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Muthumbi EM, Mwanzu A, Mbae C, Bigogo G, Karani A, Mwarumba S, Verani JR, Kariuki S, Scott JAG. The epidemiology of fecal carriage of nontyphoidal Salmonella among healthy children and adults in three sites in Kenya. PLoS Negl Trop Dis 2023; 17:e0011716. [PMID: 37883602 PMCID: PMC10629669 DOI: 10.1371/journal.pntd.0011716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/07/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Despite the importance of non-Typhoidal Salmonella (NTS) disease in Africa, epidemiologic data on carriage and transmission are few. These data are important to understand the transmission of NTS in Africa and to design control strategies. METHOD To estimate the prevalence of stool carriage of NTS in Kenya, we conducted a cross-sectional study in Kilifi, Nairobi, and Siaya, sites with a low, moderate and high incidence of invasive NTS disease, respectively. At each site, we randomly selected 100 participants in each age-group of 0-11 months, 12-59 months, 5-14 years, 15-54 years and ≥55 years. We collected stool, venous blood (for hemoglobin and malaria rapid tests), anthropometric measurements, and administered a questionnaire on Water Access Sanitation and Hygiene (WASH) practices. Stool samples were cultured on selective agar for Salmonella; suspect isolates underwent serotyping and antimicrobial susceptibility testing. RESULT Overall, 53 (3.5%) isolates of NTS were cultured from 1497 samples. Age-adjusted prevalence was 13.1% (95%CI 8.8-17.4) in Kilifi, 0.4% (95%CI 0-1.3) in Nairobi, and 0.9% (95%CI 0-2.0) in Siaya. Prevalence was highest among those aged 15-54 years (6.2%). Of 53 isolates; 5 were S. Enteritidis, 1 was S. Typhimurium. No S. Typhi was isolated. None of the risk factors were associated with carriage of NTS. All isolates were susceptible to all antibiotics tested, including ampicillin, chloramphenicol, ciprofloxacin and co-trimoxazole. CONCLUSION Prevalence of fecal carriage was high in Kilifi, an area of low incidence of invasive NTS disease and was low in areas of higher incidence in Nairobi and Siaya. The age-prevalence, risk factors, geographical and serotype distribution of NTS in carriage differs from invasive disease.
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Affiliation(s)
- Esther M. Muthumbi
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Alfred Mwanzu
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Cecilia Mbae
- Kenya Medical Research Institute–Centre for Microbiology Research, Nairobi, Kenya
| | - Godfrey Bigogo
- Kenya Medical Research Institute–Centre for Global Health Research, Kisumu, Kenya
| | - Angela Karani
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Salim Mwarumba
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Jennifer R. Verani
- U.S. Centers for Disease Control and Prevention, Division of Global Health Protection, Nairobi, Kenya
| | - Samuel Kariuki
- Kenya Medical Research Institute–Centre for Microbiology Research, Nairobi, Kenya
| | - J. Anthony G. Scott
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Akech S, Nyamwaya B, Gachoki J, Ogero M, Kigo J, Maina M, Mutua E, Ooko E, Bejon P, Mwarumba S, Bahati F, Mvera B, Musyimi R, Onsare R, Hutter J, Tanui E, Wesangula E, Turner P, Dunachie S, Lucey O, McKnight J. The CINAMR (Clinical Information Network-Antimicrobial Resistance) Project: A pilot microbial surveillance using hospitals linked to regional laboratories in Kenya: Study Protocol. Wellcome Open Res 2022; 7:256. [PMID: 37786881 PMCID: PMC10541537 DOI: 10.12688/wellcomeopenres.18289.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2022] [Indexed: 10/04/2023] Open
Abstract
Background: Antimicrobial resistance (AMR) is a global threat and is thought to be acute in low-and middle-income country (LMIC) settings, including in Kenya, but there is limited unbiased surveillance that can provide reliable estimates of its burden. Current efforts to build capacity for microbiology testing in Kenya are unlikely to result in systematic routine microbiological testing in the near term. Therefore, there is little prospect for microbiological support to inform clinical diagnoses nor for indicating the burden of AMR and for guiding empirical choice of antibiotics. Objective: We aim to build on an existing collaboration, the Clinical Information Network (CIN), to pilot microbiological surveillance using a 'hub-and-spoke' model where selected hospitals are linked to high quality microbiology research laboratories. Methods: Children admitted to paediatric wards of 12 participating hospitals will have a sample taken for blood culture at admission before antibiotics are started. Indication for blood culture will be a clinician's prescription of antibiotics. Samples will then be transported daily to the research laboratories for culture and antibiotic susceptibility testing and results relayed back to clinicians for patient management. The surveillance will take place for 6 months in each hospital. Separately, we shall conduct semi-structured interviews with frontline health workers to explore the feasibility and utility of this approach. We will also seek to understand how the availability of microbiology results might inform antibiotic stewardship, and as an interim step to the development of better national or regional laboratories linked to routine surveillance. Conclusions: If feasible, this approach is less costly and periodic 'hub-and-spoke' surveillance can be used to track AMR trends and to broadly guide empirical antibiotic guidance meaning it is likely to be more sustainable than establishing functional microbiological facilities in each hospital in a LMIC setting.
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Affiliation(s)
- Samuel Akech
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Brian Nyamwaya
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Jackline Gachoki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Morris Ogero
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce Kigo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Michuki Maina
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edna Mutua
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ednah Ooko
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Felix Bahati
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Benedict Mvera
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Robert Musyimi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Robert Onsare
- Kenya Medical Research Institute-Centre for Microbiology Research, Nairobi, Kenya
| | - Jack Hutter
- United States Army Medical Research Directorate-Africa/Kenya (USAMRD-A/K), Kombewa, Kenya
| | - Emmanuel Tanui
- Kenya Ministry of Health - AMR National Secretariat, Nairobi, Kenya
| | - Evelyn Wesangula
- Kenya Ministry of Health - AMR National Secretariat, Nairobi, Kenya
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit (COMRU), Angkor Hospital for Children, Siem Reap, Cambodia
| | - Susanna Dunachie
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, University of Mahidol, Bangkok, Thailand
| | | | - Jacob McKnight
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - CINAMR Investigators
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kenya Medical Research Institute-Centre for Microbiology Research, Nairobi, Kenya
- United States Army Medical Research Directorate-Africa/Kenya (USAMRD-A/K), Kombewa, Kenya
- Kenya Ministry of Health - AMR National Secretariat, Nairobi, Kenya
- Cambodia Oxford Medical Research Unit (COMRU), Angkor Hospital for Children, Siem Reap, Cambodia
- Mahidol-Oxford Tropical Medicine Research Unit, University of Mahidol, Bangkok, Thailand
- Imperial College London, London, UK
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Nyamwaya DK, Otiende M, Mwango L, Kariuki SM, Otieno B, Omuoyo DO, Githinji G, Kitsao BS, Karanja HK, Gitonga JN, de Laurent ZR, Davies A, Mwarumba S, Agoti CN, Thumbi SM, Hamaluba MM, Newton CR, Bejon P, Warimwe GM. Incidence of chikungunya virus infections among Kenyan children with neurological disease, 2014-2018: A cohort study. PLoS Med 2022; 19:e1003994. [PMID: 35550620 PMCID: PMC9135332 DOI: 10.1371/journal.pmed.1003994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/26/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Neurological complications due to chikungunya virus (CHIKV) infection have been described in different parts of the world, with children being disproportionately affected. However, the burden of CHIKV-associated neurological disease in Africa is currently unknown and given the lack of diagnostic facilities in routine care it is possible that CHIKV is an unrecognized etiology among children with encephalitis or other neurological illness. METHODS AND FINDINGS We estimated the incidence of CHIKV infection among children hospitalized with neurological disease in Kilifi County, coastal Kenya. We used reverse transcriptase polymerase chain reaction (RT-PCR) to systematically test for CHIKV in cerebrospinal fluid (CSF) samples from children aged <16 years hospitalized with symptoms of neurological disease at Kilifi County Hospital between January 2014 and December 2018. Clinical records were linked to the Kilifi Health and Demographic Surveillance System and population incidence rates of CHIKV infection estimated. There were 18,341 pediatric admissions for any reason during the 5-year study period, of which 4,332 (24%) had CSF collected. The most common clinical reasons for CSF collection were impaired consciousness, seizures, and coma (47%, 22%, and 21% of all collections, respectively). After acute investigations done for immediate clinical care, CSF samples were available for 3,980 admissions, of which 367 (9.2%) were CHIKV RT-PCR positive. Case fatality among CHIKV-positive children was 1.4% (95% CI 0.4, 3.2). The annual incidence of CHIKV-associated neurological disease varied between 13 to 58 episodes per 100,000 person-years among all children <16 years old. Among children aged <5 years, the incidence of CHIKV-associated neurological disease was 77 per 100,000 person-years, compared with 20 per 100,000 for cerebral malaria and 7 per 100,000 for bacterial meningitis during the study period. Because of incomplete case ascertainment due to children not presenting to hospital, or not having CSF collected, these are likely minimum estimates. Study limitations include reliance on hospital-based surveillance and limited CSF sampling in children in coma or other contraindications to lumbar puncture, both of which lead to under-ascertainment of incidence and of case fatality. CONCLUSIONS In this study, we observed that CHIKV infections are relatively more common than cerebral malaria and bacterial meningitis among children hospitalized with neurological disease in coastal Kenya. Given the wide distribution of CHIKV mosquito vectors, studies to determine the geographic extent of CHIKV-associated neurological disease in Africa are essential.
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Affiliation(s)
| | - Mark Otiende
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Lilian Mwango
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | | | | | | | | | | | | | | | | | - Alun Davies
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | | | | | - Samuel M. Thumbi
- Paul G Allen School for Global Animal Health, Washington State University, Washington, United States of America
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Center for Epidemiological Modelling and Analysis, Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | | | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - George M. Warimwe
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Gumba H, Opiyo M, Musyoki J, Mutunga M, Ngetsa C, Mwarumba S, Mosobo M, Njuguna S, Kai O, Lambisia AW, Kimani D, Cheruiyot R, Kiyuka P, Lewa C, Gicheru E, Tendwa M, Said Mohammed K, Osoti V, Makale J, Tawa B, Odundo C, Cheruiyot W, Nyamu W, Gumbi W, Mwacharo J, Nyamako L, Otieno E, Amadi D, Ouma N, Karia B, Thoya J, Karani A, Mugo D, Gichuki BM, Riako D, Mutua S, Gitonga JN, Ominde K, Wanjiku P, Mutiso A, Mwanzu A, Sein Y, Bartilol B, Mwangi S, Omuoyo DO, Morobe JM, de Laurent ZR, Mitsanze F, Mwakubia A, Rono M, Nyaguara A, Tsofa B, Bejon P, Agoti CN, Ochola-Oyier LI. Maintaining laboratory quality assurance and safety in a pandemic: Experiences from the KEMRI-Wellcome Trust Research Programme laboratory’s COVID-19 response. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.16704.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory diagnosis plays a critical role in the containment of a pandemic. Strong laboratory quality management systems (QMS) are essential for laboratory diagnostic services. However, low laboratory capacities in resource-limited countries has made the maintenance of laboratory quality assurance, especially during a pandemic, a daunting task. In this paper, we describe our experience of how we went about providing diagnostic testing services for SARS-CoV-2 through laboratory reorganization, redefining of the laboratory workflow, and training and development of COVID-19 documented procedures, all while maintaining the quality assurance processes during the COVID-19 pandemic at the Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme (KWTRP) laboratory. The KWTRP laboratory managed to respond to the COVID-19 outbreak in Kenya by providing diagnostic testing for the coastal region of the country, while maintaining its research standard quality assurance processes. A COVID-19 team comprising of seven sub-teams with assigned specific responsibilities and an organizational chart with established reporting lines were developed. Additionally, a total of four training sessions were conducted for county Rapid Response Teams (RRTs) and laboratory personnel. A total of 11 documented procedures were developed to support the COVID-19 testing processes, with three for the pre-analytical phases, seven for the analytical phase, and one for the post-analytical phase. With the workflow re-organization, the development of appropriate standard operating procedures, and training, research laboratories can effectively respond to pandemic outbreaks while maintaining research standard QMS procedures.
