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Carter MJ, Gurung M, Pokhrel B, Bijukchhe SM, Karmacharya S, Khadka B, Maharjan A, Bhattarai S, Shrestha S, Khadka B, Khulal A, Gurung S, Dhital B, Prajapati KG, Ansari I, Shah GP, Wahl B, Kandasamy R, Pradhan R, Kelly S, Voysey M, Murdoch DR, Adhikari N, Thorson S, Kelly D, Shrestha S, Pollard AJ. Childhood Invasive Bacterial Disease in Kathmandu, Nepal (2005-2013). Pediatr Infect Dis J 2022; 41:192-198. [PMID: 34955523 DOI: 10.1097/inf.0000000000003421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Invasive bacterial disease (IBD; including pneumonia, meningitis, sepsis) is a major cause of morbidity and mortality in children in low-income countries. METHODS We analyzed data from a surveillance study of suspected community-acquired IBD in children <15 years of age in Kathmandu, Nepal, from 2005 to 2013 before introduction of pneumococcal conjugate vaccines (PCV). We detailed the serotype-specific distribution of invasive pneumococcal disease (IPD) and incorporated antigen and PCR testing of cerebrospinal fluid (CSF) from children with meningitis. RESULTS Enhanced surveillance of IBD was undertaken during 2005-2006 and 2010-2013. During enhanced surveillance, a total of 7956 children were recruited of whom 7754 had blood or CSF culture results available for analysis, and 342 (4%) had a pathogen isolated. From 2007 to 2009, all 376 positive culture results were available, with 259 pathogens isolated (and 117 contaminants). Salmonella enterica serovar Typhi was the most prevalent pathogen isolated (167 cases, 28% of pathogens), followed by Streptococcus pneumoniae (98 cases, 16% pathogens). Approximately, 73% and 78% of pneumococcal serotypes were contained in 10-valent and 13-valent PCV, respectively. Most cases of invasive pneumococcal disease (IPD) were among children ≥5 years of age from 2008 onward. Antigen and PCR testing of CSF for pneumococci, Haemophilus influenzae type b and meningococci increased the number of these pathogens identified from 33 (culture) to 68 (culture/antigen/PCR testing). CONCLUSIONS S. enterica serovar Typhi and S. pneumoniae accounted for 44% of pathogens isolated. Most pneumococcal isolates were of serotypes contained in PCVs. Antigen and PCR testing of CSF improves sensitivity for IBD pathogens.
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Affiliation(s)
- Michael J Carter
- From the Department of Women and Children's Health, School of Life Course Sciences, King's College London, United Kingdom
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
- Department of Paediatrics, University of Oxford and Oxford National Institute of Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Meeru Gurung
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Bhishma Pokhrel
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Sanjeev Man Bijukchhe
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Sudhir Karmacharya
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Bijay Khadka
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Anju Maharjan
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Suraj Bhattarai
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Swosti Shrestha
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Bibek Khadka
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Animesh Khulal
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Sunaina Gurung
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Bijaya Dhital
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | | | - Imran Ansari
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Ganesh P Shah
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Brian Wahl
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Rama Kandasamy
- Department of Paediatrics, University of Oxford and Oxford National Institute of Health Research Biomedical Research Centre, Oxford, United Kingdom
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | | | - Sarah Kelly
- Department of Paediatrics, University of Oxford and Oxford National Institute of Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Merryn Voysey
- Department of Paediatrics, University of Oxford and Oxford National Institute of Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - David R Murdoch
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Neelam Adhikari
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Stephen Thorson
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Dominic Kelly
- Department of Paediatrics, University of Oxford and Oxford National Institute of Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Shrijana Shrestha
- Department of Paediatrics, Patan Academy of Health Sciences, Lalitpur, Kathmandu, Nepal
| | - Andrew J Pollard
- Department of Paediatrics, University of Oxford and Oxford National Institute of Health Research Biomedical Research Centre, Oxford, United Kingdom
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Wildes DM, Chisale M, Drew RJ, Harrington P, Watson CJ, Ledwidge MT, Gallagher J. A Systematic Review of Clinical Prediction Rules to Predict Hospitalisation in Children with Lower Respiratory Infection in Primary Care and their Validation in a New Cohort. EClinicalMedicine 2021; 41:101164. [PMID: 34712930 PMCID: PMC8529204 DOI: 10.1016/j.eclinm.2021.101164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Our goal was to identify existing clinical prediction rules for predicting hospitalisation due to lower respiratory tract infection (LRTI) in children in primary care, guiding antibiotic therapy. A validation of these rules was then performed in a novel cohort of children presenting to primary care in Malawi with World Health Organisation clinically defined pneumonia. Methods: MEDLINE & EMBASE databases were searched for studies on the development, validation and clinical impact of clinical prediction models for hospitalisation in children with lower respiratory tract infection between January 1st1946-June 30th 2021. Two reviewers screened all abstracts and titles independently. The study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews & Meta-Analyses guidelines. The BIOTOPE cohort (BIOmarkers TO diagnose PnEumonia) recruited children aged 2-59 months with WHO-defined pneumonia from two primary care facilities in Mzuzu, Malawi. Validation of identified rules was undertaken in this cohort. Findings: 1023 abstracts were identified. Following the removal of duplicates, a review of 989 abstracts was conducted leading to the identification of one eligible model. The CHARMS checklist for prediction modelling studies was utilized for evaluation. The area under the curve (AUC) of the STARWAVe rule for hospitalisation in BIOTOPE was found to be 0.80 (95% C.I of 0.75-0.85). The AUC of STARWAVe for a confirmed diagnosis of bacterial pneumonia was 0.39 (95% C.I 0.25-0.54). Interpretation: This review highlights the lack of clinical prediction rules in this area. The STARWAVe rule identified was useful in predicting hospitalisation from bacterial infection as defined. However, in the absence of a gold standard indicator for bacterial LRTI, this is a reasonable surrogate and could lead to reductions in antibiotic prescription rates, should clinical impact studies prove its utility. Further work to determine the clinical impact of STARWAVe and to identify diagnostic tests for bacterial LRTI in primary care is required.
