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Tjoa E, Joon S, Moehario LH, Loe L, Pangalila FJV. Identification of Mycoplasma pneumoniae-associated pneumonia cases among hospitalized patients using CLART® microarray technology. J Int Med Res 2022; 50:3000605221123678. [PMID: 36171729 PMCID: PMC9523878 DOI: 10.1177/03000605221123678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Objectives Community-acquired pneumonia (CAP) is a global health condition that affects populations from all age groups. The laboratory identification of Mycoplasma pneumoniae as a causative agent of CAP is challenging because of its atypical and fastidious nature. Therefore, this study assessed the diagnostic potential of PneumoCLART bacteria® in identifying M. pneumoniae as a causative agent of pneumonia in hospitalized adults. Methods This prospective study used a cross-sectional approach to assess the diagnostic potential of PneumoCLART bacteria® for detecting M. pneumoniae in sputum samples procured from 27 patients with pneumonia who required hospitalization. Results The PneumoCLART bacteria® results illustrated that 7 of 27 patients with pneumonia were positive for M. pneumoniae (26%). However, the quality of sputum varied among the M. pneumoniae-positive and M. pneumoniae-negative samples. Fifty percent of the specimens obtained from patients positive for M. pneumoniae were saliva-contaminated and unsuitable for analysis. Conclusions Because the leukocyte count was low and sputum specimens were saliva-contaminated, these findings require further validation to prove the utility of CLART® microarray technology for the identification of M. pneumoniae in pneumonia-positive patients. Conclusively, this prospective study included a small number of clinical samples, which likely affected its outcomes.
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Affiliation(s)
- Enty Tjoa
- Department of Microbiology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Shikha Joon
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Lucky Hartati Moehario
- Department of Microbiology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Luse Loe
- Department of Internal Medicine, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Franz J V Pangalila
- Internal Medicine Department, Faculty of Medicine, Universitas Tarumanagara (UNTAR), Jakarta, Indonesia
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2
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Yadav RK, Kumar D, Singh A, Ziauddin M, Singh DK. Clinical and microbial spectrum of community-acquired pneumonia in children of north India. Trop Doct 2020; 51:71-77. [PMID: 33236693 DOI: 10.1177/0049475520971595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We compared the clinical, radiological and microbial profile in children suffering from community-acquired pneumonia in rural populations of north India. A total of 125 such children were divided into two age groups of 2-12 months (Group A) and 13-60 months (Group B). After taking a history and clinical examination, routine investigations including full blood count, blood, urine, and nasopharyngeal swab culture and radiology were performed. Multiplex polymerase chain reaction for Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydia pneumoniae and Haemophilus influenzae was carried out. Failure to eat or drink was more common (40.9%) in Group A, than Group B (18.7%). Lung consolidation was more common in Group B. Blood and urine culture were found to be more positive in Group A while combined nasopharyngeal culture and multiplex polymerase chain reaction favoured more bacterial growth in Group B.
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Affiliation(s)
- Rajesh Kumar Yadav
- Professor and Head, Department of Pediatrics, Uttar Pradesh University of Medical Sciences, Etawah, India
| | - Dinesh Kumar
- Associate Professor, Department of Pediatrics, Uttar Pradesh University of Medical Sciences, Etawah, India
| | - Amit Singh
- Professor, Department of Microbiology, Uttar Pradesh University of Medical Sciences, Etawah, India
| | - Mohd Ziauddin
- Assistant Professor, Department of Pediatrics, Hind Institute of Medical Science, Sitapur, India
| | - Dinesh Kumar Singh
- Professor, Department of Pediatrics, FH Medical College and Hospital, Firozabad, India
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3
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Dong Q, Shi W, Cheng X, Chen C, Meng Q, Yao K, Qian S. Widespread of non-typeable Haemophilus influenzae with high genetic diversity after two decades use of Hib vaccine in China. J Clin Lab Anal 2019; 34:e23145. [PMID: 31846125 PMCID: PMC7171301 DOI: 10.1002/jcla.23145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The aim of this study was to analyze the microbiological characteristics of nasopharyngeal carriage Haemophilus influenzae isolates collected from children with respiratory infections in Beijing hospital and Youyang Hospital of China. METHODS The serotypes of all isolates were determined using latex agglutinated antisera (a-f). The minimum inhibitory concentrations (MICs) of 11 antibiotics were determined using E-test strips. For the beta-lactamase-negative ampicillin-resistant (BLNAR) isolates, ftsI gene was sequenced based on fragments amplified by PCR. STs of H influenzae isolates were determined by multi-locus sequence typing. RESULTS The overall carriage rate of H influenzae in the study population was 9.1% (362/3984). One hundred and ninety H influenzae isolates which were selected in our study were non-typeable (NTHi) and 44 (23.2%) of them were positive for β-lactamase. All isolates were susceptible to ceftriaxone and levofloxacin. Susceptibility rates to erythromycin and sulfamethoxazole-trimethoprim in Beijing were significantly higher than Youyang (P < .05). Thirty-six BLNAR isolates were identified. The MLST analysis showed 108 STs in 190 isolates, the most common of which were ST408 (11, 5.8%), ST914 (10, 5.3%), ST57 (9, 4.7%), and ST834 (6, 3.2%). Twelve STs were detected in both of the study sites, which covered 63 isolates. CONCLUSIONS All isolates in the present study were NTHi, which suggested widespread of this type in China. The BLNAR isolates were detected more frequently than before. Because high genetic diversity of NTHi isolates of H influenzae exists worldwide, it is important to continuously monitor these bacteria in the future.
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Affiliation(s)
- Qiaoli Dong
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, Beijing, China.,Department of Pediatrics, Affiliated Hospital of Hebei University, Baoding, China
| | - Wei Shi
- Key Laboratory of Major Diseases in Children, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xiaoping Cheng
- Youyang Hospital, People's Hospital of Chongqing Youyang County, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Changhui Chen
- Youyang Hospital, People's Hospital of Chongqing Youyang County, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinghong Meng
- Key Laboratory of Major Diseases in Children, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Kaihu Yao
- Key Laboratory of Major Diseases in Children, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, Beijing, China
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4
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A method to identify respiratory virus infections in clinical samples using next-generation sequencing. Sci Rep 2019; 9:2606. [PMID: 30796243 PMCID: PMC6384955 DOI: 10.1038/s41598-018-37483-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 11/26/2018] [Indexed: 12/30/2022] Open
Abstract
Respiratory virus infections are very common. Such infections impose an enormous economic burden and occasionally lead to death. Furthermore, every few decades, respiratory virus pandemics emerge, putting the entire world population at risk. Thus, there is an urgent need to quickly and precisely identify the infecting agent in a clinical setting. However, in many patients with influenza-like symptoms (ILS) the identity of the underlying pathogen remains unknown. In addition, it takes time and effort to individually identify the virus responsible for the ILS. Here, we present a new next-generation sequencing (NGS)-based method that enables rapid and robust identification of pathogens in a pool of clinical samples without the need for specific primers. The method is aimed at rapidly uncovering a potentially common pathogen affecting many samples with an unidentified source of disease.
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5
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van Schaik ML, Duijkers R, Paternotte N, Jansen R, Rozemeijer W, van der Reijden WA, Boersma WG. Feasibility of a quantitative polymerase chain reaction assay for diagnosing pneumococcal pneumonia using oropharyngeal swabs. Mol Biol Rep 2019; 46:1013-1021. [PMID: 30569391 PMCID: PMC7089193 DOI: 10.1007/s11033-018-4558-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/06/2018] [Indexed: 11/30/2022]
Abstract
Streptococcus pneumoniae is the most important pathogen causing community-acquired pneumonia (CAP). The current diagnostic microbial standard detects S. pneumoniae in less than 30% of CAP cases. A quantitative polymerase chain reaction (PCR) targeting autolysin (lytA) is able to increase the rate of detection. The aim of this study is validation of this quantitative PCR in vitro using different available strains and in vivo using clinical samples (oropharyngeal swabs). The PCR autolysin (lytA) was validated by testing the intra- and inter-run variability. Also, the in vitro specificity and sensitivity, including the lower limit of detection was determined. In addition, a pilot-study was performed using samples from patients (n = 28) with pneumococcal pneumonia and patients (n = 28) with a pneumonia without detection of S. pneumoniae with the current diagnostic microbial standard, but with detection of either a viral and or another bacterial pathogen to validate this test further. The intra- and inter-run variability were relatively low (SD's ranging from 0.08 to 0.96 cycle thresholds). The lower limit of detection turned out to be 1-10 DNA copies/reaction. In-vitro sensitivity and specificity of the tested specimens (8 strains carrying lytA and 6 strains negative for lytA) were both 100%. In patients with pneumococcal and non-pneumococcal pneumonia a cut-off value of 6.000 copies/mL would lead to a sensitivity of 57.1% and a specificity of 85.7%. We were able to develop a quantitative PCR targeting lytA with good in-vitro test characteristics.
