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Roberts AJ, Ong HB, Clare S, Brandt C, Harcourt K, Takele Y, Ghosh P, Toepp A, Waugh M, Matano D, Färnert A, Adams E, Moreno J, Mbuchi M, Petersen C, Mondal D, Kropf P, Wright GJ. A panel of recombinant Leishmania donovani cell surface and secreted proteins identifies LdBPK_323600.1 as a serological marker of symptomatic infection. mBio 2024:e0085924. [PMID: 38639536 DOI: 10.1128/mbio.00859-24] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Visceral leishmaniasis is a deadly infectious disease and is one of the world's major neglected health problems. Because the symptoms of infection are similar to other endemic diseases, accurate diagnosis is crucial for appropriate treatment. Definitive diagnosis using splenic or bone marrow aspirates is highly invasive, and so, serological assays are preferred, including the direct agglutination test (DAT) or rK39 strip test. These tests, however, are either difficult to perform in the field (DAT) or lack specificity in some endemic regions (rK39), making the development of new tests a research priority. The availability of Leishmania spp. genomes presents an opportunity to identify new diagnostic targets. Here, we use genome data and a mammalian protein expression system to create a panel of 93 proteins consisting of the extracellular ectodomains of the Leishmania donovani cell surface and secreted proteins. We use these panel and sera from murine experimental infection models and natural human and canine infections to identify new candidates for serological diagnosis. We observed a concordance between the most immunoreactive antigens in different host species and transmission settings. The antigen encoded by the LdBPK_323600.1 gene can diagnose Leishmania infections with high sensitivity and specificity in patient cohorts from different endemic regions including Bangladesh and Ethiopia. In longitudinal sampling of treated patients, we observed reductions in immunoreactivity to LdBPK_323600.1 suggesting it could be used to diagnose treatment success. In summary, we have identified new antigens that could contribute to improved serological diagnostic tests to help control the impact of this deadly tropical infectious disease. IMPORTANCE Visceral leishmaniasis is fatal if left untreated with patients often displaying mild and non-specific symptoms during the early stages of infection making accurate diagnosis important. Current methods for diagnosis require highly trained medical staff to perform highly invasive biopsies of the liver or bone marrow which pose risks to the patient. Less invasive molecular tests are available but can suffer from regional variations in their ability to accurately diagnose an infection. To identify new diagnostic markers of visceral leishmaniasis, we produced and tested a panel of 93 proteins identified from the genome of the parasite responsible for this disease. We found that the pattern of host antibody reactivity to these proteins was broadly consistent across naturally acquired infections in both human patients and dogs, as well as experimental rodent infections. We identified a new protein called LdBPK_323600.1 that could accurately diagnose visceral leishmaniasis infections in humans.
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Affiliation(s)
- Adam J Roberts
- Hull York Medical School, University of York, Heslington, York, United Kingdom
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Han Boon Ong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Simon Clare
- Pathogen Laboratory Support, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Cordelia Brandt
- Pathogen Laboratory Support, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Katherine Harcourt
- Pathogen Laboratory Support, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Yegnasew Takele
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Prakash Ghosh
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Angela Toepp
- College of Public Health, University of Iowa, Iowa City, USA
| | - Max Waugh
- College of Public Health, University of Iowa, Iowa City, USA
| | - Daniel Matano
- Centre for Clinical Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Anna Färnert
- Department of Medicine Solna and Center for Molecular Medicine, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Emily Adams
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Javier Moreno
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology, Instituto de Salud Carlos III, CIBER de Enfermedades Infecciosas-CIBERINFEC, Madrid, Spain
| | - Margaret Mbuchi
- Centre for Clinical Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | | | - Dinesh Mondal
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Pascale Kropf
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gavin J Wright
- Hull York Medical School, University of York, Heslington, York, United Kingdom
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology and York, Biomedical Research Institute, University of York, York, United Kingdom
