Development of nine microsatellite loci for Trypanosoma lewisi, a potential human pathogen in Western Africa and South-East Asia, and preliminary population genetics analyses

10.24072/pcjournal.188 - Peer Community Journal, Volume 2 (2022), article no. e69.

Get full text PDF Peer reviewed and recommended by PCI

Trypanosoma lewisi belongs to the so-called atypical trypanosomes that occasionally affect humans. It shares the same hosts and flea vector of other medically relevant pathogenic agents as Yersinia pestis, the agent of plague. Increasing knowledge on the population structure (reproductive mode, population size, dispersal) of this parasite thus represents a challenging but important issue. The use of polymorphic genetic markers, together with suitable population genetics tools, is a convenient way to achieve such objectives. To date, the population biology of T. lewisi is poorly known and, to our knowledge, no population genetics studies have ever been conducted. Here, we present the development of nine microsatellite markers of this species. We investigated their polymorphism in different countries from Africa and South-East Asia from DNAs extracted from the spleen of their rodent reservoirs (essentially rat species). Several amplification problems arose, especially with South-East Asian individuals. This led to retain only those individuals with complete genotypes (most of them originating from West Africa, notably Cotonou, Benin) to ensure an optimal estimate of heterozygosity. Our results pointed towards a mainly (at least 95-99%) clonal mode of propagation, a strong subdivision at the smallest scale available (i.e., urban neighborhoods, i.e. 0.250 km²), and a generation time most probably shorter than 4 months. In future studies, more extensive sampling at smaller geographic scales (i.e., households), within a one- or two-months window and with improved amplification conditions, should lead to a more precise picture of the fine population structure of this parasite.

Published online:
DOI: 10.24072/pcjournal.188
Ségard, Adeline 1; Romero, Audrey 1; Ravel, Sophie 1; Truc, Philippe 1; Dobigny, Gauthier 2; Gauthier, Philippe 2; Etougbetche, Jonas 3; Dossou, Henri-Joel 3; Badou, Sylvestre 3; Houéménou, Gualbert 3; Morand, Serge 4, 5; Chaisiri, Kittipong 6; Noûs, Camille 7; de Meeûs, Thierry 1

1 Univ Montpellier, Cirad, IRD, Intertryp, Montpellier, France
2 CBGP, IRD, Montpellier, France
3 URIB, LARBA, EPAC, Univ. Abomey-Calavi, Cotonou, Benin
4 MIVEGEC, CNRS, IRD, Montpellier Université, Montpellier, France
5 Faculty of Veterinary, Kasetsart University, Bangkok, Thailand
6 Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
7 Cogitamus laboratory, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {S\'egard, Adeline and Romero, Audrey and Ravel, Sophie and Truc, Philippe and Dobigny, Gauthier and Gauthier, Philippe and Etougbetche, Jonas and Dossou, Henri-Joel and Badou, Sylvestre and Hou\'em\'enou, Gualbert and Morand, Serge and Chaisiri, Kittipong and No\^us, Camille and de Mee\^us, Thierry},
     title = {Development of nine microsatellite loci for {<i>Trypanosoma} lewisi</i>, a potential human pathogen in {Western} {Africa} and {South-East} {Asia,} and preliminary population genetics analyses},
     journal = {Peer Community Journal},
     eid = {e69},
     publisher = {Peer Community In},
     volume = {2},
     year = {2022},
     doi = {10.24072/pcjournal.188},
     url = {}
AU  - Ségard, Adeline
AU  - Romero, Audrey
AU  - Ravel, Sophie
AU  - Truc, Philippe
AU  - Dobigny, Gauthier
AU  - Gauthier, Philippe
AU  - Etougbetche, Jonas
AU  - Dossou, Henri-Joel
AU  - Badou, Sylvestre
AU  - Houéménou, Gualbert
AU  - Morand, Serge
AU  - Chaisiri, Kittipong
AU  - Noûs, Camille
AU  - de Meeûs, Thierry
TI  - Development of nine microsatellite loci for <i>Trypanosoma lewisi</i>, a potential human pathogen in Western Africa and South-East Asia, and preliminary population genetics analyses
JO  - Peer Community Journal
PY  - 2022
DA  - 2022///
VL  - 2
PB  - Peer Community In
UR  -
UR  -
DO  - 10.24072/pcjournal.188
ID  - 10_24072_pcjournal_188
ER  - 
%0 Journal Article
%A Ségard, Adeline
%A Romero, Audrey
%A Ravel, Sophie
%A Truc, Philippe
%A Dobigny, Gauthier
%A Gauthier, Philippe
%A Etougbetche, Jonas
%A Dossou, Henri-Joel
%A Badou, Sylvestre
%A Houéménou, Gualbert
%A Morand, Serge
%A Chaisiri, Kittipong
%A Noûs, Camille
%A de Meeûs, Thierry
%T Development of nine microsatellite loci for <i>Trypanosoma lewisi</i>, a potential human pathogen in Western Africa and South-East Asia, and preliminary population genetics analyses
%J Peer Community Journal
%D 2022
%V 2
%I Peer Community In
%R 10.24072/pcjournal.188
%F 10_24072_pcjournal_188
Ségard, Adeline; Romero, Audrey; Ravel, Sophie; Truc, Philippe; Dobigny, Gauthier; Gauthier, Philippe; Etougbetche, Jonas; Dossou, Henri-Joel; Badou, Sylvestre; Houéménou, Gualbert; Morand, Serge; Chaisiri, Kittipong; Noûs, Camille; de Meeûs, Thierry. Development of nine microsatellite loci for Trypanosoma lewisi, a potential human pathogen in Western Africa and South-East Asia, and preliminary population genetics analyses. Peer Community Journal, Volume 2 (2022), article  no. e69. doi : 10.24072/pcjournal.188.