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Affiliation(s)
- M L van Schaik
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
- Department of Pulmonology, Isala clinics Zwolle, Dr. van Heesweg 2, 8025AB, Zwolle, The Netherlands
| | - R Duijkers
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - N Paternotte
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - R Jansen
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
| | - W Rozemeijer
- Department Medical Microbiology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - W A van der Reijden
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
| | - W G Boersma
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands.
- Department of Pulmonary Diseases, Northwest Hospital Group, P.O. Box 501, 1800AM, Alkmaar, The Netherlands.
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6
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Bayraç AT, Donmez SI. Selection of DNA aptamers to Streptococcus pneumonia and fabrication of graphene oxide based fluorescent assay. Anal Biochem 2018; 556:91-98. [PMID: 29964028 DOI: 10.1016/j.ab.2018.06.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/23/2018] [Accepted: 06/25/2018] [Indexed: 10/28/2022]
Abstract
Pneumococci are one of the leading causes of infections throughout the world causing problems mainly in children, elderly, and immune-deficient patients. In recent years antibiotic resistant Streptococcus pneumoniae strains become widespread. Therefore simple, rapid, and specific detection methods are needed for public health. In this study, DNA aptamer probes against S. pneumoniae were selected using bacterial Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and these probes were integrated in to a graphene oxide (GO) based fluorescent assay. Among the tested aptamers three candidates Lyd-1, Lyd-2 and Lyd-3 showed Kd values of 844.7 ± 123.6, 1984.8 ± 347.5, and 661.8 ± 111.3 nM, respectively. These candidates showed binding affinity to S. pneumoniae and no specific binding to the bacteria used in negative selection. The binding of aptamers were showed by fluorescence spectroscopy and flow cytometry. GO based label-free fluorescent assay developed using Lyd-3 aptamer had a unique detection limit of 15 cfu mL-1. Thus we believe that the selected aptamers and fabricated GO based assay has potential to be used in the detection of S. pneumoniae. Selected aptamers selectively bind to S. pneumonia with anti-pneumococcal potential and holds great potential to be used as molecular probes for identifying and targeting.
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Affiliation(s)
- Abdullah Tahir Bayraç
- Department of Bioengineering, Karamanoglu Mehmetbey University, Yunus Emre Campus, 70100 Karaman, Turkey.
| | - Sultan Ilayda Donmez
- Department of Bioengineering, Karamanoglu Mehmetbey University, Yunus Emre Campus, 70100 Karaman, Turkey
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7
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Zheng Y, Chen H, Yao M, Li X. Bacterial pathogens were detected from human exhaled breath using a novel protocol. JOURNAL OF AEROSOL SCIENCE 2018; 117:224-234. [PMID: 32226119 PMCID: PMC7094568 DOI: 10.1016/j.jaerosci.2017.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/16/2017] [Accepted: 12/21/2017] [Indexed: 05/21/2023]
Abstract
It is generally believed that influenza outbreak is associated with breath-borne transmission of viruses, however relevant evidence is little for that of respiratory bacterial infections. On another front, point-of-care infection diagnostic methods at the bedside are significantly lacking. Here, we used a newly developed protocol of integrating an exhaled breath condensate (EBC) collection device (PKU BioScreen) and Loop Mediated Isothermal Amplification (LAMP) to investigate what bacterial pathogens can be directly exhaled out from humans. Exhaled breath condensates were collected from human subjects with respiratory infection symptoms at Peking University 3rd hospital using the BioScreen. The screened bacterial pathogens included Streptococcus pneumoniae, Staphylococcus aureus, Methicillin-resistant Stphylococcus aureus (MRSA), Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia, Haemophilus influenzae, Legionella pneumophila, Mycoplasma Pneumonia, Chlamydia pneumonia, and Mycobacterium tuberculosis. The results were further compared and validated using throat swabs from the same patients by a PCR method. Here, human bacterial pathogens such as H. influenzae, P. aeruginosa, E. coli, S. aureus and MRSA were detected in exhaled breath using the developed protocol that integrates the EBC collection and LAMP. For the patients recruited from the hospital, seven types of pathogens were detected from 36.5% of them, and for the remaining subjects none of those screened bacterial pathogens was detected. Importantly, some super resistant bacteria such as MRSA were detected from the exhaled breath, suggesting that breathing might be also an important bacterial transmission route. Results from throat swabs showed that 36.2% of the subjects were found to be infected with H. influenzae, P. aeruginosa, E. coli, S. maltophilia, S. aureus and MRSA. For the EBC samples, 33.3% were found to be infected with MRSA, E. coli and P. aeruginosa. Depending on the initial pathogen load in the sample, the entire protocol (EBC-LAMP) only takes 20-60 min to complete for a respiratory infection diagnosis. For different detection methods and pathogens, the agreements between the EBC and throat swabs from the same patients were found to range from 35% to 65%. Here, we have detected several bacterial pathogens including MRSA from exhaled breath, and the developed protocol could be very useful for the bedside pathogen screening particularly in remote areas where resources are significantly limited or prohibited.
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Affiliation(s)
- Yunhao Zheng
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Haoxuan Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiaoguang Li
- Department of Infectious Diseases, Peking University Third Hospital, Peking University, Beijing 100191, China
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8
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Cleland G, Leung C, Wan Sai Cheong J, Francis J, Heney C, Nourse C. Paediatric invasive Haemophilus influenzae in Queensland, Australia, 2002-2011: Young Indigenous children remain at highest risk. J Paediatr Child Health 2018; 54:36-41. [PMID: 28871608 DOI: 10.1111/jpc.13662] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 05/26/2017] [Accepted: 06/20/2017] [Indexed: 11/27/2022]
Abstract
AIM Haemophilus influenzae continues to cause invasive disease in children despite widespread Hib immunisation. The significance of non-B serotypes continues to be investigated, with evidence of increased invasive non-typeable H. influenzae (NTHi) world-wide. The aim of this study was to examine the current epidemiological and clinical features of invasive H. influenzae disease in children in Queensland, Australia. METHODS A retrospective review was performed of all cases of invasive H. influenzae disease in children <18 years of age in Queensland between January 2002 and December 2011. Cases were identified from pathology records and data requested from treating hospitals. RESULTS Laboratory data were obtained for 144 cases and clinical/demographic data for 123 cases. The majority (72%) of cases were children <5 years of age. Annual incidence rate for all children <5 years was 7.4/100 000, and for Aboriginal and Torres Strait Islander children <5 years was 10.2/100 000. Serotype was reported for 132 isolates, 69 NTHi and 63 encapsulated strains. The most common clinical diagnoses were pneumonia, meningitis and bacteraemia without clinical focus. Of the patients, 5 patients died, and 12 had significant morbidity at hospital discharge. CONCLUSIONS While rates of invasive H. influenzae disease have decreased dramatically following the introduction of Hib vaccination, H. influenzae remains a cause of significant morbidity and mortality, and Aboriginal and Torres Strait Islander children remain particularly vulnerable.
