Abundant diversity of accessory genetic elements and associated antimicrobial resistance genes in pseudomonas aeruginosa isolates from a single Chinese hospital

Abstract

Objectives Pseudomonas aeruginosa has intrinsic antibiotic resistance and the strong ability to acquire additional resistance genes. However, a limited number of investigations provide detailed modular structure dissection and evolutionary analysis of accessory genetic elements (AGEs) and associated resistance genes (ARGs) in P. aeruginosa isolates. The objective of this study is to reveal the prevalence and transmission characteristics of ARGs by epidemiological investigation and bioinformatics analysis of AGEs of P. aeruginosa isolates taken from a Chinese hospital. Methods Draft-genome sequencing was conducted for P. aeruginosa clinical isolates (n = 48) collected from a single Chinese hospital between 2019 and 2021. The clones of P. aeruginosa isolates, type 3 secretion system (T3SS)-related virulotypes, and the resistance spectrum were identified using multilocus sequence typing (MLST), polymerase chain reaction (PCR), and antimicrobial susceptibility tests. In addition, 17 of the 48 isolates were fully sequenced. An extensive modular structure dissection and genetic comparison was applied to AGEs of the 17 sequenced P. aeruginosa isolates. Results From the draft-genome sequencing, 13 STs were identified, showing high genetic diversity. BLAST search and PCR detection of T3SS genes (exoT, exoY, exoS, and exoU) revealed that the exoS+/exoU- virulotype dominated. At least 69 kinds of acquired ARGs, involved in resistance to 10 different categories of antimicrobials, were identified in the 48 P. aeruginosa isolates. Detailed genetic dissection and sequence comparisons were applied to 25 AGEs from the 17 isolates, together with five additional prototype AGEs from GenBank. These 30 AGEs were classified into five groups -- integrative and conjugative elements (ICEs), unit transposons, IncpPBL16 plasmids, Incp60512−IMP plasmids, and IncpPA7790 plasmids. Conclusion This study provides a broad-scale and deeper genomics understanding of P. aeruginosa isolates taken from a single Chinese hospital. The isolates collected are characterized by high genetic diversity, high virulence, and multiple drug resistance. The AGEs in P. aeruginosa chromosomes and plasmids, as important genetic platforms for the spread of ARGs, contribute to enhancing the adaptability of P. aeruginosa in hospital settings.

Genetic Characteristics of Novel IncpSE5381-aadB Plasmids, Integrative and Mobilizable Elements, and Integrative and Conjugative Elements in Pseudomonas aeruginosa

“…13 IMEs typically utilize conjugation mechanisms encoded by other MGEs to achieve transfer and integration 14 while ICEs mainly use tyrosine/serine recombinases or DDE transposases for chromosomal integration and excision. 15 In previous study, a number of novel MGEs were identified in P. aeruginosa in China, such as the novel Inc groups: Inc p60512−IMP and Inc pPA7790 ; 16 Tn6852-related IMEs carrying bla PER-1 and bla CARB-2 : Tn6853; 17 Tn6417-related ICEs carrying bla VIM-1 : Tn6953; 18 and Multiple Tn1403-related transposons carrying different class 1 integrons: Tn6847, Tn6849, Tn7454, Tn7484, etc. 16,17,19 Multiple types of novel MGEs are frequently identified in China, which pose unknown challenges to the containment of bacterial resistance.…”

“…15 In previous study, a number of novel MGEs were identified in P. aeruginosa in China, such as the novel Inc groups: Inc p60512−IMP and Inc pPA7790 ; 16 Tn6852-related IMEs carrying bla PER-1 and bla CARB-2 : Tn6853; 17 Tn6417-related ICEs carrying bla VIM-1 : Tn6953; 18 and Multiple Tn1403-related transposons carrying different class 1 integrons: Tn6847, Tn6849, Tn7454, Tn7484, etc. 16,17,19 Multiple types of novel MGEs are frequently identified in China, which pose unknown challenges to the containment of bacterial resistance. It is necessary to pay close attention to the emergence of novel MGEs and their genetic evolution characteristics.…”