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Pol S, Kallonen T, Mäklin T, Sar P, Hopkins J, Soeng S, Miliya T, Ling CL, Bentley SD, Corander J, Turner P. Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing. mBio 2024; 15:e0078424. [PMID: 38682956 PMCID: PMC11237702 DOI: 10.1128/mbio.00784-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data. IMPORTANCE The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.
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Affiliation(s)
- Sreymom Pol
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Tommi Mäklin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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Katkowska M, Garbacz K, Kwapisz E, Suligowska K, Kusiak A, Cichońska D, Świetlik D. High oral carriage of multidrug resistant Gram-negative bacilli in adolescents: the SOPKARD-Junior study. Front Cell Infect Microbiol 2023; 13:1265777. [PMID: 38035342 PMCID: PMC10687414 DOI: 10.3389/fcimb.2023.1265777] [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: 07/23/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction The colonization of the oral cavity by potentially pathogenic antimicrobial-resistant bacteria in adolescents and its consequences is very poorly understood. The present study focused on the occurrence of oral colonization by Gram-negative bacilli (GNB) and their multidrug resistance, including the production of extended-spectrum β-lactamases (ESBLs) and carbapenemases, among healthy adolescents and risk factors associated with GNB colonization. Materials and methods This study was conducted as part of "A program for the early detection of risk factors for lifestyle diseases SOPKARD-Junior" (SOPKARD-Junior). Oral samples were collected from 182 adolescents from four public elementary schools in Sopot, Poland, aged 13-14 years. Bacterial strains were identified by the MALDI-TOF MS method. Screening of antimicrobial resistance was performed using a disk diffusion method. The NG-Test® CARBA-5 was used to detect and differentiate the five most widely distributed carbapenemases. Demographic and clinical data were collected and statistical analysis of risk factors was performed. Results A total of 68 out of 182 (37.4%) healthy adolescents was documented oral colonization with Gram-negative bacilli, including 50/182 (27.5%) multidrug resistant (MDR-GNB) strains. Over 60% of oral carriage concerned three main genera Enterobacter spp., Pseudomonas spp., and Serratia spp., which were detected in 22.1%, 19.1%, and 19.1% of participants, respectively. Citrobacter spp., Escherichia coli, Klebsiella spp., Hafnia spp., Aeromonas spp., Acinetobacter spp., and Stenotrophomonas spp. were also isolated. The antimicrobial resistance to ampicillin (100%), ceftazidime (69.1%), meropenem (60.3%), gentamycin (60.3%), piperacillin/tazobactam (52.9%), and piperacillin (45.6%) were the most common. Among 73.5% GNB strains multidrug resistance was observed, including all Pseudomonas spp. strains. Among MDR-GNB, 30.4% were resistant to four groups of antibiotics, half of the MDR Pseudomonas spp. strains were resistant to 10 groups of antibiotics. Extended-spectrum β-lactamases were produced by Enterobacter cloacae, Klebsiella spp., and Serratia spp. (7.4%). Colonization by ESBLs-positive GNB strains was significantly associated with recurrent respiratory infections, nasal congestion, and bronchitis (p<0.05). Conclusion Our study revealed high oral carriage of multi-drug resistant Gram-negative bacilli in healthy adolescents and the association of ESBL-producing strains with respiratory infections. Further studies on oral colonization with GNB are necessary due to the possibility of distinct infections and the acquisition of antibiotic resistance by resident microbiota.
