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Ma X, Li Y, Liang Y, Liu Y, Yu L, Li C, Liu Q, Chen L. Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia. BMC Microbiol 2020; 20:177. [PMID: 32576241 PMCID: PMC7310556 DOI: 10.1186/s12866-020-01842-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/03/2020] [Indexed: 01/25/2023] Open
Abstract
Background The rapid identification of pathogenic bacteria is important for determining an appropriate antimicrobial therapy for pneumonia, but traditional bacterial culture is time-consuming and labourious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneous detection of fifteen bacterial species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA genes and other specific genes of each pathogen were chosen as the amplification targets, amplified via multiplex polymerase chain reaction (PCR), and hybridized to oligonucleotide probes in a microarray. Results The DNA microarray detection limit was 103 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray, and 3 nontarget species from 4 clinical isolates were not detected. Additionally, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results for 99.4% (156/157) of clinical specimens were the same as those from a conventional assay. Conclusions We developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labour and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.
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Affiliation(s)
- Xiuqing Ma
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yanqin Li
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yuan Liang
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yang Liu
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Ling Yu
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Chunsun Li
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Qiqi Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Liangan Chen
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China.
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Gong X, Li J, Zhang Y, Hou S, Qu P, Yang Z, Chen S. Molecular typing of Legionella pneumophila from air-conditioning cooling waters using mip gene, SBT, and FAFLP methods. J Microbiol Methods 2017; 139:1-7. [DOI: 10.1016/j.mimet.2017.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/25/2017] [Accepted: 04/03/2017] [Indexed: 11/29/2022]
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Waites KB, Xiao L, Liu Y, Balish MF, Atkinson TP. Mycoplasma pneumoniae from the Respiratory Tract and Beyond. Clin Microbiol Rev 2017; 30:747-809. [PMID: 28539503 PMCID: PMC5475226 DOI: 10.1128/cmr.00114-16] [Citation(s) in RCA: 367] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mycoplasma pneumoniae is an important cause of respiratory tract infections in children as well as adults that can range in severity from mild to life-threatening. Over the past several years there has been much new information published concerning infections caused by this organism. New molecular-based tests for M. pneumoniae detection are now commercially available in the United States, and advances in molecular typing systems have enhanced understanding of the epidemiology of infections. More strains have had their entire genome sequences published, providing additional insights into pathogenic mechanisms. Clinically significant acquired macrolide resistance has emerged worldwide and is now complicating treatment. In vitro susceptibility testing methods have been standardized, and several new drugs that may be effective against this organism are undergoing development. This review focuses on the many new developments that have occurred over the past several years that enhance our understanding of this microbe, which is among the smallest bacterial pathogens but one of great clinical importance.
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Affiliation(s)
- Ken B Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Li Xiao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yang Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China, and Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | | | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Herrera M, Aguilar YA, Rueda ZV, Muskus C, Vélez LA. Comparison of serological methods with PCR-based methods for the diagnosis of community-acquired pneumonia caused by atypical bacteria. J Negat Results Biomed 2016; 15:3. [PMID: 26932735 PMCID: PMC4774004 DOI: 10.1186/s12952-016-0047-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/05/2016] [Indexed: 02/01/2023] Open
Abstract
Background The diagnosis of community-acquired pneumonia (CAP) caused by Legionella pneumophila, Mycoplasma pneumoniae, and Chlamydophila pneumoniae is traditionally based on cultures and serology, which have special requirements, are time-consuming, and offer delayed results that limit their clinical usefulness of these techniques. We sought to develop a multiplex PCR (mPCR) method to diagnosis these bacterial infections in CAP patients and to compare the diagnostic yields obtained from mPCR of nasopharyngeal aspirates (NPAs), nasopharyngeal swabs (NPSs), and induced sputum (IS) with those obtained with specifc PCR commercial kits, paired serology, and urinary antigen. Results A total of 225 persons were included. Of these, 10 patients showed serological evidence of L. pneumophila infection, 30 of M. pneumoniae, and 18 of C. pneumoniae; 20 individuals showed no CAP. The sensitivities were mPCR-NPS = 23.1 %, mPCR-IS = 57.1 %, Seeplex®-IS = 52.4 %, and Speed-oligo®-NPA/NPS = 11.1 %, and the specificities were mPCR-NPS = 97.1 %, mPCR-IS = 77.8 %, Seeplex®-IS = 92.6 %, and Speed-oligo®-NPA/NPS = 96.1 %. The concordance between tests was poor (kappa <0.4), except for the concordance between mPCR and the commercial kit in IS (0.67). In individuals with no evidence of CAP, positive reactions were observed in paired serology and in all PCRs. Conclusions All PCRs had good specificity but low sensitivity in nasopharyngeal samples. The sensitivity of mPCR and Seeplex® in IS was approximately 60 %; thus, better diagnostic techniques for these three bacteria are required. Electronic supplementary material The online version of this article (doi:10.1186/s12952-016-0047-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mariana Herrera
- Grupo Investigador de Problemas en Enfermedades Infecciosas (GRIPE), Sede de Investigación Universitaria, Calle 62 # 52-59, Laboratorio 630, Universidad de Antioquia, Medellín, Colombia. .,Corporación de Ciencias Básicas Biomédicas, Universidad de Antioquia UdeA, Medellín, Colombia.
| | - Yudy Alexandra Aguilar
- Grupo Investigador de Problemas en Enfermedades Infecciosas (GRIPE), Sede de Investigación Universitaria, Calle 62 # 52-59, Laboratorio 630, Universidad de Antioquia, Medellín, Colombia. .,Corporación de Ciencias Básicas Biomédicas, Universidad de Antioquia UdeA, Medellín, Colombia.
| | | | - Carlos Muskus
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia UdeA, Medellín, Colombia.
| | - Lázaro Agustín Vélez
- Grupo Investigador de Problemas en Enfermedades Infecciosas (GRIPE), Sede de Investigación Universitaria, Calle 62 # 52-59, Laboratorio 630, Universidad de Antioquia, Medellín, Colombia. .,Infectious Disease Section, School of Medicine, Universidad de Antioquia UdeA, Medellín, Colombia.
