1
|
Teh J, Biswas K, Waldvogel-Thurlow S, Broderick D, Clark ST, Johnston J, Wagner Mackenzie B, Douglas R. Paired qualitative and quantitative analysis of bacterial microcolonies in the tonsils of patients with tonsillar hyperplasia. Microbes Infect 2024; 26:105317. [PMID: 38452852 DOI: 10.1016/j.micinf.2024.105317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/03/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
The discovery of bacterial microcolonies in tonsillar tissue of patients with tonsillar hyperplasia has raised the question of their role in provoking the local immune response. Tonsils collected from patients undergoing tonsillectomy were stained for three clinically relevant bacterial taxa and lymphocytes. The bacterial composition and abundance of microcolonies was investigated using a combination of laser-microdissection, amplicon sequencing and Droplet Digital polymerase chain reaction. Microcolonies were detected in most samples (32/35) with a high prevalence of Haemophilus influenzae (78% of samples). B and T cell lymphocytes were significantly higher in the epithelium adjacent to microcolonies compared to epithelium distal to microcolonies. Furthermore, significant positive and negative correlations were identified between bacterial taxa and lymphocytes. Genus Streptococcus, which includes Group A Streptococcus (traditionally described as the main pathogen of tonsillar hyperplasia), was found in low abundance in this study. These results suggest other potential pathogens may be involved in stimulating the local immune response leading to tonsillar hyperplasia.
Collapse
Affiliation(s)
- Jackson Teh
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - Kristi Biswas
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand.
| | - Sharon Waldvogel-Thurlow
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - David Broderick
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - Sita Tarini Clark
- Te Whatu Ora - Te Toka Tumai Auckland, Health New Zealand, Auckland, 1142, New Zealand
| | - James Johnston
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand; Te Whatu Ora - Te Toka Tumai Auckland, Health New Zealand, Auckland, 1142, New Zealand
| | - Brett Wagner Mackenzie
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - Richard Douglas
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand; Te Whatu Ora - Te Toka Tumai Auckland, Health New Zealand, Auckland, 1142, New Zealand
| |
Collapse
|
2
|
Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
Collapse
Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| |
Collapse
|
3
|
Ficek M, Cieślik M, Janik M, Brodowski M, Sawczak M, Bogdanowicz R, Ryl J. Boron-doped diamond nanosheet volume-enriched screen-printed carbon electrodes: a platform for electroanalytical and impedimetric biosensor applications. Mikrochim Acta 2023; 190:410. [PMID: 37736868 PMCID: PMC10516795 DOI: 10.1007/s00604-023-05991-w] [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: 05/01/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023]
Abstract
This paper focuses on the development of a novel electrode based on boron-doped diamond nanosheet full-volume-enriched screen-printed carbon electrodes (BDDPE) for use as an impedimetric biosensor. Impedimetric biosensors offer high sensitivity and selectivity for virus detection, but their use as point-of-care devices is limited by the complexity of nanomaterials' architecture and the receptor immobilisation procedures. The study presents a two-step modification process involving the electroreduction of diazonium salt at the BDDPE and the immobilisation of antibodies using zero-length cross-linkers for a selective impedimetric biosensor of Haemophilus influenzae (Hi). The incorporation of diamond nanosheets into BDDPE leads to enhanced charge transfer and electrochemical behaviour, demonstrating greatly improved electrochemically active surface area compared with unmodified screen-printed electrodes (by 44% and 10% on average for [Ru(NH3)6]Cl2 and K3[Fe(CN)6], respectively). The presented sensing system shows high specificity towards protein D in Hi bacteria, as confirmed by negative controls against potential interference from other pathogens, with an estimated tolerance limit for interference under 12%. The Hi limit of detection by electrochemical impedance spectroscopy was 1 CFU/mL (measured at - 0.13 V vs BDDPE pseudo-reference), which was achieved in under 10 min, including 5 min sample incubation in the presence of the analyte.
Collapse
Affiliation(s)
- Mateusz Ficek
- Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Mateusz Cieślik
- Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
- Department of Analytical Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Monika Janik
- Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
- Institute of Microelectronics and Optoelectronics, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Mateusz Brodowski
- Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Mirosław Sawczak
- Szewalski Institute of Fluid-Flow Machinery, Polish Academy of Sciences, Fiszera 14, Gdańsk, Poland
| | - Robert Bogdanowicz
- Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - Jacek Ryl
- Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
| |
Collapse
|
4
|
Krumkamp R, Kohsar M, Nolte K, Hogan B, Eibach D, Jaeger A, Akenten CW, Drosten C, Boahen KG, Sarpong N, Eckerle I, Binger T, Owusu-Dabo E, May J, Kreuels B. Pathogens associated with hospitalization due to acute lower respiratory tract infections in children in rural Ghana: a case-control study. Sci Rep 2023; 13:2443. [PMID: 36765075 PMCID: PMC9916495 DOI: 10.1038/s41598-023-29410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Respiratory infections are one of the most common causes of death among children under the age of five years. Data on prevalence and relevance of specific organisms in African children are still lacking. This case-control-study investigated prevalence and relevance of specific organisms in Ghanaian children admitted to hospital with symptoms of lower respiratory tract infection (LRTI). Pharyngeal swabs were taken and tested by PCR for 19 respiratory isolates. Adjusted odds ratios (aORs) were calculated to estimate associations between isolates and admission with LRTI. Population attributable fractions (PAFs) were calculated to assess the proportion of LRTI cases due to a particular pathogen. The study included 327 cases and 562 controls. We found associations between detection and admission for LRTI for influenza (aOR 98.6; 95% confidence interval (CI) 20.0-1789.6), respiratory syncytial virus (aOR 40.2; 95% CI 7.2-758.6), H. influenzae (aOR 4.1; 95% CI 2.2-7.9) and S. pneumoniae (aOR 2.4; 95% CI 1.7-3.4). PAFs ≥ 10% were observed for S. pneumoniae (30%; 95% CI 26-42), H. influenzae (10%; 95% CI 2-19) and influenza (10%; 95% CI 2-18). This study highlights the need for heightened surveillance and development of effective vaccines for respiratory pathogens other than SARS-CoV-2 in the future.
Collapse
Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
| | - Matin Kohsar
- Division for Tropical Medicine, I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Kolja Nolte
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Deutsche Gesellschaft Für Internationale Zusammenarbeit (GIZ GmbH), Berlin, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anna Jaeger
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
| | | | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Isabella Eckerle
- Department of Medicine, University of Geneva, Geneva, Switzerland
| | - Tabea Binger
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Benno Kreuels
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany.
- Division for Tropical Medicine, I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Research Group Snakebite Envenoming, Department of Implementation Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
| |
Collapse
|
5
|
Schoonbroodt S, Ichanté JL, Boffé S, Devos N, Devaster JM, Taddei L, Rondini S, Arora AK, Pascal T, Malvaux L. Real-time PCR has advantages over culture-based methods in identifying major airway bacterial pathogens in chronic obstructive pulmonary disease: Results from three clinical studies in Europe and North America. Front Microbiol 2022; 13:1098133. [PMID: 36909845 PMCID: PMC10000296 DOI: 10.3389/fmicb.2022.1098133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/29/2022] [Indexed: 03/14/2023] Open
Abstract
Introduction We compared the performance of real-time PCR with culture-based methods for identifying bacteria in sputum samples from patients with chronic obstructive pulmonary disease (COPD) in three studies. Methods This was an exploratory analysis of sputum samples collected during an observational study of 127 patients (AERIS; NCT01360398), phase 2 study of 145 patients (NTHI-004; NCT02075541), and phase 2b study of 606 patients (NTHI-MCAT-002; NCT03281876). Bacteria were identified by culture-based microbiological methods in local laboratories using fresh samples or by real-time PCR in a central laboratory using frozen samples. Haemophilus influenzae positivity with culture was differentiated from H. haemolyticus positivity by microarray analysis or PCR. The feasibility of bacterial detection by culture-based methods on previously frozen samples was also examined in the NTHI-004 study. Results Bacterial detection results from both culture-based and PCR assays were available from 2,293 samples from AERIS, 974 from the NTHI-004 study, and 1736 from the NTHI-MCAT-002 study. Quantitative real-time PCR (qPCR) showed higher positivity rates than culture for H. influenzae (percentages for each study: 43.4% versus 26.2%, 47.1% versus 23.6%, 32.7% versus 10.4%) and Moraxella catarrhalis (12.9% versus 6.3%, 19.0% versus 6.0%, 15.5% versus 4.1%). In the NTHI-004 and NTHI-MCAT-002 studies, positivity rates were higher with qPCR for Streptococcus pneumoniae (15.6% versus 6.1%, 15.5% versus 3.8%); in AERIS, a lower rate with qPCR than with culture (11.0% versus 17.4%) was explained by misidentification of S. pseudopneumoniae/mitis isolates via conventional microbiological methods. Concordance analysis showed lowest overall agreement for H. influenzae (82.0%, 75.6%, 77.6%), due mainly to culture-negative/qPCR-positive samples, indicating lower sensitivity of the culture-based methods. The lowest positive agreement (culture-positive/qPCR-positive samples) was observed for S. pneumoniae (35.1%, 71.2%, 71.2%). Bacterial load values for each species showed a proportion of culture-negative samples with a load detected by qPCR; for some samples, the loads were in line with those observed in culture-positive samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples. Discussion Real-time PCR on frozen sputum samples has enhanced sensitivity and specificity over culture-based methods, supporting its use for the identification of common respiratory bacterial species in patients with COPD.
Collapse
|
6
|
Saadati A, Kholafazad kordasht H, Ehsani M, Hasanzadeh M, Seidi F, Shadjou N. An innovative flexible and portable DNA based biodevice towards sensitive identification of Haemophilus influenzae bacterial genome: A new platform for the rapid and low cost recognition of pathogenic bacteria using point of care (POC) analysis. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
7
|
Coleman A, Bialasiewicz S, Marsh RL, Grahn Håkansson E, Cottrell K, Wood A, Jayasundara N, Ware RS, Zaugg J, Sidjabat HE, Adams J, Ferguson J, Brown M, Roos K, Cervin A. Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children. J Pediatric Infect Dis Soc 2021; 10:468-476. [PMID: 33393596 DOI: 10.1093/jpids/piaa141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health. METHODS In total, 103 Indigenous Australian children aged 2-7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children's ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis. RESULTS Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P < .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P < .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children. CONCLUSIONS Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.
Collapse
Affiliation(s)
- Andrea Coleman
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia.,Department of Surgery-Otolaryngology, Head and Neck Surgery, Townsville University Hospital, Townsville, Australia
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Eva Grahn Håkansson
- Department of Clinical Microbiology, Umeå University and Essum AB, Umeå, Sweden
| | - Kyra Cottrell
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Amanda Wood
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | - Nadeesha Jayasundara
- Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
| | - Julian Zaugg
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia
| | - Hanna E Sidjabat
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Jasmyn Adams
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Matthew Brown
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Herston, Australia.,Department of Otolaryngology, Head and Neck Surgery, The Royal Brisbane and Women's Hospital, Brisbane, Australia
| |
Collapse
|
8
|
Binding of pDNA with cDNA using hybridization strategy towards monitoring of Haemophilus influenza genome in human plasma samples. Int J Biol Macromol 2020; 150:218-227. [DOI: 10.1016/j.ijbiomac.2020.02.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 11/24/2022]
|
9
|
Lamprecht P, Fischer N, Huang J, Burkhardt L, Lütgehetmann M, Arndt F, Rolfs I, Kerstein A, Iking-Konert C, Laudien M. Changes in the composition of the upper respiratory tract microbial community in granulomatosis with polyangiitis. J Autoimmun 2018; 97:29-39. [PMID: 30420263 DOI: 10.1016/j.jaut.2018.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/08/2018] [Accepted: 10/11/2018] [Indexed: 12/29/2022]
Abstract
Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To assess the composition of the microbial upper respiratory tract (URT) community in patients with granulomatosis with polyangiitis (GPA), we used culture-independent high-throughput methods. In this prospective clinical study, nasal swabs were collected from patients with GPA, patients with rheumatoid arthritis (RA, disease control), and healthy controls. Nasal bacterial taxa were assessed using V3-V4 region 16S rRNA amplicon sequencing. Staphylococcus aureus, Haemophilus influenza, and entero- and rhinoviruses were detected using qPCR. Unbiased metagenomic RNA sequencing (UMERS) was performed in a subset of samples to determine the relative abundance of bacterial, fungal, and viral species. A trend toward reduced microbiome diversity was detected in GPA samples compared with healthy controls. The abundance of bacterial taxa and microbial richness were significantly decreased in GPA samples compared with RA samples. The relative abundance of bacterial families shifted, with increased Planococcaceae and decreased Moraxellaceae, Tissierellaceae, Staphylococcaceae, and Propionibacteriaceae in GPA and RA. Further, decreased abundance of Corynebacteriaceae, and Aerococcaceae was observed in GPA samples. Significantly more colonization of S. aureus was seen in the nasal microbiome of GPA compared with RA and healthy control samples. H. influenzae colonization was also observed in GPA samples. UMERS detected the presence of rhinoviral sequences in some GPA samples. Thus, our study uncovered changes in the URT microbial composition in patients with GPA and RA, suggesting that both immunosuppression and disease background affect the URT microbiome. Complex alterations of host-microbiome interactions in the URT could influence chronic endonasal inflammation in GPA.
Collapse
Affiliation(s)
- Peter Lamprecht
- Department of Rheumatology & Clinical Immunology, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 46, 20246, Hamburg, Germany; German Center for Research on Infection, partner site Hamburg-Borstel-Lübeck-Riems, Germany.
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 46, 20246, Hamburg, Germany.
| | - Lia Burkhardt
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20252, Hamburg, Germany.
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 46, 20246, Hamburg, Germany.
| | - Fabian Arndt
- Department of Rheumatology and Immunology, Klinikum Bad Bramstedt, Oskar-Alexander-Strasse 26, 24576, Bad Bramstedt, Germany.
| | - Ida Rolfs
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Kiel, Arnold-Heller-Strasse 3, Haus 27, 24105, Kiel, Germany.
| | - Anja Kerstein
- Department of Rheumatology & Clinical Immunology, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
| | - Christof Iking-Konert
- Department of Nephrology and Rheumatology, Medicine III, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Martin Laudien
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Kiel, Arnold-Heller-Strasse 3, Haus 27, 24105, Kiel, Germany.
| |
Collapse
|
10
|
Prates MCM, Tamashiro E, Proenca-Modena JL, Criado MF, Saturno TH, Oliveira AS, Buzatto GP, Jesus BLS, Jacob MG, Carenzi LR, Demarco RC, Massuda ET, Aragon D, Valera FCP, Arruda E, Anselmo-Lima WT. The Relationship between Colonization by Moraxella catarrhalis and Tonsillar Hypertrophy. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2018; 2018:5406467. [PMID: 30515253 PMCID: PMC6236706 DOI: 10.1155/2018/5406467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/11/2018] [Indexed: 11/30/2022]
Abstract
We sought to investigate the prevalence of potentially pathogenic bacteria in secretions and tonsillar tissues of children with chronic adenotonsillitis hypertrophy compared to controls. Prospective case-control study comparing patients between 2 and 12 years old who underwent adenotonsillectomy due to chronic adenotonsillar hypertrophy to children without disease. We compared detection of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis by real-time PCR in palatine tonsils, adenoids, and nasopharyngeal washes obtained from 37 children with and 14 without adenotonsillar hypertrophy. We found high frequency (>50%) of Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, and Pseudomonas aeruginosa in both groups of patients. Although different sampling sites can be infected with more than one bacterium and some bacteria can be detected in different tissues in the same patient, adenoids, palatine tonsils, and nasopharyngeal washes were not uniformly infected by the same bacteria. Adenoids and palatine tonsils of patients with severe adenotonsillar hypertrophy had higher rates of bacterial coinfection. There was good correlation of detection of Moraxella catarrhalis in different sampling sites in patients with more severe tonsillar hypertrophy, suggesting that Moraxella catarrhalis may be associated with the development of more severe hypertrophy, that inflammatory conditions favor colonization by this agent. Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Moraxella catarrhalis are frequently detected in palatine tonsils, adenoids, and nasopharyngeal washes in children. Simultaneous detection of Moraxella catarrhalis in adenoids, palatine tonsils, and nasopharyngeal washes was correlated with more severe tonsillar hypertrophy.
Collapse
Affiliation(s)
- Mirela C. M. Prates
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Edwin Tamashiro
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - José L. Proenca-Modena
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP 13083-970, Brazil
| | - Miriã F. Criado
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Tamara H. Saturno
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Anibal S. Oliveira
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Guilherme P. Buzatto
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Bruna L. S. Jesus
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Marcos G. Jacob
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Lucas R. Carenzi
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Ricardo C. Demarco
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Eduardo T. Massuda
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Davi Aragon
- Department of Pediatrics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Fabiana C. P. Valera
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Eurico Arruda
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Wilma T. Anselmo-Lima
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| |
Collapse
|
11
|
Fan X, Liu X, Ji L, Cai D, Jiang J, Zhu J, Sun A, Yan J. Epidemiological analysis and rapid detection by one-step multiplex PCR assay of Haemophilus influenzae in children with respiratory tract infections in Zhejiang Province, China. BMC Infect Dis 2018; 18:414. [PMID: 30134854 PMCID: PMC6103868 DOI: 10.1186/s12879-018-3295-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Haemophilus influenzae (H. influenzae) is one of the most important pathogenic bacteria causing respiratory tract infection diseases in children. There are two main types of H. influenzae, encapsulated H. influenzae and nontypeable H. influenzae (NTHi). Serotype b of H. influenzae (Hib) used to be the main epidemic type of H. influenzae, causing the invasive infection. However, the epidemiology of invasive H. influenzae disease has changed substantially, and most invasive diseases are now caused by NTHi and other serotypes of H. influenzae. The aim of this study was to determine the main epidemic strains of H. influenzae in Zhejiang Province in China, and establish a one-step multiplex PCR assay to distinguish H. influenzae from other bacteria associated with respiratory tract infections, and distinguish encapsulated H. influenzae from NTHi. Method In this study, bacterial culture and serum agglutination testing were used to determine the most prevalent serotype of H. influenzae, and the results have served as a gold standard for clinical diagnosis. We also designed a one-step multiplex PCR assay using several kinds of standard strains of respiratory tract infection bacteria, to examine the stability, specificity, and detection limit of the PCR assays. We then used 1514 nasopharyngeal secretion (NPS) samples collected from children with respiratory tract infections to verify the specificity and sensitivity of the PCR assay. Results The bacterial culture and serum agglutination test results showed that the positive rates of H. influenzae and encapsulated H. influenzae were 18.49 and 1.18%, respectively. The PCR results showed that the detection limit of the multiplex PCR assay was 1.89 × 103 copies /μL, the ompP6 positive rate was 19.35%, and the bexA positive rate was 1.32%. The sensitivity and specificity of the multiplex PCR were 100 and 99.86%, respectively. Conclusions According to our study, the most prevalent H. influenzae subtype in Zhejiang Province was NTHi, account for 93.57%; the one-step multiplex PCR assay we established can be used as the differential detection of clinical H. influenzae strains, replacing routine bacterial culture and serum agglutination testing.
Collapse
Affiliation(s)
- Xingli Fan
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310031, Zhejiang, China.,Department of Basic Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China
| | - Xiaoxiang Liu
- Department of Basic Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China
| | - Lei Ji
- Department of Basic Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China
| | - Damin Cai
- Department of Basic Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China
| | - Jinqin Jiang
- Department of Basic Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China
| | - Jingjing Zhu
- Department of Basic Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China
| | - Aihua Sun
- Department of Basic Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China.
| | - Jie Yan
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310031, Zhejiang, China.
| |
Collapse
|
12
|
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
|
13
|
Baothong S, Sitthisak S, Kunthalert D. In vitro interference of cefotaxime at subinhibitory concentrations on biofilm formation by nontypeable Haemophilus influenzae. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2016.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
14
|
Duplex Quantitative PCR Assay for Detection of Haemophilus influenzae That Distinguishes Fucose- and Protein D-Negative Strains. J Clin Microbiol 2016; 54:2380-3. [PMID: 27335148 DOI: 10.1128/jcm.00982-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022] Open
Abstract
We have developed a specific Haemophilus influenzae quantitative PCR (qPCR) that also identifies fucose-negative and protein D-negative strains. Analysis of 100 H. influenzae isolates, 28 Haemophilus haemolyticus isolates, and 14 other bacterial species revealed 100% sensitivity (95% confidence interval [CI], 96% to 100%) and 100% specificity (95% CI, 92% to 100%) for this assay. The evaluation of 80 clinical specimens demonstrated a strong correlation between semiquantitative culture and the qPCR (P < 0.001).
Collapse
|
15
|
Post DMB, Ketterer MR, Coffin JE, Reinders LM, Munson RS, Bair T, Murphy TF, Foster ED, Gibson BW, Apicella MA. Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications. Infect Immun 2016; 84:765-74. [PMID: 26729761 PMCID: PMC4771351 DOI: 10.1128/iai.01185-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/28/2015] [Indexed: 11/20/2022] Open
Abstract
Haemophilus haemolyticus and nontypeable Haemophilus influenzae (NTHi) are closely related upper airway commensal bacteria that are difficult to distinguish phenotypically. NTHi causes upper and lower airway tract infections in individuals with compromised airways, while H. haemolyticus rarely causes such infections. The lipooligosaccharide (LOS) is an outer membrane component of both species and plays a role in NTHi pathogenesis. In this study, comparative analyses of the LOS structures and corresponding biosynthesis genes were performed. Mass spectrometric and immunochemical analyses showed that NTHi LOS contained terminal sialic acid more frequently and to a higher extent than H. haemolyticus LOS did. Genomic analyses of 10 strains demonstrated that H. haemolyticus lacked the sialyltransferase genes lic3A and lic3B (9/10) and siaA (10/10), but all strains contained the sialic acid uptake genes siaP and siaT (10/10). However, isothermal titration calorimetry analyses of SiaP from two H. haemolyticus strains showed a 3.4- to 7.3-fold lower affinity for sialic acid compared to that of NTHi SiaP. Additionally, mass spectrometric and immunochemical analyses showed that the LOS from H. haemolyticus contained phosphorylcholine (ChoP) less frequently than the LOS from NTHi strains. These differences observed in the levels of sialic acid and ChoP incorporation in the LOS structures from H. haemolyticus and NTHi may explain some of the differences in their propensities to cause disease.
Collapse
Affiliation(s)
| | | | - Jeremy E Coffin
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, USA
| | | | - Robert S Munson
- The Center for Microbial Pathogenesis at the Research Institute at Nationwide Children's Hospital and the Center for Microbial Interface Biology and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Thomas Bair
- Bioinformatics Facility, The University of Iowa, Iowa City, Iowa, USA
| | - Timothy F Murphy
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Eric D Foster
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging, Novato, California, USA Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Michael A Apicella
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
16
|
Price EP, Sarovich DS, Nosworthy E, Beissbarth J, Marsh RL, Pickering J, Kirkham LAS, Keil AD, Chang AB, Smith-Vaughan HC. Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen. BMC Genomics 2015; 16:641. [PMID: 26311542 PMCID: PMC4551764 DOI: 10.1186/s12864-015-1857-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/18/2015] [Indexed: 11/19/2022] Open
Abstract
Background Haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. Despite its clinical significance, accurate identification of H. influenzae is a non-trivial endeavour. H. haemolyticus can be misidentified as H. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. On the molecular level, frequent genetic exchange amongst Haemophilus spp. has confounded accurate identification of H. influenzae, leading to both false-positive and false-negative results with existing speciation assays. Results Whole-genome single-nucleotide polymorphism data from 246 closely related global Haemophilus isolates, including 107 Australian isolate genomes generated in this study, were used to construct a whole-genome phylogeny. Based on this phylogeny, H. influenzae could be differentiated from closely related species. Next, a H. influenzae-specific locus, fucP, was identified, and a novel TaqMan real-time PCR assay targeting fucP was designed. PCR specificity screening across a panel of clinically relevant species, coupled with in silico analysis of all species within the order Pasteurellales, demonstrated that the fucP assay was 100 % specific for H. influenzae; all other examined species failed to amplify. Conclusions This study is the first of its kind to use large-scale comparative genomic analysis of Haemophilus spp. to accurately delineate H. influenzae and to identify a species-specific molecular signature for this species. The fucP assay outperforms existing H. influenzae targets, most of which were identified prior to the next-generation genomics era and thus lack validation across a large number of Haemophilus spp. We recommend use of the fucP assay in clinical and research laboratories for the most accurate detection and diagnosis of H. influenzae infection and colonisation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1857-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Erin P Price
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. .,Menzies School of Health Research, PO Box 41096, Casuarina, NT, 0811, Australia.
| | - Derek S Sarovich
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | | | | | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Perth, WA, Australia.
