1
|
Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [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] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
Collapse
Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
2
|
Van Goethem S, Van Lint P, Willems P, Van Herendael B, Hoet K. Value of pneumococcal PCR in respiratory samples for exclusion of pneumococcal pneumonia. JAC Antimicrob Resist 2023; 5:dlad115. [PMID: 37941720 PMCID: PMC10629468 DOI: 10.1093/jacamr/dlad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
Background Streptococcus pneumoniae is the main aetiological agent in bacterial pneumonia. Therefore pneumococcal PCR is often included in respiratory multiplex PCR panels, both commercial and in-house. But respiratory PCR results for S. pneumoniae are difficult to interpret due to frequent non-pathogenic colonization on the mucosal surface of the upper airways with pneumococci or to cross-reaction of the PCR target in non-pneumococcal streptococci. In this study we investigated the value of lytA gene pneumococcal PCR in patients presenting with pneumonia. Objectives To assess the utility of lytA gene detection for S. pneumoniae in a respiratory multiplex quantitative PCR (qPCR) panel for patients presenting with pneumonia. Methods A retrospective study was conducted for lytA gene results as target for S. pneumoniae in hospitalized patients who were diagnosed with pneumonia and for which a respiratory multiplex PCR panel was performed. Patients were classified as 'probable', 'possible' or 'unlikely' of having a pneumococcal pneumonia. Results A sensitivity of 71.4% and specificity of 89.6% were found, corresponding to a negative predictive value and positive predictive value of 97.6% and 34.2%, respectively, when considering 'probable' versus 'possible/unlikely'. In the PCR-positive cases we found a statistically significant difference in semi-quantitative Ct values between the 'probable' and the 'possible/unlikely' groups. Conclusions We conclude that a negative qPCR for the lytA gene in a respiratory sample is highly predictive of a negative S. pneumoniae culture and is possibly sufficient to exclude S. pneumoniae as a causative agent. Respiratory pneumococcal PCR has a high negative predictive value for pneumococcal disease but the positive predictive value is low.
Collapse
Affiliation(s)
- Sam Van Goethem
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- Hospital Outbreak Support Team, ZAS Hospital Network, Antwerp, Belgium
| | - Philippe Van Lint
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
| | - Philippe Willems
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
| | | | - Katrien Hoet
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
| |
Collapse
|
3
|
Serigstad S, Knoop ST, Markussen DL, Ulvestad E, Bjørneklett RO, Ebbesen MH, Kommedal Ø, Grewal HMS. Diagnostic utility of oropharyngeal swabs as an alternative to lower respiratory tract samples for PCR-based syndromic testing in patients with community-acquired pneumonia. J Clin Microbiol 2023; 61:e0050523. [PMID: 37585220 PMCID: PMC10512787 DOI: 10.1128/jcm.00505-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/06/2023] [Indexed: 08/17/2023] Open
Abstract
Syndromic PCR-based analysis of lower respiratory tract (LRT) samples in patients with community-acquired pneumonia (CAP) improves the bacterial yield and time-to-results compared to culture-based methods. However, obtaining adequate sputum samples can be challenging and is frequently not prioritized in the emergency department (ED). In this study, we assess the concordance of microbiological detections between oropharyngeal- (OP) and LRT samples from patients presenting to the ED with CAP using a syndromic PCR-based respiratory panel [Biofire FilmArray Pneumonia plus (FAP plus)]. Paired OP- and high-quality LRT samples were collected from 103 patients with confirmed CAP, who had been included in a randomized controlled trial (NCT04660084) or a subsequent observational study at Haukeland University Hospital, and analyzed using the FAP plus. The LRT samples were obtained mainly by sputum induction (88%). Using the LRT samples as a reference standard, the positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement for the most common bacterial pathogens in CAP, Streptococcus pneumoniae and Haemophilus influenzae, were 85%, 99% and 95%, and 86%, 98% and 93%, respectively. For Moraxella catarrhalis, the PPA was lower (74%), while the NPA was 100%. For bacteria that are less likely causes of uncomplicated CAP (e.g., Staphylococcus aureus and Enterobacterales) the results were more divergent. In conclusion, the FAP plus detects the most common CAP pathogens S. pneumoniae and H. influenzae from OP samples with high PPAs and excellent NPAs when compared with LRT samples. For these pathogens, the PPAs for OP samples were higher than previous reports for nasopharyngeal samples. This suggests that analysis of OP samples with syndromic PCR panels could represent an alternative approach for rapid microbiological testing in the ED, especially in patients where LRT samples are difficult to obtain. Divergent results for bacteria that are less likely to cause uncomplicated CAP do, however, emphasize the need for clinical evaluation of positive test results.
Collapse
Affiliation(s)
- Sondre Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Siri T. Knoop
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Dagfinn L. Markussen
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
| | - Elling Ulvestad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Rune O. Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marit H. Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Øyvind Kommedal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Harleen M. S. Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| |
Collapse
|
4
|
Berinson B, Spenke L, Krivec L, Tanida K, Both A, Keller J, Rolvien T, Christner M, Lütgehetmann M, Aepfelbacher M, Klatte TO, Rohde H. Performance and Hypothetical Impact on Joint Infection Management of the BioFire Joint Infection Panel: a Retrospective Analysis. J Clin Microbiol 2023; 61:e0059223. [PMID: 37439678 PMCID: PMC10446873 DOI: 10.1128/jcm.00592-23] [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: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is a multiplex PCR panel which detects 31 of the most prevalent bacterial and fungal pathogens causing septic arthritis. Here, 123 cryoconserved contemporary synovial fluid samples from 120 patients underwent BJA analysis. Results were compared to those of culture-based diagnostics (standard of care [SOC]). Clinical data were collected, and the possible impact of the molecular diagnostic application on patient management was evaluated. Fifteen of 123 synovial fluid cultures grew bacterial pathogens. All on-panel pathogens (9/15) were correctly identified by the BJA. The BJA identified four additional bacterial pathogens in four SOC-negative cases. BJA sensitivity and specificity were 100% (95% confidence interval [CI], 69.2% to 100%) and 100% (95% CI, 96.8% to 100%), respectively. Compared to the SOC, the BJA would have resulted in faster provision of species identification and molecular susceptibility data by 49 h and 99 h, respectively. Clinical data analysis indicates that in BJA-positive cases, faster species ID could have led to timelier optimization of antibiotic therapy. This retrospective study demonstrates high sensitivity and specificity of the BJA to detect on-panel organisms in bacterial arthritis. The usefulness of the BJA in prosthetic-joint infections is limited, as important pathogens (i.e., coagulase negative staphylococci and Cutibacterium acnes) are not covered. Evidence from patient data analysis suggests that the assay might prove valuable for optimizing patient management in acute arthritis related to fastidious organisms or for patients who received antibiotics prior to specimen collection.
Collapse
Affiliation(s)
- Benjamin Berinson
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Spenke
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas Krivec
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Konstantin Tanida
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Both
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Keller
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Rolvien
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Orla Klatte
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
5
|
Bălan AM, Bodolea C, Trancă SD, Hagău N. Trends in Molecular Diagnosis of Nosocomial Pneumonia Classic PCR vs. Point-of-Care PCR: A Narrative Review. Healthcare (Basel) 2023; 11:healthcare11091345. [PMID: 37174887 PMCID: PMC10177880 DOI: 10.3390/healthcare11091345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Nosocomial pneumonia is one of the most frequent hospital-acquired infections. One of the types of nosocomial pneumonia is ventilator-associated pneumonia, which occurs in endotracheally intubated patients in intensive care units (ICU). Ventilator-associated pneumonia may be caused by multidrug-resistant pathogens, which increase the risk of complications due to the difficulty in treating them. Pneumonia is a respiratory disease that requires targeted antimicrobial treatment initiated as early as possible to have a good outcome. For the therapy to be as specific and started sooner, diagnostic methods have evolved rapidly, becoming quicker and simpler to perform. Polymerase chain reaction (PCR) is a rapid diagnostic technique with numerous advantages compared to classic plate culture-based techniques. Researchers continue to improve diagnostic methods; thus, the newest types of PCR can be performed at the bedside, in the ICU, so-called point of care testing-PCR (POC-PCR). The purpose of this review is to highlight the benefits and drawbacks of PCR-based techniques in managing nosocomial pneumonia.
Collapse
Affiliation(s)
- Andrei-Mihai Bălan
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Constantin Bodolea
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Sebastian Daniel Trancă
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Emergency Department, The Emergency County Hospital Cluj, 400347 Cluj-Napoca, Romania
| | - Natalia Hagău
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, "Regina Maria" Hospital, 400221 Cluj-Napoca, Romania
| |
Collapse
|
6
|
Both A, Christner M, Berinson B, Dreimann M, Viezens L, Lütgehetmann M, Aepfelbacher M, Rohde H, Stangenberg M. The added value of a commercial 16S/18S-PCR assay (UMD-SelectNA, Molzym) for microbiological diagnosis of spondylodiscitis: an observational study. Diagn Microbiol Infect Dis 2023; 106:115926. [PMID: 36963329 DOI: 10.1016/j.diagmicrobio.2023.115926] [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: 09/27/2022] [Revised: 02/14/2023] [Accepted: 02/19/2023] [Indexed: 03/26/2023]
Abstract
In spondylodiscitis, pathogen identification is important to guide therapy strategies. Here the use of an rDNA PCR assay (Molzym UMDSelectNA) for pathogen detection in spondylodiscitis was evaluated in 182 specimens from 124 spondylodiscitis patients. In 81% of specimens rDNA PCR and conventional culture produced concordant results. Compared to conventional culture, sensitivity and specificity of rDNA PCR were 75% and 83.9%, respectively. The rDNA PCR performed better than conventional culture in identification of Streptococcus spp.. However, overall sensitivity was suboptimal, e.g., in cases with low bacterial burden, and only 5 of 124 patients (4%) received a microbiological diagnosis by employing rDNA PCR. Thus, the added value of routine use of rDNA PCR on spondylodiscitis specimens is limited. Targeted use of the assay in culture-negative cases may be efficient and moderately increase diagnostic yield. The need for susceptibility information implies that 16S rDNA PCR may only be used as an add-on tool to culture.