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Mohammed KS, de Laurent ZR, Omuoyo DO, Lewa C, Gicheru E, Cheruiyot R, Bartilol B, Mutua S, Musyoki J, Gumba H, Mwacharo J, Riako D, Mwangi SJ, Gichuki BM, Nyamako L, Karani A, Karanja H, Mugo D, Gitonga JN, Njuguna S, Gumbi W, Tawa B, Tendwa M, Cheruiyot W, Sein Y, Nyambu JK, Patta SO, Thani TS, Maitha EK, Kitole B, Mwakinangu MS, Muslih BS, Otieno JO, Nyiro JU, Kiyuka P, Ndwiga L, Wamae K, Kimani D, Makale J, Morobe JM, Osoti V, Lambisia AW, Odundo C, Mwarumba S, Mutunga M, Bejon P, Tsofa B, Agoti CN, Ochola-Oyier LI. An optimization of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams. Wellcome Open Res 2022; 5:162. [PMID: 35330938 PMCID: PMC8921690 DOI: 10.12688/wellcomeopenres.16063.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2022] [Indexed: 11/28/2022] Open
Abstract
Background: The COVID-19 pandemic relies on real-time polymerase chain reaction (qRT-PCR) for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to facilitate roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers' recommendations to sustain the testing capability in a resource-limited setting. Methods: We used a SARS-CoV-2 positive control RNA sample to generate several 10-fold dilution series that were used for optimization and comparison of the performance of the four qRT-PCR assays: i) Charité Berlin primer-probe set, ii) European Virus Archive - GLOBAL (EVAg) primer-probe set, iii) DAAN premixed commercial kit and iv) Beijing Genomics Institute (BGI) premixed commercial kit. We adjusted the manufacturer- and protocol-recommended reaction component volumes for these assays and assessed the impact on cycle threshold (Ct) values. Results: The Berlin and EVAg E gene and RdRp assays reported mean Ct values within range of each other across the different titrations and with less than 5% difference. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit improved in performance following a reduction of the reaction components. Conclusion: We achieved a 2.6-fold and 4-fold increase in the number of tests per kit for the commercial kits and the primer-probe sets, respectively. All the assays had optimal performance when the primers and probes were used at 0.375X, except for the Berlin N gene assay. The DAAN kit was a reliable assay for primary screening of SARS-CoV-2 whereas the BGI kit's performance was dependent on the volumes and concentrations of both the reaction buffer and enzyme mix. Our recommendation for SARS-CoV-2 diagnostic testing in resource-limited settings is to optimize the assays available to establish the lowest volume and suitable concentration of reagents required to produce valid results.
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Affiliation(s)
| | | | | | - Clement Lewa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | - Horace Gumba
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Debra Riako
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Lydia Nyamako
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Angela Karani
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Henry Karanja
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan Njuguna
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Wilson Gumbi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Brian Tawa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Yiakon Sein
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John K. Nyambu
- Department Of Health Services, Taita-Taveta County Government, Taita-Taveta, Kenya
| | - Shem O. Patta
- Department Of Health Services, Mombasa County Government, Mombasa, Kenya
| | | | | | | | | | | | | | | | | | | | - Kevin Wamae
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | - Victor Osoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Calleb Odundo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, UK
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Gilchrist JJ, Kariuki SN, Watson JA, Band G, Uyoga S, Ndila CM, Mturi N, Mwarumba S, Mohammed S, Mosobo M, Alasoo K, Rockett KA, Mentzer AJ, Kwiatkowski DP, Hill AVS, Maitland K, Scott JAG, Williams TN. BIRC6 modifies risk of invasive bacterial infection in Kenyan children. eLife 2022; 11:77461. [PMID: 35866869 PMCID: PMC9391038 DOI: 10.7554/elife.77461] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Invasive bacterial disease is a major cause of morbidity and mortality in African children. Despite being caused by diverse pathogens, children with sepsis are clinically indistinguishable from one another. In spite of this, most genetic susceptibility loci for invasive infection that have been discovered to date are pathogen specific and are not therefore suggestive of a shared genetic architecture of bacterial sepsis. Here, we utilise probabilistic diagnostic models to identify children with a high probability of invasive bacterial disease among critically unwell Kenyan children with Plasmodium falciparum parasitaemia. We construct a joint dataset including 1445 bacteraemia cases and 1143 severe malaria cases, and population controls, among critically unwell Kenyan children that have previously been genotyped for human genetic variation. Using these data, we perform a cross-trait genome-wide association study of invasive bacterial infection, weighting cases according to their probability of bacterial disease. In doing so, we identify and validate a novel risk locus for invasive infection secondary to multiple bacterial pathogens, that has no apparent effect on malaria risk. The locus identified modifies splicing of BIRC6 in stimulated monocytes, implicating regulation of apoptosis and autophagy in the pathogenesis of sepsis in Kenyan children.
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Affiliation(s)
- James J Gilchrist
- Department of Paediatrics, University of OxfordOxfordUnited Kingdom,MRC–Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom,Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Silvia N Kariuki
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - James A Watson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Salim Mwarumba
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Shebe Mohammed
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Moses Mosobo
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Kaur Alasoo
- Institute of Computer Science, University of TartuTartuEstonia
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom,Wellcome Sanger InstituteCambridgeUnited Kingdom
| | - Adrian VS Hill
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom,The Jenner Institute, University of OxfordOxfordUnited Kingdom
| | - Kathryn Maitland
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Division of Medicine, Imperial CollegeLondonUnited Kingdom
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial CollegeLondonUnited Kingdom
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7
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Abuga KM, Muriuki JM, Uyoga SM, Mwai K, Makale J, Mogire RM, Macharia AW, Mohammed S, Muthumbi E, Mwarumba S, Mturi N, Bejon P, Scott JAG, Nairz M, Williams TN, Atkinson SH. Hepcidin regulation in Kenyan children with severe malaria and non-typhoidal Salmonella bacteremia. Haematologica 2021; 107:1589-1598. [PMID: 34498446 PMCID: PMC9244826 DOI: 10.3324/haematol.2021.279316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/09/2022] Open
Abstract
Malaria and invasive non-typhoidal Salmonella (NTS) are life-threatening infections that often co-exist in African children. The iron-regulatory hormone hepcidin is highly upregulated during malaria and controls the availability of iron, a critical nutrient for bacterial growth. We investigated the relationship between Plasmodium falciparum malaria and NTS bacteremia in all pediatric admissions aged <5 years between August 1998 and October 2019 (n=75,034). We then assayed hepcidin and measures of iron status in five groups: (1) children with concomitant severe malarial anemia (SMA) and NTS (SMA+NTS, n=16); and in matched children with (2) SMA (n=33); (3) NTS (n=33); (4) cerebral malaria (CM, n=34); and (5) community-based children. SMA and severe anemia without malaria were associated with a 2-fold or more increased risk of NTS bacteremia, while other malaria phenotypes were not associated with increased NTS risk. Children with SMA had lower hepcidin/ferritin ratios (0.10; interquartile range [IQR]: 0.03-0.19) than those with CM (0.24; IQR: 0.14-0.69; P=0.006) or asymptomatic malaria (0.19; IQR: 0.09-0.46; P=0.01) indicating suppressed hepcidin levels. Children with SMA+NTS had lower hepcidin levels (9.3 ng/mL; IQR: 4.7-49.8) and hepcidin/ferritin ratios (0.03; IQR: 0.01-0.22) than those with NTS alone (105.8 ng/mL; IQR: 17.3-233.3; P=0.02 and 0.31; IQR: 0.06-0.66; P=0.007, respectively). Since hepcidin degrades ferroportin on the Salmonella-containing vacuole, we hypothesize that reduced hepcidin in children with SMA might contribute to NTS growth by modulating iron availability for bacterial growth. Further studies are needed to understand how the hepcidin-ferroportin axis might mediate susceptibility to NTS in severely anemic children.
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Affiliation(s)
- Kelvin M. Abuga
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Department of Public Health, School of Human and Health Sciences, Pwani University, Kilifi, Kenya,Kelvin M. Abuga
| | - John Muthii Muriuki
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Sophie M. Uyoga
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Kennedy Mwai
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Epidemiology and Biostatistics Division, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Johnstone Makale
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Reagan M. Mogire
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Open University, KEMRI-Wellcome Trust Research Program – Accredited Research Center, Kilifi, Kenya
| | - Alex W. Macharia
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Open University, KEMRI-Wellcome Trust Research Program – Accredited Research Center, Kilifi, Kenya
| | - Shebe Mohammed
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Esther Muthumbi
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Salim Mwarumba
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Neema Mturi
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - J. Anthony G. Scott
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Manfred Nairz
- Department of Internal Medicine II, Medical University Innsbruck, Innsbruck, Austria
| | - Thomas N. Williams
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK,Department of Infectious Diseases and Institute of Global Health Innovation, Imperial College, London, UK
| | - Sarah H. Atkinson
- Kenya Medical Research Institute (KEMRI) Center for Geographic Medicine Research, KEMRI-Wellcome Trust Research Program, Kilifi, Kenya,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK,Department of Pediatrics, University of Oxford, Oxford, UK,Sarah H. Atkinson
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gumba H, Opiyo M, Musyoki J, Mutunga M, Ngetsa C, Mwarumba S, Mosobo M, Njuguna S, Kai O, Lambisia AW, Kimani D, Cheruiyot R, Kiyuka P, Lewa C, Gicheru E, Tendwa M, Said Mohammed K, Osoti V, Makale J, Tawa B, Odundo C, Cheruiyot W, Nyamu W, Gumbi W, Mwacharo J, Nyamako L, Otieno E, Amadi D, Ouma N, Karia B, Thoya J, Karani A, Mugo D, Gichuki BM, Riako D, Mutua S, Gitonga JN, Ominde K, Wanjiku P, Mutiso A, Mwanzu A, Sein Y, Bartilol B, Mwangi S, Omuoyo DO, Morobe JM, de Laurent ZR, Mitsanze F, Mwakubia A, Rono M, Nyaguara A, Tsofa B, Bejon P, Agoti CN, Ochola-Oyier LI. Maintaining laboratory quality assurance and safety in a pandemic: Experiences from the KEMRI-Wellcome Trust Research Programme laboratory’s COVID-19 response. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16704.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory diagnosis plays a critical role in the containment of a pandemic. Strong laboratory quality management systems (QMS) are essential for laboratory diagnostic services. However, low laboratory capacities in resource-limited countries has made the maintenance of laboratory quality assurance, especially during a pandemic, a daunting task. In this paper, we describe our experience of how we went about providing diagnostic testing services for SARS-CoV-2 through laboratory reorganization, redefining of the laboratory workflow, and training and development of COVID-19 documented procedures, all while maintaining the quality assurance processes during the COVID-19 pandemic at the Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme (KWTRP) laboratory. The KWTRP laboratory managed to respond to the COVID-19 outbreak in Kenya by providing diagnostic testing for the coastal region of the country, while maintaining its research standard quality assurance processes. A COVID-19 team comprising of seven sub-teams with assigned specific responsibilities and an organizational chart with established reporting lines were developed. Additionally, a total of four training sessions were conducted for county Rapid Response Teams (RRTs) and laboratory personnel. A total of 11 documented procedures were developed to support the COVID-19 testing processes, with three for the pre-analytical phases, seven for the analytical phase, and one for the post-analytical phase. With the workflow re-organization, the development of appropriate standard operating procedures, and training, research laboratories can effectively respond to pandemic outbreaks while maintaining research standard QMS procedures.
