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Kulkarni D, Wang X, Sharland E, Stansfield D, Campbell H, Nair H. The global burden of hospitalisation due to pneumonia caused by Staphylococcus aureus in the under-5 years children: A systematic review and meta-analysis. EClinicalMedicine 2022; 44:101267. [PMID: 35072019 PMCID: PMC8763635 DOI: 10.1016/j.eclinm.2021.101267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Pneumonia is a leading cause of childhood morbidity and mortality. This study aimed to estimate the global hospitalisation due to Staphylococcus aureus pneumonia in under-5 children. METHODS We conducted a systematic review and meta-analysis of primary studies following the PRISMA-P guidelines. We searched Medline, Embase, Global Health, CINAHL, Global Index Medicus, Scopus, China National Knowledge Infrastructure, Wanfang, and CQvip. We included studies reporting data on Staphylococcus aureus pneumonia, confirmed by detection of the pathogen in sterile-site samples in under-5 hospitalised children, published in English or Chinese language and conducted between 1st January 1990 and 4th November 2021 and between 1st January 1990 and 30th September 2020, respectively. We excluded those testing upper respiratory tract samples and not reporting data on samples with other bacteria or absence of bacteria. We screened papers against pre-specified criteria, extracted data and assessed the bacteriological quality, and combined epidemiological and microbiological quality of studies using two self-designed checklists. Pooled proportions of hospitalisation episodes for Staphylococcus aureus pneumonia amongst all-cause pneumonia and the 95% confidence intervals were calculated using the random-effects model. The review protocol was registered on PROSPERO (CRD42021236606). FINDINGS Of 26,218 studies identified, thirty-five studies enroling 20,708 hospitalised pneumonia episodes were included. Out of the total hospitalised pneumonia cases in this population, the pooled proportion of Staphylococcal pneumonia cases was 3% (95% CI 2% to 4%; I2=96%). amongst 12 studies with higher microbiological quality, the pooled estimate was 6% (95% CI 2% to 10%; I2= 98%). Based on the recent global estimates of hospitalised pneumonia in this age group, the 3% and 6% estimates represent 738 thousand and 1.48 million hospitalisations in 2019, respectively. Based on the Grading of Recommendations Assessment, Development, and Evaluation (GRADE), the overall quality of evidence was considered to be moderate. INTERPRETATION Our findings are probably an underestimate because of the unknown and the likely limited sensitivity of current testing methods for Staphylococcal pneumonia diagnosis and widespread reported use of antibiotics before recruitment (in 46% of cases). Staphylococcus aureus is an important cause of hospitalisation for pneumonia in young children globally. FUNDING Bill and Melinda Gates Foundation (OPP 1,172,551) through a prime award to John Hopkins University.
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Agha Kuchak Afshari S, Rahimi H, Hashemi SJ, Daie Ghazvini R, Badali H, Aghaei Gharehbolagh S, Rezaie S. Evaluation of PCR-reverse line blot hybridization assay for simultaneous identification of medically important saprophytic fungi. J Mycol Med 2017; 28:173-179. [PMID: 29100947 DOI: 10.1016/j.mycmed.2017.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND In immunocompromised patients suffering from invasive fungal infections, rapid identification of fungal species is important since the appropriate treatment is usually related to the responsible species. We describe here, an assay based on combination of PCR and reverse line blot hybridization (PCR/RLB) for differentiation causative agent of fungal infections. MATERIALS AND METHODS We performed PCR/RLB assay on 10 reference strains, which include Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. clavatus), Mucor circnelloides, Rhizopus oryzae, Alternaria alternata, Cladosporium herbarum, and Fusarium solani. Besides, twenty-two clinical specimens from patients with proven fungal infections were analyzed for the identification of species. The obtained results were then compared with the results of culture and sequence analysis. RESULTS The fungal species-specific oligonucleotide probes were able to distinguish between all species represented in this study with the exception of cross-reactivity between A. niger and A. fumigatus species. Two specimens, which were represented as mixed fungi in culture, were identified properly by this method. Results of the RLB assay were concordant with the culture and ITS sequencing results. CONCLUSION Our result demonstrate that the RLB assay potentially is suitable for rapid and simultaneous identification of variety fungal pathogens directly from culture as well as from clinical specimens.
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Affiliation(s)
- S Agha Kuchak Afshari
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - H Rahimi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - S J Hashemi
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - R Daie Ghazvini
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - H Badali
- Department of Medical Mycology and Parasitology, Antimicrobial Resistance Research Center (ARRC), Mazandaran University of Medical Science, Sari, Iran
| | - S Aghaei Gharehbolagh
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - S Rezaie
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Waites KB, Xiao L, Liu Y, Balish MF, Atkinson TP. Mycoplasma pneumoniae from the Respiratory Tract and Beyond. Clin Microbiol Rev 2017; 30:747-809. [PMID: 28539503 PMCID: PMC5475226 DOI: 10.1128/cmr.00114-16] [Citation(s) in RCA: 350] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mycoplasma pneumoniae is an important cause of respiratory tract infections in children as well as adults that can range in severity from mild to life-threatening. Over the past several years there has been much new information published concerning infections caused by this organism. New molecular-based tests for M. pneumoniae detection are now commercially available in the United States, and advances in molecular typing systems have enhanced understanding of the epidemiology of infections. More strains have had their entire genome sequences published, providing additional insights into pathogenic mechanisms. Clinically significant acquired macrolide resistance has emerged worldwide and is now complicating treatment. In vitro susceptibility testing methods have been standardized, and several new drugs that may be effective against this organism are undergoing development. This review focuses on the many new developments that have occurred over the past several years that enhance our understanding of this microbe, which is among the smallest bacterial pathogens but one of great clinical importance.
