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Kimemia BB, Musila L, Langat S, Odoyo E, Cinkovich S, Abuom D, Yalwala S, Khamadi S, Johnson J, Garges E, Ojwang E, Eyase F. Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics. PLoS One 2024; 19:e0296597. [PMID: 38687700 PMCID: PMC11060535 DOI: 10.1371/journal.pone.0296597] [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: 12/19/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Ticks are arachnid ectoparasites that rank second only to mosquitoes in the transmission of human diseases including bacteria responsible for anaplasmosis, ehrlichiosis, spotted fevers, and Lyme disease among other febrile illnesses. Due to the paucity of data on bacteria transmitted by ticks in Kenya, this study undertook a bacterial metagenomic-based characterization of ticks collected from Isiolo, a semi-arid pastoralist County in Eastern Kenya, and Kwale, a coastal County with a monsoon climate in the southern Kenyan border with Tanzania. A total of 2,918 ticks belonging to 3 genera and 10 species were pooled and screened in this study. Tick identification was confirmed through the sequencing of the Cytochrome C Oxidase Subunit 1 (COI) gene. Bacterial 16S rRNA gene PCR amplicons obtained from the above samples were sequenced using the MinION (Oxford Nanopore Technologies) platform. The resulting reads were demultiplexed in Porechop, followed by trimming and filtering in Trimmomatic before clustering using Qiime2-VSearch. A SILVA database pretrained naïve Bayes classifier was used to classify the Operational Taxonomic Units (OTUs) taxonomically. The bacteria of clinical interest detected in pooled tick assays were as follows: Rickettsia spp. 59.43% of pools, Coxiella burnetii 37.88%, Proteus mirabilis 5.08%, Cutibacterium acnes 6.08%, and Corynebacterium ulcerans 2.43%. These bacteria are responsible for spotted fevers, query fever (Q-fever), urinary tract infections, skin and soft tissue infections, eye infections, and diphtheria-like infections in humans, respectively. P. mirabilis, C. acnes, and C. ulcerans were detected only in Isiolo. Additionally, COI sequences allowed for the identification of Rickettsia and Coxiella species to strain levels in some of the pools. Diversity analysis revealed that the tick genera had high levels of Alpha diversity but the differences between the microbiomes of the three tick genera studied were not significant. The detection of C. acnes, commonly associated with human skin flora suggests that the ticks may have contact with humans potentially exposing them to bacterial infections. The findings in this study highlight the need for further investigation into the viability of these bacteria and the competency of ticks to transmit them. Clinicians in these high-risk areas also need to be appraised for them to include Rickettsial diseases and Q-fever as part of their differential diagnosis.
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Affiliation(s)
- Bryson Brian Kimemia
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Lillian Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
- Kenya Medical Research Institute (KEMRI), Centre for Microbiology Research, Nairobi, Kenya
| | - Solomon Langat
- Kenya Medical Research Institute (KEMRI), Centre for Virus Research, Nairobi, Kenya
| | - Erick Odoyo
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
| | - Stephanie Cinkovich
- United States Armed Forces Health Surveillance Division, Global Emerging Infections Surveillance Branch, Silver Spring, Maryland, United States of America
| | - David Abuom
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
| | - Santos Yalwala
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
| | - Samoel Khamadi
- Kenya Medical Research Institute (KEMRI), Centre for Virus Research, Nairobi, Kenya
| | - Jaree Johnson
- United States Armed Forces Pest Management Board, Silver Spring, Maryland, United States of America
| | - Eric Garges
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
| | - Elly Ojwang
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
| | - Fredrick Eyase
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa (USAMRD-A), Nairobi, Kenya
- Kenya Medical Research Institute (KEMRI), Centre for Virus Research, Nairobi, Kenya
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Langat SK, Kerich G, Cinkovich S, Johnson J, Ambale J, Yalwala S, Opot B, Garges E, Ojwang E, Eyase F. Genome sequences of Phasi Charoen-like phasivirus and Fako virus from Aedes aegypti mosquitoes collected in coastal Kenya. Microbiol Resour Announc 2023; 12:e0067823. [PMID: 37846988 PMCID: PMC10652973 DOI: 10.1128/mra.00678-23] [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] [Received: 08/13/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
We report the sequencing of two viruses, Phasi Charoen-like phasivirus (PCLV) and Fako virus (FAKV), which were detected in a pool of Aedes aegypti from Kenya. Analysis showed a high similarity of PCLV to publicly available PCLV genomes from Kenya. FAKV showed a high genetic divergence from publicly available FAKV genomes.
