Comparative whole genome phylogeny of animal, environmental and human strains confirms the genogroups organization and the diversity of Stenotrophomonas maltophilia. Comparative whole genome phylogeny of animal, environmental and human strains confirms the genogroups organization and the diversity of Stenotrophomonas maltophilia

Stenotrophomonas maltophilia (Sm) is an opportunistic environmental Gram negative bacillus responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, a genetic organization in genogroups was recently confirmed through the whole genome sequencing of human and environmental strains. Animal strains being excluded from these analyses, we sequenced the whole genome of one hundred animal strains to decipher their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the RefSeq available genomes, we performed the largest genomic analysis that included 384 non duplicated genomes from various origin (animal: 112, human: 221, environment: 36, unknown : 15). Core single nucleotide polymorphism based phylogeny and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Sm in 21 genogroups, with a basal genogroup 8 that gathered more divergent strains which can be difficult to assign to Sm species. Five new genogroups were identified and two previously described groups were divided into 2 subgroups. We compared the distribution of the host from which the strains were isolated and the genogroup affiliation and observed a clear disequilibrium in certain groups. Surprisingly, the antimicrobial resistance genes and integron and/or CALIN sequences were mainly identified in animal strains, targeting antimicrobial compounds extensively used in animals. We identified genes preferentially found in animal and coding for multidrug or metal resistance proteins. Our large whole genome analysis supports the putative contribution of animals as a reservoir of Sm strains and/or resistance genes for the human.