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Affiliation(s)
- Gavin Cleland
- Department of Paediatrics, Western Australian Country Health Service, Kimberley Region, Western Australia, Australia.,University of Western Australia, Perth, Western Australia, Australia
| | - Clare Leung
- Infection Management and Prevention Service, Lady Cilento Children's Hospital, Queensland, Australia.,University of Queensland, Brisbane, Queensland, Australia
| | - Jenny Wan Sai Cheong
- University of Queensland, Brisbane, Queensland, Australia.,Pathology Queensland, Brisbane, Queensland, Australia
| | - Joshua Francis
- Department of Paediatrics, Royal Darwin Hospital, Australia.,Northern Territory Medical Program, Flinders University, Australia.,Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Claire Heney
- Pathology Queensland, Brisbane, Queensland, Australia
| | - Clare Nourse
- Infection Management and Prevention Service, Lady Cilento Children's Hospital, Queensland, Australia.,University of Queensland, Brisbane, Queensland, Australia
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9
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Hatrongjit R, Akeda Y, Hamada S, Gottschalk M, Kerdsin A. Multiplex PCR for identification of six clinically relevant streptococci. J Med Microbiol 2017; 66:1590-1595. [DOI: 10.1099/jmm.0.000615] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Yukihiro Akeda
- Osaka University Hospital, Osaka University, Osaka, Japan
| | - Shigeyuki Hamada
- Thailand-Japan Research Collaboration Center for Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
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10
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Isothermal and Sensitive Identification of Streptococcus pneumoniae Using Loop Mediated Isothermal Amplification Assay. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2017. [DOI: 10.5812/pedinfect.61604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Wang J, Leong MC, Leong EZW, Kuan WS, Leong DT. Clinically Relevant Detection of Streptococcus pneumoniae with DNA-Antibody Nanostructures. Anal Chem 2017; 89:6900-6906. [PMID: 28548485 DOI: 10.1021/acs.analchem.7b01508] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Streptococcus pneumoniae (SP) is a pathogenic bacterium and a major cause of community-acquired pneumonia that could be fatal if left untreated. Therefore, rapid and sensitive detection of SP is crucial to enable targeted treatment during SP infections. In this study, DNA tetrahedron (DNA TH) with a hollow structure is anchored on gold electrodes to construct an electrochemical immunosensor for rapid detection of pneumococcal surface protein A (PspA) peptide and SP lysate from synthetic and actual human samples. This DNA nanostructure-based immunosensor displays excellent electrochemical activity toward PspA with a sensitive linear region from 0 to 8 ng/mL of PspA peptide and a low limit of detection (LOD) of 0.218 ng/mL. In addition, this DNA-TH-based immunosensor exhibits good sensing performance toward SP lysate in a clinically relevant linear range from 5 to 100 CFU/mL with a LOD of 0.093 CFU/mL. Along with these attractive features, this electrochemical immunosensor is able to specifically recognize and detect the PspA peptide mixed with other physiologically relevant components like bovine serum albumin (BSA) and lipopolysaccharide. In addition, our sensor could detect SP lysate even when dispersed in BSA or Escherichia coli lysate. Lastly, uncultured samples from the nasal cavity, mouth, and axilla of a human subject could be successfully determined by this well-designed electrochemical immunosensor.
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Affiliation(s)
- Jinping Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
| | - May Ching Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Eric Zhe Wei Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Win Sen Kuan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore , Singapore 117585, Singapore.,Emergency Medicine Department, National University Hospital, National University Health System , 5 Lower Kent Ridge Road, Singapore 119074, Singapore
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
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12
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Jiang L, Ren H, Zhou H, Qin T, Chen Y. Simultaneous Detection of Nine Key Bacterial Respiratory Pathogens Using Luminex xTAG ® Technology. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14030223. [PMID: 28241513 PMCID: PMC5369059 DOI: 10.3390/ijerph14030223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/13/2017] [Accepted: 02/20/2017] [Indexed: 01/26/2023]
Abstract
Early diagnosis and treatment are crucial to the outcome of lower respiratory tract infections (LRTIs). In this study, we developed an assay combining multiplex PCR and Luminex technology (MPLT) for the detection of nine important respiratory bacterial pathogens, which frequently cause LRTIs. These were Streptococcus pneumoniae, Moraxella catarrhalis, Staphylococcus aureus, Streptococcus pyogenes, Haemophilus influenzae, Mycoplasma pneumoniae, Legionella spp., Pseudomonas aeruginosa, and Klebsiella pneumoniae. Through the hybridization reaction between two new synthesized multiplex PCR products and MagPlex-TAG Microspheres, we demonstrate that the detection limits for these nine pathogens were as low as 102–103 CFU/mL. Furthermore, 86 clinical bronchoalveolar lavage fluid specimens were used to evaluate this method. Compared with the results of nine simplex real-time PCR reactions targeting these nine pathogens, this MPLT assay demonstrated a high diagnostic accuracy for Streptococcus pneumoniae (sensitivity, 87.5% and specificity, 100%). Furthermore, sensitivity and specificity for the other eight pathogens all attained 100% diagnostic accuracy. In addition, the consistency between MPLT and the nine real-time PCR reactions exceeded 98.8%. In conclusion, MPLT is a high-throughput, labor-saving and reliable method with high sensitivity and specificity for identifying nine respiratory pathogens responsible for LRTIs. Indeed, this assay may be a promising supplement to conventional methods used to diagnose LRTIs.
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Affiliation(s)
- Luxi Jiang
- 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 102206, China.
- Department of Respiratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China.
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, Hangzhou 310014, China.
| | - Hongyu Ren
- 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 102206, China.
| | - Haijian Zhou
- 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 102206, China.
| | - Tian Qin
- 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 102206, China.
| | - Yu Chen
- Department of Respiratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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13
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Torres A, Lee N, Cilloniz C, Vila J, Van der Eerden M. Laboratory diagnosis of pneumonia in the molecular age. Eur Respir J 2016; 48:1764-1778. [PMID: 27811073 DOI: 10.1183/13993003.01144-2016] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/17/2016] [Indexed: 01/20/2023]
Abstract
Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. However, with new knowledge regarding the microbiome, together with the recognition that the lungs are a dynamic microbiological ecosystem, our current concept of pneumonia is not totally realistic as this new concept of pneumonia involves a dysbiosis or alteration of the lung microbiome. A new challenge for microbiologists and clinicians has therefore arisen. There is much to learn regarding the information provided by this new diagnostic technology, which will lead to improvements in the time to antibiotic therapy, targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients. This article provides an overview of current methods of laboratory diagnosis of pneumonia in the molecular age.
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Affiliation(s)
- Antoni Torres
- Dept of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Ciber de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Nelson Lee
- Division of Infectious Diseases, Dept of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Catia Cilloniz
- Dept of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Ciber de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Jordi Vila
- Servei de Microbiologia, Hospital Clinic, ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Menno Van der Eerden
- Dept of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
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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
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15
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Community-acquired pneumonia related to intracellular pathogens. Intensive Care Med 2016; 42:1374-86. [PMID: 27276986 DOI: 10.1007/s00134-016-4394-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/14/2016] [Indexed: 01/22/2023]
Abstract
Community-acquired pneumonia (CAP) is associated with high rates of morbidity and mortality worldwide; the annual incidence of CAP among adults in Europe has ranged from 1.5 to 1.7 per 1000 population. Intracellular bacteria are common causes of CAP. However, there is considerable variation in the reported incidence between countries and change over time. The intracellular pathogens that are well established as causes of pneumonia are Legionella pneumophila, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Chlamydophila psittaci, and Coxiella burnetii. Since it is known that antibiotic treatment for severe CAP is empiric and includes coverage of typical and atypical pathogens, microbiological diagnosis bears an important relationship to prognosis of pneumonia. Factors such as adequacy of initial antibiotic or early de-escalation of therapy are important variables associated with outcomes, especially in severe cases. Intracellular pathogens sometimes appear to cause more severe disease with respiratory failure and multisystem dysfunction associated with fatal outcomes. The clinical relevance of intracellular pathogens in severe CAP has not been specifically investigated. We review the prevalence, general characteristics, and outcomes of severe CAP cases caused by intracellular pathogens.
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16
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Chavan RD, Kothari ST, Zunjarrao K, Chowdhary AS. Surveillance of acute respiratory infections in Mumbai during 2011-12. Indian J Med Microbiol 2016; 33:43-50. [PMID: 25560001 DOI: 10.4103/0255-0857.148376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Acute respiratory infections (ARIs) are a leading cause of morbidity and mortality in individuals aged less than 5 years. ARI often leads to hospitalisation, and it has been indicated that causative viral and bacterial infections go undetermined and results in the occurrence of resistant strains. The objective of the study was to assess the prevalence of various viral and bacterial infections in patients with ARIs. MATERIALS AND METHODS Two hundred samples were collected from July 2011 to July 2012 with patients suffering from ARI. Viral and bacterial infections were determined by real time reverse transcriptase polymerase chain reaction. RESULTS Influenza-like illness (ILI) consisted of 109 patients and ARI consisted of 91 patients. Pandemic influenza A H1N1 was the major viral infection with 21 (19.2%) patients in ILI as compared with 16 (17.4%) patients in ARI. Respiratory syncytial virus (RSV) was found to be 1 (0.9%) in ILI and ARI. Viral co-infections were 16 (14.4%) in ILI and 4 (4.37%) in ARI where pandemic influenza A H1N1 and influenza type B were major contributors. In bacterial infections, Streptococcus pneumoniae with 11 (10.9%) cases were predominant in both the groups. Bacterial co-infection accounted for only 1 (1.09%) case in both the groups but the most significant finding was the viral-bacterial co-infection in which Haemophilus influenzae was the major co-infecting bacteria with the influenza viruses with 4 (4.36%) cases as compared with Streptotoccus pneumoniae. CONCLUSION This data indicate the need to undertake continued surveillance that will help to better define the circulation of respiratory viruses along with the bacterial infections.