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Affiliation(s)
- Solomon K. Langat
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
- Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Gladys Kerich
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Stephanie Cinkovich
- Global Emerging Infections Surveillance Branch, Armed Forces Health Surveillance Division, Defense Health Agency, Silver Spring, Maryland, USA
- Cherokee Nation Strategic Programs, Tulsa, Oklahoma, USA
| | - Jaree Johnson
- Armed Forces Pest Management Board, Silver Spring, Maryland, USA
| | - Janet Ambale
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Santos Yalwala
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Benjamin Opot
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Eric Garges
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Elly Ojwang
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Fredrick Eyase
- Department of Entomology and Vector Borne Infections, United States Army Medical Research Directorate-Africa (USAMRD-A), Center for Clinical Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
- Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
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Langat SK, Eyase F, Bulimo W, Lutomiah J, Oyola SO, Imbuga M, Sang R. Profiling of RNA Viruses in Biting Midges ( Ceratopogonidae) and Related Diptera from Kenya Using Metagenomics and Metabarcoding Analysis. mSphere 2021; 6:e0055121. [PMID: 34643419 PMCID: PMC8513680 DOI: 10.1128/msphere.00551-21] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022] Open
Abstract
Vector-borne diseases (VBDs) cause enormous health burden worldwide, as they account for more than 17% of all infectious diseases and over 700,000 deaths each year. A significant number of these VBDs are caused by RNA virus pathogens. Here, we used metagenomics and metabarcoding analysis to characterize RNA viruses and their insect hosts among biting midges from Kenya. We identified a total of 15 phylogenetically distinct insect-specific viruses. These viruses fall into six families, with one virus falling in the recently proposed negevirus taxon. The six virus families include Partitiviridae, Iflaviridae, Tombusviridae, Solemoviridae, Totiviridae, and Chuviridae. In addition, we identified many insect species that were possibly associated with the identified viruses. Ceratopogonidae was the most common family of midges identified. Others included Chironomidae and Cecidomyiidae. Our findings reveal a diverse RNA virome among Kenyan midges that includes previously unknown viruses. Further, metabarcoding analysis based on COI (cytochrome c oxidase subunit 1 mitochondrial gene) barcodes reveal a diverse array of midge species among the insects used in the study. Successful application of metagenomics and metabarcoding methods to characterize RNA viruses and their insect hosts in this study highlights a possible simultaneous application of these two methods as cost-effective approaches to virus surveillance and host characterization. IMPORTANCE The majority of the viruses that currently cause diseases in humans and animals are RNA viruses, and more specifically arthropod-transmitted viruses. They cause diseases such as dengue, West Nile infection, bluetongue disease, Schmallenberg disease, and yellow fever, among others. Several sequencing investigations have shown us that a diverse array of RNA viruses among insect vectors remain unknown. Some of these could be ancient lineages that could aid in comprehensive studies on RNA virus evolution. Such studies may provide us with insights into the evolution of the currently pathogenic viruses. Here, we applied metagenomics to field-collected midges and we managed to characterize several RNA viruses, where we recovered complete and nearly complete genomes of these viruses. We also characterized the insect host species that are associated with these viruses. These results add to the currently known diversity of RNA viruses among biting midges as well as their associated insect hosts.
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Affiliation(s)
- Solomon K. Langat
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Fredrick Eyase
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate—Africa, Nairobi, Kenya
| | - Wallace Bulimo
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Joel Lutomiah
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Mabel Imbuga
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Rosemary Sang
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
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Koka H, Lutomiah J, Langat S, Koskei E, Nyunja A, Mutisya J, Mulwa F, Owaka S, Ofula V, Konongoi S, Eyase F, Sang R. Evidence of circulation of Orthobunyaviruses in diverse mosquito species in Kwale County, Kenya. Virol J 2021; 18:204. [PMID: 34641884 PMCID: PMC8507213 DOI: 10.1186/s12985-021-01670-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 05/03/2021] [Accepted: 09/16/2021] [Indexed: 12/05/2022] Open
Abstract
Background Arbovirus surveillance and recurrence of outbreaks in Kenya continues to reveal the re-emergence of viruses of public health importance. This calls for sustained efforts in early detection and characterization of these agents to avert future potential outbreaks. Methods A larval survey was carried out in three different sites in Kwale County, Vanga, Jego and Lunga Lunga. All containers in every accessible household and compound were sampled for immature mosquitoes. In addition, adult mosquitoes were also sampled using CO2-baited CDC light traps and BG-Sentinel traps in the three sites and also in Tsuini. The mosquitoes were knocked down using trimethylamine and stored in a liquid nitrogen shipper for transportation to the laboratory where they were identified to species, pooled and homogenized ready for testing. Results A total of 366 houses and 1730 containers were inspected. The House Index (HI), Container Index (CI) and Breateau Index (BI) for Vanga Island were (3%: 0.66: 3.66) respectively. In Jego, a rural site, the HI, CI and BI were (2.4%: 0.48: 2.4) respectively. In Lunga Lunga, a site in an urban area, the HI, CI and BI were (22.03%: 3.97: 29.7) respectively. The indices suggest that this region is at risk of arbovirus transmission given they were above the WHO threshold (CI > 1, HI > 1% and BI > 5). The most productive containers were the concrete tanks (44.4%), plastic tank (22.2%), claypot (13.3%), plastic drums (8.9%), plastic basins (4%), jerricans (1.2%) and buckets (0.3%). Over 20,200 adult mosquitoes were collected using CDC light traps, and over 9,200 using BG- sentinel traps. These mosquitoes were screened for viruses by inoculating in Vero cells. Eleven Orthobunyavirus isolates were obtained from pools of Ae. pembaensis (4), Ae. tricholabis (1), Cx. quinquefasciatus (3), Culex spp. (1) and Cx. zombaensis (2). Five of the Orthobunyaviruses were sequenced and four of these were determined to be Bunyamwera viruses while one isolate was found to be Nyando virus. One isolate remained unidentified. Conclusions These results indicate circulation of Orthobunyaviruses known to cause diverse grades of febrile illness with rash in humans in this region and highlights the need for continued monitoring and surveillance to avert outbreaks.