Collapse
Affiliation(s)
- Anna Both
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Berinson
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Dreimann
- Division of Spine Surgery, Department of Trauma and Orthopedic Surgery, University Medical Center Hamburg- Eppendorf, Hamburg, Germany
| | - Lennart Viezens
- Division of Spine Surgery, Department of Trauma and Orthopedic Surgery, University Medical Center Hamburg- Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
| | - Martin Stangenberg
- Division of Spine Surgery, Department of Trauma and Orthopedic Surgery, University Medical Center Hamburg- Eppendorf, Hamburg, Germany
| |
Collapse
|
7
|
Zhuo X, Zhao J, Wang L, Sun B, Sun L, Wang C, Li B, Fan Y, Liu Y, Cao B. Development and evaluation of a multiplex quantitative polymerase chain reaction assay for detecting bacteria associated with lower respiratory tract infection. Int J Infect Dis 2022; 122:202-211. [PMID: 35644352 DOI: 10.1016/j.ijid.2022.05.052] [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: 02/22/2022] [Revised: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES This study aimed to establish a multiplex quantitative polymerase chain reaction (MQ-PCR) assay for 12 bacterial pathogens found in lower respiratory tract infection (LRTI) and to evaluate its performance in a cohort of 211 patients with LRTI. METHODS The study was divided into two stages: a pilot study to establish the methodology and a clinical validation study to evaluate its performance. In the pilot study, we established the MQ-PCR and analyzed its performance regarding limits of detection, reproducibility, specificity, and efficiency. In the clinical validation study, we obtained 211 sputum and/or bronchoalveolar lavage fluid (BALF) samples and detected pathogens by MQ-PCR. The MQ-PCR time was 3 h from sample collection to complete pathogen detection. RESULTS The limit of detection was 1000 copies/ml, and the maximum efficiency was >95%. When cutoffs of ≥105 copies/ml in sputum and ≥104 copies/ml in BALF were applied, the sensitivity, specificity, and positive and negative predictive values of the MQ-PCR were 77% (95% confidence interval [CI] 67-88%), 94% (95% CI 93-95%), 25% (95% CI 19-31%), and 99% (95% CI 99-100%), respectively. CONCLUSIONS This study demonstrates that the new MQ-PCR assay is time-saving, more effective and sensitive, and brings us closer to mainstream adoption of quantitative molecular detection of bacteria.
Collapse
Affiliation(s)
- Xianxia Zhuo
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd
| | - Bin Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Lanhua Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Binbin Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yingmei Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.
| |
Collapse
|
8
|
Utility of Polymerase Chain Reaction in Nasopharyngeal Swabs for Identifying Respiratory Bacteria Causing Community-Acquired Pneumonia. Microbiol Spectr 2022; 10:e0037922. [PMID: 35583335 PMCID: PMC9241648 DOI: 10.1128/spectrum.00379-22] [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] [Indexed: 11/20/2022] Open
Abstract
Timely identification of a pathogen in lower respiratory tract infections (LRTI) can support appropriate antibiotics use. The difficulty of obtaining lower respiratory tract (LRT) samples limits the utility of point-of-care syndromic molecular assays. We assessed the performance of the FilmArray Pneumonia plus panel (FilmArray PP) in nasopharyngeal (NP) swab for detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Patients in the study included retrospectively consenting adults who attended the emergency department of Lausanne University Hospital between February 2019 and August 2020 for a community-acquired LRTI, with available NP swab and a high-quality LRT sample. These samples were tested with the FilmArray PP (cutoff of ≥104 copies/mL). Positive (PPA) and negative percent agreement (NPA) of FilmArray PP in NP swab were calculated, using (i) FilmArray PP in LRT sample and (ii) standard microbiological tests as reference standards. To assess the performance of a lower detection cutoff, NP samples were also tested with an in-house PCR (cutoff of ≥10 copies/mL) for S. pneumoniae and H. influenzae. Overall, 118 patients were included. FilmArray PP in LRT sample and standard microbiology tests detected S. pneumoniae in 19/118 and 12/118, H. influenzae in 44/118 and 19/118, and M. catarrhalis in 14/118 and 0/118, respectively. Using LRT FilmArray PP as reference, PPA and NPA of FilmArray PP on NP were 58% and 100% for S. pneumoniae, 61% and 100% for H. influenzae, and 57% and 99% for M. catarrhalis. Using standard diagnostic tests as reference, PPA and NPA were 58% and 96% for S. pneumoniae, 74% and 87% for H. influenzae, and indefinite and 92% for M. catarrhalis. Using a lower cutoff on NP (≥102 copies/mL), PPA was 68% for S. pneumoniae and 77% for H. influenzae with LRT FilmArray PP as reference. FilmArray PP in NP swabs has a limited PPA for identifying the most common etiologies of community-acquired LRTI irrespective of the reference standard, preventing its use for withholding antibiotics. The PCR detection cutoff does not explain the low PPA. The excellent NPA suggests the use of NP PCR results for rapidly targeted antimicrobial therapy. IMPORTANCE Timely identification of a pathogen in patients with lower respiratory tract infections is of paramount importance to avoid inappropriate antibiotic prescription. We aimed to evaluate the performance of a rapid syndromic molecular assay in nasopharyngeal swabs for identifying the most common bacterial causes of lower respiratory tract infections in adults (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis). Our data show that nasopharyngeal molecular assay has a good concordance with lower respiratory tract sample when positive but not when negative. A positive result is therefore concordant with a lower respiratory tract infection and can be used to target antibiotics. Nevertheless, a negative result does not have a good concordance, so it cannot be used to withhold antibiotics. Our findings illustrate the potential utility of these easily collected samples for the management of patients with lower respiratory tract infections.
Collapse
|
9
|
Dhoubhadel BG, Suzuki M, Ishifuji T, Yaegashi M, Asoh N, Ishida M, Hamaguchi S, Aoshima M, Yasunami M, Ariyoshi K, Morimoto K. High prevalence of multiple serotypes of pneumococci in patients with pneumonia and their associated risk factors. Thorax 2022; 77:thoraxjnl-2021-217979. [PMID: 35474029 PMCID: PMC9606540 DOI: 10.1136/thoraxjnl-2021-217979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 04/03/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Multiple serotypes of pneumococci have epidemiological and clinical implications, such as the emergence of non-vaccine serotypes and the acquisition of antimicrobial resistance. Prevalence of multiple serotypes of pneumococci in adults and their risk factors are not known. METHODS We enrolled adult patients from age ≥15 years with radiologically confirmed pneumonia in four hospitals across Japan. Pneumococcal pneumonia was defined with a pneumococcal bacterial density of ≥104/mL in sputum by lytA quantitative PCR, and serotypes were determined. Pneumonias with a single serotype were categorised as single-serotype pneumococcal pneumonia and with two or more serotypes as multiple-serotype pneumococcal pneumonia. Multivariable logistic regression was used to assess the risk factors. RESULTS 3470 patients (median age 77 years, IQR 65-85) were enrolled. Pneumococcal pneumonia was identified in 476 (18.3%, n=2605) patients. Multiple serotypes were detected in 42% of them. Risk of having multiple serotypes was low among patients who had received 23-valent pneumococcal polysaccharide vaccine (PPSV23) vaccines (adjusted OR 0.51 (95% CI 0.27 to 0.94)). Proportion of non-PCV7 PPSV23 serotypes in overall distribution of multiple serotypes was 67.4% (n=324/481) compared with 46.4% (n=128/276) in that of single serotypes (p=0.001). Serotypes 5, 9N/9L, 10A, 12/22/46, 17F and 35F were associated with multiple-serotype pneumonia, and serotypes 6A/6B, 23F, 11 and 6C/6D were associated with single-serotype pneumonia. Proportion of more invasive serotypes (serotypes 1, 5, 7F, 8) was significantly higher in multiple-serotype pneumonia (p=0.001). CONCLUSIONS Multiple serotypes of pneumococci are common in sputum of adult patients with pneumonia. The risk of multiple-serotype pneumococcal pneumonia is lower than that of single-serotype pneumococcal pneumonia among PPSV23-vaccinated patients. TRIAL REGISTRATION NUMBER UMIN000006909.
Collapse
Affiliation(s)
- Bhim Gopal Dhoubhadel
- Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Global Health, School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoko Ishifuji
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Makito Yaegashi
- Department of General Internal Medicine, Kameda Medical Center, Chiba, Japan
| | - Norichika Asoh
- Department of Internal Medicine, Juzenkai Hospital, Nagasaki, Japan
| | - Masayuki Ishida
- Department of Internal Medicine, Chikamori Hospital, Kochi, Japan
| | - Sugihiro Hamaguchi
- Department of General Internal Medicine, Fukushima Medical University, Fukushima, Japan
| | | | - Michio Yasunami
- Life Science Institute, Saga-Ken Medical Centre Koseikan, Saga, Japan
| | - Koya Ariyoshi
- Department of Global Health, School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Konosuke Morimoto
- Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| |
Collapse
|
10
|
Berneking L, Haas M, Frielinghaus L, Berinson B, Lütgehetmann M, Christner M, Aepfelbacher M, Gerlach U, Seide K, Both A, Rohde H. Evaluation of a syndromic panel polymerase chain reaction (spPCR) assay for the diagnosis of device-associated bone and joint infections (BJI). Int J Infect Dis 2022; 116:283-288. [PMID: 35031396 DOI: 10.1016/j.ijid.2022.01.013] [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: 08/11/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVE Pathogen detection is crucial for diagnosis and targeted therapy in implant-associated bone and joint infections (BJI). Culture-based microbiology regularly fails to identify causative pathogens. This study evaluated the diagnostic accuracy and clinical usefulness of a syndromic panel polymerase chain reaction (spPCR) assay targeting common BJI pathogens in tissue specimens from patients with implant-associated BJI. METHODS Results obtained by spPCR assay and a 16S rDNA PCR were compared with results obtained from a standard of care (SOC) culture-based diagnostics, serving as a gold standard. In total, 126 specimens obtained from 73 patients were analyzed. RESULTS The spPCR assay correctly identified 33/40 culture-positive samples (82.5 %) and was positive in 9/86 (10.5 %) culture-negative samples, resulting in an overall sensitivity of 84.6 % (95% confidence interval [CI] 68.79-93.59%) and specificity of 89.35% (95% CI 80.6-94.81%). The spPCR was more sensitive compared with the 16S rDNA PCR (37.5%). The spPCR identified pathogens in 7/51 (13.7%) SOC-negative patients. Re-evaluation of spPCR results in clinical context suggested their clinical significance. CONCLUSION An spPCR assay targeting common pathogens causing implant-associated BJI may help to identify causative agents in culture-negative cases. As false-negative results are possible, spPCR assays appear as an add-on approach for pathogen detection in implant-associated BJI.
