Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link

Volume 26, Number 3—March 2020

Research

Stable and Local Reservoirs of Mycobacterium ulcerans Inferred from the Nonrandom Distribution of Bacterial Genotypes, Benin

Clément Coudereau, Alban Besnard, Marie Robbe-Saule, Céline Bris, Marie Kempf, Roch Christian Johnson, Télésphore Yao Brou, Ronald Gnimavo, Sara Eyangoh, Fida Khater, and Estelle MarionComments to Author 
Author affiliations: Université d’Angers, Angers, France (C. Coudereau, A. Besnard, M. Robbe-Saule, M. Kempf, F. Khater, E. Marion); INSERM, Angers (C. Coudereau, A. Besnard, M. Robbe-Saule, M. Kempf, F. Khater, E. Marion); Centre Hospitalo-Universitaire d’Angers, Angers (C. Bris, M. Kempf); Université d'Abomey Calavi, Abomey Calavi, Benin (R.C. Johnson); Fondation Raoul Follereau, Paris, France (R.C. Johnson); Maison de la Télédétection, Montpellier, France (T.Y. Brou); Centre de Diagnostic et Traitement de la Lèpre et de l’Ulcère de Buruli, Pobè, Bénin (R. Gnimavo); International Pasteur Institute Network, Yaoundé, Cameroon (S. Eyangoh)

Main Article

Table 3

Statistical measurements of the performance of the multinomial models on a real dataset of newly sequenced genomes, Benin and Nigeria*

Locale Accuracy† Matthews correlation coefficient‡
Northern Ouémé 91.44% 0.608*
Southern Ouémé 91.73% 0.637*
Nigeria (Ogun State) 86.25% 0.371**

†Sum of the true positive and true negative divided by the total population.
‡Contingency matrix method of calculating the Pearson product–moment correlation coefficient (27). Its value ranges from −1 to +1 with +1 being a perfect positive prediction model, 0 no better than random prediction, and −1 being a model where predicted class is in total contradiction with observed class. Values indicated the strength of the relationship (*, strong positive relationship; **, moderate positive relationship).