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Affiliation(s)
- Dermot M Wildes
- gHealth Research Group, UCD Conway Institute, School of Medicine, University College Dublin, Ireland
- Corresponding author: Dr. Dermot Michael Wildes, gHealth Research Group, School of Medicine, University College Dublin, Dublin
| | - Master Chisale
- Biological Science Department, Faculty of Science, Technology & Innovations, Mzuzu University, Malawi
| | - Richard J Drew
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street, Dublin 2
| | - Peter Harrington
- gHealth Research Group, UCD Conway Institute, School of Medicine, University College Dublin, Ireland
| | - Chris J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Northern Ireland
| | - Mark T Ledwidge
- gHealth Research Group, UCD Conway Institute, School of Medicine, University College Dublin, Ireland
| | - Joe Gallagher
- gHealth Research Group, UCD Conway Institute, School of Medicine, University College Dublin, Ireland
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3
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Awori JO, Kamau A, Morpeth S, Kazungu S, Silaba M, Sande J, Karani A, Nyongesa S, Mwarumba S, Musyimi R, Bett A, Wande S, Shebe M, Ngama M, Munywoki PK, Muturi N, Nokes DJ, Feikin DR, Murdoch DR, Prosperi C, O’Brien KL, Deloria Knoll M, Hammitt LL, Scott JAG. The Etiology of Pneumonia in HIV-uninfected Children in Kilifi, Kenya: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study. Pediatr Infect Dis J 2021; 40:S29-S39. [PMID: 34448742 PMCID: PMC8448399 DOI: 10.1097/inf.0000000000002653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND In the 1980s, Streptococcus pneumoniae and Haemophilus influenzae were identified as the principal causes of severe pneumonia in children. We investigated the etiology of severe childhood pneumonia in Kenya after introduction of conjugate vaccines against H. influenzae type b, in 2001, and S. pneumoniae, in 2011. METHODS We conducted a case-control study between August 2011 and November 2013 among residents of the Kilifi Health and Demographic Surveillance System 28 days to 59 months of age. Cases were hospitalized at Kilifi County Hospital with severe or very severe pneumonia according to the 2005 World Health Organization definition. Controls were randomly selected from the community and frequency matched to cases on age and season. We tested nasal and oropharyngeal samples, sputum, pleural fluid, and blood specimens and used the Pneumonia Etiology Research for Child Health Integrated Analysis, combining latent class analysis and Bayesian methods, to attribute etiology. RESULTS We enrolled 630 and 863 HIV-uninfected cases and controls, respectively. Among the cases, 282 (44%) had abnormal chest radiographs (CXR positive), 33 (5%) died in hospital, and 177 (28%) had diagnoses other than pneumonia at discharge. Among CXR-positive pneumonia cases, viruses and bacteria accounted for 77% (95% CrI: 67%-85%) and 16% (95% CrI: 10%-26%) of pneumonia attribution, respectively. Respiratory syncytial virus, S. pneumoniae and H. influenza, accounted for 37% (95% CrI: 31%-44%), 5% (95% CrI: 3%-9%), and 6% (95% CrI: 2%-11%), respectively. CONCLUSIONS Respiratory syncytial virus was the main cause of CXR-positive pneumonia. The small contribution of H. influenzae type b and pneumococcus to pneumonia may reflect the impact of vaccine introductions in this population.
