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 28, Number 12—December 2022

Emergence and Evolutionary Response of Vibrio cholerae to Novel Bacteriophage, Democratic Republic of the Congo1

Meer T. Alam2, Carla Mavian2Comments to Author , Taylor K. Paisie, Massimiliano S. Tagliamonte, Melanie N. Cash, Angus Angermeyer, Kimberley D. Seed, Andrew Camilli, Felicien Masanga Maisha, R. Kabangwa Kakongo Senga, Marco Salemi, J. Glenn Morris, and Afsar AliComments to Author 
Author affiliations: University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, C. Mavian, T.K. Paisie, M.S. Tagliamonte, M.N. Cash, F.M. Maisha, M. Salemi, J.G. Morris, Jr., A. Ali); University of Florida College of Medicine, Gainesville (C. Mavian, T.K. Paisie, M.S. Tagliamonte, M.N. Cash, M. Salemi, J.G. Morris, Jr.); University of California, Berkeley, California, USA (A. Angermeyer, K.D. Seed); Chan Zuckerberg Biohub, San Francisco, California, USA (K.D. Seed); Tufts University School of Medicine, Boston, Massachusetts, USA (A. Camilli); Appui Medical Integre aux Activites de Laboratoire (AMI-LABO), Goma, Democratic Republic of the Congo (R.K.K. Senga); University of Goma, Goma (R.K.K. Senga); University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, A. Ali)

Main Article


Characteristics of toxigenic Vibrio cholerae O1 strains isolated from the Democratic Republic of the Congo, 2015–2017*

Strain Isolation date Province/location Serotype
Susceptibility of V. cholerae to ICP1_2017_A_DRC† Mutation in O1 antigen and other genes‡ SRA ID
Ogawa Inaba
AGC-1 2015 Apr 30 North Kivu/Kirotshe + S SRR15192533
AGC-2 2015 May 18 Goma/Buhimba + S SRR15192532
AGC-3 2015 May 20 Mutwanga + R rfbD SRR15192521
AGC-4 2015 Mar 07 Goma/Buhimba + R rfbN SRR15192516
AGC-5 2015 Mar 20 Goma/Buhimba + S SRR15192515
AGC-6 2015 Jul 26 Goma/Buhimba + R rfbV, VC0559 (hypothetical), rplE, phrA, fliD, VC0672 (hypothetical) SRR15192514
AGC-7 2015 Jun 06 Goma/Buhimba + S SRR15192513
AGC-8 2015 Aug 06 Goma/Buhimba + S SRR15192512
AGC-9 2016 Jun 20 Maniema/Kabambare + S SRR15192511
AGC-10 2016 Aug 09 Karisimbi/Hop Millitaire + R rfbD SRR15192510
AGC-11 2016 May 28 Alimbongo + R rfbD SRR15192531
AGC-12 2016 Jul 27 South Kivu/Fizi + S SRR15192530
AGC-13 2016 Aug 08 Maniema/Kimbilulenge + S SRR15192529
AGC-14 2017 May 18 Kirotshe/Rubaya + S SRR15192528
AGC-15 2017 May 31 Rutshuru/Hgr + S SRR15192527
AGC-16 2017 Jun 10 Rutshuru/Hgr + S SRR15192526
AGC-17 2017 Jul 01 Nyiragongo/Turunga + S SRR15192525
AGC-18 2017 Jul 03 Goma/Hop.Provincial + manA SRR15192524
AGC-19 2017 Jul 03 Goma/Hop.Provincial + S SRR15192523
AGC-20 2019 Jul 03 Goma/Hop.Provincial + S SRR15192522
AGC-21 2017 Jul 06 Karisimbi/Prison centrale + S SRR15192520
AGC-22 2017 Jul 14 Karisimbi/Majengo + manA SRR15192519
AGC-23 2017 Jul 19 Karisimbi/Majengo + R rfbB SRR15192518
AGC-24 2017 Jul 15 Karisimbi/Majengo + S rfbU SRR15192517

