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. 2009 Mar 30;53(6):2522–2531. doi: 10.1128/AAC.00035-09

Genomewide Identification of Genetic Determinants of Antimicrobial Drug Resistance in Pseudomonas aeruginosa▿

Andreas Dötsch 1, Tanja Becker 1, Claudia Pommerenke 1, Zofia Magnowska 2, Lothar Jänsch 2, Susanne Häussler 1,3,*
PMCID: PMC2687185  PMID: 19332674

Abstract

The emergence of antimicrobial drug resistance is of enormous public concern due to the increased risk of delayed treatment of infections, the increased length of hospital stays, the substantial increase in the cost of care, and the high risk of fatal outcomes. A prerequisite for the development of effective therapy alternatives is a detailed understanding of the diversity of bacterial mechanisms that underlie drug resistance, especially for problematic gram-negative bacteria such as Pseudomonas aeruginosa. This pathogen has impressive chromosomally encoded mechanisms of intrinsic resistance, as well as the potential to mutate, gaining resistance to current antibiotics. In this study we have screened the comprehensive nonredundant Harvard PA14 library for P. aeruginosa mutants that exhibited either increased or decreased resistance against 19 antibiotics commonly used in the clinic. This approach identified several genes whose inactivation sensitized the bacteria to a broad spectrum of different antimicrobials and uncovered novel genetic determinants of resistance to various classes of antibiotics. Knowledge of the enhancement of bacterial susceptibility to existing antibiotics and of novel resistance markers or modifiers of resistance expression may lay the foundation for effective therapy alternatives and will be the basis for the development of new strategies in the control of problematic multiresistant gram-negative bacteria.

There is accumulating evidence that appropriate antibacterial therapy administered early in the course of an infection has major implications for the outcomes of severe bacterial diseases (20, 21, 43). Patients have greatly benefited from the introduction of effective antimicrobials in the past decades; however, the frequency and spectrum of antibiotic-resistant infections have increased worldwide, and substantially higher mortality rates have been reported for patients given ineffective empirical therapy, mainly due to resistance to the agents used (39). Today, in many intensive-care units, multidrug-resistant gram-negative bacteria pose the greatest therapeutic challenge. Therefore, understanding the mechanisms of resistance and developing therapy alternatives for problematic gram-negative bacteria are of profound importance.

The increase in the incidence of multidrug resistance has been attributed to a combination of microbial characteristics, the selective pressure of antimicrobial use, and enhanced transmission of resistant organisms. This growing problem requires a comprehensive strategy that includes compliance with infection control principles, rational use of current antimicrobial agents, and the development of new active agents. The diversity of bacterial mechanisms that underlie multidrug resistance makes the development of effective new antimicrobial agents, especially against problematic species such as Pseudomonas aeruginosa, very difficult. This opportunistic gram-negative rod plays a dominant role as an infectious agent in the lungs of cystic fibrosis patients and has emerged as one of the most important human pathogens causing serious nosocomial infections. P. aeruginosa is able to thrive in various environments and utilizes a broad spectrum of virulence factors to infect different hosts, from plants and insects to humans. Due to intrinsic antibiotic resistance, P. aeruginosa infections are difficult to treat and are associated with high mortality rates (10). The intrinsic resistance to antibiotics seems to result mainly from the reduced permeability of the bacterial cell envelope and the activity of multidrug efflux pumps; however, other, yet to be discovered mechanisms might contribute.

Recent publications have aimed at identifying the intrinsic “resistome” of P. aeruginosa by screening transposon mutant libraries for the profiles of resistance to several antibiotics (7, 16, 40, 45). From these studies it has become clear that many previously unidentified genes play a role in antimicrobial resistance and that, depending on the antibiotic, there are many modifiers of the expression of resistance in P. aeruginosa.

In this study we proceeded in the identification of the P. aeruginosa resistome. We made use of a semiautomated antibiotic susceptibility test method and systematically screened the Harvard Medical School PA14 transposon mutant library (27) for mutants with either increased or decreased susceptibility to 19 different antimicrobial agents commonly used in the clinic. This approach not only uncovered novel genetic determinants of resistance in P. aeruginosa to specific antimicrobial compounds but also identified genes whose inactivation sensitized the bacteria to a broad spectrum of different antimicrobials. Our results provide valuable information for further studies aiming at predicting antibiotic resistance based on genotype and have also led to the identification of promising novel drug targets. Targets that enhance bacterial susceptibility could be the basis for the development of drugs that potentate existing antimicrobials and thus may function as chemosensitizers. Examples of such novel antimicrobial combinations are the use of inhibitors of efflux pumps in combination with tetracycline (TET) against E. coli (30) or in combination with ciprofloxacin (CIP) against P. aeruginosa (28).

MATERIALS AND METHODS

Bacterial strains.

The PA14 transposon mutant library described by Liberati et al. (27) was used to screen a comprehensive set of mutants for their resistance profiles. This library was constructed using a mariner-based transposon containing the resistance cassette aacC1, which confers resistance to gentamicin but not to tobramycin (TOB). The PAO1 transposon mutant library of the University of Washington (22) was used for verification and cross-referencing purposes. This library was constructed using two transposons derived from the IS50 element of transposon Tn5, containing a tetracycline resistance cassette.

Antimicrobial resistance screening. (i) Semiautomated susceptibility testing with Vitek 2.