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Affiliation(s)
- R D Chavan
- Departments of Virology and Immunology , Haffkine Institute for Training, Research and Testing, Parel, Mumbai, India
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17
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Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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Gadsby NJ, McHugh MP, Russell CD, Mark H, Conway Morris A, Laurenson IF, Hill AT, Templeton KE. Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections. Clin Microbiol Infect 2015; 21:788.e1-788.e13. [PMID: 25980353 PMCID: PMC4509705 DOI: 10.1016/j.cmi.2015.05.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/23/2015] [Accepted: 05/03/2015] [Indexed: 11/30/2022]
Abstract
The frequent lack of a positive and timely microbiological diagnosis in patients with lower respiratory tract infection (LRTI) is an important obstacle to antimicrobial stewardship. Patients are typically prescribed broad-spectrum empirical antibiotics while microbiology results are awaited, but, because these are often slow, negative, or inconclusive, de-escalation to narrow-spectrum agents rarely occurs in clinical practice. The aim of this study was to develop and evaluate two multiplex real-time PCR assays for the sensitive detection and accurate quantification of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. We found that all eight bacterial targets could be reliably quantified from sputum specimens down to a concentration of 100 CFUs/reaction (8333 CFUs/mL). Furthermore, all 249 positive control isolates were correctly detected with our assay, demonstrating effectiveness on both reference strains and local clinical isolates. The specificity was 98% on a panel of nearly 100 negative control isolates. Bacterial load was quantified accurately when three bacterial targets were present in mixtures of varying concentrations, mimicking likely clinical scenarios in LRTI. Concordance with culture was 100% for culture-positive sputum specimens, and 90% for bronchoalveolar lavage fluid specimens, and additional culture-negative bacterial infections were detected and quantified. In conclusion, a quantitative molecular test for eight key bacterial causes of LRTI has the potential to provide a more sensitive decision-making tool, closer to the time-point of patient admission than current standard methods. This should facilitate de-escalation from broad-spectrum to narrow-spectrum antibiotics, substantially improving patient management and supporting efforts to curtail inappropriate antibiotic use.
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Affiliation(s)
- N J Gadsby
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK.
| | - M P McHugh
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - C D Russell
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - H Mark
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - A Conway Morris
- Department of Anaesthesia, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - I F Laurenson
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - A T Hill
- Respiratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - K E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
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19
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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.
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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.
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20
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Miyashita N, Kawai Y, Tanaka T, Akaike H, Teranishi H, Wakabayashi T, Nakano T, Ouchi K, Okimoto N. Antibody responses of Chlamydophila pneumoniae pneumonia: Why is the diagnosis of C. pneumoniae pneumonia difficult? J Infect Chemother 2015; 21:497-501. [PMID: 25840889 DOI: 10.1016/j.jiac.2015.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/22/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
The ELNAS Plate Chlamydophila pneumoniae commercial test kit for the detection of anti-C. pneumoniae-specific immunoglobulin M (IgM), IgA and IgG antibodies has become available in Japan recently. To determine the optimum serum collection point for the ELNAS plate in the diagnosis of C. pneumoniae pneumonia, we analyzed the kinetics of the antibody response in patients with laboratory-confirmed C. pneumoniae pneumonia. We enrolled five C. pneumoniae pneumonia cases and collected sera from patients for several months. The kinetics of the IgM and IgG antibody responses were similar among the five patients. Significant increases in IgM and IgG antibody titer between paired sera were observed in all patients. IgM antibodies appeared approximately 2-3 weeks after the onset of illness, reached a peak after 4-5 weeks, and were generally undetectable after 3-5 months. IgG antibodies developed slowly for the first 30 days and reached a plateau approximately 3-4 months after the onset of illness. The kinetics of IgA antibody responses were different among the five patients, and significant increases in IgA antibody titer between paired sera were observed in only two patients. Although the sample size was small, the best serum collection time seemed to be approximately 3-6 weeks after onset of illness when using a single serum sample for the detection of IgM antibodies. Paired sera samples should be obtained at least 4 weeks apart. IgA antibody analysis using ELNAS may not be a useful marker for acute C. pneumoniae pneumonia.
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Affiliation(s)
- Naoyuki Miyashita
- Department of Internal Medicine I, Kawasaki Medical School, Okayama, Japan.
| | - Yasuhiro Kawai
- Department of Internal Medicine I, Kawasaki Medical School, Okayama, Japan
| | - Takaaki Tanaka
- Department of Pediatrics, Kawasaki Medical School, Okayama, Japan
| | - Hiroto Akaike
- Department of Pediatrics, Kawasaki Medical School, Okayama, Japan
| | - Hideto Teranishi
- Department of Pediatrics, Kawasaki Medical School, Okayama, Japan
| | | | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, Okayama, Japan
| | - Kazunobu Ouchi
- Department of Pediatrics, Kawasaki Medical School, Okayama, Japan
| | - Niro Okimoto
- Department of Internal Medicine I, Kawasaki Medical School, Okayama, Japan
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Trends in the epidemiology of invasive Haemophilus influenzae disease in Queensland, Australia from 2000 to 2013: what is the impact of an increase in invasive non-typable H. influenzae (NTHi)? Epidemiol Infect 2015; 143:2993-3000. [PMID: 25762194 DOI: 10.1017/s0950268815000345] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Following the introduction of vaccination against Haemophilus influenzae type b (Hib), cases of invasive encapsulated Hib disease have decreased markedly. This study aimed to examine subsequent epidemiological trends in invasive H. influenzae disease in Queensland, Australia and in particular, assess the clinical impact and public health implications of invasive non-typable H. influenzae (NTHi) strains. A multicentre retrospective study was conducted from July 2000 to June 2013. Databases of major laboratories in Queensland including Queensland Forensic and Scientific Services (jurisdictional referral laboratory for isolate typing) were examined to identify cases. Demographic, infection site, Indigenous status, serotype, and mortality data were collected. In total, 737 invasive isolates were identified, of which 586 (79·5%) were serotyped. Hib, NTHi and encapsulated non-b strains, respectively, constituted 12·1%, 69·1% and 18·8% of isolates. The predominant encapsulated non-b strains were f (45·5%) and a (27·3%) serotypes. Of isolates causing meningitis, 48·9% were NTHi, 14·9% Hib, 14·9% Hie, 10·6% Hif, 6·4% Hia and 4·3% were untyped. During the study period, there was an increase in the incidence of invasive NTHi disease (P = 0·007) with seasonal peaks in winter and spring (P 0·001) and Hib (P = 0·039) than non-Indigenous patients. In Queensland, invasive H. influenzae disease is now predominantly encountered in adults and most commonly caused by NTHi strains with demonstrated pathogenicity extending to otherwise young or immunocompetent individuals. Routine public health notification of these strains is recommended and recent available immunization options should be considered.
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22
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Di Marco E. Real-time PCR detection of Mycoplasma pneumoniae in the diagnosis of community-acquired pneumonia. Methods Mol Biol 2014; 1160:99-105. [PMID: 24740224 DOI: 10.1007/978-1-4939-0733-5_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polymerase chain reaction is a useful technique in microbial diagnostics to detect and quantify DNA or RNA of low abundance. Bacterial and viral nucleic acid can be amplified by PCR upon clinical sample extraction using specific primers for classical qualitative PCR and primers and probes for real-time PCR. Here we describe the Scorpion-probe real-time PCR-based assay that offers thermodynamic advantages due to its kinetic reaction and provides faster performances compared to a classical double-labeled probe-based assays.
