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Pulvirenti F, Giufrè M, Pentimalli TM, Camilli R, Milito C, Villa A, Sculco E, Cerquetti M, Pantosti A, Quinti I. Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency. Front Immunol 2024; 15:1371118. [PMID: 38873612 PMCID: PMC11169596 DOI: 10.3389/fimmu.2024.1371118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
Background The respiratory tract microbiome is essential for human health and well-being and is determined by genetic, lifestyle, and environmental factors. Patients with Common Variable Immunodeficiency (CVID) suffer from respiratory and intestinal tract infections, leading to chronic diseases and increased mortality rates. While CVID patients' gut microbiota have been analyzed, data on the respiratory microbiome ecosystem are limited. Objective This study aims to analyze the bacterial composition of the oropharynx of adults with CVID and its link with clinical and immunological features and risk for respiratory acute infections. Methods Oropharyngeal samples from 72 CVID adults and 26 controls were collected in a 12-month prospective study. The samples were analyzed by metagenomic bacterial 16S ribosomal RNA sequencing and processed using the Quantitative Insights Into Microbial Ecology (QIME) pipeline. Differentially abundant species were identified and used to build a dysbiosis index. A machine learning model trained on microbial abundance data was used to test the power of microbiome alterations to distinguish between healthy individuals and CVID patients. Results Compared to controls, the oropharyngeal microbiome of CVID patients showed lower alpha- and beta-diversity, with a relatively increased abundance of the order Lactobacillales, including the family Streptococcaceae. Intra-CVID analysis identified age >45 years, COPD, lack of IgA, and low residual IgM as associated with a reduced alpha diversity. Expansion of Haemophilus and Streptococcus genera was observed in patients with undetectable IgA and COPD, independent from recent antibiotic use. Patients receiving azithromycin as antibiotic prophylaxis had a higher dysbiosis score. Expansion of Haemophilus and Anoxybacillus was associated with acute respiratory infections within six months. Conclusions CVID patients showed a perturbed oropharynx microbiota enriched with potentially pathogenic bacteria and decreased protective species. Low residual levels of IgA/IgM, chronic lung damage, anti antibiotic prophylaxis contributed to respiratory dysbiosis.
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Affiliation(s)
- Federica Pulvirenti
- Reference Center for Primary Immune Deficiencies, Azienda Ospedaliero Universitaria (AOU) Policlinico Umberto I, Rome, Italy
| | - Maria Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Tancredi M. Pentimalli
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin School of Integrative Oncology (BSIO), Berlin, Germany
| | - Romina Camilli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Cinzia Milito
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Annalisa Villa
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Eleonora Sculco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Marina Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Detection of Chicken Respiratory Pathogens in Live Markets of Addis Ababa, Ethiopia, and Epidemiological Implications. Vet Sci 2022; 9:vetsci9090503. [PMID: 36136719 PMCID: PMC9501380 DOI: 10.3390/vetsci9090503] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/27/2022] [Accepted: 09/09/2022] [Indexed: 12/04/2022] Open
Abstract
A moderate to high seroprevalence of exposure to Newcastle disease (NDV), avian metapneumovirus (aMPV), infectious laryngotracheitis virus (ILTV), infectious bronchitis virus (IBV) and Mycoplasma gallisepticum (MG) has recently been reported in Ethiopia, but it is unclear to what extent these contribute to clinical cases of respiratory disease. This study investigated the presence of these pathogens in chickens exhibiting respiratory disease in two live markets in Addis Ababa. Markets were visited weekly for three months, and 18 chickens displaying respiratory clinical signs were acquired. Swab samples were taken from the choana, trachea, air sac and larynx for bacteriology and PCR tests targeting these five pathogens. PCR-positive samples were sequenced. All 18 chickens were PCR-positive for aMPV, 50% for each of Mg and NDV, 39% for IBV and 11% for ILTV. Infections with >3 pathogens were detected in 17 of 18 chickens. Potentially pathogenic bacteria such as Escherichia coli, Klebsiella spp., Streptococcus spp. and Staphylococcus were found in 16 to 44% of chickens. IBV-positive samples were of the 793B genotype. The results associate the presence of these organisms with clinical respiratory disease and are consistent with recent serological investigations, indicating a high level of exposure to multiple respiratory pathogens.