PA14 mutants were streaked onto Columbia agar plates and incubated at 37°C overnight. A sufficient number of colonies was suspended in sterile saline (0.45%) and adjusted to a 0.5 McFarland turbidity standard using a DensiChek densitometer (bioMérieux). The inoculated tube was placed in a cassette on the Vitek 2 Smart Carrier Station. The sample number was entered and associated with an antimicrobial susceptibility test (AST) card. The Smart Carrier Station cassette with the cards and the test tubes was placed on the Vitek 2 instrument, where the inoculation of the AST cards was automatically performed by the instrument.

(ii) Susceptibility testing by agar dilution.

For standard agar dilution testing, LB agar plates containing serial twofold dilutions of the antimicrobial agents to be tested were prepared, stored at 4°C, and used within 5 days. Overnight-grown P. aeruginosa mutants were diluted 1:100 in 0.9% NaCl solution and replica plated onto the LB agar containing the respective antibiotics in twofold dilutions, with duplicate plates for each single dilution. For testing of both hypersusceptible and hyperresistant mutants, susceptibility to single antibiotics belonging to six different classes was tested: piperacillin (PIP) (penicillins), meropenem (MEM) (carbapenems), ceftazidime (CAZ) (cephalosporins), CIP (fluoroquinolones), TOB (aminoglyocosides), and TET (tetracyclines). The agar plates were incubated at 37°C and read at 18 to 24 h. The MIC was considered to be the lowest concentration of an antimicrobial agent that completely inhibited growth as detected visually.

Purification of membrane proteins.

Wild-type PA14 and the PA14 oprF transposon mutants were grown overnight in 20 ml LB medium at 37°C. Cells were harvested (at 6,000 × g for 10 min) and resuspended in 100 mM CH3COOK, 5 mM (CH3COO)2Mg·4H2O, 0.2% (vol/vol) β-mercaptoethanol, 50 mM HEPES (pH 7.5) containing Complete EDTA-free protease inhibitor cocktail (Roche). Cells were lysed by a French press (four times at 1,000 lb/in2), and unbroken cells were removed by centrifugation. The supernatant was adjusted to 20% sucrose, loaded onto an isopycnic sucrose gradient (3 ml of 80% sucrose, 3 ml of 60% sucrose, 13 ml of 20% sucrose/membrane fraction, 3 ml water cushion), and ultracentrifuged (at 100,000 × g for 1 h). Membranes enriched at the 20/60% and 60/80% sucrose interphases were collected from the gradient using a Pasteur pipette and washed with water in the presence of Complete protease inhibitor cocktail (Roche). Associated proteins were rejected by carbonate extraction (17), and the remaining membrane proteins were precipitated according to the method of reference 44. Five-microgram portions of both wild-type and mutant membrane proteins were suspended in loading buffer, separated on a 12% sodium dodecyl sulfate (SDS)-polyacrylamide gel, and stained with colloidal Coomassie blue.

RESULTS AND DISCUSSION

In this study we have screened an ordered, comprehensive PA14 transposon mutant library (27) for mutants exhibiting either increased or decreased susceptibility to various antimicrobial agents. AST was performed with the Vitek 2 system (bioMérieux, Marcy l'Étoile, France). This is an automated, short-incubation broth dilution system capable of performing susceptibility testing based on bacterial growth curves. Twenty different antimicrobial agents were tested using the AST-N063 card at given concentration ranges. These included the two carbapenems ertapenem (ETP) and MEM; the two penicillins ampicillin (AMP) and PIP, both also used in combination with beta-lactam inhibitors in ampicillin-sulbactam (SAM) and piperacillin-tazobactam (TZP); the seven cephalosporins (narrow to extended spectrum), cefazolin (CFZ), cefoxitin (FOX), cefpodoxime (CPD), cefuroxime (CXM), cefotaxime (CTX), CAZ, and cefepime (FEP); the aminoglycoside TOB; the three gyrase inhibitors CIP, levofloxacin (LVX), and nalidixic acid (NAL); one tetracycline, tigecycline (TGC); and trimethoprim-sulfamethoxazole (SXT). Figure 1 summarizes the Vitek 2 MIC results for 4,676 single-gene-knockout PA14 transposon mutants. Since the MICs for wild-type PA14 were lower than the MIC calling ranges of PIP, TZP, MEM, FEP, CIP, and TOB, only mutants that exhibited an increase in the resistance profile could be detected for these antibiotics (Fig. 1). Vice versa, the MICs for wild-type PA14 were greater than the MIC calling ranges of AMP, SAM, ETP, CFZ, FOX, CPD, CXM, NAL, and TGC. Thus, for these antibiotics, only mutants that exhibited enhanced susceptibility could be detected. The MICs of CTX, CAZ, LVX, and SXT were within the given MIC calling range, and therefore both mutants that exhibited increased susceptibility and those with decreased susceptibility were identified. Additionally, the AST-N063 card includes the aminoglycoside gentamicin, which could not be used for the analysis because the transposon applied to create the PA14 mutant library carries a gentamicin resistance cassette (27).

FIG. 1.

FIG. 1.

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AST of the Harvard P. aeruginosa PA14 transposon mutant library using the Vitek 2 system. Min and Max, minimum and maximum MICs (in micrograms per milliliter) that can be determined with the Vitek 2 system. Calling ranges are also indicated by a box in each column. The MIC of each antibiotic for wild-type PA14 is given by aligning the number of wild-type PA14 isolates (shaded) horizontally with the applicable MIC on the left. Similarly, the distribution of the MICs of a particular antibiotic across all PA14 mutants is given by aligning the numbers of mutant isolates horizontally with the applicable MICs on the left. A MIC below the calling range should be read as “less than or equal to” the value given, and a MIC above the calling range should be read as “greater than or equal to” the value given. Note that the MICs for SXT are shown in the rightmost column. Failed, number of failed measurements.