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Obiero CW, Mturi N, Mwarumba S, Ngari M, Newton CR, van Hensbroek MB, Berkley JA. Clinical features of bacterial meningitis among hospitalised children in Kenya. BMC Med 2021; 19:122. [PMID: 34082778 PMCID: PMC8176744 DOI: 10.1186/s12916-021-01998-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/29/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Diagnosing bacterial meningitis is essential to optimise the type and duration of antimicrobial therapy to limit mortality and sequelae. In sub-Saharan Africa, many public hospitals lack laboratory capacity, relying on clinical features to empirically treat or not treat meningitis. We investigated whether clinical features of bacterial meningitis identified prior to the introduction of conjugate vaccines still discriminate meningitis in children aged ≥60 days. METHODS We conducted a retrospective cohort study to validate seven clinical features identified in 2002 (KCH-2002): bulging fontanel, neck stiffness, cyanosis, seizures outside the febrile convulsion age range, focal seizures, impaired consciousness, or fever without malaria parasitaemia and Integrated Management of Childhood Illness (IMCI) signs: neck stiffness, lethargy, impaired consciousness or seizures, and assessed at admission in discriminating bacterial meningitis after the introduction of conjugate vaccines. Children aged ≥60 days hospitalised between 2012 and 2016 at Kilifi County Hospital were included in this analysis. Meningitis was defined as positive cerebrospinal fluid (CSF) culture, organism observed on CSF microscopy, positive CSF antigen test, leukocytes ≥50/μL, or CSF to blood glucose ratio <0.1. RESULTS Among 12,837 admissions, 98 (0.8%) had meningitis. The presence of KCH-2002 signs had a sensitivity of 86% (95% CI 77-92) and specificity of 38% (95% CI 37-38). Exclusion of 'fever without malaria parasitaemia' reduced sensitivity to 58% (95% CI 48-68) and increased specificity to 80% (95% CI 79-80). IMCI signs had a sensitivity of 80% (95% CI 70-87) and specificity of 62% (95% CI 61-63). CONCLUSIONS A lower prevalence of bacterial meningitis and less typical signs than in 2002 meant the lower performance of KCH-2002 signs. Clinicians and policymakers should be aware of the number of lumbar punctures (LPs) or empirical treatments needed for each case of meningitis. Establishing basic capacity for CSF analysis is essential to exclude bacterial meningitis in children with potential signs.
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Affiliation(s)
- Christina W Obiero
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, P.O. Box 230 80108, Kilifi, Kenya.
- Department of Global Health, Faculty of Medicine, University of Amsterdam, Amsterdam, The Netherlands.
| | - Neema Mturi
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, P.O. Box 230 80108, Kilifi, Kenya
| | - Salim Mwarumba
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Moses Ngari
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, P.O. Box 230 80108, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Charles R Newton
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, P.O. Box 230 80108, Kilifi, Kenya
- Department of Psychiatry, University of Oxford, Oxford, UK
| | | | - James A Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, P.O. Box 230 80108, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, Nairobi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Agoti CN, Mutunga M, Lambisia AW, Kimani D, Cheruiyot R, Kiyuka P, Lewa C, Gicheru E, Tendwa M, Said Mohammed K, Osoti V, Makale J, Tawa B, Odundo C, Cheruiyot W, Nyamu W, Gumbi W, Mwacharo J, Nyamako L, Otieno E, Amadi D, Thoya J, Karani A, Mugo D, Musyoki J, Gumba H, Mwarumba S, M. Gichuki B, Njuguna S, Riako D, Mutua S, Gitonga JN, Sein Y, Bartilol B, Mwangi SJ, O. Omuoyo D, M. Morobe J, de Laurent ZR, Bejon P, Ochola-Oyier LI, Tsofa B. Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast. Wellcome Open Res 2021; 5:186. [PMID: 33134555 PMCID: PMC7590893 DOI: 10.12688/wellcomeopenres.16113.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2020] [Indexed: 12/15/2022] Open
Abstract
Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.
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Affiliation(s)
- Charles N. Agoti
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
- Department of Biomedical Sciences, Pwani University, Kilifi, Kenya
| | - Martin Mutunga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Arnold W. Lambisia
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Domtila Kimani
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Robinson Cheruiyot
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Patience Kiyuka
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Clement Lewa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Elijah Gicheru
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Metrine Tendwa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Khadija Said Mohammed
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Victor Osoti
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Johnstone Makale
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Brian Tawa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Calleb Odundo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Wesley Cheruiyot
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Wilfred Nyamu
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Wilson Gumbi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Jedidah Mwacharo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Lydia Nyamako
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Edward Otieno
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - David Amadi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Janet Thoya
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Angela Karani
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Daisy Mugo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Jennifer Musyoki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Horace Gumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Bonface M. Gichuki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Susan Njuguna
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Debra Riako
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Shadrack Mutua
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - John N. Gitonga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Yiakon Sein
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Brian Bartilol
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Shaban J. Mwangi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Donwilliams O. Omuoyo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - John M. Morobe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Zaydah R. de Laurent
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, UK
| | - Lynette Isabella Ochola-Oyier
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Benjamin Tsofa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
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Obiero CW, Mturi N, Mwarumba S, Ngari M, Newton C, Boele van Hensbroek M, Berkley JA. Clinical features to distinguish meningitis among young infants at a rural Kenyan hospital. Arch Dis Child 2021; 106:130-136. [PMID: 32819909 PMCID: PMC7841476 DOI: 10.1136/archdischild-2020-318913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/23/2020] [Accepted: 07/01/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND Detection of meningitis is essential to optimise the duration and choice of antimicrobial agents to limit mortality and sequelae. In low and middle-income countries most health facilities lack laboratory capacity and rely on clinical features to empirically treat meningitis. OBJECTIVE We conducted a diagnostic validation study to investigate the performance of clinical features (fever, convulsions, irritability, bulging fontanel and temperature ≥39°C) and WHO-recommended signs (drowsiness, lethargy, unconsciousness, convulsions, bulging fontanel, irritability or a high-pitched cry) in discriminating meningitis in young infants. DESIGN Retrospective cohort study. SETTING Kilifi County Hospital. PATIENTS Infants aged <60 days hospitalised between 2012 and 2016. MAIN OUTCOME MEASURE Definite meningitis defined as positive cerebrospinal fluid (CSF) culture, microscopy or antigen test, or leucocytes ≥0.05 x 10∧9/L. RESULTS Of 4809 infants aged <60 days included, 81 (1.7%) had definite meningitis. WHO-recommended signs had sensitivity of 58% (95% CI 47% to 69%) and specificity of 57% (95% CI 56% to 59%) for definite meningitis. Addition of history of fever improved sensitivity to 89% (95% CI 80% to 95%) but reduced specificity to 26% (95% CI 25% to 27%). Presence of ≥1 of 5 previously identified signs had sensitivity of 79% (95% CI 69% to 87%) and specificity of 51% (95% CI 50% to 53%). CONCLUSIONS Despite a lower prevalence of definite meningitis, the performance of previously identified signs at admission in predicting meningitis was unchanged. Presence of history of fever improves the sensitivity of WHO-recommended signs but loses specificity. Careful evaluation, repeated assessment and capacity for lumbar puncture and CSF microscopy to exclude meningitis in most young infants with potential signs are essential to management in this age group.
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Affiliation(s)
- Christina W Obiero
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Global Health, University of Amsterdam Faculty of Medicine, Amsterdam, Noord-Holland, The Netherlands
| | - Neema Mturi
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Salim Mwarumba
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Moses Ngari
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Charles Newton
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Psychiatry, University of Oxford Centre for Tropical Medicine and Global Health, Oxford, Oxfordshire, UK
| | - Michael Boele van Hensbroek
- Department of Global Health, University of Amsterdam Faculty of Medicine, Amsterdam, Noord-Holland, The Netherlands
| | - James Alexander Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, Nairobi, Kenya
- Nuffield Department of Medicine, University of Oxford Centre for Tropical Medicine and Global Health, Oxford, Oxfordshire, UK
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Kagia N, Kosgei P, Ooko M, Wafula L, Mturi N, Anampiu K, Mwarumba S, Njuguna P, Seale AC, Berkley JA, Bottomley C, Scott JAG, Morpeth SC. Carriage and Acquisition of Extended-spectrum β-Lactamase-producing Enterobacterales Among Neonates Admitted to Hospital in Kilifi, Kenya. Clin Infect Dis 2020; 69:751-759. [PMID: 30830952 PMCID: PMC6695508 DOI: 10.1093/cid/ciy976] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/30/2018] [Indexed: 12/18/2022] Open
Abstract
Background Infections caused by extended-spectrum β-lactamase–producing Enterobacterales (ESBL-E) among hospitalized neonates in sub-Saharan Africa pose significant clinical challenges. Data on prevalence and acquisition of ESBL-E carriage among hospitalized neonates in the region are few, and risk factors for transmission are not clearly defined. Methods In a cohort study of consecutive neonatal admissions to Kilifi County Hospital from July 2013 through August 2014, we estimated ESBL-E carriage prevalence on admission using rectal swab cultures and identified risk factors using logistic regression. Using twice-weekly follow-up swabs, we estimated the incidence and identified risk factors for ESBL-E acquisition in hospital using Poisson regression. Results The prevalence of ESBL-E carriage at admission was 10% (59/569). Cesarean delivery, older neonatal age, and smaller household size were significant risk factors. Of the 510 infants admitted without ESBL-E carriage, 238 (55%) acquired carriage during their hospital stay. The incidence of acquisition was 21.4% (95% confidence interval, 19.0%–24.0%) per day. The rate was positively associated with the number of known neonatal ESBL-E carriers and with the total number of neonates on the same ward. Conclusions Carriage of ESBL-E was common among neonates on admission, and in-hospital acquisition was rapid. The dissemination and selection of ESBL-E appears to be driven by hospital exposures, operative delivery, and neonatal ward patient density. Further attention to infection control, patient crowding, and carriage surveillance is warranted.
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Affiliation(s)
- Ngure Kagia
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Patrick Kosgei
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Michael Ooko
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Leonard Wafula
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Neema Mturi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Kirimi Anampiu
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Patricia Njuguna
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi
| | - Anna C Seale
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi.,Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom
| | - James A Berkley
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi.,Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Christian Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research- Coast, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom.,Counties Manukau District Health Board, Auckland, New Zealand
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14
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Agoti CN, Mutunga M, Lambisia AW, Kimani D, Cheruiyot R, Kiyuka P, Lewa C, Gicheru E, Tendwa M, Said Mohammed K, Osoti V, Makale J, Tawa B, Odundo C, Cheruiyot W, Nyamu W, Gumbi W, Mwacharo J, Nyamako L, Otieno E, Amadi D, Thoya J, Karani A, Mugo D, Musyoki J, Gumba H, Mwarumba S, M. Gichuki B, Njuguna S, Riako D, Mutua S, Gitonga JN, Sein Y, Bartilol B, Mwangi SJ, O. Omuoyo D, M. Morobe J, de Laurent ZR, Bejon P, Ochola-Oyier LI, Tsofa B. Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast. Wellcome Open Res 2020; 5:186. [PMID: 33134555 PMCID: PMC7590893 DOI: 10.12688/wellcomeopenres.16113.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.