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Affiliation(s)
- Ken B Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Li Xiao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yang Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China, and Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | | | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Aydemir Y, Aydemir Ö, Pekcan S, Özdemir M. Value of multiplex PCR to determine the bacterial and viral aetiology of pneumonia in school-age children. Paediatr Int Child Health 2017; 37:29-34. [PMID: 26750616 DOI: 10.1080/20469047.2015.1106080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Conventional methods for the aetiological diagnosis of community-acquired pneumonia (CAP) are often insufficient owing to low sensitivity and the long wait for the results of culture and particularly serology, and it often these methods establish a diagnosis in only half of cases. AIM To evaluate the most common bacterial and viral agents in CAP using a fast responsive PCR method and investigate the relationship between clinical/laboratory features and aetiology, thereby contributing to empirical antibiotic selection and reduction of treatment failure. METHODS In children aged 4-15 years consecutively admitted with a diagnosis of CAP, the 10 most commonly detected bacterial and 12 most commonly detected viral agents were investigated by induced sputum using bacterial culture and multiplex PCR methods. Clinical and laboratory features were compared between bacterial and viral pneumonia. RESULTS In 78 patients, at least one virus was detected in 38 (48.7%) and at least one bacterium in 32 (41%). In addition, both bacteria and viruses were detected in 16 (20.5%) patients. Overall, the agent detection rate was 69.2%. The most common viruses were respiratory syncytial virus and influenza and the most frequently detected bacteria were S. pneumoniae and H. influenzae. PCR was superior to culture for bacterial isolation (41% vs 13%, respectively). Fever, wheezing and radiological features were not helpful in differentiating between bacterial and viral CAP. White blood cell count, CRP and ESR values were significantly higher in the bacterial/mixed aetiology group than in the viral aetiology group. CONCLUSION In CAP, multiplex PCR is highly reliable, superior in detecting multiple pathogens and rapidly identifies aetiological agents. Clinical features are poor for differentiation between bacterial and viral infections. The use of PCR methods allow physicians to provide more appropriate antimicrobial therapy, resulting in a better response to treatment, and it may be possible for use as a routine service if costs can be reduced.
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Affiliation(s)
- Yusuf Aydemir
- a Departments of Pulmonology , Sakarya University , Sakarya
| | - Özlem Aydemir
- b Departments of Microbiology , Sakarya University , Sakarya , Turkey
| | - Sevgi Pekcan
- c Departments of Pediatric Pulmonology , Necmettin Erbakan University , Konya , Turkey
| | - Mehmet Özdemir
- d Departments of Microbiology , Necmettin Erbakan University , Konya , Turkey
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Abstract
The introduction of vaccination in the 1950s significantly reduced the morbidity and mortality of pertussis. However, since the 1990s, a resurgence of pertussis has been observed in vaccinated populations, and a number of causes have been proposed for this phenomenon, including improved diagnostics, increased awareness, waning immunity, and pathogen adaptation. The resurgence of pertussis highlights the importance of standardized, sensitive, and specific laboratory diagnoses, the lack of which is responsible for the large differences in pertussis notifications between countries. Accurate laboratory diagnosis is also important for distinguishing between the several etiologic agents of pertussis-like diseases, which involve both viruses and bacteria. If pertussis is diagnosed in a timely manner, antibiotic treatment of the patient can mitigate the symptoms and prevent transmission. During an outbreak, timely diagnosis of pertussis allows prophylactic treatment of infants too young to be (fully) vaccinated, for whom pertussis is a severe, sometimes fatal disease. Finally, reliable diagnosis of pertussis is required to reveal trends in the (age-specific) disease incidence, which may point to changes in vaccine efficacy, waning immunity, and the emergence of vaccine-adapted strains. Here we review current approaches to the diagnosis of pertussis and discuss their limitations and strengths. In particular, we emphasize that the optimal diagnostic procedure depends on the stage of the disease, the age of the patient, and the vaccination status of the patient.
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Affiliation(s)
- Anneke van der Zee
- Molecular Diagnostics Unit, Maasstad Hospital, Rotterdam, The Netherlands
| | | | - Frits R Mooi
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands
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Abstract
Over recent years non-culture techniques such as specific viral and bacterial nucleic acid amplification, serology and antigen detection have considerably developed and been applied within research studies to clinical samples, significantly increasing pathogen detection in pneumonia. There are promising signs of improved diagnostic yields for pneumococcal pneumonia when using molecular techniques to detect pneumococcal gene sequences in blood or by combining serum biomarkers with rapid pneumococcal urinary antigen testing. Pathogens have traditionally been difficult to detect in pneumonia and treatment is usually successful with empiric antibiotics. However, directed antibiotic treatment has significant benefits in terms of antibiotic stewardship and these new technologies make this goal a possibility, though not yet a reality.
