Genomics of Aminoglycoside Resistance in Pseudomonas aeruginosa Bloodstream Infections at a United States Academic Hospital

Abstract

Pseudomonas aeruginosa is a frequent cause of antibiotic-resistant infections. Although P. aeruginosa is intrinsically resistant to many antimicrobial agents, aminoglycosides are active against this organism in the absence of acquired resistance determinants and mutations. However, genes encoding aminoglycoside modifying enzymes (AMEs) are found in many strains that are resistant to these agents. We examined the prevalence of phenotypic resistance to the commonly used aminoglycosides gentamicin, tobramycin, and amikacin in a collection of 227 P. aeruginosa bloodstream isolates collected over two decades from a single U.S. academic medical institution. Resistance to these antibiotics was relatively stable over this time period. High-risk clones ST111 and ST298 were initially common but decreased in frequency over time. Whole genome sequencing identified relatively few AME genes in this collection compared to the published literature; only 14% of isolates contained an AME gene other than the ubiquitous aph(3’)-IIb. Of those present, only ant(2”)-Ia was associated with phenotypic resistance to gentamicin or to tobramycin. One extensively drug-resistant strain, PS1871, contained 5 AME genes, most of which were part of clusters of antibiotic resistance genes embedded within transposable elements. These findings suggest that AME genes play a relatively minor role in aminoglycoside resistance at our institution but that multidrug-resistant strains remain a problem.

High Rates of Aminoglycoside Methyltransferases Associated with Metallo-Beta-Lactamases in Multidrug-Resistant and Extensively Drug-Resistant Pseudomonas aeruginosa Clinical Isolates from a Tertiary Care Hospital in Egypt

“…16 Our results confirm findings from the USA, showing that AMEs play a relatively minor role in aminoglycoside resistance. 28 In the current study, a single aminoglycoside resistance gene was detected in 15 (45%) of the isolates, while a combination of two genes was found in three (9%), and the combination of three genes was detected in only one isolate (3%) of the 33 studied MDR P. aeruginosa strains (Table 2).…”

“… 16 Our results confirm findings from the USA, showing that AMEs play a relatively minor role in aminoglycoside resistance. 28 …”

Aminoglycoside-Modifying Enzymes Are Sufficient to Make Pseudomonas aeruginosa Clinically Resistant to Key Antibiotics

“…The most frequent AME-encoding genes in our survey of over 700 genomes were ant(2″)-I and acc(6′)-I , which are commonly found in integrons and that mediate resistance to gentamicin and tobramycin [ 44 , 45 , 46 ], and aph (3′) -VI, which is present in transposons in isolates resistant to amikacin [ 47 , 48 , 49 ]. The same genes were the most frequent AME-encoding genes in aminoglycoside-resistant isolates of P. aeruginosa in other studies [ 40 , 50 , 51 ] underscoring their importance in aminoglycoside resistance in this species. Multiple AME genes were often located on the same mobile genetic elements along with genes associated with resistance to other classes of antibiotics, and some isolates contained multiple copies of the same AME gene ( Figure 2 ; Table S3 ).…”

“…To mimic the effects of horizontal gene transfer, we introduced the cloned genes into isolates lacking mobile genetic elements. Ant (2″)-Ia and aac6′-Ib3 , which are associated with gentamicin and tobramycin resistance [ 7 , 52 ] ( Figure 3 ), conferred resistance to these antibiotics on all four isolates tested, making all of them clinically resistant while having no effect on amikacin susceptibility [ 50 , 52 ]. Similarly, aph (3′)-VIa , a frequent AME determinant in amikacin-resistant isolates of P. aeruginosa [ 7 , 29 , 40 , 51 ], made all four tested isolates resistant to this antibiotic while having no effects on tobramycin and gentamicin MICs.…”

Core Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates

“…Additionally, this species can possess 16S rRNA gene methyl transferases, which can render aminoglycosides inactive ( 26 – 28 ). Finally, the efflux pump system MexXY-OprM has been demonstrated to contribute to aminoglycoside resistance ( 29 ).…”