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Affiliation(s)
- Eddi Di Marco
- Department of Translational Medicine, Istituto Giannina Gaslini, Largo G. Gaslini 5, Genova, 16147, Italy,
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23
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Skaare D, Anthonisen IL, Caugant DA, Jenkins A, Steinbakk M, Strand L, Sundsfjord A, Tveten Y, Kristiansen BE. Multilocus sequence typing and ftsI sequencing: a powerful tool for surveillance of penicillin-binding protein 3-mediated beta-lactam resistance in nontypeable Haemophilus influenzae. BMC Microbiol 2014; 14:131. [PMID: 24884375 PMCID: PMC4039647 DOI: 10.1186/1471-2180-14-131] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/14/2014] [Indexed: 12/26/2022] Open
Abstract
Background Beta-lactam resistance in Haemophilus influenzae due to ftsI mutations causing altered penicillin-binding protein 3 (PBP3) is increasing worldwide. Low-level resistant isolates with the N526K substitution (group II low-rPBP3) predominate in most geographical regions, while high-level resistant isolates with the additional S385T substitution (group III high-rPBP3) are common in Japan and South Korea. Knowledge about the molecular epidemiology of rPBP3 strains is limited. We combined multilocus sequence typing (MLST) and ftsI/PBP3 typing to study the emergence and spread of rPBP3 in nontypeable H. influenzae (NTHi) in Norway. Results The prevalence of rPBP3 in a population of 795 eye, ear and respiratory isolates (99% NTHi) from 2007 was 15%. The prevalence of clinical PBP3-mediated resistance to ampicillin was 9%, compared to 2.5% three years earlier. Group II low-rPBP3 predominated (96%), with significant proportions of isolates non-susceptible to cefotaxime (6%) and meropenem (20%). Group III high-rPBP3 was identified for the first time in Northern Europe. Four MLST sequence types (ST) with characteristic, highly diverging ftsI alleles accounted for 61% of the rPBP3 isolates. The most prevalent substitution pattern (PBP3 type A) was present in 41% of rPBP3 isolates, mainly carried by ST367 and ST14. Several unrelated STs possessed identical copies of the ftsI allele encoding PBP3 type A. Infection sites, age groups, hospitalization rates and rPBP3 frequencies differed between STs and phylogenetic groups. Conclusions This study is the first to link ftsI alleles to STs in H. influenzae. The results indicate that horizontal gene transfer contributes to the emergence of rPBP3 by phylogeny restricted transformation. Clonally related virulent rPBP3 strains are widely disseminated and high-level resistant isolates emerge in new geographical regions, threatening current empiric antibiotic treatment. The need of continuous monitoring of beta-lactam susceptibility and a global system for molecular surveillance of rPBP3 strains is underlined. Combining MLST and ftsI/PBP3 typing is a powerful tool for this purpose.
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Affiliation(s)
- Dagfinn Skaare
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway.
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24
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Evaluation of Curetis Unyvero, a multiplex PCR-based testing system, for rapid detection of bacteria and antibiotic resistance and impact of the assay on management of severe nosocomial pneumonia. J Clin Microbiol 2014; 52:2487-92. [PMID: 24789196 DOI: 10.1128/jcm.00325-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Health care-associated pneumonia due to multidrug-resistant organisms represents a major therapeutic challenge. Unfortunately, treatment is dependent on empirical therapy, which often leads to improper and inadequate antimicrobial therapy. A rapid multiplex PCR-based Unyvero pneumonia application (UPA) assay that assists in timely decision-making has recently become available. In this study, we evaluated the performance of UPA in detecting etiological pathogens and resistance markers in patients with nosocomial pneumonia (NP). The impact of this assay on the management of severe nosocomial pneumonia was also assessed. Appropriate specimens were processed by UPA according to the manufacturer's protocol in parallel with conventional culture methods. Of the 56 patients recruited into the study, 49 (87.5%) were evaluable. Of these, 27 (55.1%) and 4 (8.2%) harbored multiple bacteria by the PCR assay and conventional culture, respectively. A single pathogen was detected in 8 (16.3%) and 4 (8.2%) patients, respectively. Thirteen different genes were detected from 38 patients, including the ermB gene (40.8%), the blaOXA-51-like gene (28.6%), the sul1 (28.6%) and int1 (20.4%) integrase genes, and the mecA and blaCTX-M genes (12.3% each). The time from sample testing to results was 4 h versus 48 to 96 h by UPA and culture, respectively. Initial empirical treatment was changed within 5 to 6 h in 33 (67.3%) patients based on the availability of UPA results. Thirty (62.2%) of the patients improved clinically. A total of 3 (6.1%) patients died, mainly from their comorbidities. These data demonstrate the potential of a multiplex PCR-based assay for accurate and timely detection of etiological agents of NP, multidrug-resistant (MDR) organisms, and resistance markers, which can guide clinicians in making early antibiotic adjustments.
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25
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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.
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Affiliation(s)
- Guma M K Abdeldaim
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, S-75185, Uppsala, Sweden
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Xirogianni A, Tsolia M, Voyiatzi A, Sioumala M, Makri A, Argyropoulou A, Paniara O, Markoulatos P, Kourea-Kremastinou J, Tzanakaki G. Diagnosis of Upper and Lower Respiratory Tract Bacterial Infections with the Use of Multiplex PCR Assays. Diagnostics (Basel) 2013; 3:222-31. [PMID: 26835676 PMCID: PMC4665534 DOI: 10.3390/diagnostics3020222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/08/2013] [Accepted: 03/21/2013] [Indexed: 11/16/2022] Open
Abstract
The investigation of respiratory infections by molecular techniques provides important information about the epidemiology of respiratory disease, especially during the post-vaccination era. The objective of the present study was the detection of bacterial pathogens directly in clinical samples from patients with upper and lower respiratory tract infections using multiplex polymerase chain reaction (PCR) assays developed in our laboratory. Clinical samples taken over a three-year period (2007–2009) and obtained from 349 patients (adults (n = 66); children (n = 283)) with signs and symptoms of certain upper or lower respiratory tract infections, consisted of: bronchoalveolar lavages (BAL, n = 83), pleural fluids (n = 29), and middle-ear aspirates (n = 237). Overall, 212 samples (61%) were confirmed by culture and/or PCR. Among the positive samples, Streptococcus pneumoniae (mainly serotype 3) was predominant (104/212; 49.0%), followed by non-typable Haemophilus influenzae (NTHi) 59/212; 27.8%) and Streptococcus pyogenes (47/212; 22%). Haemophilus influenzae type b was detected in only three samples. The underlying microbiology of respiratory infections is gradually changing in response to various selective pressures, such as vaccine use and antibiotic consumption. The application of multiplex PCR (mPCR) assays is particularly useful since it successfully identified the microorganisms implicated in acute otitis media or lower respiratory tract infections in nearly 75% of patients with a positive result compared to conventional cultures. Non-culture identification of the implicated pneumococcal serotypes is also an important issue for monitoring pneumococcal infections in the era of conjugate pneumococcal vaccines.
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Affiliation(s)
- Athanasia Xirogianni
- National Meningitis Reference Laboratory, National School of Public Health, 196, Alexandras Avenue, Athens 11521, Greece.
- School of Health Sciences, Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aiolou str, Larissa 41221, Greece.
| | - Maria Tsolia
- Second Department of Pediatrics, University of Athens School of Medicine, P. and A. Kyriakou Children's Hospital, Thevon & Levadeias str, Athens 11527, Greece.
| | - Aliki Voyiatzi
- Penteli's Children's Hospital, Microbiology Laboratory, 8 Ippokratous str., Penteli, Attiki 15236, Greece.
| | - Maria Sioumala
- National Meningitis Reference Laboratory, National School of Public Health, 196, Alexandras Avenue, Athens 11521, Greece.
| | - Antonia Makri
- Penteli's Children's Hospital, Microbiology Laboratory, 8 Ippokratous str., Penteli, Attiki 15236, Greece.
| | - Athina Argyropoulou
- "Evaggelismos" General Hospital of Athens, Microbiology Laboratory, 45-47 Ipsilantou Str, Athens 10676, Greece.
| | - Olga Paniara
- "Evaggelismos" General Hospital of Athens, Microbiology Laboratory, 45-47 Ipsilantou Str, Athens 10676, Greece.
| | - Panayotis Markoulatos
- School of Health Sciences, Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aiolou str, Larissa 41221, Greece.
| | - Jenny Kourea-Kremastinou
- National Meningitis Reference Laboratory, National School of Public Health, 196, Alexandras Avenue, Athens 11521, Greece.
| | - Georgina Tzanakaki
- National Meningitis Reference Laboratory, National School of Public Health, 196, Alexandras Avenue, Athens 11521, Greece.
