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Dusengemungu L, Gwanama C, Mubemba B. Data on fungal abundance and diversity in copper and cobalt contaminated tailing soils in Kitwe, Zambia. Data Brief 2024; 52:109951. [PMID: 38186741 PMCID: PMC10770708 DOI: 10.1016/j.dib.2023.109951] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
Mining activities in the Zambian Copperbelt Province have led to the release of heavy metal-containing waste, causing contamination in nearby areas. Despite this environmental challenge, limited knowledge exists regarding the mycobiota in copper mine sites. This study investigates fungal community structure in copper(Cu) and cobalt (Co) contaminated soils around decommisioned dams in Kitwe. Metagenomic analysis of the ITSF1 gene amplicons was used for the purpose. The composition of soil fungal communities was characterized, and the findings revealed significant insights. At the phylum level, Basidiomycota dominated the fungal profiles in the tailings (64.59%), followed by Ascomycota (21.30%), Glomeromycota (4.53%), and Rozellomycota (0.0275%). Several fungal genera, including Vanrija, Paraconiothyrium, Toxicladosporium, Neocosmospora, Septoglomus, and Fusarium, were more abundant in contaminated tailings soils, suggesting their potential in leaching, absorbing, and transforming heavy metals. In contrast, the reference soil at Mwekera National Forest exhibited different dominance patterns with four fungal phyla identified, with Basidiomycota and Ascomycota dominating most samples. Glomeromycota, known for forming arbuscular mycorrhizae with plants, were found in contaminated soils, while Rozellomycota, which can serve ecological roles in various ecosystems, were also present. Notable fungal species such as Aspergillus, Penicillium, Fusarium, and Oidiodendron demonstrated resilience to Cu and Co, the primary contaminants in the Copperbelt.
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Affiliation(s)
- Leonce Dusengemungu
- School of Mathematics and Natural Sciences, The Copperbelt University, Kitwe, Zambia
- The Copperbelt University, Africa Centre of Excellence for Sustainable Mining, Kitwe, Zambia
| | - Cousins Gwanama
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
| | - Benjamin Mubemba
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
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Mwale R, Mulavu M, Khumalo CS, Mukubesa A, Nalubamba K, Mubemba B, Changula K, Simulundu E, Chitanga S, Namangala B, Mataa L, Zulu VC, Munyeme M, Muleya W. Molecular detection and characterization of Anaplasma spp. in cattle and sable antelope from Lusaka and North-Western provinces of Zambia. Vet Parasitol Reg Stud Reports 2023; 39:100847. [PMID: 36878632 DOI: 10.1016/j.vprsr.2023.100847] [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: 06/22/2022] [Revised: 01/29/2023] [Accepted: 02/11/2023] [Indexed: 02/15/2023]
Abstract
Rickettsiales of the genus Anaplasma are globally distributed tick-borne pathogens of animals and humans with complex epidemiological cycles. Anaplasmosis is an important livestock disease in Zambia but its epidemiological information is inadequate. This study aimed to detect and characterize the species of Anaplasma present in domestic and wild ruminants in Zambia with a focus on the infection risk posed by the translocation of sable antelope (Hippotragus niger) from North-Western Province to Lusaka Province. Archived DNA samples (n = 100) extracted from whole blood (sable n = 47, cattle n = 53) were screened for Anaplasmataceae using 16S rRNA partial gene amplification followed by species confirmation using phylogenetic analysis. Out of the 100 samples, Anaplasma species were detected in 7% (4/57) of the cattle and 24% (10/43) of the sable antelope samples. Of the 14 positive samples, five were determined to be A. marginale (four from cattle and one from sable), seven were A. ovis (sable) and two were A. platys (sable). Phylogenetic analysis of the 16S rRNA partial gene sequences revealed genetic proximity between A. ovis and A. marginale, regardless of host. The detection of Anaplasma in wildlife in Zambia shows the risk of transmission of Anaplasma species associated with wildlife translocation.
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Affiliation(s)
- Rhodasi Mwale
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia
| | - Malala Mulavu
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, P.O Box 32379, Lusaka 10101, Zambia
| | - Cynthia Sipho Khumalo
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia
| | - Andrew Mukubesa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia
| | - King Nalubamba
- Department of Clinical Studies, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia
| | - Benjamin Mubemba
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, P.O Box 21692, Kitwe, Zambia
| | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia; Macha Research Trust, P.O. Box 630166, Choma, Zambia
| | - Simbarashe Chitanga
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, P.O Box 32379, Lusaka 10101, Zambia; Department of Preclinical Studies, School of Veterinary Medicine, Faculty of Health Sciences & Veterinary Medicine, University of Namibia, Namibia; School of Life Sciences, College of Agriculture, Engineering & Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Boniface Namangala
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Liywali Mataa
- Department of Veterinary Services, Ministry of Fisheries and Livestock, Lusaka 50060, Zambia
| | - Victor Chisha Zulu
- Department of Clinical Studies, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia
| | - Musso Munyeme
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, P.O Box 32379, Lusaka, Zambia.
