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Ozbay S, Ayan M, Ozsoy O, Akman C, Karcioglu O. Diagnostic and Prognostic Roles of Procalcitonin and Other Tools in Community-Acquired Pneumonia: A Narrative Review. Diagnostics (Basel) 2023; 13:diagnostics13111869. [PMID: 37296721 DOI: 10.3390/diagnostics13111869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Community-acquired pneumonia (CAP) is among the most common causes of death and one of the leading healthcare concerns worldwide. It can evolve into sepsis and septic shock, which have a high mortality rate, especially in critical patients and comorbidities. The definitions of sepsis were revised in the last decade as "life-threatening organ dysfunction caused by a dysregulated host response to infection". Procalcitonin (PCT), C-reactive protein (CRP), and complete blood count, including white blood cells, are among the most commonly analyzed sepsis-specific biomarkers also used in pneumonia in a broad range of studies. It appears to be a reliable diagnostic tool to expedite care of these patients with severe infections in the acute setting. PCT was found to be superior to most other acute phase reactants and indicators, including CRP as a predictor of pneumonia, bacteremia, sepsis, and poor outcome, although conflicting results exist. In addition, PCT use is beneficial to judge timing for the cessation of antibiotic treatment in most severe infectious states. The clinicians should be aware of strengths and weaknesses of known and potential biomarkers in expedient recognition and management of severe infections. This manuscript is intended to present an overview of the definitions, complications, and outcomes of CAP and sepsis in adults, with special regard to PCT and other important markers.
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Affiliation(s)
- Sedat Ozbay
- Department of Emergency Medicine, Sivas Numune Education and Research Hospital, Sivas 58040, Turkey
| | - Mustafa Ayan
- Department of Emergency Medicine, Sivas Numune Education and Research Hospital, Sivas 58040, Turkey
| | - Orhan Ozsoy
- Department of Emergency Medicine, Sivas Numune Education and Research Hospital, Sivas 58040, Turkey
| | - Canan Akman
- Department of Emergency Medicine, Canakkale Onsekiz Mart University, Canakkale 17100, Turkey
| | - Ozgur Karcioglu
- Department of Emergency Medicine, University of Health Sciences, Taksim Education and Research Hospital, Beyoglu, Istanbul 34098, Turkey
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2
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Ansari S, Yamaoka Y. Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance. Clin Microbiol Rev 2022; 35:e0025821. [PMID: 35404105 PMCID: PMC9491184 DOI: 10.1128/cmr.00258-21] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.
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Affiliation(s)
- Shamshul Ansari
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, USA
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
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3
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O'Hagan S, Nelson P, Speirs L, Moriarty P, Mallett P. How to interpret a paediatric blood culture. Arch Dis Child Educ Pract Ed 2021; 106:244-250. [PMID: 33637581 DOI: 10.1136/archdischild-2020-321121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 11/04/2022]
Abstract
Blood culture is one of the most important diagnostic tests in medicine, considering the significant morbidity and mortality associated with bloodstream infection (BSI). However, it is an often misused and misinterpreted test in everyday paediatric practice. In this article, we explore the evidence related to paediatric blood cultures, with the aim of providing clear and clinically-relevant recommendations for its judicious use.
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Affiliation(s)
- Shaun O'Hagan
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK shaun.o'
| | - Peter Nelson
- Clinical Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Lynne Speirs
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Paul Moriarty
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Peter Mallett
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
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4
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de Benedictis FM, Kerem E, Chang AB, Colin AA, Zar HJ, Bush A. Complicated pneumonia in children. Lancet 2020; 396:786-798. [PMID: 32919518 DOI: 10.1016/s0140-6736(20)31550-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/20/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022]
Abstract
Complicated community-acquired pneumonia in a previously well child is a severe illness characterised by combinations of local complications (eg, parapneumonic effusion, empyema, necrotising pneumonia, and lung abscess) and systemic complications (eg, bacteraemia, metastatic infection, multiorgan failure, acute respiratory distress syndrome, disseminated intravascular coagulation, and, rarely, death). Complicated community-acquired pneumonia should be suspected in any child with pneumonia not responding to appropriate antibiotic treatment within 48-72 h. Common causative organisms are Streptococcus pneumoniae and Staphylococcus aureus. Patients have initial imaging with chest radiography and ultrasound, which can also be used to assess the lung parenchyma, to identify pleural fluid; CT scanning is not usually indicated. Complicated pneumonia is treated with a prolonged course of intravenous antibiotics, and then oral antibiotics. The initial choice of antibiotic is guided by local microbiological knowledge and by subsequent positive cultures and molecular testing, including on pleural fluid if a drainage procedure is done. Information from pleural space imaging and drainage should guide the decision on whether to administer intrapleural fibrinolytics. Most patients are treated by drainage and more extensive surgery is rarely needed; in any event, in low-income and middle-income countries, resources for extensive surgeries are scarce. The clinical course of complicated community-acquired pneumonia can be prolonged, especially when patients have necrotising pneumonia, but complete recovery is the usual outcome.
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Affiliation(s)
| | - Eitan Kerem
- Department of Pediatrics, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia; Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, QLD, Australia; Centre for Healthcare Transformation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Andrew A Colin
- Division of Pediatric Pulmonology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross Children's Hospital, Cape Town, South Africa; MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Andrew Bush
- Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, UK; National Heart and Lung Institute, Imperial School of Medicine, Imperial College London, London, UK.
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5
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de Benedictis FM, Carloni I. Management of necrotizing pneumonia in children: Time for a patient-oriented approach. Pediatr Pulmonol 2019; 54:1351-1353. [PMID: 31254327 DOI: 10.1002/ppul.24412] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 11/09/2022]
Affiliation(s)
| | - Ines Carloni
- Department of Mother and Child Health, Salesi Children's Hospital, Ancona, Italy
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6
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Azzari C, Serranti D, Nieddu F, Moriondo M, Casini A, Lodi L, de Benedictis FM, De Vitis E, Cavone F, Cortimiglia M, Indolfi G, Lombardi E, Carloni I, Cutrera R, Lucenteforte E, Resti M, Ricci S. Significant impact of pneumococcal conjugate vaccination on pediatric parapneumonic effusion: Italy 2006-2018. Vaccine 2019; 37:2704-2711. [PMID: 30981627 DOI: 10.1016/j.vaccine.2019.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
Abstract
Etiology and serotyping of parapneumonic effusion (PPE) and the impact of vaccination was evaluated over a 12-year period, before and after the PCV13 introduction (2011) for Italian children From 0 to 16 years of age. Five hundred and two children were evaluated; 226 blood and 356 pleural fluid samples were obtained and tested using Realtime-PCR and culture. In the pre-PCV13 era S. pneumoniae was the most frequent pathogen identified (64/90; 71.1%) with a large predominance of serotypes 1 (42.4%), 3 (23.7%), 7F (5.1%) and 19A (11.9%). The impact of vaccination, calculated on children 0-8 years of age, demonstrated a significant reduction of PPE: with an incidence rate of 2.82 (95%CL 2.32-3.41) in the pre-PCV13 era and an age-standardized rate (ASR) of 0.66 (95% CL 0.37-1.99) in the post-PCV13 era, p < 0.0001. No increase in non-PCV13 serotypes was recorded. S. pneumoniae remained the most frequent pathogen identified in the post-PCV13 era in unvaccinated children with an unchanged serotype distribution: respectively 26/66 (39.4%), 25/66 (37.9%), 5/66 (7.6%), and 4/66 (6.1%) for 1, 3, 7F and 19A. On the other hand 7F and 19A disappeared in vaccinated children and serotype 1 and 3 decreased by 91.8% and 31.5%, respectively. Realtime PCR was significantly more sensitive than culture both in pleural fluid (79.7% vs 12.5%) and in blood (17.8% vs 7.4%). In conclusion, our findings indicate that routine immunization with PCV13 has significantly reduced the burden of childhood PPE in vaccinated children, without increasing PPE due to other bacteria and without serotype shift. Moreover, the impact of PCV13 may be underestimated due to the increase in pneumococcal surveillance in Italy. Data has also shown that Real-time PCR is an essential tool to better define the etiology of PPE and to monitor vaccination plans. Longer studies will be necessary to evaluate the role of herd protection in PPE prevention.
