Whole-Genome Analysis of Acinetobacter baumannii Strain AB43 Containing a Type I-Fb CRISPR-Cas System: Insights into the Relationship with Drug Resistance

Abstract

The CRISPR-Cas system is a bacterial and archaea adaptive immune system and is a newly recognized mechanism for controlling antibiotic resistance gene transfer. Acinetobacter baumannii (A. baumannii) is an important organism responsible for a variety of nosocomial infections. A. baumannii infections have become problematic worldwide because of the resistance of A. baumannii to multiple antibiotics. Thus, it is clinically significant to explore the relationship between the CRISPR-Cas system and drug resistance in A. baumannii. This study aimed to analyze the genomic characteristics of the A. baumannii strain AB3 containing the type I-Fb CRISPR-Cas system, which was isolated from a tertiary care hospital in China, and to investigate the relationship between the CRISPR-Cas system and antibiotic resistance in this strain. The whole-genome sequencing (WGS) of the AB43 strain was performed using Illumina and PacBio sequencing. The complete genome of AB43 consisted of a 3,854,806 bp chromosome and a 104,309 bp plasmid. The specific characteristics of the CRISPR-Cas system in AB43 are described as follows: (1) The strain AB43 carries a complete type I-Fb CRISPR-Cas system; (2) Homology analysis confirmed that the cas genes in AB43 share high sequence similarity with the same subtype cas genes; (3) A total of 28 of 105 A. baumannii AB43 CRISPR spacers matched genes in the bacteriophage genome database and the plasmid database, implying that the CRISPR-Cas system in AB43 provides immunity against invasive bacteriophage and plasmids; (4) None of the CRISPR spacers in A. baumannii AB43 were matched with antimicrobial resistance genes in the NCBI database. In addition, we analyzed the presence of antibiotic resistance genes and insertion sequences in the AB43 strain and found that the number of antibiotic resistance genes was not lower than in the “no CRISPR-Cas system” strain. This study supports the idea that the CRISPR-Cas system may inhibit drug-resistance gene expression via endogenous gene regulation, except to the published mechanism that the CRISPR-Cas system efficiently limits the acquisition of antibiotic resistance genes that make bacteria sensitive to antibiotics.

CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance

“…The relationship between drug resistance and the CRISPR-Cas system was analyzed in A. baumannii strain AB43 using the whole-genome sequencing (WGS) technique [ 362 ]. The authors identified the presence of the Type I-Fb CRISPR-Cas system in the strain AB43 and found that the cas gene in the studied strain has a higher similarity index with the similar subtype cas genes.…”

“…However, no matches for CRISPR spacers were found for AMR genes for A. baumannii strain AB43. The drug resistance mechanism in A. baumannii strain AB43 via the CRISPR-Cas system is still unclear, as the endogenous CRISPR-Cas system might be responsible for inhibition of drug resistance gene expression, which requires further research [ 342 , 362 ]. Another study using WGS identified the CRISPR-Cas system Subtype I-F in A. baumannii strain ATCC BAA1605, with a high number of spacers present in the CRISPR loci [ 363 ].…”

Sub-MIC antibiotics increased the fitness cost of CRISPR-Cas in Acinetobacter baumannii

“…Due to its robust survival capabilities, A. baumannii , a non-fermenting Gram-negative bacterium ( De Silva and Kumar, 2019 ; Muller et al, 2023 ) has become the most common source of hospital-acquired infections such as ventilator-associated pneumonia, bloodstream infections, and urinary tract infections ( Guo et al, 2022 ; Cavallo et al, 2023 ). Over the years, owing to the widespread use of antibiotics, the resistance rate of A. baumannii is continually increasing ( Peleg et al, 2008 ; Castillo-Ramirez, 2023 ), making it one of the most critical bacteria for which new antibiotics are urgently needed, as declared by the World Health Organization ( Boucher et al, 2009 ; Tacconelli et al, 2018 ).…”

“…However, with the rising rates of antibiotic resistance, there is an urgent need to explore alternative approaches to prevent resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (CRISPR-Cas) system is a remarkable immune system in prokaryotes that provides adaptive immunity against foreign genetic elements ( Kao et al, 2021 ; Mortensen et al, 2021 ), such as bacteriophages and plasmids ( Li et al, 2016 ; Guo et al, 2022 ). The CRISPR-Cas system has been classified into two categories, with six types (I-VI) and over 30 subtypes based on the composition of effector complexes ( Huang and Zhu, 2020 ).…”

“…The CRISPR-Cas system has been classified into two categories, with six types (I-VI) and over 30 subtypes based on the composition of effector complexes ( Huang and Zhu, 2020 ). In A. baumannii , the most prevalent CRISPR-Cas system type is the I-F subtype ( Guo et al, 2022 ; Wang et al, 2022 ). The I-Fb CRISPR-Cas system consists of Cas1, Cas3, Csy1, Csy2, Csy3, Csy4, and CRISPR arrays ( Wang et al, 2022 ; Camara-Wilpert et al, 2023 ).…”