in the samples, revealing that the relative abundance of APG in the APG group ranged from 2.7 to 81.3%, while the relative abundance of APG in the N-APG group ranged from 0.1 to 21.0%. Notably, a low level of APG was also detected in all 5 SPF samples. The study also identified a significant number of animal and human common bacterial pathogens, including but not limited to Gallibacterium anatis, Riemerella columbina, Enterococcus cecorum, Mycoplasma synoviae, Helicobacter hepaticus, and Staphylococcus lentus. In conclusion, 16S rRNA gene sequencing is a valuable tool for bacterial pathogen diagnosis and the discovery of novel bacterial pathogens, while conventional PCR is not reliable for diagnosis.
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Affiliation(s)
- Mei-Na Li
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Ting Wang
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Nan Wang
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Qiang Han
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Xue-Ming You
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Shuai Zhang
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Cui-Cui Zhang
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Yong-Qiang Shi
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Pei-Zhuang Qiao
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Cheng-Lian Man
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Teng Feng
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Yue-Yue Li
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China
| | - Zhuang Zhu
- Department of Basic and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
| | - Ke-Ji Quan
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China.
| | - Teng-Lin Xu
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China.
| | - George Fei Zhang
- International Joint Research Center for Microbiology and Infectious Diseases, Wohua Biotech, Binzhou, 256600, Shandong, China.
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Sasiene ZJ, LeBrun ES, Velappan N, Anderson AR, Patterson NH, Dufresne M, Farrow MA, Norris JL, Caprioli RM, Mach PM, McBride EM, Glaros TG. Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers. Analyst 2024; 149:3564-3574. [PMID: 38717518 DOI: 10.1039/d4an00325j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.
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Affiliation(s)
- Zachary J Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Erick S LeBrun
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nileena Velappan
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Austin R Anderson
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nathan H Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Melissa A Farrow
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Phillip M Mach
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Ethan M McBride
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Trevor G Glaros
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Oguni K, Fukushima S, Otsuka Y, Soejima Y, Kawaguchi M, Sazumi Y, Fujimori T, Iio K, Umakoshi N, Yamada K, Hagiya H, Otsuka F. Disseminated septic arthritis caused by Ureaplasma urealyticum in an immunocompromised patient with hypogammaglobulinemia after rituximab therapy. Infection 2024:10.1007/s15010-024-02301-1. [PMID: 38856807 DOI: 10.1007/s15010-024-02301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
PURPOSE Ureaplasma urealyticum is a rare pathogen associated with septic arthritis that predominantly affects patients with hypogammaglobulinemia. Bacterial identification of fastidious organisms is challenging because they are undetectable by routine culture testing. To the best of our knowledge, this is the first report of septic arthritis induced by U. urealyticum infection in Japan. CASE DESCRIPTION We describe the case of a 23-year-old Japanese female with secondary hypogammaglobulinemia (serum immunoglobulin level < 500 mg/dL), identified 8 years after treatment with rituximab. The patient presented with persistent fever and polyarthritis that were unresponsive to ceftriaxone and prednisolone. Contrast-enhanced computed tomography and gallium-67 scintigraphy revealed effusion and inflammation in the left sternoclavicular, hip, wrist, knee, and ankle joints. Although Gram staining and bacterial culture of the drainage fluid from the left hip joint were negative, the condition exhibited characteristics of purulent bacterial infection. The patient underwent empirical treatment with doxycycline, and her symptoms promptly resolved. Subsequent 16S ribosomal RNA (rRNA) gene sequencing of the joint fluid confirmed the presence of U. urealyticum, leading to the diagnosis of septic arthritis. Combination therapy with doxycycline and azithromycin yielded a favorable recovery from the inflammatory status and severe arthritic pain. CONCLUSION This case highlights U. urealyticum as a potential causative agent of disseminated septic arthritis, particularly in patients with hypogammaglobulinaemia. The 16S rRNA gene analysis proved beneficial for identifying pathogens in culture-negative specimens, such as synovial fluid, in suspected bacterial infections.
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Affiliation(s)
- Kohei Oguni
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan
- Department of Infectious Diseases, Okayama University Hospital, Okayama, Japan
| | - Shinnosuke Fukushima
- Department of Infectious Diseases, Okayama University Hospital, Okayama, Japan
- Department of Bacteriology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuki Otsuka
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan
| | - Yoshiaki Soejima
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan
| | - Marina Kawaguchi
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan
| | - Yosuke Sazumi
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan
| | - Takumi Fujimori
- Microbiology Division, Clinical Laboratory, Okayama University Hospital, Okayama, Japan
| | - Koji Iio
- Microbiology Division, Clinical Laboratory, Okayama University Hospital, Okayama, Japan
| | - Noriyuki Umakoshi
- Department of Radiology, Okayama University Hospital, Okayama, Japan
| | - Kazuki Yamada
- Department of Medical Materials for Musculoskeletal Reconstruction, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hideharu Hagiya
- Department of Infectious Diseases, Okayama University Hospital, Okayama, Japan
| | - Fumio Otsuka
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan.
- Department of Infectious Diseases, Okayama University Hospital, Okayama, Japan.
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Pietrzko E, Bögli S, Frick K, Ebner-Dietler S, Capone C, Imkamp F, Koliwer-Brandl H, Müller N, Keller E, Brandi G. Broad Range Eubacterial Polymerase Chain Reaction of Cerebrospinal Fluid Reduces the Time to Exclusion of and Costs Associated with Ventriculostomy-Related Infection in Hemorrhagic Stroke. Neurocrit Care 2024; 40:1109-1116. [PMID: 38087175 PMCID: PMC11147905 DOI: 10.1007/s12028-023-01888-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/31/2023] [Indexed: 01/04/2024]
Abstract
BACKGROUND Patients with hemorrhagic stroke and an external ventricular drain in situ are at risk for ventriculostomy-related-infections (VRI). Because of the contamination of the cerebrospinal fluid (CSF) with blood and the high frequency of false negative CSF culture, the diagnosis of VRI remains challenging. This study investigated the introduction of CSF broad range eubacterial polymerase chain reaction (ePCR) and its effect on frequency and duration of antibiotic therapy for VRI, neurocritical care unit (NCCU) length of stay, related costs, and outcome. METHODS Between 2020 and 2022, we prospectively included 193 patients admitted to the NCCU of the University Hospital of Zürich with hemorrhagic stroke and an external ventricular drain for more than 48 h. Patient characteristics, serum inflammatory markers, white blood cell count in CSF, use and duration of antibiotic treatment for VRI, microbiological findings (CSF cultures and ePCR tests), and NCCU length of stay were compared in patients with no infection, noncerebral infection, suspected VRI, and confirmed VRI. Data of patients with suspected VRI of this cohort were compared with a retrospective cohort of patients with suspected VRI treated at our NCCU before the introduction of CSF ePCR testing (2013-2019). RESULTS Out of 193 patients, 12 (6%) were diagnosed with a confirmed VRI, 66 (34%) with suspected VRI, 90 (47%) with a noncerebral infection, and 25 (13%) had no infection at all. Compared with the retrospective cohort of patients, the use of CSF ePCR resulted in a reduction of patients treated for suspected VRI for the whole duration of 14 days (from 51 to 11%). Furthermore, compared with the retrospective group of patients with suspected VRI (n = 67), after the introduction of CSF ePCR, patients with suspected VRI had shorter antibiotic treatment duration of almost 10 days and, hence, lower related costs with comparable outcome at 3 months. CONCLUSIONS The use of CSF ePCR to identify VRI resulted in shorter antibiotic treatment duration without changing the outcome, as compared with a retrospective cohort of patients with suspected VRI.
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Affiliation(s)
- Elisabeth Pietrzko
- Neurocritical Care Unit, Institute of Intensive Care, University Hospital of Zürich, Rämistrasse 100, 8091, Zürich, Switzerland.
| | - Stefan Bögli
- Neurocritical Care Unit, Institute of Intensive Care, University Hospital of Zürich, Rämistrasse 100, 8091, Zürich, Switzerland
- Department of Neurology, Clinical Neuroscience Center Zürich, University Hospital Zürich, Frauenklinikstrasse 26, 8091, Zürich, Switzerland
| | - Katja Frick
- Neurocritical Care Unit, Institute of Intensive Care, University Hospital of Zürich, Rämistrasse 100, 8091, Zürich, Switzerland
| | - Sabeth Ebner-Dietler
- Neurocritical Care Unit, Institute of Intensive Care, University Hospital of Zürich, Rämistrasse 100, 8091, Zürich, Switzerland
| | - Crescenzo Capone
- Neurocritical Care Unit, Institute of Intensive Care, University Hospital of Zürich, Rämistrasse 100, 8091, Zürich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 28/30, 8006, Zürich, Switzerland
| | - Hendrik Koliwer-Brandl
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 28/30, 8006, Zürich, Switzerland
| | - Nicolas Müller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Rämistrasse 100, 8091, Zürich, Switzerland
| | - Emanuela Keller
- Neurocritical Care Unit, Institute of Intensive Care, University Hospital of Zürich, Rämistrasse 100, 8091, Zürich, Switzerland
- Department of Neurosurgery, University Hospital Zürich, Frauenklinikstrasse 10, 8091, Zürich, Switzerland
| | - Giovanna Brandi
- Neurocritical Care Unit, Institute of Intensive Care, University Hospital of Zürich, Rämistrasse 100, 8091, Zürich, Switzerland
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Burban A, Słupik D, Reda A, Szczerba E, Grabowski M, Kołodzińska A. Novel Diagnostic Methods for Infective Endocarditis. Int J Mol Sci 2024; 25:1245. [PMID: 38279244 PMCID: PMC10816594 DOI: 10.3390/ijms25021245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Infective endocarditis (IE) remains a dangerous disease and continues to have a high mortality rate. Unfortunately, despite continuous improvements in diagnostic methods, in many cases, blood cultures remain negative, and the pathogen causing endocarditis is unknown. This makes targeted therapy and the selection of appropriate antibiotics impossible. Therefore, we present what methods can be used to identify the pathogen in infective endocarditis. These are mainly molecular methods, including PCR and MGS, as well as imaging methods using radiotracers, which offer more possibilities for diagnosing IE. However, they are still not widely used in the diagnosis of IE. The article summarizes in which cases we should choose them and what we are most hopeful about in further research into the diagnosis of IE. In addition, registered clinical trials that are currently underway for the diagnosis of IE are also presented.
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Affiliation(s)
- Anna Burban
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Dorota Słupik
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Aleksandra Reda
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Ewa Szczerba
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Grabowski
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Agnieszka Kołodzińska
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
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Kubiak J, Morgan A, Kirmaier A, Arnaout R, Riedel S. Universal PCR for bacteria, mycobacteria, and fungi: a 10-year retrospective review of clinical indications and patient outcomes. J Clin Microbiol 2023; 61:e0095223. [PMID: 38014970 PMCID: PMC10729690 DOI: 10.1128/jcm.00952-23] [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: 07/21/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Our work provides a retrospective analysis of universal PCR orders for bacteria, mycobacteria, and fungi across our institution across a 10-year period. We assessed the positivity rates for this diagnostic tool by test type and specimen type and, critically, studied whether and how the results influenced the outcomes from treatment change, to readmission, to death.
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Affiliation(s)
- Jeffrey Kubiak
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Alexandra Morgan
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Andrea Kirmaier
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Ramy Arnaout
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Stefan Riedel
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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Dumm RE, Glaser LJ, Rodino KG. Development of a scoring system to identify high-yield specimens for bacterial broad-range 16S rRNA gene PCR with sequencing at a tertiary care medical center. Am J Clin Pathol 2023; 160:477-482. [PMID: 37458096 DOI: 10.1093/ajcp/aqad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/25/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Broad-range bacterial polymerase chain reaction with sequencing (BRBPS) provides valuable diagnostic data, especially in cases of culture-negative infections. However, as BRBPS testing demonstrates generally low positivity, cost per impactful result can be high and commonly involves longer turnaround times compared with other methods, targeting use of this assay to high-yield situations remains a challenging goal. Diagnostic stewardship can help alleviate these challenges and increase clinical utility, yet not all laboratories have a dedicated stewardship team, and little formal guidance exists on identifying high-yield samples outside of specific clinical syndromes. In this study, we performed a retrospective review of 86 BRBPS orders from a tertiary care medical center, with a focus on identifying high-yield cases using an infectious markers scoring system, visualized inflammation or organism (VIO) score, to predict return of actionable diagnostic data. METHODS Using chart review, we evaluated how results from high VIO score or low VIO score specimens contributed to clinical management. RESULTS Testing low VIO score samples identified an organism in only 10% of samples, and of these positive results, 33% were considered to represent contamination. Despite negative routine workup and no identified pathogen via BRBPS, broad antimicrobial treatment was continued in 85% of cases with a low VIO score. In contrast, specimens with high VIO scores were more predictably positive by BRBPS, identified organisms that were universally considered pathogens, and provided opportunities to target or de-escalate antimicrobial therapy. CONCLUSIONS This study describes the VIO scoring system to guide the identification of high-yield samples and steward the appropriate use of BRBPS testing.