*R, resistant; S, susceptible; +, positive; –, negative †Susceptibility to a virulent ICP1 phage (ICP1_2017_A_DRC) determined by strains yielding either complete resistance or forming turbid plaques in response to phage infection in plaque assay. The penultimate column indicates which strains had mutations in the O1-antigen biosynthetic complex and in other genes in the chromosome, with the mutated gene designated. AGC-18, AGC-22, and AGC-24 sustained 1, 1, and 18 bp deletion mutations in the indicated gene(s), resulting in a frame shift mutation in that gene, but all other ICP1 phage-resistant isolates sustained >1 missense mutation in the O-antigen biosynthetic gene cluster. ‡As detected by analysis using single-nucleotide polymorphism, insertion/deletion, or both. §Plaques were turbid as described elsewhere (29).

Main Article

  1. World Health Organization. Cholera annual report 2020. Wkly Epidemiol Rec. 2021;96:44560.
  2. Ingelbeen  B, Hendrickx  D, Miwanda  B, van der Sande  MAB, Mossoko  M, Vochten  H, et al. Recurrent cholera outbreaks, Democratic Republic of the Congo, 2008–2017. Emerg Infect Dis. 2019;25:85664. DOIPubMedGoogle Scholar
  3. Weill  FX, Domman  D, Njamkepo  E, Tarr  C, Rauzier  J, Fawal  N, et al. Genomic history of the seventh pandemic of cholera in Africa. Science. 2017;358:7859. DOIPubMedGoogle Scholar
  4. Okeke  IN. Africa in the time of cholera: a history of pandemics from 1817 to the present [book review]. Emerg Infect Dis. 2012;18:362. DOIGoogle Scholar
  5. Moore  S, Miwanda  B, Sadji  AY, Thefenne  H, Jeddi  F, Rebaudet  S, et al. Relationship between distinct African cholera epidemics revealed via MLVA haplotyping of 337 Vibrio cholerae isolates. PLoS Negl Trop Dis. 2015;9:e00038170003817. DOIPubMedGoogle Scholar
  6. Irenge  LM, Ambroise  J, Mitangala  PN, Bearzatto  B, Kabangwa  RKS, Durant  JF, et al. Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017). PLoS Negl Trop Dis. 2020;14:e0007642. DOIPubMedGoogle Scholar
  7. Seed  KD. Battling phages: how bacteria defend against viral attack. PLoS Pathog. 2015;11:e1004847. DOIPubMedGoogle Scholar
  8. Faruque  SM, Naser  IB, Islam  MJ, Faruque  AS, Ghosh  AN, Nair  GB, et al. Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages. Proc Natl Acad Sci U S A. 2005;102:17027. DOIPubMedGoogle Scholar
  9. Huq  A, Sack  RB, Nizam  A, Longini  IM, Nair  GB, Ali  A, et al. Critical factors influencing the occurrence of Vibrio cholerae in the environment of Bangladesh. Appl Environ Microbiol. 2005;71:464554. DOIPubMedGoogle Scholar
  10. Silva-Valenzuela  CA, Camilli  A. Niche adaptation limits bacteriophage predation of Vibrio cholerae in a nutrient-poor aquatic environment. Proc Natl Acad Sci U S A. 2019;116:162732. DOIPubMedGoogle Scholar
  11. Seed  KD, Yen  M, Shapiro  BJ, Hilaire  IJ, Charles  RC, Teng  JE, et al. Evolutionary consequences of intra-patient phage predation on microbial populations. eLife. 2014;3:e03497. DOIPubMedGoogle Scholar
  12. LeGault  KN, Hays  SG, Angermeyer  A, McKitterick  AC, Johura  FT, Sultana  M, et al. Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts. Science. 2021;373:eabg2166. DOIPubMedGoogle Scholar
  13. Hussain  FA, Dubert  J, Elsherbini  J, Murphy  M, VanInsberghe  D, Arevalo  P, et al. Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages. Science. 2021;374:48892. DOIPubMedGoogle Scholar