Peer reviewed and recommended by PCI : 10.24072/pci.infections.100004

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Arnaud-Haond, S.; Alberto, F.; Teixeira, S.; Procaccini, G.; Serrão, E. A.; Duarte, C. M. Assessing genetic diversity in clonal organisms: Low diversity or low resolution? Combining power and cost efficiency in selecting markers, Journal of Heredity, Volume 96 (2005) no. 4, pp. 434-440 | DOI

[2] Arnaud-Haond, S.; Duarte, C. M.; Alberto, F.; Serrão, E. A. Standardizing methods to address clonality in population studies, Molecular Ecology, Volume 16 (2007) no. 24, pp. 5115-5139 | DOI

[3] Azad, A. F.; Radulovic, S.; Higgins, J. A.; Noden, B. H.; Troyer, J. M. Flea-borne rickettsioses: Ecologic considerations, Emerging Infectious Diseases, Volume 3 (1997) no. 3, pp. 319-327 (

[4] Balloux, F.; Lehmann, L.; De Meeûs, T. The population genetics of clonal and partially clonal diploids, Genetics, Volume 164 (2003) no. 4, pp. 1635-1644 | DOI

[5] Benjamini, Y.; Yekutieli, D. The control of the false discovery rate in multiple testing under dependency, The Annals of Statistics, Volume 29 (2001) no. 4, pp. 1165-1188 | DOI

[6] Cassan, C.; Diagne, C. A.; Tatard, C.; Gauthier, P.; Dalecky, A.; Bâ, K.; Kane, M.; Niang, Y.; Diallo, M.; Sow, A.; Brouat, C.; Bañuls, A.-L. Leishmania major and Trypanosoma lewisi infection in invasive and native rodents in Senegal, PLOS Neglected Tropical Diseases, Volume 12 (2018) no. 6 | DOI

[7] Cavalli-Sforza, L.; Edwards, A. Phylogenetic analysis: model and estimation procedures, American Journal of Human Genetics, Volume 19 (1967), pp. 233-257

[8] Chapuis, M. P.; Estoup, A. Microsatellite null alleles and estimation of population differentiation, Molecular Biology and Evolution, Volume 24 (2007) no. 3, pp. 621-631 | DOI

[9] Chau, N. V. V.; Chau, L. B.; Desquesnes, M.; Herder, S.; Lan, N. P. H.; Campbell, J. I.; Cuong, N. V.; Yimming, B.; Chalermwong, P.; Jittapalapong, S.; Franco, J. R.; Tue, N. T.; Rabaa, M. A.; Carrique-Mas, J.; Thanh, T. P. T.; Thieu, N. T. V.; Berto, A.; Hoa, N. T.; Hoang, N. V. M.; Tu, N. C.; Chuyen, N. K.; Wills, B.; Hien, T. T.; Thwaites, G. E.; Yacoub, S.; Baker, S. A clinical and epidemiological investigation of the first reported human infection with the zoonotic parasite Trypanosoma evansi in Southeast Asia, Clinical Infectious Diseases, Volume 62 (2016) no. 8, pp. 1002-1008 | DOI