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Affiliation(s)
- Rebekah E Dumm
- Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, Washington University, St Louis, MO, US
| | - Laurel J Glaser
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
| | - Kyle G Rodino
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
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Lathe R, Schultek NM, Balin BJ, Ehrlich GD, Auber LA, Perry G, Breitschwerdt EB, Corry DB, Doty RL, Rissman RA, Nara PL, Itzhaki R, Eimer WA, Tanzi RE. Establishment of a consensus protocol to explore the brain pathobiome in patients with mild cognitive impairment and Alzheimer's disease: Research outline and call for collaboration. Alzheimers Dement 2023; 19:5209-5231. [PMID: 37283269 PMCID: PMC10918877 DOI: 10.1002/alz.13076] [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: 02/08/2023] [Accepted: 03/06/2023] [Indexed: 06/08/2023]
Abstract
Microbial infections of the brain can lead to dementia, and for many decades microbial infections have been implicated in Alzheimer's disease (AD) pathology. However, a causal role for infection in AD remains contentious, and the lack of standardized detection methodologies has led to inconsistent detection/identification of microbes in AD brains. There is a need for a consensus methodology; the Alzheimer's Pathobiome Initiative aims to perform comparative molecular analyses of microbes in post mortem brains versus cerebrospinal fluid, blood, olfactory neuroepithelium, oral/nasopharyngeal tissue, bronchoalveolar, urinary, and gut/stool samples. Diverse extraction methodologies, polymerase chain reaction and sequencing techniques, and bioinformatic tools will be evaluated, in addition to direct microbial culture and metabolomic techniques. The goal is to provide a roadmap for detecting infectious agents in patients with mild cognitive impairment or AD. Positive findings would then prompt tailoring of antimicrobial treatments that might attenuate or remit mounting clinical deficits in a subset of patients.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, Chancellor's Building, University of Edinburgh Medical School, Edinburgh, UK
| | | | - Brian J. Balin
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA 19131, USA
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | | | - George Perry
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Edward B. Breitschwerdt
- Intracellular Pathogens Research Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - David B. Corry
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Richard L. Doty
- Smell and Taste Center, Department of Otorhinolaryngology: Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert A. Rissman
- Department of Neurosciences, University of California, San Diego and VA San Diego Healthcare System, La Jolla, CA
| | | | - Ruth Itzhaki
- Institute of Population Ageing, University of Oxford, Oxford, UK
| | - William A. Eimer
- Genetics and Aging Research Unit, Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
- McCance Cancer Center for Brain Health, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
- McCance Cancer Center for Brain Health, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Intracell Research Group Consortium Collaborators
- David L. Hahn (Intracell Research Group, USA), Benedict C. Albensi (Nova Southeastern, USA), James St John (Griffith University, Australia), Jenny Ekberg (Griffith University, Australia), Mark L. Nelson (Intracell Research Group, USA), Gerald McLaughlin (National Institutes of Health, USA), Christine Hammond (Philadelphia College of Osteopathic Medicine, USA), Judith Whittum-Hudson (Wayne State University, USA), Alan P. Hudson (Wayne State University, USA), Guillaume Sacco (Université Cote d’Azur, Centre Hospitalier Universitaire de Nice, CoBTek, France), Alexandra Konig (Université Cote d’Azur and CoBTek, France), Bruno Pietro Imbimbo (Chiesi Farmaceutici, Parma, Italy), Nicklas Linz (Ki Elements Ltd, Saarbrücken, Germany), Nicole Danielle Bell (Author, 'What Lurks in the Woods'), Shima T. Moein (Smell and Taste Center, Department of Otorhinolaryngology, Perelman School of Medicine, University of Philadelphia, USA), Jürgen G. Haas (Infection Medicine, University of Edinburgh Medical School, UK)
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9
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Lin WH, Tsai TS. Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene. BIOLOGY 2023; 12:1206. [PMID: 37759605 PMCID: PMC10525742 DOI: 10.3390/biology12091206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023]
Abstract
A venomous snake's oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake's oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.
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Affiliation(s)
- Wen-Hao Lin
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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10
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Rein S, Sorowka A, Grünewald T, Kremer T. Microbiologic Analysis of Hand Infections: A Prospective Study. Surg Infect (Larchmt) 2023; 24:625-631. [PMID: 37646765 DOI: 10.1089/sur.2023.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Background: Hand infections are a common problem in emergency departments. Staphylococcus aureus is the main pathogen of both hand and blood stream infections. Therefore, the aim of the present study was to evaluate the frequency and impact of bacteremia in patients with hand infections to improve the microbiologic diagnostics. Patients and Methods: A prospective study of 90 patients with acute hand infections without antimicrobial pre-treatment was performed. Blood cultures were taken pre-operatively. If positive, transesophageal echocardiography was performed to rule out infectious endocarditis. Tissue samples were microbiologically processed using standardized culture media. If negative, a broad-spectrum bacterial 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) was applied. The etiology and location of the infection, the length of hospital stay, the number of surgical interventions, and the inflammatory parameters were obtained. Results: Six patients with bacteremia (6.6%) were diagnosed, after animal bites (n = 3) and intra-articular empyema (n = 3). Pathogens included Staphylococcus pettenkoferi, Pasteurella multocida, Staphylococcus epidermidis, Staphylococcus aureus, and Bacteroides pyogenes. No case of infective endocarditis was detected. Patients with bacteremia required more surgical interventions (p = 0.002), had a longer hospital stay (p < 0.001), higher plasma C-reactive protein (CRP; p = 0.016), and a higher age (p = 0.002) compared with those without bacteremia. In 14 cases (15.6%) no pathogen was detected by culture, whereas the subsequent broad-spectrum PCR diagnosed three cases (21.4%). Conclusions: Pre-operative blood cultures in patients with hand infections are important to detect bacteremia as an essential marker of clinical severity. Those blood cultures are indicated after deep animal bites and joint empyema. A precise identification of pathogens is fundamental for an effective treatment of hand infections, for which a 16S rRNA gene PCR can contribute in culture-negative tissue samples.
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Affiliation(s)
- Susanne Rein
- Department of Plastic and Hand Surgery, Burn Unit, Hospital Sankt Georg, Leipzig, Germany
- Martin-Luther-University Halle-Wittenberg, Germany
| | - Anne Sorowka
- Department of Plastic and Hand Surgery, Burn Unit, Hospital Sankt Georg, Leipzig, Germany
| | - Thomas Grünewald
- Department of Infectious Diseases and Tropical Medicine, Hospital Chemnitz, Chemnitz, Germany
| | - Thomas Kremer
- Department of Plastic and Hand Surgery, Burn Unit, Hospital Sankt Georg, Leipzig, Germany
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11
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Batool M, Galloway-Peña J. Clinical metagenomics-challenges and future prospects. Front Microbiol 2023; 14:1186424. [PMID: 37448579 PMCID: PMC10337830 DOI: 10.3389/fmicb.2023.1186424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.
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Affiliation(s)
| | - Jessica Galloway-Peña
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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12
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Chen Y, Hu Y, Lu X. Polyethersulfone-Based Microfluidic Device Integrated with DNA Extraction on Paper and Recombinase Polymerase Amplification for the Detection of Salmonella enterica. ACS Sens 2023; 8:2331-2339. [PMID: 37228176 DOI: 10.1021/acssensors.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Rising consumption, large-scale production, and widespread distribution have been accompanied by an increase in the number of Salmonella infections reported to implicate contaminated food products. We developed a portable origami microfluidic device that enabled rapid detection of S. enterica from sample preparation to end-point detection, including nucleic acid extraction on paper dipstick without pipetting, nucleic acid amplification using isothermal recombinase polymerase amplification (RPA), and lateral flow assay for results readout. We also explored the feasibility of the polyethersulfone (PES) membrane as a new reaction matrix against the widely used chromatography paper to optimize nucleic acid amplification. Nucleic acid amplification was achieved within 20 min and demonstrated 100% specificity to S. enterica. The limit of detection of this PES-based microfluidic device was 260 CFU/mL and equivalent to RPA reaction in tube. A chromatography paper-based microfluidic device was found 1-log less in sensitivity for Salmonella detection compared to the use of PES. This PES-based microfluidic device could detect S. enterica in lettuce, chicken breast, and milk at concentrations of 6 CFU/g, 9 CFU/g, and 58 CFU/mL, respectively, after 6 h enrichment. PES has shown high compatibility to isothermal nucleic acid amplification and great potential to be implemented as an integrated sample-to-answer microfluidic device for the detection of pathogens in various food commodities.
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Affiliation(s)
- Yunxuan Chen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yaxi Hu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Food Science Program, Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Food Science and Agricultural Chemistry, McGill University, 21111 Lakeshore Road,Sainte-Anne-de-Bellevue H9X 3V9 Quebec, Canada
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13
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Killington K, Lee N, Asher R, Farrant O, Stone N. Purpura fulminans secondary to Capnocytophaga canimorsus bacteraemia following a dog bite: A case report and review of literature. Access Microbiol 2023; 5:acmi000505.v3. [PMID: 37424553 PMCID: PMC10323800 DOI: 10.1099/acmi.0.000505.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/16/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Infection due to Capnocytophaga canimorsus may result in a wide variety of clinical presentations. We present a case of life-threatening Capnocytophaga canimorsus infection with evolution of ecchymosis to purpura fulminans. Case description We present a case of a 43-year-old male with a history of excessive alcohol consumption who presented with features of sepsis following a dog bite. This was associated with a striking, widespread purpuric rash. A causative pathogen, C. canimorsus was identified through blood culture and 16S RNA sequencing. His initially purpuric rash underwent bullous transformation and was diagnosed clinically as purpura fulminans, confirmed on skin biopsy. He made a full recovery with prompt antimicrobial therapy, initially with co-amoxiclav but escalated to clindamycin and meropenem due to clinical deterioration and concerns of beta-lactamase resistance. Discussion β-Lactamase producing Capnocytophaga strains are of increasing concern. This particular concern is reflected in our case as 5 days into treatment with β-lactamase inhibitor combination therapy the patients clinical condition deteriorated but demonstrably improved on switching to a carbapenem.The development of biopsy proven purpura fulminans in this immunocompetent case is a rare severe manifestation of the previously reported manifestation of disseminated intravascular coagulation (DIC) in Capnocytophaga bacteraemia. The case reported describes characteristics common with other DIC presentations such as the presence of clinical risk factors (history of excessive alcohol consumption) and symmetrical involvement. However, an unusual feature in that initial purpuric lesions were followed by the development of a bullous appearance and peripheral necrotic features concerning for purpura fulminans and confirmed with skin biopsy.
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Affiliation(s)
| | - Nathaniel Lee
- Hospital Of Tropical Diseases, Mortimer Market, Capper St, London WC1E 6JB, UK
| | - Radha Asher
- University College Hospital London, 235 Euston Road, N1 2BU, UK
| | - Olivia Farrant
- University College Hospital London, 235 Euston Road, N1 2BU, UK
| | - Neil Stone
- University College Hospital London, 235 Euston Road, N1 2BU, UK
- Hospital Of Tropical Diseases, Mortimer Market, Capper St, London WC1E 6JB, UK
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14
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Gates L, Mistry T, Ogunbiyi O, Kite KA, Klein NJ, Sebire NJ, Alber DG. Identification of bacterial pathogens in sudden unexpected death in infancy and childhood using 16S rRNA gene sequencing. Front Microbiol 2023; 14:1171670. [PMID: 37396359 PMCID: PMC10309030 DOI: 10.3389/fmicb.2023.1171670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/05/2023] [Indexed: 07/04/2023] Open
Abstract
Background Sudden unexpected death in infancy (SUDI) is the most common cause of post-neonatal death in the developed world. Following an extensive investigation, the cause of ~40% of deaths remains unknown. It is hypothesized that a proportion of deaths are due to an infection that remains undetected due to limitations in routine techniques. This study aimed to apply 16S rRNA gene sequencing to post-mortem (PM) tissues collected from cases of SUDI, as well as those from the childhood equivalent (collectively known as sudden unexpected death in infancy and childhood or SUDIC), to investigate whether this molecular approach could help identify potential infection-causing bacteria to enhance the diagnosis of infection. Methods In this study, 16S rRNA gene sequencing was applied to de-identified frozen post-mortem (PM) tissues from the diagnostic archive of Great Ormond Street Hospital. The cases were grouped depending on the cause of death: (i) explained non-infectious, (ii) infectious, and (iii) unknown. Results and conclusions In the cases of known bacterial infection, the likely causative pathogen was identified in 3/5 cases using bacterial culture at PM compared to 5/5 cases using 16S rRNA gene sequencing. Where a bacterial infection was identified at routine investigation, the same organism was identified by 16S rRNA gene sequencing. Using these findings, we defined criteria based on sequencing reads and alpha diversity to identify PM tissues with likely infection. Using these criteria, 4/20 (20%) cases of unexplained SUDIC were identified which may be due to bacterial infection that was previously undetected. This study demonstrates the potential feasibility and effectiveness of 16S rRNA gene sequencing in PM tissue investigation to improve the diagnosis of infection, potentially reducing the number of unexplained deaths and improving the understanding of the mechanisms involved.