Collapse
Affiliation(s)
- Laura Berneking
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Michaela Haas
- Septische Unfallchirurgie und Orthopädie, BG Klinikum Hamburg, Hamburg, Germany
| | - Lisa Frielinghaus
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Berinson
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Ulf Gerlach
- Septische Unfallchirurgie und Orthopädie, BG Klinikum Hamburg, Hamburg, Germany
| | - Klaus Seide
- Septische Unfallchirurgie und Orthopädie, BG Klinikum Hamburg, Hamburg, Germany
| | - Anna Both
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
| |
Collapse
|
11
|
Boix-Palop L, Obradors M, Xercavins M, Picó-Plana E, Canales L, Dietl B, Pérez J, Garau J, Calbo E. Improvement of pneumococcal pneumonia diagnosis using quantitative real-time PCR targeting lytA in adult patients: a prospective cohort study. Clin Microbiol Infect 2021; 28:138.e1-138.e7. [PMID: 34116202 DOI: 10.1016/j.cmi.2021.05.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVES The aim of the study was to assess the performance of real-time PCR targeting the lytA gene (rtPCR-lytA) in plasma, urine and nasopharyngeal (NP) samples for the diagnosis of pneumococcal community-acquired pneumonia (P-CAP). METHODS Prospective observational study including all consecutive adults with CAP from November 2015 to May 2017. P-CAP was defined if pneumococcus was identified using conventional methods (CM) and/or a positive rtPCR-lytA was detected in blood, urine or NP samples (NP cut-off ≥8000 copies/mL). Diagnostic performance of each test was calculated. RESULTS A total of 133 individuals with CAP were included. Of these, P-CAP was diagnosed in 62 (46.6%). The proportion of P-CAP diagnosed by rtPCR-lytA methods was significantly higher than that diagnosed by CM (87.1% versus 59.7%, p 0.005). The rtPCR-lytA identified Streptococcus pneumoniae in 25 patients (40.3% of all individuals with P-CAP) whose diagnosis would have been missed by CM. NP-rtPCR-lytA allowed diagnosis of 62.3% of P-CAP. A nasopharyngeal colonization density ≥2351 copies/mL predicted P-CAP diagnosis (area under the curve = 0.82, sensitivity 83.3%, specificity 80.9%). There was a positive correlation between increasing bacterial load in blood and CURB-65 score (Spearman correlation coefficient r = 0.4, p 0.001), pneumonia severity index (r = 0.3, p 0.02) and time to clinical stability (r = 0.33, p 0.01). Median bacterial load in blood was higher in P-CAP patients with bacteraemia (0.65 × 103 versus 0 × 103 copies/mL, p 0.002), intensive care unit admission (0.68 × 103 versus 0 × 103 copies/mL, p 0.04) or mechanical ventilation (7.45 × 103 versus 0 × 103 copies/mL, p 0.04). CONCLUSIONS The use of rtPCR-lytA methods significantly increased the diagnosis of P-CAP compared with CM. Nasopharyngeal swabs rtPCR-lytA detection, with an accurate cut-off value, was the most promising among molecular methods for the diagnosis of P-CAP.
Collapse
Affiliation(s)
- Lucía Boix-Palop
- Infectious Diseases Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain; Universitat Internacional de Catalunya, Barcelona, Spain; Universitat de Barcelona, Barcelona, Spain.
| | - Meritxell Obradors
- Infectious Diseases Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | | | | | - Lydia Canales
- Radiology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Beatriz Dietl
- Infectious Diseases Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Josefa Pérez
- Microbiology Department, CatLab, Barcelona, Spain
| | - Javier Garau
- Infectious Diseases Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain; Service of Internal Medicine, Clínica Rotger, Palma de Mallorca, Spain
| | - Esther Calbo
- Infectious Diseases Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain; Universitat Internacional de Catalunya, Barcelona, Spain.
| |
Collapse
|
12
|
Abstract
PURPOSE OF REVIEW Pneumonia is the main global cause of sepsis, and has been associated with high morbidity and high short and long-term mortality rates. As it may be caused by a wide spectrum of microorganisms, microbial diagnosis is challenging and the choice of adequate therapy remains an important problem. This review focuses on recently published studies of microbiological diagnostic tests and clinical assessments for pneumonia, including community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. RECENT FINDINGS Over the past decade, the microbiological diagnosis of pneumonia has improved significantly - thanks to the development and implementation of molecular diagnostic tests for identifying the most frequent pathogens causing pneumonia and for determining their patterns of resistance. Molecular methods for the diagnosis of pneumonia focus on multiple target detection systems and pathogen detection arrays, and, more recently, have been used in combination with mass spectrometry. SUMMARY The implementation of rapid diagnostic techniques in routine clinical practice able to identify and determine the resistance patterns of the causative microbes may transform the management of pneumonia, improving the selection and administration of antimicrobial therapies especially in critically ill patients. The validation of new diagnostic technology platforms is crucial in order to assess their usefulness and to guide antimicrobial treatment in this population.
Collapse
|
13
|
Sadowy E, Hryniewicz W. Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods. Eur J Clin Microbiol Infect Dis 2020; 39:2247-2256. [PMID: 32710352 PMCID: PMC7669753 DOI: 10.1007/s10096-020-03991-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
Collapse
Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| |
Collapse
|
14
|
Pfefferle S, Christner M, Aepfelbacher M, Lütgehetmann M, Rohde H. Implementation of the FilmArray ME panel in laboratory routine using a simple sample selection strategy for diagnosis of meningitis and encephalitis. BMC Infect Dis 2020; 20:170. [PMID: 32087681 PMCID: PMC7036261 DOI: 10.1186/s12879-020-4904-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Background Infectious meningitis is a serious disease and patient outcome relies on fast and reliable diagnostics. A syndromic panel testing approach like the FilmArray ME can accelerate diagnosis and therefore decrease the time to pathogen specific therapy. Yet, its clinical utility is controversial, mainly because of a remaining uncertainty in correct interpretation of results, limited data on its performance on clinical specimens and its relatively high costs. The aim of this study was to analyze clinical performance of the assay in a real life setting at a tertiary university hospital using a pragmatic and simple sample selection strategy to reduce the overall cost burden. Methods Over a period of 18 months we received 4623 CSF samples (2338 hospitalizations, 1601 individuals). FilmArray ME analysis was restricted to CSF-samples with a high pretest probability of infectious meningitis, e.g. positive Gram-stain, samples in which leukocytes and/or bacteria were evident or urgent suspicion of infection was communicated by clinicians. N = 171 samples matched to our risk criteria and were subjected to FilmArray ME analysis. Those samples were also analyzed by reference methods: culture only (n = 45), PCR only (n = 20) or both methods (n = 106). Results 56/171 (32.75%) were FilmArray ME positive. Bacterial pathogens were detected in 30/56 (53.57%), viral pathogens were detected in 27/56 (48.21%) and yeast DNA was detected in 1/56 (1.79%) of positive samples. Double detection occurred in 2/56 samples. In 52/56 (92.86%) FilmArray ME positive samples, results could be confirmed by the reference assays (sensitivity = 96.30%, specificity =96.58%). Conclusion The FilmArray ME assay is a fast and reliable diagnostic tool for the management of infectious meningitis and can easily be implemented in routine diagnostic workflows. However, correlation of test results and underlying clinical symptoms requires experienced users and the awareness of potentially false negative or false positive results. Moreover, considering the need for antimicrobial susceptibility testing, the use of molecular tests as a stand-alone diagnostic cannot be recommended.
Collapse
Affiliation(s)
- Susanne Pfefferle
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Marc Lütgehetmann
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| |
Collapse
|
15
|
Imai K, Nemoto R, Kodana M, Tarumoto N, Sakai J, Kawamura T, Ikebuchi K, Mitsutake K, Murakami T, Maesaki S, Fujiwara T, Hayakawa S, Hoshino T, Seki M, Maeda T. Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer. Front Cell Infect Microbiol 2020; 10:11. [PMID: 32083020 PMCID: PMC7002467 DOI: 10.3389/fcimb.2020.00011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
Differentiation between mitis group streptococci (MGS) bacteria in routine laboratory tests has become important for obtaining accurate epidemiological information on the characteristics of MGS and understanding their clinical significance. The most reliable method of MGS species identification is multilocus sequence analysis (MLSA) with seven house-keeping genes; however, because this method is time-consuming, it is deemed unsuitable for use in most clinical laboratories. In this study, we established a scheme for identifying 12 species of MGS (S. pneumoniae, S. pseudopneumoniae, S. mitis, S. oralis, S. peroris, S. infantis, S. australis, S. parasanguinis, S. sinensis, S. sanguinis, S. gordonii, and S. cristatus) using the MinION nanopore sequencer (Oxford Nanopore Technologies, Oxford, UK) with the taxonomic aligner "What's in My Pot?" (WIMP; Oxford Nanopore's cloud-based analysis platform) and Kraken2 pipeline with the custom database adjusted for MGS species identification. The identities of the species in reference genomes (n = 514), clinical isolates (n = 31), and reference strains (n = 4) were confirmed via MLSA. The nanopore simulation reads were generated from reference genomes, and the optimal cut-off values for MGS species identification were determined. For 31 clinical isolates (S. pneumoniae = 8, S. mitis = 17 and S. oralis = 6) and 4 reference strains (S. pneumoniae = 1, S. mitis = 1, S. oralis = 1, and S. pseudopneumoniae = 1), a sequence library was constructed via a Rapid Barcoding Sequencing Kit for multiplex and real-time MinION sequencing. The optimal cut-off values for the identification of MGS species for analysis by WIMP and Kraken2 pipeline were determined. The workflow using Kraken2 pipeline with a custom database identified all 12 species of MGS, and WIMP identified 8 MGS bacteria except S. infantis, S. australis, S. peroris, and S. sinensis. The results obtained by MinION with WIMP and Kraken2 pipeline were consistent with the MGS species identified by MLSA analysis. The practical advantage of whole genome analysis using the MinION nanopore sequencer is that it can aid in MGS surveillance. We concluded that MinION sequencing with the taxonomic aligner enables accurate MGS species identification and could contribute to further epidemiological surveys.
Collapse
Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Rina Nemoto
- Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Masahiro Kodana
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Toru Kawamura
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kenji Ikebuchi
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
- Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Taku Fujiwara
- Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Mitsuko Seki
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| |
Collapse
|
16
|
Del Rio-Pertuz G, Gutiérrez JF, Triana AJ, Molinares JL, Robledo-Solano AB, Meza JL, Ariza-Bolívar OM, Acosta-Reyes J, Garavito A, Viasus D, Carratalà J. Usefulness of sputum gram stain for etiologic diagnosis in community-acquired pneumonia: a systematic review and meta-analysis. BMC Infect Dis 2019; 19:403. [PMID: 31077143 PMCID: PMC6509769 DOI: 10.1186/s12879-019-4048-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 04/30/2019] [Indexed: 11/28/2022] Open
Abstract
Background Implementation of sputum Gram stain in the initial assessment of community-acquired pneumonia (CAP) patients is still controversial. We performed a systematic review and meta-analysis to investigate the usefulness of sputum Gram stain for defining the etiologic diagnosis of CAP in adult patients. Methods We systematically searched the Medline, Embase, Science Direct, Scopus and LILACS databases for full-text articles. Relevant studies were reviewed by at least three investigators who extracted the data, pooled them using a random effects model, and carried out quality assessment. For each bacterium (Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Gram-negative bacilli), pooled sensitivity, specificity, positive and negative likelihood ratios were reported. Results After a review of 3539 abstracts, 20 articles were included in the present meta-analysis. The studies included yielded 5619 patients with CAP. Pooled sensitivity and pooled specificity of sputum Gram stain were 0.59 (95% CI, 0.56–0.62) and 0.87 (95% CI, 0.86–0.89) respectively for S. pneumoniae, 0.78 (95% CI, 0.72–0.84) and 0.96 (95% CI, 0.94–0.97) for H. influenzae, 0.72 (95% CI, 0.53–0.87) and 0.97 (95% CI, 0.95–0.99) for S. aureus, and 0.64 (95% CI, 0.49–0.77) and 0.99 (95% CI, 0.97–0.99) for Gram-negative bacilli. Conclusion Sputum Gram stain test is sensitive and highly specific for identifying the main causative pathogens in adult patients with CAP. Trial registration This study has been registered at PROSPERO International prospective register of systematic reviews under registration no. CRD42015015337. Electronic supplementary material The online version of this article (10.1186/s12879-019-4048-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gaspar Del Rio-Pertuz
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia
| | - Juan F Gutiérrez
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia
| | - Abel J Triana
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia
| | - Jorge L Molinares
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia
| | - Andrea B Robledo-Solano
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia
| | - José L Meza
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia
| | - Orlando M Ariza-Bolívar
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia
| | - Jorge Acosta-Reyes
- Faculty of Public Health, Division of Health Sciences, Universidad del Norte, Barranquilla, Colombia
| | - Argenis Garavito
- Clínica Medilaser S.A. - Sucursal Florencia, Fundación Universitaria Navarra, Florencia, Colombia
| | - Diego Viasus
- Faculty of Medicine, Division of Health Sciences, Hospital Universidad del Norte and Universidad del Norte, Barranquilla, Colombia.