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Kim W, Park HK, Hwang WJ, Shin HS. Simultaneous detection of Streptococcus pneumoniae, S. mitis, and S. oralis by a novel multiplex PCR assay targeting the gyrB gene. J Clin Microbiol 2013; 51:835-40. [PMID: 23269740 PMCID: PMC3592088 DOI: 10.1128/jcm.02920-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 12/17/2012] [Indexed: 01/05/2023] Open
Abstract
A multiplex PCR (mPCR) protocol was developed for simultaneous detection of the gyrB gene in Streptococcus pneumoniae, Streptococcus mitis, and Streptococcus oralis, and the specificity was evaluated using 141 coccus strains. Genomic DNAs purified from S. pneumoniae, S. mitis, and S. oralis strains were efficiently detected with size differences, whereas no PCR products were amplified from any of the reference strains tested. A pilot study of 47 human oral swab specimens was conducted in parallel, and the mPCR assay identified S. pneumoniae in 1 sample, S. mitis in 8 samples, and S. oralis in 2 samples, providing a powerful means for characterization at the level of species compared with traditional culture analysis. Our results suggest that the mPCR protocol presented here is a sensitive and promising tool for the rapid detection and discrimination of S. pneumoniae, S. mitis, and S. oralis from clinical specimens.
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hee Kuk Park
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Woo-Jin Hwang
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
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28
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Athlin S, Strålin K. The Binax NOW Streptococcus pneumoniae test applied on nasopharyngeal aspirates to support pneumococcal aetiology in community-acquired pneumonia. ACTA ACUST UNITED AC 2013; 45:425-31. [PMID: 23330980 DOI: 10.3109/00365548.2012.760843] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The use of nasopharyngeal secretions to enhance diagnostic yields of pneumococcal aetiology in community-acquired pneumonia (CAP) is of interest. We evaluated the Binax NOW Streptococcus pneumoniae immunochromatographic test (ICT) on nasopharyngeal aspirates (NPA) in order to support pneumococcal aetiology in CAP. METHODS The NPA ICT was applied on 180 adult CAP patients and 64 healthy controls. The rate of pneumococcal detection in the nasopharynx was compared to rates for lytA polymerase chain reaction (PCR) and culture on NPA. RESULTS According to blood and sputum culture and urine ICT, the test sensitivity in 59 patients with a pneumococcal aetiology was 81%. The specificity was suboptimal, with 72% negative tests among CAP patients without a pneumococcal aetiology. However, the test was positive in only 11% of patients with atypical pneumonia and in 4.7% of healthy controls. The positivity rate was higher for NPA ICT compared to culture on NPA in all CAP patients, and to both PCR and culture on NPA in non-pneumococcal non-atypical CAP patients. In 113 (63%) patients with β-lactam monotherapy, cure without treatment alteration was noted more often in cases with positive compared to negative NPA ICT at admission (91% vs 69%; p < 0.01). CONCLUSIONS The high sensitivity and the low positivity rates in patients with atypical pneumonia and healthy controls, in combination with the correlation between positive test results and clinical cure with β-lactam therapy, may support a pneumococcal aetiology in CAP in populations with low pneumococcal carriage rates.
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Affiliation(s)
- Simon Athlin
- Department of Infectious Diseases , Örebro University Hospital, Örebro, Sweden.
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Rheem I, Park J, Kim TH, Kim JW. Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens. Ann Lab Med 2012; 32:399-406. [PMID: 23130338 PMCID: PMC3486933 DOI: 10.3343/alm.2012.32.6.399] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/30/2012] [Accepted: 08/17/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In this study, we evaluated the analytical performance and clinical potential of a one-step multiplex real-time PCR assay for the simultaneous detection of 14 types of respiratory viruses using the AdvanSure RV real-time PCR Kit (LG Life Sciences, Korea). METHODS Three hundred and twenty clinical specimens were tested with the AdvanSure RV real-time PCR Kit and conventional multiplex reverse transcription (RT)-PCR assay. The assay results were analyzed and the one-step AdvanSure RV real-time PCR Kit was compared with the conventional multiplex RT-PCR assay with respect to the sensitivity and specificity of the detection of respiratory viruses. RESULTS The limit of detection (LOD) was 1.31 plaque-forming units (PFU)/mL for human rhinoviruses (hRVs), 4.93 PFU/mL for human coronavirus HCoV-229E/NL63, 2.67 PFU/mL for human coronavirus HCoV-OC43, 18.20 PFU/mL for parainfluenza virus 1 (PIV)-1, 24.57 PFU/mL for PIV-2, 1.73 PFU/mL for PIV-3, 1.79 PFU/mL for influenza virus group (Flu) A, 59.51 PFU/mL for FluB, 5.46 PFU/mL for human respiratory syncytial virus (hRSV)-A, 17.23 PFU/mL for hRSV-B, 9.99 PFU/mL for human adenovirus (ADVs). The cross-reactivity test for this assay against 23 types of non-respiratory viruses showed negative results for all viruses tested. The agreement between the one-step AdvanSure multiplex real-time PCR assay and the conventional multiplex RT-PCR assay was 98%. CONCLUSIONS The one-step AdvanSure RV multiplex real-time PCR assay is a simple assay with high potential for specific, rapid and sensitive laboratory diagnosis of respiratory viruses compared to conventional multiplex RT-PCR.
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Affiliation(s)
- Insoo Rheem
- Department of Laboratory Medicine, Dankook University College of Medicine, Cheonan, Korea
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Greve T, Møller JK. Accuracy of using the lytA gene to distinguish Streptococcus pneumoniae from related species. J Med Microbiol 2012; 61:478-482. [DOI: 10.1099/jmm.0.036574-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Thomas Greve
- Department of Clinical Microbiology, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, 8200 Aarhus N, Denmark
| | - Jens Kjølseth Møller
- Department of Clinical Microbiology, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, 8200 Aarhus N, Denmark
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Cho MC, Kim H, An D, Lee M, Noh SA, Kim MN, Chong YP, Woo JH. Comparison of sputum and nasopharyngeal swab specimens for molecular diagnosis of Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella pneumophila. Ann Lab Med 2012; 32:133-8. [PMID: 22389880 PMCID: PMC3289778 DOI: 10.3343/alm.2012.32.2.133] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/11/2011] [Accepted: 11/24/2011] [Indexed: 11/19/2022] Open
Abstract
Background Differentiation of atypical pathogens is important for community-acquired pneumonia (CAP). In this study, we compared sputum and nasopharyngeal swabs (NPS) for use in detection of Mycoplasma pneumoniae (MP), Chlamydophila pneumoniae (CP), and Legionella pneumophila (LP), using Seeplex PneumoBacter ACE Detection Assay (PneumoBacter; Seegene). Methods Sputum and NPS specimens were collected from patients in 15 hospitals. DNA was extracted from sputum using QIAamp DNA Stool Mini Kit (Qiagen) and from NPS using easyMAG (bioMérieux). Both types of specimens were evaluated by multiplex PCR using PneumoBacter. To determine the diagnostic performance of this assay, sputum samples were also tested using BD ProbeTec ET Atypical Pneumonia Assay (APA; Becton Dickinson). Results Among 217 sputum and NPS, 20 (9.2%), 2 (0.9%), and 0 sputum were positive for MP, LP, and CP, respectively, whereas 8 (3.7%) NPS were positive for MP. The sputum APA test yielded 186, 206, and 204 interpretable results for MP, LP, and CP, respectively. Of these, 21 (11.3%) were positive for MP, 2 (1.0%) were positive for LP, and 0 samples were positive for CP. Compared to APA, the sensitivity and specificity of the sputum assay for MP were 95.2% and 100.0%, respectively, whereas for the NPS assay, these were 38.1% and 93.9%. Sputum testing was more sensitive than NPS testing (P=0.002). For LP and CP diagnosis, PneumoBacter and APA tests agreed 100%. Conclusions Specimen type is crucial and sputum is preferred over NPS for simultaneous detection of MP, LP, and CP using multiplex PCR in CAP.
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Affiliation(s)
- Min-Chul Cho
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
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32
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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.
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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.
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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.