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Affiliation(s)
- Chiara Azzari
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Daniele Serranti
- Department of Pediatrics, Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Francesco Nieddu
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Maria Moriondo
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Arianna Casini
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Lorenzo Lodi
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | | | - Elisa De Vitis
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Federica Cavone
- Department of Pediatrics, Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy
| | - Martina Cortimiglia
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Giuseppe Indolfi
- Department of Pediatrics, Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Enrico Lombardi
- Department of Pediatrics, Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Ines Carloni
- Pediatric Unit, Salesi Childrens Hospital, Department of Mother and Child Health, Via Filippo Corridoni 10, 60123 Ancona, Italy.
| | - Renato Cutrera
- Ospedale Bambino Gesù, Pediatrics - Respiratory Unit, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - Ersilia Lucenteforte
- Medical Statistics, Department of Clinical and Experimental Medicine, University of Pisa, Italy.
| | - Massimo Resti
- Department of Pediatrics, Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
| | - Silvia Ricci
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Viale Pieraccini 24, 50139 Florence, Italy.
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7
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Park CE. Evaluation of the Effectiveness of Surveillance on Improving the Detection of Healthcare Associated Infections. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2019. [DOI: 10.15324/kjcls.2019.51.1.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Chang-Eun Park
- Department of Biomedical Laboratory Science, Molecular Diagnostics Research Institute, Namseoul University, Cheonan, Korea
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8
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Guiducci S, Moriondo M, Nieddu F, Ricci S, De Vitis E, Casini A, Poggi GM, Indolfi G, Resti M, Azzari C. Culture and Real-time Polymerase Chain reaction sensitivity in the diagnosis of invasive meningococcal disease: Does culture miss less severe cases? PLoS One 2019; 14:e0212922. [PMID: 30865671 PMCID: PMC6415896 DOI: 10.1371/journal.pone.0212922] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/12/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Invasive meningococcal disease (IMD) is a highly lethal disease. Diagnosis is commonly performed by culture or Realtime-PCR (qPCR). AIMS Our aim was to evaluate, retrospectively, whether culture positivity correlates with higher bacterial load and fatal outcome. Our secondary aim was to compare culture and qPCR sensitivity. METHODS The National Register for Molecular Surveillance was used as data source. Cycle threshold (CT), known to be inversely correlated with bacterial load, was used to compare bacterial load in different samples. RESULTS Three-hundred-thirteen patients were found positive for Neisseria meningitidis by qPCR, or culture, or both; 41 died (case fatality rate 13.1%); 128/143 (89.5%) blood samples and 138/144 (95.8%) CSF were positive by qPCR, 37/143 (25.9%) blood samples and 45/144 (31.2%) CSF were also positive in culture. qPCR was 3.5 times (blood) or 3.1 times (CSF) more sensitive than culture in achieving a laboratory diagnosis of IMD (OR 24.4; 95% CI 12.2-49.8; p < .10-4; Cohen's κ 0.08 for blood and OR 49.0; 95% CI 19.1-133.4; p<10-4; Cohen's κ 0.02; for CSF). Positivity of culture did not correlate with higher bacterial loads in blood (mean CT 27.7±5.71, and CT 28.1±6.03, p = 0.739 respectively in culture positive or negative samples) or in CSF (mean CT 23.1±4.9 and 24.7±5.4 respectively in positive or negative CSF samples, p = 0.11).CT values in blood from patients who died were significantly lower than in patients who survived (respectively mean 18.0, range 14-23 and mean 29.6, range 16-39; p<10-17). No deaths occurred in patients with CT in blood over 23. Positive blood cultures were found in 10/25 (40%) patients who died and in 32/163 (19.6%) patients who survived, p = 0.036, OR 2.73; 95% CL 1.025-7.215), however 60% of deaths would have remained undiagnosed with the use of culture only. CONCLUSIONS In conclusion our study demonstrated that qPCR is significantly (at least 3 times) more sensitive than culture in the laboratory confirmation of IMD. The study also demonstrated that culture negativity is not associated with lower bacterial loads and with less severe cases. On the other side, in patients with sepsis, qPCR can predict fatal outcome since higher bacterial load, evaluated by qPCR, appears strictly associated with most severe cases and fatal outcome. The study also showed that molecular techniques such as qPCR can provide a valuable addition to the proportion of diagnosed and serotyped cases of IMD.
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Affiliation(s)
- Sara Guiducci
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
- Pediatric Clinic 2, Pediatric Immunology, Meyer Children’s Hospital, Florence, Italy
| | - Maria Moriondo
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
| | - Francesco Nieddu
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
- Pediatric Clinic 2, Pediatric Immunology, Meyer Children’s Hospital, Florence, Italy
- * E-mail:
| | - Silvia Ricci
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
- Pediatric Clinic 2, Pediatric Immunology, Meyer Children’s Hospital, Florence, Italy
| | - Elisa De Vitis
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
- Pediatric Clinic 2, Pediatric Immunology, Meyer Children’s Hospital, Florence, Italy
| | - Arianna Casini
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
| | - Giovanni Maria Poggi
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
- Department of Interdisciplinary Pediatrics, Section of Medical Pediatrics, Meyer Children's Hospital, Florence, Italy
| | - Giuseppe Indolfi
- Department of Interdisciplinary Pediatrics, Section of Medical Pediatrics, Meyer Children's Hospital, Florence, Italy
| | - Massimo Resti
- Department of Interdisciplinary Pediatrics, Section of Medical Pediatrics, Meyer Children's Hospital, Florence, Italy
| | - Chiara Azzari
- Department of Health Sciences, Section of Pediatrics, University of Florence, Florence, Italy
- Pediatric Clinic 2, Pediatric Immunology, Meyer Children’s Hospital, Florence, Italy
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9
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Adebanjo T, Lessa FC, Mucavele H, Moiane B, Chauque A, Pimenta F, Massora S, Carvalho MDG, Whitney CG, Sigauque B. Pneumococcal carriage and serotype distribution among children with and without pneumonia in Mozambique, 2014-2016. PLoS One 2018; 13:e0199363. [PMID: 29944695 PMCID: PMC6019677 DOI: 10.1371/journal.pone.0199363] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/06/2018] [Indexed: 11/15/2022] Open
Abstract
Background Pneumococcal colonization is a precursor to pneumonia, and pneumococcal conjugate vaccines (PCV) can decrease vaccine-type (VT) colonization. Pneumococcal colonization studies are traditionally done among healthy children in the community; however, VT colonization prevalence may differ between these children and those with pneumonia. We assessed overall and VT pneumococcal colonization and factors associated with colonization among children with and without pneumonia after Mozambique introduced 10-valent PCV (PCV10) in 2013. Methods We used data from ongoing pneumonia surveillance in children aged <5 years and from cross-sectional nasopharyngeal colonization surveys conducted in October 2014 –April 2015 and October 2015 –May 2016. Pneumonia was defined using WHO standard criteria for radiologically confirmed pneumonia. Children with pneumonia enrolled from January 2014 –April 2016 were compared to children without pneumonia enrolled from the cross-sectional surveys. Clinical data and nasopharyngeal (NP) swabs were collected from each child. NP specimens were cultured for pneumococci, and culture-negative specimens from children with pneumonia underwent polymerase chain reaction (PCR). Results Of 778 and 927 children with and without pneumonia, 97.4% and 27.0% were exposed to antibiotics before swab collection, respectively. Based on culture, pneumococcal colonization was 45.1% for children with and 84.5% for children without pneumonia (P<0.001); VT pneumococcal colonization was 18.6% for children with and 23.4% for children without pneumonia (P = 0.02). The addition of PCR in children with pneumonia increased overall and VT-pneumococcal colonization to 79.2% and 31.1%, respectively. In multivariable analysis including PCR results, pneumonia was associated with VT pneumococcal colonization (adjusted OR: 1.4, 95%CI: 1.10–1.78). Conclusion Vaccine-type pneumococcal colonization remains common among children with and without pneumonia post-PCV10 introduction in Mozambique. In a population of children with high antibiotic exposure, the use of PCR for culture-negative NP swabs can improve assessment of pneumococcal colonization and circulating serotypes.