| | - Jordi Carratalà
- Infectious Disease Department, Hospital Universitari de Bellvitge and Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain.,Faculty of Medicine, Clinical Sciences Department, University of Barcelona, Barcelona, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0005), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
17
|
van den Munckhof EHA, de Koning MNC, Quint WGV, van Doorn LJ, Leverstein-van Hall MA. Evaluation of a stepwise approach using microbiota analysis, species-specific qPCRs and culture for the diagnosis of lower respiratory tract infections. Eur J Clin Microbiol Infect Dis 2019; 38:747-754. [DOI: 10.1007/s10096-019-03511-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/11/2019] [Indexed: 01/18/2023]
|
18
|
van Schaik ML, Duijkers R, Paternotte N, Jansen R, Rozemeijer W, van der Reijden WA, Boersma WG. Feasibility of a quantitative polymerase chain reaction assay for diagnosing pneumococcal pneumonia using oropharyngeal swabs. Mol Biol Rep 2019; 46:1013-1021. [PMID: 30569391 PMCID: PMC7089193 DOI: 10.1007/s11033-018-4558-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/06/2018] [Indexed: 11/30/2022]
Abstract
Streptococcus pneumoniae is the most important pathogen causing community-acquired pneumonia (CAP). The current diagnostic microbial standard detects S. pneumoniae in less than 30% of CAP cases. A quantitative polymerase chain reaction (PCR) targeting autolysin (lytA) is able to increase the rate of detection. The aim of this study is validation of this quantitative PCR in vitro using different available strains and in vivo using clinical samples (oropharyngeal swabs). The PCR autolysin (lytA) was validated by testing the intra- and inter-run variability. Also, the in vitro specificity and sensitivity, including the lower limit of detection was determined. In addition, a pilot-study was performed using samples from patients (n = 28) with pneumococcal pneumonia and patients (n = 28) with a pneumonia without detection of S. pneumoniae with the current diagnostic microbial standard, but with detection of either a viral and or another bacterial pathogen to validate this test further. The intra- and inter-run variability were relatively low (SD's ranging from 0.08 to 0.96 cycle thresholds). The lower limit of detection turned out to be 1-10 DNA copies/reaction. In-vitro sensitivity and specificity of the tested specimens (8 strains carrying lytA and 6 strains negative for lytA) were both 100%. In patients with pneumococcal and non-pneumococcal pneumonia a cut-off value of 6.000 copies/mL would lead to a sensitivity of 57.1% and a specificity of 85.7%. We were able to develop a quantitative PCR targeting lytA with good in-vitro test characteristics.
Collapse
Affiliation(s)
- M L van Schaik
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
- Department of Pulmonology, Isala clinics Zwolle, Dr. van Heesweg 2, 8025AB, Zwolle, The Netherlands
| | - R Duijkers
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - N Paternotte
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - R Jansen
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
| | - W Rozemeijer
- Department Medical Microbiology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - W A van der Reijden
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
| | - W G Boersma
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands.
- Department of Pulmonary Diseases, Northwest Hospital Group, P.O. Box 501, 1800AM, Alkmaar, The Netherlands.
| |
Collapse
|
19
|
Abstract
A wide variety of microorganisms are potential respiratory pathogens, and the spectrum of known pathogens for each respiratory infection syndrome has not changed markers over recent years. Detection of likely etiologic agents of respiratory infections can help direct management and can also play an important role in disease surveillance. For this purpose, we are still reliant on many traditional diagnostic tools that have been used for decades in order to determine the microbial etiology of respiratory infections. However, these tools have been increasingly supplemented by newer methods, particular molecular diagnostic techniques, which have enabled the more rapid detection of many pathogens that were previously difficult to detect. These advances have particularly lead to improvements in the ability to detect respiratory viruses and also other microorganisms that do not normally colonize the respiratory tract. Recognition of the existence of the lung microbiome has challenged the traditional views of pneumonia pathogenesis and may provide the opportunity for new diagnostic tools that are focused on more than just detection of specific known pathogens. Continued liaison between clinicians and laboratory staff is vital in order to facilitate the most cost-effective use of laboratory diagnostics.
Collapse
|
20
|
Edouard S, Al-Tawfiq JA, Memish ZA, Yezli S, Gautret P. Impact of the Hajj on pneumococcal carriage and the effect of various pneumococcal vaccines. Vaccine 2018; 36:7415-7422. [PMID: 30236632 DOI: 10.1016/j.vaccine.2018.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Islamic Hajj pilgrimage is the largest annual mass gathering in the world. The overcrowding of people promotes the acquisition, spread and transmission of respiratory pathogens, including Streptococcus pneumoniae. METHODS We conducted a methodological review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. The objective was to summarize the available data regarding the prevalence of pneumococcal carriage among Hajj pilgrims and about carriage acquisition and circulation of S. pneumoniae among pilgrims before and after participating in the Hajj according to their vaccination status. RESULTS Eight articles met eligibility criteria for pneumococcal carriage and impact of pneumococcal vaccination on carriage. Seven of them showed a significant increase in nasopharyngeal carriage of pneumococci following the pilgrimage, with acquisition rates ranging from 18 to 36%. Serotypes 3, 19F and 34 are the most common. A significant increase in antibiotic resistant strains was observed following participation in the Hajj. A lower prevalence was found in pilgrims treated with antibiotics, those who used a hand sanitizer, or those who washed their hands more frequently than usual. An increased carriage of pneumococcal serotypes included in pneumococcal vaccines (10-valent pneumococcal conjugate vaccine (PCV10), 13-valent pneumococcal conjugate vaccine (PCV13), 23-valent pneumococcal polysaccharide vaccine (PPV23)) was observed following participation in the Hajj. To date, no study has shown a significant reduction in pneumococcal carriage among pilgrims after vaccination with PPV23 or PCV. In fact, no significant difference was currently observed in the prevalence ratio of pneumococcal carriage between vaccinated and unvaccinated pilgrims. CONCLUSION The studies analyzed in this review showed an increased carriage of pneumococcus in post-Hajj pilgrims compared to pre-Hajj pilgrims, including vaccine serotypes. Further studies are needed to investigate the possible relationships between carriage, disease and vaccine in pilgrims.
Collapse
Affiliation(s)
- Sophie Edouard
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine Unit, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ziad A Memish
- Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Saber Yezli
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.
| |
Collapse
|
21
|
High HMGB1 levels in sputum are related to pneumococcal bacteraemia but not to disease severity in community-acquired pneumonia. Sci Rep 2018; 8:13428. [PMID: 30194360 PMCID: PMC6128869 DOI: 10.1038/s41598-018-31504-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/10/2018] [Indexed: 12/20/2022] Open
Abstract
During bacterial infections, damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs) activate immune cells. Here, we investigated whether plasma and sputum levels of High Mobility Group Box 1 (HMGB1), a prototypic DAMP, are associated with disease severity and aetiology in community-acquired pneumonia (CAP). In addition, in patients with pneumococcal CAP, the impact of the level of sputum lytA DNA load, a PAMP, was investigated. We studied patients hospitalised for bacterial CAP (n = 111), and samples were collected at admission. HMGB1 was determined by enzyme-linked immunosorbent assays, and pneumococcal lytA DNA load was determined by quantitative polymerase chain reaction. Plasma and sputum HMGB1 levels did not correlate to disease severity (pneumonia severity index or presence of sepsis), but high sputum HMGB1 level was correlated to pneumococcal aetiology (p = 0.002). In pneumococcal pneumonia, high sputum lytA DNA load was associated with respiratory failure (low PaO2/FiO2 ratio; p = 0.019), and high sputum HMGB1 level was associated with bacteraemia (p = 0.006). To conclude, high sputum HMGB1 was not associated with severe disease, but with pneumococcal bacteraemia, indicating a potential role for HMGB1 in bacterial dissemination. High sputum lytA was associated with severe disease.
Collapse
|
22
|
Li X, Chen B, Zhang S, Li X, Chang J, Tang Y, Wu Y, Lu X. Rapid Detection of Respiratory Pathogens for Community-Acquired Pneumonia by Capillary Electrophoresis-Based Multiplex PCR. SLAS Technol 2018; 24:105-116. [PMID: 30048599 DOI: 10.1177/2472630318787452] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Community-acquired pneumonia (CAP) is a common infectious disease linked to high rates of morbidity and mortality. Fast and accurate identification of the pathogens responsible for CAP will aid in diagnosis. We established a capillary electrophoresis-based multiplex PCR (CEMP) panel to enable the detection of viral and bacterial pathogens associated with CAP. The assay simultaneously detects and identifies the 13 common unculturable CAP viral and bacterial pathogens within 4 h. We evaluated the performance of a commercially available panel with 314 samples collected from CAP patients. We compared the results to those obtained with the liquid chip-based Luminex xTAG Respiratory Viral Panel (RVP) Fast Kit (for viruses) and the agarose gel-based Seegene PneumoBacter ACE Detection Kit (for atypical bacteria). All positive samples were further verified by the Sanger sequencing method. The sensitivity, specificity, positive predictive value, and negative predictive value of CEMP were 97.31%, 100%, 100%, and 99.85%, respectively. CEMP provides a rapid and accurate method for the high-throughput detection of pathogens in patients with CAP.
Collapse
Affiliation(s)
- Xue Li
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
| | - Bo Chen
- 3 Ningbo HEALTH Gene Technologies Co., Ltd., Ningbo, China
| | - Shaoya Zhang
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiuyuan Li
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
| | - Junxia Chang
- 4 Department of Laboratory Medicine, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Yanyan Tang
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
| | - Yong Wu
- 3 Ningbo HEALTH Gene Technologies Co., Ltd., Ningbo, China
| | - Xinxin Lu
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
| |
Collapse
|
23
|
Thakore N, Norville R, Franke M, Calderon R, Lecca L, Villanueva M, Murray MB, Cooney CG, Chandler DP, Holmberg RC. Automated TruTip nucleic acid extraction and purification from raw sputum. PLoS One 2018; 13:e0199869. [PMID: 29975759 PMCID: PMC6033430 DOI: 10.1371/journal.pone.0199869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022] Open
Abstract
Automated nucleic acid extraction from primary (raw) sputum continues to be a significant technical challenge for molecular diagnostics. In this work, we developed a prototype open-architecture, automated nucleic acid workstation that includes a mechanical homogenization and lysis function integrated with heating and TruTip purification; optimized an extraction protocol for raw sputum; and evaluated system performance on primary clinical specimens. Eight samples could be processed within 70 min. The system efficiently homogenized primary sputa and doubled nucleic acid recovery relative to an automated protocol that did not incorporate sample homogenization. Nucleic acid recovery was at least five times higher from raw sputum as compared to that of matched sediments regardless of smear or culture grade, and the automated workstation reproducibly recovered PCR-detectable DNA to at least 80 CFU mL-1 raw sputum. M. tuberculosis DNA was recovered and detected from 122/123 (99.2%) and 124/124 (100%) primary sputum and sediment extracts, respectively. There was no detectable cross-contamination across 53 automated system runs and amplification or fluorescent inhibitors (if present) were not detectable. The open fluidic architecture of the prototype automated workstation yields purified sputum DNA that can be used for any molecular diagnostic test. The ability to transfer TruTip protocols between personalized, on-demand pipetting tools and the fully automated workstation also affords public health agencies an opportunity to standardize sputum nucleic acid sample preparation procedures, reagents, and quality control across multiple levels of the health care system.
