Mancilla-Rojano Jetsi, Flores Víctor, Cevallos Miguel A, Ochoa Sara A, Parra-Flores Julio, Arellano-Galindo José, Xicohtencatl-Cortes Juan, Cruz-Córdova Ariadnna
Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico, Mexico.
Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico, Mexico.
Front Microbiol. 2024 Apr 9;15:1335997. doi: 10.3389/fmicb.2024.1335997. eCollection 2024.
INTRODUCTION: The complex, or Acb complex, consists of six species: , and . is the most clinically significant of these species and is frequently related to healthcare-associated infections (HCAIs). Clustered regularly interspaced short palindromic repeat (CRISPR) arrays and associated genes () constitute bacterial adaptive immune systems and function as variable genetic elements. This study aimed to conduct a genomic analysis of Acb complex genomes available in databases to describe and characterize CRISPR systems and genes. METHODS: Acb complex genomes available in the NCBI and BV-BRC databases, the identification and characterization of CRISPR-Cas systems were performed using CRISPRCasFinder, CRISPRminer, and CRISPRDetect. Sequence types (STs) were determined using the Oxford scheme and ribosomal multilocus sequence typing (rMLST). Prophages were identified using PHASTER and Prophage Hunter. RESULTS: A total of 293 genomes representing six Acb species exhibited CRISPR-related sequences. These genomes originate from various sources, including clinical specimens, animals, medical devices, and environmental samples. Sequence typing identified 145 ribosomal multilocus sequence types (rSTs). CRISPR-Cas systems were confirmed in 26.3% of the genomes, classified as subtypes I-Fa, I-Fb and I-Fv. Probable CRISPR arrays and genes associated with CRISPR-Cas subtypes III-A, I-B, and III-B were also detected. Some of the CRISPR-Cas systems are associated with genomic regions related to Cap4 proteins, and toxin-antitoxin systems. Moreover, prophage sequences were prevalent in 68.9% of the genomes. Analysis revealed a connection between these prophages and CRISPR-Cas systems, indicating an ongoing arms race between the bacteria and their bacteriophages. Furthermore, proteins associated with anti-CRISPR systems, such as AcrF11 and AcrF7, were identified in the and genomes. DISCUSSION: This study elucidates CRISPR-Cas systems and defense mechanisms within the Acb complex, highlighting their diverse distribution and interactions with prophages and other genetic elements. This study also provides valuable insights into the evolution and adaptation of these microorganisms in various environments and clinical settings.
引言：Acb复合体由六个菌种组成，分别为[具体菌种1]、[具体菌种2]、[具体菌种3]、[具体菌种4]、[具体菌种5]和[具体菌种6]。其中[具体菌种名称]是临床上最重要的菌种，常与医疗保健相关感染（HCAIs）有关。成簇规律间隔短回文重复序列（CRISPR）阵列及相关基因（[相关基因名称]）构成细菌的适应性免疫系统，并作为可变遗传元件发挥作用。本研究旨在对数据库中可用的Acb复合体基因组进行基因组分析，以描述和表征CRISPR系统及[相关基因名称]基因。 方法：使用CRISPRCasFinder、CRISPRminer和CRISPRDetect对NCBI和BV - BRC数据库中可用的Acb复合体基因组进行CRISPR - Cas系统的鉴定和表征。使用牛津方案和核糖体多位点序列分型（rMLST）确定序列类型（STs）。使用PHASTER和Prophage Hunter鉴定前噬菌体。 结果：代表六个Acb菌种的总共293个基因组显示出与CRISPR相关的序列。这些基因组来源于各种来源，包括临床标本、动物、医疗设备和环境样本。序列分型鉴定出145种核糖体多位点序列类型（rSTs）。在26.3%的基因组中确认了CRISPR - Cas系统，分为I - Fa、I - Fb和I - Fv亚型。还检测到与CRISPR - Cas III - A、I - B和III - B亚型相关的可能的CRISPR阵列及[相关基因名称]基因。一些CRISPR - Cas系统与与Cap4蛋白和毒素 - 抗毒素系统相关的基因组区域有关。此外，前噬菌体序列在68.9%的基因组中普遍存在。分析揭示了这些前噬菌体与CRISPR - Cas系统之间的联系，表明细菌与其噬菌体之间正在进行军备竞赛。此外，在[具体菌种1]和[具体菌种2]基因组中鉴定出了与抗CRISPR系统相关的蛋白质，如AcrF11和AcrF7。 讨论：本研究阐明了Acb复合体中的CRISPR - Cas系统和防御机制，突出了它们的多样分布以及与前噬菌体和其他遗传元件的相互作用。本研究还为这些微生物在各种环境和临床环境中的进化和适应性提供了有价值的见解。
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