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Oliwa JN, Karumbi JM, Marais BJ, Madhi SA, Graham SM. Tuberculosis as a cause or comorbidity of childhood pneumonia in tuberculosis-endemic areas: a systematic review. THE LANCET RESPIRATORY MEDICINE 2015; 3:235-43. [PMID: 25648115 DOI: 10.1016/s2213-2600(15)00028-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/19/2014] [Indexed: 11/30/2022]
Abstract
Pneumonia is a major cause of morbidity and mortality in infants and children worldwide, with most cases occurring in tuberculosis-endemic settings. Studies have emphasised the potential importance of Mycobacterium tuberculosis in acute severe pneumonia in children as a primary cause or underlying comorbidity, further emphasised by the changing aetiological range with rollout of bacterial conjugate vaccines in high mortality settings. We systematically reviewed clinical and autopsy studies done in tuberculosis-endemic settings that enrolled at least 100 children aged younger than 5 years with severe pneumonia, and that prospectively included a diagnostic approach to tuberculosis in all study participants. We noted substantial heterogeneity between studies in terms of study population and diagnostic methods. Of the 3644 patients who had culture of respiratory specimens for M tuberculosis undertaken, 275 (7·5%) were culture positive, and an acute presentation was common. Inpatient case-fatality rate for pneumonia associated with tuberculosis ranged from 4% to 21% in the four clinical studies that reported pathogen-related outcomes. Prospective studies are needed in high tuberculosis-burden settings to address whether tuberculosis is a cause or comorbidity of childhood acute severe pneumonia.
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Affiliation(s)
- Jacquie N Oliwa
- KEMRI Wellcome Trust Research Programme, Department of Public Health Research, Nairobi, Kenya.
| | - Jamlick M Karumbi
- KEMRI Wellcome Trust Research Programme, Department of Public Health Research, Nairobi, Kenya
| | - Ben J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity and The Children's Hospital at Westmead, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology and National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen M Graham
- Centre for International Child Health, University of Melbourne Department of Paediatrics and Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia; International Union Against Tuberculosis and Lung Disease, Paris, France
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Aydemir O, Aydemir Y, Ozdemir M. The role of multiplex PCR test in identification of bacterial pathogens in lower respiratory tract infections. Pak J Med Sci 2014; 30:1011-6. [PMID: 25225517 PMCID: PMC4163223 DOI: 10.12669/pjms.305.5098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/09/2014] [Accepted: 06/12/2014] [Indexed: 11/30/2022] Open
Abstract
Objectives: Lower respiratory tract infection is one of the most important causes of morbidity and mortality. However establishing a microbial diagnosis for patients with lower respiratory tract infection is still challenging and is often achieved in only half of cases by conventional methods. This study was designed to compare the fast responsive PCR method with the culture method in lower respiratory tract infections and to evaluate the reliability of multiplex PCR method. Methods: One hundred ninety seven patients with the symptoms of acute lower respiratory tract infection, and diagnosed with community-acquired pneumonia, acute exacerbation of chronic obstructive pulmonary disease and exacerbations of bronchiectasis were included in the study. Both culture and PCR methods was performed for the isolation of most commonly seen bacteria, from sputum, nasopharyngeal swabs and bronchoalveolar lavage fluid samples. Results: While at least one bacterial isolation was determined in 62 (31.5%) of all patients with culture method, this number increased to 125 (63.5%) with multiplex PCR. The bacteria most commonly identified by PCR were S. pneumoniae (32%) and H. influenzae (31%). There was a significant difference between PCR and culture in terms of multi-factor detection rates (p<0.005). Multiple bacteria were detected in only two cases in cultures; however, multiple pathogens were detected in 47 cases with PCR. Conclusions: Conventional methods, such as culture and serology are not always adequate to detect the pathogens in lower respiratory tract. Real-time PCR assays proved highly sensitive and rapid. The prevalence of bacteria and multiple agent detected by real-time PCR compared with culture was substantially higher. Widespread use of PCR methods, by providing the immediate and appropriate ''agent specific antibiotic treatment'' of LRTI, will help reduce failure and contributes to a reduction in antibiotic resistance.
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Affiliation(s)
- Ozlem Aydemir
- Ozlem Aydemir, Department of Microbiology, Sakarya University, Training and Research Hospital, Sakarya, Turkey
| | - Yusuf Aydemir
- Yusuf Aydemir, Department of Pulmonology, Faculty of Medicine, Sakarya University, Sakarya, Turkey
| | - Mehmet Ozdemir
- Mehmet Ozdemir, Faculty of Medicine, Department of Microbiology, Necmettin Erbakan University, Konya, Turkey
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Chiappini E, Venturini E, Galli L, Novelli V, de Martino M. Diagnostic features of community-acquired pneumonia in children: what's new? Acta Paediatr 2013; 102:17-24. [PMID: 24330269 DOI: 10.1111/apa.12502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AIM To critically summarise the available data on diagnosis of CAP in children, focusing on the newest findings and on the need for new studies. METHODS Eighty studies on the diagnosis of paediatric community-acquired pneumonia were scrutinised. RESULTS We found no significant associations between the signs or symptoms and aetiology of pneumonia and concluded that chest radiographs remain controversial and real-time polymerase chain reaction appears more sensitive than blood cultures. CONCLUSION Antibiotic overuse could make it difficult to differentiate viral and bacterial causes. Molecular methods provide promising tools for diagnosing infection by atypical bacteria, but are expensive and should be used selectively.