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Evaluation of a new lateral flow test for detection of Streptococcus pneumoniae and Legionella pneumophila urinary antigen. J Microbiol Methods 2015; 116:33-6. [DOI: 10.1016/j.mimet.2015.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/22/2015] [Accepted: 06/26/2015] [Indexed: 11/21/2022]
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Aydemir O, Aydemir Y, Ozdemir M. The role of multiplex PCR test in identification of bacterial pathogens in lower respiratory tract infections. Pak J Med Sci 2014; 30:1011-6. [PMID: 25225517 PMCID: PMC4163223 DOI: 10.12669/pjms.305.5098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/09/2014] [Accepted: 06/12/2014] [Indexed: 11/30/2022] Open
Abstract
Objectives: Lower respiratory tract infection is one of the most important causes of morbidity and mortality. However establishing a microbial diagnosis for patients with lower respiratory tract infection is still challenging and is often achieved in only half of cases by conventional methods. This study was designed to compare the fast responsive PCR method with the culture method in lower respiratory tract infections and to evaluate the reliability of multiplex PCR method. Methods: One hundred ninety seven patients with the symptoms of acute lower respiratory tract infection, and diagnosed with community-acquired pneumonia, acute exacerbation of chronic obstructive pulmonary disease and exacerbations of bronchiectasis were included in the study. Both culture and PCR methods was performed for the isolation of most commonly seen bacteria, from sputum, nasopharyngeal swabs and bronchoalveolar lavage fluid samples. Results: While at least one bacterial isolation was determined in 62 (31.5%) of all patients with culture method, this number increased to 125 (63.5%) with multiplex PCR. The bacteria most commonly identified by PCR were S. pneumoniae (32%) and H. influenzae (31%). There was a significant difference between PCR and culture in terms of multi-factor detection rates (p<0.005). Multiple bacteria were detected in only two cases in cultures; however, multiple pathogens were detected in 47 cases with PCR. Conclusions: Conventional methods, such as culture and serology are not always adequate to detect the pathogens in lower respiratory tract. Real-time PCR assays proved highly sensitive and rapid. The prevalence of bacteria and multiple agent detected by real-time PCR compared with culture was substantially higher. Widespread use of PCR methods, by providing the immediate and appropriate ''agent specific antibiotic treatment'' of LRTI, will help reduce failure and contributes to a reduction in antibiotic resistance.
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Affiliation(s)
- Ozlem Aydemir
- Ozlem Aydemir, Department of Microbiology, Sakarya University, Training and Research Hospital, Sakarya, Turkey
| | - Yusuf Aydemir
- Yusuf Aydemir, Department of Pulmonology, Faculty of Medicine, Sakarya University, Sakarya, Turkey
| | - Mehmet Ozdemir
- Mehmet Ozdemir, Faculty of Medicine, Department of Microbiology, Necmettin Erbakan University, Konya, Turkey
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Cantais A, Mory O, Pillet S, Verhoeven PO, Bonneau J, Patural H, Pozzetto B. Epidemiology and microbiological investigations of community-acquired pneumonia in children admitted at the emergency department of a university hospital. J Clin Virol 2014; 60:402-7. [PMID: 24915939 PMCID: PMC7106426 DOI: 10.1016/j.jcv.2014.05.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 05/02/2014] [Accepted: 05/12/2014] [Indexed: 01/15/2023]
Abstract
Systematic antimicrobials are recommended in community-acquired pneumonia of child. A large panel of bacteria and viruses was detected in 85 children exhibiting CAP. More than 60% of children with CAP exhibited an exclusive viral infection. A co-infection with at least 2 viruses was observed in >40% of the children. Data suggest that the use of antimicrobials in child's CAP should be revisited.
Background The management of children with community-acquired pneumonia (CAP) is largely influenced by the development of new molecular diagnostic tests that allow the simultaneous detection of a wide range of pathogens. Objectives Evaluation of a diagnostic approach including multiplex PCR assays for revisiting the epidemiology and etiology of CAP in children at hospital. Study design Children of all ages consulting at the Emergency Department of the University hospital of Saint-Etienne, France, during the 2012–2013 winter period were included. In addition to bacterial cultures, the following pathogens were detected using biplex commercially-available rt-PCR tests: adenovirus, respiratory syncytial virus, human metapneumovirus, bocavirus, rhinovirus/enterovirus, coronavirus, influenza viruses A and B, parainfluenza viruses, Mycoplasma pneumoniae and Chlamydophila pneumonia. Results From 85 patients with CAP, at least one pathogen was identified in 81 cases (95.3%), including 4 bacterial exclusive infections (4.7%), 53 viral exclusive infections (62.4%) and 24 mixed infections (28.2%). Coinfection by at least two viruses was observed in 37 cases (43.5%). Mean age was higher in the case of documented bacterial infection (P < 0.05). In the subgroup of viral exclusive infection, the mean age of severe cases was 2.0 years vs 3.8 years in mild and moderate cases (P < 0.05). Conclusions These findings highlight the huge proportion of CAP of viral origin, the high number of co-infection by multiple viruses and the low number of bacterial CAP, notably in children under 5 years, and address the need to re-evaluate the indications of empiric antimicrobial treatment in this age group.
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Affiliation(s)
- Aymeric Cantais
- Department of Pediatric Emergency, University-Hospital of Saint-Etienne, CHU de Saint-Etienne, 42055 Saint-Etienne Cedex 02, France
| | - Olivier Mory
- Department of Pediatric Emergency, University-Hospital of Saint-Etienne, CHU de Saint-Etienne, 42055 Saint-Etienne Cedex 02, France
| | - Sylvie Pillet
- Groupe Immunité des Muqueuses et Agents Pathogènes, EA3064, Faculty of Medicine of Saint-Etienne, University of Lyon, 42023 Saint-Etienne Cedex 02, France
| | - Paul O Verhoeven
- Groupe Immunité des Muqueuses et Agents Pathogènes, EA3064, Faculty of Medicine of Saint-Etienne, University of Lyon, 42023 Saint-Etienne Cedex 02, France
| | - Julie Bonneau
- Groupe Immunité des Muqueuses et Agents Pathogènes, EA3064, Faculty of Medicine of Saint-Etienne, University of Lyon, 42023 Saint-Etienne Cedex 02, France
| | - Hugues Patural
- Pediatric Intensive Care Unit, University-Hospital of Saint-Etienne, CHU de Saint Etienne, 42055 Saint-Etienne Cedex 02, France
| | - Bruno Pozzetto
- Groupe Immunité des Muqueuses et Agents Pathogènes, EA3064, Faculty of Medicine of Saint-Etienne, University of Lyon, 42023 Saint-Etienne Cedex 02, France.
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Application of a lateral flow test as an additional serological tool for diagnosis of Legionella infections. J Microbiol Methods 2014; 96:12-5. [DOI: 10.1016/j.mimet.2013.10.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 11/24/2022]
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Pillet S, Lardeux M, Dina J, Grattard F, Verhoeven P, Le Goff J, Vabret A, Pozzetto B. Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections. PLoS One 2013; 8:e72174. [PMID: 24058410 PMCID: PMC3751960 DOI: 10.1371/journal.pone.0072174] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 07/12/2013] [Indexed: 11/26/2022] Open
Abstract
The molecular diagnosis of respiratory infection can be performed using different commercial multiplex-based PCR kits whose performances have been previously compared individually to those of conventional techniques. This study compared the practicability and the diagnostic performances of six CE-marked kits available in 2011 on the French market, including 2 detecting viruses and atypical bacteria (from Pathofinder and Seegene companies) and 4 detecting only viruses (from Abbott, Genomica, Qiagen and Seegene companies). The respective sensitivity, specificity, accuracy and agreement of each multiplex technique were calculated by comparison to commercial duplex PCR tests (Argene/bioMérieux) used as gold standard. Eighty-eight respiratory specimens with no pathogen (n = 11), single infections (n = 33) or co-infections (n = 44) were selected to cover 9 viruses or groups of viruses and 3 atypical bacteria. All samples were extracted using the NUCLISENS® easyMAG™ instrument (bioMérieux). The overall sensitivity ranged from 56.25% to 91.67% for viruses and was below 50% with both tests for bacteria. The overall specificity was excellent (>94% for all pathogens). For each tested kit, the overall agreement with the reference test was strong for viruses (kappa test >0.60) and moderate for bacteria. After the extraction step, the hands-on time varied from 50 min to 2h30 and the complete results were available in 2h30 to 9 h. The spectrum of tested agents and the technology used to reveal the PCR products as well as the laboratory organization are determinant for the selection of a kit.