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Affiliation(s)
- Marta Katkowska
- Department of Oral Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Katarzyna Garbacz
- Department of Oral Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Kwapisz
- Department of Oral Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Klaudia Suligowska
- Department of Dental Techniques and Masticatory System Dysfunctions, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
- Department of Preventive Medicine and Education, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Aida Kusiak
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Dominika Cichońska
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Świetlik
- Division of Biostatistics and Neural Networks, Medical University of Gdansk, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
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Osei MM, Dayie NTKD, Azaglo GSK, Tettey EY, Nartey ET, Fenny AP, Manzi M, Kumar AMV, Labi AK, Opintan JA, Sampane-Donkor E. Alarming Levels of Multidrug Resistance in Aerobic Gram-Negative Bacilli Isolated from the Nasopharynx of Healthy Under-Five Children in Accra, Ghana. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10927. [PMID: 36078645 PMCID: PMC9518304 DOI: 10.3390/ijerph191710927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Nasopharyngeal carriage of aerobic Gram-negative bacilli (GNB) may precede the development of invasive respiratory infections. We assessed the prevalence of nasopharyngeal carriage of aerobic GNB and their antimicrobial resistance patterns among healthy under-five children attending seven selected day-care centres in the Accra metropolis of the Greater Accra region of Ghana from September to December 2016. This cross-sectional study analysed a total of 410 frozen nasopharyngeal samples for GNB and antimicrobial drug resistance. The GNB prevalence was 13.9% (95% CI: 10.8-17.6%). The most common GNB were Escherichia coli (26.3%), Klebsiella pneumoniae (24.6%), and Enterobacter cloacae (17.5%). Resistance was most frequent for cefuroxime (73.7%), ampicillin (64.9%), and amoxicillin/clavulanic acid (59.6%). The organisms were least resistant to gentamicin (7.0%), amikacin (8.8%), and meropenem (8.8%). Multidrug resistance (MDR, being resistant to ≥3 classes of antibiotics) was observed in 66.7% (95% CI: 53.3-77.8%). Extended-spectrum beta-lactamase (ESBL)-producing bacteria constituted 17.5% (95% CI: 9.5-29.9%), AmpC-producing bacteria constituted 42.1% (95% CI: 29.8-55.5%), and carbapenemase-producing bacteria constituted 10.5% (95% CI: 4.7-21.8%) of isolates. The high levels of MDR are of great concern. These findings are useful in informing the choice of antibiotics in empiric treatment of GNB infections and call for improved infection control in day-care centres to prevent further transmission.
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Affiliation(s)
- Mary-Magdalene Osei
- Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box GP 4236, Ghana
- FleRhoLife Research Consult, Accra P.O. Box TS 853, Ghana
| | - Nicholas T. K. D. Dayie
- Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box GP 4236, Ghana
| | - Godfred S. K. Azaglo
- Environmental Protection Agency, Starlet 91 Road, Ministries, Accra P.O. Box MB 326, Ghana
| | | | - Edmund T. Nartey
- Centre for Tropical Clinical Pharmacology & Therapeutics, University of Ghana Medical School, Accra P.O. Box GP 4236, Ghana
| | - Ama P. Fenny
- Institute of Statistical, Social and Economic Research (ISSER), University of Ghana, Accra P.O. Box LG 25, Ghana
| | - Marcel Manzi
- Department of Medical OCB, MSF-Belgium Headquarters, Rue de Bomel 65, 5000 Namur, Belgium
| | - Ajay M. V. Kumar
- International Union Against Tuberculosis and Lung Disease, 2 Rue Jean Lantier, 75001 Paris, France
- International Union Against Tuberculosis and Lung Disease, South-East Asia Office, C-6 Qutub Institutional Area, New Delhi 110016, India
- Yenepoya Medical College, Yenepoya (Deemed to Be University) University, University Road, Deralakatte, Mangalore 575018, India
| | - Appiah-Korang Labi
- World Health Organization Country Office, Roman Ridge, Accra P.O. Box MB 142, Ghana
| | - Japheth A. Opintan
- Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box GP 4236, Ghana
| | - Eric Sampane-Donkor
- Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box GP 4236, Ghana
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4
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Martens L, Kaboré B, Post A, van der Gaast-de Jongh CE, Langereis JD, Tinto H, Jacobs J, van der Ven AJ, de Mast Q, de Jonge MI. Nasopharyngeal colonisation dynamics of bacterial pathogens in patients with fever in rural Burkina Faso: an observational study. BMC Infect Dis 2022; 22:15. [PMID: 34983432 PMCID: PMC8725287 DOI: 10.1186/s12879-021-06996-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/17/2021] [Indexed: 11/29/2022] Open