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Affiliation(s)
- Tolulope Adebanjo
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- * E-mail:
| | - Fernanda C. Lessa
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Helio Mucavele
- Fundação Manhiça, Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Moçambique
| | - Benild Moiane
- Fundação Manhiça, Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Moçambique
| | - Alberto Chauque
- Fundação Manhiça, Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Moçambique
| | - Fabiana Pimenta
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Sergio Massora
- Fundação Manhiça, Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Moçambique
| | - Maria da Gloria Carvalho
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Cynthia G. Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Betuel Sigauque
- Fundação Manhiça, Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Moçambique
- John Snow Inc. (JSI) on the Maternal and Child Survival Program–MCSP (USAID Grantee), Maputo, Moçambique
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10
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Driscoll AJ, Deloria Knoll M, Hammitt LL, Baggett HC, Brooks WA, Feikin DR, Kotloff KL, Levine OS, Madhi SA, O'Brien KL, Scott JAG, Thea DM, Howie SRC, Adrian PV, Ahmed D, DeLuca AN, Ebruke BE, Gitahi C, Higdon MM, Kaewpan A, Karani A, Karron RA, Mazumder R, McLellan J, Moore DP, Mwananyanda L, Park DE, Prosperi C, Rhodes J, Saifullah M, Seidenberg P, Sow SO, Tamboura B, Zeger SL, Murdoch DR. The Effect of Antibiotic Exposure and Specimen Volume on the Detection of Bacterial Pathogens in Children With Pneumonia. Clin Infect Dis 2018; 64:S368-S377. [PMID: 28575366 PMCID: PMC5447850 DOI: 10.1093/cid/cix101] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Background. Antibiotic exposure and specimen volume are known to affect pathogen detection by culture. Here we assess their effects on bacterial pathogen detection by both culture and polymerase chain reaction (PCR) in children. Methods. PERCH (Pneumonia Etiology Research for Child Health) is a case-control study of pneumonia in children aged 1–59 months investigating pathogens in blood, nasopharyngeal/oropharyngeal (NP/OP) swabs, and induced sputum by culture and PCR. Antibiotic exposure was ascertained by serum bioassay, and for cases, by a record of antibiotic treatment prior to specimen collection. Inoculated blood culture bottles were weighed to estimate volume. Results. Antibiotic exposure ranged by specimen type from 43.5% to 81.7% in 4223 cases and was detected in 2.3% of 4863 controls. Antibiotics were associated with a 45% reduction in blood culture yield and approximately 20% reduction in yield from induced sputum culture. Reduction in yield of Streptococcus pneumoniae from NP culture was approximately 30% in cases and approximately 32% in controls. Several bacteria had significant but marginal reductions (by 5%–7%) in detection by PCR in NP/OP swabs from both cases and controls, with the exception of S. pneumoniae in exposed controls, which was detected 25% less frequently compared to nonexposed controls. Bacterial detection in induced sputum by PCR decreased 7% for exposed compared to nonexposed cases. For every additional 1 mL of blood culture specimen collected, microbial yield increased 0.51% (95% confidence interval, 0.47%–0.54%), from 2% when volume was ≤1 mL to approximately 6% for ≥3 mL. Conclusions. Antibiotic exposure and blood culture volume affect detection of bacterial pathogens in children with pneumonia and should be accounted for in studies of etiology and in clinical management.
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Affiliation(s)
- Amanda J Driscoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L Hammitt
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Daniel R Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Orin S Levine
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Katherine L O'Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Stephen R C Howie
- Medical Research Council Unit, Basse, The Gambia.,Department of Paediatrics, University of Auckland, and.,Centre for International Health, University of Otago, Dunedin, New Zealand ; Departments of
| | - Peter V Adrian
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Andrea N DeLuca
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Epidemiology and
| | | | - Caroline Gitahi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Melissa M Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Anek Kaewpan
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Angela Karani
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Ruth A Karron
- International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Razib Mazumder
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Jessica McLellan
- Medical Research Council Unit, Basse, The Gambia.,Cummings School of Medicine, University of Calgary, Alberta, Canada
| | - David P Moore
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, South Africa
| | - Lawrence Mwananyanda
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts.,University Teaching Hospital, Lusaka, Zambia
| | - Daniel E Park
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Julia Rhodes
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Md Saifullah
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Phil Seidenberg
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts.,Department of Emergency Medicine, University of New Mexico, Albuquerque
| | - Samba O Sow
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako
| | | | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; and
| | - David R Murdoch
- Department of Pathology, University of Otago, and.,Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
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11
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Katz SE, Williams DJ. Pediatric Community-Acquired Pneumonia in the United States: Changing Epidemiology, Diagnostic and Therapeutic Challenges, and Areas for Future Research. Infect Dis Clin North Am 2017; 32:47-63. [PMID: 29269189 PMCID: PMC5801082 DOI: 10.1016/j.idc.2017.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Community-acquired pneumonia (CAP) is one of the most common serious infections in childhood. This review focuses on pediatric CAP in the United States and other industrialized nations, specifically highlighting the changing epidemiology of CAP, diagnostic and therapeutic challenges, and areas for further research.
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Affiliation(s)
- Sophie E Katz
- Division of Infectious Diseases, Monroe Carell Jr. Children's Hospital at Vanderbilt, Vanderbilt University Medical Center, D-7235 Medical Center North, 1161 21st Avenue South, Nashville, TN 37232-2581, USA
| | - Derek J Williams
- Division of Hospital Medicine, Monroe Carell Jr. Children's Hospital at Vanderbilt, Vanderbilt University Medical Center, CCC 5324 Medical Center North, 1161 21st Avenue South, Nashville, TN 37232, USA.
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12
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Hansen NS, Byberg S, Hervig Jacobsen L, Bjerregaard-Andersen M, Jensen AKG, Martins C, Aaby P, Skov Jensen J, Stabell Benn C, Whittle H. Effect of early measles vaccine on pneumococcal colonization: A randomized trial from Guinea-Bissau. PLoS One 2017; 12:e0177547. [PMID: 28545041 PMCID: PMC5435222 DOI: 10.1371/journal.pone.0177547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/27/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Measles vaccine (MV) may have non-specific beneficial effects for child health and particularly seems to prevent respiratory infections. Streptococcus pneumoniae is the leading cause of bacterial pneumonia among children worldwide, and nasopharyngeal colonization precedes infection. OBJECTIVE We investigated whether providing early MV at 18 weeks of age reduced pneumococcal colonization and/or density up to 9 months of age. METHOD The study was conducted in 2013-2014 in Guinea-Bissau. Pneumococcal vaccine was not part of the vaccination program. Infants aged 18 weeks were block-randomized 2:1 to early or no early MV; at age 9 months, all children were offered MV as per current policy. Nasopharyngeal swabs were taken at baseline, age 6.5 months, and age 9 months. Pneumococcal density was determined by q-PCR. Prevalence ratios of pneumococcal colonization and recent antibiotic treatment (yes/no) by age 6.5 months (PR6.5) and age 9 months (PR9) were estimated using Poisson regression with robust variance estimates while the pneumococcal geometric mean ratio (GMR6.5 and GMR9) was obtained using OLS regression. RESULTS Analyses included 512 children; 346 early MV-children and 166 controls. At enrolment, the pneumococcal colonization prevalence was 80% (411/512). Comparing early MV-children with controls, the PR6.5 was 1.02 (95%CI = 0.94-1.10), and the PR9 was 1.04 (0.96-1.12). The GMR6.5 was 1.02 (0.55-1.89), and the GMR9 was 0.69 (0.39-1.21). Early MV-children tended to be less frequently treated with antibiotics prior to follow up (PR6.5 0.60 (0.34-1.05) and PR9 0.87 (0.50-1.53)). Antibiotic treatment was associated with considerably lower colonization rates, PR6.5 0.85 (0.71-1.01) and PR9 0.66 (0.52-0.84), as well as lower pneumococcal density, GMR6.5 0.32 (0.12-0.86) and GMR9 0.52 (0.18-1.52). CONCLUSION Early MV at age 18 weeks had no measurable effect on pneumococcal colonization prevalence or density. Higher consumption of antibiotics among controls may have blurred an effect of early MV. TRIAL REGISTRATION clinicaltrials.gov NCT01486355.
