Leptospira dzianensis and Leptospira putramalaysiae are later heterotypic synonyms of Leptospira yasudae and Leptospira stimsonii

Abstract

Leptospira dzianensis and Leptospira putramalaysiae were recently described as novel species and published almost concurrently with Leptospira yasudae and Leptospira stimsonii. Genome comparisons based on average nucleotide identity of the type strain genomes indicate that L. dzianensis and L. putramalaysiae are conspecific with L. yasudae and L. stimsonii, respectively. Based on the rules of priority, L. dzianensis should be reclassified as a later heterotypic synonym of L. yasudae, and L. putramalaysiae should be reclassified as a later heterotypic synonym of L. stimsonii.

A recent publication in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) described the novel species Leptospira yasudae and Leptospira stimsonii isolated from environmental sources [1]. Two strains were reported for each species: F1^T and B2 for L. yasudae, and Yale^T and AMB6-RJ for L. stimsonii. Almost concurrently, another publication in PLoS Neglected Tropical Diseases described 30 novel species of the genus Leptospira [2]. These species have been recently validated and listed as new names in the IJSEM on September 2020 [3]. Among those new species, L. dzianensis (strains M12A^T, L1S1, 201 702 447, 201 702 446, 201 702 418 and 201 702 445) and L. putramalaysiae (strains SSW20^T and 201702407) [2] have a close phylogenetic relationship to L. yasudae and L. stimsonii, respectively, which prompted us to clarify their taxonomic relatedness.

A comparison of the complete 16S rRNA gene sequences for the type strains showed >99.6 % identity between all two L. yasudae and six L. dzianensis strains, and 100 % identity between all two L. stimsonii and two L. putramalaysiae strains. Since draft genomes of all the strains were reported as part of their taxonomic descriptions, we performed an average nucleotide identity (ANI) analysis [4]. ANI values among L. yasudae and L. dzianensis strains ranged from 95.54 to 99.99 % (Table 1). ANI values among L. stimsonii and L. putramalaysiae strains ranged from 95.43 to 100 % (Table 2). In both cases, the ANI values were above the threshold of 95 % recommended as the cut-off point for the assignment of bacterial strains to the same species [5, 6]. We subsequently calculated the average amino acid identity (AAI) [7] and found that AAI values among L. yasudae and L. dzianensis strains ranged from 95.59 to 99.99 %. Similarly, AAI values among L. stimsonii and L. putramalaysiae strains ranged from 95.26 to 99.97 %. Taken together, our results indicate that the L. yasudae and L. dzianensis strains and the L. stimsonii and L. putramalaysiae strains are conspecific and should be accommodated within the same species.

Table 1.

ANI values obtained by pairwise comparison of the genomes of all L. yasudae and L. dzianensis strains using blast+ in JSpeciesWS

Strain	F1T	M12AT	B21	L1S1	201 702 418	201 702 445	201 702 446	201 702 447
L. yasudae F1T	100	–	–	–	–	–	–	–
L. dzianensis M12A	96.84	100	–	–	–	–	–	–
L. yasudae B21	98.93	96.96	100	–	–	–	–	–
L. dzianensis L1S1	99.06	96.94	98.96	100	–	–	–	–
L. dzianensis 201 702 418	99.04	96.90	98.92	99.99	100	–	–	–
L. dzianensis 201 702 445	95.56	96.03	95.61	95.54	95.56	100	–	–
L. dzianensis 201 702 446	95.55	96.01	95.59	95.55	95.56	100	100	–
L. dzianensis 201 702 447	95.58	95.59	95.58	95.58	95.61	100	100	100

Table 2.

ANI values obtained by pairwise comparison of the genomes of all L. stimsonii and L. putramalaysiae strains using blast+ in JSpeciesWS

Strain	YaleT	SSW20T	AMB6-RJ	201 702 407
L. stimsonii YaleT	100	–	–	–
L. putramalaysiae SSW20T	95.44	100	–	–
L. stimsonii AMB6-RJ	95.53	99.30	100	–
L. putramalaysiae 201 702 407	95.43	99.99	99.29	100

Rule 23a of the International Code of Nomenclature of Bacteria states, ‘In a given position, a species can bear only one correct epithet, that is, the earliest that is in accordance with the Rules of this Code’ [8]. Rules 23b, 24a and 24b establish the priority of names based on their dates of valid publication in the IJSEM. In this case, L. yasudae and L. stimsonii were published on March 2020 [1]. Based on the rules of priority, L. dzianensis and L. putramalaysiae are later heterotypic synonyms of L. yasudae and L. stimsonii, respectively. Consequently, we recommend the use of L. yasudae (type strain F1^T) for strains F1^T, B21, M12A, L1S1, 201 702 447, 201 702 446, 201 702 418 and 201 702 445, and the use of L. stimsonii (type strain Yale^T) for strains Yale^T, AMB6-RJ, SSW20 and 201 702 407.

It is important to mention that, despite the nomenclature change and the recommendation to use L. stimsonii and L. yasudae as species names for those strains, the results and analysis performed by Vincent et al. [2] are still valid and remain as the more updated basis for future investigations about the taxonomy and pathogenicity of the genus Leptospira.