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Affiliation(s)
- Hellen Koka
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya.
| | - Joel Lutomiah
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Solomon Langat
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Edith Koskei
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Albert Nyunja
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - James Mutisya
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Francis Mulwa
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Samuel Owaka
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Victor Ofula
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Samson Konongoi
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Fredrick Eyase
- US Army Medical Research Directorate - Kenya, P. O. Box 606-00621, Nairobi, Kenya
| | - Rosemary Sang
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
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Eyase F, Langat S, Berry IM, Mulwa F, Nyunja A, Mutisya J, Owaka S, Limbaso S, Ofula V, Koka H, Koskei E, Lutomiah J, Jarman RG, Sang R. Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak. PLoS One 2020; 15:e0241754. [PMID: 33156857 PMCID: PMC7647060 DOI: 10.1371/journal.pone.0241754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Between late 2017 and mid-2018, a chikungunya fever outbreak occurred in Mombasa, Kenya that followed an earlier outbreak in mid-2016 in Mandera County on the border with Somalia. Using targeted Next Generation Sequencing, we obtained genomes from clinical samples collected during the 2017/2018 Mombasa outbreak. We compared data from the 2016 Mandera outbreak with the 2017/2018 Mombasa outbreak, and found that both had the Aedes aegypti adapting mutations, E1:K211E and E2:V264A. Further to the above two mutations, 11 of 15 CHIKV genomes from the Mombasa outbreak showed a novel triple mutation signature of E1:V80A, E1:T82I and E1:V84D. These novel mutations are estimated to have arisen in Mombasa by mid-2017 (2017.58, 95% HPD: 2017.23, 2017.84). The MRCA for the Mombasa outbreak genomes is estimated to have been present in early 2017 (2017.22, 95% HPD: 2016.68, 2017.63). Interestingly some of the earliest genomes from the Mombasa outbreak lacked the E1:V80A, E1:T82I and E1:V84D substitutions. Previous laboratory experiments have indicated that a substitution at position E1:80 in the CHIKV genome may lead to increased CHIKV transmissibility by Ae. albopictus. Genbank investigation of all available CHIKV genomes revealed that E1:V80A was not present; therefore, our data constitutes the first report of the E1:V80A mutation occurring in nature. To date, chikungunya outbreaks in the Northern and Western Hemispheres have occurred in Ae. aegypti inhabited tropical regions. Notwithstanding, it has been suggested that an Ae. albopictus adaptable ECSA or IOL strain could easily be introduced in these regions leading to a new wave of outbreaks. Our data on the recent Mombasa CHIKV outbreak has shown that a potential Ae. albopictus adapting mutation may be evolving within the East African region. It is even more worrisome that there exists potential for emergence of a CHIKV strain more adapted to efficient transmission by both Ae. albopictus and Ae.aegypti simultaneously. In view of the present data and history of chikungunya outbreaks, pandemic potential for such a strain is now a likely possibility in the future. Thus, continued surveillance of chikungunya backed by molecular epidemiologic capacity should be sustained to understand the evolving public health threat and inform prevention and control measures including the ongoing vaccine development efforts.
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Affiliation(s)
- Fredrick Eyase
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Center for Virus Research-Kenya Medical Research Institute, Nairobi, Kenya
- Institute for Biotechnology Research-Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
- * E-mail:
| | - Solomon Langat
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Irina Maljkovic Berry
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Francis Mulwa
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Albert Nyunja
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - James Mutisya
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Samuel Owaka
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Samson Limbaso
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Center for Virus Research-Kenya Medical Research Institute, Nairobi, Kenya
| | - Victor Ofula
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Hellen Koka
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Edith Koskei
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Joel Lutomiah
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Center for Virus Research-Kenya Medical Research Institute, Nairobi, Kenya
| | - Richard G. Jarman
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Rosemary Sang
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Center for Virus Research-Kenya Medical Research Institute, Nairobi, Kenya
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Kivata MW, Mbuchi M, Eyase F, Bulimo WD, Kyanya CK, Oundo V, Mbinda WM, Sang W, Andagalu B, Soge OO, McClelland RS, Distelhorst J. Plasmid mediated penicillin and tetracycline resistance among Neisseria gonorrhoeae isolates from Kenya. BMC Infect Dis 2020; 20:703. [PMID: 32977759 PMCID: PMC7517623 DOI: 10.1186/s12879-020-05398-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 09/06/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Treatment of gonorrhea is complicated by the development of antimicrobial resistance in Neisseria gonorrhoeae (GC) to the antibiotics recommended for treatment. Knowledge on types of plasmids and the antibiotic resistance genes they harbor is useful in monitoring the emergence and spread of bacterial antibiotic resistance. In Kenya, studies on gonococcal antimicrobial resistance are few and data on plasmid mediated drug resistance is limited. The present study characterizes plasmid mediated resistance in N. gonorrhoeae isolates recovered from Kenya between 2013 and 2018. METHODS DNA was extracted from 36 sub-cultured GC isolates exhibiting varying drug resistance profiles. Whole genome sequencing was done on Illumina MiSeq platform and reads assembled de-novo using CLC Genomics Workbench. Genome annotation was performed using Rapid Annotation Subsystem Technology. Comparisons in identified antimicrobial resistance determinants were done using Bioedit sequence alignment editor. RESULTS Twenty-four (66.7%) isolates had both β-lactamase (TEM) and TetM encoding plasmids. 8.3% of the isolates lacked both TEM and TetM plasmids and had intermediate to susceptible penicillin and tetracycline MICs. Twenty-six (72%) isolates harbored TEM encoding plasmids. 25 of the TEM plasmids were of African type while one was an Asian type. Of the 36 isolates, 31 (86.1%) had TetM encoding plasmids, 30 of which harbored American TetM, whereas 1 carried a Dutch TetM. All analyzed isolates had non-mosaic penA alleles. All the isolates expressing TetM were tetracycline resistant (MIC> 1 mg/L) and had increased doxycycline MICs (up to 96 mg/L). All the isolates had S10 ribosomal protein V57M amino acid substitution associated with tetracycline resistance. No relation was observed between PenB and MtrR alterations and penicillin and tetracycline MICs. CONCLUSION High-level gonococcal penicillin and tetracycline resistance in the sampled Kenyan regions was found to be mediated by plasmid borne blaTEM and tetM genes. While the African TEM plasmid, TEM1 and American TetM are the dominant genotypes, Asian TEM plasmid, a new TEM239 and Dutch TetM have emerged in the regions.