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Affiliation(s)
- Lily Gates
- Infection, Immunity and Inflammation, UCL GOS Institute of Child Health, London, United Kingdom
| | - Talisa Mistry
- NIHR GOSH Biomedical Research Centre, Histopathology Department, Camelia Botnar Laboratories, Great Ormond Street Hospital, London, United Kingdom
| | - Olumide Ogunbiyi
- NIHR GOSH Biomedical Research Centre, Histopathology Department, Camelia Botnar Laboratories, Great Ormond Street Hospital, London, United Kingdom
| | - Kerry-Anne Kite
- Infection, Immunity and Inflammation, UCL GOS Institute of Child Health, London, United Kingdom
| | - Nigel J. Klein
- Infection, Immunity and Inflammation, UCL GOS Institute of Child Health, London, United Kingdom
| | - Neil J. Sebire
- NIHR GOSH Biomedical Research Centre, Histopathology Department, Camelia Botnar Laboratories, Great Ormond Street Hospital, London, United Kingdom
| | - Dagmar G. Alber
- Infection, Immunity and Inflammation, UCL GOS Institute of Child Health, London, United Kingdom
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15
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Aasa J, Tiselius E, Sinha I, Edman G, Wahlund M, Hedengren SS, Nilsson A, Berggren A. The Applicability of a 2-Transcript Signature to Identify Bacterial Infections in Children with Febrile Neutropenia. CHILDREN (BASEL, SWITZERLAND) 2023; 10:966. [PMID: 37371198 DOI: 10.3390/children10060966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/30/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
Febrile neutropenia is a common complication during chemotherapy in paediatric cancer care. In this setting, clinical features and current diagnostic tests do not reliably distinguish between bacterial and viral infections. Children with cancer (n = 63) presenting with fever and neutropenia were recruited for extensive microbiological and blood RNA sampling. RNA sequencing was successful in 43 cases of febrile neutropenia. These were classified as having probable bacterial infection (n = 17), probable viral infection (n = 13) and fever of unknown origin (n = 13) based on microbiological defined infections and CRP cut-off levels. RNA expression data with focus on the 2-transcript signature (FAM89A and IFI44L), earlier shown to identify bacterial infections with high specificity and sensitivity, was implemented as a disease risk score. The median disease risk score was higher in the probable bacterial infection group, -0.695 (max 2.795; min -5.478) compared to the probable viral infection group -3.327 (max 0.218; min -7.861), which in ROC analysis corresponded to a sensitivity of 0.88 and specificity of 0.54 with an AUC of 0.80. To further characterise the immune signature, analysis of significantly expressed genes and pathways was performed and upregulation of genes associated to antibacterial responses was present in the group classified as probable bacterial infection. Our results suggest that the 2-transcript signature may have a potential use as a diagnostic tool to identify bacterial infections in immunosuppressed children with febrile neutropenia.
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Affiliation(s)
- Johannes Aasa
- Division of Pediatric Oncology, Department of Women and Children's Health, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Eva Tiselius
- Division of Pediatric Oncology, Department of Women and Children's Health, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Indranil Sinha
- Division of Pediatric Oncology, Department of Women and Children's Health, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Gunnar Edman
- Department of Clinical Sciences, Karolinska Institutet, 17177 Stockholm, Sweden
- Research and Development, Norrtälje Hospital, 76145 Norrtälje, Sweden
| | | | - Shanie Saghafian Hedengren
- Division of Pediatric Oncology, Department of Women and Children's Health, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Anna Nilsson
- Division of Pediatric Oncology, Department of Women and Children's Health, Karolinska Institutet, 17177 Stockholm, Sweden
- Division of Pediatric Hematology-Oncology, Tema Barn, Astrid Lindgren Children's Hospital, 17164 Solna, Sweden
| | - Anna Berggren
- Division of Pediatric Oncology, Department of Women and Children's Health, Karolinska Institutet, 17177 Stockholm, Sweden
- Research and Development, Norrtälje Hospital, 76145 Norrtälje, Sweden
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16
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Ben-Artzi A, Horowitz DL, Mandelin AM, Tabechian D. Best practices for ultrasound-guided synovial biopsy in the United States. Best Pract Res Clin Rheumatol 2023; 37:101834. [PMID: 37263809 DOI: 10.1016/j.berh.2023.101834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023]
Abstract
The target organ in many forms of inflammatory arthritis is the synovium. However, synovial tissue has historically been perceived as either difficult to obtain or of little practical value. Ultrasound-guided synovial biopsy [UGSB] is a safe and well-tolerated bedside procedure that is established in Europe and rapidly growing in popularity in the United States. The technique can be mastered by rheumatologists who are already experienced in ultrasound-guided procedures such as joint aspirations. The USGB procedure allows the proceduralist to access small, medium, and large joints and is inexpensive and less invasive compared to surgical alternatives. The relative ease of obtaining this tissue, along with recent research suggesting that synovium may have more clinical and investigational utility than previously thought, has led clinicians and researchers to a new appreciation of the role of synovial biopsy in both the clinical and research setting. In this manuscript, the authors present recommendations on best practices for ultrasound-guided synovial biopsy in the United States, based on our initial training with well-established experts overseas and our own subsequent collective experience in performing numerous synovial biopsies in the United States over the past 7 years for both clinical and research indications. We envision a future where UGSB is more frequently incorporated in the standard diagnostic workup of arthritis and drives novel research initiatives.
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Affiliation(s)
- Ami Ben-Artzi
- Cedars Sinai Medical Center Staff Member, Los Angeles, CA, USA; Scripps Memorial Hospital Staff Member, San Diego, CA, USA.
| | - Diane L Horowitz
- Zucker School of Medicine at Hofstra/Northwell, Department of Medicine, Division of Rheumatology, Great Neck, NY, USA
| | - Arthur M Mandelin
- Northwestern University Feinberg School of Medicine, Department of Medicine, Division of Rheumatology, Chicago, IL, USA
| | - Darren Tabechian
- Department of Medicine, Division of Allergy Immunology and Rheumatology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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17
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Johnson C, Marquez C, Olson D, Ward T, Cheney S, Hulten T, Ton T, Webb CR, Dunn J. Development and performance of a multiplex PCR assay for the detection of bacteria in sterile body fluids. Future Microbiol 2023; 18:187-195. [PMID: 36820638 DOI: 10.2217/fmb-2022-0226] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Aim: To assess the performance characteristics of a lab-developed multiplex PCR assay for the detection of common bacterial pathogens associated with infections in pediatric patients from normally sterile sites, such as cerebrospinal fluid, synovial and pleural fluids. Materials & methods: A total of 272 specimens were tested by PCR and traditional culture methods to assess the presence of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, methicillin-sensitive and methicillin-resistant Staphylococcus aureus, and Kingella kingae. Results: Compared with culture, the overall positive and negative percentage agreement of the PCR were 95.9% and 74.1%, respectively. Conclusion: This sterile body fluid PCR affords a rapid and sensitive alternative for bacterial detection, allowing for more timely pathogen-directed antimicrobial therapy.
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Affiliation(s)
- Coreen Johnson
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Marquez
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Damon Olson
- Department of Pathology, Children's Minnesota, Minneapolis, MN 55404, USA
| | - Tabitha Ward
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen Cheney
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tina Hulten
- Department of Pediatrics, Section of Infectious Disease, Baylor College of Medicine, TX 77030, USA
| | - Trang Ton
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - C R Webb
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - James Dunn
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
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18
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Tuft S, Bunce C, De S, Thomas J. Utility of investigation for suspected microbial keratitis: a diagnostic accuracy study. Eye (Lond) 2023; 37:415-420. [PMID: 35102245 PMCID: PMC9905491 DOI: 10.1038/s41433-022-01952-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The true disease status of a population with suspected microbial keratitis (MK) cannot be verified. There is not an accurate (gold) reference standard to confirm infection and inter-test comparisons of sensitivity and specificity therefore lead to bias with questionable estimates of test utility. We present an alternative method to report results. METHODS We used a decision to treat as the definition for MK. We retrospectively compared the results of corneal culture and polymerase chain reaction (PCR) as these are objective tests available for the three principal groups of pathogens. We then estimated the potential contribution of positive results, either alone or in combination, to support the working diagnosis. RESULTS We included 2021 (77.4%) eyes with suspected bacterial keratitis, 365 (14.0%) with suspected acanthamoeba keratitis, and 226 (8.6%) with suspected fungal keratitis, all treated between July 2013 and December 2019. In these groups, there were 51.6% positive culture and 6.5% positive PCR results for bacteria, 19.0% and 40.5% for acanthamoeba, and 28.3% and 15.0% for fungi. Between groups the differences in the proportions of positive results from culture and PCR was statistically significant (P < 0.001). The added benefit of PCR to the result of culture in identifying a potential pathogen was 1.4% for bacteria (P = 0.6292), 24.4% for acanthamoeba (P = 0.0001), and 5.8% for fungi (P = 0.3853). CONCLUSIONS For suspected MK a comparison of the test positivity rate is an easily comprehensible outcome measure of test utility.
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Affiliation(s)
- Stephen Tuft
- Moorfields Eye Hospital, 162 City Road, London, EC1V 2PD, UK.
| | - Catey Bunce
- The Royal Marsden Hospital, 203 Fulham Rd, Chelsea, London, SW3 6JJ, UK
| | - Surjo De
- Department of Clinical Microbiology, University College London Hospitals, 235 Euston Rd, London, NW1 2BU, UK
| | - John Thomas
- Micropathology Limited, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
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19
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Rawson TM, Antcliffe DB, Wilson RC, Abdolrasouli A, Moore LSP. Management of Bacterial and Fungal Infections in the ICU: Diagnosis, Treatment, and Prevention Recommendations. Infect Drug Resist 2023; 16:2709-2726. [PMID: 37168515 PMCID: PMC10166098 DOI: 10.2147/idr.s390946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/22/2023] [Indexed: 05/13/2023] Open
Abstract
Bacterial and fungal infections are common issues for patients in the intensive care unit (ICU). Large, multinational point prevalence surveys have identified that up to 50% of ICU patients have a diagnosis of bacterial or fungal infection at any one time. Infection in the ICU is associated with its own challenges. Causative organisms often harbour intrinsic and acquired mechanisms of drug-resistance, making empiric and targeted antimicrobial selection challenging. Infection in the ICU is associated with worse clinical outcomes for patients. We review the epidemiology of bacterial and fungal infection in the ICU. We discuss risk factors for acquisition, approaches to diagnosis and management, and common strategies for the prevention of infection.
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Affiliation(s)
- Timothy M Rawson
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Hammersmith Hospital, London, UK
- Centre for Antimicrobial Optimisation, Imperial College London, Imperial College London, London, UK
- David Price Evan’s Group in Infectious Diseases and Global Health, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
- Correspondence: Timothy M Rawson, Health Protection Research Unit in Healthcare Associated Infections & Antimicrobial Resistance, Hammersmith Hospital, Du Cane Road, London, W12 0NN, United Kingdom, Email
| | - David B Antcliffe
- Centre for Antimicrobial Optimisation, Imperial College London, Imperial College London, London, UK
- Division Anaesthesia, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Richard C Wilson
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Hammersmith Hospital, London, UK
- Centre for Antimicrobial Optimisation, Imperial College London, Imperial College London, London, UK
- David Price Evan’s Group in Infectious Diseases and Global Health, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | | | - Luke S P Moore
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Hammersmith Hospital, London, UK
- Chelsea & Westminster NHS Foundation Trust, London, UK
- North West London Pathology, Imperial College Healthcare NHS Trust, London, UK
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20
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Eamsakulrat P, Santanirand P, Phuphuakrat A. Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens. Microbiol Spectr 2022; 10:e0209422. [PMID: 36374024 PMCID: PMC9769669 DOI: 10.1128/spectrum.02094-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a "gold standard," the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.