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Amarnath SK, Joshi S, Abhyankar MN, Adhikary R, Beena HB, Chugh TD, Gandhi KD, Hittinahalli V, Indumathi VA, Rajavari M, Muralidharan S, Rao SS, Roy I, Saini N. Cross-country transport and isolation and identification of Streptococcus pneumoniae by use of alternate sources of blood supplemented media among laboratories in India. Indian J Med Microbiol 2019; 37:363-369. [PMID: 32003334 DOI: 10.4103/ijmm.ijmm_19_82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background The isolation of S. pneumoniae (Sp) depends on specimen integrity / transport, media and expertise. The non-availability of sheep blood agar poses a challenge in identification of colonial morphology and identification in India. Methods Laboratories processed swabs containing either pure Sp or Sp in mixed cultures with a second (confounding) bacterium shipped across the country in cold conditions. Duplicate set of swabs was shipped back to the central laboratory to assess the impact of shipping on culture viability. The identical swab was cultured on sheep, human blood and one additional agar plate used in the laboratory. Results 46/60(77%) of cultures containing only Sp were correctly identified. In specimens where Sp was present in mixed culture, the proportion of isolates in which Sp was correctly identified varied, with most variability attributed to the particular confounding organism rather than the media. There was no discernible impact of temperature-controlled (4-6°C) transport on the isolation of Sp from culture swabs. Conclusions The study clearly elucidates the ability of laboratories for isolation of S. pneumoniae on human blood agar in resource limited settings. The results highlight the difficulties inherent in correctly identifying pathogens in mixed cultures in needs improvement using standardized tests across the study centers. The study also reaffirms the ability to transport biological specimens over long geographical distances without loss.
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Affiliation(s)
| | - Sangeeta Joshi
- Consultant Microbiologist, Manipal Hospital, Bengaluru, Karnataka, India
| | - Madhuwanti N Abhyankar
- Consultant Microbiologist, Golwilkar Metropolis Health Services, (I) Pvt. Ltd., Pune, Maharashtra, India
| | - Ranjeeta Adhikary
- Consultant Microbiologist, Manipal Hospital, Bengaluru, Karnataka, India
| | - H B Beena
- Consultant Microbiologist, Manipal Hospital, Bengaluru, Karnataka, India
| | - T D Chugh
- Sr. Consultant, Department of Microbiology, BL Kapoor Memorial Hospital, New Delhi, India
| | - K D Gandhi
- Consultant Microbiologist, Shanti Mukund Hospital, New Delhi, India
| | - Vivek Hittinahalli
- Consultant Microbiologist, Yashomati Hospital, Bengaluru, Karnataka, India
| | - V A Indumathi
- M.S. Ramaiah Medical College, Bengaluru, Karnataka, India
| | | | - S Muralidharan
- St. John's Medical College Hospital, Bengaluru, Karnataka, India
| | - S S Rao
- SS Microbiology Laboratory, Thane, Maharashtra, India
| | - I Roy
- Consultant Microbiologist, Sri Aurobindo Seva Kendra, Kolkata, West Bengal, India
| | - N Saini
- Consultant Microbiologist, Pushpanjali Hospital, New Delhi, India
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Satzke C, Dunne EM, Porter BD, Klugman KP, Mulholland EK. The PneuCarriage Project: A Multi-Centre Comparative Study to Identify the Best Serotyping Methods for Examining Pneumococcal Carriage in Vaccine Evaluation Studies. PLoS Med 2015; 12:e1001903; discussion e1001903. [PMID: 26575033 PMCID: PMC4648509 DOI: 10.1371/journal.pmed.1001903] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/09/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. METHODS AND FINDINGS Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. CONCLUSIONS Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail:
| | - Eileen M. Dunne
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Barbara D. Porter
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - E. Kim Mulholland