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Affiliation(s)
- Sylvie Pillet
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Marina Lardeux
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Julia Dina
- Laboratory of Virology, University Hospital of Caen, Caen, France
| | - Florence Grattard
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Paul Verhoeven
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Jérôme Le Goff
- Université Paris Diderot, Sorbonne Paris Cité, Microbiology Department, Saint-Louis Hospital, APHP, Paris, France
| | - Astrid Vabret
- Laboratory of Virology, University Hospital of Caen, Caen, France
| | - Bruno Pozzetto
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
- * E-mail:
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Elargoubi A, Verhoeven P, Grattard F, Stephan JL, Richard O, Pozzetto B. Acute encephalitis associated to a respiratory infection due to Chlamydophila pneumoniae. Med Mal Infect 2013; 43:345-9. [DOI: 10.1016/j.medmal.2013.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 05/25/2013] [Accepted: 06/18/2013] [Indexed: 11/15/2022]
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Two years' performance of an in-house ELISA for diagnosis of Legionnaires' disease: Detection of specific IgM and IgG antibodies against Legionella pneumophila serogroup 1, 3 and 6 in human serum. J Microbiol Methods 2013; 94:94-97. [DOI: 10.1016/j.mimet.2013.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 04/29/2013] [Accepted: 04/30/2013] [Indexed: 11/20/2022]
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Jaton-Ogay K, Bille J. Microbiological diagnosis of community-acquired respiratory tract infections by nucleic acid detection. ACTA ACUST UNITED AC 2013; 2:947-61. [PMID: 23495868 DOI: 10.1517/17530059.2.8.947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Microbiological diagnostic procedures have changed significantly over the last decade. Initially the implementation of the polymerase chain reaction (PCR) resulted in improved detection tests for microbes that were difficult or even impossible to detect by conventional methods such as culture and serology, especially in community-acquired respiratory tract infections (CA-RTI). A further improvement was the development of real-time PCR, which allows end point detection and quantification, and many diagnostic laboratories have now implemented this powerful method. OBJECTIVE At present, new performant and convenient molecular tests have emerged targeting in parallel many viruses and bacteria responsible for lower and/or upper respiratory tract infections. The range of test formats and microbial agents detected is evolving very quickly and the added value of these new tests needs to be studied in terms of better use of antibiotics, better patient management, duration of hospitalization and overall costs. CONCLUSIONS Molecular tools for a better microbial documentation of CA-RTI are now available. Controlled studies are now required to address the relevance issue of these new methods, such as, for example, the role of some newly detected respiratory viruses or of the microbial DNA load in a particular patient at a particular time. The future challenge for molecular diagnosis will be to become easy to handle, highly efficient and cost-effective, delivering rapid results with a direct impact on clinical management.
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Affiliation(s)
- Katia Jaton-Ogay
- Institute of Microbiology, University Hospital Center of Lausanne and University of Lausanne, 1011 Lausanne, Switzerland +41 21 314 40 76 ; +41 21 314 40 60 ;
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Perotin JM, Dury S, Renois F, Deslee G, Wolak A, Duval V, De Champs C, Lebargy F, Andreoletti L. Detection of multiple viral and bacterial infections in acute exacerbation of chronic obstructive pulmonary disease: a pilot prospective study. J Med Virol 2013; 85:866-73. [PMID: 23447038 PMCID: PMC7166408 DOI: 10.1002/jmv.23495] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2012] [Indexed: 01/09/2023]
Abstract
Few studies have evaluated the contribution of multiple virus and bacterial infections in acute exacerbation of chronic obstructive pulmonary disease. This study estimated the burden of multiple viral and bacterial respiratory infections in moderate to very severe chronic obstructive pulmonary disease patients that were prospectively followed-up during a 12-month pilot study. Clinical data were collected monthly and sputum was collected at the time of each acute exacerbation event. Classical culture techniques for bacteria and multiplex polymerase chain reaction (PCR) and microarray detection assays were performed to identify viral and atypical bacterial pathogens in the sputum. Overall, 51 patients were included and 45 acute exacerbation events were investigated clinically and microbiologically. Among the 45 acute exacerbation events, 44% had evidence of viral infection involving human rhinovirus (HRV) and metapneumovirus (hMPV) in 20% and 18%, respectively. Intracellular bacteria were not found in sputum by PCR. Common bacterial pathogens were identified in 42% of acute exacerbation patients, most frequently Branhamella catarrhalis, Streptococcus pneumoniae and Haemophilus influenzae. Viral or virus and bacteria co-infections were detected in 27% of acute exacerbation events (n = 12) with HRV and hMPV involved in 92% of cases. Patients with co-infections did not present greater clinical severity scores at exacerbation and more recurrence of acute exacerbation events at 3 and 6 months than those with single infections (P > 0.4). These results suggest that HRV and hMPV may be contributors or cofactors of AECOPD. These findings indicate that viral or virus and bacterial co-infections do not impact significantly on the clinical severity of acute exacerbation of chronic obstructive pulmonary disease and recurrence at 3 and 6 months.
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Affiliation(s)
- Jeanne-Marie Perotin
- Department of Respiratory Medicine, INSERM UMRS 903, University Hospital of Reims, France.
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He XY, Wang XB, Zhang R, Yuan ZJ, Tan JJ, Peng B, Huang Y, Liu EM, Fu Z, Bao LM, Zou L. Investigation of Mycoplasma pneumoniae infection in pediatric population from 12,025 cases with respiratory infection. Diagn Microbiol Infect Dis 2012; 75:22-7. [PMID: 23040512 DOI: 10.1016/j.diagmicrobio.2012.08.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 08/23/2012] [Accepted: 08/30/2012] [Indexed: 11/25/2022]
Abstract
Although Mycoplasma pneumoniae (MP) is a major pathogen of primary atypical pneumonia in children, the clinical and laboratory characteristics of MP infection in large pediatric population are less reported. Here, we retrospectively analyzed 12,025 hospitalized children with respiratory infection by using serology and polymerase chain reaction (PCR) methods simultaneously. The results showed that 2433 (20.23%) children had MP infection, which mainly occurred in November to April. The presence of sore throat and pharyngitis was peculiar to MP infection. The positive percentage of MP-DNA was higher than that of MP-IgM in children aged <1 (P < 0.0001) and 1-3 years (P < 0.0001). Moreover, the positive rate of P1 gene, the key adhesion gene for MP infection, was higher in children with MP infection than in those with other pathogens (P < 0.0001). Our work provides the clinical information of children MP infection and highlights the superiority of PCR and potential usage of P1 as a diagnosis target for MP infection.