Collapse
Affiliation(s)
- Nitu Thakore
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Ryan Norville
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Molly Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Perú, Carabayllo, Lima, Peru
| | | | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | | |
Collapse
|
24
|
Musher DM, Abers MS, Bartlett JG. Evolving Understanding of the Causes of Pneumonia in Adults, With Special Attention to the Role of Pneumococcus. Clin Infect Dis 2018; 65:1736-1744. [PMID: 29028977 PMCID: PMC7108120 DOI: 10.1093/cid/cix549] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 09/05/2017] [Indexed: 01/18/2023] Open
Abstract
Before 1945, Streptococcus pneumoniae caused more than 90% of cases of pneumonia in adults. After 1950, the proportion of pneumonia caused by pneumococcus began to decline. Pneumococcus has continued to decline; at present, this organism is identified in fewer than fewer10%-15% of cases. This proportion is higher in Europe, a finding likely related to differences in vaccination practices and smoking. Gram-negative bacilli, Staphylococcus aureus, Chlamydia, Mycoplasma, and Legionella are each identified in 2%-5% of patients with pneumonia who require hospitalization. Viruses are found in 25% of patients, up to one-third of these have bacterial coinfection. Recent studies fail to identify a causative organism in more than 50% of cases, which remains the most important challenge to understanding lower respiratory infection. Our findings have important implications for antibiotic stewardship and should be considered as new policies for empiric pneumonia management are developed.
Collapse
Affiliation(s)
- Daniel M Musher
- Departments of Medicine and Molecular Virology and Microbiology, Baylor College of Medicine.,Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Michael S Abers
- Massachusetts General Hospital.,Harvard Medical School, Boston, Massachusetts
| | - John G Bartlett
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
25
|
Wyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp Gastelaars J, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A. Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species. Open Biol 2018; 7:rsob.170074. [PMID: 28931649 PMCID: PMC5627049 DOI: 10.1098/rsob.170074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/11/2017] [Indexed: 01/08/2023] Open
Abstract
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Streptococcus pneumoniae Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands. Following this, we tested 221 streptococcal isolates in molecular assays originally assumed specific for S. pneumoniae, targeting cpsA, lytA, piaB, ply, Spn9802, zmpC and capsule-type-specific genes. Cluster analysis of S2-sequences showed grouping according to species in line with published phylogenies of streptococcal core genomes. S2-typing convincingly distinguished pneumococci from non-pneumococcal species (99.2% sensitivity, 100% specificity). Molecular assays targeting regions of lytA and piaB were 100% specific for S. pneumoniae, whereas assays targeting cpsA, ply, Spn9802, zmpC and selected serotype-specific assays (but not capsular sequence typing) showed a lack of specificity. False positive results were over-represented in species associated with carriage, although no particular confounding signal was unique for carriage isolates.
Collapse
Affiliation(s)
- Anne L Wyllie
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Sandra Bovenkerk
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Jody van Engelsdorp Gastelaars
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bart Ferwerda
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Diederik van de Beek
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Krzysztof Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands.,The Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center, Amsterdam, the Netherlands
| |
Collapse
|
26
|
Accuracy of High-Throughput Nanofluidic PCR-Based Pneumococcal Serotyping and Quantification Assays Using Sputum Samples for Diagnosing Vaccine Serotype Pneumococcal Pneumonia: Analyses by Composite Diagnostic Standards and Bayesian Latent Class Models. J Clin Microbiol 2018; 56:JCM.01874-17. [PMID: 29444834 PMCID: PMC5925721 DOI: 10.1128/jcm.01874-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/30/2018] [Indexed: 11/20/2022] Open
Abstract
The lack of reliable diagnostic tests for detecting vaccine serotype pneumococcal pneumonia (VTPP) remains a challenging issue in pneumococcal vaccine studies. This study assessed the performances of high-throughput nanofluidic PCR-based pneumococcal serotyping and quantification assay methods using sputum samples (the nanofluidic sputum quantitative PCR [Sp-qPCR] assay) to diagnose 13-valent pneumococcal conjugate VTPP compared with the performance of the serotype-specific urinary antigen detection (UAD) assay using urine samples. Adult pneumonia patients from Japan were enrolled in this study between September 2012 and August 2014. Sputum samples were subjected to the nanofluidic Sp-qPCR assay, quantitatively cultured, and serotyped by the Quellung reaction (SpQt). Urine samples were tested by the UAD method. The diagnostic performances of these tests were assessed using composite reference standards and Bayesian latent class models (BLCMs). Among 244 total patients, 27 (11.1%) tested positive with the UAD assay, while 16 (6.6%) and 34 (13.9%) tested positive with the SpQt and nanofluidic Sp-qPCR assays, respectively, with a cutoff value of ≥104 DNA copies/ml, which showed the maximum value of the Youden index. Using BLCMs, the estimated prevalence for VTPP was 12.9%, and the nanofluidic Sp-qPCR assay demonstrated the best performance (sensitivity, 90.2%; specificity, 96.9%), followed by UAD (sensitivity, 75.6%; specificity, 97.9%) and SpQt (sensitivity, 45.8%; specificity, 99.5%). However, when a higher cutoff value of ≥107 DNA copies/ml was applied, the performance of UAD became comparable to that of Sp-qPCR. The vaccine serotype-specific pneumococcal DNA load in sputum among UAD-positive patients was 3 logs higher than that among UAD-negative patients (P = 0.036). The nanofluidic Sp-qPCR assay may be accurate and useful for detecting VTPP among adults.
Collapse
|
27
|
Baggett HC, Watson NL, Deloria Knoll M, Brooks WA, Feikin DR, Hammitt LL, Howie SRC, Kotloff KL, Levine OS, Madhi SA, Murdoch DR, Scott JAG, Thea DM, Antonio M, Awori JO, Baillie VL, DeLuca AN, Driscoll AJ, Duncan J, Ebruke BE, Goswami D, Higdon MM, Karron RA, Moore DP, Morpeth SC, Mulindwa JM, Park DE, Paveenkittiporn W, Piralam B, Prosperi C, Sow SO, Tapia MD, Zaman K, Zeger SL, O'Brien KL. Density of Upper Respiratory Colonization With Streptococcus pneumoniae and Its Role in the Diagnosis of Pneumococcal Pneumonia Among Children Aged <5 Years in the PERCH Study. Clin Infect Dis 2018; 64:S317-S327. [PMID: 28575365 PMCID: PMC5850437 DOI: 10.1093/cid/cix100] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Previous studies suggested an association between upper airway pneumococcal colonization density and pneumococcal pneumonia, but data in children are limited. Using data from the Pneumonia Etiology Research for Child Health (PERCH) study, we assessed this potential association. Methods PERCH is a case-control study in 7 countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. Cases were children aged 1–59 months hospitalized with World Health Organization–defined severe or very severe pneumonia. Controls were randomly selected from the community. Microbiologically confirmed pneumococcal pneumonia (MCPP) was confirmed by detection of pneumococcus in a relevant normally sterile body fluid. Colonization density was calculated with quantitative polymerase chain reaction analysis of nasopharyngeal/oropharyngeal specimens. Results Median colonization density among 56 cases with MCPP (MCPP cases; 17.28 × 106 copies/mL) exceeded that of cases without MCPP (non-MCPP cases; 0.75 × 106) and controls (0.60 × 106) (each P < .001). The optimal density for discriminating MCPP cases from controls using the Youden index was >6.9 log10 copies/mL; overall, the sensitivity was 64% and the specificity 92%, with variable performance by site. The threshold was lower (≥4.4 log10 copies/mL) when MCPP cases were distinguished from controls who received antibiotics before specimen collection. Among the 4035 non-MCPP cases, 500 (12%) had pneumococcal colonization density >6.9 log10 copies/mL; above this cutoff was associated with alveolar consolidation at chest radiography, very severe pneumonia, oxygen saturation <92%, C-reactive protein ≥40 mg/L, and lack of antibiotic pretreatment (all P< .001). Conclusions Pneumococcal colonization density >6.9 log10 copies/mL was strongly associated with MCPP and could be used to improve estimates of pneumococcal pneumonia prevalence in childhood pneumonia studies. Our findings do not support its use for individual diagnosis in a clinical setting.
Collapse
Affiliation(s)
- Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - W Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Daniel R Feikin
- International Vaccine Access Center, and.,Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Laura L Hammitt
- International Vaccine Access Center, and.,Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Stephen R C Howie
- Medical Research Council Unit, Basse, The Gambia.,Department of Paediatrics University of Auckland, and.,Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Orin S Levine
- International Vaccine Access Center, and.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - David R Murdoch
- Department of Pathology, University of Otago, and.,Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Martin Antonio
- Medical Research Council Unit, Basse, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, and.,Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Juliet O Awori
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Vicky L Baillie
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrea N DeLuca
- International Vaccine Access Center, and.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | | | - Doli Goswami
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | | | - Ruth A Karron
- Department of International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David P Moore
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, South Africa
| | - Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom.,Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | | | - Daniel E Park
- International Vaccine Access Center, and.,Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, George Washington University, District Columbia
| | | | | | | | - Samba O Sow
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako, Mali; and
| | - Milagritos D Tapia
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Khalequ Zaman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | |
Collapse
|
28
|
lytA Quantitative PCR on Sputum and Nasopharyngeal Swab Samples for Detection of Pneumococcal Pneumonia among the Elderly. J Clin Microbiol 2017; 56:JCM.01231-17. [PMID: 29118170 PMCID: PMC5744198 DOI: 10.1128/jcm.01231-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/22/2017] [Indexed: 11/20/2022] Open
Abstract
Real-time quantitative PCR (qPCR) assay of sputum or nasopharyngeal specimens has shown promising results in the detection of pneumococcal community-acquired pneumonia (PncCAP). We applied qPCR for the autolysin gene (lytA) and compared sputum and nasopharyngeal swab (NPS) pneumococcal loads in elderly patients with community-acquired pneumonia (CAP), and specifically in patients with PncCAP, to those in patient groups with other respiratory diseases. We studied patients aged ≥65 years with radiologically confirmed CAP, clinical CAP not retrospectively radiologically confirmed, other acute respiratory infections, or stable chronic lung disease. Pneumococcal etiology of CAP was ascertained by using a combination of multiple diagnostic methods. We analyzed sputum and NPS specimens by lytA qPCR with 104 pneumococcal genome equivalents (GE)/ml as a cutoff for positivity. Among PncCAP patients, lytA qPCR detected pneumococci in 94% of the sputum samples and in large quantities (mean, 6.82 ± 1.02 log10 GE/ml) but less frequently in NPS (44%) and in smaller quantities (5.55 ± 0.92 log10 GE/ml). In all other patient groups, ≤10% of the sputum samples and <5% of the NPS samples were lytA qPCR positive; but when they were positive, the sputum pneumococcal loads were similar to those in the PncCAP patients, suggesting a pneumococcal etiology in these patients. This was supported by other pneumococcal assay results. Overall, sputum lytA qPCR positivity was more common in PncCAP patients than in the other patient groups, but the quantitative results were mainly similar. NPS lytA qPCR was less sensitive than sputum lytA qPCR in detecting PncCAP.