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Affiliation(s)
- Charles N. Agoti
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
- Department of Biomedical Sciences, Pwani University, Kilifi, Kenya
| | - Martin Mutunga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Arnold W. Lambisia
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Domtila Kimani
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Robinson Cheruiyot
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Patience Kiyuka
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Clement Lewa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Elijah Gicheru
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Metrine Tendwa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Khadija Said Mohammed
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Victor Osoti
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Johnstone Makale
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Brian Tawa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Calleb Odundo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Wesley Cheruiyot
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Wilfred Nyamu
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Wilson Gumbi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Jedidah Mwacharo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Lydia Nyamako
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Edward Otieno
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - David Amadi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Janet Thoya
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Angela Karani
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Daisy Mugo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Jennifer Musyoki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Horace Gumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Bonface M. Gichuki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Susan Njuguna
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Debra Riako
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Shadrack Mutua
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - John N. Gitonga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Yiakon Sein
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Brian Bartilol
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Shaban J. Mwangi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Donwilliams O. Omuoyo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - John M. Morobe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Zaydah R. de Laurent
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, UK
| | - Lynette Isabella Ochola-Oyier
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Benjamin Tsofa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya
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15
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Mohammed KS, de Laurent ZR, Omuoyo DO, Lewa C, Gicheru E, Cheruiyot R, Bartilol B, Mutua S, Musyoki J, Gumba H, Mwacharo J, Riako D, Mwangi SJ, Gichuki BM, Nyamako L, Karani A, Karanja H, Mugo D, Gitonga JN, Njuguna S, Gumbi W, Tawa B, Tendwa M, Cheruiyot W, Sein Y, Nyambu JK, Patta SO, Thani TS, Maitha EK, Kitole B, Mwakinangu MS, Muslih BS, Otieno JO, Nyiro JU, Kiyuka P, Ndwiga L, Wamae K, Kimani D, Makale J, Morobe JM, Osoti V, Lambisia AW, Odundo C, Mwarumba S, Mutunga M, Bejon P, Tsofa B, Agoti CN, Ochola-Oyier LI. An optimisation of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams. Wellcome Open Res 2020; 5:162. [PMID: 35330938 PMCID: PMC8921690 DOI: 10.12688/wellcomeopenres.16063.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 05/13/2024] Open
Abstract
Background: The global COVID-19 outbreak relies on a quantitative real-time polymerase chain reaction (qRT-PCR) for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2), to facilitate the roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers' recommendations to sustain the testing capability in our setting, where the supply of testing reagents is limited. Methods: Standards generated from a serially-diluted positive control and previously identified positive/negative samples were used to determine the optimal volumes of the qRT-PCR reagents and to evaluate the validity and performance of four assays: Charité Berlin and European Virus Archive - GLOBAL (EVAg) primer-probe sets, and DAAN and Beijing Genomics Institute (BGI) premixed commercial kits. A multiplex and singleplex RT-PCR kit was used with the two primer-probe sets and the recommended assay volumes of the two premixed kits were altered. Results: In comparison to the multiplex RT-PCR kit, the singleplex RT-PCR kit combined with the primer-probe sets yielded consistent cycle threshold (Ct) values across the different titrations tested. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit showed incomparable Ct values and inconsistent results between batches using the manufacturer's recommended volumes. Conclusion: We achieved a 2.5-fold and 4-fold increase in the number of tests/kit for the premixed kits and the primer-probe sets, respectively. The primer-probe set assays were reliable and consistent, and we preferred a combination of an EVAg and a Berlin target. Any inconclusive result was repeated by different individuals following the same protocol. DAAN was a consistent and reliable assay even at lower concentrations from the stated recommendations. BGI in contrast, required dilution to improve its performance and was hence an assay that was used in combination with EVAg or Berlin targets.
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Affiliation(s)
| | | | | | - Clement Lewa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | - Horace Gumba
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Debra Riako
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Lydia Nyamako
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Angela Karani
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Henry Karanja
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan Njuguna
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Wilson Gumbi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Brian Tawa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Yiakon Sein
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John K. Nyambu
- Department Of Health Services, Taita-Taveta County Government, Taita-Taveta, Kenya
| | - Shem O. Patta
- Department Of Health Services, Mombasa County Government, Mombasa, Kenya
| | | | | | | | | | | | | | | | | | | | - Kevin Wamae
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | - Victor Osoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Calleb Odundo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, UK
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16
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Gilchrist JJ, Uyoga S, Pirinen M, Rautanen A, Mwarumba S, Njuguna P, Mturi N, Hill AVS, Scott JAG, Williams TN. Risk of pneumococcal bacteremia in Kenyan children with glucose-6-phosphate dehydrogenase deficiency. BMC Med 2020; 18:148. [PMID: 32536341 PMCID: PMC7294654 DOI: 10.1186/s12916-020-01604-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/23/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency state in humans. The clinical phenotype is variable and includes asymptomatic individuals, episodic hemolysis induced by oxidative stress, and chronic hemolysis. G6PD deficiency is common in malaria-endemic regions, an observation hypothesized to be due to balancing selection at the G6PD locus driven by malaria. G6PD deficiency increases risk of severe malarial anemia, a key determinant of invasive bacterial disease in malaria-endemic settings. The pneumococcus is a leading cause of invasive bacterial infection and death in African children. The effect of G6PD deficiency on risk of pneumococcal disease is undefined. We hypothesized that G6PD deficiency increases pneumococcal disease risk and that this effect is dependent upon malaria. METHODS We performed a genetic case-control study of pneumococcal bacteremia in Kenyan children stratified across a period of falling malaria transmission between 1998 and 2010. RESULTS Four hundred twenty-nine Kenyan children with pneumococcal bacteremia and 2677 control children were included in the study. Among control children, G6PD deficiency, secondary to the rs1050828 G>A mutation, was common, with 11.2% (n = 301 of 2677) being hemi- or homozygotes and 33.3% (n = 442 of 1329) of girls being heterozygotes. We found that G6PD deficiency increased the risk of pneumococcal bacteremia, but only during a period of high malaria transmission (P = 0.014; OR 2.33, 95% CI 1.19-4.57). We estimate that the population attributable fraction of G6PD deficiency on risk of pneumococcal bacteremia in areas under high malaria transmission is 0.129. CONCLUSIONS Our data demonstrate that G6PD deficiency increases risk of pneumococcal bacteremia in a manner dependent on malaria. At the population level, the impact of G6PD deficiency on invasive pneumococcal disease risk in malaria-endemic regions is substantial. Our study highlights the infection-associated morbidity and mortality conferred by G6PD deficiency in malaria-endemic settings and adds to our understanding of the potential indirect health benefits of improved malaria control.
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Affiliation(s)
- James J Gilchrist
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. .,Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK.
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Anna Rautanen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Salim Mwarumba
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | | | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | | | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya. .,Department of Medicine, Imperial College, Norfolk Place, London, W2 1PG, UK.
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17
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Muthumbi EM, Gordon NC, Mochamah G, Nyongesa S, Odipo E, Mwarumba S, Mturi N, Etyang AO, Dance DAB, Scott JAG, Morpeth SC. Population-Based Estimate of Melioidosis, Kenya. Emerg Infect Dis 2019; 25:984-987. [PMID: 31002067 PMCID: PMC6478202 DOI: 10.3201/eid2505.180545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Melioidosis is thought to be endemic, although underdiagnosed, in Africa. We identified 5 autochthonous cases of Burkholderia pseudomallei infection in a case series in Kenya. Incidence of B. pseudomallei bacteremia in Kenya’s Kilifi County is low, at 1.5 cases per million person-years, but this result might be an underestimate.
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18
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Piper JD, Mwarumba S, Ngari M, Mvera B, Morpeth S, Berkley JA. Invasive Cronobacter species infection in infants and children admitted to a rural Kenyan hospital with a high prevalence of malnutrition. Paediatr Int Child Health 2018. [PMID: 29533163 PMCID: PMC6113899 DOI: 10.1080/20469047.2018.1446485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
For children with acute malnutrition, ready-to-use therapeutic foods (RUTF) are lifesaving treatments. In 2012, detailed testing detected Enterobacteriaceae including Cronobacter species at low levels in RUTF from all UNICEF-approved producers. Cronobacter in milk feeds has previously been associated with severe neonatal infections. Thus, given the susceptibility of severely malnourished children to invasive bacterial infections, concerns arose about the potential for Cronobacter infections from RUTF. This led to widespread production and supply problems in emergency feeding programmes. The KEMRI/Wellcome Trust Research Programme has conducted systematic surveillance for invasive bacterial infections among children admitted to Kilifi County Hospital, Kenya since 1998. 65,426 paediatric blood and cerebrospinal fluid cultures from 52,733 admissions resulted in 3953 with growth of a pathogenic organism. From the 60 Enterobacter and Cronobacter isolates, possible Cronobacter species were initially selected from their original API-20E biochemical profile, which was repeated and then confirmed using ID-32E. Only two isolates were consistent with Cronobacter species, neither case had received RUTF. Serious infection due to Cronobacter species does not have a significant burden in this population. This has important implications for the continued supply, manufacture and monitoring of emergency feeds for malnourished children.
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Affiliation(s)
- Joe D. Piper
- Child Health, Blizard Institute, Queen Mary University of London, London, UK,Clinical Research, KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi, Kenya
| | - Salim Mwarumba
- Clinical Research, KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi, Kenya
| | - Moses Ngari
- Clinical Research, KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi, Kenya,Coordination Centre, The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
| | - Benedict Mvera
- Clinical Research, KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi, Kenya
| | - Susan Morpeth
- Clinical Research, KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi, Kenya,Middlemore Hospital, Auckland, New Zealand
| | - James A. Berkley
- Clinical Research, KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi, Kenya,Coordination Centre, The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK,Corresponding author.
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19
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Gilchrist JJ, Rautanen A, Fairfax BP, Mills TC, Naranbhai V, Trochet H, Pirinen M, Muthumbi E, Mwarumba S, Njuguna P, Mturi N, Msefula CL, Gondwe EN, MacLennan JM, Chapman SJ, Molyneux ME, Knight JC, Spencer CCA, Williams TN, MacLennan CA, Scott JAG, Hill AVS. Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4. Nat Commun 2018. [PMID: 29523850 PMCID: PMC5844948 DOI: 10.1038/s41467-017-02398-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) is a major cause of bacteraemia in Africa. The disease typically affects HIV-infected individuals and young children, causing substantial morbidity and mortality. Here we present a genome-wide association study (180 cases, 2677 controls) and replication analysis of NTS bacteraemia in Kenyan and Malawian children. We identify a locus in STAT4, rs13390936, associated with NTS bacteraemia. rs13390936 is a context-specific expression quantitative trait locus for STAT4 RNA expression, and individuals carrying the NTS-risk genotype demonstrate decreased interferon-γ (IFNγ) production in stimulated natural killer cells, and decreased circulating IFNγ concentrations during acute NTS bacteraemia. The NTS-risk allele at rs13390936 is associated with protection against a range of autoimmune diseases. These data implicate interleukin-12-dependent IFNγ-mediated immunity as a determinant of invasive NTS disease in African children, and highlight the shared genetic architecture of infectious and autoimmune disease.
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Affiliation(s)
- James J Gilchrist
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. .,Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK.
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Tara C Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Holly Trochet
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Matti Pirinen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Institute for Molecular Medicine, Finland (FIMM) University of Helsinki, FI-00014, Helsinki, Finland
| | - Esther Muthumbi
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Salim Mwarumba
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | | | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi.,Pathology Department, College of Medicine, P.O. Box 360, Chichiri, Blantyre, Malawi
| | - Esther N Gondwe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi
| | - Jenny M MacLennan
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi.,Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Stephen J Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Oxford Centre for Respiratory Medicine, Churchill Hospital Site, Oxford University Hospitals, Oxford, OX3 7LE, UK
| | - Malcolm E Molyneux
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya.,Department of Medicine, Imperial College, Norfolk Place, London, W2 1PG, UK
| | - Calman A MacLennan
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi.,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. .,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
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20
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Murdoch DR, Morpeth SC, Hammitt LL, Driscoll AJ, Watson NL, Baggett HC, Brooks WA, Deloria Knoll M, Feikin DR, Kotloff KL, Levine OS, Madhi SA, O'Brien KL, Scott JAG, Thea DM, Adrian PV, Ahmed D, Alam M, Awori JO, DeLuca AN, Higdon MM, Karron RA, Kwenda G, Machuka EM, Makprasert S, McLellan J, Moore DP, Mwaba J, Mwarumba S, Park DE, Prosperi C, Sangwichian O, Sissoko S, Tapia MD, Zeger SL, Howie SRC. The Diagnostic Utility of Induced Sputum Microscopy and Culture in Childhood Pneumonia. Clin Infect Dis 2018; 64:S280-S288. [PMID: 28575362 PMCID: PMC5447842 DOI: 10.1093/cid/cix090] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background. Sputum microscopy and culture are commonly used for diagnosing the cause of pneumonia in adults but are rarely performed in children due to difficulties in obtaining specimens. Induced sputum is occasionally used to investigate lower respiratory infections in children but has not been widely used in pneumonia etiology studies. Methods. We evaluated the diagnostic utility of induced sputum microscopy and culture in patients enrolled in the Pneumonia Etiology Research for Child Health (PERCH) study, a large study of community-acquired pneumonia in children aged 1–59 months. Comparisons were made between induced sputum samples from hospitalized children with radiographically confirmed pneumonia and children categorized as nonpneumonia (due to the absence of prespecified clinical and laboratory signs and absence of infiltrate on chest radiograph). Results. One induced sputum sample was available for analysis from 3772 (89.1%) of 4232 suspected pneumonia cases enrolled in PERCH. Of these, sputum from 2608 (69.1%) met the quality criterion of <10 squamous epithelial cells per low-power field, and 1162 (44.6%) had radiographic pneumonia. Induced sputum microscopy and culture results were not associated with radiographic pneumonia, regardless of prior antibiotic use, stratification by specific bacteria, or interpretative criteria used. Conclusions. The findings of this study do not support the culture of induced sputum specimens as a diagnostic tool for pneumonia in young children as part of routine clinical practice.