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Affiliation(s)
- Elena Chiappini
- Department of Health Sciences; University of Florence; Anna Meyer Children's University Hospital; Florence Italy
| | - Elisabetta Venturini
- Department of Health Sciences; University of Florence; Anna Meyer Children's University Hospital; Florence Italy
| | - Luisa Galli
- Department of Health Sciences; University of Florence; Anna Meyer Children's University Hospital; Florence Italy
| | - Vas Novelli
- Department of Infectious Diseases; Great Ormond Street Hospital for Children NHS Trust; London UK
| | - Maurizio de Martino
- Department of Health Sciences; University of Florence; Anna Meyer Children's University Hospital; Florence Italy
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Simultaneous direct identification of genital microorganisms in voided urine using multiplex PCR-based reverse line blot assays. Methods Mol Biol 2013; 943:229-45. [PMID: 23104293 DOI: 10.1007/978-1-60327-353-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Our aim was to develop and evaluate sensitive methods that would allow simultaneous direct identification of multiple potential pathogens in clinical specimens for diagnosis and epidemiological studies, using a multiplex PCR-based reverse line blot assay. We have previously developed assays suitable for detection of bacterial respiratory and systemic pathogens. In this chapter we describe, in detail, a method developed to identify 14 genital microorganisms, for use in epidemiological studies of genital infection or colonization, using first voided urine specimens. The 14 urogenital pathogens or putative pathogens studied were Trichomonas vaginalis, Streptococcus pneumoniae, Neisseria gonorrhoeae, N. meningitidis, Chlamydia trachomatis, Ureaplasma parvum, U. urealyticum, Mycoplasma hominis, M. genitalium, Gardnerella vaginalis, Haemophilus influenzae, herpes simplex virus 1 and 2, and adenovirus. Two species-specific primer pairs and probes were designed for each target. The method was validated using a reference strain or a well-characterized clinical isolate of each target organism. In a clinical study among men attending sexual health clinics in Sydney, we used the assay to compare rates of detection of the 14 organisms in men with urethritis with those in asymptomatic controls and found the method to be sensitive, specific, convenient, and relatively inexpensive.
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Waites KB, Xiao L, Paralanov V, Viscardi RM, Glass JI. Molecular methods for the detection of Mycoplasma and ureaplasma infections in humans: a paper from the 2011 William Beaumont Hospital Symposium on molecular pathology. J Mol Diagn 2012; 14:437-50. [PMID: 22819362 PMCID: PMC3427874 DOI: 10.1016/j.jmoldx.2012.06.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 06/12/2012] [Accepted: 06/22/2012] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma and Ureaplasma species are well-known human pathogens responsible for a broad array of inflammatory conditions involving the respiratory and urogenital tracts of neonates, children, and adults. Greater attention is being given to these organisms in diagnostic microbiology, largely as a result of improved methods for their laboratory detection, made possible by powerful molecular-based techniques that can be used for primary detection in clinical specimens. For slow-growing species, such as Mycoplasma pneumoniae and Mycoplasma genitalium, molecular-based detection is the only practical means for rapid microbiological diagnosis. Most molecular-based methods used for detection and characterization of conventional bacteria have been applied to these organisms. A complete genome sequence is available for one or more strains of all of the important human pathogens in the Mycoplasma and Ureaplasma genera. Information gained from genome analyses and improvements in efficiency of DNA sequencing are expected to significantly advance the field of molecular detection and genotyping during the next few years. This review provides a summary and critical review of methods suitable for detection and characterization of mycoplasmas and ureaplasmas of humans, with emphasis on molecular genotypic techniques.
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Affiliation(s)
- Ken B Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35226, USA.
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12
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Nasopharyngeal carriage of Streptococcus pneumoniae: prevalence and risk factors in HIV-positive children in Tanzania. Int J Infect Dis 2012; 16:e753-7. [PMID: 22884165 DOI: 10.1016/j.ijid.2012.05.1037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 05/15/2012] [Accepted: 05/16/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Pneumococcal colonization of the nasopharynx is especially common in young children and is a pre-requisite for pneumococcal disease. Those with immunosuppression, such as HIV, are at higher risk of colonization and disease, especially at older ages. Currently, vaccination schedules are only offered to children under 6 months of age, despite the large impact of pneumococcal disease in older unvaccinated children with HIV. We conducted a study to assess the prevalence of, and risk factors for, pneumococcal carriage in HIV-positive children aged <15 years. METHODS We collected a single nasopharyngeal swab from 142 HIV-infected children aged 1-14 years over a 2-month period. To detect carriage of pneumococcus, these samples were cultured and serotyped; PCR was performed on negative samples. We also collected epidemiological data via survey and medical records. RESULTS The overall carriage rate was 81% and was at least 76% in those aged 5-14 years. The 7-, 10-, and 13-valent pneumococcal vaccines would cover 37%, 37%, and 49% of children with carriage, respectively. In the multivariate analysis, we identified increase in weight since last visit (p=0.028) and the existence of care-givers who had respiratory symptoms in the past week (p=0.022) as risk factors for carriage. Weight gain was also significantly associated with antiretroviral use (p=0.002). CONCLUSIONS These data illuminate the little known area of pneumococcal carriage in older HIV-infected children as well as finding novel risk factors for pneumococcal carriage, namely the association with household members who have respiratory symptoms and with an increase in the child's weight prior to swabbing. Weight gain may be due to an increase in health enabling more mobility and increasing the risk of acquiring carriage. The carriage rate observed (81%) is one of the highest recorded. Further research should address whether vaccination can prevent the acquisition of carriage and so protect against disease.