Main Article

References
  1. Sizaire  V, Nackers  F, Comte  E, Portaels  F. Mycobacterium ulcerans infection: control, diagnosis, and treatment. Lancet Infect Dis. 2006;6:288–96. DOIPubMedGoogle Scholar
  2. Asiedu  K, Etuaful  S. Socioeconomic implications of Buruli ulcer in Ghana: a three-year review. Am J Trop Med Hyg. 1998;59:1015–22. DOIPubMedGoogle Scholar
  3. Aiga  H, Amano  T, Cairncross  S, Adomako  J, Nanas  OK, Coleman  S. Assessing water-related risk factors for Buruli ulcer: a case-control study in Ghana. Am J Trop Med Hyg. 2004;71:387–92. DOIPubMedGoogle Scholar
  4. Merritt  RW, Walker  ED, Small  PL, Wallace  JR, Johnson  PD, Benbow  ME, et al. Ecology and transmission of Buruli ulcer disease: a systematic review. PLoS Negl Trop Dis. 2010;4:e911. DOIPubMedGoogle Scholar
  5. Wallace  JR, Mangas  KM, Porter  JL, Marcsisin  R, Pidot  SJ, Howden  B, et al. Mycobacterium ulcerans low infectious dose and mechanical transmission support insect bites and puncturing injuries in the spread of Buruli ulcer. PLoS Negl Trop Dis. 2017;11:e0005553. DOIPubMedGoogle Scholar
  6. Williamson  HR, Mosi  L, Donnell  R, Aqqad  M, Merritt  RW, Small  PL. Mycobacterium ulcerans fails to infect through skin abrasions in a guinea pig infection model: implications for transmission. PLoS Negl Trop Dis. 2014;8:e2770. DOIPubMedGoogle Scholar
  7. Johnson  PD, Azuolas  J, Lavender  CJ, Wishart  E, Stinear  TP, Hayman  JA, et al. Mycobacterium ulcerans in mosquitoes captured during outbreak of Buruli ulcer, southeastern Australia. Emerg Infect Dis. 2007;13:1653–60. DOIPubMedGoogle Scholar
  8. Marsollier  L, Robert  R, Aubry  J, Saint André  JP, Kouakou  H, Legras  P, et al. Aquatic insects as a vector for Mycobacterium ulcerans. Appl Environ Microbiol. 2002;68:4623–8. DOIPubMedGoogle Scholar
  9. Portaels  F, Elsen  P, Guimaraes-Peres  A, Fonteyne  PA, Meyers  WM. Insects in the transmission of Mycobacterium ulcerans infection. Lancet. 1999;353:986. DOIPubMedGoogle Scholar
  10. van der Werf  TS, Stinear  T, Stienstra  Y, van der Graaf  WT, Small  PL. Mycolactones and Mycobacterium ulcerans disease. Lancet. 2003;362:1062–4. DOIPubMedGoogle Scholar
  11. Buultjens  AH, Vandelannoote  K, Meehan  CJ, Eddyani  M, de Jong  BC, Fyfe  JAM, et al. Comparative genomics shows that Mycobacterium ulcerans migration and expansion preceded the rise of Buruli ulcer in southeastern Australia. Appl Environ Microbiol. 2018;84:e02612–7. DOIPubMedGoogle Scholar
  12. Vandelannoote  K, Phanzu  DM, Kibadi  K, Eddyani  M, Meehan  CJ, Jordaens  K, et al. Mycobacterium ulcerans population genomics to inform on the spread of Buruli ulcer across central Africa. MSphere. 2019;4:e00472–18. DOIPubMedGoogle Scholar
  13. Wu  J, Tschakert  P, Klutse  E, Ferring  D, Ricciardi  V, Hausermann  H, et al. Buruli ulcer disease and its association with land cover in southwestern Ghana. PLoS Negl Trop Dis. 2015;9:e0003840. DOIPubMedGoogle Scholar
  14. Bolz  M, Bratschi  MW, Kerber  S, Minyem  JC, Um Boock  A, Vogel  M, et al. Locally confined clonal complexes of Mycobacterium ulcerans in two Buruli ulcer endemic regions of Cameroon. PLoS Negl Trop Dis. 2015;9:e0003802. DOIPubMedGoogle Scholar
  15. Vandelannoote  K, Meehan  CJ, Eddyani  M, Affolabi  D, Phanzu  DM, Eyangoh  S, et al. Multiple introductions and recent spread of the emerging human pathogen Mycobacterium ulcerans across Africa. Genome Biol Evol. 2017;9:414–26. DOIPubMedGoogle Scholar
  16. Kambarev  S, Corvec  S, Chauty  A, Marion  E, Marsollier  L, Pecorari  F. Draft genome sequence of Mycobacterium ulcerans S4018 isolated from a patient with an active Buruli ulcer in Benin, Africa. Genome Announc. 2017;5:e00248–17. DOIPubMedGoogle Scholar
  17. Andrew  S. FastQC: a quality control tool for high throughput sequence data. 2010 [cited 2019 Apr 1].
  18. Bolger  AM, Lohse  M, Usadel  B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20. DOIPubMedGoogle Scholar
  19. Seemann  T. Snippy: fast bacterial variant calling from NGS reads. 2015 [cited 2019 Apr 1].
  20. Li  H, Durbin  R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60. DOIPubMedGoogle Scholar
  21. Stinear  TP, Seemann  T, Pidot  S, Frigui  W, Reysset  G, Garnier  T, et al. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res. 2007;17:192–200. DOIPubMedGoogle Scholar