[10] Coombs, J. A.; Letcher, B. H.; Nislow, K. H. create: a software to create input files from diploid genotypic data for 52 genetic software programs, Molecular Ecology Resources, Volume 8 (2008) no. 3, pp. 578-580 | DOI

[11] De Meeûs, T. Statistical decision from k test series with particular focus on population genetics tools: a DIY notice, Infection Genetics and Evolution, Volume 22 (2014), pp. 91-93 | DOI

[12] De Meeûs, T. Genetic identities and local inbreeding in pure diploid clones with homoplasic markers: SNPs may be misleading, Infection Genetics and Evolution, Volume 33 (2015), pp. 227-232 | DOI

[13] De Meeûs, T. Revisiting FIS, FST, Wahlund effects, and Null alleles, Journal of Heredity, Volume 109 (2018) no. 4, pp. 446-456 | DOI

[14] De Meeûs, T.; Chan, C. T.; Ludwig, J. M.; Tsao, J. I.; Patel, J.; Bhagatwala, J.; Beati, L. Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the U.S.A., Peer Community Journal, Volume 1 (2021), p. e40 | DOI

[15] De Meeûs, T.; Guégan, J. F.; Teriokhin, A. T. MultiTest V.1.2, a program to binomially combine independent tests and performance comparison with other related methods on proportional data, BMC Bioinformatics, Volume 10 (2009) no. 1, p. 443 | DOI

[16] De Meeûs, T.; Humair, P. F.; Grunau, C.; Delaye, C.; Renaud, F. Non-Mendelian transmission of alleles at microsatellite loci: an example in Ixodes ricinus, the vector of Lyme disease, International Journal for Parasitology, Volume 34 (2004) no. 8, pp. 943-950 | DOI

[17] De Meeûs, T.; Lehmann, L.; Balloux, F. Molecular epidemiology of clonal diploids: A quick overview and a short DIY (do it yourself) notice, Infection Genetics and Evolution, Volume 6 (2006) no. 2, pp. 163-170 | DOI

[18] De Meeûs, T.; McCoy, K. D.; Prugnolle, F.; Chevillon, C.; Durand, P.; Hurtrez-Boussès, S.; Renaud, F. Population genetics and molecular epidemiology or how to "débusquer la bête", Infection Genetics and Evolution, Volume 7 (2007) no. 2, pp. 308-332 | DOI

[19] De Meeûs, T.; Noûs, C. A simple procedure to detect, test for the presence of stuttering, and cure stuttered data with spreadsheet programs, Peer Community Journal, Volume 2 (2022), p. e52 | DOI

[20] Dobigny, G.; Gauthier, P.; Houéménou, G.; Dossou, H. J.; Badou, S.; Etougbétché, J.; Tatard, C.; Truc, P. Spatio-temporal survey of small mammal-borne Trypanosoma lewisi in Cotonou, Benin, and the potential risk of human infection, Infection Genetics and Evolution, Volume 75 (2019), p. 103967 | DOI

[21] Dobigny, G.; Poirier, P.; Hima, K.; Cabaret, O.; Gauthier, P.; Tatard, C.; Costa, J. M.; Bretagne, S. Molecular survey of rodent-borne Trypanosoma in Niger with special emphasis on T. lewisi imported by invasive black rats, Acta Tropica, Volume 117 (2011) no. 3, pp. 183-188 | DOI

[22] Doke, P. P.; Kar, A. A fatal case of Trypanosoma lewisi in Maharashtra, India, Annals of Tropical Medicine and Public Health, Volume 4 (2011) no. 2, pp. 91-95 | DOI

[23] Fox, J. The R commander: a basic statistics graphical user interface to R, Journal of Statistical Software, Volume 14 (2005) no. 9, pp. 1-42 | DOI

[24] Fox, J. Extending the R commander by "plug in" packages, R News, Volume 7 (2007) no. 3, pp. 46-52 (

[25] Goudet, J. FSTAT (Version 1.2): A computer program to calculate F-statistics, Journal of Heredity, Volume 86 (1995) no. 6, pp. 485-486 | DOI

[26] Goudet, J. Fstat (ver. 2.9.4), a program to estimate and test population genetics parameters. Updated from Goudet (1995), 2003 (

