Ambroa Antón, Blasco Lucia, López María, Pacios Olga, Bleriot Inés, Fernández-García Laura, González de Aledo Manuel, Ortiz-Cartagena Concha, Millard Andrew, Tomás María
Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain.
Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain.
Front Microbiol. 2022 Feb 17;12:784949. doi: 10.3389/fmicb.2021.784949. eCollection 2021.
To optimize phage therapy, we need to understand how bacteria evolve against phage attacks. One of the main problems of phage therapy is the appearance of bacterial resistance variants. The use of genomics to track antimicrobial resistance is increasingly developed and used in clinical laboratories. For that reason, it is important to consider, in an emerging future with phage therapy, to detect and avoid phage-resistant strains that can be overcome by the analysis of metadata provided by whole-genome sequencing. Here, we identified genes associated with phage resistance in 18 clinical strains belonging to the ST-2 clonal complex during a decade (Ab2000 vs. 2010): 9 from 2000 to 9 from 2010. The presence of genes putatively associated with phage resistance was detected. Genes detected were associated with an abortive infection system, restriction-modification system, genes predicted to be associated with defense systems but with unknown function, and CRISPR-Cas system. Between 118 and 171 genes were found in the 18 clinical strains. On average, 26% of these genes were detected inside genomic islands in the 2000 strains and 32% in the 2010 strains. Furthermore, 38 potential CRISPR arrays in 17 of 18 of the strains were found, as well as 705 proteins associated with CRISPR-Cas systems. A moderately higher presence of these genes in the strains of 2010 in comparison with those of 2000 was found, especially those related to the restriction-modification system and CRISPR-Cas system. The presence of these genes in genomic islands at a higher rate in the strains of 2010 compared with those of 2000 was also detected. Whole-genome sequencing and bioinformatics could be powerful tools to avoid drawbacks when a personalized therapy is applied. In this study, it allows us to take care of the phage resistance in clinical strains to prevent a failure in possible phage therapy.
为了优化噬菌体疗法，我们需要了解细菌如何针对噬菌体攻击进行进化。噬菌体疗法的主要问题之一是细菌耐药变体的出现。利用基因组学追踪抗菌药物耐药性在临床实验室中越来越多地得到发展和应用。因此，在噬菌体疗法的新兴未来，考虑通过分析全基因组测序提供的元数据来检测和避免可克服的噬菌体抗性菌株非常重要。在此，我们在十年间（2000年与2010年相比）确定了18株属于ST-2克隆复合体的临床菌株中与噬菌体抗性相关的基因：2000年的9株与2010年的9株。检测到了可能与噬菌体抗性相关的基因的存在。检测到的基因与流产感染系统、限制修饰系统、预测与防御系统相关但功能未知的基因以及CRISPR-Cas系统有关。在这18株临床菌株中发现了118至171个基因。平均而言，这些基因在2000年菌株的基因组岛中的检出率为26%，在2010年菌株中的检出率为32%。此外，在18株中的17株中发现了38个潜在的CRISPR阵列，以及705种与CRISPR-Cas系统相关的蛋白质。与2000年的菌株相比，发现这些基因在2010年的菌株中存在程度略高，尤其是与限制修饰系统和CRISPR-Cas系统相关的基因。与2000年的菌株相比，也检测到这些基因在2010年的菌株中以更高的比例存在于基因组岛中。当应用个性化疗法时，全基因组测序和生物信息学可能是避免缺点的有力工具。在本研究中，它使我们能够关注临床菌株中的噬菌体抗性，以防止可能的噬菌体疗法失败。