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Affiliation(s)
- Nadja Skadkær Hansen
- Research Center for Vitamins and Vaccines (CVIVA), Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
| | - Stine Byberg
- Research Center for Vitamins and Vaccines (CVIVA), Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
| | - Lars Hervig Jacobsen
- Research Center for Vitamins and Vaccines (CVIVA), Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
| | - Morten Bjerregaard-Andersen
- Research Center for Vitamins and Vaccines (CVIVA), Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
- Department of Endocrinology, Odense University Hospital, Odense, Denmark
| | - Aksel Karl Georg Jensen
- Research Center for Vitamins and Vaccines (CVIVA), Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
- Section of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Cesario Martins
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
| | - Peter Aaby
- Research Center for Vitamins and Vaccines (CVIVA), Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
| | - Jørgen Skov Jensen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Christine Stabell Benn
- Research Center for Vitamins and Vaccines (CVIVA), Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
- Odense Patient data Explorative Network, Odense University Hospital/Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Hilton Whittle
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
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13
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Microbial Etiology of Pneumonia: Epidemiology, Diagnosis and Resistance Patterns. Int J Mol Sci 2016; 17:ijms17122120. [PMID: 27999274 PMCID: PMC5187920 DOI: 10.3390/ijms17122120] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/05/2016] [Accepted: 12/13/2016] [Indexed: 11/16/2022] Open
Abstract
Globally, pneumonia is a serious public health concern and a major cause of mortality and morbidity. Despite advances in antimicrobial therapies, microbiological diagnostic tests and prevention measures, pneumonia remains the main cause of death from infectious disease in the world. An important reason for the increased global mortality is the impact of pneumonia on chronic diseases, along with the increasing age of the population and the virulence factors of the causative microorganism. The increasing number of multidrug-resistant bacteria, difficult-to-treat microorganisms, and the emergence of new pathogens are a major problem for clinicians when deciding antimicrobial therapy. A key factor for managing and effectively guiding appropriate antimicrobial therapy is an understanding of the role of the different causative microorganisms in the etiology of pneumonia, since it has been shown that the adequacy of initial antimicrobial therapy is a key factor for prognosis in pneumonia. Furthermore, broad-spectrum antibiotic therapies are sometimes given until microbiological results are available and de-escalation cannot be performed quickly. This review provides an overview of microbial etiology, resistance patterns, epidemiology and microbial diagnosis of pneumonia.
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14
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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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15
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Pleural effusion with negative culture: a challenge for pneumococcal diagnosis in children. Diagn Microbiol Infect Dis 2016; 86:200-4. [PMID: 27527890 DOI: 10.1016/j.diagmicrobio.2016.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 11/23/2022]
Abstract
BACKGROUND Pneumococcal parapneumonic effusion seems to be increasing in children in the postvaccine era and is frequently associated with negative culture. Due to the low yield of culture, culture-independent tools are evaluated. METHODS Culture-negative pleural fluid specimens from 38 children with parapneumonic effusion were examined for pneumococcal lytA by quantitative polymerase chain reaction (qPCR) and soluble antigen (C-polysaccharide) using an immunochromatographic test (BinaxNow Streptococcus pneumoniae). RESULTS In 81% (30/37) and 63% (24/38) of the specimens, a positive result was obtained by qPCR and antigen detection, respectively. Most mismatches were observed in specimens with low quantities of pneumococcal DNA and a negative antigen test. CONCLUSIONS Our results suggest an imperfect relationship between the 2 described methods. The immunochromatographic assay is a simple diagnostic tool, which can be used when resources are limited, and even after antibiotic use, but negative results may require confirmation through a more sensitive test, such as qPCR.
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16
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Yoshii Y, Shimizu K, Morozumi M, Chiba N, Ubukata K, Uruga H, Hanada S, Wakui H, Ito S, Takasaka N, Minagawa S, Kojima J, Numata T, Hara H, Kawaishi M, Saito K, Araya J, Kaneko Y, Nakayama K, Kishi K, Kuwano K. Identification of pathogens by comprehensive real-time PCR versus conventional methods in community-acquired pneumonia in Japanese adults. Infect Dis (Lond) 2016; 48:782-8. [PMID: 27329337 DOI: 10.1080/23744235.2016.1193788] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) has high morbidity and mortality. Unfortunately, the pathogen detection rate using conventional culture methods is relatively low. We compared comprehensive real-time polymerase chain reaction (real-time PCR) analysis of nasopharyngeal swab specimens (NPS) and sputum samples against conventional methods for ability to detect causative pathogens of CAP. METHODS We prospectively enrolled adult CAP patients, including those with prior antibiotic use, from December 2012 to May 2014. For each patient, causative pathogens were investigated conventionally and by real-time PCR that can identify 6 bacterial and 11 viral pathogens. RESULTS Patients numbered 92 (mean age, 63 years; 59 male), including 30 (33%) with prior antibiotic use. Considering all patients, identification of causative pathogens by real-time PCR was significantly more frequent than by conventional methods in all patients (72% vs. 57%, p = 0.018). In patients with prior antibiotic use, identification rates also differed significantly (PCR, 77%; conventional, 50%; p = 0.027). Mixed infections were more frequent according to real-time PCR than conventional methods (26% vs. 4%, p < 0.001). By the real-time PCR, Streptococcus pneumoniae was most frequently identified (38%) as a causative pathogen, followed by Haemophilus influenzae (37%) and Mycoplasma pneumoniae (5%). PCR also identified viral pathogens (21%), with sensitivity enhanced by simultaneous examination of both NPS and sputum samples rather than only NPS samples. CONCLUSIONS Real-time PCR of NPS and sputum samples could better identify bacterial and viral pathogens in CAP than conventional methods, both overall and in patients with prior antibiotic treatment.
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Affiliation(s)
- Yutaka Yoshii
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Kenichiro Shimizu
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Miyuki Morozumi
- b Department of Infectious Diseases , Keio University School of Medicine , Tokyo , Japan
| | - Naoko Chiba
- b Department of Infectious Diseases , Keio University School of Medicine , Tokyo , Japan
| | - Kimiko Ubukata
- b Department of Infectious Diseases , Keio University School of Medicine , Tokyo , Japan
| | - Hironori Uruga
- c Department of Respiratory Medicine , Respiratory Center, Toranomon Hospital , Tokyo , Japan
| | - Shigeo Hanada
- c Department of Respiratory Medicine , Respiratory Center, Toranomon Hospital , Tokyo , Japan
| | - Hiroshi Wakui
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Saburo Ito
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Naoki Takasaka
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Shunsuke Minagawa
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Jun Kojima
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Takanori Numata
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Hiromichi Hara
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Makoto Kawaishi
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Keisuke Saito
- d Department of Respiratory Medicine , The Jikei University Daisan Hospital , Tokyo , Japan
| | - Jun Araya
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Yumi Kaneko
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Katsutoshi Nakayama
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
| | - Kazuma Kishi
- c Department of Respiratory Medicine , Respiratory Center, Toranomon Hospital , Tokyo , Japan
| | - Kazuyoshi Kuwano
- a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan
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17
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Habets MN, Cremers AJH, Bos MP, Savelkoul P, Eleveld MJ, Meis JF, Hermans PWM, Melchers WJ, de Jonge MI, Diavatopoulos DA. A novel quantitative PCR assay for the detection of Streptococcus pneumoniae using the competence regulator gene target comX. J Med Microbiol 2015; 65:129-136. [PMID: 26628261 DOI: 10.1099/jmm.0.000204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Streptococcus pneumoniae is responsible for an estimated 1.6 million deaths worldwide every year. While rapid detection and timely treatment with appropriate antibiotics is preferred, this is often difficult due to the amount of time that detection with blood cultures takes. In this study, a novel quantitative PCR assay for the detection of Streptococcus pneumoniae was developed. To identify novel targets, we analysed the pneumococcal genome for unique, repetitive DNA sequences. This approach identified comX, which is conserved and present in duplicate copies in Streptococcus pneumoniae but not in other bacterial species. Comparison with lytA, the current 'gold standard' for detection by quantitative PCR, demonstrated an analytic specificity of 100% for both assays on a panel of 10 pneumococcal and 18 non-pneumococcal isolates, but a reduction of 3.5 quantitation cycle values (± 0.23 sem), resulting in an increased analytical detection rate of comX. We validated our assay on DNA extracted from the serum of 30 bacteraemic patients who were blood culture positive for Streptococcus pneumoniae and 51 serum samples that were culture positive for other bacteria. This resulted in a similar clinical sensitivity between the comX and lytA assays (47%) and in a diagnostic specificity of 98.2 and 100% for the lytA and comX assays, respectively. In conclusion, we have developed a novel quantitative PCR assay with increased analytical sensitivity for the detection of Streptococcus pneumoniae, which may be used to develop a rapid bedside test for the direct detection of Streptococcus pneumoniae in clinical specimens.