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Gill CJ, Mwananyanda L, MacLeod WB, Kwenda G, Pieciak RC, Etter L, Bridges D, Chikoti C, Chirwa S, Chimoga C, Forman L, Katowa B, Lapidot R, Lungu J, Matoba J, Mwinga G, Mubemba B, Mupila Z, Muleya W, Mwenda M, Ngoma B, Nakazwe R, Nzara D, Pawlak N, Pemba L, Saasa N, Simulundu E, Yankonde B, Thea DM. What is the prevalence of COVID-19 detection by PCR among deceased individuals in Lusaka, Zambia? A postmortem surveillance study. BMJ Open 2022; 12:e066763. [PMID: 36600354 PMCID: PMC9729848 DOI: 10.1136/bmjopen-2022-066763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia. DESIGN A systematic, postmortem prevalence study. SETTING A busy, inner-city morgue in Lusaka. PARTICIPANTS We sampled a random subset of all decedents who transited the University Teaching Hospital morgue. We sampled the posterior nasopharynx of decedents using quantitative PCR. Prevalence was weighted to account for age-specific enrolment strategies. INTERVENTIONS Not applicable-this was an observational study. PRIMARY OUTCOMES Prevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time. SECONDARY OUTCOMES Shifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates. RESULTS From 1118 decedents enrolled between January and June 2021, COVID-19 was detected among 32.0% (358/1116). Roughly four COVID-19+ community deaths occurred for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only ~10% of COVID-19+ deaths were identified in life. During peak transmission periods, COVID-19 was detected in ~90% of all deaths. We observed three waves of transmission that peaked in July 2020, January 2021 and ~June 2021: the AE.1 lineage and the Beta and Delta variants, respectively. PCR signals were strongest among those whose deaths were deemed 'probably due to COVID-19', and weakest among children, with an age-dependent increase in PCR signal intensity. CONCLUSIONS COVID-19 was common among deceased individuals in Lusaka. Antemortem testing was rarely done, and almost never for community deaths. Suspicion that COVID-19 was the cause of deaths was highest for those with a respiratory syndrome and lowest for individuals <19 years.
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Affiliation(s)
- Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Lawrence Mwananyanda
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Geoffrey Kwenda
- Biomedical Sciences, University of Zambia, Ridgeway Campus, Lusaka, Lusaka, Zambia
| | - Rachel C Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Lauren Etter
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Daniel Bridges
- Program for Applied Technology in Health (PATH), Lusaka, Zambia
| | | | | | | | - Leah Forman
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Ben Katowa
- Macha Research Trust, Choma, Southern Province, Zambia
| | - Rotem Lapidot
- Pediatric Infectious Diseases, Boston Medical Center, Brookline, Massachusetts, USA
| | | | - Japhet Matoba
- Macha Research Trust, Choma, Southern Province, Zambia
| | | | - Benjamin Mubemba
- Wildlife Sciences, The Copperbelt University, Kitwe, Copperbelt, Zambia
| | | | - Walter Muleya
- Biomedical Sciences, University of Zambia School of Veterinary Medicine, Lusaka, Lusaka, Zambia
| | - Mulenga Mwenda
- Program for Applied Technology in Health, Lusaka, Zambia
| | | | - Ruth Nakazwe
- Biomedical Sciences, University of Zambia University Teaching Hospital, Lusaka, Lusaka, Zambia
| | | | - Natalie Pawlak
- Tufts University School of Medicine, Boston, Massachusetts, USA
| | | | - Ngonda Saasa
- University of Zambia School of Veterinary Medicine, Lusaka, Zambia
| | | | | | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
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4
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Dusengemungu L, Gwanama C, Simuchimba G, Mubemba B. Potential of bioaugmentation of heavy metal contaminated soils in the Zambian Copperbelt using autochthonous filamentous fungi. Front Microbiol 2022; 13:1045671. [PMID: 36532421 PMCID: PMC9752026 DOI: 10.3389/fmicb.2022.1045671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2023] Open
Abstract
There is great potential to remediate heavy metal contaminated environments through bioaugmentation with filamentous fungi. However, these fungi have been poorly investigated in most developing countries, such as Zambia. Therefore, the present study aimed at isolating indigenous filamentous fungi from heavy metal contaminated soil and to explore their potential for use in bioaugmentation. The conventional streak plate method was used to isolate fungi from heavy metal-contaminated soil. Filamentous fungal isolates were identified using morphological and molecular techniques. The radial growth diameter technique was used to evaluate heavy metal tolerance of the fungi. The most abundant and highly tolerant fungi, identified as Aspergillus transmontanensis, Cladosporium cladosporioides, and Geotrichum candidum species, were used to bioremediate heavy metal contaminated soil samples with uncontaminated soil sample being employed as a control. A maximum tolerance index (TI) between 0.7 and 11.0 was observed for A. transmontanensis, and G. candidum while C. cladosporioides displayed the TI between 0.2 and 1.2 in the presence of 1,000 ppm of Cu, Co, Fe, Mn, and Zn. The interspecific interaction was analyzed to determine the compatibility among isolates. Our results showed mutual intermingling between the three evaluated fungal species, which confirms their common influence in biomineralization of heavy metals in contaminated soils. Maximum bio-removal capacities after 90 days were 72% for Cu, 99.8% for Co, 60.6% for Fe, 82.2% for Mn, and 100% for both Pb and Zn. This study has demonstrated the potential of highly resistant autochthonous fungal isolates to remediate the heavy metal contamination problem.