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Affiliation(s)
- Pruke Eamsakulrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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21
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Pitashny M, Kadry B, Shalaginov R, Gazit L, Zohar Y, Szwarcwort M, Stabholz Y, Paul M. NGS in the clinical microbiology settings. Front Cell Infect Microbiol 2022; 12:955481. [PMID: 36339334 PMCID: PMC9627026 DOI: 10.3389/fcimb.2022.955481] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Abstract
We hypothesized that targeted NGS sequencing might have an advantage over Sanger sequencing, especially in polymicrobial infections. The study included 55 specimens from 51 patients. We compared targeted NGS to Sanger sequencing in clinical samples submitted for Sanger sequencing. The overall concordance rate was 58% (32/55) for NGS vs. Sanger. NGS identified 9 polymicrobial and 2 monomicrobial infections among 19 Sanger-negative samples and 8 polymicrobial infections in 11 samples where a 16S gene was identified by gel electrophoresis, but could not be mapped to an identified pathogen by Sanger. We estimated that NGS could have contributed to patient management in 6/18 evaluated patients and thus has an advantage over Sanger sequencing in certain polymicrobial infections.
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Affiliation(s)
- Milena Pitashny
- Clinical and Research Microbiome Center, Research Division, Rambam Health Care Campus, Haifa, Israel
- Clinical Microbiology Laboratories, Laboratories Division, Rambam Health Care Campus, Haifa, Israel
- *Correspondence: Milena Pitashny,
| | - Balqees Kadry
- Clinical and Research Microbiome Center, Research Division, Rambam Health Care Campus, Haifa, Israel
| | - Raya Shalaginov
- Clinical Microbiology Laboratories, Laboratories Division, Rambam Health Care Campus, Haifa, Israel
| | - Liat Gazit
- Clinical Microbiology Laboratories, Laboratories Division, Rambam Health Care Campus, Haifa, Israel
| | - Yaniv Zohar
- Pathology Institute, Rambam Health Care Campus, Haifa, Israel
| | - Moran Szwarcwort
- Clinical Microbiology Laboratories, Laboratories Division, Rambam Health Care Campus, Haifa, Israel
| | - Yoav Stabholz
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Mical Paul
- Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
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22
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Ragothaman KK, Elmarsafi TX, Mobaraki A, Zarick CS, Evans KK, Steinberg JS, Attinger CE, Kim PJ. Evaluation of Polymerase Chain Reaction in the Identification and Quantification of Clinically Relevant Bacterial Species in Lower Extremity Wound Infections. J Foot Ankle Surg 2022; 61:713-718. [PMID: 34895822 DOI: 10.1053/j.jfas.2020.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 02/03/2023]
Abstract
Identification of bacteria by polymerase chain reaction (PCR) is known to be more sensitive than culture, which brings to question the clinical applicability of the results. In this study, we evaluate the ability of PCR to detect clinically relevant bacterial species in lower extremity wound infections requiring operative debridement, as well as the quantitative change in biodiversity and bacterial load reflected by PCR during the course of treatment. Thirty-four infected lower extremity were examined by analysis of 16S ribosomal RNA subunit and by culture. McNemar's test was used to measure the concordance of clinically relevant bacterial species identified by PCR compared to culture during each debridement. Change in wound biodiversity from initial presentation to final closure was evaluated by Wilcoxon signed-rank test. Kaplan-Meier survival curve was used to characterize change in measured bacterial load over the course of operative debridement. A total of 15 and 12 clinically relevant bacterial species were identified by PCR and culture, respectively. The most common bacterial species identified were Coagulase-negative Staphylococcus, Staphylococcus aureus, and Enterococcus spp. PCR was less likely to detect Enterococcus spp. on initial debridement and Coagulase-negative Staphylococcus on closure in this study population. A significant decrease in mean number of clinically relevant species detected from initial debridement to closure was reflected by culture (p = .0188) but not by PCR (p = .1848). Both PCR (p = .0128) and culture (p = .0001) depicted significant reduction in mean bacterial load from initial debridement to closure. PCR is able to identify common clinically relevant bacterial species in lower extremity surgical wound infections. PCR displays increased sensitivity compared to culture with relation to detection of biodiversity, rather than bacterial load. Molecular diagnostics and conventional culture may serve a joint purpose to assist with rendering clinical judgment in complex wound infections.
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Affiliation(s)
- Kevin K Ragothaman
- Foot and Ankle Surgeon, Foot and Ankle Associates, Los Gatos and Cupertino, CA.
| | | | | | - Caitlin S Zarick
- Assistant Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - Karen K Evans
- Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - John S Steinberg
- Assistant Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - Christopher E Attinger
- Professor, Department of Plastic Surgery, Georgetown University School of Medicine, Washington, DC
| | - Paul J Kim
- Professor, Departments of Plastic and Orthopaedic Surgery, University of Texas Southwestern, Dallas, TX
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23
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Mularoni A, Mikulska M, Barbera F, Graziano E, Medaglia AA, Di Carlo D, Monaco F, Bellavia D, Cascio A, Raffa G, Sciacca S, Luca A, Pilato M, Conaldi PG. Molecular Analysis With 16S rRNA PCR/Sanger Sequencing and Molecular Antibiogram Performed on DNA Extracted From Valve Improve Diagnosis and Targeted Therapy of Infective Endocarditis: A Prospective Study. Clin Infect Dis 2022; 76:e1484-e1491. [PMID: 35686318 PMCID: PMC9907470 DOI: 10.1093/cid/ciac452] [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: 03/29/2022] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Molecular analysis (MA) on heart valve (HV) improves the microbiologic diagnosis of infectious endocarditis (IE). The main drawback of MA is the lack of antimicrobial susceptibility information. METHODS We conducted a prospective cohort observational study of consecutive adult patients from April 2012 to May 2021 who underwent valve surgery at our hospital. The performance of MA, blood cultures (BC) and valve cultures (VC), and the diagnostic and therapeutic impact of MA were evaluated. Molecular antibiogram results were compared to culture-based antimicrobial susceptibility testing (AST). RESULTS A total of 137 patients with definite IE and 52 patients with no IE were enrolled in the study. Among IE cases BC, VC, and MA were positive in 75 (55%), 30 (22%), and 120 (88%) of IE cases, respectively. Among 62 cases of BC-negative IE (BCNE), 57 achieved diagnosis with MA. MA led to a change of antimicrobial therapy in 92% of BCNE. MA was negative in 100% of patients with no IE. Molecular antibiogram performed on 17 valve specimens that resulted positive for pathogens potential carrier of genes encoding for multidrug resistant mechanisms showed 100% concordance with AST. CONCLUSIONS MA showed a high specificity and sensitivity in etiological diagnosis of IE. Molecular antibiogram could overcome the major limitation of MA that is the lack of susceptibility testing. We advocate for the inclusion of MA among diagnostic criteria for IE and for a more extensive use of molecular antibiogram when the culture result is negative, and MA is the only positive test.
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Affiliation(s)
- Alessandra Mularoni
- Correspondence: A. Mularoni, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Via Ernesto Tricomi 5, 90100, Palermo, Italy ()
| | - Malgorzata Mikulska
- Division of Infectious Diseases, University of Genoa (DISSAL), Genova, Italy,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Floriana Barbera
- Pathology Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Elena Graziano
- Infectious Diseases Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy,Infectious and Tropical Diseases Unit, Department of Medicine and Surgery, University of Insubria, ASST-Sette Laghi, Varese, Italy
| | | | - Daniele Di Carlo
- Pathology Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Francesco Monaco
- Pathology Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Diego Bellavia
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Antonio Cascio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Infectious Diseases Unit, University of Palermo, Palermo, Italy
| | - Giuseppe Raffa
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Sergio Sciacca
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Angelo Luca
- Department of Diagnostic and Therapeutic Services, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Michele Pilato
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
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24
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Multiple Polymerase Chain Reaction for Direct Detection of Bloodstream Infection After Cardiac Surgery in a PICU. Crit Care Explor 2022; 4:e0707. [PMID: 35651736 PMCID: PMC9150881 DOI: 10.1097/cce.0000000000000707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Nosocomial infections are a prevalent cause of death and complications in critically ill children. Conventional cultures are able to detect only up to 25% of bacteremia. Several studies have suggested that molecular tests could be a faster and effective tool for detection of bacterial infections. The objective of this study is to compare molecular tests for bacterial detection in whole blood samples, with routine blood culture for the diagnosis of nosocomial bloodstream infections (BSIs).
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25
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Thevis M, Leow TYS, Bekkers S, Otten J, Waterval JJ, Derks J, Buil JB, Kunst DPM, Jansen TTG. Diagnosis, treatment and prognosis of otomastoiditis induced by Fusobacterium necrophorum: A retrospective multicentre cohort study. Anaerobe 2022; 76:102587. [PMID: 35595214 DOI: 10.1016/j.anaerobe.2022.102587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/01/2022]
Abstract
OBJECTIVES Otomastoiditis caused by the anaerobic Fusobacterium necrophorum (F. necrophorum) often induces severe complications, such as meningitis and sinus thrombosis. Early diagnosis is difficult, partly because little is known about specific early signs. Comprehensive research about clinically chosen antimicrobial therapy has not been done yet and prognostic information about otomastoiditis caused by F. necrophorum is scarce. More knowledge about this subject is required. METHODS In this retrospective cohort study, we included all cases of otomastoiditis caused by F. necrophorum treated in two university medical centres in the Netherlands during the past 10 years. Data was gathered from patient records and analysed using independent sample T-tests and Chi2-tests. RESULTS This study reveals that otomastoiditis caused by F. necrophorum potentially induces neurological sequelae. Thereby, 80% of all included patients (n = 16) needed readmission within six months due to recurrence or complications of otomastoiditis caused by F. necrophorum. Mean (range) of age, CRP and temperature were 4.5 years (0.9-29.3), 243 mg/L (113-423) and 40 °C (37-41). All patients were hospitalized and treated with antibiotics, mostly metronidazole (n = 13/16) and a β -lactam (n = 15/16). Additional treatment contained low molecular weight heparin (83%, n = 10/12), dexamethasone (78%, n = 7/9) and/or surgery (80%, n = 12/16, whereof 9/12 mastoidectomy). CONCLUSIONS Patients and/or their parents need to be informed about this potential unfortunate prognosis when otomastoiditis caused by F. necrophorum is diagnosed. To improve early diagnosis, otomastoiditis caused by F. necrophorum should be suspected and therefore immediately cultured when a) young children present with otomastoiditis, with b) high CRP values, and/or c) vomiting and decreased consciousness.
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Affiliation(s)
- Madelon Thevis
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| | - Theresa Y S Leow
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| | - Stijn Bekkers
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| | - Josje Otten
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Maastricht University Medical Center, P. Debyelaan 25, 6229, HX, Maastricht, the Netherlands.
| | - Jerome J Waterval
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Maastricht University Medical Center, P. Debyelaan 25, 6229, HX, Maastricht, the Netherlands.
| | - Jolanda Derks
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| | - Jochem B Buil
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Dirk P M Kunst
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Maastricht University Medical Center, P. Debyelaan 25, 6229, HX, Maastricht, the Netherlands.
| | - Thijs T G Jansen
- Dutch Academic Alliance Skull Base Pathology, Radboud University Medical Center, Maastricht University Medical Center+, Nijmegen/Maastricht, the Netherlands; Department of Otorhinolaryngology - Head and Neck Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
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26
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Egli K, Risch M, Risch L, Bodmer T. Comparison of an automated DNA extraction and 16S rDNA real time PCR/sequencing diagnostic method using optimized reagents with culture during a 15-month study using specimens from sterile body sites. BMC Microbiol 2022; 22:119. [PMID: 35501697 PMCID: PMC9063205 DOI: 10.1186/s12866-022-02542-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/18/2022] [Indexed: 11/25/2022] Open
Abstract
Background 16S rDNA-PCR for the identification of a bacterial species is an established method. However, the DNA extraction reagents as well as the PCR reagents may contain residual bacterial DNA, which consequently generates false-positive PCR results. Additionally, previously used methods are frequently time-consuming. Here, we describe the results obtained with a new technology that uses DNA-free reagents for automated DNA extraction and subsequent real time PCR using sterile clinical specimens. Results In total, we compared 803 clinical specimens using real time PCR and culturing. The clinical specimens were mainly of orthopedic origin received at our diagnostic laboratory. In 595 (74.1%) samples, the results were concordant negative, and in 102 (12.7%) the results were concordant positive. A total of 170 (21.2%) clinical specimens were PCR-positive, of which 62 (36.5% from PCR positive, 7.7% in total) gave an additional benefit to the patient since only the PCR result was positive. Many of these 62 positive specimens were strongly positive based on crossingpoint values (54% < Cp 30), and these 62 positive clinical specimens were diagnosed as medically relevant as well. Thirty-eight (4.2%) clinical specimens were culture-positive (25 of them were only enrichment culture positive) but PCR-negative, mainly for S. epidermidis, S. aureus and C. acnes. The turnaround times for negative specimens were 4 hours (automated DNA extraction and real time PCR) and 1 working day for positive specimens (including Sanger sequencing). Melting-curve analysis of SYBR Green-PCR enables the differentiation of specific and unspecific PCR products. Using Ripseq, even mixed infections of 2 bacterial species could be resolved. Conclusions For endocarditis cases, the added benefit of PCR is obvious. The crucial innovations of the technology enable timely reporting of explicit reliable results for adequate treatment of patients. Clinical specimens with truly PCR-positive but culture-negative results represent an additional benefit for patients. Very few results at the detection limit still have to be critically examined.