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Affiliation(s)
- Marrit N Habets
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amelieke J H Cremers
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Paul Savelkoul
- Microbiome, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, VU University Medical Center, The Netherlands
- Department of Medical Microbiology, Maastricht University Medical Center, The Netherlands
| | - Marc J Eleveld
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter W M Hermans
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willem J Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dimitri A Diavatopoulos
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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18
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Abstract
BACKGROUND South Africa introduced the 7-valent pneumococcal conjugate vaccine (PCV7) in 2009 and PCV13 in 2011. The etiology and incidence of childhood empyema in an 8-year period overlapping the introduction of PCV was investigated. METHODS Children younger than 12 years admitted with empyema at a tertiary pediatric hospital in Cape Town, South Africa, from December 2006 to December 2011 (cohort A) and January 2012 to December 2014 (cohort B) were investigated. Pathogens were identified by culture of pleural fluid and blood. In addition, polymerase chain reaction targeting bacterial pathogens and Streptococcus pneumoniae serotypes was conducted on pleural fluid in a subset of patients enrolled 2009-2011. RESULTS Cohort A: 142 children were prospectively enrolled, with a median age of 17 months (interquartile range 8-43). Most (92%) children were unimmunized with PCV. S. pneumoniae and Staphylococcus aureus were the most common culture-identified pathogens (each 25 of 142; 18%); polymerase chain reaction of pleural fluid increased yield of S. pneumoniae detection by 31% [26 of 54 (48%) vs. 9 of 54 (17%), P < 0.001]. Serotypes were identified for 24 of 26 (92%) patients with S. pneumoniae, of which 22 of 24 (92%) were included in PCV13. Cohort B: 22 patients were retrospectively identified. No pathogen was found in 12 of 22 (54.5%) patients and S. pneumoniae in 1 patient (4.5%). Empyema incidence declined by 50% in cohort B compared with that of cohort A (4.2 vs. 10.4 cases per 1000 pneumonia admissions; risk ratio: 0.5; 95% confidence incidence: 0.3-0.7). CONCLUSION S. pneumoniae is the commonest cause of childhood empyema in South Africa. PCV has been highly effective at reducing empyema incidence in South African children.
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19
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Azzari C, Moriondo M, Di Pietro P, Di Bari C, Resti M, Mannelli F, Esposito S, Castelli-Gattinara G, Campa A, de Benedictis FM, Bona G, Comarella L, Holl K, Marchetti F. The burden of bacteremia and invasive diseases in children aged less than five years with fever in Italy. Ital J Pediatr 2015; 41:92. [PMID: 26589787 PMCID: PMC4654905 DOI: 10.1186/s13052-015-0189-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 10/12/2015] [Indexed: 11/29/2022] Open
Abstract
Background Invasive diseases (ID) caused by Streptococcus pneumoniae (S. pneumoniae), Haemophilus influenzae (H. influenzae), and Neisseria meningitidis are a major public health problem worldwide. Comprehensive data on the burden of bacteremia and ID in Italy, including data based on molecular techniques, are needed. Methods We conducted a prospective, multi-centre, hospital-based study (GSK study identifier: 111334) to assess the burden of bacteremia and ID among children less than five years old with a fever of 39 °C or greater. Study participation involved a single medical examination, collection of blood for polymerase chain reaction (PCR) and blood culture, and collection of an oropharyngeal swab for colonization analysis by PCR. Results Between May 2008 and June 2009, 4536 patients were screened, 944 were selected and 920 were enrolled in the study. There were 225 clinical diagnoses of ID, 9.8 % (22) of which were bacteremic. A diagnosis of sepsis was made for 38 cases, 5.3 % (2) of which were bacteremic. Among the 629 non-ID diagnoses, 1.6 % (10) were bacteremic. Among the 34 bacteremic cases, the most common diagnoses were community-acquired pneumonia (15/34), pleural effusion (4/34) and meningitis (4/34). S. pneumoniae was the most frequently detected bacteria among bacteremic cases (29/34) followed by H. influenzae (3/34). Ninety percent (27/30) of bacteremic patients with oropharyngeal swab results were colonized with the studied bacterial pathogens compared to 46.1 % (402/872) of non-bacteremic cases (p < 0.001). PCV7 (7-valent pneumococcal conjugate vaccine) vaccination was reported for 55.9 % (19/34) of bacteremic cases. S. pneumoniae serotypes were non-vaccine serotypes in children who had been vaccinated. Mean duration of hospitalization was longer for bacteremic cases versus non-bacteremic cases (13.6 versus 5.8 days). Conclusions These results confirm that S. pneumoniae is one of the pathogens frequently responsible for invasive disease.
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Affiliation(s)
- Chiara Azzari
- Division of Pediatric Immunology, Department of Health Sciences, University of Florence and Anna Meyer Children's University Hospital, Florence, Italy.
| | - Maria Moriondo
- Division of Pediatric Immunology, Department of Health Sciences, University of Florence and Anna Meyer Children's University Hospital, Florence, Italy.
| | - Pasquale Di Pietro
- Istituto Giannina Gaslini, Ospedale Pediatrico IRCCS, Via Gerolamo Gaslini 5, 16148, Genoa, Italy.
| | - Cesare Di Bari
- Azienda Ospedaliera Universitaria, Policlinico Consorziale di Bari, Piazza Giulio Cesare 11, 70124, Bari, Italy.
| | - Massimo Resti
- Anna Meyer Children's University Hospital, Florence, Italy.
| | | | - Susanna Esposito
- Pediatric Highly Intensive Care Unit, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Guido Castelli-Gattinara
- Paediatric Division, Bambino Gesù Children Hospital, v. Aurelia Km.30, 00100 Palidoro, Rome, Italy.
| | - Antonio Campa
- Ospedale Santobono, Via Fiore Mario 6, 80129, Naples, Italy.
| | | | - Gianni Bona
- Azienda Ospedaliera Maggiore della Carita', Corso Mazzini, n. 18, Novara, 28100, Italy.
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20
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Tempia S, Wolter N, Cohen C, Walaza S, von Mollendorf C, Cohen AL, Moyes J, de Gouveia L, Nzenze S, Treurnicht F, Venter M, Groome MJ, Madhi SA, von Gottberg A. Assessing the impact of pneumococcal conjugate vaccines on invasive pneumococcal disease using polymerase chain reaction-based surveillance: an experience from South Africa. BMC Infect Dis 2015; 15:450. [PMID: 26496761 PMCID: PMC4620746 DOI: 10.1186/s12879-015-1198-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022] Open
Abstract
Background The use of molecular diagnostic techniques for the evaluation of the impact of pneumococcal conjugate vaccines (PCVs) has not been documented. We aimed to evaluate the impact of PCVs on invasive pneumococcal disease (IPD) using polymerase chain reaction (PCR)-based techniques and compare with results obtained from culture-based methods. Methods We implemented two independent surveillance programs for IPD among individuals hospitalized at one large surveillance site in Soweto, South Africa during 2009–2012: (i) PCR-based (targeting the lytA gene) syndromic pneumonia surveillance; and (ii) culture-based laboratory surveillance. Positive samples were serotyped. The molecular serotyping assay included targets for 42 serotypes including all serotypes/serogroups included in the 7-valent (PCV-7) and 13-valent (PCV-13) PCV. The Quellung reaction was used for serotyping of culture-positive cases. We calculated the change in rates of IPD (lytA- or culture-positive) among HIV-uninfected children aged <2 years from the year of PCV-7 introduction (2009) to the post-vaccine years (2011 or 2012). Results During the study period there were 607 lytA-positive and 1,197 culture-positive cases that were serotyped. Samples with lytA cycle threshold (Ct)-values ≥35 (30.2 %; 123/407) were significantly less likely to have a serotype/serogroup detected for serotypes included in the molecular serotyping assay than those with Ct-values <35 (78.0 %; 156/200) (p < 0.001). From 2009 to 2012 rates of PCV-7 serotypes/serogroups decreased −63.8 % (95 % CI: −79.3 % to −39.1 %) among lytA-positive cases and −91.7 % (95 % CI: −98.8 % to −73.6 %) among culture-positive cases. Rates of lytA-positive non-vaccine serotypes/serogroups also significantly decreased (−71.7 %; 95 % CI: −81.1 % to −58.5 %) over the same period. Such decline was not observed among the culture-positive non-vaccine serotypes (1.2 %; 95 % CI: −96.7 % to 58.4 %). Conclusions Significant downward trends in IPD PCV-7 serotype-associated rates were observed among patients tested by PCR or culture methods; however trends of non-vaccine serotypes/serogroups differed between the two groups. Misclassifications of serotypes/serogroups, affecting the use of non-vaccine serotypes as a control group, may have occurred due to the low performance of the serotyping assay among lytA-positive cases with high Ct-values. Until PCR methods improve further, culture methods should continue to be used to monitor the effects of PCV vaccination programs on IPD incidence. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1198-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefano Tempia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA. .,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa. .,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Claire von Mollendorf
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Adam L Cohen
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA. .,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
| | - Susan Nzenze
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
| | - Florette Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
| | - Marietjie Venter
- Division of Global Health Protection, Centers for Disease Control and Prevention, Pretoria, South Africa.
| | - Michelle J Groome
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.