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Affiliation(s)
- Leonce Dusengemungu
- School of Mathematics and Natural Sciences, The Copperbelt University, Kitwe, Zambia
- Africa Centre of Excellence for Sustainable Mining, The Copperbelt University, Kitwe, Zambia
| | - Cousins Gwanama
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
| | - Grant Simuchimba
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
| | - Benjamin Mubemba
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
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5
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Katowa B, Kalonda A, Mubemba B, Matoba J, Shempela DM, Sikalima J, Kabungo B, Changula K, Chitanga S, Kasonde M, Kapona O, Kapata N, Musonda K, Monze M, Tembo J, Bates M, Zumla A, Sutcliffe CG, Kajihara M, Yamagishi J, Takada A, Sawa H, Chilengi R, Mukonka V, Muleya W, Simulundu E. Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern. Viruses 2022; 14:v14091865. [PMID: 36146671 PMCID: PMC9504048 DOI: 10.3390/v14091865] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.
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Affiliation(s)
- Ben Katowa
- Macha Research Trust, Choma 20100, Zambia
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Benjamin Mubemba
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe 50100, Zambia
- Department of Biomedical Sciences, School of Medicine, Copperbelt University, Ndola 50100, Zambia
| | | | | | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia
| | - Boniface Kabungo
- Southern Provincial Health Office, Ministry of Health, Choma 20100, Zambia
| | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Simbarashe Chitanga
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia
- Department of Preclinical Studies, School of Veterinary Medicine, University of Namibia, Windhoek Private Bag 13301, Namibia
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Mpanga Kasonde
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Otridah Kapona
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Nathan Kapata
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Mwaka Monze
- Virology Laboratory, University Teaching Hospital, Lusaka 10101, Zambia
| | - John Tembo
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka 10101, Zambia
| | - Matthew Bates
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka 10101, Zambia
- School of Life and Environmental Sciences, University of Lincoln, Lincoln, Lincolnshire LN6 7TS, UK
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London NW3 2PF, UK
| | - Catherine G. Sutcliffe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Division of International Research Promotion, Hokkaido University International Institute for Zoonosis Control, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Global Virus Network, 725 W Lombard Street, Baltimore, MD 21201, USA
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
- Republic of Zambia State House, Lusaka 10101, Zambia
| | - Victor Mukonka
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Edgar Simulundu
- Macha Research Trust, Choma 20100, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Correspondence:
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6
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Mubemba B, Mburu MM, Changula K, Muleya W, Moonga LC, Chambaro HM, Kajihara M, Qiu Y, Orba Y, Hayashida K, Sutcliffe CG, Norris DE, Thuma PE, Ndubani P, Chitanga S, Sawa H, Takada A, Simulundu E. Current knowledge of vector-borne zoonotic pathogens in Zambia: A clarion call to scaling-up "One Health" research in the wake of emerging and re-emerging infectious diseases. PLoS Negl Trop Dis 2022; 16:e0010193. [PMID: 35120135 PMCID: PMC8849493 DOI: 10.1371/journal.pntd.0010193] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 07/06/2021] [Revised: 02/16/2022] [Accepted: 01/24/2022] [Indexed: 12/19/2022] Open
Abstract
Background Although vector-borne zoonotic diseases are a major public health threat globally, they are usually neglected, especially among resource-constrained countries, including those in sub-Saharan Africa. This scoping review examined the current knowledge and identified research gaps of vector-borne zoonotic pathogens in Zambia. Methods and findings Major scientific databases (Web of Science, PubMed, Scopus, Google Scholar, CABI, Scientific Information Database (SID)) were searched for articles describing vector-borne (mosquitoes, ticks, fleas and tsetse flies) zoonotic pathogens in Zambia. Several mosquito-borne arboviruses have been reported including Yellow fever, Ntaya, Mayaro, Dengue, Zika, West Nile, Chikungunya, Sindbis, and Rift Valley fever viruses. Flea-borne zoonotic pathogens reported include Yersinia pestis and Rickettsia felis. Trypanosoma sp. was the only tsetse fly-borne pathogen identified. Further, tick-borne zoonotic pathogens reported included Crimean-Congo Haemorrhagic fever virus, Rickettsia sp., Anaplasma sp., Ehrlichia sp., Borrelia sp., and Coxiella burnetii. Conclusions This study revealed the presence of many vector-borne zoonotic pathogens circulating in vectors and animals in Zambia. Though reports of human clinical cases were limited, several serological studies provided considerable evidence of zoonotic transmission of vector-borne pathogens in humans. However, the