Abstract
Background Nasopharyngeal colonisation with clinically relevant bacterial pathogens is a risk factor for severe infections, such as pneumonia and bacteraemia. In this study, we investigated the determinants of nasopharyngeal carriage in febrile patients in rural Burkina Faso. Methods From March 2016 to June 2017, we recruited 924 paediatric and adult patients presenting with fever, hypothermia or suspicion of severe infection to the Centre Medical avec Antenne Chirurgicale Saint Camille de Nanoro, Burkina Faso. We recorded a broad range of clinical data, collected nasopharyngeal swabs and tested them for the presence of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Klebsiella pneumoniae by quantitative polymerase chain reaction. Using logistic regression, we investigated the determinants of carriage and aimed to find correlations with clinical outcome. Results Nasopharyngeal colonisation with S. pneumoniae, H. influenzae and M. catarrhalis was highly prevalent and strongly dependent on age and season. Females were less likely to be colonised with S. pneumoniae (OR 0.71, p = 0.022, 95% CI 0.53–0.95) and M. catarrhalis (OR 0.73, p = 0.044, 95% CI 0.54–0.99) than males. Colonisation rates were highest in the age groups < 1 year and 1–2 years of age and declined with increasing age. Colonisation also declined towards the end of the rainy season and rose again during the beginning of the dry season. K. pneumoniae prevalence was low and not significantly correlated with age or season. For S. pneumoniae and H. influenzae, we found a positive association between nasopharyngeal carriage and clinical pneumonia [OR 1.75, p = 0.008, 95% CI 1.16–2.63 (S. pneumoniae) and OR 1.90, p = 0.004, 95% CI 1.23–2.92 (H. influenzae)]. S. aureus carriage was correlated with mortality (OR 4.01, p < 0.001, 95% CI 2.06–7.83), independent of bacteraemia caused by this bacterium. Conclusions Age, sex and season are important determinants of nasopharyngeal colonisation with S. pneumoniae, H. influenzae and M. catarrhalis in patients with fever in Burkina Faso. S. pneumoniae and H. influenzae carriage is associated with clinical pneumonia and S. aureus carriage is associated with mortality in patients with fever. These findings may help to understand the dynamics of colonisation and the associated transmission of these pathogens. Furthermore, understanding the determinants of nasopharyngeal colonisation and the association with disease could potentially improve the diagnosis of febrile patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06996-7.
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Affiliation(s)
- Liesbeth Martens
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud university medical center, Nijmegen, the Netherlands. .,Department of Medical Microbiology, Radboud university medical center, Nijmegen, the Netherlands. .,Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands.
| | - Bérenger Kaboré
- Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands.,Department of Internal Medicine, Radboud university medical center, Nijmegen, the Netherlands.,Institut de Recherche en Sciences de la Santé/Clinical Research Unit of Nanoro, Nanoro, Burkina Faso
| | - Annelies Post
- Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands.,Department of Internal Medicine, Radboud university medical center, Nijmegen, the Netherlands
| | - Christa E van der Gaast-de Jongh
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud university medical center, Nijmegen, the Netherlands.,Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands
| | - Jeroen D Langereis
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud university medical center, Nijmegen, the Netherlands.,Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands
| | - Halidou Tinto
- Institut de Recherche en Sciences de la Santé/Clinical Research Unit of Nanoro, Nanoro, Burkina Faso
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - André J van der Ven
- Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands.,Department of Internal Medicine, Radboud university medical center, Nijmegen, the Netherlands
| | - Quirijn de Mast
- Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands.,Department of Internal Medicine, Radboud university medical center, Nijmegen, the Netherlands
| | - Marien I de Jonge
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud university medical center, Nijmegen, the Netherlands.,Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, the Netherlands
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5