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Panpradist N, Toley BJ, Zhang X, Byrnes S, Buser JR, Englund JA, Lutz BR. Swab sample transfer for point-of-care diagnostics: characterization of swab types and manual agitation methods. PLoS One 2014; 9:e105786. [PMID: 25181250 PMCID: PMC4152222 DOI: 10.1371/journal.pone.0105786] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 07/24/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The global need for disease detection and control has increased effort to engineer point-of-care (POC) tests that are simple, robust, affordable, and non-instrumented. In many POC tests, sample collection involves swabbing the site (e.g., nose, skin), agitating the swab in a fluid to release the sample, and transferring the fluid to a device for analysis. Poor performance in sample transfer can reduce sensitivity and reproducibility. METHODS In this study, we compared bacterial release efficiency of seven swab types using manual-agitation methods typical of POC devices. Transfer efficiency was measured using quantitative PCR (qPCR) for Staphylococcus aureus under conditions representing a range of sampling scenarios: 1) spiking low-volume samples onto the swab, 2) submerging the swab in excess-volume samples, and 3) swabbing dried sample from a surface. RESULTS Excess-volume samples gave the expected recovery for most swabs (based on tip fluid capacity); a polyurethane swab showed enhanced recovery, suggesting an ability to accumulate organisms during sampling. Dry samples led to recovery of ∼20-30% for all swabs tested, suggesting that swab structure and volume is less important when organisms are applied to the outer swab surface. Low-volume samples led to the widest range of transfer efficiencies between swab types. Rayon swabs (63 µL capacity) performed well for excess-volume samples, but showed poor recovery for low-volume samples. Nylon (100 µL) and polyester swabs (27 µL) showed intermediate recovery for low-volume and excess-volume samples. Polyurethane swabs (16 µL) showed excellent recovery for all sample types. This work demonstrates that swab transfer efficiency can be affected by swab material, structure, and fluid capacity and details of the sample. Results and quantitative analysis methods from this study will assist POC assay developers in selecting appropriate swab types and transfer methods.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Bhushan J. Toley
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Xiaohong Zhang
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Samantha Byrnes
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Joshua R. Buser
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Janet A. Englund
- Program in Infectious Diseases, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington, Seattle, Washington, United States of America
- * E-mail: (JAE); (BRL)
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- * E-mail: (JAE); (BRL)
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Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, Henao-Restrepo AM, Leach AJ, Klugman KP, Porter BD, Sá-Leão R, Scott JA, Nohynek H, O'Brien KL. Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 2014; 32:165-79. [PMID: 24331112 DOI: 10.1016/j.vaccine.2013.08.062] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/25/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022]
Abstract
In 2003 the World Health Organization (WHO) convened a working group and published a set of standard methods for studies measuring nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus). The working group recently reconvened under the auspices of the WHO and updated the consensus standard methods. These methods describe the collection, transport and storage of nasopharyngeal samples, as well as provide recommendations for the identification and serotyping of pneumococci using culture and non-culture based approaches. We outline the consensus position of the working group, the evidence supporting this position, areas worthy of future research, and the epidemiological role of carriage studies. Adherence to these methods will reduce variability in the conduct of pneumococcal carriage studies undertaken in the context of pneumococcal vaccine trials, implementation studies, and epidemiology studies more generally so variability in methodology does not confound the interpretation of study findings.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Centre for International Child Health, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia.