  22. Guindon  S, Dufayard  JF, Lefort  V, Anisimova  M, Hordijk  W, Gascuel  O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21. DOIPubMedGoogle Scholar
  23. Hodcroft  E. TreeCollapserCL. 2012 [cited 2019 Apr 1].
  24. Kulldorff  M. SatScan: software for the spatial and space-time scan statistics. 2019 [cited 2019 Apr 1].
  25. Team QGIS Development. QGIS Geographic Information System. Project OSGF. 2019 [cited 2019 Apr 1].
  26. R Core Team. R: a language and environment for statistical computing. Computing RFfS. 2019 [cited 2019 Apr 1].
  27. Powers  DMW. Evaluation: from precision, recall and F-Measure to ROC, informedness, markedness, and correlation. J Mach Learn Technol. 2011;2:37–63.
  28. Bennett  SD, Lowther  SA, Chingoli  F, Chilima  B, Kabuluzi  S, Ayers  TL, et al. Assessment of water, sanitation and hygiene interventions in response to an outbreak of typhoid fever in Neno District, Malawi. PLoS One. 2018;13:e0193348. DOIPubMedGoogle Scholar
  29. Davies  HG, Bowman  C, Luby  SP. Cholera - management and prevention. J Infect. 2017;74(Suppl 1):S66–73. DOIPubMedGoogle Scholar
  30. Mitjà  O, Marks  M, Bertran  L, Kollie  K, Argaw  D, Fahal  AH, et al. Integrated control and management of neglected tropical skin diseases. PLoS Negl Trop Dis. 2017;11:e0005136. DOIPubMedGoogle Scholar
  31. Brou  T, Broutin  H, Elguero  E, Asse  H, Guegan  JF. Landscape diversity related to Buruli ulcer disease in Côte d’Ivoire. PLoS Negl Trop Dis. 2008;2:e271. DOIPubMedGoogle Scholar
  32. Landier  J, Gaudart  J, Carolan  K, Lo Seen  D, Guégan  JF, Eyangoh  S, et al. Spatio-temporal patterns and landscape-associated risk of Buruli ulcer in Akonolinga, Cameroon. PLoS Negl Trop Dis. 2014;8:e3123. DOIPubMedGoogle Scholar
  33. Marion  E, Landier  J, Boisier  P, Marsollier  L, Fontanet  A, Le Gall  P, et al. Geographic expansion of Buruli ulcer disease, Cameroon. Emerg Infect Dis. 2011;17:551–3. DOIPubMedGoogle Scholar
  34. Nackers  F, Johnson  RC, Glynn  JR, Zinsou  C, Tonglet  R, Portaels  F. Environmental and health-related risk factors for Mycobacterium ulcerans disease (Buruli ulcer) in Benin. Am J Trop Med Hyg. 2007;77:834–6. DOIPubMedGoogle Scholar
  35. Pouillot  R, Matias  G, Wondje  CM, Portaels  F, Valin  N, Ngos  F, et al. Risk factors for buruli ulcer: a case control study in Cameroon. PLoS Negl Trop Dis. 2007;1:e101. DOIPubMedGoogle Scholar
  36. Raghunathan  PL, Whitney  EA, Asamoa  K, Stienstra  Y, Taylor  TH Jr, Amofah  GK, et al. Risk factors for Buruli ulcer disease (Mycobacterium ulcerans Infection): results from a case-control study in Ghana. Clin Infect Dis. 2005;40:1445–53. DOIPubMedGoogle Scholar
  37. Wagner  T, Benbow  ME, Burns  M, Johnson  RC, Merritt  RW, Qi  J, et al. A Landscape-based model for predicting Mycobacterium ulcerans infection (Buruli Ulcer disease) presence in Benin, West Africa. EcoHealth. 2008;5:69–79. DOIPubMedGoogle Scholar
  38. Röltgen  K, Stinear  TP, Pluschke  G. The genome, evolution and diversity of Mycobacterium ulcerans. Infect Genet Evol. 2012;12:522–9. DOIPubMedGoogle Scholar
  39. Demangel  C, Stinear  TP, Cole  ST. Buruli ulcer: reductive evolution enhances pathogenicity of Mycobacterium ulcerans. Nat Rev Microbiol. 2009;7:50–60. DOIPubMedGoogle Scholar
  40. Rondini  S, Käser  M, Stinear  T, Tessier  M, Mangold  C, Dernick  G, et al. Ongoing genome reduction in Mycobacterium ulcerans. Emerg Infect Dis. 2007;13:1008–15. DOIPubMedGoogle Scholar
  41. Yerramilli  A, Tay  EL, Stewardson  AJ, Fyfe  J, O’Brien  DP, Johnson  PDR. The association of rainfall and Buruli ulcer in southeastern Australia. PLoS Negl Trop Dis. 2018;12:e0006757. DOIPubMedGoogle Scholar
  42. Tanser  FC, Le Sueur  D. The application of geographical information systems to important public health problems in Africa. Int J Health Geogr. 2002;1:4. DOIPubMedGoogle Scholar
  43. Carpi  G, Walter  KS, Bent  SJ, Hoen  AG, Diuk-Wasser  M, Caccone  A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics. 2015;16:434. DOIPubMedGoogle Scholar

Main Article

Page created: February 20, 2020
Page updated: February 20, 2020
Page reviewed: February 20, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external