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Affiliation(s)
- Mary Wandia Kivata
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P. O Box 62,000-00200, Thika, Kenya
- Department of Biological and Physical Science, Karatina University (KarU), P. O Box 1957-10101, Karatina, Kenya
| | - Margaret Mbuchi
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
- Kenya Medical Research Institute (KEMRI), P. O Box 54840-00200, Nairobi, Kenya
| | - Fredrick Eyase
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P. O Box 62,000-00200, Thika, Kenya
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
| | - Wallace Dimbuson Bulimo
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
- School of Medicine, Department of Biochemistry, University of Nairobi, P. O Box 30197, GPO, Nairobi, 00100 Kenya
| | - Cecilia Katunge Kyanya
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
| | - Valerie Oundo
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
| | - Wilton Mwema Mbinda
- Department of Chemistry and Biochemistry, Pwani University, P. O Box 195-80108, Mombasa, Kenya
| | - Willy Sang
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
- Kenya Medical Research Institute (KEMRI), P. O Box 54840-00200, Nairobi, Kenya
| | - Ben Andagalu
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
| | - Olusegun O. Soge
- Departments of Global Health and Medicine, University of Washington, 325 9th Avenue, Box 359931, Seattle, WA 98104 USA
| | - Raymond Scott McClelland
- Departments of Medicine, Epidemiology, and Global Health, University of Washington, 325 9th Avenue, Box 359931, Seattle, WA 98104 USA
| | - John Distelhorst
- U.S. Army Medical Research Directorate-Africa, P. O Box 606, Village Market, Nairobi, 00621 Kenya
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Maljkovic Berry I, Eyase F, Pollett S, Konongoi SL, Joyce MG, Figueroa K, Ofula V, Koka H, Koskei E, Nyunja A, Mancuso JD, Jarman RG, Sang R. Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak. Am J Trop Med Hyg 2020; 100:1249-1257. [PMID: 30860010 PMCID: PMC6493958 DOI: 10.4269/ajtmh.18-0980] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 01/03/2023] Open
Abstract
In 2016, a chikungunya virus (CHIKV) outbreak was reported in Mandera, Kenya. This was the first major CHIKV outbreak in the country since the global reemergence of this virus in Kenya in 2004. We collected samples and sequenced viral genomes from this outbreak. All Kenyan genomes contained two mutations, E1:K211E and E2:V264A, recently reported to have an association with increased infectivity, dissemination, and transmission in the Aedes aegypti vector. Phylogeographic inference of temporal and spatial virus relationships showed that this variant emerged within the East, Central, and South African lineage between 2005 and 2008, most probably in India. It was also in India where the first large outbreak caused by this virus appeared, in New Delhi, 2010. More importantly, our results also showed that this variant is no longer contained to India. We found it present in several major outbreaks, including the 2016 outbreaks in Pakistan and Kenya, and the 2017 outbreak in Bangladesh. Thus, this variant may have a capability of driving large CHIKV outbreaks in different regions of the world. Our results point to the importance of continued genomic-based surveillance and prompt urgent vector competence studies to assess the level of vector susceptibility and virus transmission, and the impact this might have on this variant's epidemic potential and global spread.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Fredrick Eyase
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Samson Limbaso Konongoi
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya.,United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Michael Gordon Joyce
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland.,Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Katherine Figueroa
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Victor Ofula
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Helen Koka
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Edith Koskei
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Albert Nyunja
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - James D Mancuso
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Rosemary Sang
- United States Army Medical Research Directorate - Kenya, Nairobi, Kenya
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8
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Kyany'a C, Eyase F, Odundo E, Kipkirui E, Kipkemoi N, Kirera R, Philip C, Ndonye J, Kirui M, Ombogo A, Koech M, Bulimo W, Hulseberg CE. First report of Entamoeba moshkovskii in human stool samples from symptomatic and asymptomatic participants in Kenya. Trop Dis Travel Med Vaccines 2019; 5:23. [PMID: 31890239 PMCID: PMC6918706 DOI: 10.1186/s40794-019-0098-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/14/2019] [Indexed: 11/10/2022]
Abstract
Entamoeba moshkovskii is a member of the Entamoeba complex and a colonizer of the human gut. We used nested polymerase chain reaction (PCR) to differentiate Entamoeba species in stool samples that had previously been screened by microscopy. Forty-six samples were tested, 23 of which had previously been identified as Entamoeba complex positive by microscopy. Of the 46 specimens tested, we identified nine (19.5%) as E. moshkovskii-positive. In seven of these nine E. moshkovskii-positive samples, either E. dispar or E. histolytica (or both) were also identified, suggesting that co-infections may be common. E. moshkovskii was also detected in both symptomatic and asymptomatic participants. To the best of our knowledge, this is the first report of E. moshkovskii in Kenya.