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | | |
Collapse
|
17
|
Wang H, Gu X, Weng Y, Xu T, Fu Z, Peng W, Yu W. Quantitative analysis of pathogens in the lower respiratory tract of patients with chronic obstructive pulmonary disease. BMC Pulm Med 2015; 15:94. [PMID: 26286268 PMCID: PMC4543462 DOI: 10.1186/s12890-015-0094-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/05/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Bacterial infection of the lower respiratory tract is believed to play a major role in the pathogenesis of chronic obstructive pulmonary disease (COPD) and acute exacerbations of COPD (AECOPD). This study investigates the potential relationship between AECOPD and the load of six common bacterial pathogens in the lower respiratory tract using real-time quantitative PCR (RT-qPCR) in COPD patients. METHODS Protected specimen brush (PSB) and bronchoalveolar lavage fluid (BALF) samples from the lower respiratory tract of 66 COPD patients and 33 healthy subjects were collected by bronchoscopy. The load of Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Pseudomonos aeruginosa, Haemophilus influenzeae, and Moraxella catarrhalis were detected by RT-qPCR. RESULTS High Klebsiella pneumoniae, Pseudomonos aeruginosa, Haemophilus influenzeae and Moraxella catarrhalis burden were detected by RT-qPCR in both PSB and BALF samples obtained from stable COPD and AECOPD patients compared with healthy subjects. The load of the above four pathogenic strains in PSB and BALF samples obtained from AECOPD patients were significantly higher compared with stable COPD patients. Finally, positive correlations between bacterial loads and inflammatory mediators such as neutrophil count and cytokine levels of IL-1β, IL-6 and IL-8, as well as negative correlations between bacterial loads and the forced expiratory volume in one second (FEV1) % predicted, forced vital capacity (FVC) % predicted, and FEV1/FVC ratio, were detected. CONCLUSIONS These findings suggest that increased bacterial loads mediated inflammatory response in the lower respiratory tract and were associated with AECOPD. In addition, these results provide guidance for antibiotic therapy of AECOPD patients.
Collapse
Affiliation(s)
- Huaying Wang
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Xiao Gu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Yuesong Weng
- Clinical Laboratory, First Hospital, 58 Liuting Road, Ningbo City, Zhejiang Province, 315010, P. R. China
| | - Tao Xu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Zhongming Fu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Weidong Peng
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China
| | - Wanjun Yu
- Department of Respiratory Diseases, Affiliated Yinzhou Hospital, College of Medicine, Ningbo University, 251 East Baizhang Road, Ningbo City, Zhejiang Province, 315040, P. R. China.
| |
Collapse
|
18
|
Coughlan H, Reddington K, Tuite N, Boo TW, Cormican M, Barrett L, Smith TJ, Clancy E, Barry T. Comparative genome analysis identifies novel nucleic acid diagnostic targets for use in the specific detection of Haemophilus influenzae. Diagn Microbiol Infect Dis 2015; 83:112-6. [PMID: 26166209 DOI: 10.1016/j.diagmicrobio.2015.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 11/25/2022]
Abstract
Haemophilus influenzae is recognised as an important human pathogen associated with invasive infections, including bloodstream infection and meningitis. Currently used molecular-based diagnostic assays lack specificity in correctly detecting and identifying H. influenzae. As such, there is a need to develop novel diagnostic assays for the specific identification of H. influenzae. Whole genome comparative analysis was performed to identify putative diagnostic targets, which are unique in nucleotide sequence to H. influenzae. From this analysis, we identified 2H. influenzae putative diagnostic targets, phoB and pstA, for use in real-time PCR diagnostic assays. Real-time PCR diagnostic assays using these targets were designed and optimised to specifically detect and identify all 55H. influenzae strains tested. These novel rapid assays can be applied to the specific detection and identification of H. influenzae for use in epidemiological studies and could also enable improved monitoring of invasive disease caused by these bacteria.
Collapse
Affiliation(s)
- Helena Coughlan
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland; Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Nina Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Teck Wee Boo
- Department of Clinical Microbiology, University College Hospital, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland, Galway, Ireland
| | - Louise Barrett
- National Centre of Sensor Research, School of Physical Sciences, Biomedical Diagnostics Institute, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Terry J Smith
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland; Molecular Diagnostics Research Group (MDRG), School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Eoin Clancy
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland; Molecular Diagnostics Research Group (MDRG), School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| |
Collapse
|
19
|
Safaeyan F, Nahaei MR, Seifi SJ, Kafil HS, Sadeghi J. Quantitative detection of Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae in patients with new influenza A (H1N1)/2009 and influenza A/2010 virus infection. GMS HYGIENE AND INFECTION CONTROL 2015; 10:Doc06. [PMID: 25914868 PMCID: PMC4399408 DOI: 10.3205/dgkh000249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Viral influenza is a seasonal infection associated with significant morbidity and mortality. In the United States more than 35,000 deaths and 200,000 hospitalizations are recorded annually due to influenza. Secondary bacterial infections or co-infections associated with cases of influenza are a leading cause of severe morbidity and mortality, especially among high-risk groups such as the elderly and young children. AIM The aim of the present study was the quantitative detection of S. aureus, S. pneumoniae and H. influenzae in a group of patients with seasonal influenza A, influenza A (H1N1) pandemic 2009, and patients with symptoms of respiratory infection, but the negative for H1N1 serving as control group. METHOD In total, 625 patients suspected respiratory infection from April 2009 to April 2010 were studied. There were 58 patients with influenza A H1N1 and 567 patients negative for influenza A H1N1. From November 2010 to February 2011, 158 patients with respiratory symptoms were analyzed for seasonal influenza A. There were 25 patients with seasonal influenza A. To check the colonization status among the healthy individuals 62 healthy persons were further investigated. Individual were screened in parallel. The choices of special genes were amplified from clinical specimens using real-time PCR with a cutoff of 10(4) CFU/mL to differentiate colonization from infection in respiratory tract. RESULTS S. aureus, S. pneumoniae and H. influenzae were detected in 12%, 26% and 33% of patients with H1N1, while the corresponding figures were 9%, 19%, and 31% for H1N1 negative patients. Among patients with seasonal influenza A 12% S. aureus, 24% S. pneumoniae, and 32% H. influenzae co-infections were detected, while influenza negative control group yielded 5% S. aureus, 11% S. pneumoniae, and 10% H. influenzae, respectively. CONCLUSION The results of this study indicated that the serotype of pandemic H1N1 2009 did not increase incidence of secondary infection with S. aureus, S. pneumoniae and H. influenzae. Quantitative detection of secondary bacterial infection by QR-PCR can help us for distinguishing colonization from infection and controlling misuse of antibiotics and bacterial drug resistances.
Collapse
Affiliation(s)
- Firouzeh Safaeyan
- Tuberculosis & Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Nahaei
- Tuberculosis & Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sirus Jedary Seifi
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
20
|
Edin A, Granholm S, Koskiniemi S, Allard A, Sjöstedt A, Johansson A. Development and laboratory evaluation of a real-time PCR assay for detecting viruses and bacteria of relevance for community-acquired pneumonia. J Mol Diagn 2015; 17:315-24. [PMID: 25772704 PMCID: PMC7185852 DOI: 10.1016/j.jmoldx.2015.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 12/19/2014] [Accepted: 01/08/2015] [Indexed: 02/01/2023] Open
Abstract
Community-acquired pneumonia may present with similar clinical symptoms, regardless of viral or bacterial cause. Diagnostic assays are needed to rapidly discriminate between causes, because this will guide decisions on appropriate treatment. Therefore, a quantitative real-time PCR (qPCR) assay with duplex reactions targeting eight bacteria and six viruses was developed. Technical performance was examined with linear plasmids. Upper and lower respiratory tract specimens were used to compare the qPCR assay with standard microbiological methods. The limit of detection was 5 to 20 DNA template copies with approximately 1000-fold differences in concentrations of the two competing templates. SDs for positive controls were <5%. The use of the qPCR assay resulted in 113 positive identifications in 94 respiratory specimens compared with 38 by using standard diagnostics. Diagnostic accuracy of the qPCR assay varied between 60% positive agreement with standard tests for Streptococcus pneumoniae and 100% for Mycoplasma pneumoniae, Moraxella catarrhalis, and Staphylococcus aureus. Negative percentage of agreement was >95% for M. pneumoniae, Streptococcus pyogenes, respiratory syncytial virus, and influenza A virus; whereas it was only 56% for Haemophilus influenzae. Multiple microbial agents were identified in 19 of 44 sputum and 19 of 50 nasopharynx specimens. We conclude that in parallel qPCR detection of the targeted respiratory bacteria and viruses is feasible. The results indicate good technical performance of the assay in clinical specimens.