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Sankar S, Ramamurthy M, Nandagopal B, Srikanth P, Venkatraman G, Sridharan G. Molecular and nanotechnologic approaches to etiologic diagnosis of infectious syndromes. Mol Diagn Ther 2011; 15:145-58. [PMID: 21766906 PMCID: PMC7100041 DOI: 10.1007/bf03256405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Infectious diseases are a major global public health problem. Multiple agents are now recognized to cause indistinguishable illnesses. The term ‘syndrome’ applies to such situations, for which early and rapid diagnosis of the infecting agent would enable prompt and appropriate therapy. Public health physicians would also get timely information on the specific etiology of the infectious syndrome, facilitating intervention at the community level in the face of outbreaks or epidemics. A variety of molecular techniques have been evaluated for rapid diagnosis of infectious syndromes. These techniques include real-time multiplex PCR, DNA microarray, loop-mediated isothermal amplification, and other similar assays. This review surveys such state-of-the-art technologies.
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Affiliation(s)
- Sathish Sankar
- Division of Biomedical Research, Sri Narayani Hospital and Research Centre, Thirumalaikodi, Sripuram, Vellore, Tamil Nadu, India.
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Cao Y, Kong F, Zhou F, Xiao M, Wang Q, Duan Y, Kesson AM, McPhie K, Gilbert GL, Dwyer DE. Genotyping of human adenoviruses using a PCR-based reverse line blot hybridisation assay. Pathology 2011; 43:488-94. [PMID: 21670723 DOI: 10.1097/pat.0b013e328348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Human adenoviruses are common pathogens associated with a broad spectrum of disease. There is a growing clinical interest in typing clinical isolates since it is becoming increasingly clear that individual serotypes are associated with different disease spectra, virulence, severity of consequences, and outbreaks. Current methods cannot detect all known adenoviruses simultaneously and rapidly. We designed a practical adenovirus typing method with polymerase chain reaction (PCR)-based reverse line blot hybridisation assay (RLB) using hypervariable region-7 (HVR-7) in the hexon gene. METHODS A PCR-RLB assay was developed based on HVR-7 in the hexon region for potentially genotyping 51 adenovirus serotypes by hybridisation of 62 genotype-specific probes using amplicons generated from one genus-specific primer pair. Single PCR and sequencing were performed for confirmation of RLB results. Eighty-seven previously serotyped clinical isolates (representing 28 serotypes) were studied. RESULTS Thirty-two different genotypes were detected by RLB from 87 adenovirus isolates, of which 82 isolates showed consistent results with sequencing. Another five isolates revealed evidence by RLB of co-infection, and were confirmed with a combination of genotype-specific single PCR and sequencing. CONCLUSIONS In comparison to sequencing and serological methods, the advantages of the RLB assay include: (1) rapid genotyping of multiple samples in a single run; (2) successful detection of co-infection; (3) detection of subgenotype variants. This will allow rapid and inexpensive characterisation of adenovirus infections and outbreaks.
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Affiliation(s)
- Yongyan Cao
- Research Laboratory for Infectious Skin Diseases, Department of Dermatology, Wuhan First Hospital, Wuhan, PR China
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Strachan RE, Cornelius A, Gilbert GL, Gulliver T, Martin A, McDonald T, Nixon GM, Roseby R, Ranganathan S, Selvadurai H, Smith G, Soto-Martinez M, Suresh S, Teoh L, Thapa K, Wainwright CE, Jaffe A. Bacterial causes of empyema in children, Australia, 2007-2009. Emerg Infect Dis 2011; 17:1839-45. [PMID: 22000353 PMCID: PMC3310657 DOI: 10.3201/eid1710.101825] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An increase in the incidence of empyema worldwide could be related to invasive pneumococcal disease caused by emergent nonvaccine replacement serotypes. To determine bacterial pathogens and pneumococcal serotypes that cause empyema in children in Australia, we conducted a 2-year study of 174 children with empyema. Blood and pleural fluid samples were cultured, and pleural fluid was tested by PCR. Thirty-two (21.0%) of 152 blood and 53 (33.1%) of 160 pleural fluid cultures were positive for bacteria; Streptococcus pneumoniae was the most common organism identified. PCR identified S. pneumoniae in 74 (51.7%) and other bacteria in 19 (13.1%) of 145 pleural fluid specimens. Of 53 samples in which S. pneumoniae serotypes were identified, 2 (3.8%) had vaccine-related and 51 (96.2%) had nonvaccine serotypes; 19A (n = 20; 36.4%), 3 (n = 18; 32.7%), and 1 (n = 8; 14.5%) were the most common. High proportions of nonvaccine serotypes suggest the need to broaden vaccine coverage.