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Affiliation(s)
- Cecilia Kyany'a
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya.,Jomo Kenyatta University of Science and Technology, P.O Box 62000-00200, Nairobi, Kenya
| | - Fredrick Eyase
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya.,Jomo Kenyatta University of Science and Technology, P.O Box 62000-00200, Nairobi, Kenya
| | - Elizabeth Odundo
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Erick Kipkirui
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Nancy Kipkemoi
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Ronald Kirera
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Cliff Philip
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Janet Ndonye
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Mary Kirui
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Abigael Ombogo
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Margaret Koech
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Wallace Bulimo
- United States Army Medical Research Directorate-Africa, P.O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Christine E Hulseberg
- 3United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland USA
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9
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Chepkorir E, Tchouassi DP, Konongoi SL, Lutomiah J, Tigoi C, Irura Z, Eyase F, Venter M, Sang R. Serological evidence of Flavivirus circulation in human populations in Northern Kenya: an assessment of disease risk 2016-2017. Virol J 2019; 16:65. [PMID: 31101058 PMCID: PMC6525424 DOI: 10.1186/s12985-019-1176-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 02/25/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
Background Yellow fever, Dengue, West Nile and Zika viruses are re-emerging mosquito-borne Flaviviruses of public health concern. However, the extent of human exposure to these viruses and associated disease burden in Kenya and Africa at large remains unknown. We assessed the seroprevalence of Yellow fever and other Flaviviruses in human populations in West Pokot and Turkana Counties of Kenya. These areas border Uganda, South Sudan and Ethiopia where recent outbreaks of Yellow fever and Dengue have been reported, with possibility of spillover to Kenya. Methodology Human serum samples collected through a cross-sectional survey in West Pokot and Turkana Counties were screened for neutralizing antibodies to Yellow fever, Dengue-2, West Nile and Zika virus using the Plaque Reduction Neutralization Test (PRNT). Seroprevalence was compared by county, site and important human demographic characteristics. Adjusted odds ratios (aOR) were estimated using Firth logistic regression model. Results Of 877 samples tested, 127 neutralized with at least one of the four flaviviruses (14.5, 95% CI 12.3–17.0%), with a higher proportion in Turkana (21.1%, n = 87/413) than in West Pokot (8.6%, n = 40/464). Zika virus seroprevalence was significantly higher in West Pokot (7.11%) than in Turkana County (0.24%; χ2P < 0.0001). A significantly higher Yellow fever virus seroprevalence was also observed in Turkana (10.7%) compared to West Pokot (1.29%; χ2 P < 0.0001). A high prevalence of West Nile virus was detected in Turkana County only (10.2%) while Dengue was only detected in one sample, from West Pokot. The odds of infection with West Nile virus was significantly higher in males than in females (aOR = 2.55, 95% CI 1.22–5.34). Similarly, the risk of Zika virus infection in West Pokot was twice higher in males than females (aOR = 2.01, 95% CI 0.91–4.41). Conclusion Evidence of neutralizing antibodies to West Nile and Zika viruses indicates that they have been circulating undetected in human populations in these areas. While the observed Yellow Fever prevalence in Turkana and West Pokot Counties may imply virus activity, we speculate that this could also be as a result of vaccination following the Yellow Fever outbreak in the Omo river valley, South Sudan and Uganda across the border. Electronic supplementary material The online version of this article (10.1186/s12985-019-1176-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Chepkorir
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya. .,Center for Viral Zoonoses, Department of Medical Virology, University of Pretoria, P. O. Box 323, Arcadia, 0007, South Africa.
| | - D P Tchouassi
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - S L Konongoi
- Center for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - J Lutomiah
- Center for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - C Tigoi
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - Z Irura
- Division of Disease Surveillance and Response, Ministry of Health, P. O. Box 20781-00202, Nairobi, Kenya
| | - F Eyase
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 606, Village Market, Nairobi, Kenya
| | - M Venter
- Center for Viral Zoonoses, Department of Medical Virology, University of Pretoria, P. O. Box 323, Arcadia, 0007, South Africa
| | - R Sang
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
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10
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Morobe JM, Nyiro JU, Brand S, Kamau E, Gicheru E, Eyase F, Otieno GP, Munywoki PK, Agoti CN, Nokes DJ. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome Open Res 2019; 3:128. [PMID: 30483602 PMCID: PMC6234744 DOI: 10.12688/wellcomeopenres.14836.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Accepted: 03/22/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections, resulting in a significant public health burden. The virus circulates as many different types (168), each generating strong homologous, but weak heterotypic, immunity. The influence of these features on transmission patterns of HRV in the community is understudied. Methods: Nasopharyngeal swabs were collected from patients with symptoms of acute respiratory infection (ARI) at nine out-patient facilities across a Health and Demographic Surveillance System between December 2015 and November 2016. HRV was diagnosed by real-time RT-PCR, and the VP4/VP2 genomic region of the positive samples sequenced. Phylogenetic analysis was used to determine the HRV types. Classification models and G-test statistic were used to investigate HRV type spatial distribution. Demographic characteristics and clinical features of ARI were also compared. Results: Of 5,744 NPS samples collected, HRV was detected in 1057 (18.4%), of which 817 (77.3%) were successfully sequenced. HRV species A, B and C were identified in 360 (44.1%), 67 (8.2%) and 390 (47.7%) samples, respectively. In total, 87 types were determined: 39, 10 and 38 occurred within species A, B and C, respectively. HRV types presented heterogeneous temporal patterns of persistence. Spatially, identical types occurred over a wide distance at similar times, but there was statistically significant evidence for clustering of types between health facilities in close proximity or linked by major road networks. Conclusion: This study records a high prevalence of HRV in out-patient presentations exhibiting high type diversity. Patterns of occurrence suggest frequent and independent community invasion of different types. Temporal differences of persistence between types may reflect variation in type-specific population immunity. Spatial patterns suggest either rapid spread or multiple invasions of the same type, but evidence of similar types amongst close health facilities, or along road systems, indicate type partitioning structured by local spread.