| | - Shabir A Madhi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Estimation of the Impact of Meningococcal Serogroup C Universal Vaccination in Italy and Suggestions for the Multicomponent Serogroup B Vaccine Introduction. J Immunol Res 2015; 2015:710656. [PMID: 26351649 PMCID: PMC4553333 DOI: 10.1155/2015/710656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/31/2015] [Accepted: 04/15/2015] [Indexed: 02/02/2023] Open
Abstract
In Italy, the meningococcal C conjugate vaccine (MenC) has been offered in most regions since 2009-2010. The incidence of Invasive Meningococcal Disease (IMD) was 0.25 confirmed cases per 100,000 in 2011, but this may be considerably underestimated due to underdetection and underreporting. This study estimates the impact of the MenC universal vaccination (URV) in the Puglia region by assessing the completeness of three registration sources (notifications, hospitalizations, and laboratory surveillance). Capture-recapture analysis was performed on meningococcal meningitis collected within 2001-2013. The impact of URV among ≤ 18-year-olds was assessed by attributable benefit, preventable fraction, and prevented fraction. Missed opportunities for vaccination were evaluated from surveillance of IMD. The proportion of detected serogroups was applied to the number of IMD in the postvaccination period to compute the cases still preventable. The sensitivity of the three sources was 36.7% (95% CI: 17.5%-57.9%) and registrations lost nearly 28 cases/year in the period. Attributable benefit of URV was -0.5 cases per 100,000, preventable fraction 19.6%, and prevented fraction 31.3%. Three adolescent cases missed the opportunity to be vaccinated. The multicomponent serogroup B meningococcal vaccine has the potential to further prevent at least three other cases/year. Vaccination strategy against serogroup B together with existing programmes makes IMD a 100% vaccine-preventable disease.
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Gianchecchi E, Torelli A, Piccini G, Piccirella S, Montomoli E. Neisseria meningitidisinfection: who, when and where? Expert Rev Anti Infect Ther 2015; 13:1249-63. [DOI: 10.1586/14787210.2015.1070096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Berti E, Chiappini E, Orlandini E, Galli L, de Martino M. Pertussis is still common in a highly vaccinated infant population. Acta Paediatr 2014; 103:846-9. [PMID: 24716812 DOI: 10.1111/apa.12655] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/08/2014] [Accepted: 04/07/2014] [Indexed: 11/30/2022]
Abstract
AIM To provide epidemiological data on pertussis in a highly vaccinated paediatric population, focusing on the age of the infected children. METHODS We analysed data from the regional hospital discharge database on children hospitalised for pertussis in Tuscany, Italy, from January 2000 to December 2012. RESULTS A total of 279 cases were recorded. The majority of hospitalised children were infants (75.6%), who had the highest rate of complications (24.2%) of any age group and a crude mortality rate of 9.47 per 1000. The overall hospitalisation rate decreased significantly during the study period, from 4.23 to 2.82 per 100 000, but when we analysed the data by age groups, we found notable differences. Hospitalisation rates in the 1- to 4-year-old age group decreased significantly from 2.82 in the year 2000 to zero per 100 000 in 2012 and decreased significantly in the 5- to 9-year-old age group over the same period, from 6.58 to 0.63 per 100 000. Overall hospitalisation rates in the infant group remained high at 53.14 per 100 000, with three peaks due to periodic pertussis outbreaks. CONCLUSION Pertussis is still a relevant health concern in infants who are unvaccinated or incompletely immunised, both in terms of morbidity and mortality.
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Affiliation(s)
- Elettra Berti
- Department of Sciences for Health Sciences; Anna Meyer Children's University Hospital; University of Florence; Florence Italy
| | - Elena Chiappini
- Department of Sciences for Health Sciences; Anna Meyer Children's University Hospital; University of Florence; Florence Italy
| | - Elisa Orlandini
- Information Technology Section; Tuscany Regional Government Department of Right to Health and Solidarity Policies; Florence Italy
| | - Luisa Galli
- Department of Sciences for Health Sciences; Anna Meyer Children's University Hospital; University of Florence; Florence Italy
| | - Maurizio de Martino
- Department of Sciences for Health Sciences; Anna Meyer Children's University Hospital; University of Florence; Florence Italy
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Challenges of using molecular serotyping for surveillance of pneumococcal disease. J Clin Microbiol 2014; 52:3271-6. [PMID: 24958802 DOI: 10.1128/jcm.01061-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent advances in the molecular identification and serotyping of Streptococcus pneumoniae are useful for culture-negative samples; however, there are limitations associated with these methods. We aimed to assess the value of molecular assays for invasive pneumococcal disease (IPD) surveillance in South Africa from 2010 through 2012. Nonviable isolates and culture-negative clinical specimens were tested for the lytA gene and, if positive, were serotyped, using real-time PCRs. Multinomial regression analysis was used to determine the maximum lytA cycle threshold (CT) value useful for predicting the ability to detect a serotype for the sample. The χ(2) test was used to compare the prevalence of serotypes between viable/nonviable isolates and culture-negative clinical specimens. Of 11,224 IPD cases reported, 1,091 (10%) were culture-negative samples and 981 (90%) of these were lytA positive. Samples with a lytA CT value of ≥35 were significantly less likely to be serotyped. A serotype/group was determined for 87% (737/844) of samples with a lytA CT value of <35, of which 60% (443/737) were identified as individual serotypes. The serotype prevalence did not differ significantly between isolates and culture-negative specimens. Although molecular serotyping added 7% (737/11,224) serotyping data, the inability to resolve 40% of samples to single serotypes remains a challenge for serotype-specific data analysis.
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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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Distribution of invasive meningococcal B disease in Italian pediatric population: implications for vaccination timing. Vaccine 2013; 32:1187-91. [PMID: 24120548 DOI: 10.1016/j.vaccine.2013.09.055] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 11/23/2022]
Abstract
Neisseria meningitidis group B (MenB) is a leading cause of meningitis and sepsis. A new vaccine has been recently licensed. The aim of the present study was to evaluate the epidemiology of MenB disease in pediatric age and define the optimal age for vaccination. All patients aged 0-18 years admitted with a diagnosis of meningitis or sepsis to the 83 participating Italian pediatric hospitals were included in the study. Blood and/or cerebrospinal fluid (CSF) samples were tested by Realtime-PCR and/or culture. One hundred and thirty-six cases (mean age 5.0 years, median 2.7) of MenB disease were found. Among these, 96/136 (70.6%) were between 0 and 5 years, 61/136 (44.9%) were between 0 and 2 years. Among the latter, 39/61 (63.9%) occurred during the first year of life with highest incidence between 4 and 8 months. A case-fatality rate of 13.2% was found, with 27.8% cases below 12 months. Sepsis lethality was 24.4%. RT-PCR was significantly more sensitive than culture: 82 patients were tested at the same time by both methods, either in blood or in CSF; MenB was found by RT-PCR in blood or CSF in 81/82 cases (98.8%), culture identified 27/82 (32.9%) infections (Cohen's Kappa 0.3; McNemar's: p<10⁻⁵). The study shows that the highest incidence of disease occurs in the first year of age, with a peak between 4 and 8 months of life; 30% of deaths occur before 12 months. The results suggest that the greatest prevention could be obtained starting MenB vaccination in the first months of life; a catch-up strategy up to the fifth year of life could be considered. Our results also confirm that Realtime PCR is significantly more sensitive than culture. In those countries where only isolate positive infections are counted as cases, the incidence of MenB infection results highly underestimated.
