Mobile Carbapenemase Genes in Pseudomonas aeruginosa

Abstract

Carbapenem-resistant Pseudomonas aeruginosa is one of the major concerns in clinical settings impelling a great challenge to antimicrobial therapy for patients with infections caused by the pathogen. While membrane permeability, together with derepression of the intrinsic beta-lactamase gene, is the global prevailing mechanism of carbapenem resistance in P. aeruginosa, the acquired genes for carbapenemases need special attention because horizontal gene transfer through mobile genetic elements, such as integrons, transposons, plasmids, and integrative and conjugative elements, could accelerate the dissemination of the carbapenem-resistant P. aeruginosa. This review aimed to illustrate epidemiologically the carbapenem resistance in P. aeruginosa, including the resistance rates worldwide and the carbapenemase-encoding genes along with the mobile genetic elements responsible for the horizontal dissemination of the drug resistance determinants. Moreover, the modular mobile elements including the carbapenemase-encoding gene, also known as the P. aeruginosa resistance islands, are scrutinized mostly for their structures.

Keywords: Pseudomonas aeruginosa; carbapenem resistance; carbapenemase; genomic islands; mobile genetic elements; molecular epidemiology.

FIGURE 1

Carbapenem drugs. The backbone of carbapenems is in a box. The C-1 position replaced from the sulfur atom in the penicillin backbone is indicated with a red dot. The important R1 and R3 positions are indicated with red letters. Ertapenem with a bulky R3 residue, which does not have enough affinity to be active against Pseudomonas aeruginosa, is presented with the other three carbapenems having antipseudomonal activity.

FIGURE 2

A stereoview of PBP3 of Pseudomonas aeruginosa complexed with meropenem (PDB ID, 3PBR) and the interaction of the meropenem in the ligand pocket of PBP3 (Han et al., 2010). The structure of PBP3 is colored by secondary structure, and the meropenem is in a ball-and-stick presentation. The molecular surface of PBP3 in the binding pocket is presented with the interacting amino acid residue complex with meropenem in a ball-and-stick presentation.

FIGURE 3

Rates of imipenem resistance in Pseudomonas aeruginosa worldwide in 2018. All the data were extracted from the Antimicrobial Testing Leadership and Surveillance run by Pfizer (last updated on October 30, 2019) (Pfizer, 2020), except for the data from South Korea (unpublished data). The actual resistance rates are indicated per continent as follows: Africa [three participating countries: Morocco (N = 79, 22.8%), Nigeria (N = 38, 13.2%), South Africa (N = 98, 21.4%)]; Asia [10 participating countries: China (N = 386, 33.2%), Hong Kong (N = 25, 24%), India (N = 125, 29.6%), Japan (N = 75, 8%), Malaysia (N = 55, 21.8%), Philippines (N = 74, 18.9%), Singapore (N = 25, 16%), South Korea (N = 127, 18.1%), Taiwan (N = 99, 9.1%), and Thailand (N = 75, 16%)]; Europe [24 participating countries: Belgium (N = 150, 21.3%), Croatia (N = 78, 35.9%), Czech Republic (N = 102, 29.4%), Denmark (N = 25, 8%), Finland (N = 19, 0%), France (N = 248, 20.2%), Germany (N = 248, 27.4%), Greece (N = 75, 30.7%), Hungary (N = 100, 42%), Ireland (N = 64, 18.8%), Italy (N = 242, 28.5%), Latvia (N = 24, 33.3%), Lithuania (N = 50, 22%), Poland (N = 101, 39.6%), Portugal (N = 99, 32.3%), Romania (N = 99, 45.5%), Russia (N = 194, 48.5%), Netherlands (N = 40, 17.5%), Spain (N = 273, 19.4%), Sweden (N = 25, 8%), Switzerland (N = 50, 10%), Turkey (N = 60, 43.3%), Ukraine (N = 53, 54.7%), and United Kingdom (N = 158, 19.6%)]; Mid and South America [10 participating countries: Brazil (N = 116, 16.4%), Chile (N = 75, 49.3%), Colombia (N = 124, 30.7%), Costa Rica (N = 22, 13.6%), Dominican Republic (N = 24, 12.5%), Guatemala (N = 55, 16.4%), Mexico (N = 146, 42.5%), Panama (N = 32, 37.5%), and Venezuela (N = 64, 45.3%)]; North America [two participating countries: Canada (N = 197, 27.4%) and the United States (N = 588, 21.4%),]; Middle East [four participating countries: Israel (N = 100, 12%), Jordan (N = 24, 29.2%), Kuwait (N = 76, 44.7%), and Saudi Arabia (N = 26, 38.5%)]; and Oceania [a single participating country: Australia (N = 99, 7.1%)].