[27] Goudet, J.; Raymond, M.; de Meeüs, T.; Rousset, F. Testing Differentiation in Diploid Populations, Genetics, Volume 144 (1996) no. 4, pp. 1933-1940 | DOI

[28] Hedrick, P. W. A standardized genetic differentiation measure, Evolution, Volume 59 (2005) no. 8, pp. 1633-1638 | DOI

[29] Hoare, C. A. The Trypanosomes of Mammals. A zoological Monograph, Volume 1, Blackwell Scientific Publications, Oxford, 1972, p. 749

[30] Ibrahim, M. A. M.; Weber, J. S.; Ngomtcho, S. C. H.; Signaboubo, D.; Berger, P.; Hassane, H. M.; Kelm, S. Diversity of trypanosomes in humans and cattle in the HAT foci Mandoul and Maro, Southern Chad-A matter of concern for zoonotic potential?, Plos Neglected Tropical Diseases, Volume 15 (2021) no. 6, p. e0009323 | DOI

[31] Kaboré, J.; MacLeod, A.; Jamonneau, V.; Ilboudo, H.; Duffy, C.; Camara, M.; Camara, O.; Belem, A. M. G.; Bucheton, B.; De Meeûs, T. Population genetic structure of Guinea Trypanosoma brucei gambiense isolates according to host factors, Infection, Genetics and Evolution, Volume 11 (2011) no. 5, pp. 1129-1135 | DOI

[32] Koffi, M.; De Meeûs, T.; Bucheton, B.; Solano, P.; Camara, M.; Kaba, D.; Cuny, G.; Ayala, F. J.; Jamonneau, V. Population genetics of Trypanosoma brucei gambiense, the agent of sleeping sickness in Western Africa, Proceedings of the National Academy of Sciences of the United States of America, Volume 106 (2009) no. 1, pp. 209-214 | DOI

[33] Lepais, O.; Chancerel, E.; Boury, C.; Salin, F.; Manicki, A.; Taillebois, L.; Dutech, C.; Aissi, A.; Bacles, C. F.; Daverat, F.; Launey, S.; Guichoux, E. Fast sequence-based microsatellite genotyping development workflow, PeerJ, Volume 8 (2020) | DOI

[34] Lun, Z. R.; Wen, Y. Z.; Uzureau, P.; Lecordier, L.; Lai, D. H.; Lan, Y. G.; Desquesnes, M.; Geng, G. Q.; Yang, T. B.; Zhou, W. L.; Jannin, J. G.; Simarro, P. P.; Truc, P.; Vincendeau, P.; Pays, E. Resistance to normal human serum reveals Trypanosoma lewisi as an underestimated human pathogen, Molecular Biochemical Parasitology, Volume 199 (2015) no. 1-2, pp. 58-61 | DOI

[35] Manangwa, O.; De Meeûs, T.; Grébaut, P.; Segard, A.; Byamungu, M.; Ravel, S. Detecting Wahlund effects together with amplification problems : cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania, Molecular Ecology Resources, Volume 19 (2019) no. 3, pp. 757-772 | DOI

[36] Meglécz, E.; Pech, N.; Gilles, A.; Dubut, V.; Hingamp, P.; Trilles, A.; Grenier, R.; Martin, J. F. QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate, Molecular Ecology Resources, Volume 14 (2014) no. 6, pp. 1302-1313 | DOI

[37] Meirmans, P. G.; Hedrick, P. W. Assessing population structure: FST and related measures, Molecular Ecology Resources, Volume 11 (2011) no. 1, pp. 5-18 | DOI

[38] Mills, J. N.; Yates, T. L.; Childs, J. E.; Parmenter, R. R.; Ksiazek, T. G.; Rollin, P. E.; Peters, C. J. Guidelines for working with rodents potentially infected with hantavirus, Journal of Mammalogy, Volume 76 (1995) no. 3, pp. 716-722 | DOI

[39] Nei, M.; Chesser, R. K. Estimation of fixation indices and gene diversities, Annals of Human Genetics, Volume 47 (1983) no. Pt 3, p. 253-9 | DOI

[40] Pumhom, P.; Morand, S.; Tran, A.; Jittapalapong, S.; Desquesnes, M. Trypanosoma from rodents as potential source of infection in human-shaped landscapes of South-East Asia, Vet Parasitol, Volume 208 (2015) no. 3-4, pp. 174-180 | DOI

[41] R-Core-Team R: A Language and Environment for Statistical Computing, Version 3.6.3 (2020-02-29), R Foundation for Statistical Computing, Vienna, Austria, 2020 (