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Affiliation(s)
- David R Murdoch
- Department of Pathology, University of Otago, and
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology London School of Hygiene & Tropical Medicine, United Kingdom
- Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Laura L Hammitt
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Amanda J Driscoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | | | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Daniel R Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Orin S Levine
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Katherine L O'Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology London School of Hygiene & Tropical Medicine, United Kingdom
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Peter V Adrian
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Muntasir Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Juliet O Awori
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Andrea N DeLuca
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Epidemiology, and
| | - Melissa M Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Ruth A Karron
- International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, and
- Zambia Center for Applied Health Research and Development, Lusaka
| | | | - Sirirat Makprasert
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Jessica McLellan
- Medical Research Council Unit, Basse, The Gambia
- University of Calgary Cummings School of Medicine, Alberta, Canada
| | - David P Moore
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, and
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, Johannesburg, South Africa
| | - John Mwaba
- Zambia Center for Applied Health Research and Development, Lusaka
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Daniel E Park
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, George Washington University
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, and
| | - Ornuma Sangwichian
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Seydou Sissoko
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako
| | - Milagritos D Tapia
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Stephen R C Howie
- Medical Research Council Unit, Basse, The Gambia
- Department of Paediatrics, University of Auckland, and
- Centre for International Health, University of Otago, Dunedin, New Zealand
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21
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Driscoll AJ, Karron RA, Morpeth SC, Bhat N, Levine OS, Baggett HC, Brooks WA, Feikin DR, Hammitt LL, Howie SRC, Knoll MD, Kotloff KL, Madhi SA, Scott JAG, Thea DM, Adrian PV, Ahmed D, Alam M, Anderson TP, Antonio M, Baillie VL, Dione M, Endtz HP, Gitahi C, Karani A, Kwenda G, Maiga AA, McClellan J, Mitchell JL, Morailane P, Mugo D, Mwaba J, Mwansa J, Mwarumba S, Nyongesa S, Panchalingam S, Rahman M, Sawatwong P, Tamboura B, Toure A, Whistler T, O'Brien KL, Murdoch DR. Standardization of Laboratory Methods for the PERCH Study. Clin Infect Dis 2018; 64:S245-S252. [PMID: 28575358 PMCID: PMC5447855 DOI: 10.1093/cid/cix081] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1–59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory.
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Affiliation(s)
| | - Ruth A Karron
- Center for Immunization Research, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom.,Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Niranjan Bhat
- International Vaccine Access Center, and.,Center for Vaccine Innovation and Access, PATH, and
| | - Orin S Levine
- International Vaccine Access Center, and.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W Abdullah Brooks
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Daniel R Feikin
- International Vaccine Access Center, and.,Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Laura L Hammitt
- International Vaccine Access Center, and.,Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Stephen R C Howie
- Medical Research Council Unit, Basse, The Gambia.,Department of Paediatrics, University of Auckland, and.,Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Shabir A Madhi
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Peter V Adrian
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Dilruba Ahmed
- InternationalCentre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Muntasir Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka
| | - Trevor P Anderson
- Microbiology Department, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Martin Antonio
- Medical Research Council Unit, Basse, The Gambia.,Department of Pathogen Biology, London School of Hygiene & Tropical Medicine, United Kingdom.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Vicky L Baillie
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Michel Dione
- Medical Research Council Unit, Basse, The Gambia.,International Livestock Research Institute, Kampala, Uganda
| | - Hubert P Endtz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab.,Department of Clinical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands.,Fondation Mérieux, Lyon, France
| | - Caroline Gitahi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Angela Karani
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Medicine, University of Medicine, and.,Zambia Center for Applied Health Research and Development, Lusaka
| | | | - Jessica McClellan
- Medical Research Council Unit, Basse, The Gambia.,Cummings School of Medicine, University of Calgary, Canada
| | - Joanne L Mitchell
- Microbiology Department, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Palesa Morailane
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Daisy Mugo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - John Mwaba
- Zambia Center for Applied Health Research and Development, Lusaka.,Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - James Mwansa
- Zambia Center for Applied Health Research and Development, Lusaka.,Cummings School of Medicine, University of Calgary, Canada
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Sammy Nyongesa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Sandra Panchalingam
- Department of Medicine, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore; and
| | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka
| | - Pongpun Sawatwong
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | | | - Aliou Toure
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako
| | - Toni Whistler
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - David R Murdoch
- Microbiology Department, Canterbury Health Laboratories, Christchurch, New Zealand.,Department of Pathology, University of Otago, Christchurch, New Zealand
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22
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Wang L, Ko ER, Gilchrist JJ, Pittman KJ, Rautanen A, Pirinen M, Thompson JW, Dubois LG, Langley RJ, Jaslow SL, Salinas RE, Rouse DC, Moseley MA, Mwarumba S, Njuguna P, Mturi N, Williams TN, Scott JAG, Hill AVS, Woods CW, Ginsburg GS, Tsalik EL, Ko DC. Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis. Sci Adv 2017; 3:e1602096. [PMID: 28345042 PMCID: PMC5342653 DOI: 10.1126/sciadv.1602096] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/03/2017] [Indexed: 06/06/2023]
Abstract
Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mouse model demonstrate that the methionine salvage pathway is a regulator of sepsis that can accurately predict prognosis in patients. Pathway-based genome-wide association analysis of nontyphoidal Salmonella bacteremia showed a strong enrichment for single-nucleotide polymorphisms near the components of the methionine salvage pathway. Measurement of the pathway's substrate, methylthioadenosine (MTA), in two cohorts of sepsis patients demonstrated increased plasma MTA in nonsurvivors. Plasma MTA was correlated with levels of inflammatory cytokines, indicating that elevated MTA marks a subset of patients with excessive inflammation. A machine-learning model combining MTA and other variables yielded approximately 80% accuracy (area under the curve) in predicting death. Furthermore, mice infected with Salmonella had prolonged survival when MTA was administered before infection, suggesting that manipulating MTA levels could regulate the severity of the inflammatory response. Our results demonstrate how combining genetic data, biomolecule measurements, and animal models can shape our understanding of disease and lead to new biomarkers for patient stratification and potential therapeutic targeting.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Emily R. Ko
- Duke Regional Hospital, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
| | - James J. Gilchrist
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, U.K
| | - Kelly J. Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
| | - Matti Pirinen
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
| | - J. Will Thompson
- Proteomics and Metabolomics Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura G. Dubois
- Proteomics and Metabolomics Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Raymond J. Langley
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA
| | - Sarah L. Jaslow
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raul E. Salinas
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - D. Clayburn Rouse
- Division of Laboratory Animal Resources, Duke University Medical Center, Durham, NC 27710, USA
| | - M. Arthur Moseley
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
- Proteomics and Metabolomics Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Salim Mwarumba
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
| | - Patricia Njuguna
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
| | - Neema Mturi
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
| | | | | | - Thomas N. Williams
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
- Department of Medicine, Imperial College, Norfolk Place, London W2 1PG, U.K
| | - J. Anthony G. Scott
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, U.K
| | - Adrian V. S. Hill
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Christopher W. Woods
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Medical Service, Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
| | - Geoffrey S. Ginsburg
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
| | - Ephraim L. Tsalik
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
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23
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Seale AC, Davies MR, Anampiu K, Morpeth SC, Nyongesa S, Mwarumba S, Smeesters PR, Efstratiou A, Karugutu R, Mturi N, Williams TN, Scott JAG, Kariuki S, Dougan G, Berkley JA. Invasive Group A Streptococcus Infection among Children, Rural Kenya. Emerg Infect Dis 2016; 22:224-32. [PMID: 26811918 PMCID: PMC4734542 DOI: 10.3201/eid2202.151358] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
These infections cause serious illness, especially in neonates. To determine the extent of group A Streptococcus (GAS) infections in sub-Saharan Africa and the serotypes that cause disease, we analyzed surveillance data for 64,741 hospital admissions in Kilifi, Kenya, during 1998–2011. We evaluated incidence, clinical presentations, and emm types that cause invasive GAS infection. We detected 370 cases; of the 369 for which we had data, most were skin and soft tissue infections (70%), severe pneumonia (23%), and primary bacteremia (14%). Overall case-fatality risk was 12%. Incidence of invasive GAS infection was 0.6 cases/1,000 live births among neonates, 101/100,000 person-years among children <1 year of age, and 35/100,000 among children <5 years of age. Genome sequencing identified 88 emm types. GAS causes serious disease in children in rural Kenya, especially neonates, and the causative organisms have considerable genotypic diversity. Benefit from the most advanced GAS type–specific vaccines may be limited, and efforts must be directed to protect against disease in regions of high incidence.
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24
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Muthumbi E, Morpeth SC, Ooko M, Mwanzu A, Mwarumba S, Mturi N, Etyang AO, Berkley JA, Williams TN, Kariuki S, Scott JAG. Invasive Salmonellosis in Kilifi, Kenya. Clin Infect Dis 2015; 61 Suppl 4:S290-301. [PMID: 26449944 PMCID: PMC4596936 DOI: 10.1093/cid/civ737] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Invasive salmonelloses are a major cause of morbidity and mortality in Africa, but the incidence and case fatality of each disease vary markedly by region. We aimed to describe the incidence, clinical characteristics, and antimicrobial susceptibility patterns of invasive salmonelloses among children and adults in Kilifi, Kenya. METHODS We analyzed integrated clinical and laboratory records for patients presenting to the Kilifi County Hospital between 1998 and 2014. We calculated incidence, and summarized clinical features and multidrug resistance. RESULTS Nontyphoidal Salmonella (NTS) accounted for 10.8% and 5.8% of bacteremia cases in children and adults, respectively, while Salmonella Typhi accounted for 0.5% and 2.1%, respectively. Among 351 NTS isolates serotyped, 160 (45.6%) were Salmonella Enteritidis and 152 (43.3%) were Salmonella Typhimurium. The incidence of NTS in children aged <5 years was 36.6 per 100 000 person-years, being highest in infants aged <7 days (174/100 000 person-years). The overall incidence of NTS in children varied markedly by location and declined significantly during the study period; the pattern of dominance of the NTS serotypes also shifted from Salmonella Enteritidis to Salmonella Typhimurium. Risk factors for invasive NTS disease were human immunodeficiency virus infection, malaria, and malnutrition; the case fatality ratio was 22.1% (71/321) in children aged <5 years and 36.7% (11/30) in adults. Multidrug resistance was present in 23.9% (84/351) of NTS isolates and 46.2% (12/26) of Salmonella Typhi isolates. CONCLUSIONS In Kilifi, the incidence of invasive NTS was high, especially among newborn infants, but typhoid fever was uncommon. NTS remains an important cause of bacteremia in children <5 years of age.