| | - Paul Turner
- Microbiology Department, Angkor Hospital for Children, Siem Reap, Kingdom of Cambodia; Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anni Virolainen-Julkunen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Peter V Adrian
- MRC/Wits Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Kim M Hare
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Respiratory and Meningeal Pathogens Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Barbara D Porter
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - J Anthony Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; London School of Hygiene & Tropical Medicine, London, UK
| | - Hanna Nohynek
- Vaccine Programme Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Katherine L O'Brien
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Trends in asymptomatic nasopharyngeal colonization with streptococcus pneumoniae after introduction of the 13-valent pneumococcal conjugate vaccine in Calgary, Canada. Pediatr Infect Dis J 2014; 33:724-30. [PMID: 24463806 DOI: 10.1097/inf.0000000000000267] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND We previously reported serotype-specific trends in pneumococcal nasopharyngeal colonization soon after introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in mid-2002. Our current aim is to describe later trends after PCV7 and early trends after PCV13 vaccine introduction in 2010. METHODS The Calgary Area Streptococcus pneumoniae Epidemiology Research team conducted 10 point-prevalence surveys of pneumococcal nasopharyngeal colonization in healthy children aged 12 and 18 months and 4.5 years biannually from 2003 to 2005 (previously reported) and annually in 2006, 2010, 2011 and 2012. RESULTS For surveys conducted during 2010-2012, the proportion colonized was 13.2% compared with 19.9% in surveys conducted during 2003-2006 (P < 0.001). Vaccination with 2 or more doses of PCV7 or PCV13, older age and recent antibiotic use reduced the odds of colonization with any pneumococcus. By 2012, 94% of all isolates were nonvaccine serotypes with 11A, 15A/B/C, 22F, 23A/B and 35B/F representing 75% of all isolates. CONCLUSIONS Pneumococcal nasopharyngeal colonization has changed profoundly since the introduction of conjugate vaccines and overall colonization by pneumococcus has declined in recent years. By 2012, nonvaccine serotypes have nearly completely replaced vaccine serotypes. The impact on clinical disease remains to be seen.
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Dube FS, Kaba M, Whittaker E, Zar HJ, Nicol MP. Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children. PLoS One 2013; 8:e68097. [PMID: 23840817 PMCID: PMC3694050 DOI: 10.1371/journal.pone.0068097] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 05/24/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A better understanding of the epidemiology of nasopharyngeal carriage of Streptococcus pneumoniae is important to assess the impact of vaccination and the pathogenesis of pneumococcal disease. We compared the recovery of S. pneumoniae from nylon flocked, Dacron and rayon swabs. METHODS The recovery of S. pneumoniae from mocked specimens using flocked, Dacron and rayon swabs were compared by culture. The yield from paired nasopharyngeal (NP) samples obtained from healthy children sampled with flocked and Dacron swabs was also determined using culture and lytA-targeted real-time polymerase chain reaction (qPCR). RESULTS Using mock specimen, the percentage recovery of S. pneumoniae ATCC 49619 (serotype 19F) strain from the flocked swabs was 100%, while it was 41% from Dacron swabs and 7% from rayon swabs. Similar results were observed for S. pneumoniae serotypes 1 and 5. S. pneumoniae was cultured from 18 of 42 (43%) paired NP samples from the healthy children (median age 8 [interquartile range (IQR) 5-16] months). The median number of colony-forming units (CFU) recovered from flocked swabs was two-fold higher (8.8×10(4) CFU/mL [IQR, 2.0×10(2) - 4.0×10(5) CFU/mL]) than Dacron swabs (3.7×10(4) CFU/mL [IQR, 4.0×10(2)-3.2×10(5) CFU/mL], p = 0.17). Using lytA-targeted qPCR from paired NP samples, the median copy number of S. pneumoniae detected from flocked swabs was significantly higher than from Dacron swabs (3.0×10(5) genome copies/mL [IQR, 1.3×10(2)-1.8×10(6)] vs. 9.3×10(4) genome copies/mL [IQR, 7.0×10(1)-1.1×10(6)]; p = 0.005). CONCLUSION Flocked swabs released more S. pneumoniae compared to both Dacron and rayon swabs from mock specimens. Similarly, higher bacterial loads were detected by qPCR from flocked swabs compared with Dacron swabs from healthy children.