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Affiliation(s)
| | | | - Lorenz Risch
- Dr Risch, 3097, Liebefeld, Switzerland.,Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
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27
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Salina A, Schumann DM, Franchetti L, Jahn K, Purkabiri K, Müller R, Strobel W, Khanna N, Tamm M, Stolz D. Multiplex bacterial PCR in the bronchoalveolar lavage fluid of non-intubated patients with suspected pulmonary infection: a quasi-experimental study. ERJ Open Res 2022; 8:00595-2021. [PMID: 35479296 PMCID: PMC9035597 DOI: 10.1183/23120541.00595-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/23/2022] [Indexed: 11/05/2022] Open
Abstract
Background Early pathogen identification in pulmonary infection is crucial to guide antibacterial therapy and decrease length of hospital stay. We hypothesise that compared to conventional diagnostic methods, a multiplex bacterial polymerase chain reaction assay has a higher diagnostic yield in bronchoalveolar lavage (BAL) fluid and improved clinical outcomes in patients with suspicion of pulmonary infection. Methods A prospective, monocentric, quasi-experimental, observational study was carried out. Unselected patients with suspected pulmonary infection who underwent bronchoscopy with BAL were included in the study over a period of 1 year. In addition to conventional diagnostic methods, a multiplex PCR bacterial assay was performed in BAL on a 2 week on: 1 week off pre-determined schedule. No therapeutic recommendations were provided to the treating physician. Results 605 cases were included, 54% of whom were immunosuppressed. Conventional diagnostic methods detected 56% of the bacteria evidenced by PCR. PCR failed to detect bacteria in 4% of the cases with a positive conventional diagnostic result. After bronchoscopy, 42% of the patients received antibacterial therapy for pulmonary infection for a median of 12 antibiotic days. There was no statistically significant difference in length of hospital stay (median 8 versus 8; p=0.839), antibiotic exposure (median 11 versus 14; p=0.362) or number of antibiotics prescribed (median 2 versus 2; p=0.595) between the two groups. Conclusions A multiplex bacterial PCR detected more bacteria in BAL fluid than conventional diagnostic methods. However, without a specific antibiotic stewardship approach and a clear understanding of the clinical implications of a positive or negative PCR result, the PCR results did not influence clinical outcomes.
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Affiliation(s)
- Anna Salina
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Desiree M Schumann
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Léo Franchetti
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Kathleen Jahn
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Kurosch Purkabiri
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Raphael Müller
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Werner Strobel
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Nina Khanna
- Clinic of Infectiology and Hospital Hygiene, University Hospital Basel, Basel, Switzerland
| | - Michael Tamm
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Daiana Stolz
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland.,Faculty of Medicine, Clinic of Respiratory Medicine, Medical Center, University of Freiburg, Freiburg, Germany
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28
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Determining the Clinical Utility of 16S rRNA Sequencing in the Management of Culture-Negative Pediatric Infections. Antibiotics (Basel) 2022; 11:antibiotics11020159. [PMID: 35203762 PMCID: PMC8868208 DOI: 10.3390/antibiotics11020159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
The use of 16S rRNA sequencing in culture-negative infections has improved identification of bacterial pathogens in select scenarios, but its clinical impact requires further elucidation, especially in the pediatric population. This retrospective study aims to determine the clinical utility of 16S rRNA sequencing on the clinical management of pediatric culture-negative infections in our institution. Significant clinical utility was identified in 30 (40.5%) of 74 clinical samples (p < 0.0001). Of all specimens, pulmonary samples yielded the most clinical utility (n = 9, 30%), followed equally by joint fluid (n = 6, 20%) and bone (n = 6, 20%), with no difference between fluid and fresh tissue specimens (p = 0.346). Although the difference was not statistically significant (p = 0.4111), the overall use of broad-spectrum coverage was decreased. The median number of antibiotics was decreased from two to one (p < 0.0001) based on 16S rRNA sequencing results. The results suggest that 16S rRNA sequencing has a significant impact on decreasing the number of antibiotics used in the treatment of pediatric culture-negative infections. 16S rRNA sequencing performed on pulmonary specimens has the highest likelihood of identifying a pathogen compared to other specimen types. Additional cost–benefit analysis needs to be completed to further determine clinical benefit.
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29
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Tuft S, Somerville TF, Li JPO, Neal T, De S, Horsburgh MJ, Fothergill JL, Foulkes D, Kaye S. Bacterial keratitis: identifying the areas of clinical uncertainty. Prog Retin Eye Res 2021; 89:101031. [PMID: 34915112 DOI: 10.1016/j.preteyeres.2021.101031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
Bacterial keratitis is a common corneal infection that is treated with topical antimicrobials. By the time of presentation there may already be severe visual loss from corneal ulceration and opacity, which may persist despite treatment. There are significant differences in the associated risk factors and the bacterial isolates between high income and low- or middle-income countries, so that general management guidelines may not be appropriate. Although the diagnosis of bacterial keratitis may seem intuitive there are multiple uncertainties about the criteria that are used, which impacts the interpretation of investigations and recruitment to clinical studies. Importantly, the concept that bacterial keratitis can only be confirmed by culture ignores the approximately 50% of cases clinically consistent with bacterial keratitis in which investigations are negative. The aetiology of these culture-negative cases is unknown. Currently, the estimation of bacterial susceptibility to antimicrobials is based on data from systemic administration and achievable serum or tissue concentrations, rather than relevant corneal concentrations and biological activity in the cornea. The provision to the clinician of minimum inhibitory concentrations of the antimicrobials for the isolated bacteria would be an important step forward. An increase in the prevalence of antimicrobial resistance is a concern, but the effect this has on disease outcomes is yet unclear. Virulence factors are not routinely assessed although they may affect the pathogenicity of bacteria within species and affect outcomes. New technologies have been developed to detect and kill bacteria, and their application to bacterial keratitis is discussed. In this review we present the multiple areas of clinical uncertainty that hamper research and the clinical management of bacterial keratitis, and we address some of the assumptions and dogma that have become established in the literature.
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Affiliation(s)
- Stephen Tuft
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Tobi F Somerville
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Ji-Peng Olivia Li
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, UK.
| | - Timothy Neal
- Department of Clinical Microbiology, Liverpool Clinical Laboratories, Liverpool University Hospital NHS Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK.
| | - Surjo De
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London, NW1 2PG, UK.
| | - Malcolm J Horsburgh
- Department of Infection and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7BX, UK.
| | - Joanne L Fothergill
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Daniel Foulkes
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Stephen Kaye
- Department of Eye and Vision Sciences, University of Liverpool, 6 West Derby Street, Liverpool, L7 8TX, UK.
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30
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Abstract
PURPOSE OF REVIEW Poststernotomy mediastinitis (PSM) remains a serious infection and is significantly associated with high morbidity, short-term and long-term mortality. Gram-negative bacteria (GNB) are an underestimated cause of PSM, and there is little information on the risk factors, prevention, diagnosis and management of GNB PSM. RECENT FINDINGS The pathogenesis of PSM is the result of a complex and multifactorial interplay between intraoperative wound contamination, host-related and surgical host factors but GNB are probably mostly translocated from other host site infections. GNB are frequent cause of PSM (18-38% of cases) and GNB PSM have shown to more frequently polymicrobial (20-44%). GNG PSM has shown to occur earlier than Gram-positive PSM. Early diagnosis is crucial to successful treatment. The management of PSM needs a combination of culture-directed antimicrobial therapy and an early extensive surgical debridement with either immediate or delayed closure of the sternal space. Antibiotic treatment choice and duration should be based on clinical evaluation, evolution of inflammatory markers, microbiological tests and imaging studies. Mortality has shown to be significantly higher with GNB PSM compared with other causes and the inappropriateness of initial antibiotic therapy may explain the worse outcome of GNB PSM. SUMMARY GNB PSM is usually undervalued in the setting of PSM and have shown to be a frequent cause of inappropriate treatment with adverse prognostic potential. There is a need for efforts to improve knowledge to prevent and adequately treat GNB PSM.
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31
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Bouza E, de Alarcón A, Fariñas MC, Gálvez J, Goenaga MÁ, Gutiérrez-Díez F, Hortal J, Lasso J, Mestres CA, Miró JM, Navas E, Nieto M, Parra A, Pérez de la Sota E, Rodríguez-Abella H, Rodríguez-Créixems M, Rodríguez-Roda J, Sánchez Espín G, Sousa D, Velasco García de Sierra C, Muñoz P, Kestler M. Prevention, Diagnosis and Management of Post-Surgical Mediastinitis in Adults Consensus Guidelines of the Spanish Society of Cardiovascular Infections ( SEICAV), the Spanish Society of Thoracic and Cardiovascular Surgery ( SECTCV) and the Biomedical Research Centre Network for Respiratory Diseases ( CIBERES). J Clin Med 2021; 10:5566. [PMID: 34884268 PMCID: PMC8658224 DOI: 10.3390/jcm10235566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 01/04/2023] Open
Abstract
This is a consensus document of the Spanish Society of Cardiovascular Infections (SEICAV), the Spanish Society of Thoracic and Cardiovascular Surgery (SECTCV) and the Biomedical Research Centre Network for Respiratory Diseases (CIBERES). These three entities have brought together a multidisciplinary group of experts that includes anaesthesiologists, cardiac and cardiothoracic surgeons, clinical microbiologists, infectious diseases and intensive care specialists, internal medicine doctors and radiologists. Despite the clinical and economic consequences of sternal wound infections, to date, there are no specific guidelines for the prevention, diagnosis and management of mediastinitis based on a multidisciplinary consensus. The purpose of the present document is to provide evidence-based guidance on the most effective diagnosis and management of patients who have experienced or are at risk of developing a post-surgical mediastinitis infection in order to optimise patient outcomes and the process of care. The intended users of the document are health care providers who help patients make decisions regarding their treatment, aiming to optimise the benefits and minimise any harm as well as the workload.
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Affiliation(s)
- Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañon University Hospital, Gregorio Marañon Health Research Institute, Complutense University of Madrid, CIBER of Respiratory Diseases—CIBERES, 28007 Madrid, Spain; (E.B.); (M.R.-C.); (P.M.)
| | | | | | - Juan Gálvez
- Virgen Macarena University Hospital, 41009 Seville, Spain;
| | | | - Francisco Gutiérrez-Díez
- Cardiovascular Surgery Department, Marques de Valdecilla University Hospital, 39008 Santander, Cantabria, Spain;
| | - Javier Hortal
- Anesthesia and Intensive Care Department, Gregorio Marañon University Hospital, 28007 Madrid, Spain;
| | - José Lasso
- Plastic Surgery Department, Gregorio Marañon University Hospital, 28007 Madrid, Spain;
| | - Carlos A. Mestres
- Department of Cardiac Surgery, University Hospital Zurich, 8091 Zurich, Switzerland;
| | - José M. Miró
- Infectious Diseases Services, Hospital Clinic-IDIBAPS, University of Barcelona, 08036 Barcelona, Spain;
| | - Enrique Navas
- Infectious Diseases Department, Ramón y Cajal University Hospital, 28034 Madrid, Spain;
| | - Mercedes Nieto
- Cardiovascular Unit, Intensive Care Department, San Carlos Clinical Hospital, 28040 Madrid, Spain;
| | - Antonio Parra
- Department of Radiology, Marquez de Valdecilla University Hospital, 39008 Santander, Cantabria, Spain;
| | | | - Hugo Rodríguez-Abella
- Cardiac Surgery Department, Gregorio Marañon University Hospital, 28007 Madrid, Spain;
| | - Marta Rodríguez-Créixems
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañon University Hospital, Gregorio Marañon Health Research Institute, Complutense University of Madrid, CIBER of Respiratory Diseases—CIBERES, 28007 Madrid, Spain; (E.B.); (M.R.-C.); (P.M.)
| | | | - Gemma Sánchez Espín
- Heart Clinical Management Unit, Virgen de la Victoria University Hospital, 29006 Malaga, Spain;
| | - Dolores Sousa
- Infectious Diseases Department, A Coruña Hospital Complex, 15006 A Coruña, Spain;
| | | | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañon University Hospital, Gregorio Marañon Health Research Institute, Complutense University of Madrid, CIBER of Respiratory Diseases—CIBERES, 28007 Madrid, Spain; (E.B.); (M.R.-C.); (P.M.)
| | - Martha Kestler
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañon University Hospital, Gregorio Marañon Health Research Institute, Complutense University of Madrid, CIBER of Respiratory Diseases—CIBERES, 28007 Madrid, Spain; (E.B.); (M.R.-C.); (P.M.)