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O'Sullivan MVN, Zhou F, Sintchenko V, Kong F, Gilbert GL. Multiplex PCR and reverse line blot hybridization assay (mPCR/RLB). J Vis Exp 2011:2781. [PMID: 21847083 PMCID: PMC3211120 DOI: 10.3791/2781] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Multiplex PCR/Reverse Line Blot Hybridization assay allows the detection of up to 43 molecular targets in 43 samples using one multiplex PCR reaction followed by probe hybridization on a nylon membrane, which is re-usable. Probes are 5' amine modified to allow fixation to the membrane. Primers are 5' biotin modified which allows detection of hybridized PCR products using streptavidin-peroxidase and a chemiluminescent substrate via photosensitive film. With low setup and consumable costs, this technique is inexpensive (approximately US$2 per sample), high throughput (multiple membranes can be processed simultaneously) and has a short turnaround time (approximately 10 hours). The technique can be utilized in a number of ways. Multiple probes can be designed to detect sequence variation within a single amplified product, or multiple products can be amplified simultaneously, with one (or more) probes used for subsequent detection. A combination of both approaches can also be used within a single assay. The ability to include multiple probes for a single target sequence makes the assay highly specific. Published applications of mPCR/RLB include detection of antibiotic resistance genes(1,2), typing of methicillin-resistant Staphylococcus aureus(3-5) and Salmonella sp(6), molecular serotyping of Streptococcus pneumoniae(7,8), Streptococcus agalactiae(9) and enteroviruses(10,11), identification of Mycobacterium sp(12), detection of genital(13-15) and respiratory tract(16) and other(17) pathogens and detection and identification of mollicutes(18). However, the versatility of the technique means the applications are virtually limitless and not restricted to molecular analysis of micro-organisms. The five steps in mPCR/RLB are a) Primer and Probe design, b) DNA extraction and PCR amplification c) Preparation of the membrane, d) Hybridization and detection, and e) Regeneration of the Membrane.
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17
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Cuevas LE. The urgent need for new diagnostics for symptomatic tuberculosis in children. Indian J Pediatr 2011; 78:449-55. [PMID: 21188551 DOI: 10.1007/s12098-010-0354-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 12/08/2010] [Indexed: 11/28/2022]
Abstract
TB is a major public health problem causing 9 million cases, of which 10%-15% occur in children each year. Historically, children have received lower priority within TB control activities because they are considered less infectious than smear-positive adults. This review argues that TB is a public health problem in children and that poor awareness of the magnitude of the problem emanates from the lack of suitable pediatric diagnostic tests for TB and the characteristics of the disease in young children. New TB diagnostics, approved for use in adults have not been evaluated in children, although there is limited evidence that some of these tests hold promise and should be assessed. There are several approaches that could be used to improve the performance of tests in pediatric patients. These include improved methods for specimen collection and processing. The value of collecting specimens from multiple anatomical sites to shorten the diagnostic process and improve sensitivity was reported recently and the combination of expectorated sputum, nasopharyngeal aspirate, induce sputum and gastric aspirate may result in a similar yield than specimens collected over consecutive days. Methods for sample collection such as fine needle aspiration biopsy should be used more frequently and the Microscopic Observation Drug Sensitivity (MODS) assay has higher sensitivity than LJ culture. There is however very scanty evidence of the performance of other promising tests such as the fully automated NAAT (Xpert) and Line Probe Assays and loop mediated isothermal amplification. Although the future holds promise, increased support from international organizations and funding agencies is needed to promote the evaluation and development of new diagnostics that are suitable for TB in children.
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Affiliation(s)
- Luis E Cuevas
- UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases, Geneva, Switzerland.
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18
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Zahn LM, Ma X, Altman NS, Zhang Q, Wall PK, Tian D, Gibas CJ, Gharaibeh R, Leebens-Mack JH, dePamphilis CW, Ma H. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biol 2010; 11:R101. [PMID: 20950453 PMCID: PMC3218657 DOI: 10.1186/gb-2010-11-10-r101] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/03/2010] [Accepted: 10/15/2010] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Molecular genetic studies of floral development have concentrated on several core eudicots and grasses (monocots), which have canalized floral forms. Basal eudicots possess a wider range of floral morphologies than the core eudicots and grasses and can serve as an evolutionary link between core eudicots and monocots, and provide a reference for studies of other basal angiosperms. Recent advances in genomics have enabled researchers to profile gene activities during floral development, primarily in the eudicot Arabidopsis thaliana and the monocots rice and maize. However, our understanding of floral developmental processes among the basal eudicots remains limited. RESULTS Using a recently generated expressed sequence tag (EST) set, we have designed an oligonucleotide microarray for the basal eudicot Eschscholzia californica (California poppy). We performed microarray experiments with an interwoven-loop design in order to characterize the E. californica floral transcriptome and to identify differentially expressed genes in flower buds with pre-meiotic and meiotic cells, four floral organs at preanthesis stages (sepals, petals, stamens and carpels), developing fruits, and leaves. CONCLUSIONS Our results provide a foundation for comparative gene expression studies between eudicots and basal angiosperms. We identified whorl-specific gene expression patterns in E. californica and examined the floral expression of several gene families. Interestingly, most E. californica homologs of Arabidopsis genes important for flower development, except for genes encoding MADS-box transcription factors, show different expression patterns between the two species. Our comparative transcriptomics study highlights the unique evolutionary position of E. californica compared with basal angiosperms and core eudicots.