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Affiliation(s)
- John Mwita Morobe
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, +254, Kenya.,Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Samuel Brand
- Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Elijah Gicheru
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Fredrick Eyase
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, +254, Kenya
| | - Grieven P Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Public Health, Pwani University, Kilifi, +254, Kenya
| | - C N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Public Health, Pwani University, Kilifi, +254, Kenya
| | - D J Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK.,Public Health, Pwani University, Kilifi, +254, Kenya
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11
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Konongoi SL, Nyunja A, Ofula V, Owaka S, Koka H, Koskei E, Eyase F, Langat D, Mancuso J, Lutomiah J, Sang R. Human and entomologic investigations of chikungunya outbreak in Mandera, Northeastern Kenya, 2016. PLoS One 2018; 13:e0205058. [PMID: 30308064 PMCID: PMC6181335 DOI: 10.1371/journal.pone.0205058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/19/2018] [Indexed: 01/14/2023] Open
Abstract
Chikungunya is a reemerging vector borne pathogen associated with severe morbidity in affected populations. Lamu, along the Kenyan coast was affected by a major chikungunya outbreak in 2004. Twelve years later, we report on entomologic investigations and laboratory confirmed chikungunya cases in northeastern Kenya. Patient blood samples were received at the Kenya Medical Research Institute (KEMRI) viral hemorrhagic fever laboratory and the immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against chikungunya and dengue. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus, alphavirus and chikungunya specific primers were used to detect acute infections and representative PCR positive samples sequenced to confirm the circulating strain. Immature mosquitoes were collected from water-holding containers indoors and outdoors in the affected areas in northeastern Kenya. A total of 189 human samples were tested; 126 from Kenya and 63 from Somalia. 52.9% (100/189) tested positive for Chikungunya virus (CHIKV) by either IgM ELISA or RT-PCR. Sequence analysis of selected samples revealed that the virus was closely related to that from China (2010). 29% (55/189) of the samples, almost all from northeastern Kenya or with a history of travel to northern Kenya, tested positive for dengue IgM antibodies. Entomologic risk assessment revealed high house, container and Breteau indices of, 14.5, 41.9 and 17.1% respectively. Underground water storage tanks were the most abundant, 30.1%, of which 77.4% were infested with Aedes aegypti mosquitoes. These findings confirm the presence of active chikungunya infections in the northeastern parts of Kenya. The detection of dengue IgM antibodies concurrently with chikungunya virus circulation emphasizes on the need for improved surveillance systems and diagnostic algorithms with the capacity to capture multiple causes of arbovirus infections as these two viruses share common vectors and eco-systems. In addition sustained entomological surveillance and vector control programs targeting most productive containers are needed to monitor changes in vector densities, for early detection of the viruses and initiate vector control efforts to prevent possible outbreaks.
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Affiliation(s)
- Samson Limbaso Konongoi
- Kenya Medical Research Institute, Nairobi, Kenya
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Albert Nyunja
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Victor Ofula
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Samuel Owaka
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Hellen Koka
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Edith Koskei
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Fredrick Eyase
- United States Army Medical Research Directorate, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Daniel Langat
- Kenya Ministry of Health -Division of Disease Surveillance and Response, Nairobi, Kenya
| | - James Mancuso
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Joel Lutomiah
- Kenya Medical Research Institute, Nairobi, Kenya
- United States Army Medical Research Directorate, Nairobi, Kenya
| | - Rosemary Sang
- Kenya Medical Research Institute, Nairobi, Kenya
- United States Army Medical Research Directorate, Nairobi, Kenya
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12
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Morobe JM, Nyiro JU, Brand S, Kamau E, Gicheru E, Eyase F, Otieno GP, Munywoki PK, Agoti C, Nokes D. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome Open Res 2018; 3:128. [DOI: 10.12688/wellcomeopenres.14836.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2018] [Indexed: 01/02/2023] Open
Abstract
Background: Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections, resulting in a significant public health burden. The virus circulates as many different types (~160), each generating strong homologous, but weak heterotypic, immunity. The influence of these features on transmission patterns of HRV in the community is understudied. Methods: Nasopharyngeal swabs were collected from patients with symptoms of acute respiratory infection (ARI) at nine out-patient facilities across a Health and Demographic Surveillance System between December 2015 and November 2016. HRV was diagnosed by real-time RT-PCR, and the VP4/VP2 genomic region of the positive samples sequenced. Phylogenetic analysis was used to determine the HRV types. Classification models and G-test statistic were used to investigate HRV type spatial distribution. Demographic characteristics and clinical features of ARI were also compared. Results: Of 5,744 NPS samples collected, HRV was detected in 1057 (18.4%), of which 817 (77.3%) were successfully sequenced. HRV species A, B and C were identified in 360 (44.1%), 67 (8.2%) and 390 (47.7%) samples, respectively. In total, 87 types were determined: 39, 10 and 38 occurred within species A, B and C, respectively. HRV types presented heterogeneous temporal patterns of persistence. Spatially, identical types occurred over a wide distance at similar times, but there was statistically significant evidence for clustering of types between health facilities in close proximity or linked by major road networks. Conclusion: This study records a high prevalence of HRV in out-patient presentations exhibiting high type diversity. Patterns of occurrence suggest frequent and independent community invasion of different types. Temporal differences of persistence between types may reflect variation in type-specific population immunity. Spatial patterns suggest either rapid spread or multiple invasions of the same type, but evidence of similar types amongst close health facilities, or along road systems, indicate type partitioning structured by local spread.
