Vibrio cholerae multifaceted adaptive strategies in response to bacteriophage predation in an endemic region of the Democratic Republic of the Congo

Abstract

Bacteriophage predation of toxigenic Vibrio cholerae O1 (the causative agent of cholera) has been linked with seasonal patterns of disease and with clinical response to infection in humans 1-4. However, we still lack a clear demonstration of how the interplay between bacteria and bacteriophage can influence shifts in strain populations. We analyzed toxigenic V. cholerae O1 isolated from patients in the Great Lakes, a cholera endemic region of the Democratic Republic of the Congo (DRC), between 2013-2017. Bayesian phylogeography shows that all strains derived from the East Africa T10 introduction event5, consistent with establishment of a regional endemic focus, and identified two major lineages, with the most recent correlating to ST515, a cholera cluster previously found in the Lake Kivu and expanding northward6. We also identified a novel ICP1 bacteriophage, genetically distinct from previous ICP1 isolates detected in Asia 7,8, from stool samples of cholera patients. The presence of phages in specific regions of the DRC resulted in the independent emergence, along both internal and external branches of the cholera phylogeny, of distinct mutational pathways in genes of the O1 biosynthetic gene cluster associated with phage resistance. Our data evidence, for the first time, V. cholerae multi-peaked adaptive landscape during outbreaks, and a complex co-evolutionary dynamic linked to presence of predatory phages

Development of a Monoclonal Antibody to a Vibriophage as a Proxy for Vibrio cholerae Detection

“…The sample collections analyzed were from previously published Institutional Review Board (IRB) approved studies; the recruitment, consent, enrollment, and procedures are described ( 16 , 19 , 38 , 39 ). In the first collection, stool samples from the Bangladesh study were obtained September to December 2015 at a district hospital and a subdistrict hospital in the remote northern district of Netrokona ( 38 ).…”

“…ICP1, a member of the Myoviridae bacteriophage family, is the most prevalent phage excreted in cholera patient’s stool during the episode of an epidemic ( 14 , 16 , 17 ). ICP1 phage is specific to V. cholerae O1 and has been in other geographical locations, including India and Africa (South Sudan and Democratic Republic of Congo [DRC]) ( 16 – 19 ).…”

Development of a monoclonal antibody to a vibriophage as a proxy forVibrio choleraedetection

“…The sample collections analyzed were from previously published IRB approved studies; the recruitment, consent, enrollment and procedures are described (16, 19, 33, 34). In the first collection, stool samples from the Bangladesh study were obtained during September to December 2015 at a district hospital and a subdistrict hospital in the remote northern district of Netrokona (33).…”

“…Alignment of Bangladesh (Bd) (14) and Goma ICP1 (19) bacteriophage ORF75 ( A ) and ORF122 ( B ) protein sequences by Clustal Omega (EMBL-EBI). Alignment is shown by symbols.…”

“…ICP1, a member of Myoviridae bacteriophage family is the most prevalent phage excreted in cholera patient's stool during the episode of an epidemic (14,16,17). ICP1 phage is specific to V. cholerae O1 and has been in other geographical locations including India and Africa (South Sudan and Democratic Republic of Congo (DRC)) (16)(17)(18)(19).…”