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Liu YF, Gao Y, Chen MF, Cao B, Yang XH, Wei L. Etiological analysis and predictive diagnostic model building of community-acquired pneumonia in adult outpatients in Beijing, China. BMC Infect Dis 2013; 13:309. [PMID: 23834931 PMCID: PMC3728139 DOI: 10.1186/1471-2334-13-309] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/05/2013] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Etiological epidemiology and diagnosis are important issues in adult community-acquired pneumonia (CAP), and identifying pathogens based on patient clinical features is especially a challenge. CAP-associated main pathogens in adults include viruses as well as bacteria. However, large-scale epidemiological investigations of adult viral CAP in China are still lacking. In this study, we analyzed the etiology of adult CAP in Beijing, China and constructed diagnostic models based on combinations of patient clinical factors. METHODS A multicenter cohort was established with 500 adult CAP outpatients enrolled in Beijing between November 2010 to October 2011. Multiplex and quantitative real-time fluorescence PCR were used to detect 15 respiratory viruses and mycoplasma pneumoniae, respectively. Bacteria were detected with culture and enzyme immunoassay of the Streptococcus pneumoniae urinary antigen. Univariate analysis, multivariate analysis, discriminatory analysis and Receiver Operating Characteristic (ROC) curves were used to build predictive models for etiological diagnosis of adult CAP. RESULTS Pathogens were detected in 54.2% (271/500) of study patients. Viruses accounted for 36.4% (182/500), mycoplasma pneumoniae for 18.0% (90/500) and bacteria for 14.4% (72/500) of the cases. In 182 of the patients with viruses, 219 virus strains were detected, including 166 single and 53 mixed viral infections. Influenza A virus represented the greatest proportion with 42.0% (92/219) and 9.1% (20/219) in single and mixed viral infections, respectively. Factors selected for the predictive etiological diagnostic model of viral CAP included cough, dyspnea, absence of chest pain and white blood cell count (4.0-10.0) × 10(9)/L, and those of mycoplasma pneumoniae CAP were being younger than 45 years old and the absence of a coexisting disease. However, these models showed low accuracy levels for etiological diagnosis (areas under ROC curve for virus and mycoplasma pneumoniae were both 0.61, P < 0.05). CONCLUSIONS Greater consideration should be given to viral and mycoplasma pneumoniae infections in adult CAP outpatients. While predictive etiological diagnostic models of viral and mycoplasma pneumoniae based on combinations of demographic and clinical factors may provide indications of etiology, diagnostic confirmation of CAP remains dependent on laboratory pathogen test results.
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Affiliation(s)
- Ya-Fen Liu
- Peking University People's Hospital, Department of Infectious Disease, Peking University Hepatology Institute, Beijing 100044, P R China
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Cvitkovic Spik V, Beovic B, Pokorn M, Drole Torkar A, Vidmar D, Papst L, Seme K, Kogoj R, Müller Premru M. Improvement of pneumococcal pneumonia diagnostics by the use of rt-PCR on plasma and respiratory samples. ACTA ACUST UNITED AC 2013; 45:731-7. [PMID: 23826792 DOI: 10.3109/00365548.2013.804631] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The aim of the study was to assess the performance of a real-time polymerase chain reaction (rt-PCR) assay on plasma and respiratory samples for the diagnosis of pneumococcal pneumonia. METHODS Three hundred and forty patients (160 children and 180 adults) with community-acquired pneumonia were included prospectively from January 2011 to May 2012. Blood samples were obtained simultaneously for culture and rt-PCR targeting the lytA gene. Respiratory samples were also obtained: nasopharyngeal swab in nearly all patients and sputum or tracheal aspirate when available. RESULTS Streptococcus pneumoniae was detected in 222 (65%) of 340 patients: 143 (89%) children and 79 (44%) adults. Pneumonia was assigned as definite pneumococcal in 96 (28.2%) of 340 patients, according to S. pneumoniae detected in blood: in 54 (33.8%) children - by rt-PCR in 51 (31.9%) and by culture in 5 (3.1%); and in 42 (23.3%) adults - by rt-PCR in 41 (22.8%) and by culture in 12 (6.7%). Pneumonia was considered as probably pneumococcal in 19 (10.6%) adults according to S. pneumoniae detected in sputum/tracheal aspirate, by rt-PCR in 19 and by culture in 5. In 18 adults and 89 children with S. pneumoniae detected only in the nasopharynx, pneumonia was considered as possibly pneumococcal; however it should be noted that nasopharyngeal colonization with S. pneumoniae is also common in children with other aetiologies of pneumonia. CONCLUSIONS rt-PCR on plasma and other samples performed significantly better than culture for the detection of pneumococcal pneumonia (p < 0.0005) in children and adults.
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Affiliation(s)
- Vesna Cvitkovic Spik
- From the Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana
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Abstract
PURPOSE OF REVIEW This review discusses unsolved problems concerning pediatric community-acquired pneumonia (CAP) and identifies the areas of research that need to be developed. RECENT FINDINGS Diagnosing pediatric CAP and the required hospitalization are difficult problems especially in the presence of mild signs and symptoms. It is frequently not possible to identify the cause of this disease, and this explains why antibiotics are unnecessarily prescribed in some cases. The treatment recommendations for severe CAP are better defined than those for mild and moderate CAP. SUMMARY It is possible to prepare recommendations for most of the problems that emerge in severe cases of pediatric CAP even though its cause can also be difficult to identify. However, the recommended approach to mild or moderate cases is always based on mainly moderate or poor quality evidence. There is an urgent need for further studies aimed at defining first-line and second-line antibiotic therapy for mild and moderate CAP. In the absence of new data, it is necessary to be aware that a substantial number of patients will not be optimally treated.
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Esposito S, Marchese A, Tozzi AE, Rossi GA, Da Dalt L, Bona G, Pelucchi C, Schito GC, Principi N. Bacteremic pneumococcal community-acquired pneumonia in children less than 5 years of age in Italy. Pediatr Infect Dis J 2012; 31:705-10. [PMID: 22426300 DOI: 10.1097/inf.0b013e31825384ae] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND This study was designed to determine the proportion of bacteremic pneumococcal cases in a group of pediatric subjects with community-acquired pneumonia (CAP), the importance of the different serotypes and the impact of the currently available pneumococcal conjugate vaccines (PCVs). METHODS The study involved children who were ≤5 years with radiographically confirmed CAP admitted to hospital in Italy between September 2008 and March 2011. A diagnosis of laboratory-confirmed bacteremic pneumococcal CAP was made in the presence of a culture and/or real-time polymerase chain reaction (PCR) positive for Streptococcus pneumoniae. RESULTS A total of 510 children were included in the study. Pneumococcal CAP was diagnosed in 73 cases (14.3%): S. pneumoniae was identified by means of positive real-time PCR in 67 cases (91.8%), a positive blood culture in 1 (1.4%) and both in 5 (6.8%). Complicated pneumonia was observed significantly more often in the pneumococcal-positive cases (P=0.02) and empyema was the main complication (P=0.007). Serotype 19A was most frequently encountered (17 cases; 25.8%), followed by serotypes 14 (10 cases, 15.1%), 4 (5 cases, 7.6%) and 3 (4 cases, 6.1%). The theoretical coverage offered by the available PCVs was calculated to be 31% for PCV7, 37% for PCV10 and 71% for PCV13. CONCLUSIONS In Italy, bacteremic pneumococcal CAP accounts for a significant number of CAP cases in children who were ≤5 years, with serotypes 19A and 14 being the most frequent. This suggests that PCV13 is the best means of preventing pneumococcal CAP.
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Affiliation(s)
- Susanna Esposito
- Department of Maternal and Pediatric Sciences, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Bradley JS, Byington CL, Shah SS, Alverson B, Carter ER, Harrison C, Kaplan SL, Mace SE, McCracken GH, Moore MR, St Peter SD, Stockwell JA, Swanson JT. The management of community-acquired pneumonia in infants and children older than 3 months of age: clinical practice guidelines by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America. Clin Infect Dis 2011; 53:e25-76. [PMID: 21880587 PMCID: PMC7107838 DOI: 10.1093/cid/cir531] [Citation(s) in RCA: 991] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 07/08/2011] [Indexed: 02/07/2023] Open
Abstract
Evidenced-based guidelines for management of infants and children with community-acquired pneumonia (CAP) were prepared by an expert panel comprising clinicians and investigators representing community pediatrics, public health, and the pediatric specialties of critical care, emergency medicine, hospital medicine, infectious diseases, pulmonology, and surgery. These guidelines are intended for use by primary care and subspecialty providers responsible for the management of otherwise healthy infants and children with CAP in both outpatient and inpatient settings. Site-of-care management, diagnosis, antimicrobial and adjunctive surgical therapy, and prevention are discussed. Areas that warrant future investigations are also highlighted.
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Affiliation(s)
- John S Bradley
- Department of Pediatrics, University of California San Diego School of Medicine and Rady Children's Hospital of San Diego, San Diego, California, USA.