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Teoh T, McNamara R, Powell J, O’Connell NH, Dunne CP. A retrospective observational study of the impact of 16s and 18s ribosomal RNA PCR on antimicrobial treatment over seven years: A tertiary hospital experience. PLoS One 2021; 16:e0258552. [PMID: 34637486 PMCID: PMC8509882 DOI: 10.1371/journal.pone.0258552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 01/15/2023] Open
Abstract
Background Although culture-based methods remain a staple element of microbiology analysis, advanced molecular methods increasingly supplement the testing repertoire. Since the advent of 16s and 18s ribosomal RNA PCR in the 2000s, there has been interest in its utility for pathogen detection. Nonetheless, studies assessing the impact on antimicrobial prescribing are limited. We report a single-centre experience of the influence of 16s and 18s PCR testing on antimicrobial treatment, including a cost-analysis. Methods Data were collected retrospectively for all samples sent for 16s and 18s PCR testing between January 2014 and December 2020. Results were compared to any culture-based result. Assessment focused on any change of antimicrobial treatment based on PCR result, or use of the result as supportive evidence for microbiological diagnosis. Results 310 samples relevant to 268 patients were referred for 16s/18s rRNA PCR testing during the period. Culture was performed for 234 samples. Enrichment culture was performed for 83 samples. 82 of 300 samples sent for 16s PCR had positive results (20.8%). When culture was performed, enrichment reduced the outcome of 16s PCR only positive results (4/36 [11.1%] versus 14/35 [40.0%], p = 0.030 where a pathogen found). 18s PCR yielded 9 positive results from 67 samples. The 16s PCR result influenced antimicrobial change for 6 patients (2.2%). We estimated the cost for 16s PCR testing to result in one significant change in antimicrobial therapy to be €3,340. 18s PCR did not alter antimicrobial treatment. Conclusion There was limited impact of 16s PCR results on antimicrobial treatments. Relevance to practice was affected by relatively long turn-around-time for results. Utility may be increased in specialised surgical centres, or by reducing turn-around-time. Enrichment culture should be considered on samples where 16s PCR is requested. There remains limited evidence for use of 18s PCR in clinical management, and further studies in this area are likely warranted.
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Affiliation(s)
- TeeKeat Teoh
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
| | - Rachel McNamara
- Department of Medicine and Infectious Diseases, University Hospital Limerick, Limerick, Ireland
| | - James Powell
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
| | - Nuala H. O’Connell
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
| | - Colum P. Dunne
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
- * E-mail:
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Anton-Vazquez V, Dworakowski R, Cannata A, Amin-Youssef G, Gunning M, Papachristidis A, MacCarthy P, Baghai M, Deshpande R, Khan H, Byrne J, Fife A. 16S rDNA PCR for the aetiological diagnosis of culture-negative infective endocarditis. Infection 2021; 50:243-249. [PMID: 34490592 DOI: 10.1007/s15010-021-01690-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Culture-negative infective endocarditis (IE) accounts for 7-31% of all cases. Metagenomics has contributed to improving the aetiological diagnosis of IE patients undergoing valve surgery. We assessed the impact of 16S ribosomal DNA gene polymerase chain reaction (16S rDNA PCR) in the aetiological diagnosis of culture-negative IE. METHODS Between January 2016 and January 2020, clinical data from culture-negative IE patients were reviewed retrospectively. Identification of bacteria was performed using 16S rDNA PCR in heart valve specimens. RESULTS 36 out of 313 patients (12%) with culture-negative IE had their valve tissue specimens submitted for 16S rDNA PCR. 16S rDNA PCR detected and identified bacterial nucleic acid in heart valve tissue significantly more frequently compared to valve culture alone 25(70%) vs 5(12%); p < 0.05. Mean age was 57 years (SD 18) and 80% were male. Native and aortic valve were involved in 76% and 52% of cases, respectively. Streptococcus spp. (n 15) were the most commonly detected organisms, followed by bacteria of the HACEK group (Haemophilus parainfluenzae 2, Aggregatibacter actinomycetemcomitans 1), nutritionally variant streptococci (Abiotrophia defectiva 2), and one each of Staphylococcus aureus, Corynebacterium pseudodiphtheriticum, Helcococcus kunzii, Neisseria gonorrhoeae, Tropheryma whipplei. CONCLUSION 16S rDNA PCR may be a useful diagnostic tool for the identification of the causative organism in culture-negative IE. Efforts towards a shorter turnaround time for results should be consider and further studies assessing the clinical impact of this technique in culture-negative IE are needed.
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Affiliation(s)
- Vanesa Anton-Vazquez
- Department of Medical Microbiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK.
| | - Rafal Dworakowski
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Antonio Cannata
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - George Amin-Youssef
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Margaret Gunning
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Alexandros Papachristidis
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Phil MacCarthy
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Max Baghai
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Ranjit Deshpande
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Habib Khan
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Jonathan Byrne
- Department of Cardiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Amanda Fife
- Department of Medical Microbiology, Kings College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
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Liu X, Bu S, Wei H, Wang Z, Yu S, Li Z, Hao Z, He X, Wan J. Visual assay of Escherichia coli O157:H7 based on an isothermal strand displacement and hybrid chain reaction amplification strategy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3379-3385. [PMID: 34235517 DOI: 10.1039/d1ay00644d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Here, we describe a simple, sensitive, and enzyme-free method for visual point-of-care detection of 16S rRNA of Escherichia coli O157:H7 based on an isothermal strand displacement-hybrid chain reaction (ISD-HCR) and lateral flow strip (LFS). In this study, the secondary structure of 16S rRNA of E. coli O157:H7 was unwound by two helper oligonucleotides to expose the single-strand-specific nucleic acid sequence. The free specific sequence promoted the toehold-mediated strand displacement reaction to output a large number of FITC-labeled single-stranded DNA probes (capture probe [CP]). The 3'-end sequence of the reporter probe propagated a chain reaction of hybridization events between the two hairpin probes modified with biotin to form long nicked DNA polymers with multiple biotins (RP-HCR complexes); the free CP and RP-HCR complexes then form CP/RP-HCR complexes. The biotin-labeled double-stranded DNA CP/RP-HCR polymers then introduced numerous streptavidin (SA)-labeled gold nanoparticles (AuNPs) on the LFS. The accumulation of AuNPs produced a characteristic red band, which enabled visual detection of changes in the signal of 16S rRNA of E. coli O157:H7. The current approach could detect E. coli O157:H7 at concentrations as low as 102 CFU mL-1 without instrumentation. This approach thus provides a simple, sensitive, and low-cost tool for point-of-care detection of pathogenic bacteria, especially in resource-limited countries.
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Affiliation(s)
- Xiu Liu
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun 130022, China.
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Itoh N, Murakami H, Ishibana Y, Yoshida M, Watari T, Otsuka Y. A case of Salmonella osteomyelitis mimicking a malignant tumor of the humerus in an immunocompetent adult patient identified using broad-range polymerase chain reaction with sequencing of a biopsied specimen. J Infect Chemother 2021; 27:1769-1773. [PMID: 34400093 DOI: 10.1016/j.jiac.2021.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/22/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Salmonella infections are associated with gastroenteritis, enteric fever, bacteremia, focal infection, and chronic carrier state. Cases of Salmonella osteomyelitis are uncommon and mainly occur in individuals with immunosuppressive conditions. Herein, we report a case of Salmonella osteomyelitis that required differentiation from malignancy in an immunocompetent adult patient. CASE PRESENTATION A 31-year-old previously healthy male truck driver presented with a 2-week history of pain in his left upper arm. He had fallen off the back of a truck 2 months previously and injured the left side of his body. He also had bloody diarrhea and fever. Computed tomography and magnetic resonance imaging revealed a lesion that appeared to be a bone tumor in the left humerus, and the patient was referred to our cancer center from another clinic. Culture of a biopsy specimen of the left humerus was negative; however, the consensus sequence in broad-range polymerase chain reaction (PCR) showed the highest similarity to the 16S rRNA gene of Salmonella enterica subspecies enterica. Curettage of the left humerus was performed, and the patient was administered levofloxacin for 6 weeks. He recovered left arm function and had no recurrence during 2 months of follow-up. CONCLUSIONS When the culture of blood or biopsy specimens is negative in situations wherein a specific infection is suspected, broad-range PCR with sequencing should be considered to determine the causative organism.
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Affiliation(s)
- Naoya Itoh
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden Chikusa-ku, Nagoya, Aichi, 464-8681, Japan; Collaborative Chairs Emerging and Reemerging Infectious Diseases, National Center for Global Health and Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Hiromi Murakami
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Yuichi Ishibana
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Masahiro Yoshida
- Section of Orthopedic Surgery, Aichi Cancer Center Hospital, 1-1 Kanokoden Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Tomohisa Watari
- Department of Clinical Laboratory, Kameda Medical Center, 929 Higashi-cho, Kamogawa, Chiba, 296-8602, Japan
| | - Yoshihito Otsuka
- Department of Clinical Laboratory, Kameda Medical Center, 929 Higashi-cho, Kamogawa, Chiba, 296-8602, Japan
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Price TK, Realegeno S, Mirasol R, Tsan A, Chandrasekaran S, Garner OB, Yang S. Validation, Implementation, and Clinical Utility of Whole Genome Sequence-Based Bacterial Identification in the Clinical Microbiology Laboratory. J Mol Diagn 2021; 23:1468-1477. [PMID: 34384892 DOI: 10.1016/j.jmoldx.2021.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 12/16/2022] Open
Abstract
The application of next-generation sequencing extends from microbial identification to epidemiologic insight and antimicrobial resistance prediction. Despite this potential, the roadblock for clinical laboratories lies in implementation and validation of such complex technology and data analysis. Here, we describe a validation study using whole-genome sequencing (WGS) for pan-bacterial identification (ID) in a clinical laboratory setting, and discuss the clinical relevance. A diverse set of 125 bacterial isolates, including a subset of isolates without genus (25) and/or species (10) ID, were analyzed by de novo assembly and reference genome mapping. The 16S rRNA, rpoB, and groEL genes were used for ID. Using WGS, 100% (89 of 89) and 89% (79 of 89) of isolates were identified to the genus and species levels, respectively. WGS also provided improved results for the majority of isolates (25 of 35) that were reported originally with genus-only or descriptive IDs. Chart review identified cases in which improved genus and/or species level ID by WGS may have had a positive impact on patient care. Reasons included the use of an ineffective antibiotic owing to unclear ID, use of antibiotics when not clinically indicated, and help with an outbreak investigation. The implementation of next-generation sequencing in a clinical microbiology setting is a challenging but necessary task. Our study provides a model for the validation and implementation of bacterial ID by WGS in such a setting.
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Affiliation(s)
- Travis K Price
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Susan Realegeno
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Ruel Mirasol
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Allison Tsan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Sukantha Chandrasekaran
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
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O'Hagan S, Nelson P, Speirs L, Moriarty P, Mallett P. How to interpret a paediatric blood culture. Arch Dis Child Educ Pract Ed 2021; 106:244-250. [PMID: 33637581 DOI: 10.1136/archdischild-2020-321121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 11/04/2022]
Abstract
Blood culture is one of the most important diagnostic tests in medicine, considering the significant morbidity and mortality associated with bloodstream infection (BSI). However, it is an often misused and misinterpreted test in everyday paediatric practice. In this article, we explore the evidence related to paediatric blood cultures, with the aim of providing clear and clinically-relevant recommendations for its judicious use.