Collapse
Affiliation(s)
- Alicia Edin
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Susanne Granholm
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Satu Koskiniemi
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Annika Allard
- Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden
| | - Anders Sjöstedt
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
| |
Collapse
|
21
|
Latham R, Zhang B, Tristram S. Identifying Haemophilus haemolyticus and Haemophilus influenzae by SYBR Green real-time PCR. J Microbiol Methods 2015; 112:67-9. [PMID: 25753676 DOI: 10.1016/j.mimet.2015.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
SYBR Green real time PCR assays for protein D (hpd), fuculose kinase (fucK) and [Cu, Zn]-superoxide dismutase (sodC) were designed for use in an algorithm for the identification of Haemophilus influenzae and H. haemolyticus. When tested on 127 H. influenzae and 60 H. haemolyticus all isolates were identified correctly.
Collapse
Affiliation(s)
- Roger Latham
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia.
| | - Bowen Zhang
- School of Health Sciences, University of Tasmania, Launceston, Australia.
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Australia.
| |
Collapse
|
22
|
Pickering J, Richmond PC, Kirkham LAS. Molecular tools for differentiation of non-typeable Haemophilus influenzae from Haemophilus haemolyticus. Front Microbiol 2014; 5:664. [PMID: 25520712 PMCID: PMC4251515 DOI: 10.3389/fmicb.2014.00664] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/15/2014] [Indexed: 12/18/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus are closely related bacteria that reside in the upper respiratory tract. NTHi is associated with respiratory tract infections that frequently result in antibiotic prescription whilst H. haemolyticus is rarely associated with disease. NTHi and H. haemolyticus can be indistinguishable by traditional culture methods and molecular differentiation has proven difficult. This current review chronologically summarizes the molecular approaches that have been developed for differentiation of NTHi from H. haemolyticus, highlighting the advantages and disadvantages of each target and/or technique. We also provide suggestions for the development of new tools that would be suitable for clinical and research laboratories.
Collapse
Affiliation(s)
- Janessa Pickering
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia
| | - Peter C Richmond
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia ; Centre for Vaccine and Infectious Disease Research, Telethon Kids Institute, The University of Western Australia Perth, WA, Australia
| | - Lea-Ann S Kirkham
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia ; Centre for Vaccine and Infectious Disease Research, Telethon Kids Institute, The University of Western Australia Perth, WA, Australia
| |
Collapse
|
23
|
Kloepfer KM, Lee WM, Pappas TE, Kang TJ, Vrtis RF, Evans MD, Gangnon RE, Bochkov YA, Jackson DJ, Lemanske RF, Gern JE. Detection of pathogenic bacteria during rhinovirus infection is associated with increased respiratory symptoms and asthma exacerbations. J Allergy Clin Immunol 2014; 133:1301-7, 1307.e1-3. [PMID: 24698319 DOI: 10.1016/j.jaci.2014.02.030] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/21/2014] [Accepted: 02/14/2014] [Indexed: 01/26/2023]
Abstract
BACKGROUND Detection of either viral or bacterial pathogens is associated with wheezing in children; however, the influence of both bacteria and viruses on illness symptoms has not been described. OBJECTIVE We evaluated bacterial detection during the peak rhinovirus season in children with and without asthma to determine whether an association exists between bacterial infection and the severity of rhinovirus-induced illnesses. METHODS Three hundred eight children (166 with asthma and 142 without asthma) aged 4 to 12 years provided 5 consecutive weekly nasal samples during September and scored cold and asthma symptoms daily. Viral diagnostics and quantitative PCR for Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were performed on all nasal samples. RESULTS Detection rates were 53%, 17%, and 11% for H influenzae, S pneumoniae, and M catarrhalis, respectively, with detection of rhinovirus increasing the risk of detecting bacteria within the same sample (odds ratio [OR], 2.0; 95% CI, 1.4-2.7; P < .0001) or the following week (OR, 1.6; 95% CI, 1.1-2.4; P = .02). In the absence of rhinovirus, S pneumoniae was associated with increased cold symptoms (mean, 2.7 [95% CI, 2.0-3.5] vs 1.8 [95% CI, 1.5-2.2]; P = .006) and moderate asthma exacerbations (18% [95% CI, 12% to 27%] vs 9.2% [95% CI, 6.7% to 12%]; P = .006). In the presence of rhinovirus, S pneumoniae was associated with increased moderate asthma exacerbations (22% [95% CI, 16% to 29%] vs 15% [95% CI, 11% to 20%]; P = .01). Furthermore, M catarrhalis detected alongside rhinovirus increased the likelihood of experiencing cold symptoms, asthma symptoms, or both compared with isolated detection of rhinovirus (OR, 2.0 [95% CI, 1.0-4.1]; P = .04). Regardless of rhinovirus status, H influenzae was not associated with respiratory symptoms. CONCLUSION Rhinovirus infection enhances detection of specific bacterial pathogens in children with and without asthma. Furthermore, these findings suggest that M catarrhalis and S pneumoniae contribute to the severity of respiratory tract illnesses, including asthma exacerbations.
Collapse
Affiliation(s)
- Kirsten M Kloepfer
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Ind.
| | - Wai Ming Lee
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Tressa E Pappas
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Theresa J Kang
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Rose F Vrtis
- Department of Medicine, University of Wisconsin-Madison, Madison, Wis
| | - Michael D Evans
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis
| | - Ronald E Gangnon
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis; Department of Medicine, University of Wisconsin-Madison, Madison, Wis
| | - Robert F Lemanske
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis; Department of Medicine, University of Wisconsin-Madison, Madison, Wis
| | - James E Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wis; Department of Medicine, University of Wisconsin-Madison, Madison, Wis
| |
Collapse
|
24
|
Nørskov-Lauritsen N. Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans. Clin Microbiol Rev 2014; 27:214-40. [PMID: 24696434 PMCID: PMC3993099 DOI: 10.1128/cmr.00103-13] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The aim of this review is to provide a comprehensive update on the current classification and identification of Haemophilus and Aggregatibacter species with exclusive or predominant host specificity for humans. Haemophilus influenzae and some of the other Haemophilus species are commonly encountered in the clinical microbiology laboratory and demonstrate a wide range of pathogenicity, from life-threatening invasive disease to respiratory infections to a nonpathogenic, commensal lifestyle. New species of Haemophilus have been described (Haemophilus pittmaniae and Haemophilus sputorum), and the new genus Aggregatibacter was created to accommodate some former Haemophilus and Actinobacillus species (Aggregatibacter aphrophilus, Aggregatibacter segnis, and Aggregatibacter actinomycetemcomitans). Aggregatibacter species are now a dominant etiology of infective endocarditis caused by fastidious organisms (HACEK endocarditis), and A. aphrophilus has emerged as an important cause of brain abscesses. Correct identification of Haemophilus and Aggregatibacter species based on phenotypic characterization can be challenging. It has become clear that 15 to 20% of presumptive H. influenzae isolates from the respiratory tracts of healthy individuals do not belong to this species but represent nonhemolytic variants of Haemophilus haemolyticus. Due to the limited pathogenicity of H. haemolyticus, the proportion of misidentified strains may be lower in clinical samples, but even among invasive strains, a misidentification rate of 0.5 to 2% can be found. Several methods have been investigated for differentiation of H. influenzae from its less pathogenic relatives, but a simple method for reliable discrimination is not available. With the implementation of identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry, the more rarely encountered species of Haemophilus and Aggregatibacter will increasingly be identified in clinical microbiology practice. However, identification of some strains will still be problematic, necessitating DNA sequencing of multiple housekeeping gene fragments or full-length 16S rRNA genes.
Collapse
|
25
|
Frickmann H, Christner M, Donat M, Berger A, Essig A, Podbielski A, Hagen RM, Poppert S. Rapid discrimination of Haemophilus influenzae, H. parainfluenzae, and H. haemolyticus by fluorescence in situ hybridization (FISH) and two matrix-assisted laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS) platforms. PLoS One 2013; 8:e63222. [PMID: 23646201 PMCID: PMC3639997 DOI: 10.1371/journal.pone.0063222] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 04/01/2013] [Indexed: 12/12/2022] Open
Abstract
Background Due to considerable differences in pathogenicity, Haemophilus influenzae, H. parainfluenzae and H. haemolyticus have to be reliably discriminated in routine diagnostics. Retrospective analyses suggest frequent misidentifications of commensal H. haemolyticus as H. influenzae. In a multi-center approach, we assessed the suitability of fluorescence in situ hybridization (FISH) and matrix-assisted laser-desorption-ionization time-of-flight mass-spectrometry (MALDI-TOF-MS) for the identification of H. influenzae, H. parainfluenzae and H. haemolyticus to species level. Methodology A strain collection of 84 Haemophilus spp. comprising 50 H. influenzae, 25 H. parainfluenzae, 7 H. haemolyticus, and 2 H. parahaemolyticus including 77 clinical isolates was analyzed by FISH with newly designed DNA probes, and two different MALDI-TOF-MS systems (Bruker, Shimadzu) with and without prior formic acid extraction. Principal Findings Among the 84 Haemophilus strains analyzed, FISH led to 71 correct results (85%), 13 uninterpretable results (15%), and no misidentifications. Shimadzu MALDI-TOF-MS resulted in 59 correct identifications (70%), 19 uninterpretable results (23%), and 6 misidentifications (7%), using colony material applied directly. Bruker MALDI-TOF-MS with prior formic acid extraction led to 74 correct results (88%), 4 uninterpretable results (5%) and 6 misidentifications (7%). The Bruker MALDI-TOF-MS misidentifications could be resolved by the addition of a suitable H. haemolyticus reference spectrum to the system's database. In conclusion, no analyzed diagnostic procedure was free of errors. Diagnostic results have to be interpreted carefully and alternative tests should be applied in case of ambiguous test results on isolates from seriously ill patients.