disease burden in humans attributable to vector-borne zoonotic infections could not be ascertained from the available reports and this precludes the formulation of national policies that could help in the control and mitigation of the impact of these diseases in Zambia. Therefore, there is an urgent need to scale-up “One Health” research in emerging and re-emerging infectious diseases to enable the country to prepare for future epidemics, including pandemics. Despite vector-borne zoonoses being a major public health threat globally, they are often overlooked, particularly among resource-constrained countries in sub-Saharan Africa, including Zambia. Therefore, we reviewed the current knowledge and identified research gaps of vector-borne zoonotic pathogens in Zambia. We focussed on mosquito-, tick-, flea- and tsetse fly-borne zoonotic pathogens reported in the country. Although we found evidence of circulation of several vector-borne zoonotic pathogens among vectors, animals and humans, clinical cases in humans were rarely reported. This suggests sparse capacity for diagnosis of vector-borne pathogens in healthcare facilities in the country and possibly limited awareness and knowledge of the local epidemiology of these infectious agents. Establishment of facility-based surveillance of vector-borne zoonoses in health facilities could provide valuable insights on morbidity, disease severity, and mortalities associated with infections as well as immune responses. In addition, there is also need for increased genomic surveillance of vector-borne pathogens in vectors and animals and humans for a better understanding of the molecular epidemiology of these diseases in Zambia. Furthermore, vector ecology studies aimed at understanding the drivers of vector abundance, pathogen host range (i.e., including the range of vectors and reservoirs), parasite-host interactions and factors influencing frequency of human-vector contacts should be prioritized. The study revealed the need for Zambia to scale-up One Health research in emerging and re-emerging infectious diseases to enable the country to be better prepared for future epidemics, including pandemics.
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Affiliation(s)
- Benjamin Mubemba
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe, Zambia
- Department of Biomedical Sciences, School of Medicine, Copperbelt University, Ndola, Zambia
| | | | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lavel C. Moonga
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Herman M. Chambaro
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Division of International Research Promotion, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kyoko Hayashida
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Catherine G. Sutcliffe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Douglas E. Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | | | | | - Simbarashe Chitanga
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Namibia, Windhoek, Namibia
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of International Research Promotion, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
- Global Virus Network, Baltimore, Maryland, United States of America
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
- * E-mail: (AT); (ES)
| | - Edgar Simulundu
- Macha Research Trust, Choma, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- * E-mail: (AT); (ES)
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7
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Hockings KJ, Mubemba B, Avanzi C, Pleh K, Düx A, Bersacola E, Bessa J, Ramon M, Metzger S, Patrono LV, Jaffe JE, Benjak A, Bonneaud C, Busso P, Couacy-Hymann E, Gado M, Gagneux S, Johnson RC, Kodio M, Lynton-Jenkins J, Morozova I, Mätz-Rensing K, Regalla A, Said AR, Schuenemann VJ, Sow SO, Spencer JS, Ulrich M, Zoubi H, Cole ST, Wittig RM, Calvignac-Spencer S, Leendertz FH. Leprosy in wild chimpanzees. Nature 2021; 598:652-656. [PMID: 34646009 PMCID: PMC8550970 DOI: 10.1038/s41586-021-03968-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 11/18/2020] [Accepted: 08/27/2021] [Indexed: 11/08/2022]
Abstract
Humans are considered as the main host for Mycobacterium leprae1, the aetiological agent of leprosy, but spillover has occurred to other mammals that are now maintenance hosts, such as nine-banded armadillos and red squirrels2,3. Although naturally acquired leprosy has also been described in captive nonhuman primates4-7, the exact origins of infection remain unclear. Here we describe leprosy-like lesions in two wild populations of western chimpanzees (Pan troglodytes verus) in Cantanhez National Park, Guinea-Bissau and Taï National Park, Côte d'Ivoire, West Africa. Longitudinal monitoring of both populations revealed the progression of disease symptoms compatible with advanced leprosy. Screening of faecal and necropsy samples confirmed the presence of M. leprae as the causative agent at each site and phylogenomic comparisons with other strains from humans and other animals show that the chimpanzee strains belong to different and rare genotypes (4N/O and 2F). These findings suggest that M. leprae may be circulating in more wild animals than suspected, either as a result of exposure to humans or other unknown environmental sources.