Interestingly, while there was significant overlap of mutants identified in this and previous screens for the “intrinsic” resistome of the PA14 strain (7, 40, 44), only four mutants were identified both in our PA14 screen and a published Tb and 59.20 strain screen for antibiotic resistance (16). It is known that, while all P. aeruginosa strains share a large common set of “core genes,” their genetic repertoire exhibits great variation in the “accessory genome,” which has substantial influence on the phenotype of the strain. Although most of the mutations identified in the two studies affect common (core) genes of P. aeruginosa, the (accessory) genetic background might strongly affect the actual resistance phenotype.

Identification of hypersusceptible P. aeruginosa mutants.

Using this global approach, we identified 40 PA14 mutants that exhibited enhanced susceptibility to at least 2 out of 13 antibiotics or antibiotic combinations (Table 1). Since the Vitek 2 system records MICs on the basis of bacterial growth, we included the growth rates of these mutants in Table 1 (determined from the maximum slope of the growth curve of the AST control; the growth rate of the wild-type control was defined as 1.0). Some mutants exhibited slight growth advantages, whereas others grew more slowly than the wild type and did not reach the maximal optical density (not shown). However, no mutant exhibited serious growth alterations.

TABLE 1.

List of mutants hypersusceptible to at least two different antibiotics

PA14 gene locus PAO1 ortholog Gene name Growthb Log2 change in the MICa of:
SAMc,d ETPc,d CTXc CAZc LVXc NALc,d TGCc,d SXTc
PA14_05530 PA0425 mexA 1.07 −1f,g −3f,g −1f,g ≤−1f,g ≤−1g −1g −2f ≤−2
PA14_05540 PA0426 mexB 1.03 −2f −4f −2f ≤−1f ≤−1g −1g ≤−2
PA14_07430 PA0572 1.05 −1f,g −1f ≤−1f ≤−1g −1
PA14_07770 PA0595 ostA 0.94 ≤−1f −1
PA14_54410 PA0764 mucB 1.35 −1f,g ≤−1f,g ≤−1g −1
PA14_54330 PA0770e rnc 0.78 ≤−1f ≤−1 −1f
PA14_53970 PA0794 1.19 −1f ≤−1f ≤−1g −1
PA14_53000 PA0871 phhB 0.66 −1g ≤−1f ≤−2
PA14_52260 PA0928 1.39 −1f ≤−1f ≤−1g −1
PA14_51780 PA0967 ruvB 1.15 −1f ≤−1f ≤−1 −1
PA14_51320 PA1005 1.01 ≤−1f ≤−1g −1
PA14_49320 PA1167 0.95 −1g −1f ≤−1f ≤−1g −1
PA14_47230 PA1316 1.01 −2g −1f ≤−1f −1
PA14_41570 PA1777 oprF 1.17 −1f,g −2f −1f,g ≤−1f,g ≤−1f,g ≤−4f ≤−2
PA14_40620 PA1848 1.39 −1f,g ≤−1f,g ≤−1g −1
PA14_38530 PA2008 fahA 0.77 −1 −1g −1f ≤−1f
PA14_30290 PA2615e ftsK 1.31 −3f −2f ≤−1f ≤−1f
PA14_27920 PA2800 1.18 ≤−1g −2f −1
PA14_25110 PA3011 topA 0.88 −2f,g −1f,g ≤−1f,g ≤−4f
PA14_23890 PA3110 0.89 −2f,g −1f ≤−1f
PA14_23360 PA3160 wzz 1.12 ≤−1f ≤−1g −1f
PA14_22370 PA3233 1.07 ≤−1g −2f −1
PA14_20730 PA3351 flgM 1.00 −1 −1f,g ≤−1f,g −1
PA14_17170 PA3647e ompH 1.07 −1f ≤−1f ≤−1f −2 −1
PA14_16890 PA3670 0.92 −2 −1 ≤−1 ≤−1g −1
PA14_14910 PA3800 1.07 −1f ≤−1f ≤−1f,g −1
PA14_12400 PA3976 thiE 1.12 −1f,g ≤−1f,g ≤−1g −1
PA14_12030 PA4005 0.85 −2g ≤−1f
PA14_08780 PA4269 rpoC 0.96 −1f,g ≤−1f,g ≤−1g −1f
PA14_57690 PA4441 1.00 −2g −1f ≤−1f ≤−1g −1
PA14_57880 PA4456 1.05 ≤−1g −1 −1
PA14_57910 PA4459e 1.31 −1 ≤−1f ≤−1 ≤−4 −1
PA14_62560 PA4727 pcnB 1.09 −1f ≤−1f ≤−1g −2 −1
PA14_62770 PA4745e nusA 0.86 −3g −1f ≤−1f ≤−1f −1f −1
PA14_62880 PA4753 0.89 −2g ≤−1f
PA14_64190 PA4853e fis 1.06 ≤−1 −1 −1
PA14_68670 PA5198 1.22 −2 −1 ≤−1 ≤−1
PA14_69810 PA5288 glnK 0.71 −2g −1
PA14_70980 PA5375 betT1 1.23 −1f,g ≤−1f,g ≤−1f,g −1g −1
PA14_15750 —e 0.81 −1 −1f ≤−1f ≤−1 −2f
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a

Data are given only for those antibiotics for which a change in the MIC could be detected; only negative MIC changes are displayed.

b

Maximum growth rate of the mutant growth control relative to the growth of the wild type.

c

Retesting by agar dilution was performed using antibiotics of the same class: PIP for β-lactams (SAM), MEM for carbapenems (ETP), CAZ for cephalosporins (CAZ), CIP for quinolones (LVX, NAL), and TET for tetracyclines (TGC). SXT was not retested by agar dilution.

d

The MIC for the wild-type PA14 strain was above the calling range (Fig. 1); the MIC change was calculated based on an assumed MIC for the wild type of twice the upper limit of the calling range.

e

No PAO1 transposon mutant available. —, no PAO1 ortholog.

f

MIC change consistent with agar dilution testing of the PA14 mutant using an antibiotic of the same class.

g

MIC change consistent with agar dilution testing of the PAO1 mutant using an antibiotic of the same class.