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Affiliation(s)
- Juliet O. Awori
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Alice Kamau
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Susan Morpeth
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Sidi Kazungu
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Micah Silaba
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | | | - Angela Karani
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Sammy Nyongesa
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Salim Mwarumba
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Robert Musyimi
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Anne Bett
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Siti Wande
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Mohammed Shebe
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Mwanajuma Ngama
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Patrick K. Munywoki
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Neema Muturi
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - D. James Nokes
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- School of Life Sciences and WIDER, University of Warwick, Coventry, United Kingdom
| | - Daniel R. Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katherine L. O’Brien
- 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
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J. Anthony G. Scott
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Nuffield Department of Tropical Medicine, Oxford University, Oxford, United Kingdom
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Bunthi C, Rhodes J, Thamthitiwat S, Higdon MM, Chuananon S, Amorninthapichet T, Paveenkittiporn W, Chittaganpitch M, Sawatwong P, Hammitt LL, Feikin DR, Murdoch DR, Deloria-Knoll M, O’Brien KL, Prosperi C, Maloney SA, Baggett HC, Akarasewi P. Etiology and Clinical Characteristics of Severe Pneumonia Among Young Children in Thailand: Pneumonia Etiology Research for Child Health (PERCH) Case-Control Study Findings, 2012-2013. Pediatr Infect Dis J 2021; 40:S91-S100. [PMID: 34448748 PMCID: PMC8448397 DOI: 10.1097/inf.0000000000002768] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pneumonia remains the leading cause of death among children <5 years of age beyond the neonatal period in Thailand. Using data from the Pneumonia Etiology Research for Child Health (PERCH) Study, we provide a detailed description of pneumonia cases and etiology in Thailand to inform local treatment and prevention strategies in this age group. METHODS PERCH, a multi-country case-control study, evaluated the etiology of hospitalized cases of severe and very severe pneumonia among children 1-59 months of age. The Thailand site enrolled children for 24 consecutive months during January 2012-February 2014 with staggered start dates in 2 provinces. Cases were children hospitalized with pre-2013 WHO-defined severe or very severe pneumonia. Community controls were randomly selected from health services registries in each province. Analyses were restricted to HIV-negative cases and controls. We calculated adjusted odds ratios (ORs) and 95% CIs comparing organism prevalence detected by nasopharyngeal/oropharyngeal (NP/OP) polymerase chain reaction between cases and controls. The PERCH Integrated Analysis (PIA) used Bayesian latent variable analysis to estimate pathogen-specific etiologic fractions and 95% credible intervals. RESULTS Over 96% of both cases (n = 223) and controls (n = 659) had at least 1 organism detected; multiple organisms were detected in 86% of cases and 88% of controls. Among 98 chest Radiograph positive (CXR+) cases, respiratory syncytial virus (RSV) had the highest NP/OP prevalence (22.9%) and the strongest association with case status (OR 20.5; 95% CI: 10.2, 41.3) and accounted for 34.6% of the total etiologic fraction. Tuberculosis (TB) accounted for 10% (95% CrI: 1.6-26%) of the etiologic fraction among CXR+ cases. DISCUSSION More than one-third of hospitalized cases of severe and very severe CXR+ pneumonia among children 1-59 months of age in Thailand were attributable to RSV. TB accounted for 10% of cases, supporting evaluation for TB among children hospitalized with pneumonia in high-burden settings. Similarities in pneumonia etiology in Thailand and other PERCH sites suggest that global control strategies based on PERCH study findings are relevant to Thailand and similar settings.
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Affiliation(s)
- Charatdao Bunthi
- From the Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Julia Rhodes
- From the Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Somsak Thamthitiwat
- From the Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Melissa M. Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | | | | | - Pongpun Sawatwong
- From the Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Laura L. Hammitt
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Daniel R. Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand; Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Maria Deloria-Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katherine L. O’Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Susan A. Maloney
- Division of Global HIV and TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA
| | - Henry C. Baggett
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, GA
| | - Pasakorn Akarasewi
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
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Deloria Knoll M, Prosperi C, Baggett HC, Brooks WA, Feikin DR, Hammitt LL, Howie SR, Kotloff KL, Madhi SA, Murdoch DR, Scott JAG, Thea DM, O’Brien KL. Introduction to the Site-specific Etiologic Results From the Pneumonia Etiology Research for Child Health (PERCH) Study. Pediatr Infect Dis J 2021; 40:S1-S6. [PMID: 34448739 PMCID: PMC8448396 DOI: 10.1097/inf.0000000000002778] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2020] [Indexed: 11/26/2022]
Abstract
The Pneumonia Etiology Research for Child Health (PERCH) study evaluated the etiology of severe and very severe pneumonia in children hospitalized in 7 African and Asian countries. Here, we summarize the highlights of in-depth site-specific etiology analyses published separately in this issue, including how etiology varies by age, mortality status, malnutrition, severity, HIV status, and more. These site-specific results impart important lessons that can inform disease control policy implications.