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Inghammar M, Borand L, Goyet S, Rammaert B, Te V, Lorn Try P, Guillard B, Buchy P, Vong S, Tek Chheng E, Cavailler P, Mayaud C, Tarantola A. Community-acquired pneumonia and Gram-negative bacilli in Cambodia-incidence, risk factors and clinical characteristics. Trans R Soc Trop Med Hyg 2019; 112:57-63. [PMID: 29579302 PMCID: PMC6018679 DOI: 10.1093/trstmh/try022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 03/07/2018] [Indexed: 11/13/2022] Open
Abstract
Background In Western settings, community-acquired pneumonia (CAP) due to Gram-negative bacilli (GNB) is relatively rare. Previous studies from Asia, however, indicate a higher prevalence of GNB in CAP, but data, particularly from Southeast Asia, are limited. Methods This is a prospective observational study of 1451 patients ≥15 y of age with CAP from two hospitals in Cambodia between 2007 and 2010. The proportion of GNB was estimated. Risk factors and clinical characteristics of CAP due to GNB were assessed using logistic regression models. Results The prevalence of GNB was 8.6% in all CAP patients and 15.8% among those with a valid respiratory sample. GNB infection was independently associated with diabetes, higher leucocyte count and CAP severity. Mortality was higher in patients with CAP due to GNB. Conclusions We found a high proportion of GNB in a population hospitalized for CAP in Cambodia. Given the complex antimicrobial sensitivity patterns of certain GNBs and the rapid emergence of multidrug-resistant GNB, microbiological laboratory capacity should be strengthened and prospective clinical trials comparing empiric treatment algorithms according to the severity of CAP are needed.
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Affiliation(s)
- Malin Inghammar
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia.,Lund University, Department of Clinical Sciences Lund, Section for Infection Medicine, Lund, Sweden
| | - Laurence Borand
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Sophie Goyet
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Blandine Rammaert
- Université de Poitiers, Service de maladies infectieuses et tropicales, CHU de Poitiers, Poitiers, France.,INSERM U1070, Pôle Biologie Santé, Poitiers, France
| | - Vantha Te
- Takeo Provincial Hospital, Takeo, Cambodia
| | | | - Bertrand Guillard
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Philippe Buchy
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia.,GlaxoSmithKline Vaccines R&D Asia-Pacific, Scientific Affairs and Public Health, Singapore
| | - Sirenda Vong
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Eap Tek Chheng
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Philippe Cavailler
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Charles Mayaud
- Service de Pneumologie, Hôpital Tenon, Assistance Publique des Hôpitaux de Paris, Université Paris VI, France
| | - Arnaud Tarantola
- Institut Pasteur du Cambodge, Reseau International des Instituts Pasteur, Phnom Penh, Cambodia
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6
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Peto L, Nadjm B, Horby P, Ngan TTD, van Doorn R, Van Kinh N, Wertheim HFL. The bacterial aetiology of adult community-acquired pneumonia in Asia: a systematic review. Trans R Soc Trop Med Hyg 2014; 108:326-37. [PMID: 24781376 PMCID: PMC4023908 DOI: 10.1093/trstmh/tru058] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is a major cause of adult mortality in Asia. Appropriate empirical treatment depends on knowledge of the pathogens commonly responsible. However, assessing the aetiological significance of identified organisms is often difficult, particularly with sputum isolates that might represent contamination with oropharyngeal flora. METHODS A systematic review of all adult CAP aetiology studies from Asia, excluding the Middle East, published in English between 1 January 1990 and 1 March 2012 was conducted. Forty-eight studies reporting on 10 423 patients were included, representing data from China, India, Indonesia, Japan, Malaysia, The Philippines, Singapore, South Korea, Taiwan, Thailand and Vietnam. Data from large parts of Asia were unavailable and there was substantial heterogeneity in methodology. RESULTS As in western studies, Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella spp. and Haemophilus influenzae were all significant pathogens. However, compared with western studies, S. pneumoniae was of less relative importance. Gram-negative bacilli and Mycobacterium tuberculosis were more important, and in northeast Thailand Burkholderia pseudomallei was a major pathogen. CONCLUSION These data have major implications for diagnostic strategies and empirical treatment. Narrow-spectrum antibiotics targeting S. pneumoniae may be inappropriate in many Asian settings, and agents active against TB may lead to partial response and delayed TB diagnosis.