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Affiliation(s)
- Xiao-yan He
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, Chongqing 400014, China
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Waites KB, Xiao L, Paralanov V, Viscardi RM, Glass JI. Molecular methods for the detection of Mycoplasma and ureaplasma infections in humans: a paper from the 2011 William Beaumont Hospital Symposium on molecular pathology. J Mol Diagn 2012; 14:437-50. [PMID: 22819362 PMCID: PMC3427874 DOI: 10.1016/j.jmoldx.2012.06.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 06/12/2012] [Accepted: 06/22/2012] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma and Ureaplasma species are well-known human pathogens responsible for a broad array of inflammatory conditions involving the respiratory and urogenital tracts of neonates, children, and adults. Greater attention is being given to these organisms in diagnostic microbiology, largely as a result of improved methods for their laboratory detection, made possible by powerful molecular-based techniques that can be used for primary detection in clinical specimens. For slow-growing species, such as Mycoplasma pneumoniae and Mycoplasma genitalium, molecular-based detection is the only practical means for rapid microbiological diagnosis. Most molecular-based methods used for detection and characterization of conventional bacteria have been applied to these organisms. A complete genome sequence is available for one or more strains of all of the important human pathogens in the Mycoplasma and Ureaplasma genera. Information gained from genome analyses and improvements in efficiency of DNA sequencing are expected to significantly advance the field of molecular detection and genotyping during the next few years. This review provides a summary and critical review of methods suitable for detection and characterization of mycoplasmas and ureaplasmas of humans, with emphasis on molecular genotypic techniques.
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Affiliation(s)
- Ken B Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35226, USA.
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Xu D, Li S, Chen Z, Du L. Reply to "how to diagnose Mycoplasma pneumoniae etiology in a child with pneumonia". Eur J Pediatr 2012; 171:595-6. [PMID: 22081242 DOI: 10.1007/s00431-011-1594-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 09/21/2011] [Indexed: 10/17/2022]
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Poritz MA, Blaschke AJ, Byington CL, Allen L, Nilsson K, Jones DE, Thatcher SA, Robbins T, Lingenfelter B, Amiott E, Herbener A, Daly J, Dobrowolski SF, Teng DHF, Ririe KM. FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection. PLoS One 2011; 6:e26047. [PMID: 22039434 PMCID: PMC3198457 DOI: 10.1371/journal.pone.0026047] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 09/16/2011] [Indexed: 12/19/2022] Open
Abstract
The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the "FilmArray", which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon.
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Affiliation(s)
- Mark A Poritz
- Idaho Technology, Inc., Salt Lake City, Utah, United States of America.
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Panagariya A, Sharma AK, Dev A, Kankane A, Sharma B, Dubey P. Reversible neurological syndromes with atypical pneumonia. Ann Indian Acad Neurol 2011; 14:127-9. [PMID: 21808478 PMCID: PMC3141478 DOI: 10.4103/0972-2327.82806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 04/02/2010] [Accepted: 07/30/2010] [Indexed: 11/11/2022] Open
Abstract
Simultaneous or sequential involvement of lungs is frequently encountered with neurological syndromes like meningoencephalitis, cerebellitis, aseptic meningitis, transverse myelitis, or multiple cranial nerve palsies. However, pulmonary involvement is frequently overlooked when all the attention of physician is diverted to neurological disorder. Prompt and early recognition of such potentially treatable association is required to improve diagnostic and therapeutic outcome. We report six patients presenting with various neurological manifestations like meningitis, meningoencephalitis, and myelits associated with atypical pneumonia. With proper clinical correlation and relevant investigations, all of them were diagnosed in time and had remarkable recovery with appropriate treatment.
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Affiliation(s)
- Ashok Panagariya
- Department of Neurology, SMS Medical College & Attached Hospitals, Jaipur, Rajashthan, India
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Xu D, Li S, Chen Z, Du L. Detection of Mycoplasma pneumoniae in different respiratory specimens. Eur J Pediatr 2011; 170:851-8. [PMID: 21107602 DOI: 10.1007/s00431-010-1360-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 11/12/2010] [Indexed: 11/26/2022]
Abstract
UNLABELLED Mycoplasma pneumoniae (M. pneumoniae) is an important community-acquired pneumonia pathogen. Serological test and polymerase chain reaction (PCR) assay are the two main laboratory tests to detect M. pneumoniae now. Little information was compared about the sensitivity and specificity of PCR using different specimens including bronchoalveolar lavage (BAL) and nasopharyngeal aspirate (NPA). The aim of the present study was to evaluate diagnostic values of different specimens by fluorescence quantitative real-time PCR and to find clinical features helpful to diagnose M. pneumoniae pneumonia (MPP). Four hundred and six hospitalized pneumonia children were studied. M. pneumoniae DNA in NPA and BAL samples were detected by fluorescence quantitative real-time PCR. M. pneumoniae-specific IgM was tested by ELISA. MPP were diagnosed based on positive M. pneumoniae-specific IgM in 101 (24.9%) children. The median ages of MPP and non-MPP children were 4.1 and 2.4 years, respectively, with significant difference between them (p < 0.001). Laboratory results including leukocyte count, neutrophil percentage, immunoglobulins, except serum IgM, subgroups of T lymphocyte, and BAL cell count had no significant differences in MPP and non-MPP. BAL macrophage cell percentage was lower in BAL-PCR positive children (p = 0.003), while BAL neutrophil percentage was higher in BAL-PCR positive children (p = 0.007). PCR from NPA and BAL were similar in diagnostic parameters, including sensitivity, specificity, PPV, and NPV (78.6%, 63.4%, 39.8%, and 90.6% for NPA-PCR, respectively; 70.3%, 58.7%, 36.0%, and 85.6% for BAL-PCR, respectively). CONCLUSIONS NPA is better than BAL as PCR sample in MPP diagnosis for similar performance in PCR assay, cheap, and less invasive. BAL is useful in defining local inflammatory condition. Age is the only prefigurative factor in MPP.