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Affiliation(s)
- Kimberley J Hockings
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
- Centre for Research in Anthropology (CRIA - NOVA FCSH), Lisbon, Portugal
| | - Benjamin Mubemba
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe, Zambia
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Kamilla Pleh
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Ariane Düx
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Elena Bersacola
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
- Centre for Research in Anthropology (CRIA - NOVA FCSH), Lisbon, Portugal
| | - Joana Bessa
- Centre for Research in Anthropology (CRIA - NOVA FCSH), Lisbon, Portugal
- Department of Zoology, University of Oxford, Oxford, UK
| | - Marina Ramon
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Sonja Metzger
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Livia V Patrono
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Jenny E Jaffe
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Andrej Benjak
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Camille Bonneaud
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Philippe Busso
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Emmanuel Couacy-Hymann
- Laboratoire National d'Appui au Développement Agricole/Laboratoire Central de Pathologie Animale, Bingerville, Côte d'Ivoire
| | - Moussa Gado
- Programme National de Lutte Contre la Lèpre, Ministry of Public Health, Niamey, Niger
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Roch C Johnson
- Centre Interfacultaire de Formation et de Recherche en Environnement pour le Développement Durable, University of Abomey-Calavi, Jericho, Cotonou, Benin
- Fondation Raoul Follereau, Paris, France
| | - Mamoudou Kodio
- Centre National d'Appui à la Lutte Contre la Maladie, Bamako, Mali
| | | | - Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Kerstin Mätz-Rensing
- Pathology Unit, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Aissa Regalla
- Instituto da Biodiversidade e das Áreas Protegidas, Dr. Alfredo Simão da Silva (IBAP), Bissau, Guinea-Bissau
| | - Abílio R Said
- Instituto da Biodiversidade e das Áreas Protegidas, Dr. Alfredo Simão da Silva (IBAP), Bissau, Guinea-Bissau
| | | | - Samba O Sow
- Centre National d'Appui à la Lutte Contre la Maladie, Bamako, Mali
| | - John S Spencer
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Markus Ulrich
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Hyacinthe Zoubi
- Programme National d'Elimination de la Lèpre, Dakar, Senegal
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Roman M Wittig
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Fabian H Leendertz
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.
- Helmholtz Institute for One Health, Greifswald, Germany.
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8
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Velu RM, Kwenda G, Libonda L, Chisenga CC, Flavien BN, Chilyabanyama ON, Simunyandi M, Bosomprah S, Sande NC, Changula K, Muleya W, Mburu MM, Mubemba B, Chitanga S, Tembo J, Bates M, Kapata N, Orba Y, Kajihara M, Takada A, Sawa H, Chilengi R, Simulundu E. Mosquito-Borne Viral Pathogens Detected in Zambia: A Systematic Review. Pathogens 2021; 10:pathogens10081007. [PMID: 34451471 PMCID: PMC8401848 DOI: 10.3390/pathogens10081007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/30/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Emerging and re-emerging mosquito-borne viral diseases are a threat to global health. This systematic review aimed to investigate the available evidence of mosquito-borne viral pathogens reported in Zambia. A search of literature was conducted in PubMed and Google Scholar for articles published from 1 January 1930 to 30 June 2020 using a combination of keywords. Eight mosquito-borne viruses belonging to three families, Togaviridae, Flaviviridae and Phenuiviridae were reported. Three viruses (Chikungunya virus, Mayaro virus, Mwinilunga virus) were reported among the togaviruses whilst four (dengue virus, West Nile virus, yellow fever virus, Zika virus) were among the flavivirus and only one virus, Rift Valley fever virus, was reported in the Phenuiviridae family. The majority of these mosquito-borne viruses were reported in Western and North-Western provinces. Aedes and Culex species were the main mosquito-borne viral vectors reported. Farming, fishing, movement of people and rain patterns were among factors associated with mosquito-borne viral infection in Zambia. Better diagnostic methods, such as the use of molecular tools, to detect the viruses in potential vectors, humans, and animals, including the recognition of arboviral risk zones and how the viruses circulate, are important for improved surveillance and design of effective prevention and control measures.
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Affiliation(s)
- Rachel Milomba Velu
- Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (C.C.C.); (O.N.C.); (M.S.); (S.B.); (R.C.)
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia; (N.C.S.); (A.T.); (E.S.)
- Correspondence: (R.M.V.); (H.S.)
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka P.O. Box 50110, Zambia; (G.K.); (S.C.)
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka P.O. Box 32379, Zambia
| | - Liyali Libonda
- Department of Disease Control and Prevention, School of Medicine and Health Sciences, Eden University, Lusaka P.O. Box 37727, Zambia; (L.L.); (B.N.F.)
| | - Caroline Cleopatra Chisenga
- Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (C.C.C.); (O.N.C.); (M.S.); (S.B.); (R.C.)
| | - Bumbangi Nsoni Flavien
- Department of Disease Control and Prevention, School of Medicine and Health Sciences, Eden University, Lusaka P.O. Box 37727, Zambia; (L.L.); (B.N.F.)
| | | | - Michelo Simunyandi
- Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (C.C.C.); (O.N.C.); (M.S.); (S.B.); (R.C.)
| | - Samuel Bosomprah
- Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (C.C.C.); (O.N.C.); (M.S.); (S.B.); (R.C.)
- Department of Biostatistics, School of Public Health, University of Ghana, Accra P.O. Box LG13, Ghana
| | - Nicholus Chintu Sande
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia; (N.C.S.); (A.T.); (E.S.)
| | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia;
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia;
| | | | - Benjamin Mubemba
- Department of Zoology and Aquatic Sciences, School of Natural Resources, Copperbelt University, Kitwe P.O. Box 21692, Zambia;
| | - Simbarashe Chitanga
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka P.O. Box 50110, Zambia; (G.K.); (S.C.)