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Affiliation(s)
- Leon Peto
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi and Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7LJ, UK
| | - Behzad Nadjm
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi and Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7LJ, UK
| | - Peter Horby
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi and Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7LJ, UK
| | | | - Rogier van Doorn
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi and Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7LJ, UK
| | | | - Heiman F L Wertheim
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi and Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7LJ, UK
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7
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Cobey S, Lipsitch M. Pathogen diversity and hidden regimes of apparent competition. Am Nat 2012; 181:12-24. [PMID: 23234842 DOI: 10.1086/668598] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Competition through cross-reacting host immune responses, a form of apparent competition, is a major driver of pathogen evolution and diversity. Most models of pathogens have focused on intraspecific interactions to explain observed patterns. Two recent experiments suggested that Haemophilus influenzae, a common nasopharyngeal colonizer of humans, might alter the immune environment in a way that favors otherwise less fit serotypes of another common pathogen, pneumococcus. Using a computational model, we demonstrate that H. influenzae, if it consistently raises the fitness of the less fit serotypes, can strongly promote pneumococcal diversity. However, the effects of H. influenzae are so sensitive to the prevalence of H. influenzae that this species is unlikely to be the main driver of serotype coexistence. Interactions that significantly affect diversity could furthermore be extremely difficult to detect through co-occurrence analysis alone. These results suggest that small differences in strains' adaptations to different immunological regimes, which are shaped by coinfections with other pathogens, can have dramatic effects on strain dynamics and patterns of phenotypic variation. Studies of microbial communities might therefore benefit from the use of varied approaches to infer the presence of indirect interactions.
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Affiliation(s)
- Sarah Cobey
- Center for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
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8
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Nelson KE, Jones-Nelson B. Pathogen Genomics and the Potential for Understanding Diseases in the Developing World. ADVANCES IN MICROBIAL ECOLOGY 2012. [PMCID: PMC7120252 DOI: 10.1007/978-1-4614-2182-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Approximately 46% and 32% of deaths among children under five globally occur in sub-Saharan Africa and South Asia, respectively. Over 80% of the 4.2 million child deaths in Africa are caused by infectious diseases, sharply contrasted to Europe where 39% of the 0.15 million child deaths are attributable to infectious diseases (Fig. 5.1) (Black et al. 2010). Hence, despite the remarkable public health advancements in hygiene, sanitation, antimicrobial drugs and vaccine strategies of the twenty-first century, the burden of infectious diseases remains unacceptably high in the developing world.
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Affiliation(s)
- Karen E. Nelson
- J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, 20850 Maryland USA
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9
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Coudeyras S, Forestier C. Microbiote et probiotiques : impact en santé humaine. Can J Microbiol 2010; 56:611-50. [DOI: 10.1139/w10-052] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
All accessible mucous membranes of the human body are colonized by an abundant and diversified microbial flora called microbiota. Recent studies have shown that these microorganisms, long regarded as purely commensal, have essential beneficial effects on human health. Thus, numerous human ailments are linked to dysbiosis; that is, imbalances in the microflora composition. The administration of probiotic microorganisms could, in some situations, provide substantial relief from such disorders. These live microorganisms, which, according to the definition, confer a health benefit to the host when administered in adequate amounts, are often derived from human flora and belong mostly to lactic acid bacteria, in particular to the genus Lactobacillus . The constant improvement of knowledge of the role of human microbiota and the growing popularity of probiotics are now opening the door to new prophylactic and therapeutic strategies in human health.