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Affiliation(s)
- Dan Xu
- Department of Pulmonology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang Province, People's Republic of China
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Elverdal PL, Svarrer CW, Jørgensen CS, Skovsted IC, Uldum SA. Development and validation of ELISA for detection of antibodies to Legionella pneumophila serogroup 1, 3 and 6 in human sera. J Microbiol Methods 2011; 86:298-303. [PMID: 21664386 DOI: 10.1016/j.mimet.2011.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 05/28/2011] [Accepted: 05/29/2011] [Indexed: 11/28/2022]
Abstract
The aim of this study was to determine whether separate measurement of immunoglobulin (Ig) M and G antibodies to Legionella (L.) pneumophila serogroups (sg) 1, 3 and 6 as single antigens can facilitate an early diagnosis of Legionnaires' disease. The developed ELISA was evaluated and compared with an in-house indirect Legionella immunofluorescence antibody test (IFAT) measuring Total Ig. A total of 193 sera from 128 patients with confirmed L. pneumophila infections were used to assess the sensitivity of the developed ELISA. The sensitivity was assessed in different time-periods after onset of symptoms. It was found that the sensitivity of the test increased during the first month of infection, IgM being the most sensitive; ranging from 13% in the first week after onset of symptoms, 45% in the second week to 84% in the third week; in the fourth (and beyond) week a drop to 67% was observed. The IFAT detecting L. pneumophila sg 1-6 had a sensitivity of 11%, 27%, 80% and 59%, respectively, during these time-periods. The test with the lowest sensitivity was the IgG ELISA (0%, 21%, 36% and 52%), but by combining the IgG results with the IgM results, the overall sensitivity of the assay was improved (13%, 48%, 88% and 70%). This study confirms that detection of IgG and IgM antibodies by ELISA is an important diagnostic tool especially during the initial phase of the disease, when supported by other tests like the urinary antigen test, PCR or culture. Furthermore, we showed that the ELISA is suitable for the detection of significant changes in antibody levels in paired serum samples. It was found that the sensitivity was higher for the ELISA assays than for the IFAT. Both the in-house IgM ELISA and the IFAT had a low false positive rate, while a 14% false positive rate was found for the IgG ELISA among serum samples from patients with other infections.
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Affiliation(s)
- Pernille L Elverdal
- Unit of Atypical Pneumonia, Department of Microbiological Surveillance and Research, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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Update on the Detection and Characterization of Bacterial Pathogens by Nucleic Acid Amplification. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Allegra S, Girardot F, Grattard F, Berthelot P, Helbig J, Pozzetto B, Riffard S. Evaluation of an immunomagnetic separation assay in combination with cultivation to improveLegionella pneumophilaserogroup 1 recovery from environmental samples. J Appl Microbiol 2011; 110:952-61. [DOI: 10.1111/j.1365-2672.2011.04955.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zarogoulidis P, Alexandropoulou I, Romanidou G, Konstasntinidis TG, Terzi E, Saridou S, Stefanis A, Zarogoulidis K, Constantinidis TC. Community-acquired pneumonia due to Legionella pneumophila, the utility of PCR, and a review of the antibiotics used. Int J Gen Med 2011; 4:15-9. [PMID: 21403787 PMCID: PMC3056326 DOI: 10.2147/ijgm.s15654] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Introduction There are at least 40 types of Legionella bacteria, half of which are capable of producing disease in humans. The Legionella pneumophila bacterium, the root cause of Legionnaires’ disease, causes 90% of legionellosis cases. Case presentation We describe the case of a 60-year-old woman with a history of diabetes mellitus and arterial hypertension who was admitted to our hospital with fever and symptoms of respiratory infection, diarrhea, and acute renal failure. We used real-time polymerase chain reaction (PCR) to detect L. pneumophila DNA in peripheral blood and serum samples and urine antigen from a patient with pneumonia. Legionella DNA was detected in all two sample species when first collected. Conclusion Since Legionella is a cause of 2% to 15% of all community-acquired pneumonias that require hospitalization, legionellosis should be taken into account in an atypical pulmonary infection and not be forgotten. Moreover, real-time PCR should be considered a useful diagnostic method.
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Affiliation(s)
- Paul Zarogoulidis
- Regional Laboratory of Public Health, East Macedonia-Thrace, Komotini, Greece.
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Loens K, Goossens H, Ieven M. Acute respiratory infection due to Mycoplasma pneumoniae: current status of diagnostic methods. Eur J Clin Microbiol Infect Dis 2010; 29:1055-69. [PMID: 20526788 PMCID: PMC7088226 DOI: 10.1007/s10096-010-0975-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 05/18/2010] [Indexed: 11/30/2022]
Abstract
Because of the absence of well-standardized both in-house and FDA-approved commercially available diagnostic tests, the reliable diagnosis of respiratory infection due to Mycoplasma pneumoniae remains difficult. In addition, no formal external quality assessment schemes which would allow to conclude about the performance of M. pneumoniae diagnostic tests exist. In this review, the current state of knowledge of M. pneumoniae-associated respiratory infections in the context of epidemiological studies published during the past 5 years is discussed, with particular emphasis on the diagnostic strategies used and their impact on results. The role of M. pneumoniae as a cause of respiratory tract infections (RTIs) differs from study to study due to geographical and epidemiological differences, as well as to the application of different diagnostic techniques and criteria used.
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Affiliation(s)
- K Loens
- Department of Microbiology, Vaccine and Infectious Disease Institute (VIDI), University of Antwerp, Antwerp, Belgium.
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Corrêa RDA, Lundgren FLC, Pereira-Silva JL, Frare e Silva RL, Cardoso AP, Lemos ACM, Rossi F, Michel G, Ribeiro L, Cavalcanti MADN, de Figueiredo MRF, Holanda MA, Valery MIBDA, Aidê MA, Chatkin MN, Messeder O, Teixeira PJZ, Martins RLDM, da Rocha RT. Brazilian guidelines for community-acquired pneumonia in immunocompetent adults - 2009. J Bras Pneumol 2010; 35:574-601. [PMID: 19618038 DOI: 10.1590/s1806-37132009000600011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Accepted: 04/23/2009] [Indexed: 01/30/2023] Open
Abstract
Community-acquired pneumonia continues to be the acute infectious disease that has the greatest medical and social impact regarding morbidity and treatment costs. Children and the elderly are more susceptible to severe complications, thereby justifying the fact that the prevention measures adopted have focused on these age brackets. Despite the advances in the knowledge of etiology and physiopathology, as well as the improvement in preliminary clinical and therapeutic methods, various questions merit further investigation. This is due to the clinical, social, demographical and structural diversity, which cannot be fully predicted. Consequently, guidelines are published in order to compile the most recent knowledge in a systematic way and to promote the rational use of that knowledge in medical practice. Therefore, guidelines are not a rigid set of rules that must be followed, but first and foremost a tool to be used in a critical way, bearing in mind the variability of biological and human responses within their individual and social contexts. This document represents the conclusion of a detailed discussion among the members of the Scientific Board and Respiratory Infection Committee of the Brazilian Thoracic Association. The objective of the work group was to present relevant topics in order to update the previous guidelines. We attempted to avoid the repetition of consensual concepts. The principal objective of creating this document was to present a compilation of the recent advances published in the literature and, consequently, to contribute to improving the quality of the medical care provided to immunocompetent adult patients with community-acquired pneumonia.
