Long-term Persistence of an Extensively Drug-Resistant Subclade of Globally Distributed Pseudomonas aeruginosa Clonal Complex 446 in an Academic Medical Center

Abstract

Background: Antimicrobial resistance (AMR) is a major challenge in the treatment of infections caused by Pseudomonas aeruginosa. Highly drug-resistant infections are disproportionally caused by a small subset of globally distributed P. aeruginosa sequence types (STs), termed "high-risk clones." We noted that clonal complex (CC) 446 (which includes STs 298 and 446) isolates were repeatedly cultured at 1 medical center and asked whether this lineage might constitute an emerging high-risk clone.

Methods: We searched P. aeruginosa genomes from collections available from several institutions and from a public database for the presence of CC446 isolates. We determined antibacterial susceptibility using microbroth dilution and examined genome sequences to characterize the population structure of CC446 and investigate the genetic basis of AMR.

Results: CC446 was globally distributed over 5 continents. CC446 isolates demonstrated high rates of AMR, with 51.9% (28/54) being multidrug-resistant (MDR) and 53.6% of these (15/28) being extensively drug-resistant (XDR). Phylogenetic analysis revealed that most MDR/XDR isolates belonged to a subclade of ST298 (designated ST298*) of which 100% (21/21) were MDR and 61.9% (13/21) were XDR. XDR ST298* was identified repeatedly and consistently at a single academic medical center from 2001 through 2017. These isolates harbored a large plasmid that carries a novel antibiotic resistance integron.

Conclusions: CC446 isolates are globally distributed with multiple occurrences of high AMR. The subclade ST298* is responsible for a prolonged epidemic (≥16 years) of XDR infections at an academic medical center. These findings indicate that CC446 is an emerging high-risk clone deserving further surveillance.

Keywords: Pseudomonas aeruginosa; antimicrobial resistance; high-risk clone; phylogenetics; plasmid.

Figure 1.

Clonal complex definition and global distribution of CC446. A, Global optimal eBURST diagram showing sequence types in CC446. The likely founder of the clonal complex (ST446) is indicated in light green, and subgroup founders (ST298 and ST1963) are indicated in dark green. B, World map indicating countries where CC446 isolates have been detected. Countries with at least 1 isolate associated with a genome analyzed in this study are shaded blue. Countries in which a CC446 isolate has been reported but no genome was available are shaded in black.

Figure 2.

Characterization of the plasmid pPABL048. A, Description of the antimicrobial resistance (AMR) class I integron in1697 of pPABL048. in1697 consists of a 5’ conserved segment (5’-CS) with the integrase intI1 and promoter Pc, AMR cassettes, and a 3’ conserved segment (3’-CS) of qacE∆1 and sul1. Complete attC recombination sites were identified downstream of qacF and aadB, and truncated attC sites were identified downstream of blaOXA-10 and aad10Ae. in1697 appears to be part of a transposable-like element that includes a partial tni transposon operon and has as its borders IRi and IRt (25-bp imperfect [92% identity] inverted repeats). B, Diagram of pPABL048 with rings (from in to out) showing guanine-cytosine (GC) skew, GC%, coding sequences, and position in base pairs. The location of in1697 is highlighted in red.

Figure 3.

Recombination-corrected maximum likelihood phylogenetic tree of the CC446 isolates included in this study based on core genome alignment to the chromosome of PABL048. A, Midpoint-rooted circular tree annotated (from inner to outer rings) with sequence type, collection of origin, and the presence of in1697. B, Unrooted radial tree with sequence type and subclade indicated by blue (ST446), green (ST298), and gray (ST298*) outlines. Isolates collected from NMH are indicated with purple circles. Abbreviations: BWH, Brigham and Women’s Hospital; Hosp_Env, Hospital Environment; NCBI, National Center for Biotechnology Information; NMH, Northwestern Memorial Hospital; SNV, single-nucleotide variant; PASP, Pseudomonas aeruginosa Spain.

Figure 4.

Time-scaled phylogenetic tree of ST298* isolates. Tips indicate date of isolation. Root is the estimated last common ancestor of these isolates (mean, 1980.9; 95% highest posterior density interval, 1973.8–1987.4). The presence of in1697 is indicated by shaded bars on the right, with light gray indicating heterogenous presence in only some colonies for a given isolate.