FIGURE 4

Worldwide identification of the carbapenemase-producing Pseudomonas aeruginosa. Reports of class A [Klebsiella pneumoniae carbapenemase (KPC) and Guiana extended-spectrum beta-lactamase (GES) with amino acid alteration at aa 170], class B [Verona integron-encoded MBL (VIM), imipenemase (IMP), New Delhi MBL (NDM), and others], and class D (OXA) carbapenemases are indicated in a geographic map. The references used for the map drawing are indicated in the main text.

FIGURE 5

Epidemic carbapenemase-producing high-risk Pseudomonas aeruginosa clones identified worldwide. Regional dissemination of specific P. aeruginosa clones identified through multilocus sequence typing (MLST) is indicated in color on a geographic map, and the carbapenemases produced are indicated at the region. The number of countries with reports of the P. aeruginosa clone are indicated in the figure legends. References are indicated in the main text.

FIGURE 6

Transposable units identified in Pseudomonas aeruginosa carrying the carbapenemase-encoding genes. The red arrow indicates the genes for antimicrobial resistance, and those with yellow letters inside indicate the genes for carbapenemase. Yellow arrows depict insertion sequences, and those in orange indicate transposase/resolvase.

FIGURE 7

Mechanisms of replicative transposition of the transposons. (A) Insertion sequence with a common region (ISCR)-mediated rolling circle replicative transposition is involved in rolling circle replication. ISCR elements lack terminal inverted repeats, and a single copy of the element is able to transpose adjacent DNA sequences (Toleman et al., 2006). (B) A Tn3-mediated copy-and-paste replicative transposition requires both a transposase and a resolvase. The transposon is replicated, joining the donor and the recipient in a cointegrate, which is resolved to give the donor and the recipient of the transposon (Grindley, 1983).

FIGURE 8

Organization of the integron and the process of capturing and exchanging the gene cassettes. The open arrow indicates the open reading frame and is colored based on its function: the antimicrobial resistance gene is in red or in magenta, the attC gene is in green, and the intI1 gene is in orange. The open box indicates the attI locus. The integron is organized as a functional platform including the intI1 gene and the attI locus and a cassette array assembled through the acquisition of gene cassettes structured with an open reading frame and an attC locus. Expression of the gene cassettes is dependent on the common promoter, Pc, and the level of expression depends on the distance from the Pc. The IntI1 integrase binds to the attC locus of the excised gene cassette to help circularize the cassette (Collis et al., 1993; Hall and Collis, 1995).

FIGURE 9

Transposons giving mobility to integrons. Transposons are indicated in scale with the component. The accession number of each sequence is indicated in brackets. Arrows indicate open reading frames with filled colors that differ by function: yellow, transposition; orange, class 1 integrase; red, antimicrobial resistance; green, heavy metal resistance (Radstrom et al., 1994; Minakhina et al., 1999; Shi et al., 2018).

FIGURE 10

Schematic presentation of the structure of genomic islands belonging to the three groups. The schematic structure is presented for the three groups of genomic islands: (A) Group 1 resistance islands equipping the tyrosine-based integrase gene at the 5’ terminal and the conjugative transfer machinery gene cluster at the 3’ terminus, (B) Group 2 resistance islands carrying a transposition module of a whole or a partial TniABQR component, (C) and the others. The genes are indicated with open arrows and colored based on function: genes for integration and recombination of the genomic island are in yellow, genes for antimicrobial resistance (AMR) are in red, genes for heavy metal resistance (HMR) are in green, the intI1 gene is in orange, conjugative transfer module mostly composed of the type 4 pili assembly genes is in black, and the core gene is in gray. The open box indicates inverted repeats (IRs) left and right, named the attL and attR loci for integration conjugative elements.