[42] Rossi, J. P.; Kadaouré, I.; Godefroid, M.; Dobigny, G. Landscape epidemiology in urban environments: The example of rodent-borne Trypanosoma in Niamey, Niger, Infection Genetics and Evolution, Volume 63 (2018), pp. 307-315 | DOI

[43] Saitou, N.; Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees., Molecular Biology and Evolution, Volume 4 (1987), pp. 406-425 | DOI

[44] Ségard, A.; Roméro, A.; Ravel, S.; Truc, P.; Gauthier, D.; Gauthier, P.; Dossou, H.-J.; Sylvestre, B.; Houéménou, G.; Morand, S.; Chaisiri, K.; Noûs, C.; De Meeûs, T. Development of nine microsatellite loci for Trypanosoma lewisi, a potential human pathogen in Western Africa and South-East Asia, and preliminary population genetics analyses, Supplementary File S1, Zenodo, 2022 | DOI

[45] Séré, M.; Kabore, J.; Jamonneau, V.; Belem, A. M. G.; Ayala, F. J.; De Meeûs, T. Null allele, allelic dropouts or rare sex detection in clonal organisms : simulations and application to real data sets of pathogenic microbes, Parasites and Vectors, Volume 7 (2014), p. 331 | DOI

[46] Sikes, R. S.; Gannon, W. L. Guidelines of the American Society of Mammalogists for the use of wild mammals in research, Journal of Mammalogy, Volume 92 (2011) no. 1, pp. 235-253 | DOI

[47] Takezaki, N.; Nei, M. Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA, Genetics, Volume 144 (1996) no. 1, pp. 389-399 | DOI

[48] Tatard, C.; Garba, M.; Gauthier, P.; Hima, K.; Artige, E.; Dossou, D.; Gagare, S.; Genson, G.; Truc, P.; Dobigny, G. Rodent-borne Trypanosoma from cities and villages of Niger and Nigeria: A special role for the invasive genus Rattus?, Acta Tropica, Volume 171 (2017), pp. 151-158 | DOI

[49] Teriokhin, A. T.; De Meeûs, T.; Guegan, J. F. On the power of some binomial modifications of the Bonferroni multiple test, Zhurnal Obshchei Biologii, Volume 68 (2007), pp. 332-340

[50] Truc, P.; Büscher, P.; Cuny, G.; Gonzatti, M. I.; Jannin, J.; Joshi, P.; Juyal, P.; Lun, Z. R.; Mattioli, R.; Pays, E.; Simarro, P. P.; Teixeira, M. M.; Touratier, L.; Vincendeau, P.; Desquesnes, M. Atypical human infections by animal trypanosomes, PLoS Neglected Tropical Diseases, Volume 7 (2013) no. 9, p. e2256 | DOI

[51] Truc, P.; Jamonneau, V.; N'Guessan, P.; N'Dri, L.; Diallo, P. B.; Cuny, G. Trypanosoma brucei ssp. and T-congolense: mixed human infection in Cote d'Ivoire, Transactions of the Royal Society of Tropical Medicine and Hygiene, Volume 92 (1998) no. 5, pp. 537-538 | DOI

[52] Wabale, V.; Nalage, P.; Joshi, A.; Bharadwaj, R.; Desphande, K.; Chowdhary, A. Human Asian trypanosomiasis due to Trypanosoma evansi: a rare case, The Journal of Advances in Parasitology, Volume 2 (2015) no. 3, pp. 65-68 | DOI

[53] Wang, J. Does GST underestimate genetic differentiation from marker data?, Molecular Ecology, Volume 24 (2015) no. 14, pp. 3546-3558 | DOI

[54] Weir, B.; Cockerham, C. Estimating F-statistics for the analysis of population structure, Evolution, Volume 38 (1984), pp. 1358-1370 | DOI

[55] Wright, S. The interpretation of population structure by F-statistics with special regard to system of mating, Evolution, Volume 19 (1965), pp. 395-420 | DOI

[56] Zhang, X.; Li, S. J.; Li, Z. Y.; He, C. Y.; Hide, G.; Lai, D. H.; Lun, Z. R. Cell cycle and cleavage events during in vitro cultivation of bloodstream forms of Trypanosoma lewisi, a zoonotic pathogen, Cell Cycle, Volume 18 (2019) no. 5, pp. 552-567 | DOI

Cited by Sources: