Abstract
Pseudomonas aeruginosa is noted for its intrinsic antibiotic resistance and capacity of acquiring additional resistance genes. In this study, the genomes of nine clinical P. aeruginosa isolates were fully sequenced. An extensive genetic comparison was applied to 18 P. aeruginosa accessory genetic elements (AGEs; 13 of them were sequenced in this study and located within P. aeruginosa chromosomes) that were divided into four groups: five related integrative and conjugative elements (ICEs), four related integrative and mobilizable elements (IMEs), five related unit transposons, and two related IMEs and their two derivatives. At least 45 resistance genes, involved in resistance to 10 different categories of antibiotics and heavy metals, were identified from these 18 AGEs. A total of 10 β-lactamase genes were identified from 10 AGEs sequenced herein, and nine of them were captured within class 1 integrons, which were further integrated into ICEs and IMEs with intercellular mobility, and also unit transposons with intracellular mobility. Through this study, we identified for the first time 20 novel MGEs, including four ICEs Tn6584, Tn6585, Tn6586, and Tn6587; three IMEs Tn6853, Tn6854, and Tn6878; five unit transposons Tn6846, Tn6847, Tn6848, Tn6849, and Tn6883; and eight integrons In1795, In1778, In1820, In1784, In1775, In1774, In1789, and In1799. This was also the first report of two resistance gene variants blaCARB-53 and catB3s, and a novel ST3405 isolate of P. aeruginosa. The data presented here denoted that complex transposition and homologous recombination promoted the assembly and integration of AGEs with mosaic structures into P. aeruginosa chromosomes.
Highlights
Pseudomonas aeruginosa is a major opportunistic pathogen and a leading cause of morbidity and mortality in cystic fibrosis patients and immunocompromised individuals (Alvarez-Ortega et al, 2011)
This work presented the complete sequences of 13 P. aeruginosa chromosomal AGEs, which could be divided into four groups: four Tn6417-related integrative and conjugative elements (ICEs) Tn6584, Tn6585, Tn6586 and Tn6587; two Tn6852-related integrative and mobilizable elements (IMEs) Tn6853 and Tn6854; four Tn1403related unit transposons Tn6846, Tn6847, Tn6848 and Tn6849; and one Tn6877-related IME Tn6878 and its two derivatives dfrA12 region and blaVEB-3 region
Of the 10 b-lactamase genes in the 10 chromosomal AGEs sequenced in this study, nine were associated with class 1 integrons
Summary
Pseudomonas aeruginosa is a major opportunistic pathogen and a leading cause of morbidity and mortality in cystic fibrosis patients and immunocompromised individuals (Alvarez-Ortega et al, 2011). MGEs play critical roles in the accumulation and spread of antibiotic resistance genes in P. aeruginosa (Botelho et al, 2019). Among these genetic platforms, the integrative and conjugative elements (ICEs) are transposons which encode self-integration and -conjugation modules, typically including attL (attachment site at the left end), int (integrase), xis (excisionase), rlx (relaxase), oriT (origin of conjugative replication), cpl (coupling protein), a P (TivB)- or F (TivF)type T4SS gene set (mating pair formation), and attR (attachment site at the right end) (Botelho and Schulenburg, 2020). The Tn3-family unit transposons carry a core transposition module typically composed of tnpA (transposase), tnpR (resolvase), and res (resolution site), with a pair of terminal inverted repeats IRL/ IRR (Nicolas et al, 2015)
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