  14. Seed  KD, Bodi  KL, Kropinski  AM, Ackermann  HW, Calderwood  SB, Qadri  F, et al. Evidence of a dominant lineage of Vibrio cholerae-specific lytic bacteriophages shed by cholera patients over a 10-year period in Dhaka, Bangladesh. MBio. 2011;2:e0033410. DOIPubMedGoogle Scholar
  15. Angermeyer  A, Das  MM, Singh  DV, Seed  KD. Analysis of 19 highly conserved Vibrio cholerae bacteriophages isolated from environmental and patient sources over a twelve-year period. Viruses. 2018;10:10. DOIPubMedGoogle Scholar
  16. Ali  A, Chen  Y, Johnson  JA, Redden  E, Mayette  Y, Rashid  MH, et al. Recent clonal origin of cholera in Haiti. Emerg Infect Dis. 2011;17:699701. DOIPubMedGoogle Scholar
  17. O’Hara  BJ, Barth  ZK, McKitterick  AC, Seed  KD. A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome. PLoS Genet. 2017;13:e1006838. DOIPubMedGoogle Scholar
  18. Lemey  P, Rambaut  A, Drummond  AJ, Suchard  MA. Bayesian phylogeography finds its roots. PLOS Comput Biol. 2009;5:e1000520. DOIPubMedGoogle Scholar
  19. Grenfell  BT, Pybus  OG, Gog  JR, Wood  JL, Daly  JM, Mumford  JA, et al. Unifying the epidemiological and evolutionary dynamics of pathogens. Science. 2004;303:32732. DOIPubMedGoogle Scholar
  20. Drummond  AJ, Rambaut  A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007;7:214. DOIPubMedGoogle Scholar
  21. Hasegawa  M, Kishino  H, Yano  T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22:16074. DOIPubMedGoogle Scholar
  22. Leaché  AD, Banbury  BL, Felsenstein  J, de Oca  AN, Stamatakis  A. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Syst Biol. 2015;64:103247. DOIPubMedGoogle Scholar
  23. Minin  VN, Bloomquist  EW, Suchard  MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 2008;25:145971. DOIPubMedGoogle Scholar
  24. Strimmer  K, Pybus  OG. Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol. 2001;18:2298305. DOIPubMedGoogle Scholar
  25. Hall  MD, Woolhouse  ME, Rambaut  A. The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study. Virus Evol. 2016;2:vew003. DOIPubMedGoogle Scholar
  26. Lemey  P, Kosakovsky Pond  SL, Drummond  AJ, Pybus  OG, Shapiro  B, Barroso  H, et al. Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLOS Comput Biol. 2007;3:e29. DOIPubMedGoogle Scholar
  27. Mavian  C, Paisie  TK, Alam  MT, Browne  C, Beau De Rochars  VM, Nembrini  S, et al. Toxigenic Vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems. Proc Natl Acad Sci U S A. 2020;117:7897904. DOIPubMedGoogle Scholar
  28. Seed  KD, Faruque  SM, Mekalanos  JJ, Calderwood  SB, Qadri  F, Camilli  A. Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1. PLoS Pathog. 2012;8:e1002917. DOIPubMedGoogle Scholar
  29. Seed  KD, Lazinski  DW, Calderwood  SB, Camilli  A. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature. 2013;494:48991. DOIPubMedGoogle Scholar
  30. Kamp  HD, Patimalla-Dipali  B, Lazinski  DW, Wallace-Gadsden  F, Camilli  A. Gene fitness landscapes of Vibrio cholerae at important stages of its life cycle. PLoS Pathog. 2013;9:e1003800. DOIPubMedGoogle Scholar
  31. Oechslin  F. Resistance development to bacteriophages occurring during bacteriophage therapy. Viruses. 2018;10:10. DOIPubMedGoogle Scholar

Main Article

1Previously presented at Epidemics—8th International Conference on Infectious Diseases Dynamics [online], November 30–December 3, 2021.

2These authors contributed equally to this article.

Page created: October 18, 2022
Page updated: November 21, 2022
Page reviewed: November 21, 2022
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.