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Odoyo E, Matano D, Tiria F, Georges M, Kyanya C, Wahome S, Mutai W, Musila L. Environmental contamination across multiple hospital departments with multidrug-resistant bacteria pose an elevated risk of healthcare-associated infections in Kenyan hospitals. Antimicrob Resist Infect Control 2023; 12:22. [PMID: 36978195 PMCID: PMC10053033 DOI: 10.1186/s13756-023-01227-x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Healthcare-associated infections (HAIs) are often caused by multidrug-resistant (MDR) bacteria contaminating hospital environments which can cause outbreaks as well as sporadic transmission. METHODS This study systematically sampled and utilized standard bacteriological culture methods to determine the numbers and types of MDR Enterococcus faecalis/faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli (ESKAPEE) from high-touch environments of five Kenyan hospitals; level 6 and 5 hospitals (A, B, and C), and level 4 hospitals (D and E), in 2018. Six hundred and seventeen high-touch surfaces across six hospital departments; surgical, general, maternity, newborn, outpatient and pediatric were sampled. RESULTS 78/617 (12.6%) of the sampled high-touch surfaces were contaminated with MDR ESKAPEE; A. baumannii, 23/617 (3.7%), K. pneumoniae, 22/617 (3.6%), Enterobacter species, 19/617 (3.1%), methicillin resistant S. aureus (MRSA), 5/617 (0.8%), E. coli, 5/617 (0.8%), P. aeruginosa, 2/617 (0.3%), and E. faecalis and faecium, 2/617 (0.3%). Items found in patient areas, such as beddings, newborn incubators, baby cots, and sinks were the most frequently contaminated. Level 6 and 5 hospitals, B, 21/122 (17.2%), A, 21/122 (17.2%), and C, 18/136 (13.2%), were more frequently contaminated with MDR ESKAPEE than level 4 hospitals; D, 6/101 (5.9%), and E, 8/131 (6.1%). All the sampled hospital departments were contaminated with MDR ESKAPEE, with high levels observed in newborn, surgical and maternity. All the A. baumannii, Enterobacter species, and K. pneumoniae isolates were non-susceptible to piperacillin, ceftriaxone and cefepime. 22/23 (95.6%) of the A. baumannii isolates were non-susceptible to meropenem. In addition, 5 K. pneumoniae isolates were resistant to all the antibiotics tested except for colistin. CONCLUSION The presence of MDR ESKAPEE across all the hospitals demonstrated gaps in infection prevention practices (IPCs) that should be addressed. Non-susceptibility to last-line antibiotics such as meropenem threatens the ability to treat infections.
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Affiliation(s)
- Erick Odoyo
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | - Daniel Matano
- Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Fredrick Tiria
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | - Martin Georges
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | - Cecilia Kyanya
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya
| | | | - Winnie Mutai
- Department of Medical Microbiology, Faculty of Health Sciences, University of Nairobi, P.O. Box 30197- 00100, Nairobi, Kenya
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Nairobi, Kenya.
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Muriuki CW, Ogonda LA, Kyanya C, Matano D, Masakhwe C, Odoyo E, Musila L. Phenotypic and Genotypic Characteristics of Uropathogenic Escherichia coli Isolates from Kenya. Microb Drug Resist 2021; 28:31-38. [PMID: 34297634 PMCID: PMC8792489 DOI: 10.1089/mdr.2020.0432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 11/13/2022] Open
Abstract
Introduction: Uropathogenic Escherichia coli (UPECs) are a significant cause of urinary tract infections (UTIs). In Kenya, UTIs are typically treated with β-lactam antibiotics without antibiotic susceptibility testing, which could accelerate antibiotic resistance among UPEC strains. Aim: This study determined the occurrence of UPEC producing extended-spectrum β-lactamases (ESBLs), the genes conferring resistance to β-lactams, and the phylogenetic groups associated with ESBLs in Kenyan UPECs. Methodology: Ninety-five UPEC isolates from six Kenyan hospitals were tested for ESBL and plasmid-mediated AmpC β-lactamase (pAmpC) production by combined disk diffusion and disk approximation tests, respectively. Real-time and conventional polymerase chain reactions (PCRs) were used to detect three ESBL and six pAmpC genes, respectively, and phylogenetic groups were assigned by a quadruplex PCR method. Results: Twenty-four percent UPEC isolates were ESBL producers with blaCTX-M (95.6%), blaTEM (95.6%), and blaSHV (21.7%) genes detected. Sixteen isolates had blaCTX-M/TEM, whereas five had blaTEM/CTX-M/SHV. A total of 5/23 ESBLs were cefoxitin resistant, but no AmpC genes were detected. The UPECs belonged predominantly to phylogenetic groups B2 (31/95; 32.6%) and D (30/95; 31.6%), while groups B2 and A had the most ESBL producers. Conclusions: β-Lactam antibiotics have reduced utility for treating UTIs as a quarter of UPECs were ESBL producing. Single or multiple ESBL genes were present in UPECs, belonging primarily to phylogenetic groups B2 and A.