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Affiliation(s)
- Guma M K Abdeldaim
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Strålin K, Olcén P, Törnqvist E, Holmberg H. Definite, probable, and possible bacterial aetiologies of community-acquired pneumonia at different CRB-65 scores. ACTA ACUST UNITED AC 2010; 42:426-34. [PMID: 20141490 DOI: 10.3109/00365540903552353] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
According to the recommendations of the Swedish Community-Acquired Pneumonia (CAP) guidelines, the selection of empirical antibiotic therapy should be based on the CRB-65 rule. The guidelines recommend empirical therapy directed predominantly against Streptococcus pneumoniae for patients with low CRB-65 scores and broad-spectrum therapy for patients with high CRB-65 scores. In order to study the utility of the recommendations, we analyzed the data from an aetiological study previously performed on 235 hospitalized adult CAP patients at our medical centre. A definite, probable, or possible bacterial aetiology was noted in 194 cases (83%), including 112 cases (48%) with S. pneumoniae aetiology. The following frequencies of definite-probable aetiologies were noted in the patients with CRB-65 score 0-1 (n=155) and CRB-65 score 2-4 (n=80): S. pneumoniae 30% and 35%, Haemophilus influenzae 6.5% and 14% (p=0.063), Mycoplasma pneumoniae 15% and 5.0% (p=0.019), Chlamydophila species 2.6% and 1.2%, Legionella pneumophila 1.9% and 0%, and Staphylococcus aureus 1.3% and 1.2%, respectively. The high frequency of S. pneumoniae in the study supports the recommendations to predominantly cover this bacterium in the empirical therapy of patients with low CRB-65 scores. In the case of treatment failure in these patients, the study indicates that coverage against M. pneumoniae and H. influenzae should be considered.
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Affiliation(s)
- Kristoffer Strålin
- Department of Infectious Diseases, Orebro University Hospital, Orebro, Sweden.
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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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Shieh WJ, Blau DM, Denison AM, Deleon-Carnes M, Adem P, Bhatnagar J, Sumner J, Liu L, Patel M, Batten B, Greer P, Jones T, Smith C, Bartlett J, Montague J, White E, Rollin D, Gao R, Seales C, Jost H, Metcalfe M, Goldsmith CS, Humphrey C, Schmitz A, Drew C, Paddock C, Uyeki TM, Zaki SR. 2009 pandemic influenza A (H1N1): pathology and pathogenesis of 100 fatal cases in the United States. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 177:166-75. [PMID: 20508031 DOI: 10.2353/ajpath.2010.100115] [Citation(s) in RCA: 333] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the spring of 2009, a novel influenza A (H1N1) virus emerged in North America and spread worldwide to cause the first influenza pandemic since 1968. During the first 4 months, over 500 deaths in the United States had been associated with confirmed 2009 pandemic influenza A (H1N1) [2009 H1N1] virus infection. Pathological evaluation of respiratory specimens from initial influenza-associated deaths suggested marked differences in viral tropism and tissue damage compared with seasonal influenza and prompted further investigation. Available autopsy tissue samples were obtained from 100 US deaths with laboratory-confirmed 2009 H1N1 virus infection. Demographic and clinical data of these case-patients were collected, and the tissues were evaluated by multiple laboratory methods, including histopathological evaluation, special stains, molecular and immunohistochemical assays, viral culture, and electron microscopy. The most prominent histopathological feature observed was diffuse alveolar damage in the lung in all case-patients examined. Alveolar lining cells, including type I and type II pneumocytes, were the primary infected cells. Bacterial co-infections were identified in >25% of the case-patients. Viral pneumonia and immunolocalization of viral antigen in association with diffuse alveolar damage are prominent features of infection with 2009 pandemic influenza A (H1N1) virus. Underlying medical conditions and bacterial co-infections contributed to the fatal outcome of this infection. More studies are needed to understand the multifactorial pathogenesis of this infection.
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Affiliation(s)
- Wun-Ju Shieh
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G-32, Atlanta, GA 30333, USA.
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Park HK, Yoon JW, Shin JW, Kim JY, Kim W. rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol Lett 2010; 305:58-64. [DOI: 10.1111/j.1574-6968.2010.01913.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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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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39
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Jung CL, Lee MA, Chung WS. Clinical Evaluation of the Multiplex PCR Assay for the Detection of Bacterial Pathogens in Respiratory Specimens from Patients with Pneumonia. ACTA ACUST UNITED AC 2010. [DOI: 10.5145/kjcm.2010.13.1.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chae Lim Jung
- Department of Laboratory Medicine, School of Medicine, Ewha Womans University, Seoul, Korea
| | - Mi Ae Lee
- Department of Laboratory Medicine, School of Medicine, Ewha Womans University, Seoul, Korea
| | - Wha Soon Chung
- Department of Laboratory Medicine, School of Medicine, Ewha Womans University, Seoul, Korea
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40
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Park J, Kim JK, Rheem I, Kim J. Evaluation of SeeplexTM Pneumobacter Multiplex PCR Kit for the Detection of Respiratory Bacterial Pathogens in Pediatric Patients. Ann Lab Med 2009; 29:307-13. [DOI: 10.3343/kjlm.2009.29.4.307] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Joowon Park
- Department of Laboratory Medicine, Dankook University Hospital, Cheonan, Korea
| | - Jae Kyoung Kim
- Department of Laboratory Medicine, Dankook University Hospital, Cheonan, Korea
| | - Insoo Rheem
- Department of Laboratory Medicine, Dankook University Hospital, Cheonan, Korea
| | - Jongwan Kim
- Department of Laboratory Medicine, Dankook University Hospital, Cheonan, Korea
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Detection of Haemophilus influenzae in respiratory secretions from pneumonia patients by quantitative real-time polymerase chain reaction. Diagn Microbiol Infect Dis 2009; 64:366-73. [PMID: 19446978 DOI: 10.1016/j.diagmicrobio.2009.03.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 03/26/2009] [Accepted: 03/27/2009] [Indexed: 11/20/2022]
Abstract
A quantitative real-time polymerase chain reaction (PCR) based on the omp P6 gene was developed to detect Haemophilus influenzae. Its specificity was determined by analysis of 29 strains of 11 different Haemophilus spp. and was compared with PCR assays having other target genes: rnpB, 16S rRNA, and bexA. The method was evaluated on nasopharyngeal aspirates from 166 adult patients with community-acquired pneumonia. When 10(4) DNA copies/mL was used as cutoff limit for the method, P6 PCR had a sensitivity of 97.5% and a specificity of 96.0% compared with the culture. Of 20 culture-negative but P6 PCR-positive cases, 18 were confirmed by fucK PCR as H. influenzae. Five (5.9%) of 84 nasopharyngeal aspirates from adult controls tested PCR positive. We conclude that the P6 real-time PCR is both sensitive and specific for identification of H. influenzae in respiratory secretions. Quantification facilitates discrimination between disease-causing H. influenzae strains and commensal colonization.
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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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Abdeldaim G, Herrmann B, Korsgaard J, Olcén P, Blomberg J, Strålin K. Is quantitative PCR for the pneumolysin (ply) gene useful for detection of pneumococcal lower respiratory tract infection? Clin Microbiol Infect 2009; 15:565-70. [PMID: 19416297 DOI: 10.1111/j.1469-0691.2009.02714.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pneumolysin (ply) gene is widely used as a target in PCR assays for Streptococcus pneumoniae in respiratory secretions. However, false-positive results with conventional ply-based PCR have been reported. The aim here was to study the performance of a quantitative ply-based PCR for the identification of pneumococcal lower respiratory tract infection (LRTI). In a prospective study, fibreoptic bronchoscopy was performed in 156 hospitalized adult patients with LRTI and 31 controls who underwent bronchoscopy because of suspicion of malignancy. Among the LRTI patients and controls, the quantitative ply-based PCR applied to bronchoalveolar lavage (BAL) fluid was positive at >or=10(3) genome copies/mL in 61% and 71% of the subjects, at >or=10(5) genome copies/mL in 40% and 58% of the subjects, and at >or=10(7) genome copies/mL in 15% and 3.2% of the subjects, respectively. Using BAL fluid culture, blood culture, and/or a urinary antigen test, S. pneumoniae was identified in 19 LRTI patients. As compared with these diagnostic methods used in combination, quantitative ply-based PCR showed sensitivities and specificities of 89% and 43% at a cut-off of 10(3) genome copies/mL, of 84% and 66% at a cut-off of 10(5) genome copies/mL, and of 53% and 90% at a cut-off of 10(7) genome copies/mL, respectively. In conclusion, a high cut-off with the quantitative ply-based PCR was required to reach acceptable specificity. However, as a high cut-off resulted in low sensitivity, quantitative ply-based PCR does not appear to be clinically useful. Quantitative PCR methods for S. pneumoniae using alternative gene targets should be evaluated.