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13
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Lutomiah J, Barrera R, Makio A, Mutisya J, Koka H, Owaka S, Koskei E, Nyunja A, Eyase F, Coldren R, Sang R. Dengue Outbreak in Mombasa City, Kenya, 2013-2014: Entomologic Investigations. PLoS Negl Trop Dis 2016; 10:e0004981. [PMID: 27783626 PMCID: PMC5082659 DOI: 10.1371/journal.pntd.0004981] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 08/16/2016] [Indexed: 01/26/2023] Open
Abstract
Dengue outbreaks were first reported in East Africa in the late 1970s to early 1980s including the 1982 outbreak on the Kenyan coast. In 2011, dengue outbreaks occurred in Mandera in northern Kenya and subsequently in Mombasa city along the Kenyan coast in 2013-2014. Following laboratory confirmation of dengue fever cases, an entomologic investigation was conducted to establish the mosquito species, and densities, causing the outbreak. Affected parts of the city were identified with the help of public health officials. Adult Ae. aegypti mosquitoes were collected using various tools, processed and screened for dengue virus (DENV) by cell culture and RT-PCR. All containers in every accessible house and compound within affected suburbs were inspected for immatures. A total of 2,065 Ae. aegypti adults were collected and 192 houses and 1,676 containers inspected. An overall house index of 22%, container index, 31.0% (indoor = 19; outdoor = 43) and Breteau index, 270.1, were observed, suggesting that the risk of dengue transmission was high. Overall, jerry cans were the most productive containers (18%), followed by drums (17%), buckets (16%), tires (14%) and tanks (10%). However, each site had specific most-productive container-types such as tanks (17%) in Kizingo; Drums in Nyali (30%) and Changamwe (33%), plastic basins (35%) in Nyali-B and plastic buckets (81%) in Ganjoni. We recommend that for effective control of the dengue vector in Mombasa city, all container types would be targeted. Measures would include proper covering of water storage containers and eliminating discarded containers outdoors through a public participatory environmental clean-up exercise. Providing reliable piped water to all households would minimize the need for water storage and reduce aquatic habitats. Isolation of DENV from male Ae. aegypti mosquitoes is a first observation in Kenya and provides further evidence that transovarial transmission may have a role in DENV circulation and/or maintenance in the environment.
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Affiliation(s)
- Joel Lutomiah
- Arbovirus/Viral Hemorrhagic Fever Laboratory, Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Roberto Barrera
- Entomology and Ecology Activity, Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Albina Makio
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - James Mutisya
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Hellen Koka
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Samuel Owaka
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Edith Koskei
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Albert Nyunja
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Fredrick Eyase
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Rodney Coldren
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
| | - Rosemary Sang
- Arbovirus/Viral Hemorrhagic Fever Laboratory, Center for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- United States Army Medical Research Directorate—Kenya (USAMRD-K), Nairobi, Kenya
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14
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Achieng AO, Ingasia LA, Juma DW, Cheruiyot AC, Okudo CA, Yeda RA, Cheruiyot J, Akala HM, Johnson J, Andangalu B, Eyase F, Jura WGZO, Kamau E. Reduced in vitro doxycycline susceptibility in plasmodium falciparum field isolates from Kenya is associated with PfTetQ KYNNNN sequence polymorphism. Antimicrob Agents Chemother 2014; 58:5894-9. [PMID: 25070109 PMCID: PMC4187988 DOI: 10.1128/aac.02788-13] [Citation(s) in RCA: 11] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/18/2014] [Indexed: 11/20/2022] Open
Abstract
Doxycycline is widely used for malaria prophylaxis by international travelers. However, there is limited information on doxycycline efficacy in Kenya, and genetic polymorphisms associated with reduced efficacy are not well defined. In vitro doxycycline susceptibility profiles for 96 Plasmodium falciparum field isolates from Kenya were determined. Genetic polymorphisms were assessed in P. falciparum metabolite drug transporter (Pfmdt) and P. falciparum GTPase tetQ (PftetQ) genes. Copy number variation of the gene and the number of KYNNNN amino acid motif repeats within the protein encoded by PftetQ were determined. Reduced in vitro susceptibility to doxycycline was defined by 50% inhibitory concentrations (IC50s) of ≥35,000 nM. The odds ratio (OR) of having 2 PfTetQ KYNNNN amino acid repeats in isolates with IC50s of >35,000 nM relative to those with IC50s of <35,000 nM is 15 (95% confidence interval [CI], 3.0 to 74.3; P value of <0.0002). Isolates with 1 copy of the Pfmdt gene had a median IC50 of 6,971 nM, whereas those with a Pfmdt copy number of >1 had a median IC50 of 9,912 nM (P = 0.0245). Isolates with 1 copy of PftetQ had a median IC50 of 6,370 nM, whereas isolates with a PftetQ copy number of >1 had a median IC50 of 3,422 nM (P < 0.0007). Isolates with 2 PfTetQ KYNNNN motif repeats had a median IC50 of 26,165 nM, whereas isolates with 3 PfTetQ KYNNNN repeats had a median IC50 of 3,352 nM (P = 0.0023). PfTetQ sequence polymorphism is associated with a reduced doxycycline susceptibility phenotype in Kenyan isolates and is a potential marker for susceptibility testing.