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Affiliation(s)
- Sophie Coudeyras
- Université Clermont 1, UFR Pharmacie, Laboratoire de Bactériologie, Clermont Ferrand, France
| | - Christiane Forestier
- Université Clermont 1, UFR Pharmacie, Laboratoire de Bactériologie, Clermont Ferrand, France
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10
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Lima ABM, de Oliveira Leão LSN, Oliveira LSDC, Pimenta FC. Nasopharyngeal Gram-Negative bacilli colonization in brazilian children attending day-care centers. Braz J Microbiol 2010; 41:24-7. [PMID: 24031458 PMCID: PMC3768626 DOI: 10.1590/s1517-83822010000100005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 02/18/2009] [Accepted: 07/24/2009] [Indexed: 11/22/2022] Open
Abstract
This study aimed at determining prevalence and resistance profile of Gram-negative bacilli isolated from nasopharynx of children attending day-care centers in Goiânia (Brazil). P. aeruginosa (100.0%), E. coli (50.0%), K. pneumoniae (35.3%), and E. aerogenes (16.7%) were the most frequent multi-drug resistant microorganisms isolated. No production of ESBL was detected.
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Affiliation(s)
- Ana Beatriz Mori Lima
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás , Goiânia, GO , Brasil
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Cotton MF, Wasserman E, Smit J, Whitelaw A, Zar HJ. High incidence of antimicrobial resistant organisms including extended spectrum beta-lactamase producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus in nasopharyngeal and blood isolates of HIV-infected children from Cape Town, South Africa. BMC Infect Dis 2008; 8:40. [PMID: 18380900 PMCID: PMC2329621 DOI: 10.1186/1471-2334-8-40] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 04/01/2008] [Indexed: 12/02/2022] Open
Abstract
Background There is little information on nasopharyngeal (NP) flora or bacteremia in HIV-infected children. Our aim was to describe the organisms and antimicrobial resistance patterns in children enrolled in a prospective study comparing daily and three times weekly trimethoprim-sulfamethoxazole (TMP-SMX) and isoniazid (INH) or placebo prophylaxis. Methods NP swabs were taken at baseline from HIV-infected children enrolled in the study. Standard microbiological techniques were used. Children were grouped according to previous or current exposure to TMP-SMX and whether enrolled to the study during a period of hospitalization. Blood culture results were also recorded within 12 months of baseline. Results Two hundred and three children, median age 1.8 (Interquartile [IQ]: 0.7–4) years had NP swabs submitted for culture. One hundred and eighty-four (90.7%) had either stage B or C HIV disease. One hundred and forty-one (69.8%) were receiving TMP-SMX and 19 (9.4%) were on antiretroviral therapy. The majority, 168 (82%) had a history of hospitalization and 91 (44.8%) were enrolled during a period of hospitalization. Thirty-two subjects (16.2%) died within 12 months of study entry. One hundred and eighty-one potential pathogens were found in 167 children. The most commonly isolated organisms were Streptococcus pneumoniae (48: 22.2%), Gram-negative respiratory organisms (Haemophilus influenzae and Moraxella catarrhalis) (47: 21.8%), Staphylococcus aureus (44: 20.4%), Enterobacteriaceae 32 (14.8%) and Pseudomonas 5 (2.3%). Resistance to TMP-SMX occurred in > 80% of pathogens except for M. catarrhalis (2: 18.2% of tested organisms). TMP-SMX resistance tended to be higher in those receiving it at baseline (p = 0.065). Carriage of Methicillin resistant S. aureus (MRSA) was significantly associated with being on TMP-SMX at baseline (p = 0.002). Minimal inhibitory concentrations (MIC) to penicillin were determined for 18 S. pneumoniae isolates: 7 (38.9%) were fully sensitive (MIC ≤ 0.06 μg/ml), 9 (50%) had intermediate resistance (MIC 0.12 – 1 μg/ml) and 2 (11.1%) had high level resistance (MIC ≥2 μg/ml). Fifty percent of Enterobacteriaceae produced extended spectrum beta-lactamases (ESBL) (resistant to third generation cephalosporins) and 56% were resistant to gentamicin. Seventy-seven percent of S. aureus were MRSA. Carriage of resistant organisms was not associated with hospitalization. On multivariate logistic regression, risk factors for colonization with Enterobacteriaceae were age ≤ one year (Odds ratio 4.4; 95% Confidence Interval 1.9–10.9; p = 0.0008) and CDC stage C disease (Odds ratio 3.6; 95% Confidence Interval 1.5–8.6; p = 0.005) Nineteen (9.4%) subjects had 23 episodes of bacteremia. Enterobacteriaceae were most commonly isolated (13 of 25 isolates), of which 6 (46%) produced ESBL and were resistant to gentamicin. Conclusion HIV-infected children are colonized with potential pathogens, most of which are resistant to commonly used antibiotics. TMP-SMX resistance is extremely common. Antibiotic resistance is widespread in colonizing organisms and those causing invasive disease. Antibiotic recommendations should take cognizance of resistance patterns. Antibiotics appropriate for ESBL-producing Enterobacteriaceae and MRSA should be used for severely ill HIV-infected children in our region. Further study of antibiotic resistance patterns in HIV-infected children from other areas is needed.