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Affiliation(s)
- Felix S. Dube
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Mamadou Kaba
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Elizabeth Whittaker
- Academic Department of Paediatrics, Wright–Fleming Institute, Imperial College London, St Mary's Campus, London, United Kingdom
- Department of Paediatrics and Child Health, University of Cape Town, South Africa
- Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, University of Cape Town, South Africa
- Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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Saleem M, Naz M, Waris A, Muneer B, Khurshid R. Screening of pneumococcal pneumonia by amplification of pneumolysin gene in children visiting hospitals in lahore, pakistan. IRANIAN JOURNAL OF PEDIATRICS 2012; 22:524-30. [PMID: 23430764 PMCID: PMC3533155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 06/04/2012] [Accepted: 06/22/2012] [Indexed: 10/26/2022]
Abstract
OBJECTIVE Streptococcus pneumoniae is a common worldwide potential pathogen causing pneumonia among children and the detection of pneumococcal infections by conventional culturing techniques is cumbersome. The present study describes a comparative analysis of sensitive nested-PCR and bacterial culture in pediatric patients with clinical and radiological indication of S. pneumoniae infection. METHODS PCR was performed using outer primers to amplify a 348-bp region and inner primers a 208-bp region of the pneumolysin gene. For pneumolysin PCR assay, DNA from peripheral blood and middle ear fluid (MEF) samples was extracted by salting out method. The sensitivity of the assay was evaluated with about 0.06 pg of purified S. pneumoniae genomic DNA. FINDINGS Among 90 MEF culture negative samples from acute otitis media pediatric patients, 8.8% pneumolysin-PCR positivity was detected, demonstrating the sensitivity and reliability of PCR for rapid pneumonia evaluation. Binomial test of proportionality performed on (SPSS 17) gives P< 0.05 indicating that PCR technique is statistically significant and sensitive in the diagnosis of S. pneumoniae infection. CONCLUSION The research work evaluated the effectiveness and efficacy of nested-PCR for detecting S. pneumoniae in pediatric patients with clinical and radiological confirmation of bacterial infection. This simplified method permitted quick selection of the patients and played a significant role in preliminary management of pneumococcal infections.
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Affiliation(s)
- Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, Pakistan,Corresponding Author:Address: University of the Punjab,Institute of Biochemistry and Biotechnology. E-mail:
| | - Mamoona Naz
- Institute of Biochemistry and Biotechnology, University of the Punjab, Pakistan
| | - Asma Waris
- Institute of Biochemistry and Biotechnology, University of the Punjab, Pakistan
| | - Bushra Muneer
- Institute of Industrial Biotechnology, Govt. College University, Pakistan
| | - Rukhshan Khurshid
- Department of Biochemistry, Fatima Jinnah Medical College, Lahore, Pakistan
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Gladstone RA, Jefferies JM, Faust SN, Clarke SC. Sampling methods for the study of pneumococcal carriage: a systematic review. Vaccine 2012; 30:6738-44. [PMID: 22981760 DOI: 10.1016/j.vaccine.2012.08.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/20/2012] [Accepted: 08/31/2012] [Indexed: 10/27/2022]
Abstract
Streptococcus pneumoniae is an important pathogen worldwide. Accurate sampling of S. pneumoniae carriage is central to surveillance studies before and following conjugate vaccination programmes to combat pneumococcal disease. Any bias introduced during sampling will affect downstream recovery and typing. Many variables exist for the method of collection and initial processing, which can make inter-laboratory or international comparisons of data complex. In February 2003, a World Health Organisation working group published a standard method for the detection of pneumococcal carriage for vaccine trials to reduce or eliminate variability. We sought to describe the variables associated with the sampling of S. pneumoniae from collection to storage in the context of the methods recommended by the WHO and those used in pneumococcal carriage studies since its publication. A search of published literature in the online PubMed database was performed on the 1st June 2012, to identify published studies that collected pneumococcal carriage isolates, conducted after the publication of the WHO standard method. After undertaking a systematic analysis of the literature, we show that a number of differences in pneumococcal sampling protocol continue to exist between studies since the WHO publication. The majority of studies sample from the nasopharynx, but the choice of swab and swab transport media is more variable between studies. At present there is insufficient experimental data that supports the optimal sensitivity of any standard method. This may have contributed to incomplete adoption of the primary stages of the WHO detection protocol, alongside pragmatic or logistical issues associated with study design. Consequently studies may not provide a true estimate of pneumococcal carriage. Optimal sampling of carriage could lead to improvements in downstream analysis and the evaluation of pneumococcal vaccine impact and extrapolation to pneumococcal disease control therefore further in depth comparisons would be of value.