Collapse
Affiliation(s)
- Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.
Collapse
Affiliation(s)
- Max Maurin
- Laboratoire de Bactériologie, Département des Agents Infectieux, Institut de Biologie et Pathologie, CHU de Grenoble, Université Joseph Fourier Grenoble 1, France.
| |
Collapse
|
27
|
Pedersen KS, Stege H, Jensen TK, Guedes R, Ståhl M, Nielsen JP, Hjulsager C, Larsen LE, Angen Ø. Diagnostic performance of fecal quantitative real-time polymerase chain reaction for detection of Lawsonia intracellularis-associated proliferative enteropathy in nursery pigs. J Vet Diagn Invest 2013; 25:336-40. [PMID: 23536614 DOI: 10.1177/1040638713480499] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) tests for detection and quantification of Lawsonia intracellularis in feces from pigs have been developed. The objective of the current study was to evaluate the diagnostic performance of a fecal qPCR test for detection of nursery pigs with L. intracellularis-associated proliferative enteropathy (PE) under field conditions. Furthermore, the diagnostic performance for different subpopulations of pigs was investigated, including pigs infected or noninfected with Porcine circovirus-2, Brachyspira pilosicoli, and Escherichia coli. The diagnostic performance was evaluated in terms of diagnostic sensitivity and specificity. Data from pigs originating from 20 herds with antibiotic treatment requiring diarrhea outbreaks from a prior study were reused. Before treatment, pigs were randomly selected for histological and immunohistochemical examination of intestinal segments and fecal quantification of L. intracellularis by qPCR. A total of 313 pigs (157 without diarrhea, 156 with diarrhea) were included in the statistical analysis, and 37 pigs (11.8%) were classified as PE positives (defined as proliferative histological lesions in combination with L. intracellularis demonstration by immunohistochemistry). Lawsonia intracellularis was detected by qPCR in feces from 91 pigs (29.1%). A nonparametric receiver operating characteristic (ROC) analysis provided an area under the ROC curve (0.93) and an optimal cutoff value of 4.8 log10 L. intracellularis bacteria/g feces. This cutoff provided a diagnostic sensitivity of 0.84 and diagnostic specificity of 0.93. The diagnostic sensitivity and specificity were significantly different between herds (P < 0.0001). Numerically, diagnostic sensitivity and specificity were different between subpopulations of pigs, but no significant differences were demonstrated.
Collapse
Affiliation(s)
- Ken Steen Pedersen
- HERD-Centre for Herd Oriented Education, Research and Development, Department of Large Animal Sciences, University of Copenhagen, Groennegaardsvej 2, DK-1870 Frederiksberg C, Denmark.
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Abdeldaim GMK, Strålin K, Olcén P, Blomberg J, Mölling P, Herrmann B. Quantitative fucK gene polymerase chain reaction on sputum and nasopharyngeal secretions to detect Haemophilus influenzae pneumonia. Diagn Microbiol Infect Dis 2013; 76:141-6. [PMID: 23541117 DOI: 10.1016/j.diagmicrobio.2013.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/08/2013] [Accepted: 02/19/2013] [Indexed: 11/26/2022]
Abstract
A quantitative polymerase chain reaction (PCR) for the fucK gene was developed for specific detection of Haemophilus influenzae. The method was tested on sputum and nasopharyngeal aspirate (NPA) from 78 patients with community-acquired pneumonia (CAP). With a reference standard of sputum culture and/or serology against the patient's own nasopharyngeal isolate, H. influenzae etiology was detected in 20 patients. Compared with the reference standard, fucK PCR (using the detection limit 10(5) DNA copies/mL) on sputum and NPA showed a sensitivity of 95.0% (19/20) in both cases, and specificities of 87.9% (51/58) and 89.5% (52/58), respectively. In a receiver operating characteristic curve analysis, sputum fucK PCR was found to be significantly superior to sputum P6 PCR for detection of H. influenzae CAP. NPA fucK PCR was positive in 3 of 54 adult controls without respiratory symptoms. In conclusion, quantitative fucK real-time PCR provides a sensitive and specific identification of H. influenzae in respiratory secretions.
Collapse
Affiliation(s)
- Guma M K Abdeldaim
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, S-75185, Uppsala, Sweden
| | | | | | | | | | | |
Collapse
|
29
|
Zhu B, Xiao D, Zhang H, Zhang Y, Gao Y, Xu L, Lv J, Wang Y, Zhang J, Shao Z. MALDI-TOF MS distinctly differentiates nontypable Haemophilus influenzae from Haemophilus haemolyticus. PLoS One 2013; 8:e56139. [PMID: 23457514 PMCID: PMC3573053 DOI: 10.1371/journal.pone.0056139] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/05/2013] [Indexed: 11/19/2022] Open
Abstract
Nontypable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus exhibit different pathogenicities, but to date, there remains no definitive and reliable strategy for differentiating these strains. In this study, we evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a potential method for differentiating NTHi and H. haemolyticus. The phylogenetic analysis of concatenated 16S rRNA and recombinase A (recA) gene sequences, outer membrane protein P6 gene sequencing and single-gene PCR were used as reference methods. The original reference database (ORD, provided with the Biotyper software) and new reference database (NRD, extended with Chinese strains) were compared for the evaluation of MALDI-TOF MS. Through a search of the ORD, 76.9% of the NTHi (40/52) and none of the H. haemolyticus (0/20) strains were identified at the species level. However, all NTHi and H. haemolyticus strains used for identification were accurately recognized at the species level when searching the NRD. From the dendrogram clustering of the main spectra projections, the Chinese and foreign H. influenzae reference strains were categorized into two distinct groups, and H. influenzae and H. haemolyticus were also separated into two categories. Compared to the existing methods, MALDI-TOF MS has the advantage of integrating high throughput, accuracy and speed. In conclusion, MALDI-TOF MS is an excellent method for differentiating NTHi and H. haemolyticus. This method can be recommended for use in appropriately equipped laboratories.
Collapse
Affiliation(s)
- Bingqing Zhu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Di Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Huifang Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yongchan Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yuan Gao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Li Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Jing Lv
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, People’s Republic of China
| | - Yingtong Wang
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Jianzhong Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- * E-mail: (ZS); (JZ)
| | - Zhujun Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- * E-mail: (ZS); (JZ)
| |
Collapse
|
30
|
Abdeldaim GMK, Herrmann B. PCR detection of Haemophilus influenzae from respiratory specimens. Methods Mol Biol 2013; 943:115-23. [PMID: 23104285 DOI: 10.1007/978-1-60327-353-4_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The detection of Haemophilus influenzae by conventional methods like culture is time-consuming and may give false-negative results, especially during ongoing antibiotic treatment. Therefore, non-culture based methods that are sensitive, specific, and rapid are valuable for early diagnosis and effective therapy. Here we describe a quantitative real-time PCR assay based on the outer membrane P6 gene omp6, to detect H. influenzae and its application on respiratory tract specimens.
