Abstract
As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin–antitoxin (T–A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.
Highlights
Pseudomonas aeruginosa is a glucose non-fermentative Gramnegative bacillus that can adapt to various ecological niches, such as soil, marshes, coastal marine habitats, and plant and animal tissues [1,2]
P. aeruginosa PA1 was resistant or intermediate-resistant to most of the antibiotics tested (24 out of 29; Figure 1D), including 16 kinds of antibiotics that belong to β-lactams and 8 kinds of antibiotics that belong to nitrofurans, amphenicols, tetracyclines, sulfonamides, quinolones and aminoglycosides
PA1 was sensitive to only five of the tested antibiotics, including polymyxin B and E that belong to polypeptides, amikacin and tobramycin that belong to aminoglycosides, and meropenem that belongs to β-lactams
Summary
Pseudomonas aeruginosa is a glucose non-fermentative Gramnegative bacillus that can adapt to various ecological niches, such as soil, marshes, coastal marine habitats, and plant and animal tissues [1,2]. P. aeruginosa causes a wide range of syndromes in humans; in some instances, its infection is fatal and considered an increasingly notorious pathogen in nosocomial infection [3]. P. aeruginosa is significantly associated with respiratory tract infections, burn infections and urinary-tract infections in catheterized patients [4]. It is the dominant pathogen in cystic fibrosis (CF) lung disease, with single lineage persisting throughout the whole life of a patient [5]. In infections among patients with CF, endocarditis and periodontitis, P. aeruginosa can form biofilms. P. aeruginosa can resist numerous antibiotics because of intrinsic drug resistance. The prevention and treatment of P. aeruginosa are very difficult because of biofilm formation and drug resistance [6,7]
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