The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole genome sequencing of human and environmental strains. Animal strains being poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 non-duplicated genomes with various origins (animal: 104, human: 226, environment: 30, unknown: 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified and two previously described groups were further divided into two subgroups, each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or CALIN sequences targeting antimicrobial compounds extensively used in animals, were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole genome analysis performed by us supports the hypothesis of putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans.

Importance:

Given its naturally large antimicrobial resistance profile, Smc is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As an environmental group of microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype or MALDI-TOF based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act a reservoir for mobile resistance genes. Some genogroups seem to be clearly associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.

该嗜麦芽窄食单复合体（Smc）包含机会性环境革兰氏阴性杆菌，负责人类和动物的多种感染。除了其巨大的遗传多样性之外，最近通过人类和环境菌株的全基因组测序证实了其在基因组中的遗传组织。在这些分析中代表性较弱的动物品系，我们对93个动物品系的整个基因组进行了测序，以确定其遗传背景和特征。将这些数据与81个新测序的人类菌株以及RefSeq的基因组结合起来，我们进行了基因组分析，其中包括375个具有不同起源的非重复基因组（动物：104；人类：226；环境：30；未知：15）。系统发育分析和基于全基因组平均核苷酸同一性的聚类证实并指定了Smc在至少20个基因组中的遗传组织。确定了两个新的基因组，并将两个先前描述的组进一步分为两个亚组。比较从不同宿主类型分离的菌株及其基因组隶属关系，我们观察到某些组明显不平衡。出人意料的是，主要在动物品系中鉴定了靶向广泛用于动物的抗微生物化合物的一些抗微生物抗性基因，整合素和/或CALIN序列。我们还鉴定了通常在编码外排系统的动物品系中发现的基因。我们进行的大型全基因组分析的结果支持了假设的假设，认为动物是动物的储存库。确定了两个新的基因组，并将两个先前描述的组进一步分为两个亚组。比较从不同宿主类型分离的菌株及其基因组隶属关系，我们观察到某些组明显不平衡。出人意料的是，主要在动物品系中鉴定了靶向广泛用于动物的抗微生物化合物的一些抗微生物抗性基因，整合素和/或CALIN序列。我们还鉴定了通常在编码外排系统的动物品系中发现的基因。我们进行的大型全基因组分析的结果支持了假设的假设，认为动物是动物的储存库。确定了两个新的基因组，并将两个先前描述的组进一步分为两个亚组。比较从不同宿主类型分离的菌株及其基因组隶属关系，我们观察到某些组明显不平衡。出人意料的是，主要在动物品系中鉴定了靶向广泛用于动物的抗微生物化合物的一些抗微生物抗性基因，整合素和/或CALIN序列。我们还鉴定了通常在编码外排系统的动物品系中发现的基因。我们进行的大型全基因组分析的结果支持了假设的假设，认为动物是动物的储存库。比较从不同宿主类型分离的菌株及其基因组隶属关系，我们观察到某些组明显不平衡。出人意料的是，主要在动物品系中鉴定了靶向广泛用于动物的抗微生物化合物的一些抗微生物抗性基因，整合素和/或CALIN序列。我们还鉴定了通常在编码外排系统的动物品系中发现的基因。我们进行的大型全基因组分析的结果支持了假设的假设，认为动物是动物的储存库。比较从不同宿主类型分离的菌株及其基因组隶属关系，我们观察到某些组明显不平衡。出人意料的是，主要在动物品系中鉴定了一些广泛用于动物中的靶向抗微生物化合物的抗微生物抗性基因，整合素和/或CALIN序列。我们还鉴定了通常在编码外排系统的动物品系中发现的基因。我们进行的大型全基因组分析的结果支持了假设的假设，认为动物是动物的储存库。我们还鉴定了通常在编码外排系统的动物品系中发现的基因。我们进行的大型全基因组分析的结果支持了假设的假设，认为动物是动物的储存库。我们还鉴定了通常在编码外排系统的动物品系中发现的基因。我们进行的大型全基因组分析的结果支持了假设的假设，认为动物是动物的储存库。嗜麦芽窄食单胞菌复杂菌株和/或人类菌株的抗性基因。

重要性：

鉴于其自然而然的抗微生物耐药性，Smc是免疫抑制和囊性纤维化患者的一组新兴病原体。作为一种环境微生物，对人类的适应是了解该过程涉及的遗传和代谢选择机制的机会。由于动物品系的数据不足，先前报道的基因组组织不完整。我们对93种动物起源的菌株进行了全基因组测序，从而增加了这个难题的缺失。除了描述系统发育组织外，我们还证实了Smc的遗传多样性，这无法通过常规表型或基于MALDI-TOF的实验室测试来估计。动物品系似乎在Smc的多样性中起关键作用，并且可以充当移动抗性基因的贮藏库。一些基因组似乎与特定宿主明显相关。这种关联的遗传支持和决定因素/相应基因的作用需要探索。