Collapse
|
29
|
Athlin S, Lidman C, Lundqvist A, Naucler P, Nilsson AC, Spindler C, Strålin K, Hedlund J. Management of community-acquired pneumonia in immunocompetent adults: updated Swedish guidelines 2017. Infect Dis (Lond) 2017; 50:247-272. [PMID: 29119848 DOI: 10.1080/23744235.2017.1399316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Based on expert group work, Swedish recommendations for the management of community-acquired pneumonia in adults are here updated. The management of sepsis-induced hypotension is addressed in detail, including monitoring and parenteral therapy. The importance of respiratory support in cases of acute respiratory failure is emphasized. Treatment with high-flow oxygen and non-invasive ventilation is recommended. The use of statins or steroids in general therapy is not found to be fully supported by evidence. In the management of pleural infection, new data show favourable effects of tissue plasminogen activator and deoxyribonuclease installation. Detailed recommendations for the vaccination of risk groups are afforded.
Collapse
Affiliation(s)
- Simon Athlin
- a Department of Infectious Diseases , Örebro University Hospital , Örebro , Sweden.,b Faculty of Medicin and Health , Örebro University , Örebro , Sweden
| | - Christer Lidman
- c Unit of Infectious Diseases, Department of Medicine Solna , Karolinska Institutet , Stockholm , Sweden.,d Department of Infectious Diseases , Karolinska University Hospital , Stockholm , Sweden
| | - Anders Lundqvist
- e Department of Infectious Diseases , Södra Älvsborgs Hospital , Borås , Sweden
| | - Pontus Naucler
- c Unit of Infectious Diseases, Department of Medicine Solna , Karolinska Institutet , Stockholm , Sweden.,d Department of Infectious Diseases , Karolinska University Hospital , Stockholm , Sweden
| | - Anna C Nilsson
- f Infectious Disease Research Unit, Department of Translational Medicine , Lund University , Malmö , Sweden
| | - Carl Spindler
- d Department of Infectious Diseases , Karolinska University Hospital , Stockholm , Sweden
| | - Kristoffer Strålin
- b Faculty of Medicin and Health , Örebro University , Örebro , Sweden.,d Department of Infectious Diseases , Karolinska University Hospital , Stockholm , Sweden.,g Unit of Infectious Diseases, Department of Medicine Huddinge , Karolinska Institutet , Stockholm , Sweden
| | - Jonas Hedlund
- c Unit of Infectious Diseases, Department of Medicine Solna , Karolinska Institutet , Stockholm , Sweden.,d Department of Infectious Diseases , Karolinska University Hospital , Stockholm , Sweden
| |
Collapse
|
30
|
Brotons P, Bassat Q, Lanaspa M, Henares D, Perez-Arguello A, Madrid L, Balcells R, Acacio S, Andres-Franch M, Marcos MA, Valero-Rello A, Muñoz-Almagro C. Nasopharyngeal bacterial load as a marker for rapid and easy diagnosis of invasive pneumococcal disease in children from Mozambique. PLoS One 2017; 12:e0184762. [PMID: 28910402 PMCID: PMC5599037 DOI: 10.1371/journal.pone.0184762] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Current diagnostic methods for detection of Streptococcus pneumoniae in children with suspected invasive pneumococcal disease have limitations of accuracy, timeliness, and patient convenience. This study aimed to determine the performance of pneumococcal load quantified with a real-time polymerase-chain reaction in nasopharyngeal samples to diagnose invasive pneumococcal disease in children. METHODS Matched case-control study of patients <5 years of age with invasive pneumococcal disease admitted to the Manhiça District Hospital (Mozambique) and asymptomatic controls recruited in different periods between 2006 and 2014. Cases were confirmed by a positive bacterial culture for S. pneumoniae in blood or cerebrospinal fluid. Nasopharyngeal aspirates were collected from cases and controls and pneumococcal density was quantified by lytA real-time polymerase-chain reaction. RESULTS Thirty cases (median age 12.8 months) and sixty controls (median age 11.7 months) were enrolled and 70% of them were male. Nasopharyngeal pneumococcal carriage was high in both groups: 28/30 (93.3%) for cases vs. 53/60 (88.3%) for controls (p = 0.71). Mean nasopharyngeal pneumococcal load was identified as a marker for invasive pneumococcal disease (7.0 log10 copies/mL in cases vs. 5.8 log10 copies/mL in controls, p<0.001) and showed good discriminatory power (AUC-ROC: 82.1%, 95% CI 72.5%-91.8%). A colonization density of 6.5 log10 copies/mL was determined as the optimal cut-off value to distinguish cases from controls (sensitivity 75.0%, specificity 73.6%). CONCLUSION Use of non-invasive nasopharyngeal aspirates coupled with rapid and accurate quantification of pneumococcal load by real-time polymerase chain reaction has the potential to become a useful surrogate marker for early diagnosis of invasive pneumococcal disease in children.
Collapse
Affiliation(s)
- Pedro Brotons
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Quique Bassat
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain
- Universidad Europea de Madrid, Madrid, Spain
| | - Miguel Lanaspa
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | - Desiree Henares
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
| | - Amaresh Perez-Arguello
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
| | - Lola Madrid
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | | | | | - Maria Andres-Franch
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Angeles Marcos
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ana Valero-Rello
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
- * E-mail:
| |
Collapse
|
31
|
Edouard S, Al-Tawfiq JA, Memish ZA, Yezli S, Gautret P. WITHDRAWN: Impact of the Hajj on pneumococcal carriage and the effect of various pneumococcal vaccines. Vaccine 2017:S0264-410X(17)31028-9. [PMID: 28780980 DOI: 10.1016/j.vaccine.2017.03.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/25/2017] [Accepted: 03/01/2017] [Indexed: 12/27/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Sophie Edouard
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée-Infection, Marseille, France
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine Unit, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ziad A Memish
- Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Saber Yezli
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Philippe Gautret
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée-Infection, Marseille, France.
| |
Collapse
|
32
|
Mika M, Maurer J, Korten I, Allemann A, Aebi S, Brugger SD, Qi W, Frey U, Latzin P, Hilty M. Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case-control study. MICROBIOME 2017; 5:85. [PMID: 28738889 PMCID: PMC5525364 DOI: 10.1186/s40168-017-0302-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/06/2017] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case-control study using samples from a longitudinal infant cohort from Switzerland. We compared pneumococcal carriage and the nasal microbiota within the first year of life of healthy infants vaccinated with either PCV7 (n = 20, born in 2010) or PCV13 (n = 21, born between 2011 and 2013). Nasal swabs were collected every second week (n = 763 in total). Pneumococcal carriage was analyzed by quantitative PCR of the pneumococcal-specific lytA gene. Analysis of the bacterial core microbiota was performed based on 16S rRNA sequencing and subsequent oligotyping. We exclusively performed oligotyping of the core microbiota members, which were defined as the five most abundant bacterial families (Moraxellaceae, Streptococcaceae, Staphylococcaceae, Corynebacteriaceae, and Pasteurellaceae). Linear mixed effect (LME) and negative binomial regression models were used for statistical analyses. RESULTS We found a higher number of samples positive for pneumococcal carriage in PCV7- compared to PCV13-vaccinated infants (LME model; P = 0.01). In contrast, infants vaccinated in the PCV13 era had an increased alpha diversity as measured by the richness and the Shannon Diversity Index (LME model; P = 0.003 and P = 0.01, respectively). Accordingly, the PCV13 era was associated with clusters of a higher diversity than PCV7-associated clusters. Furthermore, infants vaccinated with PCV13 had a higher binary-based within-subject microbiota similarity, as well as a decreased Jensen-Shannon distance over time as compared to PCV7-vaccinated infants, indicating a higher microbiota stability in the PCV13 era (LME model and t test; P = 0.06 and P = 0.03, respectively). CONCLUSIONS We hypothesize that the higher diversity and stability of the upper airway microbiota in the PCV13 era is the result of the lower pneumococcal carriage rate. This seems to indicate that the nasal bacterial microbiota of infants has changed in recent years as compared to the beginning of this study.
Collapse
Affiliation(s)
- Moana Mika
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Josua Maurer
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Silvio D Brugger
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Weihong Qi
- Functional Genomics Center, Swiss Federal Institute of Technology Zurich/University of Zurich, Zurich, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland.
- Department of Infectious Diseases, University Hospital, Bern, Switzerland.
| |
Collapse
|
33
|
Gillis HD, Lang ALS, ElSherif M, Martin I, Hatchette TF, McNeil SA, LeBlanc JJ. Assessing the diagnostic accuracy of PCR-based detection of Streptococcus pneumoniae from nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: a Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study. BMJ Open 2017; 7:e015008. [PMID: 28600368 PMCID: PMC5623389 DOI: 10.1136/bmjopen-2016-015008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/28/2017] [Accepted: 04/12/2017] [Indexed: 12/02/2022] Open
Abstract
STUDY DESIGN Detection and serotyping of Streptococcus pneumoniae are important to assess the impact of pneumococcal vaccines. This study describes the diagnostic accuracy of PCR-based detection of S. pneumoniae directly from nasopharyngeal (NP) swabs collected for respiratory virus studies. METHODS Active surveillance for community-acquired pneumonia (CAP) in hospitalised adults was performed from December 2010 to 2013. Detection of pneumococcal CAP (CAPSpn) was performed by urine antigen detection (UAD), identification of S. pneumoniae in sputum or blood cultures. S. pneumoniae was detected in NP swabs using lytA and cpsA real-time PCR, and serotyping was performed using conventional and real-time multiplex PCRs. For serotyping, the Quellung reaction, PCR-based serotyping or a serotype-specific UAD was used. RESULTS NP swab results were compared against CAP cases where all pneumococcal tests were performed (n=434), or where at least one test was performed (n=1616). CAPSpn was identified in 22.1% (96/434) and 14.9% (240/1616), respectively. The sensitivity of NP swab PCR for the detection of S. pneumoniae was poor for CAPSpn (35.4% (34/96) and 34.17% (82/240)), but high specificity was observed (99.4% (336/338) and 97.89% (1347/1376)). Of the positive NP swabs, a serotype could be deduced by PCR in 88.2% (30/34) and 93.9% (77/82), respectively. CONCLUSIONS While further optimisation may be needed to increase the sensitivity of PCR-based detection, its high specificity suggests there is a value for pneumococcal surveillance. With many laboratories archiving specimens for influenza virus surveillance, this specimen type could provide a non-culture-based method for pneumococcal surveillance.