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Affiliation(s)
- Esther Muthumbi
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
| | - Susan C. Morpeth
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine
| | - Michael Ooko
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
| | - Alfred Mwanzu
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
| | - Salim Mwarumba
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
| | - Neema Mturi
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
| | - Anthony O. Etyang
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine
| | - James A. Berkley
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
- Nuffield Department of Clinical Medicine, Oxford University, United Kingdom
| | - Thomas N. Williams
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
- Nuffield Department of Clinical Medicine, Oxford University, United Kingdom
| | - Samuel Kariuki
- Centre for Microbiological Research, Kenya Medical Research Institute, Nairobi
| | - J. Anthony G. Scott
- Kenya Medical Research Institute–Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine
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25
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Hassall OW, Thitiri J, Fegan G, Hamid F, Mwarumba S, Denje D, Wambua K, Mandaliya K, Maitland K, Bates I. Safety and efficacy of allogeneic umbilical cord red blood cell transfusion for children with severe anaemia in a Kenyan hospital: an open-label single-arm trial. Lancet Haematol 2015; 2:e101-7. [PMID: 26687795 PMCID: PMC4722332 DOI: 10.1016/s2352-3026(15)00005-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/16/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND In sub-Saharan Africa, children are frequently admitted with severe anaemia needing an urgent blood transfusion, but blood is often unavailable. When conventional blood supplies are inadequate, allogeneic umbilical cord blood could be a feasible alternative. The aim of this study was to assess the safety and efficacy of cord blood transfusion in children with severe anaemia. METHODS Between June 26, 2007, and May 20, 2008, 413 children needing an urgent blood transfusion were admitted to Kilifi District Hospital in Kenya. Of these, 87 children were eligible for our study--ie, younger than 12 years, no signs of critical illness, and haemoglobin 100 g/L or lower (if aged 3 months or younger) or 40 g/L or lower (if older than 3 months). Cord blood was donated at Coast Provincial General Hospital, Mombasa, and screened for transfusion-transmitted infections and bacterial contamination. Red blood cells were stored vertically at 2-6°C to enable sedimentation. After transfusion, children were monitored closely for adverse events and followed up for 28 days. The primary outcome measure was the frequency and nature of adverse reactions associated with the transfusion. Secondary outcomes were the changes in haemoglobin concentrations 24 h and 28 days after transfusion, compared with pretransfusion levels. This trial is registered on ISRCTN.com, number ISRCTN66687527. FINDINGS Of the 87 children eligible for the study, cord blood was unavailable for 24, six caregivers declined consent, and two children were withdrawn before transfusion. Therefore, 55 children received umbilical cord red blood cells from 74 donations. Ten (18%) children had ten serious adverse events and 43 (78%) had 94 adverse events; the most frequent adverse events were anaemia (n=14), weight loss (n=12), and vomiting (n=10). An independent expert panel judged none of these adverse events to be probably or certainly caused by the cord blood transfusion (one-sided 97·5% CI 0-6·5). Haemoglobin increased by a median of 26 g/L (IQR 21-31) 24 h after transfusion and by 50 g/L (10-68) a median of 29 days (28-35) after transfusion. INTERPRETATION These preliminary data suggest that cord blood could be an important supplementary source of blood for transfusion in children in sub-Saharan Africa. Further studies are needed to compare the safety and efficacy of cord blood with conventional adult-donated blood for transfusions. Challenges associated with cost, infrastructure, and scale up also need investigating. FUNDING Wellcome Trust.
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Affiliation(s)
- Oliver W Hassall
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya; Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Johnstone Thitiri
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Greg Fegan
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Fauzat Hamid
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Salim Mwarumba
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Kongo Wambua
- Regional Blood Transfusion Centre, Mombasa, Kenya
| | - Kishor Mandaliya
- Coast Provincial General Hospital, Mombasa, Kenya; Regional Blood Transfusion Centre, Mombasa, Kenya
| | - Kathryn Maitland
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya; Department of Paediatrics, Imperial College London, London, UK
| | - Imelda Bates
- Liverpool School of Tropical Medicine, Liverpool, UK
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Webb C, Ngama M, Ngatia A, Shebbe M, Morpeth S, Mwarumba S, Bett A, Nokes DJ, Seale AC, Kazungu S, Munywoki P, Hammitt LL, Scott JAG, Berkley JA. Treatment failure among Kenyan children with severe pneumonia--a cohort study. Pediatr Infect Dis J 2012; 31:e152-7. [PMID: 22692700 PMCID: PMC3691501 DOI: 10.1097/inf.0b013e3182638012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND Pneumonia is the leading cause of childhood mortality worldwide. The World Health Organization recommends presumptive treatment based on clinical syndromes. Recent studies raise concerns over the frequency of treatment failure in Africa. METHODS We applied a definition of treatment failure to data prospectively collected from children who were 2-59 months of age with severe, or very severe, pneumonia admitted to Kilifi District Hospital, Kenya, from May 2007 through May 2008 and treated using World Health Organization guidelines. The primary outcome was treatment failure at 48 hours. RESULTS Of 568 children, median age 11 months, 165 (29%) had very severe pneumonia, 30 (5.3%) a positive HIV test and 62 (11%) severe malnutrition. One hundred eleven (20%; 95% confidence interval: 17-23%) children failed treatment at 48 hours and 34 (6.0%) died; 22 (65%) deaths occurred before 48 hours. Of 353 children with severe pneumonia, without HIV or severe malnutrition, 42 (12%) failed to respond at 48 hours, 15 (4.3%) failed at 5 days and 1 child (0.3%) died. Among 215 children with either severe pneumonia complicated by HIV or severe malnutrition, or very severe pneumonia, 69 (32%) failed to treatment at 48 hours, 47 (22%) failed at 5 days and 33 (16%) died. Treatment failure at 48 hours was associated with shock, bacteremia, very severe pneumonia, oxygen saturation in hemoglobin <95%, severe malnutrition, HIV and age <1 year in multivariable models. CONCLUSIONS In this setting, few children with uncomplicated severe pneumonia fail treatment or die under current guidelines. Deaths mainly occurred early and may be reduced by improving prevention, prehospital care and treatment of sepsis.
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Affiliation(s)
- Clare Webb
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Mwanajuma Ngama
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Anthony Ngatia
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Mohammed Shebbe
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Susan Morpeth
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Salim Mwarumba
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Ann Bett
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
,Department of Biological Sciences, University of Warwick, Coventry, UK.
| | - Anna C. Seale
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sidi Kazungu
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Patrick Munywoki
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - Laura L. Hammitt
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
| | - J. Anthony G. Scott
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - James A. Berkley
- Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research - Coast, PO Box 230, Kilifi, 80108, Kenya.
,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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Hammitt LL, Kazungu S, Morpeth SC, Gibson DG, Mvera B, Brent AJ, Mwarumba S, Onyango CO, Bett A, Akech DO, Murdoch DR, Nokes DJ, Scott JAG. A preliminary study of pneumonia etiology among hospitalized children in Kenya. Clin Infect Dis 2012; 54 Suppl 2:S190-9. [PMID: 22403235 PMCID: PMC3297554 DOI: 10.1093/cid/cir1071] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pneumonia is the leading cause of childhood death in the developing world. Higher-quality etiological data are required to reduce this mortality burden. METHODS We conducted a case-control study of pneumonia etiology among children aged 1-59 months in rural Kenya. Case patients were hospitalized with World Health Organization-defined severe pneumonia (SP) or very severe pneumonia (VSP); controls were outpatient children without pneumonia. We collected blood for culture, induced sputum for culture and multiplex polymerase chain reaction (PCR), and obtained oropharyngeal swab specimens for multiplex PCR from case patients, and serum for serology and nasopharyngeal swab specimens for multiplex PCR from case patients and controls. RESULTS Of 984 eligible case patients, 810 (84%) were enrolled in the study; 232 (29%) had VSP. Blood cultures were positive in 52 of 749 case patients (7%). A predominant potential pathogen was identified in sputum culture in 70 of 417 case patients (17%). A respiratory virus was detected by PCR from nasopharyngeal swab specimens in 486 of 805 case patients (60%) and 172 of 369 controls (47%). Only respiratory syncytial virus (RSV) showed a statistically significant association between virus detection in the nasopharynx and pneumonia hospitalization (odds ratio, 12.5; 95% confidence interval, 3.1-51.5). Among 257 case patients in whom all specimens (excluding serum specimens) were collected, bacteria were identified in 24 (9%), viruses in 137 (53%), mixed viral and bacterial infection in 39 (15%), and no pathogen in 57 (22%); bacterial causes outnumbered viral causes when the results of the case-control analysis were considered. CONCLUSIONS A potential etiology was detected in >75% of children admitted with SP or VSP. Except for RSV, the case-control analysis did not detect an association between viral detection in the nasopharynx and hospitalization for pneumonia.
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Affiliation(s)
- Laura L Hammitt
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
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Hassall OW, Thitiri J, Fegan G, Pole L, Mwarumba S, Denje D, Wambua K, Lowe B, Parry CM, Mandaliya K, Maitland K, Bates I. The microbiologic safety of umbilical cord blood transfusion for children with severe anemia in Mombasa, Kenya. Transfusion 2011; 52:1542-51. [PMID: 22221267 DOI: 10.1111/j.1537-2995.2011.03487.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Severe anemia requiring blood transfusion is common in hospitalized young children in sub-Saharan Africa but blood is often in short supply. Umbilical cord blood may be a useful source of blood if microbiologic safety concerns can be addressed. STUDY DESIGN AND METHODS Cord blood, donated on the labor ward at the provincial hospital in Mombasa, was cultured soon after collection (screening culture) and after a period of storage (poststorage culture). Conventional blood transfused to children at the hospital was cultured only at the time of issue (poststorage culture). Maternal sera (cord blood) and conventional blood donations were also screened for transfusion-transmitted infection. RESULTS At poststorage culture, the overall contamination rate of cord blood was one-third that of conventional blood (13/449 vs. 38/434; odds ratio [OR], 0.31; 95% confidence interval [CI], 0.15-0.61) and for bacteria of high pathogenic potential it was half that of conventional blood (4/449 vs. 7/434; OR, 0.55; 95% CI, 0.12-2.18). Screening cultures were positive in 50% (2/4) of cord blood packs where an organism of high pathogenic potential was isolated at poststorage culture. Cord blood donors had a lower seroreactivity than conventional donors for human immunodeficiency virus (OR, 0.63; 95% CI, 0.29-1.18), hepatitis B virus (OR, 0.32; 95% CI, 0.16-0.59), and hepatitis C virus (OR, 0.20; 95% CI, 0.24-0.76). For syphilis, initial seroreactivity in cord blood donors was 3.8% compared to 1.8% in conventional blood donors (OR, 2.10; 95% CI, 1.15-3.60) but was 0.5% after retesting. CONCLUSION With respect to bacterial contamination and seroreactivity for transfusion-transmitted infection, the safety of cord blood in Mombasa compares favorably with conventional blood. Clinical trials of cord blood transfusion are justified.
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Affiliation(s)
- Oliver W Hassall
- Centre for Geographic Medicine Research, Kenya Medical Research Institute, Kenya.
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Aiken AM, Mturi N, Njuguna P, Mohammed S, Berkley JA, Mwangi I, Mwarumba S, Kitsao BS, Lowe BS, Morpeth SC, Hall AJ, Khandawalla I, Scott JAG. Risk and causes of paediatric hospital-acquired bacteraemia in Kilifi District Hospital, Kenya: a prospective cohort study. Lancet 2011; 378:2021-2027. [PMID: 22133536 PMCID: PMC3242162 DOI: 10.1016/s0140-6736(11)61622-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND In sub-Saharan Africa, community-acquired bacteraemia is an important cause of illness and death in children. Our aim was to establish the magnitude and causes of hospital-acquired (nosocomial) bacteraemia in African children. METHODS We reviewed prospectively collected surveillance data of 33,188 admissions to Kilifi District Hospital, Kenya, between April 16, 2002, and Sept 30, 2009. We defined bacteraemia as nosocomial if it occurred 48 h or more after admission. We estimated the per-admission risk, daily rate, effect on mortality, and microbial cause of nosocomial bacteraemia and analysed risk factors by multivariable Cox regression. The effect on morbidity was measured as the increase in hospital stay by comparison with time-matched patients without bacteraemia. FINDINGS The overall risk of nosocomial bacteraemia during this period was 5·9/1000 admissions (95% CI 5·2-6·9) but we recorded an underlying rise in risk of 27% per year. The incidence was 1·0/1000 days in hospital (0·87-1·14), which is about 40 times higher than that of community-acquired bacteraemia in the same region. Mortality in patients with nosocomial bacteraemia was 53%, compared with 24% in community-acquired bacteraemia and 6% in patients without bacteraemia. In survivors, nosocomial bacteraemia lengthened hospital stay by 10·1 days (3·0-17·2). Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Acinetobacter spp, group D streptococci, and Pseudomonas aeruginosa accounted for three-quarters of nosocomial infections. Nosocomial bacteraemia was significantly associated with severe malnutrition (hazard ratio 2·52, 95% CI 1·79-3·57) and blood transfusion in children without severe anaemia (4·99; 3·39-7·37). INTERPRETATION Our findings show that although nosocomial bacteraemia is rare, it has serious effects on morbidity and mortality, and the microbiological causes are distinct from those of community-acquired bacteraemia. Nosocomial infections are largely unrecognised or undocumented as a health risk in low-income countries, but they are likely to become public health priorities as awareness of their occurrence increases and as other prominent childhood diseases are progressively controlled. FUNDING Wellcome Trust.