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Affiliation(s)
- Angela O Achieng
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya Department of Zoology, School of Biological and Physical Sciences, Maseno University, Maseno, Kenya
| | - Luiser A Ingasia
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Dennis W Juma
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Agnes C Cheruiyot
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya Department of Zoology, School of Biological and Physical Sciences, Maseno University, Maseno, Kenya
| | - Charles A Okudo
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Redemptah A Yeda
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Jelagat Cheruiyot
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Hoseah M Akala
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Jacob Johnson
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Ben Andangalu
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Fredrick Eyase
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
| | - Walter G Z O Jura
- Department of Zoology, School of Biological and Physical Sciences, Maseno University, Maseno, Kenya
| | - Edwin Kamau
- Department of Emerging Infectious Diseases-Global Emerging Infections Surveillance and Response System (DEID-GEIS) Program, United States Army Medical Research Unit-Kenya (USAMRU-K), Kenya Medical Research Institute (KEMRI)-Walter Reed Project, Kisumu, Kenya
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Juma BW, Wadegu M, Makio A, Kirera R, Eyase F, Awinda G, Kamanza J, Schnabel D, Wurapa EK. A Survey of Biosafety and Biosecurity Practices in the United States Army Medical Research Unit-Kenya (USAMRU-K). Appl Biosaf 2014. [DOI: 10.1177/153567601401900104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Meshack Wadegu
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
| | - Albina Makio
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
| | - Ronald Kirera
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
| | - Fredrick Eyase
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
| | - George Awinda
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
| | - John Kamanza
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
| | - David Schnabel
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
| | - Eyako K. Wurapa
- United States Army Medical Research Unit—Kenya, Nairobi, Kenya
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Ogutu BR, Onyango KO, Koskei N, Omondi EK, Ongecha JM, Otieno GA, Obonyo C, Otieno L, Eyase F, Johnson JD, Omollo R, Perkins DJ, Akhwale W, Juma E. Efficacy and safety of artemether-lumefantrine and dihydroartemisinin-piperaquine in the treatment of uncomplicated Plasmodium falciparum malaria in Kenyan children aged less than five years: results of an open-label, randomized, single-centre study. Malar J 2014; 13:33. [PMID: 24472156 PMCID: PMC3916309 DOI: 10.1186/1475-2875-13-33] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [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] [Received: 08/13/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND This open-label, randomized study evaluated efficacy and safety of artemether-lumefantrine (AL) and dihydroartemisinin-piperaquine (DP) in treatment of uncomplicated falciparum malaria in children below five years of age, to build evidence on use of AL as first-line treatment and DP as second-line treatment in Kenya. METHODS A total of 454 children aged six to 59 months with uncomplicated falciparum malaria were randomized (1:1) to receive AL dispersible or DP paediatric tablets and followed up for 42 days. Primary efficacy variable was corrected adequate clinical and parasitological response (ACPR) rate on day 28. Secondary variables included corrected (day 14, 28 and 42), uncorrected (day 3, 14, 28 and 42) cure rates, parasitological failure at days 3, 14 and 42. Acceptability and tolerability of both drugs were assessed by caregiver questionnaire. RESULTS On day 28, corrected ACPR rates for AL dispersible and DP paediatric were 97.8% (95% CI: 94.9-99.3) and 99.1% (95% CI: 96.8-99.9), respectively, in intention-to-treat population, with no significant treatment differences noted between AL dispersible and DP paediatric arms. Additionally, no significant differences were observed for PCR corrected cure rates on days 14 and ACPR on day 42 for AL dispersible (100%; 96.8%) and DP paediatric (100%; 98.7%). Similarly, for PCR uncorrected cure rates, no significant differences were seen on days 3, 14, 28, and 42 for AL dispersible (99.1%; 98.7%; 81.1%; 67.8%) and DP paediatric (100%; 100%; 87.7%; 70.5%). Parasite clearance was rapid, with approximately 90% clearance achieved in 40 hours in both treatment arms. Incidence of adverse events was related to underlying disease; malaria being reported in both treatment arms. One serious adverse event was noted in AL dispersible (0.42%) arm, not related to study drug. Adherence to treatment regimen was higher for children treated with AL dispersible (93.6%) compared to DP paediatric (85.6%). Acceptability of AL dispersible regimen was assessed as being significantly better than DP paediatric. CONCLUSIONS AL and DP were both efficacious and well tolerated, and had similar effects at day 42 on risk of recurrent malaria. No signs of Plasmodium falciparum tolerance to artemisinins were noted. TRIAL REGISTRATION PACTR201111000316370.
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Affiliation(s)
- Bernhards R Ogutu
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
- Walter Reed Project/Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Kevin O Onyango
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Nelly Koskei
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Edgar K Omondi
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - John M Ongecha
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Godfrey A Otieno
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
- Walter Reed Project/Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Charles Obonyo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Lucas Otieno
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
- Walter Reed Project/Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Fredrick Eyase
- Walter Reed Project/Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jacob D Johnson
- Walter Reed Project/Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Raymond Omollo
- Drugs for Neglected Disease Initiative, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Willis Akhwale
- Department of Disease Control and Prevention, Ministry of Public Health and Sanitation, Nairobi, Kenya
| | - Elizabeth Juma
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
- Division of Malaria Control, Ministry of Public Health and Sanitation, Nairobi, Kenya
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Walsh DS, Meyers WM, Odindo A, Bulimo WD, Schnabel DC, Waitumbi JN, Onyango D, Portaels F, Otieno W, Eyase F. Clinical and Molecular Evidence for a Case of Buruli Ulcer (Mycobacterium ulcerans Infection) in Kenya. Am J Trop Med Hyg 2009; 81:1110-3. [DOI: 10.4269/ajtmh.2009.09-0313] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Mbaisi A, Liyala P, Eyase F, Achilla R, Akala H, Wangui J, Mwangi J, Osuna F, Alam U, Smoak BL, Davis JM, Kyle DE, Coldren RL, Mason C, Waters NC. Drug susceptibility and genetic evaluation of Plasmodium falciparum isolates obtained in four distinct geographical regions of Kenya. Antimicrob Agents Chemother 2004; 48:3598-601. [PMID: 15328137 PMCID: PMC514731 DOI: 10.1128/aac.48.9.3598-3601.2004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The drug resistance profiles of Plasmodium falciparum isolated from four regions in Kenya were analyzed for drug resistance profiles. We observed variability in resistance to a broad range of antimalarial drugs across Kenya as determined from in vitro drug susceptibility screening and genotyping analysis.
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