- School of Veterinary Medicine, University of Namibia, Windhoek Private Bag 13301, Namibia
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - John Tembo
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka Private Bag RW1X Ridgeway, Lusaka P.O. Box 10101, Zambia; (J.T.); (M.B.)
| | - Matthew Bates
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka Private Bag RW1X Ridgeway, Lusaka P.O. Box 10101, Zambia; (J.T.); (M.B.)
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK
| | - Nathan Kapata
- Zambia National Public Health Institute, Ministry of Health, Lusaka P.O. Box 30205, Zambia;
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N 20 W10, Kita-ku, Sapporo 001-0020, Japan;
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N 20 W10, Kita-ku, Sapporo 001-0020, Japan;
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia; (N.C.S.); (A.T.); (E.S.)
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka P.O. Box 32379, Zambia
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N 20 W10, Kita-ku, Sapporo 001-0020, Japan;
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia; (N.C.S.); (A.T.); (E.S.)
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka P.O. Box 32379, Zambia
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N 20 W10, Kita-ku, Sapporo 001-0020, Japan;
- Global Virus Network, 725 W Lombard St., Baltimore, MD 21201, USA
- Correspondence: (R.M.V.); (H.S.)
| | - Roma Chilengi
- Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (C.C.C.); (O.N.C.); (M.S.); (S.B.); (R.C.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka P.O. Box 32379, Zambia; (N.C.S.); (A.T.); (E.S.)
- Macha Research Trust, Choma P.O. Box 630166, Zambia;
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9
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Mubemba B, Chanove E, Mätz-Rensing K, Gogarten JF, Düx A, Merkel K, Röthemeier C, Sachse A, Rase H, Humle T, Banville G, Tchoubar M, Calvignac-Spencer S, Colin C, Leendertz FH. Yaws Disease Caused by Treponema pallidum subspecies pertenue in Wild Chimpanzee, Guinea, 2019. Emerg Infect Dis 2021; 26:1283-1286. [PMID: 32441635 PMCID: PMC7258472 DOI: 10.3201/eid2606.191713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Yaws-like lesions are widely reported in wild African great apes, yet the causative agent has not been confirmed in affected animals. We describe yaws-like lesions in a wild chimpanzee in Guinea for which we demonstrate infection with Treponema pallidum subsp. pertenue. Assessing the conservation implications of this pathogen requires further research.
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10
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Chitanga S, Chibesa K, Sichibalo K, Mubemba B, Nalubamba KS, Muleya W, Changula K, Simulundu E. Molecular Detection and Characterization of Rickettsia Species in Ixodid Ticks Collected From Cattle in Southern Zambia. Front Vet Sci 2021; 8:684487. [PMID: 34164457 PMCID: PMC8215536 DOI: 10.3389/fvets.2021.684487] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/20/2021] [Indexed: 12/24/2022] Open
Abstract
Tick-borne zoonotic pathogens are increasingly becoming important across the world. In sub-Saharan Africa, tick-borne pathogens identified include viruses, bacteria and protozoa, with Rickettsia being the most frequently reported. This study was conducted to screen and identify Rickettsia species in ticks (Family Ixodidae) infesting livestock in selected districts of southern Zambia. A total of 236 ticks from three different genera (Amblyomma, Hyalomma, and Rhipicephalus) were collected over 14 months (May 2018-July 2019) and were subsequently screened for the presence of Rickettsia pathogens based on PCR amplification targeting the outer membrane protein B (ompB). An overall Rickettsia prevalence of 18.6% (44/236) was recorded. Multi-locus sequencing and phylogenetic characterization based on the ompB, ompA, 16S rRNA and citrate synthase (gltA) genes revealed the presence of Rickettsia africae (R. africae), R. aeschlimannii-like species and unidentified Rickettsia species. While R. aeschlimannii-like species are being reported for the first time in Zambia, R. africae has been reported previously, with our results showing a wider distribution of the bacteria in the country. Our study reveals the potential risk of human infection by zoonotic Rickettsia species and highlights the need for increased awareness of these infections in Zambia's public health systems.