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Affiliation(s)
- R A Gladstone
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, UK
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Hammitt LL, Murdoch DR, Scott JAG, Driscoll A, Karron RA, Levine OS, O'Brien KL. Specimen collection for the diagnosis of pediatric pneumonia. Clin Infect Dis 2012; 54 Suppl 2:S132-9. [PMID: 22403227 PMCID: PMC3693496 DOI: 10.1093/cid/cir1068] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diagnosing the etiologic agent of pneumonia has an essential role in ensuring the most appropriate and effective therapy for individual patients and is critical to guiding the development of treatment and prevention strategies. However, establishing the etiology of pneumonia remains challenging because of the relative inaccessibility of the infected tissue and the difficulty in obtaining samples without contamination by upper respiratory tract secretions. Here, we review the published and unpublished literature on various specimens available for the diagnosis of pediatric pneumonia. We discuss the advantages and limitations of each specimen, and discuss the rationale for the specimens to be collected for the Pneumonia Etiology Research for Child Health study.
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Affiliation(s)
- Laura L Hammitt
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
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Gritzfeld JF, Roberts P, Roche L, El Batrawy S, Gordon SB. Comparison between nasopharyngeal swab and nasal wash, using culture and PCR, in the detection of potential respiratory pathogens. BMC Res Notes 2011; 4:122. [PMID: 21489228 PMCID: PMC3084159 DOI: 10.1186/1756-0500-4-122] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 04/13/2011] [Indexed: 11/16/2022] Open
Abstract
Background Nasopharyngeal carriage of potential pathogens is important as it is both the major source of transmission and the prerequisite of invasive disease. New methods for detecting carriage could improve comfort, accuracy and laboratory utility. The aims of this study were to compare the sensitivities of a nasopharyngeal swab (NPS) and a nasal wash (NW) in detecting potential respiratory pathogens in healthy adults using microbiological culture and PCR. Results Healthy volunteers attended for nasal washing and brushing of the posterior nasopharynx. Conventional and real-time PCR were used to detect pneumococcus and meningococcus. Statistical differences between the two nasal sampling methods were determined using a nonparametric Mann-Whitney U test; differences between culture and PCR methods were determined using the McNemar test. Nasal washing was more comfortable for volunteers than swabbing (n = 24). In detection by culture, the NW was significantly more likely to detect pathogens than the NPS (p < 0.00001). Overall, there was a low carriage rate of pathogens in this sample; no significant difference was seen in the detection of bacteria between culture and PCR methods. Conclusions Nasal washing and PCR may provide effective alternatives to nasopharyngeal swabbing and classical microbiology, respectively.
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Affiliation(s)
- Jenna F Gritzfeld
- Respiratory Infection Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.
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Optimal sampling sites and methods for detection of pathogens possibly causing community-acquired lower respiratory tract infections. J Clin Microbiol 2008; 47:21-31. [PMID: 19020070 DOI: 10.1128/jcm.02037-08] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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