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Affiliation(s)
- Alexander M Aiken
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; London School of Hygiene and Tropical Medicine, London, UK.
| | - Neema Mturi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Ministry of Medical Services, Kilifi District Hospital, Kilifi, Kenya
| | - Patricia Njuguna
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Ministry of Medical Services, Kilifi District Hospital, Kilifi, Kenya
| | - Shebe Mohammed
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Ministry of Medical Services, Kilifi District Hospital, Kilifi, Kenya
| | - James A Berkley
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK
| | - Isaiah Mwangi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Barnes S Kitsao
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Brett S Lowe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK
| | - Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK
| | - Andrew J Hall
- London School of Hygiene and Tropical Medicine, London, UK
| | - Iqbal Khandawalla
- Ministry of Medical Services, Kilifi District Hospital, Kilifi, Kenya
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya; Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK
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Scott JAG, Berkley JA, Mwangi I, Ochola L, Uyoga S, Macharia A, Ndila C, Lowe BS, Mwarumba S, Bauni E, Marsh K, Williams TN. Relation between falciparum malaria and bacteraemia in Kenyan children: a population-based, case-control study and a longitudinal study. Lancet 2011; 378:1316-23. [PMID: 21903251 PMCID: PMC3192903 DOI: 10.1016/s0140-6736(11)60888-x] [Citation(s) in RCA: 231] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Many investigators have suggested that malaria infection predisposes individuals to bacteraemia. We tested this hypothesis with mendelian randomisation studies of children with the malaria-protective phenotype of sickle-cell trait (HbAS). METHODS This study was done in a defined area around Kilifi District Hospital, Kilifi, Kenya. We did a matched case-control study to identify risk factors for invasive bacterial disease, in which cases were children aged 3 months to 13 years who were admitted to hospital with bacteraemia between Sept 16, 1999, and July 31, 2002. We aimed to match two controls, by age, sex, location, and time of recruitment, for every case. We then did a longitudinal case-control study to assess the relation between HbAS and invasive bacterial disease as malaria incidence decreased. Cases were children aged 0-13 years who were admitted to hospital with bacteraemia between Jan 1, 1999, and Dec 31, 2007. Controls were born in the study area between Jan 1, 2006, and June 23, 2009. Finally, we modelled the annual incidence of bacteraemia against the community prevalence of malaria during 9 years with Poisson regression. RESULTS In the matched case-control study, we recruited 292 cases-we recruited two controls for 236, and one for the remaining 56. Sickle-cell disease, HIV, leucocyte haemozoin pigment, and undernutrition were positively associated with bacteraemia and HbAS was strongly negatively associated with bacteraemia (odds ratio 0·36; 95% CI 0·20-0·65). In the longitudinal case-control study, we assessed data from 1454 cases and 10,749 controls. During the study period, the incidence of admission to hospital with malaria per 1000 child-years decreased from 28·5 to 3·45, with a reduction in protection afforded by HbAS against bacteraemia occurring in parallel (p=0·0008). The incidence of hospital admissions for bacteraemia per 1000 child-years also decreased from 2·59 to 1·45. The bacteraemia incidence rate ratio associated with malaria parasitaemia was 6·69 (95% CI 1·31-34·3) and, at a community parasite prevalence of 29% in 1999, 62% (8·2-91) of bacteraemia cases were attributable to malaria. INTERPRETATION Malaria infection strongly predisposes individuals to bacteraemia and can account for more than half of all cases of bacteraemia in malaria-endemic areas. Interventions to control malaria will have a major additional benefit by reducing the burden of invasive bacterial disease. FUNDING Wellcome Trust.
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Affiliation(s)
- J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- INDEPTH Network, Accra, Ghana
- Correspondence to: Dr Anthony Scott, KEMRI-Wellcome Trust Programme, Centre for Geographic Medicine Research-Coast, P O Box 230, Kilifi, Kenya
| | - James A Berkley
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Isaiah Mwangi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Lucy Ochola
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Sophie Uyoga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Alexander Macharia
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Carolyne Ndila
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Brett S Lowe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Salim Mwarumba
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Evasius Bauni
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kevin Marsh
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Thomas N Williams
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- INDEPTH Network, Accra, Ghana
- Department of Paediatrics, University of Oxford, Oxford, UK
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Duncan S, Thiong'o AN, Macharia M, Wamuyu L, Mwarumba S, Mvera B, Smith AD, Morpeth S, Graham SM, Sanders EJ. High prevalence of quinolone resistance in Neisseria gonorrhoeae in coastal Kenya. Sex Transm Infect 2011; 87:231. [PMID: 21307154 DOI: 10.1136/sti.2010.048777] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Williams TN, Uyoga S, Macharia A, Ndila C, McAuley CF, Opi DH, Mwarumba S, Makani J, Komba A, Ndiritu MN, Sharif SK, Marsh K, Berkley JA, Scott JAG. Bacteraemia in Kenyan children with sickle-cell anaemia: a retrospective cohort and case-control study. Lancet 2009; 374:1364-70. [PMID: 19747721 PMCID: PMC2768782 DOI: 10.1016/s0140-6736(09)61374-x] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND In sub-Saharan Africa, more than 90% of children with sickle-cell anaemia die before the diagnosis can be made. The causes of death are poorly documented, but bacterial sepsis is probably important. We examined the risk of invasive bacterial diseases in children with sickle-cell anaemia. METHODS This study was undertaken in a rural area on the coast of Kenya, with a case-control approach. We undertook blood cultures on all children younger than 14 years who were admitted from within a defined study area to Kilifi District Hospital between Aug 1, 1998, and March 31, 2008; those with bacteraemia were defined as cases. We used two sets of controls: children recruited by random sampling in the same area into several studies undertaken between Sept 1, 1998, and Nov 30, 2005; and those born consecutively within the area between May 1, 2006, and April 30, 2008. Cases and controls were tested for sickle-cell anaemia retrospectively. FINDINGS We detected 2157 episodes of bacteraemia in 38 441 admissions (6%). 1749 of these children with bacteraemia (81%) were typed for sickle-cell anaemia, of whom 108 (6%) were positive as were 89 of 13 492 controls (1%). The organisms most commonly isolated from children with sickle-cell anaemia were Streptococcus pneumoniae (44/108 isolates; 41%), non-typhi Salmonella species (19/108; 18%), Haemophilus influenzae type b (13/108; 12%), Acinetobacter species (seven of 108; 7%), and Escherichia coli (seven of 108; 7%). The age-adjusted odds ratio for bacteraemia in children with sickle-cell anaemia was 26.3 (95% CI 14.5-47.6), with the strongest associations for S pneumoniae (33.0, 17.4-62.8), non-typhi Salmonella species (35.5, 16.4-76.8), and H influenzae type b (28.1, 12.0-65.9). INTERPRETATION The organisms causing bacteraemia in African children with sickle-cell anaemia are the same as those in developed countries. Introduction of conjugate vaccines against S pneumoniae and H influenzae into the childhood immunisation schedules of African countries could substantially affect survival of children with sickle-cell anaemia. FUNDING Wellcome Trust, UK.
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Hassall O, Maitland K, Pole L, Mwarumba S, Denje D, Wambua K, Lowe B, Parry C, Mandaliya K, Bates I. Bacterial contamination of pediatric whole blood transfusions in a Kenyan hospital. Transfusion 2009; 49:2594-8. [PMID: 19682331 PMCID: PMC2939982 DOI: 10.1111/j.1537-2995.2009.02344.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND: Hospitalized children in sub-Saharan Africa frequently receive whole blood transfusions for severe anemia. The risk from bacterial contamination of blood for transfusion in sub-Saharan Africa is not known. This study assessed the frequency of bacterial contamination of pediatric whole blood transfusions at a referral hospital in Kenya. STUDY DESIGN AND METHODS: This was an observational study. Over the course of 1 year, bacteriologic cultures were performed on 434 of the 799 blood packs issued to children by the blood bank of Coast Provincial General Hospital, Mombasa. Clinical outcome was not assessed. RESULTS: Forty-four bacterial contaminants were isolated from 38 blood packs—an overall contamination frequency of 8.8% (95% confidence interval, 6.1%-11.4%). Sixty-four percent of the bacteria isolated were Gram-negative. Many of the isolates are usually found in the environment and the most likely source of contamination was considered to be the hospital blood bank. CONCLUSION: Bacterial contamination of whole blood may be a significant but unrecognized hazard of blood transfusion for children in sub-Saharan Africa. Further work is needed to clarify the extent of the problem and its clinical consequences. Increased awareness and adherence to basic principles of asepsis in the hospital blood bank may be important immediate interventions.
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Affiliation(s)
- Oliver Hassall
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute/Wellcome Trust Research Programme, Kilifi, Kenya
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Scott JAG, Mwarumba S, Ngetsa C, Njenga S, Lowe BS, Slack MPE, Berkley JA, Mwangi I, Maitland K, English M, Marsh K. Progressive increase in antimicrobial resistance among invasive isolates of Haemophilus influenzae obtained from children admitted to a hospital in Kilifi, Kenya, from 1994 to 2002. Antimicrob Agents Chemother 2005; 49:3021-4. [PMID: 15980390 PMCID: PMC1168672 DOI: 10.1128/aac.49.7.3021-3024.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Etest susceptibilities to amoxicillin, chloramphenicol, and trimethoprim-sulfamethoxazole of 240 invasive isolates of Haemophilus influenzae cultured from children in rural Kenya were 66%, 66%, and 38%, respectively. Resistance increased markedly over 9 years and was concentrated among serotype b isolates. In Africa, the increasing cost of treating resistant infections supports economic arguments for prevention through conjugate H. influenzae type b immunization.
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Affiliation(s)
- J Anthony G Scott
- Wellcome Trust/Kenya Medical Research Institute, Centre for Geographic Medicine Research--Coast, P.O. Box 230, Kilifi, Kenya.
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Bejon P, Mwangi I, Ngetsa C, Mwarumba S, Berkley JA, Lowe BS, Maitland K, Marsh K, English M, Scott JAG. Invasive Gram-negative bacilli are frequently resistant to standard antibiotics for children admitted to hospital in Kilifi, Kenya. J Antimicrob Chemother 2005; 56:232-5. [PMID: 15905304 DOI: 10.1093/jac/dki145] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To determine the pattern of resistance among Gram-negative bacilli causing invasive bacterial disease for the antibiotics that are already in common use in Kilifi, Kenya and for two potential alternatives, ciprofloxacin and cefotaxime. Also, to determine whether prevalence and severity of resistance was increasing over time, to identify patients who are particularly at risk of resistant infections, and to explore which factors are associated with the development of resistance in our setting. METHODS We used Etest to study antibiotic susceptibility patterns of 90 Gram-negative bacilli cultured in blood or CSF from paediatric inpatients over 8 years. RESULTS Susceptibility to amoxicillin 28%, cefotaxime 95% and ciprofloxacin 99% did not vary significantly with age. Susceptibilities for isolates from children aged less than 14 days were: chloramphenicol, 81%; trimethoprim/sulfamethoxazole, 71%; and gentamicin, 91%. From older children, susceptibilities were: chloramphenicol, 62%; trimethoprim/sulfamethoxazole, 39%; and gentamicin, 73%. Chloramphenicol susceptibility was significantly more common among non-typhi salmonellae than other species (79% versus 53%, P < 0.0005). The combination of gentamicin and chloramphenicol covered 91% of all isolates. The prevalence of resistance did not increase over time and was not more common in patients with HIV or malnutrition. Age was the only clinical feature that predicted resistance. CONCLUSIONS Gentamicin or chloramphenicol alone was suboptimal therapy for Gram-negative sepsis, although in this retrospective study, there was no association between resistance and mortality.