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Affiliation(s)
- Ricardo de Amorim Corrêa
- Universidade Federal de Minas Gerais - UFMG, Federal University of Minas Gerais - School of Medicine, Belo Horizonte, Brazil
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te Witt R, van Leeuwen WB, van Belkum A. Specific Diagnostic Tests for Atypical Respiratory Tract Pathogens. Infect Dis Clin North Am 2010. [DOI: 10.1016/j.idc.2009.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Carrillo J, Gutiérrez J, García F, Muñoz A, Villegas E, Rojas J, Sorlózano A, Rojas A. Development and evaluation of a multiplex test for the detection of atypical bacterial DNA in community-acquired pneumonia during childhood. Clin Microbiol Infect 2009; 15:473-80. [DOI: 10.1111/j.1469-0691.2009.02711.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Diederen BMW, Van Der Eerden MM, Vlaspolder F, Boersma WG, Kluytmans JAJW, Peeters MF. Detection of respiratory viruses and Legionella spp. by real-time polymerase chain reaction in patients with community acquired pneumonia. ACTA ACUST UNITED AC 2009; 41:45-50. [PMID: 18821175 DOI: 10.1080/00365540802448799] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We conducted a study on throat swabs obtained from a group of hospitalized patients with community acquired pneumonia (CAP). Throat swab specimens from 242 adults admitted to hospital with CAP were tested. In total, 1 or more aetiological agents were identified by real-time PCR in 55 (23%) patients. The most frequently detected pathogens were coronavirus (17%), parainfluenza virus (6%) and influenza virus (4%). Overall, viral pathogens were identified by conventional techniques in 7 (2%) patients, and real-time PCR in 50 (21%) patients (p<0.0001). The diagnostic yield increased from 137 cases (57% of patients using conventional microbiological assays) to 158 cases (65% of patients using real-time PCR assays and conventional microbiological assays; p=0.06). A significantly higher percentage of mortality was present in patients with a mixed bacterial and viral infection. L. pneumophila PCR was positive in only 3 out of 11 cases (27%) of Legionnaires' disease (LD). This study demonstrates that real-time PCR can increase the number of microbiological detections of respiratory pathogens, mainly as a result of detection of respiratory viruses.
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Affiliation(s)
- Bram M W Diederen
- Regional Laboratory of Public Health Haarlem, Haarlem, Haarlem, The Netherlands.
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29
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Higgins RR, Lombos E, Tang P, Rohoman K, Maki A, Brown S, Jamieson F, Drews SJ. Verification of the ProPneumo-1 assay for the simultaneous detection of Mycoplasma pneumoniae and Chlamydophila pneumoniae in clinical respiratory specimens. Ann Clin Microbiol Antimicrob 2009; 8:10. [PMID: 19284712 PMCID: PMC2655279 DOI: 10.1186/1476-0711-8-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 03/10/2009] [Indexed: 11/23/2022] Open
Abstract
Background Mycoplasma pneumoniae and Chlamydophila pneumoniae are major causes of lower and upper respiratory infections that are difficult to diagnose using conventional methods such as culture. The ProPneumo-1 (Prodesse, Waukesha, WI) assay is a commercial multiplex real-time PCR assay for the simultaneous detection of M. pneumoniae and/or C. pneumoniae DNA in clinical respiratory samples. Objective The aim of this study was to evaluate the sensitivity and specificity of the ProPneumo-1, a newly developed commercial multiplex real-time PCR assay. Methods A total of 146 clinical respiratory specimens, collected from 1997 to 2007, suspected of C. pneumoniae or M. pneumoniae infections were tested retrospectively. Nucleic acid was extracted using an automated NucliSense easyMag (bioMerieux, Netherlands). We used a "Home-brew" monoplex real-time assay as the reference method for the analysis of C. pneumoniae and culture as the reference method for the analysis of M. pneumoniae. For discordant analysis specimens were re-tested using another commercial multiplex PCR, the PneumoBacter-1 assay (Seegene, Korea). Results Following discordant analysis, the sensitivity of the ProPneumo-1 assay for pathogens, C. pneumoniae or M. pneumoniae, was 100%. The specificity of the ProPneumo-1 assay, however, was 100% for C. pneumoniae and 98% for M. pneumoniae. The limits of detection were 1 genome equivalent (Geq) per reaction for pathogens, M. pneumoniae and C. pneumoniae. Due to the multipex format of the ProPneumo-1 assay, we identified 5 additional positive specimens, 2 C. pneumoniae in the M. pneumoniae-negative pool and 3 M. pneumoniae in the C. pneumoniae-negative pool. Conclusion The ProPneumo-1 assay is a rapid, sensitive and effective method for the simultaneous detection of M. pneumoniae and C. pneumoniae directly in respiratory specimens.
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Affiliation(s)
- Rachel R Higgins
- Ontario Public Health Laboratories, Ministry of Health and Long-Term Care, Toronto, Ontario, Canada.
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Evaluation of a nested-PCR-derived sequence-based typing method applied directly to respiratory samples from patients with Legionnaires' disease. J Clin Microbiol 2009; 47:981-7. [PMID: 19225096 DOI: 10.1128/jcm.02071-08] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence-based typing (SBT) is a powerful method based on the sequencing of seven genes of Legionella pneumophila isolates. SBT performed directly on clinical samples has been used only in a limited number of cases. In our study, its efficiency was tested with 63 legionellosis respiratory samples. Sixty-three clinical samples, which included 23 samples from sporadic cases and 40 collected during four French outbreaks, confirmed by culture or urinary antigen testing and all positive by L. pneumophila quantitative PCR were subtyped by SBT according to the European Working Group for Legionella Infections standard scheme. Only 28.6% of the samples provided nucleotide sequences by SBT. Nested-PCR-based SBT (NPSBT) applied to the same respiratory samples was thus evaluated with new PCR primers surrounding the first set of primers used for the SBT. Sequencing results were obtained with 90.5% of the samples. Complete allelic profiles (seven genes sequenced) were obtained for 3.2% versus 53.9% of the samples by SBT and NPSBT, respectively. More importantly, of the 28 culture-negative samples, only 4 did not give any sequencing results. Taken together, NPSBT applied directly to clinical specimens significantly improved epidemiological typing compared to the initial SBT, in particular when no isolates are available.
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Abstract
Objectifs Depuis les dix dernières années, l’introduction de la biologie moléculaire et l’automatisation ont radicalement changé les pratiques dans les laboratoires de microbiologie clinique. L’amélioration de la communication entre les microbiologistes et les cliniciens ainsi que les évolutions technologiques telles que la standardisation et le développement de tests diagnostics plus rapides ont conduit à une réorganisation des laboratoires de microbiologie. Méthodes Jusqu’à présent la prescription des examens ciblait un diagnostic étiologique précis, actuellement l’évolution se fait vers le diagnostic par syndrome incluant un panel de tests regroupant les étiologies responsables d’un syndrome donné y compris les pathogènes émergents. Résultats et conclusions Dans cette revue, nous avons résumé les développements technologiques les plus récents en matière de diagnostic microbiologique adapté au diagnostic par syndrome incluant les stratégies de diagnostic exhaustif, les DNA microarray et les microarray antigéniques.