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Affiliation(s)
- Laura M Zahn
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: American Association for the Advancement of Science, 1200 New York Avenue NW, Washington DC 20005, USA
| | - Xuan Ma
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- The Intercollege Graduate Program in Cell and Developmental Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Naomi S Altman
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qing Zhang
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: 2367 Setter Run Lane, State College, PA 16802, USA
| | - P Kerr Wall
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: BASF Plant Science, 26 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Donglan Tian
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cynthia J Gibas
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Raad Gharaibeh
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - James H Leebens-Mack
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602, USA
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hong Ma
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- The Intercollege Graduate Program in Cell and Developmental Biology, The Pennsylvania State University, University Park, PA 16802, USA
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
- Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
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19
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Wang H, Kong F, Wang B, Mckechnie ML, Gilbert GL. Multiplex polymerase chain reaction-based reverse line blot hybridization assay to detect common genital pathogens. Int J STD AIDS 2010; 21:320-5. [PMID: 20498099 DOI: 10.1258/ijsa.2009.008481] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The objective of the present paper is to develop and apply a multiplex polymerase chain reaction (mPCR) based reverse line blot (RLB) hybridization assay to facilitate the diagnosis of genital infections by detection of seven recognized or putative genital pathogens (Neisseria gonorrhoeae, Chlamydia trachomatis, Ureaplasma urealyticum, Ureaplasma parvum, Mycoplasma genitalium, Mycoplasma hominis and Trichomonas vaginalis). Species-specific biotin-labelled primer pairs were used in a single mPCR to amplify target regions in each of seven pathogens. The amplified biotin-labelled PCR products were hybridized with membrane-bound-specific oligonucleotide probes and were detected by chemiluminescence. Two hundred and eleven specimens (104 male urethral and 107 female vaginal swabs), collected from patients with suspected genital infections attending the Wuhan First Hospital Sexually Transmitted Diseases (STD) clinic, were tested by mPCR/RLB and results were confirmed by single PCR using different species-specific targets. The sensitivity of the assay was assessed using dilutions of positive DNA controls with known copy numbers, for each target. The assay correctly identified all reference strains and detected potential pathogens in a high proportion of clinical specimens. There was no cross-reaction between the seven pathogens. The mPCR/RLB can detect <or= 10(2) copies of the target gene fragments. Comparison of mPCR/RLB and single PCR assays showed discrepant results in six of 211 (2.8%) clinical specimens, which were positive by mPCR/RLB assay, but negative by the corresponding single PCR. Nested PCR on the six discrepant specimens gave results consistent with those of mPCR/RLB. In conclusion, the mPCR/RLB hybridization assay is sensitive and specific, and able to rapidly detect genital pathogens in clinical specimens.
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Affiliation(s)
- H Wang
- Research Laboratory for Infectious Skin Diseases, Department of Dermatology, Wuhan First Hospital, Wuhan 430022, P R China
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20
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Sy MG, Robinson JL. Community-acquired Moraxella catarrhalis pneumonia in previously healthy children. Pediatr Pulmonol 2010; 45:674-8. [PMID: 20575092 DOI: 10.1002/ppul.21243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND The aim of this study was to determine if Moraxella catarrhalis is a common cause of community acquired pneumonia in children with no chronic medical problems. A secondary goal was to describe the clinical features of children with M. catarrhalis pneumonia. METHODS A systematic literature search was conducted for (i) case series of pediatric community-acquired pneumonia (CAP) where one or more diagnostic tests for M. catarrhalis were applied to all cases and (ii) case reports of previously healthy children with proven M. catarrhalis pneumonia. RESULTS There were nine case series describing a total of 1,500 children with CAP. The number of children tested and yield was as follows: blood cultures 0/402 (0%); sputum cultures 15/157 (10%); nasopharyngeal, or postnasal cultures 129/521 (25%); sputum or nasopharyngeal cultures 0/74 (0%) (one study allowed either); nucleic acid amplification testing 2/100 (2%); serology 30/976 (3%). There were eight case reports of CAP with M. catarrhalis in previously well children. Children were ages 3 weeks to 7 years of age (median 14 months). Six of 8 (75%) children required mechanical ventilation. All survived. CONCLUSION It is common to detect M. catarrhalis in upper respiratory secretions in children with pneumonia, but bacteremia or seroconversion is rare. There are only eight well-documented case reports CAP due to M. catarrhalis in previously well children, with there being no distinctive features in the eight cases described to date. This organism is likely a rare cause of CAP in previously healthy children.
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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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22
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Pozzetto B, Grattard F, Pillet S. Multiplex PCR theranostics of severe respiratory infections. Expert Rev Anti Infect Ther 2010; 8:251-3. [PMID: 20192677 PMCID: PMC7103703 DOI: 10.1586/eri.09.131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Bruno Pozzetto
- Laboratory of Bacteriology–Virology–Hygiene, University of Lyon – GIMAP EA 3064, University-Hospital of Saint-Etienne, 15 rue Ambroise Paré, 42023 Saint-Etienne cedex 02, France.