Collapse
Affiliation(s)
- Hayley D Gillis
- Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Amanda L S Lang
- Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada
| | - May ElSherif
- Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Irene Martin
- National Microbiology Laboratory (NML), Winnipeg, Manitoba, Canada
| | - Todd F Hatchette
- Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shelly A McNeil
- Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason J LeBlanc
- Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
34
|
Bjarnason A, Lindh M, Westin J, Andersson LM, Baldursson O, Kristinsson KG, Gottfredsson M. Utility of oropharyngeal real-time PCR for S. pneumoniae and H. influenzae for diagnosis of pneumonia in adults. Eur J Clin Microbiol Infect Dis 2017; 36:529-536. [PMID: 27822652 PMCID: PMC5309271 DOI: 10.1007/s10096-016-2829-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022]
Abstract
A lack of sensitive tests and difficulties obtaining representative samples contribute to the challenge in identifying etiology in pneumonia. Upper respiratory tract swabs can be easily collected and analyzed with real-time PCR (rtPCR). Common pathogens such as S. pneumoniae and H. influenzae can both colonize and infect the respiratory tract, complicating the interpretation of positive results. Oropharyngeal swabs were collected (n = 239) prospectively from adults admitted to hospital with pneumonia. Analysis with rtPCR targeting S. pneumoniae and H. influenzae was performed and results compared with sputum cultures, blood cultures, and urine antigen testing for S. pneumoniae. Different Ct cutoff values were applied to positive tests to discern colonization from infection. Comparing rtPCR with conventional testing for S. pneumoniae in patients with all tests available (n = 57) resulted in: sensitivity 87 %, specificity 79 %, PPV 59 % and NPV 94 %, and for H. influenzae (n = 67): sensitivity 75 %, specificity 80 %, PPV 45 % and NPV 94 %. When patients with prior antimicrobial exposure were excluded sensitivity improved: 92 % for S. pneumoniae and 80 % for H. influenzae. Receiver operating characteristic curve analysis demonstrated for S. pneumoniae: AUC = 0.65 (95 % CI 0.51-0.80) and for H. influenzae: AUC = 0.86 (95 % CI 0.72-1.00). Analysis of oropharyngeal swabs using rtPCR proved both reasonably sensitive and specific for diagnosing pneumonia caused by S. pneumoniae and H. influenzae. This method may be a useful diagnostic adjunct to other methods and of special value in patients unable to provide representative lower airway samples.
Collapse
Affiliation(s)
- A Bjarnason
- Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - M Lindh
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden
| | - J Westin
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden
| | - L-M Andersson
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden
| | - O Baldursson
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - K G Kristinsson
- Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland
| | - M Gottfredsson
- Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland.
- Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland.
- Division of Infectious Diseases, Landspitali University Hospital, Fossvogur, 108, Reykjavik, Iceland.
| |
Collapse
|
35
|
Torres A, Lee N, Cilloniz C, Vila J, Van der Eerden M. Laboratory diagnosis of pneumonia in the molecular age. Eur Respir J 2016; 48:1764-1778. [PMID: 27811073 DOI: 10.1183/13993003.01144-2016] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/17/2016] [Indexed: 01/20/2023]
Abstract
Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. However, with new knowledge regarding the microbiome, together with the recognition that the lungs are a dynamic microbiological ecosystem, our current concept of pneumonia is not totally realistic as this new concept of pneumonia involves a dysbiosis or alteration of the lung microbiome. A new challenge for microbiologists and clinicians has therefore arisen. There is much to learn regarding the information provided by this new diagnostic technology, which will lead to improvements in the time to antibiotic therapy, targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients. This article provides an overview of current methods of laboratory diagnosis of pneumonia in the molecular age.
Collapse
Affiliation(s)
- Antoni Torres
- Dept of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Ciber de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Nelson Lee
- Division of Infectious Diseases, Dept of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Catia Cilloniz
- Dept of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Ciber de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Jordi Vila
- Servei de Microbiologia, Hospital Clinic, ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Menno Van der Eerden
- Dept of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| |
Collapse
|
36
|
Murdoch DR. How recent advances in molecular tests could impact the diagnosis of pneumonia. Expert Rev Mol Diagn 2016; 16:533-40. [PMID: 26891612 PMCID: PMC7103682 DOI: 10.1586/14737159.2016.1156536] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 12/21/2022]
Abstract
Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm.
Collapse
Affiliation(s)
- David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, and Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| |
Collapse
|
37
|
Hatori K, Ohki S, Miki T, Hirai H, Yasuhara K, Obayashi T. Infected abdominal aortic aneurysm caused by Streptococcus pneumoniae diagnosed using polymerase chain reaction. Surg Case Rep 2016; 1:83. [PMID: 26943412 PMCID: PMC4572041 DOI: 10.1186/s40792-015-0085-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/08/2015] [Indexed: 11/28/2022] Open
Abstract
We report the case of a 55-year-old man who initially visited the emergency department of our hospital owing to fever, headache, and neck stiffness. He was diagnosed with meningitis because cerebrospinal fluid culture was positive for Streptococcus pneumoniae. After intravenous antibiotic treatment, the patient’s condition returned to normal. On hospital day 20, he complained of lumbar pain with abdominal distension. Because an abdominal computed tomography (CT) scan showed a small sacciform infrarenal abdominal aortic aneurysm, an infected aneurysm was suspected. However, cerebrospinal fluid and blood cultures were negative for S. pneumoniae. Seven days later, a second abdominal CT was performed that showed rapid expansion of the sacciform infrarenal abdominal aortic aneurysm. The patient was diagnosed with an infected abdominal aortic aneurysm and underwent surgery for resection of the aneurysm and in situ reconstruction with a rifampicin-soaked vascular prosthesis. Although blood and aneurysmal tissue cultures were negative for S. pneumoniae, the autolysin (lytA) gene, which is the target gene of S. pneumoniae, was detected in the abdominal aortic wall by using polymerase chain reaction (PCR). Therefore, appropriate molecular diagnostic techniques can be used for the rapid detection of pathogens. An accurate diagnosis can be used to direct postoperative antibiotic therapy.
Collapse
Affiliation(s)
- Kyohei Hatori
- Department of Cardiovascular Surgery, Isesaki Municipal Hospital, 12-1 Tsunatori-honmachi, Isesaki, Gunma, 372-0812, Japan.
| | - Satoshi Ohki
- Department of Cardiovascular Surgery, Isesaki Municipal Hospital, 12-1 Tsunatori-honmachi, Isesaki, Gunma, 372-0812, Japan
| | - Takao Miki
- Department of Cardiovascular Surgery, Isesaki Municipal Hospital, 12-1 Tsunatori-honmachi, Isesaki, Gunma, 372-0812, Japan
| | - Hanako Hirai
- Department of Cardiovascular Surgery, Isesaki Municipal Hospital, 12-1 Tsunatori-honmachi, Isesaki, Gunma, 372-0812, Japan
| | - Kiyomitsu Yasuhara
- Department of Cardiovascular Surgery, Isesaki Municipal Hospital, 12-1 Tsunatori-honmachi, Isesaki, Gunma, 372-0812, Japan
| | - Tamiyuki Obayashi
- Department of Cardiovascular Surgery, Isesaki Municipal Hospital, 12-1 Tsunatori-honmachi, Isesaki, Gunma, 372-0812, Japan
| |
Collapse
|
38
|
Gadsby NJ, Russell CD, McHugh MP, Mark H, Conway Morris A, Laurenson IF, Hill AT, Templeton KE. Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia. Clin Infect Dis 2016; 62:817-823. [PMID: 26747825 PMCID: PMC4787606 DOI: 10.1093/cid/civ1214] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/24/2015] [Indexed: 01/22/2023] Open
Abstract
Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP. Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns. Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients. Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy.
Collapse
Affiliation(s)
- Naomi J Gadsby
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Clark D Russell
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh.,College of Medicine and Veterinary Medicine, University of Edinburgh
| | - Martin P McHugh
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Harriet Mark
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | | | - Ian F Laurenson
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Adam T Hill
- Respiratory Medicine, Royal Infirmary of Edinburgh, United Kingdom
| | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| |
Collapse
|
39
|
Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
40
|
Ganaie FA, Govindan V, Ravi Kumar KL. Standardisation and evaluation of a quantitative multiplex real-time PCR assay for the rapid identification of Streptococcus pneumoniae. Pneumonia (Nathan) 2015; 6:57-66. [PMID: 31641579 PMCID: PMC5922331 DOI: 10.15172/pneu.2015.6/559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 06/19/2015] [Indexed: 12/14/2022] Open
Abstract
Rapid diagnosis of Streptococcus pneumoniae can play a significant role in decreasing morbidity and mortality of infection. The accurate diagnosis of pneumococcal disease is hampered by the difficulties in growing the isolates from clinical specimens and also by misidentification. Molecular methods have gained popularity as they offer improvement in the detection of causative pathogens with speed and ease. The present study aims at validating and standardising the use of 4 oligonucleotide primer-probe sets (pneumolysin [ply], autolysin [lytA], pneumococcal surface adhesion A [psaA] and Spn9802 [DNA fragment]) in a single-reaction mixture for the detection and discrimination of S. pneumoniae. Here, we validate a quantitative multiplex real-time PCR (qmPCR) assay with a panel consisting of 43 S. pneumoniae and 29 non-pneumococcal isolates, 20 culture positive, 26 culture negative and 30 spiked serum samples. A standard curve was obtained using S. pneumoniae ATCC 49619 strain and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene was used as an endogenous internal control. The experiment showed high sensitivity with lower limit of detection equivalent to 4 genome copies/µl. The efficiency of the reaction was 100% for ply, lytA, Spn9802 and 97% for psaA. The test showed sensitivity and specificity of 100% with culture isolates and serum specimens. This study demonstrates that qmPCR analysis of sera using 4 oligonucleotide primers appears to be an appropriate method for the genotypic identification of S. pneumoniae infection.