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Nolte FS. Molecular diagnostics for detection of bacterial and viral pathogens in community-acquired pneumonia. Clin Infect Dis 2008; 47 Suppl 3:S123-6. [PMID: 18986277 PMCID: PMC7107880 DOI: 10.1086/591392] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Traditional microbiological methods for detection of respiratory tract pathogens can be slow, are often not sensitive, may not distinguish infection from colonization, and are influenced by previous antibiotic therapy. Molecular diagnostic tests for common and atypical causative pathogens of community-acquired pneumonia have the potential to dramatically increase the diagnostic yield and decrease the time required to render results. Unfortunately, these tests often lack standardization and are not widely available. Consideration should be given to the development and evaluation of companion molecular diagnostic tests for detection of respiratory pathogens in future clinical trials of antimicrobials intended to treat community-acquired pneumonia.
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Affiliation(s)
- Frederick S Nolte
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston 29425-9080, USA.
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Atkinson TP, Balish MF, Waites KB. Epidemiology, clinical manifestations, pathogenesis and laboratory detection of Mycoplasma pneumoniae infections. FEMS Microbiol Rev 2008; 32:956-73. [PMID: 18754792 DOI: 10.1111/j.1574-6976.2008.00129.x] [Citation(s) in RCA: 313] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Since its initial description in the 1940s and eventual elucidation as a highly evolved pathogenic bacterium, Mycoplasma pneumoniae has come to be recognized as a worldwide cause of primary atypical pneumonia. Beyond its ability to cause severe lower respiratory illness and milder upper respiratory symptoms it has become apparent that a wide array of extrapulmonary infectious and postinfectious events may accompany the infections in humans caused by this organism. Autoimmune disorders and chronic diseases such as asthma and arthritis are increasingly being associated with this mycoplasma, which frequently persists in individuals for prolonged periods. The reductive evolutionary process that has led to the minimal genome of M. pneumoniae suggests that it exists as a highly specialized parasitic bacterium capable of residing in an intracellular state within the respiratory tissues, occasionally emerging to produce symptoms. This review includes discussion of some of the newer aspects of our knowledge on this pathogen, characteristics of clinical infections, how it causes disease, the recent emergence of macrolide resistance, and the status of laboratory diagnostic methods.
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Utility of real-time PCR for diagnosis of Legionnaires' disease in routine clinical practice. J Clin Microbiol 2007; 46:671-7. [PMID: 18094136 DOI: 10.1128/jcm.01196-07] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The main aim of our study was to determine the added value of PCR for the diagnosis of Legionnaires' disease (LD) in routine clinical practice. The specimens were samples submitted for routine diagnosis of pneumonia from December 2002 to November 2005. Patients were evaluated if, in addition to PCR, the results of at least one of the following diagnostic tests were available: (i) culture for Legionella spp. on buffered charcoal yeast extract agar or (ii) detection of Legionella pneumophila antigen in urine specimens. Of the 151 evaluated patients, 37 (25%) fulfilled the European Working Group on Legionella Infections criteria for a confirmed case of LD (the "gold standard"). An estimated sensitivity, specificity, and overall percent agreement of 86% (32 of 37; 95% confidence interval [CI] = 72 to 95%), 95% (107 of 112; 95% CI = 90 to 98%), and 93% (139 of 149), respectively, were found for 16S rRNA-based PCR, and corresponding values of 92% (34 of 37; 95% CI = 78 to 98%), 98% (110 of 112; 95% CI = 93 to 100%), and 97% (144 of 149), respectively, were found for the mip gene-based PCR. A total of 35 patients were diagnosed by using the urinary antigen test, and 34 were diagnosed by the 16S rRNA-based PCR. With the mip gene PCR one more case of LD (n = 36; not significant) was detected. By combining urinary antigen test and the mip gene PCR, LD was diagnosed in an additional 4 (11%) patients versus the use of the urinary antigen test alone. The addition of a L. pneumophila-specific mip gene PCR to a urinary antigen test is useful in patients with suspected LD who produce sputum and might allow the early detection of a significant number of additional patients.
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Epidemiological, molecular, and clinical features of enterovirus respiratory infections in French children between 1999 and 2005. J Clin Microbiol 2007; 46:206-13. [PMID: 18003804 DOI: 10.1128/jcm.01414-07] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enteroviruses (EVs) can induce nonspecific respiratory tract infections in children, but their epidemiological, virological, and clinical features remain to be assessed. In the present study, we analyzed 252 EV-related infection cases (median age of subjects, 5.1 years) diagnosed among 11,509 consecutive children visiting emergency departments within a 7-year period in the north of France. EV strains were isolated from nasopharyngeal samples by viral cell culture, identified by seroneutralization assay, and genetically compared by partial amplification and sequencing of the VP1 gene. The respiratory syndromes (79 [31%] of 252 EV infections) appeared as the second most common EV-induced pediatric pathology after meningitis (111 [44%] of 252 cases) (44 versus 31%, P < 10(-3)), contributing to lower respiratory tract infection (LRTI) in 43 (54%) of 79 EV respiratory infection cases. Bronchiolitis was the most common EV-induced LRTI (34 [43%] of 79 cases, P < 10(-3)) occurring more often in infants aged 1 to 12 months (P = 0.0002), with spring-fall seasonality. Viruses ECHO 11, 6, and 13 were the more frequently identified respiratory strains (24, 13, and 11%, respectively). The VP1 gene phylogenetic analysis showed the concomitant or successive circulation of genetically distinct EV respiratory strains (species A or B) during the same month or annual epidemic period. Our findings indicated that respiratory tract infections accounted for the 30% of EV-induced pediatric pathologies, contributing to LRTIs in 54% of these cases. Moreover, the concomitant or successive circulation of genetically distinct EV strains indicated the possibility of pediatric repeated respiratory infections within the same epidemic season.
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Elverdal P, Jørgensen CS, Uldum SA. Comparison and evaluation of four commercial kits relative to an in-house immunofluorescence test for detection of antibodies against Legionella pneumophila. Eur J Clin Microbiol Infect Dis 2007; 27:149-52. [DOI: 10.1007/s10096-007-0410-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 10/12/2007] [Indexed: 10/22/2022]
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Diederen BMW. Legionella spp. and Legionnaires' disease. J Infect 2007; 56:1-12. [PMID: 17980914 DOI: 10.1016/j.jinf.2007.09.010] [Citation(s) in RCA: 262] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 09/18/2007] [Accepted: 09/19/2007] [Indexed: 11/24/2022]
Abstract
Infection with Legionella spp. is an important cause of community- and hospital-acquired pneumonia, occurring both sporadically and in outbreaks. Infection with Legionella spp. ranks among the three most common causes of severe pneumonia in the community setting, and is isolated in 1-40% of cases of hospital-acquired pneumonia. There are no clinical features unique to Legionnaires' disease. Macrolides and fluoroquinolones are the most widely used drugs in treatment. The availability of a good diagnostic repertoire, suitable for accurately diagnosing LD, constitutes the basis for the early recognition and treatment of the individual patient as well as for effective measures for prevention and control. This review summarizes the available information regarding the microbiology, clinical presentation, diagnosis and treatment of LD, with an emphasis on the laboratory diagnosis of infection with Legionella spp.