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Affiliation(s)
- Maria Deloria Knoll
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Christine Prosperi
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Henry C. Baggett
- Division of Global Health Protection, 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, Bangladesh
| | - Daniel R. Feikin
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L. Hammitt
- From the 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, Kenya
| | - Stephen R.C. Howie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Basse, The Gambia
- Department of Paediatrics University of Auckland, New Zealand
| | - Karen L. Kotloff
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Shabir A. Madhi
- 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 Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - J. Anthony G. Scott
- Kenya Medical Research Institute—Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Donald M. Thea
- Department of Global Health and Development, Boston University School of Public Health, Boston, Massachusetts
| | - Katherine L. O’Brien
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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6
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Chen Y, Roberts CS, Ou W, Petigara T, Goldmacher GV, Fancourt N, Knoll MD. Deep learning for classification of pediatric chest radiographs by WHO's standardized methodology. PLoS One 2021; 16:e0253239. [PMID: 34153076 PMCID: PMC8216551 DOI: 10.1371/journal.pone.0253239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/31/2021] [Indexed: 11/05/2022] Open
Abstract
Background The World Health Organization (WHO)-defined radiological pneumonia is a preferred endpoint in pneumococcal vaccine efficacy and effectiveness studies in children. Automating the WHO methodology may support more widespread application of this endpoint. Methods We trained a deep learning model to classify pneumonia CXRs in children using the World Health Organization (WHO)’s standardized methodology. The model was pretrained on CheXpert, a dataset containing 224,316 adult CXRs, and fine-tuned on PERCH, a pediatric dataset containing 4,172 CXRs. The model was then tested on two pediatric CXR datasets released by WHO. We also compared the model’s performance to that of radiologists and pediatricians. Results The average area under the receiver operating characteristic curve (AUC) for primary endpoint pneumonia (PEP) across 10-fold validation of PERCH images was 0.928; average AUC after testing on WHO images was 0.977. The model’s classification performance was better on test images with high inter-observer agreement; however, the model still outperformed human assessments in AUC and precision-recall spaces on low agreement images. Conclusion A deep learning model can classify pneumonia CXR images in children at a performance comparable to human readers. Our method lays a strong foundation for the potential inclusion of computer-aided readings of pediatric CXRs in vaccine trials and epidemiology studies.
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Affiliation(s)
- Yiyun Chen
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
- * E-mail:
| | - Craig S. Roberts
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Wanmei Ou
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Tanaz Petigara
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | | | - Nicholas Fancourt
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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7
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Martines RB, Ritter JM, Gary J, Shieh WJ, Ordi J, Hale M, Carrilho C, Ismail M, Traore CB, Ndibile BE, Sava S, Arjuman F, Kamal M, Rahman MM, Blau DM, Zaki SR. Pathology and Telepathology Methods in the Child Health and Mortality Prevention Surveillance Network. Clin Infect Dis 2020; 69:S322-S332. [PMID: 31598668 DOI: 10.1093/cid/ciz579] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This manuscript describes the Child Health and Mortality Prevention Surveillance (CHAMPS) network approach to pathologic evaluation of minimally invasive tissue sampling (MITS) specimens, including guidelines for histopathologic examination and further diagnostics with special stains, immunohistochemistry, and molecular testing, as performed at the CHAMPS Central Pathology Laboratory (CPL) at the Centers for Disease Control and Prevention, as well as techniques for virtual discussion of these cases (telepathology) with CHAMPS surveillance locations. Based on review of MITS from the early phase of CHAMPS, the CPL has developed standardized histopathology-based algorithms for achieving diagnoses from MITS and telepathology procedures in conjunction with the CHAMPS sites, with the use of whole slide scanners and digital image archives, for maximizing concurrence and knowledge sharing between site and CPL pathologists. These algorithms and procedures, along with lessons learned from initial implementation of these approaches, guide pathologists at the CPL and CHAMPS sites through standardized diagnostics of MITS cases, and allow for productive, real-time case discussions and consultations.
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Affiliation(s)
- Roosecelis B Martines
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jana M Ritter
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joy Gary
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wun-Ju Shieh
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jaume Ordi
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Spain
| | - Martin Hale
- Division of Anatomical Pathology, University of the Witswatersrand, Johannesburg, South Africa
| | - Carla Carrilho
- Department of Pathology, Faculty of Medicine, Eduardo Mondlane University and Maputo Central Hospital, Mozambique
| | - Mamudo Ismail
- Department of Pathology, Faculty of Medicine, Eduardo Mondlane University and Maputo Central Hospital, Mozambique
| | - Cheick Boudadari Traore
- Department of Pathological Anatomy and Cytology, University Hospital of Point G, Bamako, Mali
| | | | - Solomon Sava
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Kisumu County, Kenya
| | - Farida Arjuman
- National Institute of Cancer Research and Hospital, Dhaka, Bangladesh
| | - Mohammed Kamal
- Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | | | - Dianna M Blau
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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8
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Piedra PA. Long-Term Healthcare Costs Associated With Respiratory Syncytial Virus Infection in Children: The Domino Effect. J Infect Dis 2020; 221:1205-1207. [PMID: 30982897 DOI: 10.1093/infdis/jiz161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/12/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Pedro A Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas
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9
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Carugati M, Morlacchi LC, Peri AM, Alagna L, Rossetti V, Bandera A, Gori A, Blasi F. Challenges in the Diagnosis and Management of Bacterial Lung Infections in Solid Organ Recipients: A Narrative Review. Int J Mol Sci 2020; 21:E1221. [PMID: 32059371 PMCID: PMC7072844 DOI: 10.3390/ijms21041221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/31/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Respiratory infections pose a significant threat to the success of solid organ transplantation, and the diagnosis and management of these infections are challenging. The current narrative review addressed some of these challenges, based on evidence from the literature published in the last 20 years. Specifically, we focused our attention on (i) the obstacles to an etiologic diagnosis of respiratory infections among solid organ transplant recipients, (ii) the management of bacterial respiratory infections in an era characterized by increased antimicrobial resistance, and (iii) the development of antimicrobial stewardship programs dedicated to solid organ transplant recipients.