We retested the susceptibility profiles of these 40 mutants for six antimicrobials (PIP, MEM, CIP, TET, CAZ, and TOB) by using the agar dilution method and also confirmed the increased-susceptibility phenotype with the respective independent mutants from the PAO1 transposon mutant library (22). Table 1 lists the MIC changes for these mutants, most of which could be confirmed to be hypersusceptible to several different antibiotics. Five of the 40 mutants could not be confirmed to be hypersusceptible by the agar dilution method (PA3670, PA4456, PA4459, the fis mutant, and PA5198).

Mutations within the MexAB-oprM multidrug efflux pump, several outer membrane proteins, and proteins involved in DNA replication, recombination, and repair confer hypersensitivity.

As expected, the two mutants harboring a transposon insertion within the mexA and mexB genes, encoding the major intrinsic multidrug MexAB-oprM efflux pump in P. aeruginosa (26, 35), exhibited the most pronounced overall susceptibility. They exhibited enhanced sensitivity to all classes of antibiotics tested in this screen. However, we also identified six mutants with insertions in genes involved in cell envelope biogenesis as being hypersusceptible. These included mutants with insertions in wzz, encoding a protein shown to be important for determining the length of the O-antigen side chain attached to lipopolysaccharide (LPS) and to influence serum resistance (24); PA2800, encoding a conserved hypothetical protein (putative lipoprotein); and genes encoding the outer membrane proteins OstA, OprF, OmpH, and BetT1. Outer membrane proteins are key molecules with regard to the interface between the cell and its environment, and these proteins have been suggested to influence the intrinsic resistance to antibiotics. Using a proteomic approach, P. aeruginosa OmpH has been demonstrated to be an antibiotic resistance-related protein (32), and a Vibrio vulnificus ompH mutant showed enhanced sensitivity to SDS and polymyxin B (2).

Ethanol tolerance in Escherichia coli appears to involve increased production of the betT-encoded choline transporter (18), which also confers general protection against osmotic stress by mediating the uptake of choline, the precursor of the compatible solute glycine betaine (46). OstA has been suggested to contribute to n-hexane resistance by reducing the influx of n-hexane in E. coli (1). Furthermore, disruption of the OstA protein in Helicobacter pylori resulted in altered membrane permeability, sensitivity to organic solvents, and susceptibility to antibiotics (11).

OprF is the most common outer membrane protein in P. aeruginosa and has been studied extensively. It is a nonspecific porin, permitting passive diffusion of small polar nutrients. Since the pore changes its channel size according to the growth conditions, this could affect outer-membrane permeability. OprF is also a promising candidate for vaccine development and is involved in maintaining cell shape and growth in a low-osmolarity environment (38, 48). Furthermore, it has recently been reported that the binding of human gamma interferon to OprF activates quorum-sensing-dependent expression of virulence determinants (49). The role of OprF in antibiotic resistance remains controversial (6). It has been suggested that loss of this protein may be involved in the multiple-antibiotic-resistance phenotype (33, 37), and it has been proposed that OprF has a role in antibiotic uptake in P. aeruginosa (9, 19, 47). As shown in this study, loss of OprF induced susceptibility to a very broad spectrum of antimicrobials, such as SAM, ETP, CTX, CAZ, LVX, SXT, and TGC, whereas growth was not affected (Table 1). As shown in Fig. 2 the OprF protein is completely absent from the outer membrane proteins, confirming that the oprF transposon mutant in the PA14 strain background has lost expression of a functional OprF protein.

FIG. 2.

FIG. 2.

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SDS-polyacrylamide gel electrophoresis of membrane proteins. In contrast to wild-type PA14 (lane 1), the PA14 oprF mutant (lane 2) is missing the OprF band at 37.6 kDa (arrow). Lane M, prestained PageRuler protein ladder (Fermentas).

Within this global screen for hypersensitive P. aeruginosa mutants, we also identified a mucB mutant exhibiting enhanced susceptibility to CTX, CAZ, LVX, and TGC. Inactivation of mucB causes conversion to mucoidy (29), and mucoid clinical isolates have been shown to tend toward more susceptible phenotypes (4).

In accordance with our findings, and despite the use of a different screening method, a recent study of the complex CIP resistome has identified the PA14 outer membrane protein betT1 and oprF transposon mutants as CIP hypersusceptible (7). Furthermore, the study revealed that several strains with mutations of genes involved in DNA replication and repair (ruvA, recG, xerD, sss) display increased CIP sensitivity, as do strains with mutations of ftsK, involved in cell division and chromosome partitioning. Our screen also revealed three genes encoding proteins involved in DNA replication, recombination, and repair (topA, fis, ruvB), mutations of which confer broad-spectrum hypersensitivity, and we also identified the ftsK mutant, exhibiting hypersusceptibility to ETP, CTX, CAZ, and LVX. It has recently been suggested that bactericidal antibiotics induce cellular death by a common mechanism involving the generation of deleterious hydroxyl radicals (25). It thus seems reasonable that the intrinsic “resistome” involves not only multidrug efflux pumps and proteins that maintain the integrity of the cellular outer membrane but also proteins that shield DNA from damaging agents and are involved in DNA repair processes. Proteins of similar functional categories have recently been determined to be of major importance for the E. coli and P. aeruginosa intrinsic resistomes (16, 42).