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Affiliation(s)
- Simbarashe Chitanga
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
- Department of Pathobiology, School of Veterinary Medicine, University of Namibia, Windhoek, Namibia
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kennedy Chibesa
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
- Centre for Infectious Diseases Research in Zambia, Lusaka, Zambia
| | - Karen Sichibalo
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Benjamin Mubemba
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe, Zambia
- Department of Biomedical Sciences, School of Medicine, Copperbelt University, Ndola, Zambia
| | - King S. Nalubamba
- Department of Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary Sciences, University of Zambia, Lusaka, Zambia
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Macha Research Trust, Choma, Zambia
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11
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Mubemba B, Gogarten JF, Schuenemann VJ, Düx A, Lang A, Nowak K, Pléh K, Reiter E, Ulrich M, Agbor A, Brazzola G, Deschner T, Dieguez P, Granjon AC, Jones S, Junker J, Wessling E, Arandjelovic M, Kuehl H, Wittig RM, Leendertz FH, Calvignac-Spencer S. Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue. Microb Genom 2020; 6:mgen000463. [PMID: 33125317 PMCID: PMC7725339 DOI: 10.1099/mgen.0.000463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/29/2019] [Accepted: 10/13/2020] [Indexed: 01/28/2023] Open
Abstract
Many non-human primate species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue, the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while T. pallidum subsp. pallidum causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other T. pallidum subspecies found in humans also occur in non-human primates and how the genomic diversity of non-human primate T. pallidum subsp. pertenue lineages is distributed across hosts and space. We observed orofacial and genital lesions in sooty mangabeys (Cercocebus atys) in Taï National Park, Côte d'Ivoire and collected swabs and biopsies from symptomatic animals. We also collected non-human primate bones from 8 species in Taï National Park and 16 species from 11 other sites across sub-Saharan Africa. Samples were screened for T. pallidum DNA using polymerase chain reactions (PCRs) and we used in-solution hybridization capture to sequence T. pallidum genomes. We generated three nearly complete T. pallidum genomes from biopsies and swabs and detected treponemal DNA in bones of six non-human primate species in five countries, allowing us to reconstruct three partial genomes. Phylogenomic analyses revealed that both orofacial and genital lesions in sooty mangabeys from Taï National Park were caused by T. pallidum subsp. pertenue. We showed that T. pallidum subsp. pertenue has infected non-human primates in Taï National Park for at least 28 years and has been present in two non-human primate species that had not been described as T. pallidum subsp. pertenue hosts in this ecosystem, western chimpanzees (Pan troglodytes verus) and western red colobus (Piliocolobus badius), complementing clinical evidence that started accumulating in Taï National Park in 2014. More broadly, simian T. pallidum subsp. pertenue strains did not form monophyletic clades based on host species or the symptoms caused, but rather clustered based on geography. Geographical clustering of T. pallidum subsp. pertenue genomes might be compatible with cross-species transmission of T. pallidum subsp. pertenue within ecosystems or environmental exposure, leading to the acquisition of closely related strains. Finally, we found no evidence for mutations that confer antimicrobial resistance.
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Affiliation(s)
- Benjamin Mubemba
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
- Department of Wildlife Sciences, Copperbelt University, Kitwe, Zambia
| | - Jan F. Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
- Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Verena J. Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
| | - Alexander Lang
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
| | - Kathrin Nowak
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
| | - Kamilla Pléh
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jessica Junker
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Erin Wessling
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar Kuehl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Leipzig, Germany
| | - Roman M. Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fabian H. Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institut, Berlin, Germany
- Viral Evolution, Robert Koch Institute, Berlin, Germany
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12
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Simulundu E, Mupeta F, Chanda-Kapata P, Saasa N, Changula K, Muleya W, Chitanga S, Mwanza M, Simusika P, Chambaro H, Mubemba B, Kajihara M, Chanda D, Mulenga L, Fwoloshi S, Shibemba AL, Kapaya F, Zulu P, Musonda K, Monze M, Sinyange N, Mazaba ML, Kapin'a M, Chipimo PJ, Hamoonga R, Simwaba D, Ngosa W, Morales AN, Kayeyi N, Tembo J, Bates M, Orba Y, Sawa H, Takada A, Nalubamba KS, Malama K, Mukonka V, Zumla A, Kapata N. First COVID-19 case in Zambia - Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries. Int J Infect Dis 2020; 102:455-459. [PMID: 33035675 PMCID: PMC7537667 DOI: 10.1016/j.ijid.2020.09.1480] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 09/14/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/19/2022] Open
Abstract
Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 h of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient’s SARS-CoV-2 strain showed that it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa.
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Affiliation(s)
- Edgar Simulundu
- Macha Research Trust, Choma, Zambia; University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.
| | | | | | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.
| | - Katendi Changula
- University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.
| | - Walter Muleya
- University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.
| | - Simbarashe Chitanga
- University of Zambia, School of Health Sciences, Lusaka, Zambia; Hokkaido University, Research Centre for Zoonosis Control, Sapporo, Japan.
| | | | | | - Herman Chambaro
- Hokkaido University, Research Centre for Zoonosis Control, Sapporo, Japan.
| | - Benjamin Mubemba
- Copperbelt University, School of Natural Resources, Kitwe, Zambia.
| | - Masahiro Kajihara
- Hokkaido University, Research Centre for Zoonosis Control, Sapporo, Japan.
| | | | | | | | | | - Fred Kapaya
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Paul Zulu
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | | | - Nyambe Sinyange
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Mazyanga L Mazaba
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Muzala Kapin'a
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Peter J Chipimo
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Raymond Hamoonga
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Davie Simwaba
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - William Ngosa
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Albertina N Morales
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - Nkomba Kayeyi
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
| | - John Tembo
- HerpeZ and UNZA-UCLMS Project, University Teaching Hospital, Lusaka, Zambia.
| | - Mathew Bates
- HerpeZ and UNZA-UCLMS Project, University Teaching Hospital, Lusaka, Zambia.
| | - Yasuko Orba
- Hokkaido University, Research Centre for Zoonosis Control, Sapporo, Japan.
| | - Hirofumi Sawa
- University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.
| | - Ayato Takada
- University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.
| | - King S Nalubamba
- University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.
| | | | - Victor Mukonka
- Division of Infection and Immunity, CCM, University College London, London, United Kingdom.
| | - Alimuddin Zumla
- Division of Infection and Immunity, CCM, University College London, London, United Kingdom; University College London Hospitals NHS Foundation Trust NIHR Biomedical Research Centre, London, United Kingdom.
| | - Nathan Kapata
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia.
