We recovered 17 B. neotomae WGS datasets from public repositories as assemblies or raw reads (last accessed May 31, 2023): ERR1894830, GCA_000158715, GCA_000712255, GCA_000742255, GCA_900446125, SRR004305, SRR004306, SRR032598, SRR857216, SRR4038991 (all 10 strains 5K33), ERR2993140 (MLVA31), GCA_900446115, SRR4038990 (5E1169), GCA_900446105 (6D152), ERR473742 (babohCR62), ERR1845156 (bneohCR2), and ERR1845155 (bneohCR1) (Appendix Table 2). We merged 3 records (SRR004305, SRR004306, SRR032598) corresponding to the same biosample.

The Brucella strain collection maintained by APHA contained 5 and INRAE/BCCN, 7 B. neotomae strains (6,7). We recorded APHA and corresponding BCCN identifiers for each strain (Appendix Table 1). We produced and analyzed sequence data (Appendix). The 12 B. neotomae sequence datasets produced for this report were SRR22273182–8 (BCCN collection corresponding to primary names 6G152, 5E1169, 5E1266, 7E1260, 6H8988, and 5G239 and 1 unknown primary name) and SRR22414766–70 (APHA collection corresponding to primary names 7E164 and 5E1266 and 3 unknown primary names). We deposited sequences in the National Center for Biotechnology BioProject database as PRJNA901374 (BCCN) and PRJNA905663 (APHA) (Appendix Table 2).

Figure 1

Figure 1. Brucella neotomaephylogeny. Maximum parsimony tree was derived from wgSNP data. We investigated 27 datasets and identified 149 SNPs; tree size is 151 substitutions (homoplasy 1.5%). Circles are colored according...

We generated a maximum parsimony tree from the 149 SNPs identified among the 27 B. neotomae sequence datasets, including 15 public and 12 newly sequenced WGS datasets (Figure 1; Appendix Tables 1, 2). The whole-genome SNP (wgSNP) genotype of the most recent common ancestor (MRCA) of known B. neotomae lineages descends into 2 groups (Figure 1): the group containing type strain 5K33 corresponds to sequence type (ST) 22 in the Brucella multilocus sequence typing scheme MLST21, the other to ST120 (7). The limited available information about the sampling site of each strain from rodents in the Great Salt Lake Desert in Utah, USA, is consistent with congruence between B. neotomae phylogeny and the geography of the Great Salt Lake region, but further data are needed to robustly test this association (Appendix).

Figure 2

Figure 2. Rooted Brucella neotomaephylogeny of 16 selected datasets. Maximum parsimony tree was derived from wgSNP data; 205 SNPs in tree, tree size 207 substitutions (homoplasy 1%). Branch lengths >1...

We show a different representation of the wgSNP phylogenetic analysis after removal of duplicates and of 1 dataset with relatively lower coverage (Figure 2; GenBank accession no. GCA_900446105 from strain 6D152). Because we removed the WGS datasets with partial coverage, the new tree contained 205 SNPs. The distances from MRCA to tips were similar: maximum 76 SNPs (to strain 7E1260) and minimum 56 SNPs (to strain APHA#65–197). The 3 whole-genome datasets from Costa Rica, including the human isolates bneohCR1 and bneohCR2 and the isolate babohCR62 entered as B. abortus in the European Nucleotide Archive database, remained identical in wgSNP genotype to strain 5G239 (BCCN#R34) in spite of the increased resolution. We still observed a coincident wgSNP genotype when we considered only these 4 strains, in sharp contrast with a report of human cases that indicated the corresponding genomes differed by 164 SNPs (4).

Our findings demonstrate that the strains isolated during 1955–1964 in the Great Salt Lake Desert in Utah display notable intraspecies genetic diversity despite being isolated from a geographically limited location, within a limited time frame, and from the same host species. In contrast, the datasets from wgSNP analysis of isolates from Costa Rica were identical despite having been isolated 4 years apart and in different areas of Costa Rica (5). Of note, datasets from analysis of isolates from Costa Rica were identical to data from 1 B. neotomae strain, 5G239, from the Great Salt Lake region. Finding an identical genotype in human cases from Costa Rica >3,000 km and >50 years apart in a different species from the Great Salt Lake discovery is remarkable in light of the diversity of strains noted in the geographically limited location in Utah and reported absence of rats of genus Neotoma in Costa Rica (5). Full understanding of the zoonotic potential of B. neotomae requires further exploration, including additional sampling of rodents and human cases in the US Southwest and Central America.