Novel Chromosome-Borne Accessory Genetic Elements Carrying Multiple Antibiotic Resistance Genes in Pseudomonas aeruginosa

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 bla_CARB-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.

Keywords: Pseudomonas aeruginosa; ST3405; blaCARB-53; catB3s; mobile genetic elements; β-lactam resistance.

Figure 1

Heatmap of prevalence of resistance genes. The original data are shown in Table S2.

Figure 2

Comparison of five related ICEs Tn6417, Tn6584, Tn6585, Tn6586, and Tn6587. Genes are denoted by arrows. Genes, MGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥90%), light orange (nucleotide identity <90%). The accession number of Tn6417 (Valot et al., 2014) used as reference is EU696790.

Figure 3

Comparison of Tn6532, Tn6807, Tn6808 and Tn6809, and organization of In1784. Shown are five Tn6346-related transposons (A) and one integron In1784 (B). Genes are denoted by arrows. Genes, MGEs, and other features are colored based on their functional classification. Shading denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains DHS01, SE5352, SE5331, 31130, and 201330, respectively. The accession number of Tn6346 (Ng et al., 2009) used as reference is EU696790.

Figure 4

Organization of four related IMEs Tn6852, Tn6853, Tn6854, and Tn6855. Genes are denoted by arrows. Genes, MGEs, and other features are colored based on their functional classification. Shading denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains PA38182, YT12746 and YTSEY8, and the plasmid pHNAH8I-1 of strain AHM7C8I, respectively. The accession number of Tn6852 (Witney et al., 2014) used as reference is HG530068.

Figure 5

Organization of five related unit transposons Tn1403, Tn6846, Tn6847, Tn6848, and Tn6849. Shown are five Tn1403-related regions (A) and two Tn6489b-related transposons (B). Genes are denoted by arrows. Genes, MGEs, and other features are colored based on their functional classification. Shading denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains SE5357, YTSEY8, YT12746, and YTSEY8, respectively. The accession numbers of Tn1403 (Stokes et al., 2007) and Tn6489b (Jiang et al., 2020) used as reference are AF313472 and MF344569, respectively.

Figure 6

Organization of two related IMEs Tn6877 and Tn6878, and their derivatives dfrA12 region and bla_VEB-3 region. Genes are denoted by arrows. Genes, MGEs, and other features are colored based on their functional classification. Shading denotes regions of homology (nucleotide identity ≥95%). The accession number of Tn6877 (Espinosa-Camacho et al., 2017) used as reference is CP021775.

Figure 7

Comparison of Tn6882, Tn6883, and related regions. Shown are five Tn21-related regions (A) and VR3_In1799/VR2_In27 (B). Genes are denoted by arrows. Genes, MGEs, and other features are colored based on their functional classification. Shading denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains Pa58, SE5429, and SE5458, respectively. The accession numbers of Tn21 (Partridge et al., 2001) and IS26–rmtB–qepA–IS26 unit (Yamane et al., 2007) used as reference are AF071413 and AB263754, respectively.