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Affiliation(s)
- Manuela Carugati
- Internal Medicine Department, Division of Infectious Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (A.M.P.); (L.A.); (A.B.); (A.G.)
- Division of Infectious Diseases and International Health, Duke University, Durham, NC 27710, USA
| | - Letizia Corinna Morlacchi
- Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (L.C.M.); (V.R.); (F.B.)
| | - Anna Maria Peri
- Internal Medicine Department, Division of Infectious Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (A.M.P.); (L.A.); (A.B.); (A.G.)
| | - Laura Alagna
- Internal Medicine Department, Division of Infectious Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (A.M.P.); (L.A.); (A.B.); (A.G.)
| | - Valeria Rossetti
- Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (L.C.M.); (V.R.); (F.B.)
| | - Alessandra Bandera
- Internal Medicine Department, Division of Infectious Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (A.M.P.); (L.A.); (A.B.); (A.G.)
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milano, Italy
| | - Andrea Gori
- Internal Medicine Department, Division of Infectious Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (A.M.P.); (L.A.); (A.B.); (A.G.)
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milano, Italy
- Centre for Multidisciplinary Research in Health Science, 20122 Milano, Italy
| | - Francesco Blasi
- Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, 20122 Milano, Italy; (L.C.M.); (V.R.); (F.B.)
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milano, Italy
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10
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Rhee C, Kharod GA, Schaad N, Furukawa NW, Vora NM, Blaney DD, Crump JA, Clarke KR. Global knowledge gaps in acute febrile illness etiologic investigations: A scoping review. PLoS Negl Trop Dis 2019; 13:e0007792. [PMID: 31730635 PMCID: PMC6881070 DOI: 10.1371/journal.pntd.0007792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 11/27/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Acute febrile illness (AFI), a common reason for people seeking medical care globally, represents a spectrum of infectious disease etiologies with important variations geographically and by population. There is no standardized approach to conducting AFI etiologic investigations, limiting interpretation of data in a global context. We conducted a scoping review to characterize current AFI research methodologies, identify global research gaps, and provide methodological research standardization recommendations. METHODOLOGY/FINDINGS Using pre-defined terms, we searched Medline, Embase, and Global Health, for publications from January 1, 2005-December 31, 2017. Publications cited in previously published systematic reviews and an online study repository of non-malarial febrile illness etiologies were also included. We screened abstracts for publications reporting on human infectious disease, aimed at determining AFI etiology using laboratory diagnostics. One-hundred ninety publications underwent full-text review, using a standardized tool to collect data on study characteristics, methodology, and laboratory diagnostics. AFI case definitions between publications varied: use of self-reported fever as part of case definitions (28%, 53/190), fever cut-off value (38·0°C most commonly used: 45%, 85/190), and fever measurement site (axillary most commonly used: 19%, 36/190). Eighty-nine publications (47%) did not include exclusion criteria, and inclusion criteria in 13% (24/190) of publications did not include age group. No publications included study settings in Southern Africa, Micronesia & Polynesia, or Central Asia. We summarized standardized reporting practices, specific to AFI etiologic investigations that would increase inter-study comparability. CONCLUSIONS Wider implementation of standardized AFI reporting methods, with multi-pathogen disease detection, could improve comparability of study findings, knowledge of the range of AFI etiologies, and their contributions to the global AFI burden. These steps can guide resource allocation, strengthen outbreak detection and response, target prevention efforts, and improve clinical care, especially in resource-limited settings where disease control often relies on empiric treatment. PROSPERO: CRD42016035666.
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Affiliation(s)
- Chulwoo Rhee
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Grishma A. Kharod
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Nicolas Schaad
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Nathan W. Furukawa
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Neil M. Vora
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - David D. Blaney
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John A. Crump
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, United States of America
- Centre for International Health, University of Otago, New Zealand
| | - Kevin R. Clarke
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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11
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Aston SJ, Ho A, Jary H, Huwa J, Mitchell T, Ibitoye S, Greenwood S, Joekes E, Daire A, Mallewa J, Everett D, Nyirenda M, Faragher B, Mwandumba HC, Heyderman RS, Gordon SB. Etiology and Risk Factors for Mortality in an Adult Community-acquired Pneumonia Cohort in Malawi. Am J Respir Crit Care Med 2019; 200:359-369. [PMID: 30625278 PMCID: PMC6680311 DOI: 10.1164/rccm.201807-1333oc] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/09/2019] [Indexed: 01/12/2023] Open
Abstract
Rationale: In the context of rapid antiretroviral therapy rollout and an increasing burden of noncommunicable diseases, there are few contemporary data describing the etiology and outcome of community-acquired pneumonia (CAP) in sub-Saharan Africa.Objectives: To describe the current etiology of CAP in Malawi and identify risk factors for mortality.Methods: We conducted a prospective observational study of adults hospitalized with CAP to a teaching hospital in Blantyre, Malawi. Etiology was defined by blood culture, Streptococcus pneumoniae urinary antigen detection, sputum mycobacterial culture and Xpert MTB/RIF, and nasopharyngeal aspirate multiplex PCR.Measurements and Main Results: In 459 patients (285 [62.1%] males; median age, 34.7 [interquartile range, 29.4-41.9] yr), 30-day mortality was 14.6% (64/439) and associated with male sex (adjusted odds ratio, 2.60 [95% confidence interval, 1.17-5.78]), symptom duration greater than 7 days (2.78 [1.40-5.54]), tachycardia (2.99 [1.48-6.06]), hypoxemia (4.40 [2.03-9.51]), and inability to stand (3.59 [1.72-7.50]). HIV was common (355/453; 78.4%), frequently newly diagnosed (124/355; 34.9%), but not associated with mortality. S. pneumoniae (98/458; 21.4%) and Mycobacterium tuberculosis (75/326; 23.0%) were the most frequently identified pathogens. Viral infection occurred in 32.6% (148/454) with influenza (40/454; 8.8%) most common. Bacterial-viral coinfection occurred in 9.1% (28/307). Detection of M. tuberculosis was associated with mortality (adjusted odds ratio, 2.44 [1.19-5.01]).Conclusions: In the antiretroviral therapy era, CAP in Malawi remains predominantly HIV associated, with a large proportion attributable to potentially vaccine-preventable pathogens. Strategies to increase early detection and treatment of tuberculosis and improve supportive care, in particular the correction of hypoxemia, should be evaluated in clinical trials to address CAP-associated mortality.