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Affiliation(s)
- G Abdeldaim
- Department of Clinical Microbiology, Uppsala University Hospital, Uppsala, Sweden
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Development of a single-tube polymerase chain reaction assay for the simultaneous detection of Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus spp. directly in clinical samples. Diagn Microbiol Infect Dis 2008; 63:121-6. [PMID: 19027257 DOI: 10.1016/j.diagmicrobio.2008.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 09/29/2008] [Accepted: 09/30/2008] [Indexed: 11/21/2022]
Abstract
This study describes the development and evaluation of a multiplex single-tube polymerase chain reaction assay for the simultaneous detection of Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus spp. used as target species-specific or genus-specific genes. The assay enables the detection of 5 to 50 pg of bacterial DNA. The sensitivity of the assay was evaluated as 100% for P. aeruginosa, S. aureus, and Streptococcus spp., and 94.3% for H. influenzae; the specificity was 100% for all 4 microorganisms (positive predictive value, 100%; negative predictive value, 98.2%). The assay permits rapid and accurate detection of these 4 microorganisms in a wide range of clinical samples such as whole blood, cerebrospinal, ear, pleural and ophthalmic fluids, as well as bronchoalveolar lavage and bronchial secretions.
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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: 306] [Impact Index Per Article: 19.1] [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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Effect of erythromycin on bronchial hyperreactivity and inflammation in ovalbumin-sensitized brown Norway rats. Respir Physiol Neurobiol 2008; 161:267-72. [PMID: 18430615 DOI: 10.1016/j.resp.2008.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 02/25/2008] [Accepted: 02/28/2008] [Indexed: 11/21/2022]
Abstract
To evaluate the effect of erythromycin on bronchial hyperreactivity, inflammation, and T-cell related cytokine mRNA expression in rats sensitized to ovalbumin, three experimental groups of 10 brown Norway rats each were sensitized by breathing aerosolized ovalbumin. From day 1 to day 15, one group was given oral erythromycin 80 mg/kg/day, another group oral erythromycin 20mg/kg/day, and the third group oral saline only. A fourth control group of 10 rats breathed aerosolized saline. After sensitization, the three experimental groups were provoked by breathing ovalbumin, with the controls again breathing saline. The rats were then anesthetized and paralyzed, and pulmonary function tests were performed at baseline and after varying doses of acetylcholine. Bronchoalveolar lavage (BAL) fluid and lung tissues were examined for expression of mRNA for T-cell cytokines. Our results showed that erythromycin had no beneficial effects on pulmonary function and lung inflammation in the two erythromycin-treated experimental groups compared with the saline experimental group. Th2-related cytokines and their mRNA expression in the three experimental groups were higher than in controls but did not differ among the experimental groups. In conclusion, erythromycin does not prevent bronchial hyperreactivity or an inflammatory response in ovalbumin-sensitized rats.
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Toward a quantitative DNA-based definition of pneumococcal pneumonia: a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment. Diagn Microbiol Infect Dis 2008; 60:143-50. [DOI: 10.1016/j.diagmicrobio.2007.08.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 08/21/2007] [Accepted: 08/26/2007] [Indexed: 11/19/2022]
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Lam WY, Yeung ACM, Tang JW, Ip M, Chan EWC, Hui M, Chan PKS. Rapid multiplex nested PCR for detection of respiratory viruses. J Clin Microbiol 2007; 45:3631-40. [PMID: 17804659 PMCID: PMC2168518 DOI: 10.1128/jcm.00280-07] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory tract infections can be caused by a heterogeneous group of viruses and bacteria that produce similar clinical presentations. Specific diagnosis therefore relies on laboratory investigation. This study developed and evaluated five groups of multiplex nested PCR assays that could simultaneously detect 21 different respiratory pathogens: influenza A virus (H1N1, H3N2, and H5N1); influenza B virus; parainfluenza virus types 1, 2, 3, 4a, and 4b; respiratory syncytial virus A and B; human rhinoviruses; human enteroviruses; human coronaviruses OC43 and 229E; severe acute respiratory syndrome coronavirus; human metapneumoviruses; Mycoplasma pneumoniae; Chlamydophila pneumoniae; Legionella pneumophila; and adenoviruses (A to F). These multiplex nested PCRs adopted fast PCR technology. The high speed of fast PCR (within 35 min) greatly improved the efficiency of these assays. The results show that these multiplex nested PCR assays are specific and more sensitive (100- to 1,000-fold) than conventional methods. Among the 303 clinical specimens tested, the multiplex nested PCR achieved an overall positive rate of 48.5% (95% confidence interval [CI], 42.9 to 54.1%), which was significantly higher than that of virus isolation (20.1% [95% CI, 15.6 to 24.6%]) and that of direct detection by immunofluorescence assay (13.5% [95% CI, 9.7 to 17.4%]). The improved sensitivity was partly due to the higher sensitivity of multiplex nested PCR than that of conventional methods in detecting cultivatable viruses. Moreover, the ability of the multiplex nested PCR to detect noncultivatable viruses, particularly rhinoviruses, coronavirus OC43, and metapneumoviruses, contributed a major gain (15.6%) in the overall positive rate. In conclusion, rapid multiplex nested PCR assays can improve the diagnostic yield for respiratory infections to allow prompt interventive actions to be taken.
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Affiliation(s)
- W Y Lam
- Department of Microbiology, The Chinese University of Hong Kong, 1/F Clinical Science Building, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
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Kumar S, Hammerschlag MR. Acute respiratory infection due to Chlamydia pneumoniae: current status of diagnostic methods. Clin Infect Dis 2007; 44:568-76. [PMID: 17243062 DOI: 10.1086/511076] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 10/19/2006] [Indexed: 12/11/2022] Open
Abstract
Reliable diagnosis of respiratory infection due to Chlamydia pneumoniae and investigation of its role in chronic diseases remain difficult because of the absence of well-standardized and commercially available diagnostic tests. In 2001, the US Centers for Disease Control and Prevention published recommendations for standardizing the diagnostic approach. In this review, we discuss the current state of knowledge of C. pneumoniae-associated respiratory infections in the context of epidemiological studies published during the past 5 years, with particular emphasis on the diagnostic strategies used and their impact on results. The single most likely factor underlying wide variations in data is the significant interstudy variation of the choice of diagnostic methods and criteria used. Adoption of a more unified approach, both for choices of diagnostic methods and for validation of new molecular assays, is long overdue and will be critically important for development of a standardized test for clinical laboratories.
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Affiliation(s)
- Swati Kumar
- Division of Infectious Diseases, Department of Pediatrics, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA.
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Lin SH, Kuo PH, Hsueh PR, Yang PC, Kuo SH. Sputum bacteriology in hospitalized patients with acute exacerbation of chronic obstructive pulmonary disease in Taiwan with an emphasis on Klebsiella pneumoniae and Pseudomonas aeruginosa. Respirology 2007; 12:81-7. [PMID: 17207030 DOI: 10.1111/j.1440-1843.2006.00999.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND OBJECTIVE Bacterial infection is one of the major causes of acute exacerbation of COPD (AECOPD). This study was undertaken to investigate the microbiology of AECOPD. METHODS Medical records from 494 episodes of AECOPD in patients admitted to the National Taiwan University Hospital from January 2000 to June 2004 were reviewed. Severity of COPD was classified according to the 2003 Global Initiative for Chronic Obstructive Lung Disease guideline. RESULTS Potential pathogenic microorganisms were isolated from patients in 328 (66.4%) episodes of AECOPD. The predominant bacteria were Klebsiella pneumoniae (19.6%), Pseudomonas aeruginosa (16.8%) and Haemophilus influenzae (7.5%), followed by Acinetobacter baumannii (6.9%), Enterobacter species (6.1%) and Staphylococcus aureus (6.1%). The incidence of Streptococcus pneumoniae was 2.4%. Spirometry results obtained within 1 year of the exacerbation were available in 186 cases. K. pneumoniae was more frequently isolated in stage I COPD (39.1%) than stage II (16.6%), III (13.8%) and IV (9.4%). No glucose non-fermentative Gram-negative bacilli were isolated in stage I patients. Multivariate logistic regression analysis revealed that P. aeruginosa (odds ratio (OR) 3.19; 95% confidence interval (CI): 1.21-8.38), intubation (OR 14.81; 95% CI: 5.08-43.12) and age (OR 1.1; 95% CI: 1.03-1.17) were independent risk factors for mortality. CONCLUSIONS Klebsiella pneumoniae and P. aeruginosa are the most common sputum pathogens in hospitalized patients with AECOPD in Taiwan, with the former being more commonly isolated from mild COPD and the latter associated with poor clinical outcome. These results should be considered when deciding which antibiotics should initially be used to treat patients with AECOPD.
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