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Affiliation(s)
- Mark F Cotton
- Department of Paediatrics, Faculty of Health Sciences, Stellenbosch University, Cape Town South Africa.
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Wolf B, Rey LC, Moreira LB, Milatovic D, Fleer A, Verhoef J, Roord JJ. Carriage of gram-negative bacilli in young Brazilian children with community-acquired pneumonia. Int J Infect Dis 2002; 5:155-9. [PMID: 11724673 DOI: 10.1016/s1201-9712(01)90091-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Gram-negative bacilli are not infrequently encountered as etiologic organisms of pneumonia in children in warm-climate countries. OBJECTIVES To investigate the nasopharyngeal carriage rate and antimicrobial susceptibility patterns of gram-negative bacilli colonizing children with community-acquired pneumonia in Fortaleza, Brazil. METHODS A single nasopharyngeal specimen was collected from children 2 months to 5 years of age presenting at one of the three children's hospitals in Fortaleza and fulfilling the World Health Organization criteria for pneumonia. Randomly recruited healthy children from public daycare centers and immunization clinics served as controls. RESULTS The study included 912 children, 482 (53%) with pneumonia and 430 (47%) controls. Aerobic gram-negative bacilli were seen in 79 (16%) of the 482 children with pneumonia and 51 (12%) of the 430 healthy controls. Nonfermentative gram-negative bacilli were seen in 85 (18%) of children with pneumonia and 54 (13%) of healthy controls. Neither gender, nutritional status, season, previous hospital admission nor antibiotic use was associated with carriage with gram-negative bacilli. However, pneumonia was associated with increased carriage, whereas concomitant colonization with Streptococcus pneumoniae or Haemophilus influenzae was associated with decreased carriage with gram-negative bacilli. Only 36% of all Escherichia species and 76% of all Klebsiella isolates were susceptible to cotrimoxazole; 90% of all Acinetobacter species were susceptible to gentamicin. CONCLUSION Nasopharyngeal carriage with gram-negative bacilli, in particular with Acinetobacter species, is common and associated with a clinical diagnosis of community-acquired pneumonia in children in Fortaleza, Brazil.
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Affiliation(s)
- B Wolf
- Department of Pediatrics, St. Lucas Andreas Hospital, Amsterdam, The Netherlands.
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Abstract
Este artigo revisa os efeitos do envelhecimento, tabagismo, DPOC, insuficiência cardíaca, colonização da orofaringe, aspiração (micro e macro), alcoolismo, cirrose hepática, deficiência nutricional, imunossupressão e fatores ambientais sobre o risco de adquirir pneumonia na comunidade e sua gravidade. Na segunda parte, é feita revisão sobre a ação profilática das vacinas antiinfluenza e antipneumococo, assim como a ação das drogas antivirais, na profilaxia e tratamento das pneumonias adquiridas na comunidade.
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