Collapse
Affiliation(s)
- Guma M K Abdeldaim
- Department of Clinical Microbiology, Uppsala, University Hospital, Uppsala, Sweden
| | | |
Collapse
|
31
|
Density interactions among Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus in the nasopharynx of young Peruvian children. Pediatr Infect Dis J 2013; 32:72-7. [PMID: 22935873 PMCID: PMC3525793 DOI: 10.1097/inf.0b013e318270d850] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus are commonly carried in the nasopharynx of young children, and have been speculated to interact with each other. Although earlier studies used cultures alone to assess these interactions, the addition of real-time quantitative polymerase chain reaction (qPCR) provides further insight into these interactions. We compared results of culture and qPCR for the detection of these 3 bacteria in 446 nasopharynx samples collected from 360 healthy young children in a prospective cohort study in the Peruvian Andes. Patterns of concurrent bacterial colonization were studied using repeated measures logistic regression models with generalized estimating equations. Spearman correlation coefficients were used to assess correlations among bacterial densities. At a bacterial density <10 colony forming units/mL measured by qPCR, culture detected significantly less carriers (P < 0.0001) for all 3 pathogens, than at a bacterial density >10 colony forming units/mL. In addition, there was a positive association between S. pneumoniae and H. influenzae colonization measured by both culture (odds ratio [OR] 3.11-3.17, P < 0.001) and qPCR (OR 1.95-1.97, P < 0.01). The densities of S. pneumoniae and H. influenzae, measured by qPCR, were positively correlated (correlation coefficient 0.32, P < 0.001). A negative association was found between the presence of S. pneumoniae and Staphylococcus aureus in carriage with both culture (OR 0.45, P = 0.024) and qPCR (OR 0.61, P < 0.05). The impact of density on detection by culture and the observed density-related interactions support use of qPCR in additional studies to examine vaccine effects on diverse bacterial species.
Collapse
|
32
|
Meyler KL, Meehan M, Bennett D, Cunney R, Cafferkey M. Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples. Diagn Microbiol Infect Dis 2012; 74:356-62. [DOI: 10.1016/j.diagmicrobio.2012.08.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 06/29/2012] [Accepted: 08/19/2012] [Indexed: 11/26/2022]
|
33
|
Pedersen KS, Ståhl M, Guedes RMC, Angen Ø, Nielsen JP, Jensen TK. Association between faecal load of lawsonia intracellularis and pathological findings of proliferative enteropathy in pigs with diarrhoea. BMC Vet Res 2012; 8:198. [PMID: 23092367 PMCID: PMC3514390 DOI: 10.1186/1746-6148-8-198] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
Background The study was designed to investigate correlation between histological findings of Lawsonia intracellularis in porcine cases of diarrhoea and the quantitative detection of Lawsonia intracellularis in faeces. A total of 156 pigs (10 to 70 days post weaning) with diarrhoea were randomly selected from 20 herds: The pigs were subjected to necropsy, histopathology, immunohistochemistry and faecal quantification of Lawsonia intracellularis by real time PCR. Results The median Lawsonia intracellularis excretion was significantly higher in pigs with gross lesions of proliferative enteropathy (median excretion: 5.92 log10 bacteria/g faeces) compared to pigs without gross lesions of proliferative enteropathy (median excretion: <3.3 log10 bacteria/g faeces) (P<0.001). Spearman’s correlation coefficient between the measureable PE lesions and L. intracellularis excretion was 0.50 (P<0.001). A significantly increasing trend in Lawsonia intracellularis excretion level for increasing proliferative enteropathy histopathology and immunohistochemistry scores was demonstrated (P<0.001; P<0.001). Spearman’s correlation coefficient between the histopathology scores and L. intracellularis excretion was 0.67 (P<0.001). Spearman’s correlation coefficient between the IHC scores and L. intracellularis excretion was 0.77 (P<0.001). Conclusions The histological and quantitative PCR detection of Lawsonia intracellularis were correlated in pigs with diarrhoea. Overall the results suggest that clinically important levels for Lawsonia intracellularis excretion in faeces may be established. Such clinical threshold levels may be used in practice to confirm a diagnosis of Lawsonia intracellularis associated diarrhoea.
Collapse
Affiliation(s)
- Ken Steen Pedersen
- HERD - Centre for Herd oriented Education, Research and Development, Department of Large Animal Sciences, University of Copenhagen, Groennegaardsvej 2, Frederiksberg C 1870, Denmark.
| | | | | | | | | | | |
Collapse
|
34
|
Hammitt LL, Murdoch DR, Scott JAG, Driscoll A, Karron RA, Levine OS, O'Brien KL. Specimen collection for the diagnosis of pediatric pneumonia. Clin Infect Dis 2012; 54 Suppl 2:S132-9. [PMID: 22403227 PMCID: PMC3693496 DOI: 10.1093/cid/cir1068] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diagnosing the etiologic agent of pneumonia has an essential role in ensuring the most appropriate and effective therapy for individual patients and is critical to guiding the development of treatment and prevention strategies. However, establishing the etiology of pneumonia remains challenging because of the relative inaccessibility of the infected tissue and the difficulty in obtaining samples without contamination by upper respiratory tract secretions. Here, we review the published and unpublished literature on various specimens available for the diagnosis of pediatric pneumonia. We discuss the advantages and limitations of each specimen, and discuss the rationale for the specimens to be collected for the Pneumonia Etiology Research for Child Health study.
Collapse
Affiliation(s)
- Laura L Hammitt
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Molecular surveillance of true nontypeable Haemophilus influenzae: an evaluation of PCR screening assays. PLoS One 2012; 7:e34083. [PMID: 22470516 PMCID: PMC3314702 DOI: 10.1371/journal.pone.0034083] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/21/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Unambiguous identification of nontypeable Haemophilus influenzae (NTHi) is not possible by conventional microbiology. Molecular characterisation of phenotypically defined NTHi isolates suggests that up to 40% are Haemophilus haemolyticus (Hh); however, the genetic similarity of NTHi and Hh limits the power of simple molecular techniques such as PCR for species discrimination. METHODOLOGY/PRINCIPAL FINDINGS Here we assess the ability of previously published and novel PCR-based assays to identify true NTHi. Sixty phenotypic NTHi isolates, classified by a dual 16S rRNA gene PCR algorithm as NTHi (n = 22), Hh (n = 27) or equivocal (n = 11), were further characterised by sequencing of the 16S rRNA and recA genes then interrogated by PCR-based assays targeting the omp P2, omp P6, lgtC, hpd, 16S rRNA, fucK and iga genes. The sequencing data and PCR results were used to define NTHi for this study. Two hpd real time PCR assays (hpd#1 and hpd#3) and the conventional iga PCR assay were equally efficient at differentiating study-defined NTHi from Hh, each with a receiver operator characteristic curve area of 0.90 [0.83; 0.98]. The hpd#1 and hpd#3 assays were completely specific against a panel of common respiratory bacteria, unlike the iga PCR, and the hpd#3 assay was able to detect below 10 copies per reaction. CONCLUSIONS/SIGNIFICANCE Our data suggest an evolutionary continuum between NTHi and Hh and therefore no single gene target could completely differentiate NTHi from Hh. The hpd#3 real time PCR assay proved to be the superior method for discrimination of NTHi from closely related Haemophilus species with the added potential for quantification of H. influenzae directly from specimens. We suggest the hpd#3 assay would be suitable for routine NTHi surveillance and to assess the impact of antibiotics and vaccines, on H. influenzae carriage rates, carriage density, and disease.
Collapse
|
36
|
Evaluation of new biomarker genes for differentiating Haemophilus influenzae from Haemophilus haemolyticus. J Clin Microbiol 2012; 50:1422-4. [PMID: 22301020 DOI: 10.1128/jcm.06702-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR detecting the protein D (hpd) and fuculose kinase (fucK) genes showed high sensitivity and specificity for identifying Haemophilus influenzae and differentiating it from H. haemolyticus. Phylogenetic analysis using the 16S rRNA gene demonstrated two distinct groups for H. influenzae and H. haemolyticus.
Collapse
|
37
|
Woodhead M, Blasi F, Ewig S, Garau J, Huchon G, Ieven M, Ortqvist A, Schaberg T, Torres A, van der Heijden G, Read R, Verheij TJM. Guidelines for the management of adult lower respiratory tract infections--summary. Clin Microbiol Infect 2012; 17 Suppl 6:1-24. [PMID: 21951384 DOI: 10.1111/j.1469-0691.2011.03602.x] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This document is an update of Guidelines published in 2005 and now includes scientific publications through to May 2010. It provides evidence-based recommendations for the most common management questions occurring in routine clinical practice in the management of adult patients with LRTI. Topics include management outside hospital, management inside hospital (including community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), acute exacerbations of bronchiectasis) and prevention. The target audience for the Guideline is thus all those whose routine practice includes the management of adult LRTI.