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Affiliation(s)
- Shaun O'Hagan
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK shaun.o'
| | - Peter Nelson
- Clinical Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Lynne Speirs
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Paul Moriarty
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Peter Mallett
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
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Akiyama T, Imamura H, Fukui N, Sakai N. Helicobacter cinaedi-infected chronic subdural hematoma mimicking an expanding hematoma: A case report. Surg Neurol Int 2021; 12:288. [PMID: 34221619 PMCID: PMC8247720 DOI: 10.25259/sni_387_2021] [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: 04/20/2021] [Accepted: 05/18/2021] [Indexed: 11/21/2022] Open
Abstract
Background: We present the rare case of a spontaneous intracranial subdural empyema caused by Helicobacter cinaedi in a preexisting chronic subdural hematoma (CSDH). Case Description: A 72-year-old man with a history of the right CSDH that remained radiologically unchanged for the past 2 years with conservative management was transferred to our hospital because of fever and convulsive seizure. Systemic sources of infection were not identified. Fever and extremely high levels of serum C-reactive protein (CRP) spontaneously improved without antibacterial therapy. One month after the fever disappeared, brain computed tomography (CT) showed an increase in CSDH size. Mildly elevated CRP levels persisted without fever. Interval changes in shape on CT and hyperintense signals on diffusion-weighted magnetic resonance imaging (DWI) within the CSDH were observed with no neurological deficits. Five months later, the patient underwent craniotomy for a progressively enlarged CSDH. An infected organized hematoma was found, and copious pus was evacuated. Subsequently, an infected subdural hematoma (ISH) was diagnosed. Although bacterial cultures of the purulent specimen were negative, H. cinaedi was identified by gene sequencing analysis. Six months post antibiotic therapy, the ISH was under control, and abnormal DWI signals disappeared. Conclusion: To the best of our knowledge, this is the first report of ISH caused by H. cinaedi. This case suggests that ISH can follow a chronic course, mimicking the progressive expansion of subdural hematoma, and that H. cinaedi should be considered as a causative organism of ISH especially when conventional cultures are negative.
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Affiliation(s)
- Tomoaki Akiyama
- Department of Neurosurgery, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Hirotoshi Imamura
- Department of Neurosurgery, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Nobuyuki Fukui
- Department of Neurosurgery, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Nobuyuki Sakai
- Department of Neurosurgery, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
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Malczynski M, Zhu A, Zembower T, Qi C. Diagnostic performance of Ion 16S metagenomics kit and Ion reporter metagenomics workflow for bacterial pathogen detection in culture-negative clinical specimens from sterile sources. Diagn Microbiol Infect Dis 2021; 101:115451. [PMID: 34237647 DOI: 10.1016/j.diagmicrobio.2021.115451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 12/17/2022]
Abstract
PCR-based deep sequencing of 16S rRNA gene allows for detection of a wide array of bacterial pathogens in culture-negative specimens. Ion 16S metagenomics kit and Ion Reporter metagenomics workflow (Ion 16S mNGS) provides an end-to-end solution with integrated workflow. Ninety-eight clinical samples with the diagnosis generated with 16S rRNA gene PCR/chain termination (Sanger) sequencing (16S CS) was used to assess the performance of Ion 16S mNGS. Compared to species level detection of 16S CS, the Ion 16S mNGS had 88% sensitivity and 76% specificity. When accounting for genus level of detection, the Ion 16S mNGS had 100% sensitivity. Notably, Ion 16S mNGS generated diagnosis in 13% of 16S CS and culture-negative samples. In addition, Ion 16S mNGS had the advantage of detecting more than 1 pathogen in 16S CS positive samples. We showed that the workflow had high reproducibility.
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Affiliation(s)
- Michael Malczynski
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA
| | - Alex Zhu
- Northwestern University, Evanston, IL, USA
| | - Teresa Zembower
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA; Northwestern University, Evanston, IL, USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chao Qi
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA; Northwestern University, Evanston, IL, USA; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Onder AM, Cuff CF, Liang X, Billings AA, Onder S, Yu JJ, King JA. Detecting the prevalence of bacterial colonization on tunneled cuffed hemodialysis catheters using quantitative PCR targeting 16S rRNA and scanning electron microscopy. J Vasc Access 2021; 23:743-753. [PMID: 33855873 DOI: 10.1177/11297298211009016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Tunneled cuffed hemodialysis catheters (TCC) get colonized by microorganisms, increasing risk for catheter related bacteremia (CRB). Our objective was to detect the prevalence of bacterial colonization of TCC by using quantitative PCR (qPCR) targeting 16S rRNA and by determining the intraluminal adherent biological material (ABM) coverage. METHODS A total of 45 TCC were investigated. The 16S rRNA qPCR technique was used to detect bacterial colonization after scraping the intraluminal ABM. Proximal, middle, and distal TCC were evaluated by scanning electron microscopy (SEM) to determine the percentage (%) of intraluminal ABM coverage. All catheters were cultured following sonication. RESULTS A total of 45 TCC were removed: 7 due to CRB, 3 for suspected CRB and 35 were removed for non-infectious etiologies. Bacterial colonization was detected in 27 TCC by documenting 16S rRNA qPCR (+) results (60%). Seven of these 16S rRNA qPCR (+) catheters were removed due to CRB. There was no difference in demographic, clinical, or laboratory values between the 16S rRNA (+) versus (-) TCC. The 16S rRNA qPCR (-) outcome was highly associated with CRB-free status with negative predictive value of 100%. Bacterial colonization was documented in 10 TCC using catheter cultures (22%), which was significantly less compared to qPCR method (p = 0.0002). ABM were detected in all catheter pieces, with mean intraluminal surface coverage (ABMC) of 68.4 ± 26.1%. ABM was unlikely to be microbial biofilm in at least 36% of removed TCC as their 16S rRNA qPCR and catheter culture results were both negative. CONCLUSIONS Detecting bacterial colonization of TCC was significantly higher with 16S rRNA qPCR compared to catheter cultures. The 16S rRNA qPCR (-) cannot be predicted and was strongly associated with absence of CRB. Intraluminal ABM was not associated with microbial presence in about 1/3 of the TCC. These pieces of evidence may help to improve prophylactic strategies against CRB.
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Affiliation(s)
- Ali Mirza Onder
- Department of Pediatrics, West Virginia University, School of Medicine, Morgantown, WV, USA.,Division of Pediatric Nephrology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Christopher F Cuff
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, School of Medicine, Morgantown, WV, USA
| | - Xiaobing Liang
- Department of Biochemistry, West Virginia University, School of Medicine, Morgantown, WV, USA
| | | | - Songul Onder
- Department of Medicine, West Virginia University, School of Medicine, Morgantown, WV, USA.,Department of Medicine, University of Tennessee, School of Medicine, Memphis, TN, USA
| | - Jing Jie Yu
- Department of Biochemistry, West Virginia University, School of Medicine, Morgantown, WV, USA
| | - Judy Ann King
- Department of Pathology, West Virginia University, School of Medicine, Morgantown, WV, USA.,Department of Pathology and Translational Pathobiology, Louisiana State University Health Shreveport, Shreveport, LA, USA
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Mao YC, Chuang HN, Shih CH, Hsieh HH, Jiang YH, Chiang LC, Lin WL, Hsiao TH, Liu PY. An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota. PLoS Negl Trop Dis 2021; 15:e0009331. [PMID: 33857127 PMCID: PMC8078740 DOI: 10.1371/journal.pntd.0009331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/27/2021] [Accepted: 03/25/2021] [Indexed: 01/11/2023] Open
Abstract
Naja atra is a major venomous snake found in Taiwan. The bite of this snake causes extensive wound necrosis or necrotizing soft tissue infection. Conventional microbial culture-based techniques may fail to identify potential human pathogens and render antibiotics ineffective in the management of wound infection. Therefore, we evaluated 16S Sanger sequencing and next-generation sequencing (NGS) to identify bacterial species in the oropharynx of N. atra. Using conventional microbial culture methods and the VITEK 2 system, we isolated nine species from snakebite wounds. On the basis of the 16S Sanger sequencing of bacterial clones from agar plates, we identified 18 bacterial species in the oropharynx of N. atra, including Morganella morganii, Proteus vulgaris, and Proteus mirabilis, which were also present in the infected bite wound. Using NGS of 16S metagenomics, we uncovered more than 286 bacterial species in the oropharynx of N. atra. In addition, the bacterial species identified using 16S Sanger sequencing accounted for only 2% of those identified through NGS of 16S metagenomics. The bacterial microbiota of the oropharynx of N. atra were modeled better using NGS of 16S metagenomics compared to microbial culture-based techniques. Stenotrophomonas maltophilia, Acinetobacter baumannii, and Proteus penneri were also identified in the NGS of 16S metagenomics. Understanding the bacterial microbiota that are native to the oropharynx of N. atra, in addition to the bite wound, may have additional therapeutic implications regarding empiric antibiotic selection for managing N. atra bites. Naja atra bites induce extensive wound necrotizing soft tissue infections in a substantial proportion of patients. Empiric antibiotic administration in snakebite patients is a common practice, but clinical reports indicate that this treatment was ineffective in preventing secondary infection given that the microbiota of the infected wound and oropharynx of the culprit snake were not properly established. In this study, only 9 species were detected in cobra bites using a conventional microbial culture method and the VITEK 2 system, whereas 18 species were detected in the cobra oropharynx using microbial culture-based 16S Sanger sequencing. Among these, Morganella morganii, Proteus vulgaris, and Proteus mirabilis were identified as common bacteria. Compared to microbial culture-based 16S Sanger sequencing, NGS-based 16S metagenomic sequencing detected more than 286 bacterial species. Stenotrophomonas maltophilia, Acinetobacter baumannii, and Proteus penneri only appeared with 16S metagenomic sequencing. These results suggest that NGS-based 16S metagenomic sequencing is a better tool for uncovering the bacterial microbiota of the N. atra oropharynx, which may help in developing a proper therapeutic strategy for patients with N. atra bites.
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Affiliation(s)
- Yan-Chiao Mao
- Department of Emergency Medicine, Division of Clinical Toxicology, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- Department of Medicine, Division of Clinical Toxicology and Occupational Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Environmental and Occupational Health Sciences, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Han-Ni Chuang
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chien-Hung Shih
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Han-Hsueh Hsieh
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Han Jiang
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Liao-Chun Chiang
- Department of Emergency Medicine, Division of Clinical Toxicology, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- Department of Medicine, Division of Clinical Toxicology and Occupational Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Environmental and Occupational Health Sciences, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- National Tsing Hua University, College of Life Sciences, Hsinchu, Taiwan
| | - Wen-Loung Lin
- Taichung Wildlife Conservation Group, Taichung, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (T-HH); (P-YL)
| | - Po-Yu Liu
- Department of Internal Medicine, Division of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (T-HH); (P-YL)
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Bourbour S, Emaneini M, Jabalameli M, Mortazavi SMJ, Tahmasebi MN, Taghizadeh A, Sharafatvaziri A, Beigverdi R, Jabalameli F. Efficacy of 16S rRNA variable regions high-resolution melt analysis for bacterial pathogens identification in periprosthetic joint infections. BMC Microbiol 2021; 21:112. [PMID: 33849440 PMCID: PMC8045251 DOI: 10.1186/s12866-021-02164-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/22/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Accurate and rapid identification of microorganisms causing periprosthetic joint infections (PJIs) are necessary for choosing an appropriate antibiotic therapy. Therefore, molecular techniques are suggested for diagnosis in suspected PJIs. The Broad-range PCR and High-Resolution Melt Analysis (HRMA) were evaluated for the identification of causative organisms of PJIs in this study. RESULTS For 47 of 63 specimens, both the culture and broad-range PCR were positive. The culture was found to be able of organism's detection in 74.6% (47/63) of patients. Of 47 positive cultures, 11 (23.4%) were polymicrobial and 36 (76.59%) were monomicrobial cultures, in which 34 (91.89%) cases were detected by HRM assay. The sensitivity, specificity of HRMA vs monomicrobial culture were 91.89, 93.75%, respectively. The sensitivity, specificity of total HRMA (mono + poly) vs culture were 82.92, 93.75%. CONCLUSIONS HRM assay coupled with broad-range PCR are effective screening, rapid, and relatively cost-effective methods for discrimination of PJIs especially in aiding culture method. Using computer programs such as the Matlab-2018b program for HRM data analysis is also valuable and helpful in diagnosis.
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Affiliation(s)
- Samaneh Bourbour
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Jabalameli
- Department of Orthopedic Surgery, Shafa Yahyaiyan Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Javad Mortazavi
- Department of Orthopedic Surgery, Imam Khomaini Hospital, Tehran University of Medical Sciences, knee and hip surgeon, Tehran, Iran
| | - Mohamad Naghi Tahmasebi
- Department of Orthopedic Surgery, Imam Khomaini Hospital, Tehran University of Medical Sciences, knee and hip surgeon, Tehran, Iran
| | - Amirheckmat Taghizadeh
- School of Electrical and Computer engineering, college of engineering, University of Tehran, Tehran, Iran
| | - Arash Sharafatvaziri
- Department of Orthopedic Surgery, Imam Khomaini Hospital, Tehran University of Medical Sciences, knee and hip surgeon, Tehran, Iran
| | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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43
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Ursenbach A, Schramm F, Séverac F, Hansmann Y, Lefebvre N, Ruch Y, Argemi X. Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study. BMC Infect Dis 2021; 21:190. [PMID: 33602178 PMCID: PMC7890971 DOI: 10.1186/s12879-021-05892-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). Conclusion In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05892-4.