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13
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Gogarten JF, Düx A, Mubemba B, Pléh K, Hoffmann C, Mielke A, Müller-Tiburtius J, Sachse A, Wittig RM, Calvignac-Spencer S, Leendertz FH. Tropical rainforest flies carrying pathogens form stable associations with social nonhuman primates. Mol Ecol 2019; 28:4242-4258. [PMID: 31177585 DOI: 10.1111/mec.15145] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/28/2019] [Indexed: 11/27/2022]
Abstract
Living in groups provides benefits but also incurs costs such as attracting disease vectors. For example, synanthropic flies associate with human settlements, and higher fly densities increase pathogen transmission. We investigated whether such associations also exist in highly mobile nonhuman primate (NHP) Groups. We studied flies in a group of wild sooty mangabeys (Cercocebus atys atys) and three communities of wild chimpanzees (Pan troglodytes verus) in Taï National Park, Côte d'Ivoire. We observed markedly higher fly densities within both mangabey and chimpanzee groups. Using a mark-recapture experiment, we showed that flies stayed with the sooty mangabey group for up to 12 days and for up to 1.3 km. We also tested mangabey-associated flies for pathogens infecting mangabeys in this ecosystem, Bacillus cereus biovar anthracis (Bcbva), causing sylvatic anthrax, and Treponema pallidum pertenue, causing yaws. Flies contained treponemal (6/103) and Bcbva (7/103) DNA. We cultured Bcbva from all PCR-positive flies, confirming bacterial viability and suggesting that this bacterium might be transmitted and disseminated by flies. Whole genome sequences of Bcbva isolates revealed a diversity of Bcbva, probably derived from several sources. We conclude that flies actively track mangabeys and carry infectious bacterial pathogens; these associations represent an understudied cost of sociality and potentially expose many social animals to a diversity of pathogens.
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Affiliation(s)
- Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Biology, McGill University, Montreal, QC, Canada.,Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.,Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Benjamin Mubemba
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Department of Wildlife Sciences, Copperbelt University, Kitwe, Zambia
| | - Kamilla Pléh
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Constanze Hoffmann
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Alexander Mielke
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Andreas Sachse
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Roman M Wittig
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
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14
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Abstract
In early 2014, abortions and death of ruminants were reported on farms in Maputo and Gaza Provinces, Mozambique. Serologic analysis and quantitative and conventional reverse transcription PCR confirmed the presence of Rift Valley fever virus. The viruses belonged to lineage C, which is prevalent among Rift Valley fever viruses in southern Africa.
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15
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Abstract
Translocation is one of the fundamental tools in wildlife management but only if appropriately undertaken. In 2009, 30 black lechwe antelopes were suddenly translocated from the State House Habitat (STH) into the newly established Lusaka National Park (LNP). However, within 4 months of being translocated to LNP, 28 black lechwes (93%) died. A pathological report produced by veterinarians following a postmortem examination suggested no disease incidence affected the antelopes. The food quality of LNP was tested and compared to that in the STH and the antelopes' native habitat of the Bangweulu wetlands (BGW) to establish if variations in food quality were responsible for the antelopes' mortality. The findings suggest that the food quality in LNP was greatly inferior to that in STH, which could explain the observed high mortality of the antelopes in LNP. Further, the quality of food in LNP did not widely differ from that in the BGW, suggesting that the antelopes might not have survived had they been translocated to their native habitat, as they had already adapted to feeding on highly nutritious supplementary feed at the STH.
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Affiliation(s)
| | - Lackson Chama
- b Department of Zoology and Aquatic Sciences , School of Natural Resources, Copperbelt University , Riverside , Kitwe , Zambia
| | - Stanford Siachoono
- b Department of Zoology and Aquatic Sciences , School of Natural Resources, Copperbelt University , Riverside , Kitwe , Zambia
| | - Benjamin Mubemba
- b Department of Zoology and Aquatic Sciences , School of Natural Resources, Copperbelt University , Riverside , Kitwe , Zambia
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16
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Mubemba B, Thompson P, Odendaal L, Coetzee P, Venter E. Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis. J Virol Methods 2017; 243:10-14. [DOI: 10.1016/j.jviromet.2017.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
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17
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Fafetine JM, Coetzee P, Mubemba B, Nhambirre O, Neves L, Coetzer J, Venter EH. Rift Valley Fever Outbreak in Livestock, Mozambique, 2014. Emerg Infect Dis 2016. [DOI: 10.3201/eid2212/160310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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