Collapse
Affiliation(s)
- Feroze A Ganaie
- Department of Microbiology, Kempegowda Institute of Medical Sciences, Hospital and Research Centre, K.R Road, V.V Puram, Bangalore, 560004 India
| | - Vandana Govindan
- Department of Microbiology, Kempegowda Institute of Medical Sciences, Hospital and Research Centre, K.R Road, V.V Puram, Bangalore, 560004 India
| | - K L Ravi Kumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences, Hospital and Research Centre, K.R Road, V.V Puram, Bangalore, 560004 India
| |
Collapse
|
41
|
Clinical and Microbiological Factors Associated with High Nasopharyngeal Pneumococcal Density in Patients with Pneumococcal Pneumonia. PLoS One 2015; 10:e0140112. [PMID: 26466142 PMCID: PMC4605601 DOI: 10.1371/journal.pone.0140112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 09/22/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND We aimed to study if certain clinical and/or microbiological factors are associated with a high nasopharyngeal (NP) density of Streptococcus pneumoniae in pneumococcal pneumonia. In addition, we aimed to study if a high NP pneumococcal density could be useful to detect severe pneumococcal pneumonia. METHODS Adult patients hospitalized for radiologically confirmed community-acquired pneumonia were included in a prospective study. NP aspirates were collected at admission and were subjected to quantitative PCR for pneumococcal DNA (Spn9802 DNA). Patients were considered to have pneumococcal etiology if S. pneumoniae was detected in blood culture and/or culture of respiratory secretions and/or urinary antigen test. RESULTS Of 166 included patients, 68 patients had pneumococcal DNA detected in NP aspirate. Pneumococcal etiology was noted in 57 patients (84%) with positive and 8 patients (8.2%) with negative test for pneumococcal DNA (p<0.0001). The median NP pneumococcal density of DNA positive patients with pneumococcal etiology was 6.83 log10 DNA copies/mL (range 1.79-9.50). In a multivariate analysis of patients with pneumococcal etiology, a high pneumococcal density was independently associated with severe pneumonia (Pneumonia Severity Index risk class IV-V), symptom duration ≥2 days prior to admission, and a medium/high serum immunoglobulin titer against the patient's own pneumococcal serotype. NP pneumococcal density was not associated with sex, age, smoking, co-morbidity, viral co-infection, pneumococcal serotype, or bacteremia. Severe pneumococcal pneumonia was noted in 28 study patients. When we studied the performance of PCR with different DNA cut-off levels for detection of severe pneumococcal pneumonia, we found sensitivities of 54-82% and positive predictive values of 37-56%, indicating suboptimal performance. CONCLUSIONS Pneumonia severity, symptom duration ≥2 days, and a medium/high serum immunoglobulin titer against the patient's own serotype were independently associated with a high NP pneumococcal density. NP pneumococcal density has limited value for detection of severe pneumococcal pneumonia.
Collapse
|
42
|
Detection and prediction of Streptococcus pneumoniae serotypes directly from nasopharyngeal swabs using PCR. J Med Microbiol 2015; 64:836-844. [DOI: 10.1099/jmm.0.000097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
43
|
Sanchez JL, Cooper MJ, Myers CA, Cummings JF, Vest KG, Russell KL, Sanchez JL, Hiser MJ, Gaydos CA. Respiratory Infections in the U.S. Military: Recent Experience and Control. Clin Microbiol Rev 2015; 28:743-800. [PMID: 26085551 PMCID: PMC4475643 DOI: 10.1128/cmr.00039-14] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This comprehensive review outlines the impact of military-relevant respiratory infections, with special attention to recruit training environments, influenza pandemics in 1918 to 1919 and 2009 to 2010, and peacetime operations and conflicts in the past 25 years. Outbreaks and epidemiologic investigations of viral and bacterial infections among high-risk groups are presented, including (i) experience by recruits at training centers, (ii) impact on advanced trainees in special settings, (iii) morbidity sustained by shipboard personnel at sea, and (iv) experience of deployed personnel. Utilizing a pathogen-by-pathogen approach, we examine (i) epidemiology, (ii) impact in terms of morbidity and operational readiness, (iii) clinical presentation and outbreak potential, (iv) diagnostic modalities, (v) treatment approaches, and (vi) vaccine and other control measures. We also outline military-specific initiatives in (i) surveillance, (ii) vaccine development and policy, (iii) novel influenza and coronavirus diagnostic test development and surveillance methods, (iv) influenza virus transmission and severity prediction modeling efforts, and (v) evaluation and implementation of nonvaccine, nonpharmacologic interventions.
Collapse
Affiliation(s)
- Jose L Sanchez
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Michael J Cooper
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | | | - James F Cummings
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Kelly G Vest
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Kevin L Russell
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Joyce L Sanchez
- Mayo Clinic, Division of General Internal Medicine, Rochester, Minnesota, USA
| | - Michelle J Hiser
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA Oak Ridge Institute for Science and Education, Postgraduate Research Participation Program, U.S. Army Public Health Command, Aberdeen Proving Ground, Aberdeen, Maryland, USA
| | - Charlotte A Gaydos
- International STD, Respiratory, and Biothreat Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, Maryland, USA
| |
Collapse
|
44
|
Gadsby NJ, McHugh MP, Russell CD, Mark H, Conway Morris A, Laurenson IF, Hill AT, Templeton KE. Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections. Clin Microbiol Infect 2015; 21:788.e1-788.e13. [PMID: 25980353 PMCID: PMC4509705 DOI: 10.1016/j.cmi.2015.05.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/23/2015] [Accepted: 05/03/2015] [Indexed: 11/30/2022]
Abstract
The frequent lack of a positive and timely microbiological diagnosis in patients with lower respiratory tract infection (LRTI) is an important obstacle to antimicrobial stewardship. Patients are typically prescribed broad-spectrum empirical antibiotics while microbiology results are awaited, but, because these are often slow, negative, or inconclusive, de-escalation to narrow-spectrum agents rarely occurs in clinical practice. The aim of this study was to develop and evaluate two multiplex real-time PCR assays for the sensitive detection and accurate quantification of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. We found that all eight bacterial targets could be reliably quantified from sputum specimens down to a concentration of 100 CFUs/reaction (8333 CFUs/mL). Furthermore, all 249 positive control isolates were correctly detected with our assay, demonstrating effectiveness on both reference strains and local clinical isolates. The specificity was 98% on a panel of nearly 100 negative control isolates. Bacterial load was quantified accurately when three bacterial targets were present in mixtures of varying concentrations, mimicking likely clinical scenarios in LRTI. Concordance with culture was 100% for culture-positive sputum specimens, and 90% for bronchoalveolar lavage fluid specimens, and additional culture-negative bacterial infections were detected and quantified. In conclusion, a quantitative molecular test for eight key bacterial causes of LRTI has the potential to provide a more sensitive decision-making tool, closer to the time-point of patient admission than current standard methods. This should facilitate de-escalation from broad-spectrum to narrow-spectrum antibiotics, substantially improving patient management and supporting efforts to curtail inappropriate antibiotic use.
Collapse
Affiliation(s)
- N J Gadsby
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK.
| | - M P McHugh
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - C D Russell
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - H Mark
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - A Conway Morris
- Department of Anaesthesia, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - I F Laurenson
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - A T Hill
- Respiratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - K E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| |
Collapse
|
45
|
Abstract
PURPOSE OF REVIEW This review examines the epidemiology, diagnosis, prognosis, treatment and prevention of community-acquired pneumonia (CAP) in adults. RECENT FINDINGS CAP is a significant cause of morbidity and mortality. Streptococcus pneumoniae is the most common CAP pathogen; however, microbial cause varies by geographic location and host factors. Identification of a microbial cause in CAP remains challenging - 30-65% of cases do not have a pathogen isolated. The use of molecular techniques in addition to culture, serology and urinary antigen testing has improved diagnostic yield. Scoring systems are useful for CAP prognostication and site of care decisions. Studies evaluating novel biomarkers including pro-B-type natriuretic peptide and procalcitonin suggest potential adjunctive roles in CAP prognosis. Guideline-based treatment for CAP has changed little in recent years. Effective and timely antimicrobial therapy is crucial in optimizing outcomes and should be based on local antimicrobial susceptibility patterns. Macrolides may have additional anti-inflammatory properties and a mortality benefit in severe CAP. Preventive strategies include immunization and modification of specific patient risk factors. SUMMARY CAP is common and causes considerable morbidity and mortality. A comprehensive approach including advanced diagnostic testing, effective and timely antimicrobial therapy and prevention is required to optimize CAP outcomes.
Collapse
|
46
|
Genomic load from sputum samples and nasopharyngeal swabs for diagnosis of pneumococcal pneumonia in HIV-infected adults. J Clin Microbiol 2014; 52:4224-9. [PMID: 25253798 DOI: 10.1128/jcm.01553-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quantitative lytA real-time PCR (rtPCR) results from nasopharyngeal (NP) swabs distinguish community-acquired pneumococcal pneumonia (CAP) from asymptomatic colonization. The use of an optimized cutoff value improved pneumococcal etiology determination compared to that of traditional diagnostic methods. Here, we compare the utility of lytA rtPCR from induced sputum and from NP swabs. Pneumococcus was considered the cause of CAP in HIV-infected South African adults if blood culture, induced-sputum culture or Gram stain, urine antigen test, or whole-blood lytA rtPCR revealed pneumococcus or if lytA rtPCR from NP swabs gave a result of >8,000 copies/ml. lytA rtPCR was also performed on induced sputum. Pneumococcus was detected by lytA rtPCR from sputum in 149 (67.1%) of 222 patients with available induced sputum, whereas the results of either Gram stain or culture of sputum were positive in 105 of 229 patients (45.9%; P < 0.001). The mean copy numbers from sputum were higher when the sputum cultures were positive than when the sputum cultures were negative (7.9 versus 5.6 log10 copies/ml; P < 0.001). Against the composite diagnostic standard, a cutoff value of 10,000 copies/ml for good-quality sputum lytA rtPCR had a sensitivity of 78.1% and a specificity of 80.0%. This cutoff value performed similarly to the previously identified cutoff value of 8,000 copies/ml for NP swab lytA rtPCR (area under the curve receiver operating characteristic [AUC-ROC], 80.4% for sputum of any quality versus 79.6% for NP swabs). The AUC-ROC for good-quality sputum was 83.2%. Overall, lytA rtPCR performs similarly well on induced sputum as on NP swabs for most patients but performs slightly better if good-quality sputum can be obtained. Due to the ease of specimen collection, NP swabs may be preferable for the diagnosis of pneumococcal pneumonia.
Collapse
|
47
|
Gritzfeld JF, Cremers AJH, Ferwerda G, Ferreira DM, Kadioglu A, Hermans PWM, Gordon SB. Density and duration of experimental human pneumococcal carriage. Clin Microbiol Infect 2014; 20:O1145-51. [PMID: 24995531 PMCID: PMC4313687 DOI: 10.1111/1469-0691.12752] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 02/03/2023]
Abstract
The density and duration of pneumococcal carriage are considered to affect the likelihood of transmission and invasive disease. Because of its importance in both spreading and causing disease, carriage has been suggested as an endpoint in future vaccine studies. Culture is the current gold standard for detection, but may not be sensitive enough to detect changes at low density. Healthy adult volunteers received an intranasal inoculation of Streptococcus pneumoniae serotype 6B. Pneumococcal density in nasal washes collected at six time-points post-inoculation was determined by culture and quantitative PCR (qPCR). Natural pneumococcal carriers detected at initial screening were followed in parallel. In 331 nasal washes from 79 volunteers, the sensitivity and specificity of pneumococcal detection by qPCR, as compared with culture, were 92.3% and 75.9%. The estimation of pneumococcal density by culture and qPCR was highly correlated (rs = 0.73, p <0.0001), although qPCR had a lower detection limit. Pneumococcal density fluctuated within a carriage episode, and occasionally fell below the detection limit of both methods. The duration of carriage episodes was underestimated when only one method was used. Similar fluctuations in density were observed in natural carriers. Pneumococcal carriage is a dynamic event. Culture and qPCR are complementary for surveying the density and duration of pneumococcal carriage episodes.
Collapse
Affiliation(s)
- J F Gritzfeld
- Respiratory Infection Group, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | | | | | | | | |
Collapse
|