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Affiliation(s)
- B M W Diederen
- Regional Laboratory of Public Health Haarlem, Boerhaavelaan 26, 2035 RC Haarlem, The Netherlands.
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Ieven M. Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections. J Clin Virol 2007; 40:259-76. [PMID: 17977063 PMCID: PMC7108459 DOI: 10.1016/j.jcv.2007.08.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 08/20/2007] [Indexed: 12/03/2022]
Abstract
For the detection of respiratory viruses conventional culture techniques are still considered as the gold standard. However, results are mostly available too late to have an impact on patient management. The latest developments include appropriate DNA- and RNA-based amplification techniques (both NASBA and PCR) for the detection of an extended number of agents responsible for LRTI. Real time amplification, the latest technical progress, produces, within a considerable shorter time, results with a lower risk of false positives. As results can be obtained within the same day, patient management with appropriate therapy or reduction of unnecessary antibiotic therapy in LRTI will be possible. A number of technical aspects of these amplification assays, and their advantages are discussed. The availability and use of these new diagnostic tools in virology has contributed to a better understanding of the role of respiratory viruses in LRTI. The increasing importance of the viral agents, Mycoplasma pneumoniae and Chlamydophila pneumoniae in ARI is illustrated. A great proportion of ARI are caused by viruses, but their relative importance depends on the spectrum of agents covered by the diagnostic techniques and on the populations studied, the geographical location and the season. The discovery of new viruses is ongoing; examples are the hMPV and the increasing number of coronaviruses. Indications for the use of these rapid techniques in different clinical situations are discussed. Depending on the possibilities, the laboratory could optimize its diagnostic strategy by applying a combination of immunofluorescence for the detection of RSV an IFL, and a combination of real-time amplification tests for other respiratory viruses and the atypical agents. When implementing a strategy, a compromise between sensitivity, clinical utility, turn around time and cost will have to be found.
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Affiliation(s)
- Margareta Ieven
- Laboratory for Microbiology, Vaccine & Infectious Disease Institute (VIDI), University Hospital Antwerp, University of Antwerp, Wilrijkstraat 10, B-2650 Edegem, Belgium.
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Rodríguez Vidigal FF, Vera Tomé A, Muñoz Sanz A. Chlamydophila pneumoniae, un posible agente causal del síndrome mononucleósico. Med Clin (Barc) 2007; 129:156. [PMID: 17663971 DOI: 10.1157/13107494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Legionnaires’ Disease. INFECTIOUS DISEASES IN CRITICAL CARE 2007. [PMCID: PMC7122631 DOI: 10.1007/978-3-540-34406-3_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The incidence of legionnaires’ disease (LD) seems to increase with age, particularly in males [36]. It was considered an infrequent cause of pneumonia in the past, but it currently ranks second to pneumococcus in the list of etiologic agents of severe community-acquired pneumonia (CAP) of bacterial origin [2, 24, 60, 89]. Considering less severe cases, in a series of 145 pneumonias in which BCYE culture, serology and the Legionella urinary antigen (LUA) test were systematically applied, Vergis et al. [91] reported a prevalence of LD of 13.7%. In another series of 392 adult patients with CAP treated in a university hospital, Sopena et al. found a prevalence of 12.5%, and LD was the second cause of pneumonia [83].
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Honderlick P, Philippe B, Picard C, Thaler F, Couderc LJ. [Simultaneous detection by multiplex PCR of atypical bacterial pathogens involved in infections of respiratory tract. Is it useful for the microbiological diagnosis of respiratory infections]. PATHOLOGIE-BIOLOGIE 2006; 54:467-9. [PMID: 17027196 DOI: 10.1016/j.patbio.2006.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 07/21/2006] [Indexed: 05/12/2023]
Abstract
The aim was to evaluate the "strategical place" of the new commercial test Chlamylege (Argene-Biosoft-France) which allows the simultaneous detection in respiratory samples of Chlamydophila pneumoniae, Mycoplasma pneumoniae and most Legionella species using a PCR multiplex. 41 patients with an atypical pneumonia were included, all standard procedures of diagnosis were done and in addition the chamylege test. A pathogen was identified in 12 patients, an other microorganisms than the 3 targeted by our study was found in 8 patients. 4 positive PCR were obtained, 3 with M. pneumoniae and 1 with Legionella pneumophila 1. That means that for 29 patients no aetiology was found. Among them 23 clearly improved under antibiotic treatment. Though that PCR multiplex is an attractive test, easy to perform, sensitive, specific and convenient, we need further studies to approach the place of this PCR test in the diagnosis of multifaceted atypical pneumonia. We also need to know if the cost associated with the microbiological diagnosis (culture, serology, immunofluorescence, urinary antigen test, PCR...) for atypical pneumonia worth value? An algorithm as to be drawn to determine the value of intensive microbiological investigation. An other point to discuss, may be this kind of rapid and multiplex PCR technique could lead to spare the use of some antibiotics.
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Affiliation(s)
- P Honderlick
- Service de microbiologie, hôpital Foch, 40, rue Worth, 92150 Suresnes cedex, France.
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Abstract
PURPOSE OF REVIEW Mycoplasma pneumoniae is associated with a wide range of central nervous system diseases, most importantly with childhood encephalitis. This review summarizes and discusses recent findings in the field of M. pneumoniae central nervous system infections in context with previously published findings, with reference to clinical spectrum, pathogenesis, diagnosis, and treatment. RECENT FINDINGS Further insight into the pathogenesis has been provided by studies on cytokine production and autoantibody formation. Some new manifestations have been described (e.g. Kluver-Bucy syndrome, intracranial hypertension). Anecdotal descriptions on the association of M. pneumoniae with uncommon neurologic diseases remain to be confirmed by additional reports, however, especially when aetiologic diagnosis relied exclusively on serology. New knowledge on treatment options targeting the immune system has been provided by isolated reports. Recent diagnostic advances refer to general methods (polymerase chain reaction, serology), without specific reference to neurologic disease. SUMMARY M. pneumoniae must be considered as causative agent of various neurologic diseases. The recent literature shows, however, that the clinical spectrum of M. pneumoniae central nervous system disease is still not well defined. In addition, the main future challenges are the investigation of the pathogenesis of M. pneumoniae central nervous system disease and the establishment of therapeutic approaches.
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Affiliation(s)
- Florian Daxboeck
- Clinical Institute for Hygiene and Medical Microbiology, Division of Hospital Hygiene, Medical University Vienna, Vienna General Hospital, Vienna, Austria.
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Murdoch DR. Impact of rapid microbiological testing on the management of lower respiratory tract infection. Clin Infect Dis 2005; 41:1445-7. [PMID: 16231255 DOI: 10.1086/497145] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 07/20/2005] [Indexed: 11/03/2022] Open
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