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Affiliation(s)
- Stephen J. Aston
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Liverpool School of Tropical of Medicine, Liverpool, United Kingdom
| | - Antonia Ho
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Hannah Jary
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Liverpool School of Tropical of Medicine, Liverpool, United Kingdom
| | - Jacqueline Huwa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
| | - Tamara Mitchell
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
| | - Sarah Ibitoye
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Liverpool School of Tropical of Medicine, Liverpool, United Kingdom
| | - Simon Greenwood
- Department of Radiology, Royal Liverpool University Hospital NHS Trust, Liverpool, United Kingdom
| | - Elizabeth Joekes
- Department of Radiology, Royal Liverpool University Hospital NHS Trust, Liverpool, United Kingdom
| | - Arthur Daire
- Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Jane Mallewa
- Queen Elizabeth Central Hospital, Blantyre, Malawi
- College of Medicine, University of Malawi, Blantyre, Malawi
| | - Dean Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; and
| | | | - Brian Faragher
- Liverpool School of Tropical of Medicine, Liverpool, United Kingdom
| | - Henry C. Mwandumba
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Liverpool School of Tropical of Medicine, Liverpool, United Kingdom
| | - Robert S. Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Stephen B. Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
- Liverpool School of Tropical of Medicine, Liverpool, United Kingdom
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12
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Foresti S, Perego MR, Carugati M, Casati A, Malafronte C, Manzoni M, Badolato R, Gori A, Achilli F. The hidden hypothesis: A disseminated tuberculosis case. Int J Infect Dis 2019; 85:88-91. [PMID: 31150844 DOI: 10.1016/j.ijid.2019.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022] Open
Abstract
CASE PRESENTATION 77-year-old former smoker admitted because of fatigue and abdominal distention. Past medical history positive for two previous hospitalizations for pericardial and pleural effusions (no diagnosis achieved). At admission erythrocyte sedimentation rate was 122mm per hour. Baseline investigations revealed ascitic, pleural and pericardial effusion. Effusions were tapped: neoplastic cells and acid-fast bacilli (AFB) were not identified, aerobic and mycobacterial culture resulted negative. QuantiFERON TB-Gold test was negative. Total body PET-CT and autoimmunity panel were negative. A neoplastic process was considered the most likely explanation. Before signing off the patient to comfort care, a reassessment was performed and an exposure to tuberculosis during childhood was documented. Because of constrictive pericarditis, pericardiectomy was performed: histologic examination showed chronic pericardial inflammation without granulomas, but Ziehl-Neelsen stain identified AFB and PCR was positive for Mycobacterium tuberculosis complex. Patient was started on anti-TB therapy with resolution of the effusions in the following months. Genes associated with defects in innate immunity were sequences and dentritic cells were studied, but no alterations were identified. DISCUSSION A Bayesian approach to clinical decision making should be recommended. Interpretation of diagnostic tests should take into account the imperfect diagnostic performance of the majority of these tests. Further studies to investigate genetic susceptibility to tuberculosis are needed.
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Affiliation(s)
- Sergio Foresti
- Division of Infectious Diseases, Ospedale San Gerardo ASST Monza, Via Pergolesi 33, Monza, Italy.
| | - Maria Rita Perego
- Division of Internal Medicine, Ospedale San Gerardo ASST Monza, Via Pergolesi 33, Monza, Italy.
| | - Manuela Carugati
- Division of Infectious Diseases, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, Milan, Italy; Division of Infectious Diseases, Duke University, 300 Trent Drive, Durham, USA.
| | - Anna Casati
- Division of Cardiology, Ospedale San Gerardo ASST Monza, Via Pergolesi 33, Monza, Italy.
| | - Cristina Malafronte
- Division of Cardiology, Ospedale San Gerardo ASST Monza, Via Pergolesi 33, Monza, Italy.
| | - Marco Manzoni
- Department of Medicine and Surgery, Pathology Section, University of Milano-Bicocca, Milan, Italy.
| | - Raffaele Badolato
- Division of Paediatrics, Università degli Studi di Brescia, P.le Ospedali Civili di Brescia 1, Brescia, Italy.
| | - Andrea Gori
- Division of Infectious Diseases, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Via Festa del Perdono 7, Milan, Italy.
| | - Felice Achilli
- Division of Cardiology, Ospedale San Gerardo ASST Monza, Via Pergolesi 33, Monza, Italy.