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Affiliation(s)
- Catherine Wawira Muriuki
- Department of Biomedical Science and Technology, School of Biological and Physical Science, Maseno University, Maseno, Kenya.,Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Kenya/Kenya Medical Research Institute, Nairobi, Kenya
| | - Lilian Adhiambo Ogonda
- Department of Biomedical Science and Technology, School of Biological and Physical Science, Maseno University, Maseno, Kenya
| | - Cecilia Kyanya
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Kenya/Kenya Medical Research Institute, Nairobi, Kenya
| | - Daniel Matano
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Kenya/Kenya Medical Research Institute, Nairobi, Kenya
| | - Clement Masakhwe
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Kenya/Kenya Medical Research Institute, Nairobi, Kenya
| | - Erick Odoyo
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Kenya/Kenya Medical Research Institute, Nairobi, Kenya
| | - Lillian Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Kenya/Kenya Medical Research Institute, Nairobi, Kenya
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Odoyo E, Matano D, Georges M, Tiria F, Wahome S, Kyany’a C, Musila L. Ten Thousand-Fold Higher than Acceptable Bacterial Loads Detected in Kenyan Hospital Environments: Targeted Approaches to Reduce Contamination Levels. Int J Environ Res Public Health 2021; 18:ijerph18136810. [PMID: 34201911 PMCID: PMC8297338 DOI: 10.3390/ijerph18136810] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022]
Abstract
Microbial monitoring of hospital surfaces can help identify target areas for improved infection prevention and control (IPCs). This study aimed to determine the levels and variations in the bacterial contamination of high-touch surfaces in five Kenyan hospitals and identify the contributing modifiable risk factors. A total of 559 high-touch surfaces in four departments identified as high risk of hospital-acquired infections were sampled and examined for bacterial levels of contamination using standard bacteriological culture methods. Bacteria were detected in 536/559 (95.9%) surfaces. The median bacterial load on all sampled surfaces was 6.0 × 104 CFU/cm2 (interquartile range (IQR); 8.0 × 103–1.0 × 106). Only 55/559 (9.8%) of the sampled surfaces had acceptable bacterial loads, <5 CFU/cm². Cleaning practices, such as daily washing of patient sheets, incident rate ratio (IRR) = 0.10 [95% CI: 0.04–0.24], providing hand wash stations, IRR = 0.25 [95% CI: 0.02–0.30], having running water, IRR = 0.19 [95% CI: 0.08–0.47] and soap for handwashing IRR = 0.21 [95% CI: 0.12–0.39] each significantly lowered bacterial loads. Transporting dirty linen in a designated container, IRR = 72.11 [95% CI: 20.22–257.14], increased bacterial loads. The study hospitals can best reduce the bacterial loads by improving waste-handling protocols, cleaning high-touch surfaces five times a day and providing soap at the handwash stations.
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Affiliation(s)
- Erick Odoyo
- United States Army Medical Research Directorate-Africa, Nairobi P.O. Box 606-00621, Kenya; (E.O.); (M.G.); (F.T.); (C.K.)
| | - Daniel Matano
- Kenya Medical Research Institute, Nairobi P.O. Box 54848-00200, Kenya;
| | - Martin Georges
- United States Army Medical Research Directorate-Africa, Nairobi P.O. Box 606-00621, Kenya; (E.O.); (M.G.); (F.T.); (C.K.)
| | - Fredrick Tiria
- United States Army Medical Research Directorate-Africa, Nairobi P.O. Box 606-00621, Kenya; (E.O.); (M.G.); (F.T.); (C.K.)
| | - Samuel Wahome
- Independent Researcher, Nairobi P.O. Box 64-20300, Kenya;
| | - Cecilia Kyany’a
- United States Army Medical Research Directorate-Africa, Nairobi P.O. Box 606-00621, Kenya; (E.O.); (M.G.); (F.T.); (C.K.)
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, Nairobi P.O. Box 606-00621, Kenya; (E.O.); (M.G.); (F.T.); (C.K.)