- † Author for correspondence
| | - Florence Grattard
- Laboratory of Bacteriology–Virology–Hygiene, University of Lyon – GIMAP EA 3064, University-Hospital of Saint-Etienne, 15 rue Ambroise Paré, 42023 Saint-Etienne cedex 02, France
| | - Sylvie Pillet
- Laboratory of Bacteriology–Virology–Hygiene, University of Lyon – GIMAP EA 3064, University-Hospital of Saint-Etienne, 15 rue Ambroise Paré, 42023 Saint-Etienne cedex 02, France
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23
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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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Gilbert GL, Selgelid M. Populations, Patients, Germs and Genes: Ethics Of Genomics and Informatics in Communicable Disease Control. INFECTIOUS DISEASE INFORMATICS 2010. [PMCID: PMC7122797 DOI: 10.1007/978-1-4419-1327-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
This chapter will explore the ways in which genomics (and the informatics tools needed to analyze and interpret them) could, potentially, transform our understanding of infectious disease epidemiology, improve disease management and prevention and save lives. The integration of microbiological, clinical and environmental data into personalized clinical decision support and risk assessment tools will improve both the care of patients with infectious diseases and public health protection. Integrated electronic health information systems will be faster, safer and more cost-effective than the current inefficient miscellany of individual medical records and disease surveillance systems. Technical, commercial and economic barriers to system implementation are unlikely to be insurmountable, but the largely uncharted ethical hazards are potentially more challenging. Prospective evaluation of clinical and public health impact and cost-effectiveness of new diagnostic and surveillance methods and information systems, designed to protect privacy and security of health data without placing unnecessary restrictions on access to essential public health data, will be needed. The interests, priorities and concerns of all stakeholders, including patients and potential patients, health professionals and administrators, public health officials and politicians, must be openly debated and addressed. Otherwise, unnecessary delays or a failure to implement better systems will allow unnecessary suffering and preventable mortality to continue.
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PCR using blood for diagnosis of invasive pneumococcal disease: systematic review and meta-analysis. J Clin Microbiol 2009; 48:489-96. [PMID: 20007385 DOI: 10.1128/jcm.01636-09] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The use of molecular-based methods for the diagnosis of bacterial infections in blood is appealing, but they have not yet passed the threshold for clinical practice. A systematic review of prospective and case-control studies assessing the diagnostic utility of PCR directly with blood samples for the diagnosis of invasive pneumococcal disease (IPD) was performed. A broad search was conducted to identify published and unpublished studies. Two reviewers independently extracted the data. Summary estimates for sensitivity and specificity with 95% confidence intervals (CIs) were calculated by using the hierarchical summary receiver operating characteristic method. The effects of sample processing, PCR type, the gene-specific primer, study design, the participants' age, and the source of infection on the diagnostic odds ratios were assessed through meta-regression. Twenty-nine studies published between 1993 and 2009 were included. By using pneumococcal bacteremia for case definition and healthy people or patients with bacteremia caused by other bacteria as controls (22 studies), the summary estimates for sensitivity and specificity were 57.1% (95% CI, 45.7 to 67.8%) and 98.6% (95% CI, 96.4 to 99.5%), respectively. When the controls were patients suspected of having IPD without pneumococcal bacteremia (26 studies), the respective values were 66.4% (95% CI, 55.9 to 75.6%) and 87.8% (95% CI, 79.5 to 93.1%). With lower degrees of proof for IPD (any culture or serology result and the clinical impression), the sensitivity of PCR decreased and the specificity increased. All analyses were highly heterogeneous. The use of nested PCR and being a child were associated with low specificity, while the use of a cohort study design was associated with a low sensitivity. The lack of an appropriate reference standard might have caused underestimation of the performance of the PCR. Currently available methods for PCR with blood samples for the diagnosis of IPD lack the sensitivity and specificity necessary for clinical practice.
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Identification of pathogenic Nocardia species by reverse line blot hybridization targeting the 16S rRNA and 16S-23S rRNA gene spacer regions. J Clin Microbiol 2009; 48:503-11. [PMID: 19955277 DOI: 10.1128/jcm.01761-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although 16S rRNA gene sequence analysis is employed most often for the definitive identification of Nocardia species, alternate molecular methods and polymorphisms in other gene targets have also enabled species determinations. We evaluated a combined Nocardia PCR-based reverse line blot (RLB) hybridization assay based on 16S and 16S-23S rRNA gene spacer region polymorphisms to identify 12 American Type Culture Collection and 123 clinical Nocardia isolates representing 14 species; results were compared with results from 16S rRNA gene sequencing. Thirteen 16S rRNA gene-based (two group-specific and 11 species-specific) and five 16S-23S spacer-targeted (two taxon-specific and three species-specific) probes were utilized. 16S rRNA gene-based probes correctly identified 124 of 135 isolates (sensitivity, 92%) but were unable to identify Nocardia paucivorans strains (n = 10 strains) and a Nocardia asteroides isolate with a novel 16S rRNA gene sequence. Nocardia farcinica and Nocardia cyriacigeorgica strains were identified by the sequential use of an N. farcinica-"negative" probe and a combined N. farcinica/N. cyriacigeorgica probe. The assay specificity was high (99%) except for weak cross-reactivity between the Nocardia brasiliensis probe with the Nocardia thailandica DNA product; however, cross-hybridization with closely related nontarget species may occur. The incorporation of 16S-23S rRNA gene spacer-based probes enabled the identification of all N. paucivorans strains. The overall sensitivity using both probe sets was >99%. Both N. farcinica-specific 16S-23S rRNA gene spacer-directed probes were required to identify all N. farcinica stains by using this probe set. The study demonstrates the utility of a combined PCR/RLB assay for the identification of clinically relevant Nocardia species and its potential for studying subtypes of N. farcinica. Where species assignment is ambiguous or not possible, 16S rRNA gene sequencing is recommended.
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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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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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