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13
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Velaphi SC, Westercamp M, Moleleki M, Pondo T, Dangor Z, Wolter N, von Gottberg A, Shang N, Demirjian A, Winchell JM, Diaz MH, Nakwa F, Okudo G, Wadula J, Cutland C, Schrag SJ, Madhi SA. Surveillance for incidence and etiology of early-onset neonatal sepsis in Soweto, South Africa. PLoS One 2019; 14:e0214077. [PMID: 30970036 PMCID: PMC6457488 DOI: 10.1371/journal.pone.0214077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/06/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Globally, over 400,000 neonatal deaths in 2015 were attributed to sepsis, however, the incidence and etiologies of these infections are largely unknown in low-middle income countries. We aimed to determine incidence and etiology of community-acquired early-onset (<72 hours age) sepsis (EOS) using culture and molecular diagnostics. METHODS This was a prospective observational study, in which we conducted a surveillance for pathogens using a combination of blood culture and a polymerase chain reaction (PCR)-based test. Blood culture was performed on all neonates with suspected EOS. Among the subset fulfilling criteria for protocol-defined EOS, blood and nasopharyngeal (NP) respiratory swabs were tested by quantitative real-time reverse-transcriptase PCR using a Taqman Array Card (TAC) with 15 bacterial and 12 viral targets. Blood and NP samples from 312 healthy newborns were also tested by TAC to estimate background positivity rates. We used variant latent-class methods to attribute etiologies and calculate pathogen-specific proportions and incidence rates. RESULTS We enrolled 2,624 neonates with suspected EOS and from these 1,231 newborns met criteria for protocol-defined EOS (incidence- 39.3/1,000 live-births). Using the partially latent-class modelling, only 26.7% cases with protocol-defined EOS had attributable etiology, and the largest pathogen proportion were Ureaplasma spp. (5.4%; 95%CI: 3.6-8.0) and group B Streptococcus (GBS) (4.8%; 95%CI: 4.1-5.8), and no etiology was attributable for 73.3% of cases. Blood cultures were positive in 99/1,231 (8.0%) with protocol-defined EOS (incidence- 3.2/1,000 live-births). Leading pathogens on blood culture included GBS (35%) and viridans streptococci (24%). Ureaplasma spp. was the most common organism identified on TAC among cases with protocol-defined EOS. CONCLUSION Using a combination of blood culture and a PCR-based test the common pathogens isolated in neonates with sepsis were Ureaplasma spp. and GBS. Despite documenting higher rates of protocol-defined EOS and using a combination of tests, the etiology for EOS remains elusive.
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Affiliation(s)
- Sithembiso C. Velaphi
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Matthew Westercamp
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Malefu Moleleki
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tracy Pondo
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Ziyaad Dangor
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and School of Pathology, Faculty of Health Sciences, 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 (NHLS), and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nong Shang
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Alicia Demirjian
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Jonas M. Winchell
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Maureen H. Diaz
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Firdose Nakwa
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Grace Okudo
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology and Infectious Diseases, NHLS, South Africa and School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Clare Cutland
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie J. Schrag
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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14
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le Roux DM, Nicol MP, Myer L, Vanker A, Stadler JAM, von Delft E, Zar HJ. Lower Respiratory Tract Infections in Children in a Well-vaccinated South African Birth Cohort: Spectrum of Disease and Risk Factors. Clin Infect Dis 2019; 69:1588-1596. [DOI: 10.1093/cid/ciz017] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Childhood lower respiratory tract infections (LRTIs) cause substantial morbidity and under-5 child mortality. The epidemiology of LRTI is changing in low- and middle-income countries with expanding access to conjugate vaccines, yet there are few data on the incidence and risk factors for LRTI in these settings.
Methods
A prospective birth cohort enrolled mother–infant pairs in 2 communities near Cape Town, South Africa. Active surveillance for LRTI was performed for the first 2 years of life over 4 respiratory seasons. Comprehensive data collection of risk factors was done through 2 years of life. World Health Organization definitions were used to classify clinical LRTI and chest radiographs.
Results
From March 2012 to February 2017, 1143 children were enrolled and followed until 2 years of age. Thirty-two percent of children were exposed to antenatal maternal smoking; 15% were born at low birth weights. Seven hundred ninety-five LRTI events occurred in 429 children by February 2017; incidence of LRTI was 0.51 and 0.25 episodes per child-year in the first and second years of life, respectively. Human immunodeficiency virus (HIV)–exposed, uninfected infants (vs HIV-unexposed infants) were at increased risk of hospitalized LRTI in the first 6 months of life. In regression models, male sex, low birth weight, and maternal smoking were independent risk factors for both ambulatory and hospitalized LRTI; delayed or incomplete vaccination was associated with hospitalized LRTI.