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Affiliation(s)
- Axel Ursenbach
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France.
| | - Frédéric Schramm
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France
| | - François Séverac
- Service de Santé Publique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yves Hansmann
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nicolas Lefebvre
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvon Ruch
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Xavier Argemi
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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Jakobsen TH, Xu Y, Bay L, Schønheyder HC, Jakobsen T, Bjarnsholt T, Thomsen TR. Sampling challenges in diagnosis of chronic bacterial infections. J Med Microbiol 2021; 70. [PMID: 33410733 DOI: 10.1099/jmm.0.001302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In recent decades there has been an increase in knowledge of the distribution, species diversity and growth patterns of bacteria in human chronic infections. This has challenged standard diagnostic methods, which have undergone a development to both increase the accuracy of testing as well as to decrease the occurrence of contamination. In particular, the introduction of new technologies based on molecular techniques into the clinical diagnostic process has increased detection and identification of infectious pathogens. Sampling is the first step in the diagnostic process, making it crucial for obtaining a successful outcome. However, sampling methods have not developed at the same speed as molecular identification. The heterogeneous distribution and potentially small number of pathogenic bacterial cells in chronic infected tissue makes sampling a complicated task, and samples must be collected judiciously and handled with care. Clinical sampling is a step in the diagnostic process that may benefit from innovative methods based on current knowledge of bacteria present in chronic infections. In the present review, we describe and discuss different aspects that complicate sampling of chronic infections. The purpose is to survey representative scientific work investigating the presence and distribution of bacteria in chronic infections in relation to various clinical sampling methods.
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Affiliation(s)
- Tim Holm Jakobsen
- Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Yijuan Xu
- Bio- and Environmental Technology, Danish Technological Institute, Taastrup, Denmark
- Center for Microbial Communities, Department of Chemistry and Biosciences, Aalborg University, Aalborg, Denmark
| | - Lene Bay
- Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Carl Schønheyder
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Thomas Jakobsen
- Department of Orthopaedics, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Thomas Bjarnsholt
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Trine Rolighed Thomsen
- Bio- and Environmental Technology, Danish Technological Institute, Taastrup, Denmark
- Center for Microbial Communities, Department of Chemistry and Biosciences, Aalborg University, Aalborg, Denmark
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Selva Pandiyan A, Siva Ganesa Karthikeyan R, Rameshkumar G, Sen S, Lalitha P. Identification of Bacterial and Fungal Pathogens by rDNA Gene Barcoding in Vitreous Fluids of Endophthalmitis Patients. Semin Ophthalmol 2021; 35:358-364. [PMID: 33390091 DOI: 10.1080/08820538.2020.1864416] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Purpose: To identify the bacterial and fungal pathogens in ocular samples of clinically suspected endophthalmitis patients by conventional culture methods and 16S and 28S rDNA gene sequencing respectively. Methods: A total of 88 patients with clinically suspected endophthalmitis were included in this study. Under sterile operating conditions, a vitreous fluid (0.1-0.2 ml) was obtained by pars plana vitrectomy procedure. The samples were processed for conventional microbiology methods and PCR. PCR targeting 16S rDNA gene for bacteria and 28S rDNA gene for fungus were performed individually using the MightyAmp DNA Polymerase Ver. 2 (TaKaRa China) kit. The PCR amplified samples were sequenced and aligned using CLUSTAL-W tool. The phylogenetic tree was constructed by Neighborhood joining along with the reference sequences downloaded from NCBI database using MEGA X software. Results: 67 Post-operative, 12 Endogenous and 9 traumatic endophthalmitis patients were included as study subjects. By the direct culturing bacterial growth was observed in 17 samples and fungal growth in three samples. PCR was positive for all the culture positive samples, in addition 14 were positive in culture negative samples. The predominant species identified in gram-positive bacteria were Staphylococcus spp., and Pseudomonas spp. in the gram-negative group. Both PCR and culture identified only three samples positive for fungal pathogens which were identified as Aspergillus fumigatus, Candida albicans, and Exerohilum rostratum. Conclusions: PCR based molecular diagnosis is more sensitive than the conventional gold standard culture methods in endophthalmitis. Bacterial pathogens were found to be the predominant in causing endophthalmitis than fungal pathogens.
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Affiliation(s)
| | | | | | - Sagnik Sen
- Department of Vitreoretinal Services, Aravind Eye Hospital , Madurai, India
| | - Prajna Lalitha
- Department of Ocular Microbiology, Aravind Eye Hospital , Madurai, India
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46
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Somerville TF, Corless CE, Sueke H, Neal T, Kaye SB. 16S Ribosomal RNA PCR Versus Conventional Diagnostic Culture in the Investigation of Suspected Bacterial Keratitis. Transl Vis Sci Technol 2020; 9:2. [PMID: 33344046 PMCID: PMC7718820 DOI: 10.1167/tvst.9.13.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/20/2020] [Indexed: 01/17/2023] Open
Abstract
Purpose The purpose of this study was to compare conventional diagnostic culture (CDC) to 16S ribosomal RNA polymerase chain reaction (PCR) analysis for diagnosing bacterial keratitis. Methods Samples collected from 100 consecutive patients presenting to the Royal Liverpool University Hospital with bacterial keratitis were processed using CDC and 16S PCR analysis. Results The overall detection rate using both methods was 36%. Of these, 72.2% (26/36) were detected by PCR and 63.9% (23/36) isolated by CDC (P = 0.62). Using a combination of both PCR and CDC increased the detection rate for pathogenic bacteria by 13% compared to using CDC alone (P = 0.04). In CDC negative samples, 16S PCR identified more pathogens than CDC in 16S PCR negative samples. Neither order of sample collection nor prior antimicrobial use affected the detection rate. Conclusions 16S rRNA gene PCR performed in addition to CDC on corneal samples from patients with clinically suspected bacterial keratitis led to additional pathogen detection. Translational Relevance 16S rRNA gene PCR should be developed to become an additional part of clinical service for patients with bacterial keratitis rather than used in isolation.
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Affiliation(s)
- Tobi F Somerville
- Department of Eye and Vision Sciences, University of Liverpool, Liverpool, UK.,St. Paul's Eye Unit, Liverpool University Hospitals NHS Trust, Liverpool, UK
| | - Caroline E Corless
- Department of Microbiology, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Trust, Liverpool, UK
| | - Henri Sueke
- Department of Eye and Vision Sciences, University of Liverpool, Liverpool, UK.,St. Paul's Eye Unit, Liverpool University Hospitals NHS Trust, Liverpool, UK
| | - Timothy Neal
- Department of Microbiology, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Trust, Liverpool, UK
| | - Stephen B Kaye
- Department of Eye and Vision Sciences, University of Liverpool, Liverpool, UK.,St. Paul's Eye Unit, Liverpool University Hospitals NHS Trust, Liverpool, UK
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47
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Umbilical Cord-Derived CD362 + Mesenchymal Stromal Cells Attenuate Polymicrobial Sepsis Induced by Caecal Ligation and Puncture. Int J Mol Sci 2020; 21:ijms21218270. [PMID: 33158246 PMCID: PMC7672591 DOI: 10.3390/ijms21218270] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) have a multimodal, immunomodulatory mechanism of action and are now in clinical trials for single organ and systemic sepsis. However, a number of practicalities around source, homogeneity and therapeutic window remain to be determined. Here, we utilised conditioned medium from CD362+-sorted umbilical cord-human MSCs (UC-hMSCs) for a series of in vitro anti-inflammatory assays and the cryopreserved MSCs themselves in a severe (Series 1) or moderate (Series 2+3) caecal ligation and puncture (CLP) rodent model. Surviving animals were assessed at 48 h post injury induction. MSCs improved human lung, colonic and kidney epithelial cell survival following cytokine activation. In severe systemic sepsis, MSCs administered at 30 min enhanced survival (Series 1), and reduced organ bacterial load. In moderate systemic sepsis (Series 2), MSCs were ineffective when delivered immediately or 24 h later. Of importance, MSCs delivered 4 h post induction of moderate sepsis (Series 3) were effective, improving serum lactate, enhancing bacterial clearance from tissues, reducing pro-inflammatory cytokine concentrations and increasing antimicrobial peptides in serum. While demonstrating benefit and immunomodulation in systemic sepsis, therapeutic efficacy may be limited to a specific point of disease onset, and repeat dosing, MSC enhancement or other contingencies may be necessary.
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48
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Abd El-Aziz NK, Gharib AA, Mohamed EAA, Hussein AH. Real-time PCR versus MALDI-TOF MS and culture-based techniques for diagnosis of bloodstream and pyogenic infections in humans and animals. J Appl Microbiol 2020; 130:1630-1644. [PMID: 33073430 DOI: 10.1111/jam.14862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
AIMS This study was applied to evaluate the usefulness of a high-throughput sample preparation protocol prior to the application of quantitative real-time PCR (qPCR) for the early diagnosis of bloodstream and pyogenic infections in humans and animals compared to matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and classical culture. METHODS AND RESULTS Saponin-mediated selective host cell lysis combined with DNase-1 was applied for processing of whole blood and pus clinical samples collected from suspected cases of septicaemia and pyogenic infections in humans and animals. The pre-PCR processing strategy enabled the recovery of microbial cells with no changes in their colony forming units immediately after the addition of saponin. DNase-1 was efficient for removing the DNAs from the host cells as well as dead cells with damaged cell membranes. The metagenomic qPCR and MALDI-TOF MS could identify the bacterial community of sepsis at species level with a concordance of 97·37% unlike the conventional culture. According to qPCR results, Staphylococcus aureus (24·24%) was predominated in animal pyogenic infections, whereas Klebsiella pneumonia (31·81%) was commonly detected in neonatal sepsis. CONCLUSIONS Saponin combined with DNase-1 allowed the efficient recovery of microbial DNA from blood and pus samples in sepsis using qPCR assay. SIGNIFICANCE AND IMPACT OF THE STUDY Metagenomic qPCR could identify a broad range of bacteria directly from blood and pus with more sensitivity, higher discriminatory power and shorter turnaround time than those using MALDI-TOF MS and conventional culture. This might allow a timely administration of a prompt treatment.
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Affiliation(s)
- N K Abd El-Aziz
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A A Gharib
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - E A A Mohamed
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A H Hussein
- Avian and Rabbit Medicine Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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49
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Bonnet C, Chehaibou I, Ghaffari R, Jackson NJ, Bostan C, Hubschman JP, Harissi-Dagher M, Aldave AJ. Idiopathic Vitritis after Boston Type 1 Keratoprosthesis Implantation: Incidence, Risk Factors and Outcomes in a Multicentric Cohort. Ocul Immunol Inflamm 2020; 30:769-775. [DOI: 10.1080/09273948.2020.1826541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Clemence Bonnet
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Ophthalmology Department, AP-HP, Cochin Hospital, Paris University, Paris, France
| | - Ismael Chehaibou
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Ophthalmology Department, Université De Paris, AP-HP, Hôpital Lariboisière, Paris, France
| | - Reza Ghaffari
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Nicholas J. Jackson
- Department of Medicine Statistics Core, University of California, Los Angeles, Los Angeles, California, USA
| | - Cristina Bostan
- Department of Ophthalmology, Centre Hospitalier De l’Université De Montréal, Montréal, Québec, Canada
| | - Jean-Pierre Hubschman
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Mona Harissi-Dagher
- Department of Ophthalmology, Centre Hospitalier De l’Université De Montréal, Montréal, Québec, Canada
| | - Anthony J. Aldave
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
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50
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Kerkhoff AD, Rutishauser RL, Miller S, Babik JM. Clinical Utility of Universal Broad-Range Polymerase Chain Reaction Amplicon Sequencing for Pathogen Identification: A Retrospective Cohort Study. Clin Infect Dis 2020; 71:1554-1557. [PMID: 31907545 PMCID: PMC7486847 DOI: 10.1093/cid/ciz1245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/02/2020] [Indexed: 12/20/2022] Open
Abstract
We assessed the real-world utility of universal broad-range polymerase chain reaction sequencing for pathogen detection. Among 1062 clinical samples, 107/1062 (10.1%) had a clinically significant, positive result, with substantial variation by specimen type. Clinical management was changed in 44/1062 (4.1%). These data can help maximize utility of this emerging diagnostic.
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Affiliation(s)
- Andrew D Kerkhoff
- Division of HIV, Infectious Diseases, and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, Department of Medicine, University of California, San Francisco, California, USA
| | - Rachel L Rutishauser
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Jennifer M Babik
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, USA
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