Identification of antibiotic-resistant P. aeruginosa mutants.

We also screened the library for mutants that exhibited increases in the MICs of the 10 antibiotics where resistance could be determined, because the MIC for the wild-type PA14 strain was within or below the MIC calling range. A total of 193 mutants showing increased resistance to at least one antibiotic are listed in Table 2.

TABLE 2.

List of mutants showing increased resistance

PA14 gene locus PAO1 ortholog Gene name Growthb Log2 change in the MICa of:
PIPc TZPc MEMc FEPc CTX CAZ CIPc LVX TOBc SXT
PA14_01080 PA0089 0.71 ≥2 1
PA14_01100 PA0090 0.90 ≥5 ≥5 2 1 1
PA14_01720 PA0140 ahpF 1.14 1 1 1 ≥2 1
PA14_02770 PA0227 1.00 2 1 1 1
PA14_03050 PA0247 pobA 0.97 2 *
PA14_03760 PA0287 1.04 1 1 1 ≥2 1 1 1
PA14_04110 PA0316 serA 1.18 1 1 1 ≥2 1
PA14_04430 PA0339 0.86 ≥5 4 1 1
PA14_04980 PA0381 thiG 0.74 ≥5 4 1
PA14_05050 PA0387 1.10 1 1 1 ≥2 1 1
PA14_05310 PA0407 gshB 0.63 1 1 2 1
PA14_05410 PA0415 0.84 1 1 ≥2 1 1
PA14_05620 PA0432 sahH 0.45 1 1 1 1 3 1
PA14_06010 PA0460 0.99 ≥5 4 1 1
PA14_06260 PA0479 1.40 1 ≥2 1
PA14_06950 PA0533 0.98 2 1 1 ≥2 1 1
PA14_07070 PA0545 0.90 1 1 ≥2 1 1
PA14_07780 PA0596 1.18 1 1 1 ≥2 1
PA14_07790 PA0597 1.15 2 1 1 ≥2 1
PA14_07950 PA0610 prtN 0.85 2 1 1
PA14_08520 PA0666 1.15 1 1 1 ≥2 1 1
PA14_08540 PA0667 0.92 2 1 1 ≥2 1 1 1
PA14_53820 PA0807 0.94 1 1 1 ≥2 1
PA14_53380 PA0842 1.03 1 1 1 ≥2 1 1
PA14_52510 PA0908 1.02 2 1 1 ≥2 1 1
PA14_52050 PA0944 purN 0.31 2 * 1 1 1
PA14_51880 PA0958 oprD 0.99 3 1
PA14_50980 PA1032 pac 0.82 ≥5 1 1
PA14_50250 PA1095 1.07 ≥5 4 2 ≥2 1
PA14_50140 PA1101 fliF 0.98 1 1 2 ≥2 1
PA14_49320 PA1167 0.95 ≥5
PA14_49280 PA1171 0.75 ≥5 2 1 1 1
PA14_48840 PA1195 0.85 ≥5 1 1 1 1
PA14_47930 PA1259 0.83 ≥5 4 1 1 1
PA14_47300 PA1310 phnW 1.15 1 1 1 ≥2 1 1 1
PA14_47230 PA1316 1.01 ≥5
PA14_46960 PA1338 ggt 1.07 1 1 1 ≥2 1 1
PA14_46850 PA1347 0.99 1 1 1 ≥2 1
PA14_46840 PA1348 0.89 1 1 3 1 ≥2 1 1
PA14_45980 PA1428 1.07 1 1 1 ≥2 1 1
PA14_45580 PA1459 0.65 1 1 ≥2 1 *
PA14_44440 PA1549 0.85 2 2 2 ≥2 2 1
PA14_43950 PA1588 sucC 0.74 1 1 1 ≥2 1 1
PA14_43920 PA1590 braB 1.03 1 1 1 ≥2 1 1
PA14_43900 PA1592 0.88 4 1
PA14_43670 PA1611 1.05 ≥5 2 1
PA14_43310 PA1639 0.85 1 1 1 ≥2 1 1
PA14_43270 PA1643 1.11 1 1 1 ≥2 1
PA14_41710 PA1767 1.12 2 1 1 1 ≥2 1 1
PA14_41530 PA1781 nirB 1.21 1 1 1 ≥2 1
PA14_40980 PA1821 1.12 ≥5 4 1
PA14_39420 PA1942 0.85 2 1 1 1 1
PA14_38350 PA2023 galU 1.16 ≥5 ≥5 1 3 ≥2 2
PA14_37550 PA2085 0.82 ≥5 4 1 1 1
PA14_37530 PA2086 1.23 1 1 1 ≥2 1
PA14_37310 PA2110 0.97 2 1 1
PA14_37030 PA2130 cupA3 1.26 1 1 1 ≥2 1
PA14_36280 PA2198 0.81 2 1
PA14_36170 PA2207 0.94 4 1
PA14_34540 PA2326 0.93 ≥5 1 2 1 1
PA14_33720 PA2394 pvdN 1.05 ≥5 1 1
PA14_32860 PA2455 0.90 ≥5 4 1 1
PA14_32590 PA2478 1.11 1 1 1 ≥2 1 1
PA14_32470 PA2487 1.14 1 1 1 ≥2 1
PA14_31850 PA2529 1.08 1 1 1 ≥2 1 1
PA14_31820 PA2531 1.24 ≥5 1
PA14_31810 PA2532 tpx 1.11 2 1 2 ≥2 1
PA14_31400 PA2561 1.01 ≥5 1 1
PA14_30840 PA2571 1.01 ≥5 4 1 1 1
PA14_29970 PA2641 nuoF 0.91 2 1 1 1
PA14_29930 PA2643 nuoH 0.96 2 1 ≥2 1
PA14_29920 PA2644 nuoI 1.03 2 1 1 ≥2 1
PA14_29900 PA2645 nuoJ 0.91 1 1 ≥2 1
PA14_29880 PA2647d nuoL 0.90 2 1 ≥2 1
PA14_29880 PA2647d nuoL 1.02 2 1 ≥2 1 1
PA14_29320 PA2691 1.14 1 1 1 ≥2 1 1
PA14_29290 PA2693 0.84 ≥5 ≥5 2 4 1 2
PA14_29220 PA2700 1.10 1 1 1 ≥2 1 1
PA14_27950 PA2797 0.77 1 1 1 ≥2 1 1 1
PA14_26960 PA2871 1.11 1 1 1 ≥2 1
PA14_25880 PA2951 etfA 0.74 4 1 ≥2 1
PA14_25840 PA2953 1.05 2
PA14_25820 PA2955 0.90 2 1 ≥2 1 1
PA14_25630 PA2970 rpmF 0.97 2
PA14_25420 PA2989 0.92 ≥5 4 1 1 1
PA14_25080 PA3014 foaA 0.95 1 1 1 ≥2 1 1
PA14_25060 PA3015 0.87 2 1