- Correspondence:
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Kyany'a C, Nyasinga J, Matano D, Oundo V, Wacira S, Sang W, Musila L. Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya. BMC Microbiol 2019; 19:245. [PMID: 31694531 PMCID: PMC6836327 DOI: 10.1186/s12866-019-1597-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 05/27/2019] [Accepted: 09/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The increase and spread of virulent-outbreak associated, methicillin and vancomycin resistant (MRSA/VRSA) Staphylococcus aureus require a better understanding of the resistance and virulence patterns of circulating and emerging strains globally. This study sought to establish the resistance phenotype, and strains of 32 non-duplicate clinical MRSA and MSSA S. aureus isolates from four Kenyan hospitals, identify their resistance and virulence genes and determine the genetic relationships of MRSA with global strains. METHODS Antimicrobial susceptibility profiles were determined on a Vitek 2, genomic DNA sequenced on an Illumina Miseq and isolates typed in-silico. Resistance and virulence genes were identified using ARIBA and phylogenies generated using RAxML. RESULTS The MRSA isolates were 100% susceptible to vancomycin, teicoplanin, linezolid, and tigecycline. Nine distinct CC, 12 ST and 15 spa types including the novel t17826 and STs (4705, 4707) were identified with CC8 and CC152 predominating. MRSA isolates distributed across 3 CCs; CC5-ST39 (1), CC8 - ST241 (4), a novel CC8-ST4705 (1), ST8 (1) and CC152 (1). There was > 90% phenotype-genotype concordance with key resistance genes identified only among MRSA isolates: gyrA, rpoB, and parC mutations, mecA, ant (4')-lb, aph (3')-IIIa, ermA, sat-4, fusA, mphC and msrA. Kenyan MRSA isolates were genetically diverse and most closely related to Tanzanian and UK isolates. There was a significant correlation between map, hlgA, selk, selq and cap8d virulence genes and severe infections. CONCLUSION The findings showed a heterogeneous S. aureus population with novel strain types. Though limited by the low number of isolates, this study begins to fill gaps and expand our knowledge of S. aureus epidemiology while uncovering interesting patterns of distribution of strain types which should be further explored. Although last-line treatments are still effective, the potential for outbreaks of both virulent and resistant strains remain, requiring sustained surveillance of S. aureus populations.
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Affiliation(s)
- Cecilia Kyany'a
- Kenya Medical Research Institute, P. O. Box 54840-00200, Nairobi, Kenya.,The United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Justin Nyasinga
- Technical University of Kenya, P.O. Box 52428-00200, Nairobi, Kenya
| | - Daniel Matano
- Kenya Medical Research Institute, P. O. Box 54840-00200, Nairobi, Kenya.,The United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Valerie Oundo
- Kenya Medical Research Institute, P. O. Box 54840-00200, Nairobi, Kenya.,The United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Simon Wacira
- Kenya Medical Research Institute, P. O. Box 54840-00200, Nairobi, Kenya.,The United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Willie Sang
- Kenya Medical Research Institute, P. O. Box 54840-00200, Nairobi, Kenya
| | - Lillian Musila
- Kenya Medical Research Institute, P. O. Box 54840-00200, Nairobi, Kenya. .,The United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya.
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Nyasinga J, Kyany'a C, Okoth R, Oundo V, Matano D, Wacira S, Sang W, Musembi S, Musila L. A six-member SNP assay on the iPlex MassARRAY platform provides a rapid and affordable alternative for typing major African Staphylococcus aureus types. Access Microbiol 2019; 1:e000018. [PMID: 32974514 PMCID: PMC7471782 DOI: 10.1099/acmi.0.000018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 11/23/2018] [Accepted: 03/03/2019] [Indexed: 11/18/2022] Open
Abstract
Purpose Data on the clonal distribution of Staphylococcus aureus in Africa are scanty, partly due to the high costs and long turnaround times imposed by conventional genotyping methods such as spa and multilocus sequence typing (MLST), which means there is a need for alternative typing approaches. This study evaluated the discriminatory power, cost of and time required for genotyping Kenyan staphylococcal isolates using iPlex MassARRAY compared to conventional methods. Methodology Fifty-four clinical S. aureus isolates from three counties were characterized using iPlex MassARRAY, spa and MLST typing methods. Ten single-nucleotide polymorphisms (SNPs) from the S. aureus MLST loci were assessed by MassARRAY. >Results The MassARRAY assay identified 14 unique SNP genotypes, while spa typing and MLST revealed 22 spa types and 21 sequence types (STs) that displayed unique regional distribution. spa type t355 (ST152) was the dominant type overall while t037/t2029 (ST 241) dominated among the methicillin-resistant S. aureus (MRSA) isolates. MassARRAY showed 83 % and 82 % accuracy against spa typing and MLST, respectively, in isolate classification. Moreover, MassARRAY identified all MRSA strains and a novel spa type. MassARRAY had a reduced turnaround time (<12 h) compared to spa typing (4 days) and MLST (20 days). The MassARRAY reagent and consumable costs per isolate were approximately $18 USD compared to spa typing ($30 USD) and MLST ($126 USD). Conclusion This study demonstrated that iPlex MassARRAY can be adapted as a useful surveillance tool to provide a faster, more affordable and fairly accurate method for genotyping African S. aureus isolates to identify clinically significant genotypes, MRSA strains and emerging strain types.
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Affiliation(s)
- Justin Nyasinga
- Kenyatta University, Nairobi, Kenya.,Technical University of Kenya, Nairobi, Kenya
| | - Cecilia Kyany'a
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Raphael Okoth
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Valerie Oundo
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Daniel Matano
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Simon Wacira
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Willie Sang
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Lillian Musila
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
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