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Real-time PCR improves Helicobacter pylori detection in patients with peptic ulcer bleeding. PLoS One 2011; 6:e20009. [PMID: 21625499 PMCID: PMC3098855 DOI: 10.1371/journal.pone.0020009] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 04/19/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND AIMS Histological and rapid urease tests to detect H. pylori in biopsy specimens obtained during peptic ulcer bleeding episodes (PUB) often produce false-negative results. We aimed to examine whether immunohistochemistry and real-time PCR can improve the sensitivity of these biopsies. PATIENTS AND METHODS We selected 52 histology-negative formalin-fixed paraffin-embedded biopsy specimens obtained during PUB episodes. Additional tests showed 10 were true negatives and 42 were false negatives. We also selected 17 histology-positive biopsy specimens obtained during PUB to use as controls. We performed immunohistochemistry staining and real-time PCR for 16S rRNA, ureA, and 23S rRNA for H. pylori genes on all specimens. RESULTS All controls were positive for H. pylori on all PCR assays and immunohistochemical staining. Regarding the 52 initially negative biopsies, all PCR tests were significantly more sensitive than immunohistochemical staining (p<0.01). Sensitivity and specificity were 55% and 80% for 16S rRNA PCR, 43% and 90% for ureA PCR, 41% and 80% for 23S rRNA PCR, and 7% and 100% for immunohistochemical staining, respectively. Combined analysis of PCR assays for two genes were significantly more sensitive than ureA or 23S rRNA PCR tests alone (p<0.05) and marginally better than 16S rRNA PCR alone. The best combination was 16S rRNA+ureA, with a sensitivity of 64% and a specificity of 80%. CONCLUSIONS Real-time PCR improves the detection of H. pylori infection in histology-negative formalin-fixed paraffin-embedded biopsy samples obtained during PUB episodes. The low reported prevalence of H. pylori in PUB may be due to the failure of conventional tests to detect infection.
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Marchese A, Esposito S, Coppo E, Rossi GA, Tozzi A, Romano M, Da Dalt L, Schito GC, Principi N. Detection of Streptococcus pneumoniae and identification of pneumococcal serotypes by real-time polymerase chain reaction using blood samples from Italian children ≤ 5 years of age with community-acquired pneumonia. Microb Drug Resist 2011; 17:419-24. [PMID: 21510746 DOI: 10.1089/mdr.2011.0031] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is a leading cause of severe life-threatening infections. Laboratory identification and serotyping of this pathogens is desirable to monitor vaccine impact and coverage; however, especially in pediatric patients, the yield of traditional microbiological diagnostic procedures can be very low. The aim of this study was to develop real-time polymerase chain reaction (PCR)-based assays to be performed directly on blood samples to identify the most common capsular serotypes causing pneumonia in Italian children (≤ 5 years of ages) after the introduction of the 7-valent conjugate vaccine. Our real-time PCR-based assays showed high sensitivity (at least 35 fg of pneumococcal DNA), and they were validated with 49 well-characterized pneumococcal isolates, 8 nonpneumococcal isolates, 13 simulated blood clinical samples loaded with S. pneumoniae of known serotypes, and 46 blood clinical samples. All the strains tested and the simulated blood clinical samples were correctly typed by the technique. Real-time PCR allowed serotyping in 37/46 children ≤ 5 years of age (80.4%) in whom pneumonia was diagnosed in four Italian hospitals. Non-PCV7 serotypes accounted for at least 47.8% (22/46) of cases, serotype 19A being the most common (34.7%, 16/46). Although, it is not known at present whether the incidence of 19A serotype is attributable to the use of PCV7 only, expanding pneumococcal serotype coverage has clearly the potential to prevent a larger number of pneumonias in Italian children less than ≤ 5 years of age. Molecular methods are of increasing importance in the diagnosis of pneumococcal pneumonia and in monitoring serotype distribution and replacement.
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Affiliation(s)
- Anna Marchese
- Dipartimento Interdisciplinare di Scienze Chiaurgiche e Diagnostiche Integrate, Sezione di Microbiologia, University of Genoa, Genoa, Italy.
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35
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Azzari C, Cortimiglia M, Moriondo M, Canessa C, Lippi F, Ghiori F, Becciolini L, de Martino M, Resti M. Pneumococcal DNA is not detectable in the blood of healthy carrier children by real-time PCR targeting the lytA gene. J Med Microbiol 2011; 60:710-714. [PMID: 21349984 PMCID: PMC3167920 DOI: 10.1099/jmm.0.028357-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The diagnosis of invasive pneumococcal disease (IPD) is currently based on culture methods, which lack sensitivity, especially after antibiotic therapy. Molecular methods have improved sensitivity and do not require viable bacteria; however, their use is complicated by reports of low specificity with some assays. The present study investigated the specificity of a real-time PCR targeting lytA for the detection of IPD. A group of 147 healthy children, aged 6 months to 16 years (mean 6.4 years, median 4.9 years, interquartile range 6.4 years), who were in hospital for routine examinations, were tested for pneumococcal carrier status and for the presence of detectable pneumococcal DNA in their blood by real-time PCR targeting the pneumococcal lytA gene. In addition, 35 culture-positive biological samples were analysed. Urine was examined for the presence of pneumococcal DNA and C-polysaccharide antigen. Carriage was detected in 77 of the 147 subjects (52.4 %); however, regardless of carrier status, none of the subjects had a positive result from blood. Analysis of the culture-positive biological samples yielded positive results in 100 % (15/15) of cerebrospinal fluid samples and 95 % (19/20) of blood samples. All urine samples from healthy carriers were negative for DNA, whilst antigenuria was detected in 44/77 carriers (57.1 %). In conclusion, real-time PCR is both sensitive and specific and can be a useful tool in the routine diagnosis of IPD. Its sensitivity, which surpasses that of other methods for this purpose, does not come at the cost of reduced specificity.
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Affiliation(s)
- Chiara Azzari
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Martina Cortimiglia
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Maria Moriondo
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Clementina Canessa
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Francesca Lippi
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Federica Ghiori
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Laura Becciolini
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Maurizio de Martino
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
| | - Massimo Resti
- Department of Paediatrics, Anna Meyer Children's University Hospital, Florence, Italy
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Picazo J, Ruiz-Contreras J, Hernandez B, Sanz F, Gutierrez A, Cercenado E, Meseguer M, Delgado-Iribarren A, Rodriguez-Avial I, Méndez C. Clonal and clinical profile of Streptococcus pneumoniae serotype 19A causing pediatric invasive infections: A 2-year (2007–2009) laboratory-based surveillance in Madrid. Vaccine 2011; 29:1770-6. [DOI: 10.1016/j.vaccine.2010.12.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/22/2010] [Accepted: 12/22/2010] [Indexed: 10/18/2022]
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Realtime PCR is more sensitive than multiplex PCR for diagnosis and serotyping in children with culture negative pneumococcal invasive disease. PLoS One 2010; 5:e9282. [PMID: 20174571 PMCID: PMC2824814 DOI: 10.1371/journal.pone.0009282] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 01/28/2010] [Indexed: 11/19/2022] Open
Abstract
Background Pneumococcal serotyping is usually performed by Quellung reaction, considered the gold standard test. However the method cannot be used on culture-negative samples. Molecular methods can be a useful alternative. The aim of the study was to evaluate the use of Multiplex-sequential-PCR (MS-PCR) or Realtime-PCR on blood samples for diagnosis and serotyping of invasive pneumococcal disease (IPD) in a pediatric clinical setting. Methodology/Principal Findings Sensitivity and specificity of MS-PCR and Realtime-PCR have been evaluated both on 46 well characterized pneumococcal isolates and on 67 clinical samples from children with culture-negative IPD. No difference in sensitivity and specificity between MS-PCR and Realtime PCR was found when the methods were used on isolates: both methods could type 100% isolates and the results were always consistent with culture-based methods. On the contrary, when used on clinical samples 43/67 (64.2%) were typeable by MS-PCR and 61/67 (91.0%) by Realtime-PCR (p = 0.0004,K Cohen 0.3, McNemar's p<0.001). Non-typeability by MS-PCR was associated in 18/20 cases (90.0%) with low bacterial load. The difference between the two methods was present both when they were used on normally sterile fluids (respectively 31/33 (93.9%) typeable samples for Realtime-PCR and 24/33 (72.7%) for MS-PCR, p = 0.047, 95%CL 0.03–0.98; K Cohen 0.3; McNemar's p = 0.0016) and when they were used on nasopharyngeal swabs (respectively 30/34 (88.2%) typeable samples for Realtime-PCR and 19/34 (55.9%) for MS-PCR, p = 0.007, 95%CL 0.04–0.66); the presence of multiple pneumococcal serotypes in nasopharyngeal swabs was found more frequently by Realtime PCR (19/30; 63.3%) than by Multiplex-sequential PCR (3/19; 15.8%; p = 0.003;95%CL 1.87–39.97). Conclusions/Significance In conclusion, both MS-PCR and Realtime PCR can be used for pneumococcal serotyping of most serotypes/serogroups directly on clinical samples from culture-negative patients but Realtime-PCR appears more sensitive.
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