PA14_25050 PA3016 1.05 1 1 1 ≥2 1 1
PA14_24690 PA3047 0.92 2 1 1 ≥2 2 1
PA14_24490 PA3063 pelB 0.93 1 1 ≥2 1 1
PA14_24150 PA3093 1.23 2 1 1 ≥2 1
PA14_23670 PA3127 1.01 2 1 1 1 1
PA14_23470 PA3141 wbpM 0.88 1 1 1 ≥2 1
PA14_23240 PA3170 0.93 ≥5 1 1
PA14_23210 PA3172 0.90 2 1 1 ≥2 1 1
PA14_22910 PA3194d edd 0.46 1 2
PA14_22910 PA3194d edd 0.42 1 2
PA14_22480 PA3224 1.01 2
PA14_22330 PA3236 1.03 1 ≥2 1
PA14_21990 PA3247 0.93 1 1 1 ≥2 1 1
PA14_21860 PA3259 1.26 1 1 ≥2 1
PA14_21410 PA3296 phoA 1.01 ≥2
PA14_21050 PA3324 0.83 ≥5 4 1 1
PA14_20730 PA3351 flgM 1.00 3
PA14_19910 PA3416 1.24 1 1 1 ≥2 1
PA14_19340 PA3462 0.97 2 1
PA14_19170 PA3472 0.87 ≥5 1
PA14_18080 PA3574 0.88 2 1 1 1 ≥2 1 1
PA14_18060 PA3575 1.07 1 1 1 ≥2 1 1
PA14_18050 PA3576 0.93 2 1 1 ≥2 1 1
PA14_17500 PA3620 mutS 1.26 1 1 ≥2 1
PA14_16890 PA3670 0.92 ≥5
PA14_16500 PA3702 wspR 0.81 ≥5 ≥5 1 ≥2 1
PA14_16470 PA3704 1.05 1 1 1 ≥2 1
PA14_16280 PA3721 1.05 1 1 1 ≥2 1
PA14_16130 PA3733 1.13 1 1 1 ≥2 1 1 1
PA14_14520 PA3826 0.90 1 1 ≥2 1 1
PA14_14470 PA3831 pepA 0.67 2 1 1 ≥2 1 2 1
PA14_14380 PA3837 0.93 ≥5 3 1 1
PA14_11900 PA4016 1.16 2 1 1 ≥2 1
PA14_11760 PA4025 0.92 2 1 1
PA14_10800 PA4109 ampR 1.08 3 3 1 ≥2 3 1 1 1
PA14_09550 PA4204 1.09 ≥2
PA14_09480 PA4210 phzA1 1.21 1 1 1 ≥2 1
PA14_09300 PA4223 0.99 1 ≥2
PA14_55770 PA4292 1.11 1 ≥2 1
PA14_56620 PA4354 1.09 1 1 1 ≥2 1 1
PA14_56640 PA4355 1.13 1 1 1 ≥2 1
PA14_57080 PA4392 1.03 ≥2
PA14_57210 PA4402 argJ 1.00 1 1 1 ≥2 3 1
PA14_57260 PA4406 lpxC 0.98 ≥2
PA14_57540 PA4429 0.87 2 2 ≥2 2 1
PA14_57560 PA4430 0.77 1 1 ≥2 1
PA14_57570 PA4431 0.84 1 1 ≥2 1 1
PA14_57850 PA4454 1.06 ≥5 4 1 1 1
PA14_57950 PA4463 1.09 ≥5 1 1 1
PA14_58260 PA4490 0.85 2 1 1 1
PA14_58850 PA4536 0.83 1 1 1 ≥2 1
PA14_60860 PA4600 nfxB 0.79 1 3 3 1
PA14_60990 PA4609 radA 0.89 ≥
PA14_62630 PA4733 acsB 1.02 1 1 1 ≥2 1 1
PA14_63040 PA4766 0.91 2 1 1 1
PA14_63210 PA4781 0.88 ≥5 4 1
PA14_63580 PA4811 fdnH 0.97 2 1 1
PA14_63970 PA4838 1.07 2 1 1 ≥2 1 1
PA14_65250 PA4939 1.11 1 1 1 ≥2 1 1
PA14_65280 PA4942 hflK 1.05 1 1 1 ≥2 1 1
PA14_65320 PA4945 miaA 0.65 2 2 1 1 1 1 1
PA14_65350 PA4946d mutL 1.30 2 1 1 ≥2 1 1
PA14_65350 PA4946d mutL 1.12 1 1 1 ≥2 1
PA14_65750 PA4974 1.01 2
PA14_66120 PA5001 0.89 2 1 1 ≥2 3 1
PA14_66150 PA5003 1.11 2 1 1 ≥2 2 1
PA14_66480 PA5028 1.16 1 1 1 ≥2 1 1
PA14_66580 PA5037 0.96 2 1 1
PA14_66600 PA5038 aroB 0.55 4 4 3 ≥2 3 1 2
PA14_67270 PA5094 0.99 ≥2
PA14_67530 PA5114 1.09 ≥5 4 1 1
PA14_67670 PA5124 ntrB 0.93 ≥5 4 1
PA14_68580 PA5192 pckA 1.05 2 1 1 1 1
PA14_68610 PA5193 hslO 0.78 ≥5 ≥5 1 1
PA14_68680 PA5199 envZ 1.06 1 1 1 ≥2 1 1
PA14_68730 PA5203 gshA 0.59 2
PA14_68800 PA5208 0.91 1 1 1 ≥2 1 1
PA14_69000 PA5224 pepP 0.72 2 1 2 1 1 1
PA14_69170 PA5238 0.89 1 1 ≥2
PA14_69270 PA5246 0.87 ≥5 1
PA14_70860 PA5369 0.84 1 1 ≥2 1 1
PA14_71630 PA5427 adhA 1.10 1 1 1 ≥2 1
PA14_71700 PA5433 1.09 1 1 1 ≥2 1 1
PA14_72140 PA5466 1.11 1 1 1 ≥2 1 1
PA14_73200 PA5551 1.19 1 1 1 ≥2 1
PA14_73370 PA5565d gidA 0.62 2
PA14_73370 PA5565d gidA 0.78 1 1 2 1 1
PA14_73410 PA5568 0.81 2 1 1 1 1
PA14_14420 1.03 1 1 1 ≥2 1 1
PA14_15540 1.13 1 1 1 ≥2 1 1
PA14_15600 0.93 1 1 1 ≥2 1 1
PA14_18070 0.92 2 2 1 2 ≥2 1 1
PA14_23420 0.83 2 1 1 ≥2 1 1
PA14_23430 1.21 1 1 1 ≥2 1 1
PA14_23460 orfN 0.92 2 1 1 ≥2 1 1
PA14_28520 0.91 1 1 1 ≥2 1 1
PA14_43090 0.91 1 1 1 2 1 1
PA14_44230 1.19 1 1 1 ≥2 1
PA14_51950 1.04 1 1 1 ≥2 1 1
PA14_54750 1.17 1 1 1 ≥2 1
PA14_58760 pilC 0.73 2 1 1 ≥2 1 1
PA14_66100 1.08 1 1 1 ≥2 1 1
PA14_30210d clpS 1.20 3 4 1 ≥2 3 1
PA14_30210d clpS 1.18 3 1 1 ≥2 1 1
PA14_60280d fimU 0.82 2 1 1 ≥2 1 1
PA14_60280d fimU 0.80 1 1 1 ≥2 1
Open in a new tab
a

