Gómez-Martínez Jessica, Rocha-Gracia Rosa Del Carmen, Bello-López Elena, Cevallos Miguel Angel, Castañeda-Lucio Miguel, Sáenz Yolanda, Jiménez-Flores Guadalupe, Cortés-Cortés Gerardo, López-García Alma, Lozano-Zarain Patricia
Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico.
Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico.
Antibiotics (Basel). 2023 May 7;12(5):866. doi: 10.3390/antibiotics12050866.
The genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. (a variant of ) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that was most prevalent in the genomes of urinary samples and and in sputum samples. This study provides evidence regarding the genetic variability among isolated from different niches.
基因组可以发生变化以适应不同的生态位。我们比较了来自墨西哥一家医院的4个基因组和来自GenBank的59个来自不同生态位（如尿液、痰液和环境）的基因组。ST分析表明，GenBank的三个生态位的基因组中存在高风险STs（ST235、ST773和ST27），而墨西哥基因组的STs（ST167、ST2731和ST549）与GenBank基因组不同。系统发育分析表明，基因组是根据其ST而不是其生态位进行聚类的。在分析基因组内容时，我们观察到环境基因组具有参与适应环境的基因，而这些基因在临床样本中未发现，并且它们的耐药机制是抗生素耐药相关基因的突变。相比之下，GenBank的临床基因组在染色体的可移动/可动员遗传元件中具有耐药基因，除了墨西哥基因组，其耐药基因大多存在于质粒中。这与CRISPR-Cas和抗CRISPR的存在有关；然而，墨西哥菌株仅具有质粒和CRISPR-Cas。对碳青霉烯类具有更高活性的（一种变体）在痰液基因组中更为普遍。毒力组分析表明，在尿液样本的基因组中最为普遍，而在痰液样本中最为普遍。本研究提供了关于从不同生态位分离出的之间遗传变异性的证据。