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Affiliation(s)
- Philip Bejon
- Wellcome Trust/Kenya Medical Research Institute (KEMRI), Centre for Geographic Medicine Research -- Coast, Kilifi, Kenya
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Abstract
AIMS To describe the clinical features and outcome of bacteraemia due to Staphylococcus aureus in children admitted to a rural Kenyan hospital. METHODS Retrospective case review of all children with a positive blood culture for S aureus admitted to Kilifi District Hospital, Kenya, between January 1996 and December 2001. RESULTS Ninety seven children (median age 17 months, range 1 day to 12 years; 46 male) with bacteraemia due to S aureus were identified, accounting for 5% of all positive blood cultures; 10 were considered to be nosocomially acquired. A focus that was clinically consistent with staphylococcal infection was identified in 52 cases; of these, 88% had multiple foci. Children with a focus were likely to be older, present later, and have a longer duration of hospital stay. Most children in this group (90%) received intravenous cloxacillin on admission in contrast to none of those without a focus. In the former group, mortality was only 6% compared to 47% among those without a focus; 10/13 neonates without an apparent staphylococcal focus died compared to none of the 11 with a focus. Eight of the 10 neonates in the former group died within 48 hours of admission, before empirical antibiotics could be changed to include cloxacillin. CONCLUSIONS Children most at risk of death associated with bacteraemia due to S aureus are least likely to have clinical features traditionally associated with this infection.
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Affiliation(s)
- S Ladhani
- Centre for Geographic Medicine Research, Coast, KEMRI, Kenya.
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English M, Ngama M, Musumba C, Wamola B, Bwika J, Mohammed S, Ahmed M, Mwarumba S, Ouma B, McHugh K, Newton C. Causes and outcome of young infant admissions to a Kenyan district hospital. Arch Dis Child 2003; 88:438-43. [PMID: 12716721 PMCID: PMC1719579 DOI: 10.1136/adc.88.5.438] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AIMS To provide a comprehensive description of young infant admissions to a first referral level health facility in Kenya. These data, currently lacking, are important given present efforts to standardise their care through the integrated management of childhood illness (IMCI) and for prioritising both health care provision and disease prevention strategies. METHODS Prospective, 18 month observational study in a Kenyan district hospital of all admissions less than 3 months of age to the paediatric ward. RESULTS A total of 1080 infants were studied. Mortality was 18% overall, though in those aged 0-7 days it was 34%. Within two months of discharge a further 5% of infants aged <60 days on admission had died. Severe infection and prematurity together accounted for 57% of inpatient deaths in those aged <60 days, while jaundice and tetanus accounted for another 27%. S pneumoniae, group B streptococcus, E coli, and Klebsiella spp. were the most common causes of invasive bacterial disease. Hypoxaemia, hypoglycaemia, and an inability to feed were each present in more than 20% of infants aged 0-7 days. Both hypoxaemia and the inability to feed were associated with inpatient death (OR 3.8 (95% CI 2.5 to 5.8) and 7.4 (95% CI 4.8 to 11.2) respectively). CONCLUSIONS Young infants contribute substantially to paediatric inpatient mortality at the first referral level, highlighting the need both for basic supportive care facilities and improved disease prevention strategies.
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Affiliation(s)
- M English
- Centre for Geographic Medicine Research-Coast, KEMRI/Wellcome Trust Research Laboratories, PO Box 230, Kilifi, Kenya.
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Oundo JO, Muli F, Kariuki S, Waiyaki PG, Iijima Y, Berkley J, Kokwaro GO, Ngetsa CJ, Mwarumba S, Torto R, Lowe B. Non-typhi salmonella in children with severe malaria. East Afr Med J 2002; 79:633-9. [PMID: 12678446 DOI: 10.4314/eamj.v79i12.8670] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To determine the association between Plasmodium falciparum malaria and non-typhi Salmonella in children. DESIGN Cross-sectional hospital based study. SETTING Kilifi District Hospital (KDH) between January 1997 and June 2001. SUBJECTS Children aged between three months to 123 months (mean age 28.28 months) and who had been admitted to the paediatric or High Dependency Research Ward (HDRW) of the KDH. METHODS A total of 19, 118 blood cultures routinely obtained for all admissions and 1,820 clinically indicated stools samples were obtained from 9,147 children admitted with malaria. The specimens were cultured and antibiotic sensitivity done using standard laboratory procedures with stringent internal and external quality control in place. RESULTS The total bacterial pathogens isolated from blood and stool were 1,395/19,118 (7.3%) and 342/1,820 (19%) respectively. Non-typhi salmonella consisted of 260/1,395 (18.6%) of the positive blood cultures and 92/324 (28.4%) of the stool cultures out of which a total of 101 NTS occurred in children with severe malaria. Out of the 9,147 malaria cases admitted, 101/9,147 (1.10%) had concomitant NTS infection. NTS with severe malaria as a proportion of all malaria admissions for the period varied between 0.8% and 1.5%. There was a significant association (p-value=0.032) between clinical outcome of death and female sex of the patient. The NTS isolates which occurred with severe malaria showed various levels of antibiotic resistance. They were resistant to ampicillin (35%), chloramphenicol (18%), gentamicin (22%), cefuroxime (29%), sulphamethoxazole-trimethoprim (39%), ciprofloxacin (3%), cefotaxime (14%), amoxycillin-clavulanic acid (26%) and tobramycin (18.0%). Multidrug resistance (MDR) was seen in 34 (33.6%) of the isolates. CONCLUSIONS NTS and severe malaria occurring together are a problem in this area and that a large number of the isolates are MDR. An elaborate case-controlled study is required to elucidate the chain of events of both NTS and malaria parasite co-existence.
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Affiliation(s)
- J O Oundo
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
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Khamala JK, Mwarumba S, Lewa P, Lowe B. Vibrio cholerae 01 strain resistant to vibriostatic compound 0/129 isolated from cholera cases in Kilifi, Kenya. East Afr Med J 2002; 79:560. [PMID: 12635766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Abstract
BACKGROUND The diagnosis of acute bacterial meningitis in children is difficult in sub-Saharan Africa, because the clinical features overlap with those of other common diseases, and laboratory facilities are inadequate in many areas. We have assessed the value of non-laboratory tests and incomplete laboratory data in diagnosing childhood acute bacterial meningitis in this setting. METHODS We prospectively studied 905 children undergoing lumbar puncture at a rural district hospital in Kenya over 1 year. We related microbiological findings and cerebrospinal-fluid (CSF) laboratory measurements to tests that would typically be available at such a hospital. FINDINGS Acute bacterial meningitis was proven in 45 children (5.0% [95% CI 3.7-6.6]) and probable in 26 (2.9% [1.9-4.2]). 21 of the 71 cases of proven or probable acute bacterial meningitis had neither neck stiffness nor turbid CSF. In eight of 45 children with proven disease the CSF leucocyte count was less than 10x10(6)/L or leucocyte counting was not possible because of blood-staining. The presence of either a leucocyte count of 50x10(6)/L or more or a CSF/blood glucose ratio of 0.10 or less detected all but two of the 45 children with proven acute bacterial meningitis; these two samples were grossly blood-stained. INTERPRETATION The diagnosis of childhood acute bacterial meningitis is likely to be missed in a third of cases at district hospitals in sub-Saharan Africa without adequate and reliable laboratory resources. CSF culture facilities are expensive and difficult to maintain, and greater gains could be achieved with facilities for accurate leucocyte counting and glucose measurement.
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Affiliation(s)
- J A Berkley
- Centre for Geographic Medicine Research (Coast), PO Box 230, Kilifi, Kenya.
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Abstract
Bacteraemia associated with severe malaria in childhood is a sporadically reported phenomenon but its incidence and clinical importance are unknown. We have reviewed clinical and laboratory data from 783 Kenyan children sequentially admitted with a primary diagnosis of severe malaria. The overall incidence of bacteraemia in children with severe malaria was 7.8% (95% CI 5.5-10.0); however, in children under 30 months of age the incidence was 12.0% (95% CI 8.3-15.7). The presence of bacteraemia was associated with a 3-fold increase in mortality (33.3% vs. 10.4%, P < 0.001). We conclude that invasive bacterial disease may contribute to the pathophysiology of the clinical syndrome of severe malaria in an important subgroup of children. We recommend that young children with severe malaria be treated with broad-spectrum antibiotics in addition to antimalarial drugs.
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Affiliation(s)
- J Berkley
- Centre for Geographic Medicine Research, Coast, Kilifi, Kenya.
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Abstract
Cerebral malaria (CM) and acute bacterial meningitis (ABM) are the two common causes of impaired consciousness in children presenting to hospital in sub-Sahara Africa. Since the clinical features of the two diseases may be very similar, treatment is often guided by the initial laboratory findings. However, no detailed studies have examined the extent to which the laboratory findings in these two diseases may overlap. We reviewed data from 555 children with impaired consciousness admitted to Kilifi District Hospital, Kenya. Strictly defined groups were established based on the malaria slide, cerebrospinal fluid (CSF) leucocyte count and the results of blood and CSF culture and CSF bacterial antigen testing. Our data suggests significant overlap in the initial CSF findings between CM and ABM. The absolute minimum proportions of children with impaired consciousness and malaria parasitaemia who also had definite bacterial meningitis were 4% of all children and 14% of children under 1 year of age. The estimated maximum proportion of all children with impaired consciousness and malaria parasitaemia in whom the diagnosis was dual or unclear was at least 13%. The finding of malaria parasites in the blood of an unconscious child in sub-Saharan Africa is not sufficient to establish a diagnosis of cerebral malaria, and acute bacterial meningitis must be actively excluded in all cases.
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Affiliation(s)
- J A Berkley
- Centre for Geographic Medicine Research, Coast, Kilifi, Kenya.
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Scott JA, Hall AJ, Hannington A, Edwards R, Mwarumba S, Lowe B, Griffiths D, Crook D, Marsh K. Serotype distribution and prevalence of resistance to benzylpenicillin in three representative populations of Streptococcus pneumoniae isolates from the coast of Kenya. Clin Infect Dis 1998; 27:1442-50. [PMID: 9868658 DOI: 10.1086/515013] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
As surveillance data from sub-Saharan Africa are few, three representative populations of Streptococcus pneumoniae isolates were examined in Kenya for serotype distribution and Etest minimum inhibitory concentrations (MICs) of benzylpenicillin: (1) 75 lung aspirate or blood culture isolates from 301 consecutive adult patients with pneumonia, (2) 112 invasive isolates from continuous pediatric inpatient surveillance over 4 years, and (3) 97 nasopharyngeal isolates from systematically selected sick children. The proportions with benzylpenicillin MICs of > or = 0.1 microgram/mL were 0.27, 0.29, and 0.47, respectively. Vaccine-related serotypes accounted for 96% of invasive isolates from children and 90% of those from human immunodeficiency virus (HIV)-seropositive adults. Serotype 1 accounted for 44% of pneumococci from HIV-seronegative patients but only 5% of those from HIV-seropositive patients (P = .0002). Of serotype 1 isolates, 98% were susceptible to benzylpenicillin, but serogroups 13, 14, 19, and 23 were strongly associated with an MIC of > or = 0.1 microgram/mL.
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Affiliation(s)
- J A Scott
- Kenya Medical Research Institute, CRC, Kilifi Research Unit, Kenya
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