Only those mutants for which at least a fourfold increase in the MIC was obtained are listed; only positive MIC changes are displayed. *, failed measurement.

b

Maximum growth rate of the mutant growth control relative to the growth of the wild type.

c

The MIC for the wild-type PA14 strain was below the calling range (Fig. 1); the change in the MIC was calculated based on an assumed MIC for the wild type of 0.5 times the lower limit of the calling range.

d

Independent strains with the transposon in different positions within the gene.

Nineteen of those mutants were retested for antibiotic resistance using the agar dilution method with PIP, MEM, CIP, TET, CAZ, and TOB, and we also confirmed the increased resistance profile with the respective independent isolates from the PAO1 transposon mutant library (Table 3).

TABLE 3.

Retesting of mutants exhibiting increased resistance

PA14 gene locus PAO1 ortholog Gene name Log2 change in the MICa of:
PIPb MEMb CAZ CIPb TOBb
PA14_01100 PA0090 ≥5d,e 1
PA14_51880 PA0958 oprD 3d
PA14_50250 PA1095 ≥5d,e 1d
PA14_46840 PA1348 1d,e 3d 1
PA14_44440 PA1549 2d,e 2d 1d,e
PA14_38350 PA2023 galU ≥5d,e 1d 2d
PA14_29290 PA2693 ≥5d,e 2 2
PA14_22480 PA3224 2d,e
PA14_16500 PA3702 wspR ≥5d,e 1d
PA14_14470 PA3831 pepA 2d,e 1d,e
PA14_10800 PA4109 ampR 3d,e 3d 1d
PA14_57540 PA4429c 2 2 1d
PA14_57570 PA4431 1d,e 1d 1d
PA14_58260 PA4490 2d,e 1e
PA14_60860 PA4600 nfxB 3d,e
PA14_66600 PA5038 aroB 4d,e 3d 1d
PA14_68610 PA5193 hslO ≥5d,e
PA14_18070 —c 2 1d 1d
PA14_30210 —c clpS 3d,e 3d
Open in a new tab
a

Only positive MIC changes are displayed.

b

The MIC for the wild-type PA14 strain was below the calling range (Fig. 1); the MIC change was calculated based on an assumed MIC for the wild type of 0.5 times the lower limit of the calling range.

c

No PAO1 transposon mutant available. —, no PAO1 ortholog.

d

MIC change consistent with agar dilution testing of the PA14 mutant with the same antibiotic.

e

MIC change consistent with agar dilution testing of the PAO1 mutant with the same antibiotic.