Conclusions
LRTI incidence was high in the first year of life, with substantial morbidity. Strategies to ameliorate harmful exposures are needed to reduce LRTI burden in vulnerable populations.
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Affiliation(s)
- David M le Roux
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Department of Paediatrics, New Somerset Hospital, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | - Landon Myer
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Aneesa Vanker
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Jacob A M Stadler
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Eckart von Delft
- Department of Paediatrics, Paarl Hospital, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
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15
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Watson NL, Prosperi C, Driscoll AJ, Higdon MM, Park DE, Sanza M, DeLuca AN, Awori JO, Goswami D, Hammond E, Hossain L, Johnson C, Kamau A, Kuwanda L, Moore DP, Neyzari O, Onwuchekwa U, Parker D, Sapchookul P, Seidenberg P, Shamsul A, Siazeele K, Srisaengchai P, Sylla M, Levine OS, Murdoch DR, O'Brien KL, Wolff M, Deloria Knoll M. Data Management and Data Quality in PERCH, a Large International Case-Control Study of Severe Childhood Pneumonia. Clin Infect Dis 2018; 64:S238-S244. [PMID: 28575357 PMCID: PMC5447839 DOI: 10.1093/cid/cix080] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The Pneumonia Etiology Research for Child Health (PERCH) study is the largest multicountry etiology study of pediatric pneumonia undertaken in the past 3 decades. The study enrolled 4232 hospitalized cases and 5325 controls over 2 years across 9 research sites in 7 countries in Africa and Asia. The volume and complexity of data collection in PERCH presented considerable logistical and technical challenges. The project chose an internet-based data entry system to allow real-time access to the data, enabling the project to monitor and clean incoming data and perform preliminary analyses throughout the study. To ensure high-quality data, the project developed comprehensive quality indicator, data query, and monitoring reports. Among the approximately 9000 cases and controls, analyzable laboratory results were available for ≥96% of core specimens collected. Selected approaches to data management in PERCH may be extended to the planning and organization of international studies of similar scope and complexity.
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Affiliation(s)
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Amanda J Driscoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Melissa M Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - 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
| | | | - Andrea N DeLuca
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Juliet O Awori
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Doli Goswami
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | | | - Lokman Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | | | - Alice Kamau
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Locadiah Kuwanda
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, and
| | - David P Moore
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, and.,Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, Johannesberg, South Africa
| | | | - Uma Onwuchekwa
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako
| | - David Parker
- Medical Research Council Unit, Basse, The Gambia
| | - Patranuch Sapchookul
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Phil Seidenberg
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts.,Department of Emergency Medicine, University of New Mexico, Albuquerque
| | | | | | - Prasong Srisaengchai
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Mamadou Sylla
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako
| | - 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
| | - David R Murdoch
- Department of Pathology, University of Otago, and.,Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Katherine L O'Brien
- 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
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16
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Malosh RE, Martin ET, Ortiz JR, Monto AS. The risk of lower respiratory tract infection following influenza virus infection: A systematic and narrative review. Vaccine 2017; 36:141-147. [PMID: 29157959 PMCID: PMC5736984 DOI: 10.1016/j.vaccine.2017.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/07/2017] [Indexed: 01/18/2023]
Abstract
Background Lower respiratory tract infections (LRTI) are a major cause of morbidity and mortality worldwide, particularly in young children and older adults. Influenza is known to cause severe disease but the risk of developing LRTI following influenza virus infection in various populations has not been systematically reviewed. Such data are important for estimating the impact specific influenza vaccine programs would have on LRTI outcomes in a community. We sought to review the published literature to determine the risk of developing LRTI following an influenza virus infection in individuals of any age. Methods and findings We conducted a systematic review to identify prospective studies that estimated the incidence of LRTI following laboratory-confirmed influenza virus infection. We searched PubMed, Medline, and Embase databases for relevant literature. We supplemented this search with a narrative review of influenza and LRTI. The systematic review identified two prospective studies that both followed children less than 5 years. We also identified one additional pediatric study from our narrative review meeting the study inclusion criteria. Finally, we summarized recent case-control studies on the etiology of pneumonia in both adults and children. Conclusions There is a dearth of prospective studies evaluating the risk of developing LRTI following influenza virus infection. Determining the burden of severe LRTI that is attributable to influenza is necessary to estimate the benefits of influenza vaccine on this important public health outcome. Vaccine probe studies are an efficient way to evaluate these questions and should be encouraged going forward.
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Affiliation(s)
- Ryan E Malosh
- University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, MI, United States
| | | | - Arnold S Monto
- University of Michigan School of Public Health, Ann Arbor, MI, United States.
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17
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Weinberg GA. Respiratory syncytial virus mortality among young children. LANCET GLOBAL HEALTH 2017; 5:e951-e952. [DOI: 10.1016/s2214-109x(17)30348-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 08/29/2017] [Indexed: 11/16/2022]
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