Circulating genotypes of Leptospira in French Polynesia : An 9-year molecular epidemiology surveillance follow-up study

Background Leptospirosis is a widespread zoonosis with global impact, particularly among vulnerable populations in resource-poor settings in tropical countries. Rodents have been considered to be the main reservoir of the disease; however, a wide variety of mammals can act as hosts as well. Here we examine the genetic diversity ofLeptospirastrains from biological samples of patients and animals in French Polynesia (FP) from 2011 to 2019. Methodology/Principal findings From 2011 to 2019, we have collected 444 blood samples from patients diagnosed as having leptospirosis. The limited volume of clinical material and low amount of leptospiral DNA in blood samples led us to develop a nested PCR targeting thesecYlocus that enabled us to amplify and sequence 244 samples (55%). In addition, 20Leptospirastrains recovered from the blood of patients from 2002 to 2011 were sequenced and fully characterized at the serogroup level and used as reference strains for the association of different phylogenetic branches with respective serogroups. ThesecYsequences were compared with publicly available sequences from patients and animal reservoirs in FP (n = 79). We identified rats as the main source of infection forL.borgpeterseniiserogroup Ballum andL.interrogansserogroup Icterohaemorrhagiae, dogs as the main source of infection forL.interrogansserogroup Australis, and farm pigs as the main source of infection forL.interrogansserogroups Pomona or Canicola.L.interroganswas associated with the most severe infections with 10 and 5 fatal cases due to serogroups Icterohaemorrhagiae and Australis, respectively. Mortality was significantly associated with older age (p-value < 0.001). Conclusions/Significance We described the population dynamics of leptospires circulating among patients in FP, including two patients who were reinfected with unrelatedLeptospiragenotypes, and clarified the local role of the animal reservoirs in the transmission route of leptospirosis to humans. RoutineLeptospiragenotyping directly on biological samples should allow the epidemiological follow-up of circulating strains and assess the impact of control interventions on disease transmission. Author summary PathogenicLeptospiraare the causative agents for leptospirosis, a neglected zoonosis occurring worldwide with the highest incidence of the disease found in the Pacific region, including French Polynesia (FP). In this study, a nested PCR of blood specimens allowed a high isolation frequency ofLeptospiraDNA among patients with febrile illness in FP. InfectingLeptospiraisolates were characterized by sequencing of thesecYgene from 244 clinical samples from 2011 to 2019. The genotypes have been assigned toLeptospiraspecies and serogroups by comparing thesecYsequences with the genomes of strains isolated prior to 2011 in FP. This study therefore enables to follow the distribution of genotypes/serogroups over a 18-year time period. Leptospiral sequences from patients were also compared withsecYsequences from different animal reservoirs from a previous study in FP showing that not only rats but also dogs and pigs might play an important role in the circulation of pathogenicLeptospirastrains in FP. Further progress in our understanding of the epidemiology ofLeptospiracirculating genotypes should contribute to the implementation of prevention and intervention measures to reduce the risk of leptospirosis transmission in FP.