Collapse
Affiliation(s)
- M Woodhead
- Department of Respiratory Medicine, Manchester Royal Infirmary, Oxford Road, Manchester, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Cope EK, Goldstein-Daruech N, Kofonow JM, Christensen L, McDermott B, Monroy F, Palmer JN, Chiu AG, Shirtliff ME, Cohen NA, Leid JG. Regulation of virulence gene expression resulting from Streptococcus pneumoniae and nontypeable Haemophilus influenzae interactions in chronic disease. PLoS One 2011; 6:e28523. [PMID: 22162775 PMCID: PMC3230614 DOI: 10.1371/journal.pone.0028523] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 11/09/2011] [Indexed: 01/25/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a common inflammatory disease of the sinonasal cavity mediated, in part, by polymicrobial communities of bacteria. Recent molecular studies have confirmed the importance of Streptococcus pneumoniae and nontypeable Haemophilus influenzae (NTHi) in CRS. Here, we hypothesize that interaction between S. pneumoniae and NTHi mixed-species communities cause a change in bacterial virulence gene expression. We examined CRS as a model human disease to validate these polymicrobial interactions. Clinical strains of S. pneumoniae and NTHi were grown in mono- and co-culture in a standard biofilm assay. Reverse transcriptase real-time PCR (RTqPCR) was used to measure gene expression of key virulence factors. To validate these results, we investigated the presence of the bacterial RNA transcripts in excised human tissue from patients with CRS. Consequences of physical or chemical interactions between microbes were also investigated. Transcription of NTHi type IV pili was only expressed in co-culture in vitro, and expression could be detected ex vivo in diseased tissue. S. pneumoniae pyruvate oxidase was up-regulated in co-culture, while pneumolysin and pneumococcal adherence factor A were down-regulated. These results were confirmed in excised human CRS tissue. Gene expression was differentially regulated by physical contact and secreted factors. Overall, these data suggest that interactions between H. influenzae and S. pneumoniae involve physical and chemical mechanisms that influence virulence gene expression of mixed-species biofilm communities present in chronically diseased human tissue. These results extend previous studies of population-level virulence and provide novel insight into the importance of S. pneumoniae and NTHi in CRS.
Collapse
Affiliation(s)
- Emily K Cope
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Woodhead M, Blasi F, Ewig S, Garau J, Huchon G, Ieven M, Ortqvist A, Schaberg T, Torres A, van der Heijden G, Read R, Verheij TJM. Guidelines for the management of adult lower respiratory tract infections--full version. Clin Microbiol Infect 2011; 17 Suppl 6:E1-59. [PMID: 21951385 PMCID: PMC7128977 DOI: 10.1111/j.1469-0691.2011.03672.x] [Citation(s) in RCA: 586] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This document is an update of Guidelines published in 2005 and now includes scientific publications through to May 2010. It provides evidence-based recommendations for the most common management questions occurring in routine clinical practice in the management of adult patients with LRTI. Topics include management outside hospital, management inside hospital (including community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), acute exacerbations of bronchiectasis) and prevention. Background sections and graded evidence tables are also included. The target audience for the Guideline is thus all those whose routine practice includes the management of adult LRTI.
Collapse
Affiliation(s)
- M Woodhead
- Department of Respiratory Medicine, Manchester Royal Infirmary, Oxford Road, Manchester, UK.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Wang X, Mair R, Hatcher C, Theodore MJ, Edmond K, Wu HM, Harcourt BH, Carvalho MDGS, Pimenta F, Nymadawa P, Altantsetseg D, Kirsch M, Satola SW, Cohn A, Messonnier NE, Mayer LW. Detection of bacterial pathogens in Mongolia meningitis surveillance with a new real-time PCR assay to detect Haemophilus influenzae. Int J Med Microbiol 2011; 301:303-9. [PMID: 21276750 DOI: 10.1016/j.ijmm.2010.11.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/12/2010] [Accepted: 11/14/2010] [Indexed: 11/25/2022] Open
Abstract
Since the implementation of Haemophilus influenzae (Hi) serotype b vaccine, other serotypes and non-typeable strains have taken on greater importance as a cause of Hi diseases. A rapid and accurate method is needed to detect all Hi regardless of the encapsulation status. We developed 2 real-time PCR (rt-PCR) assays to detect specific regions of the protein D gene (hpd). Both hpd assays are very specific and sensitive for detection of Hi. Of the 63 non-Hi isolates representing 21 bacterial species, none was detected by the hpd #1 assay, and only one of 2 H. aphrophilus isolates was detected by the hpd #3 assay. The hpd #1 and #3 assays detected 97% (229/237) and 99% (234/237) of Hi isolates, respectively, and were superior for detection of both typeable and non-typeable Hi isolates, as compared to previously developed rt-PCR targeting ompP2 or bexA. The diagnostic sensitivity and specificity of these rt-PCR assays were assessed on cerebrospinal fluid specimens collected as part of meningitis surveillance in Ulaanbaatar, Mongolia. The etiology (Neisseria meningitidis, Hi, and Streptococcus pneumoniae) of 111 suspected meningitis cases was determined by conventional methods (culture and latex agglutination), previously developed rt-PCR assays, and the new hpd assays. The rt-PCR assays were more sensitive for detection of meningitis pathogens than other classical methods and improved detection from 50% (56/111) to 75% (83/111). The hpd #3 assay identified a non-b Hi that was missed by the bexA assay and other methods. A sensitive rt-PCR assay to detect both typeable and non-typeable Hi is a useful tool for improving Hi disease surveillance especially after Hib vaccine introduction.
Collapse
Affiliation(s)
- Xin Wang
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center of Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Abdeldaim GMK, Strålin K, Korsgaard J, Blomberg J, Welinder-Olsson C, Herrmann B. Multiplex quantitative PCR for detection of lower respiratory tract infection and meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis. BMC Microbiol 2010; 10:310. [PMID: 21129171 PMCID: PMC3016321 DOI: 10.1186/1471-2180-10-310] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 12/03/2010] [Indexed: 11/10/2022] Open
Abstract
Background Streptococcus pneumoniae and Haemophilus influenzae cause pneumonia and as Neisseria meningitidis they are important agents of meningitis. Although several PCR methods have been described for these bacteria the specificity is an underestimated problem. Here we present a quantitative multiplex real-time PCR (qmPCR) for detection of S. pneumoniae (9802 gene fragment), H. influenzae (omp P6 gene) and N. meningitidis (ctrA gene). The method was evaluated on bronchoalveolar lavage (BAL) samples from 156 adults with lower respiratory tract infection (LRTI) and 31 controls, and on 87 cerebrospinal fluid (CSF) samples from meningitis patients. Results The analytical sensitivity was not affected by using a combined mixture of reagents and a combined DNA standard (S. pneumoniae/H. influenzae/N. meningitidis) in single tubes. By blood- and BAL-culture and S. pneumoniae urinary antigen test, S. pneumoniae and H. influenzae were aetiological agents in 21 and 31 of the LTRI patients, respectively. These pathogens were identified by qmPCR in 52 and 72 of the cases, respectively, yielding sensitivities and specificities of 95% and 75% for S. pneumoniae, and 90% and 65% for H. influenzae, respectively. When using a cut-off of 105 genome copies/mL for clinical positivity the sensitivities and specificities were 90% and 80% for S. pneumoniae, and 81% and 85% for H. influenzae, respectively. Of 44 culture negative but qmPCR positive for H. influenzae, 41 were confirmed by fucK PCR as H. influenzae. Of the 103 patients who had taken antibiotics prior to sampling, S. pneumoniae and H. influenzae were identified by culture in 6% and 20% of the cases, respectively, and by the qmPCR in 36% and 53% of the cases, respectively. In 87 CSF samples S. pneumoniae and N. meningitidis were identified by culture and/or 16 S rRNA in 14 and 10 samples and by qmPCR in 14 and 10 samples, respectively, giving a sensitivity of 100% and a specificity of 100% for both bacteria. Conclusions The PCR provides increased sensitivity and the multiplex format facilitates diagnosis of S. pneumoniae, H. influenzae and N. meningitidis and the assay enable detection after antibiotic treatment has been installed. Quantification increases the specificity of the etiology for pneumonia.
Collapse
Affiliation(s)
- Guma M K Abdeldaim
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | |
Collapse
|
42
|
Ridderberg W, Fenger MG, Nørskov-Lauritsen N. Haemophilus influenzae may be untypable by the multilocus sequence typing scheme due to a complete deletion of the fucose operon. J Med Microbiol 2010; 59:740-742. [PMID: 20185549 DOI: 10.1099/jmm.0.018424-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Winnie Ridderberg
- Department of Clinical Microbiology, Aarhus University Hospital Skejby, DK-8200 Aarhus N, Denmark
| | - Mette G Fenger
- Department of Clinical Microbiology, Aarhus University Hospital Skejby, DK-8200 Aarhus N, Denmark
| | - Niels Nørskov-Lauritsen
- Department of Clinical Microbiology, Aarhus University Hospital Skejby, DK-8200 Aarhus N, Denmark
| |
Collapse
|