As expected, in our Vitek 2 screen we were able to identify various genes that have previously been reported to be involved in the alteration of the bacterial susceptibility profile. Among these genes were nfxB, whose inactivation has been shown to lead to MexCD-OprJ-overproducing efflux mutants exhibiting resistance to gyrase inhibitors and FEP (36); oprD, involved in carbapenem resistance (34); ampR, encoding the transcriptional regulator of chromosomal AmpC beta-lactamase in P. aeruginosa (3); and lpxC. lpxC mutants exhibit increased resistance to CTX, and LpxC inhibitors have been demonstrated to show antibiotic properties. A recently discovered LpxC inhibitor was proven to control the growth of E. coli and P. aeruginosa with an efficacy rivaling that of CIP (5). We furthermore identified a galU mutant exhibiting increased cephalosporin and PIP resistance. A galU mutant was previously identified in a screen for aminoglycoside resistance (15), and it has been speculated that loss of the A- and B-band polysaccharides due to the impaired conversion of glucose-1-phosphate to UDP glucose (14) results in reduced antibacterial activity due to a lack of aminoglycoside binding to the bacterial cell (23). Interestingly, we also identified a wbpM mutant that exhibits increased resistance toward the cephalosporins and PIP. Insertional inactivation of wbpM has been shown to result in mutants exhibiting three distinct LPS phenotypes (14), suggesting that an altered LPS phenotype affects susceptibility not only to aminoglycosides but also to beta-lactam antibiotics.

We furthermore identified mutS and mutL mutants that exhibited increased resistance profiles. Mutation within mutS or mutL has been reported to lead to hypermutable phenotypes exhibiting a 100- to 1,000-fold-increased rate of spontaneous mutation (31). These mutants show enhanced acquisition of antibiotic resistance through the accumulation of secondary mutations and are frequently found in chronic lung infections in cystic fibrosis (12, 31). The radA, PA1767, PA5001, and ahpF mutants also exhibited antibiotic resistance in our screen; all of them were picked in a previous screen of the PA14 mutant library for decreased susceptibility to different antibiotics (CIP, TOB, and CAZ). Among those genes, only radA has been shown to be involved in the expression of an enhanced mutation frequency (45).

Aminoglycoside antibiotics must traverse the bacterial cytoplasmic membrane prior to initiating lethal effects, a process that seems to be dependent on the proton motive force (8, 13, 41). Thus, resistance may be the result of a decreased aminoglycoside uptake. We found that a strain with a mutation in a gene encoding a protein involved in the production and maturation of cytochrome c oxidase (PA1549) exhibited enhanced resistance to tobramycin. The respective PA14 transposon mutant has already been identified in a global screen for novel genetic determinants of aminoglycoside resistance (40). The reason that the screen by Schurek et al. identified a significantly larger number of mutants (40) might be that the tobramycin MIC for the wild-type PA14 strain was below the calling range in the present study, and therefore small MIC changes might have been missed.

Inactivation of the nuoABDEFGHIJKLMN operon, coding for the proton translocating type I NADH oxidoreductase, did not result in enhanced resistance to TOB, as observed by Schurek et al. (40); however, we found enhanced resistance to the cephalosporins (especially CTX) and PIP.

Concluding remarks.

One approach to producing a new generation of useful antimicrobial compounds involves sensitization of the bacteria to existing antibiotics by identifying targets for increasing susceptibility. Our finding that not only the loss of efflux pumps but also the loss of, e.g., OprF entails pronounced hypersusceptibility to various antibiotics belonging to different classes identifies OprF as a possible target candidate for the development of an attractive chemosensitizer.

We acknowledge that the approach of screening a transposon mutant library for mutants exhibiting increased resistance profiles is far from being comprehensive. Only nonessential genes can be identified, and this screen will miss small mutations or a combination of several mutations that lead to the evolution of antibiotic-resistant strains in the clinical setting. Nevertheless, screening of the Harvard PA14 transposon mutant library proved to be sufficient to detect many genes already predicted to play a role in P. aeruginosa resistance, and we identified a large number of previously unknown genes that modified the expression of resistance to many different antibiotics and that might turn out to be targets of clinical relevance. As the technology of high-throughput sequencing and comparative genome hybridization evolves very rapidly, it will be a very challenging task for the near future to identify novel genetic markers of antibiotic resistance and modifiers of resistance expression via genomewide association studies and to combine these data with the “resistome” data from our study and other studies. The prediction of the antibiotic resistance profiles of clinical strains based on their genotypes will be a major advance for the rapid and reliable detection of antimicrobial resistance in modern microbiological diagnostics and will contribute significantly to the efficient control of multiresistance.

Acknowledgments

Perfect technical assistance by Katharina Smaluch is gratefully acknowledged. We thank Jörg Overhage for helpful discussions.

The financial support of the Helmholtz-Gemeinschaft is gratefully acknowledged. A.D. is a recipient of a predoctoral stipend provided by the DFG-sponsored International Research Training Group “Pseudomonas: Pathogenicity and Biotechnology”.

Footnotes

▿

Published ahead of print on 30 March 2009.

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