AAC Accepts, published online ahead of print on 22 December 2014 Antimicrob. Agents Chemother. doi:10.1128/AAC.04809-14 Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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Activity of eravacycline against Enterobacteriaceae and Acinetobacter baumannii, including

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multidrug-resistant isolates, from New York City

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Marie Abdallaha, Olawole Olafisoyea, Christopher Cortesb, Carl Urbanb, David Landmana, John

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Qualea#

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Division of Infectious Diseases, SUNY Downstate Medical Center, Brooklyn, NY, USAa; The

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Dr. James J. Rahal Jr. Division of Infectious Diseases, New York Hospital Queens, Flushing,

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NY, USAb

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Corresponding author: John Quale Email: [email protected]

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Running title: Eravacycline activity against Gram negative bacilli

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ABSTRACT

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Eravacycline demonstrated in vitro activity against a contemporary collection of over 4000

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Gram-negative pathogens from New York City hospitals, with MIC50/MIC90 values for

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Escherichia coli of 0.12/0.5 µg/ml, Klebsiella pneumoniae of 0.25/1 µg/ml, Enterobacter

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aerogenes of 0.25/1 µg/ml, E. cloacae 0.5/1of µg/ml, and A. baumannii of 0.5/1 µg/ml. Activity

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was retained against multidrug-resistant isolates, including those expressing KPC and OXA

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carbapenemases. For A. baumannii, eravacycline MICs correlated with increased expression of

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the gene adeB.

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Nosocomial infections with multidrug-resistant Gram-negative bacilli come with considerable

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clinical and economic burden. Carbapenem-resistant Enterobacteriaceae and Acinetobacter

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baumannii have become commonplace in many medical centers around the world. In the United

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States, and particularly New York City, spread of Enterobacteriaceae possessing the

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carbapenemase KPC and A. baumannii possessing OXA-type carbapenemases has been

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especially problematic (1-3). Since these isolates are often also resistant to aminoglycosides and

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fluoroquinolones, therapeutic options are very limited. Often the therapy of last resort are the

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polymyxins; however there are lingering issues regarding dosing, susceptibility testing, and

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resistance with these agents (4,5). As a result, the need for novel antibacterial agents with

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activity against multidrug-resistant isolates has been voiced (6).

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Eravacycline is a novel fluorocycline of the tetracycline class, being developed for both

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intravenous and oral use, which has broad spectrum activity against Gram-negative and Gram-

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positive aerobic and anaerobic pathogens (7). Like tigecycline, eravacycline is not affected by

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many of the tetracycline-specific resistance mechanisms found in Gram-negative bacteria,

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including acquired efflux systems and ribosomal protection proteins (7,8). In this report, we

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determined the activity of eravacycline against Enterobacteriaceae and A. baumannii endemic to

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medical centers in New York City.

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For a three month period spanning November 2013 – January 2014, all single patient isolates

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of E coli, K. pneumoniae, Enterobacter spp., and A. baumannii were collected from eleven

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hospitals in Brooklyn and Queens, NY. Susceptibility tests were performed in a central research

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laboratory using the broth microdilution (for tigecycline and eravacycline) or agar dilution (all

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other agents) methods, according to CLSI standards (9). Ceftriaxone-resistant isolates were

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tested, by PCR, for the presence of blaKPC and blaOXA-23-type and blaOXA-24-type using previously

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described primers (1,10). Isolates of K. pneumoniae with blaKPC and A. baumannii with blaOXA23-

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type underwent

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described (2). Isolates were considered related if there was a 0-1 band difference. Finally, select

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isolates of K. pneumoniae were also examined for mutations in genes encoding RamR and

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ribosomal S10 proteins, using previously described primers and PCR conditions (11).

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genetic fingerprinting by the rep-PCR method with ERIC-2 primer, as previously

To examine the mechanisms contributing to eravacycline resistance in A. baumannii,

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susceptibility testing was performed using a collection of previously characterized isolates (12).

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Expression of adeB, abeM, and ompA was determined by real time RT-PCR and normalized to

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that of A. baumannii ATCC 19606, as previously described (12). Multiple regression analysis

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was used to determine any correlation between expression of efflux genes adeB, abeM, and porin

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gene ompA with eravacycline MIC values. In addition, gene silencing of adeB was performed to

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further determine the role of this efflux system in eravacycline resistance. Two previously-

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characterized isolates of A. baumannii were selected based on their disparate expression of adeB

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and susceptibility to kanamycin. Insertional inactivation of the adeB gene was performed by

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amplifying a 979 bp fragment of the gene (AccuPrime Pfx DNA polymerase, Invitrogen Corp.,

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Carlsbad, CA). The amplicon was inserted into the pCR-Blunt II-TOPO vector using the Zero

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Blunt TOPO PCR Cloning Kit (Invitrogen Corp.). The plasmid was introduced into the clinical

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isolates by electroporation. Transformants were selected from plates containing 250 µg/ml of

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kanamycin. The presence of the insert in adeB was confirmed by PCR amplification and DNA

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sequencing using an M13 forward primer and a primer (5’-TTGGGCTGATATTACAGGGG-3’)

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located upstream to the insert.

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A total of 2866 isolates of E. coli were gathered during the three month surveillance study.

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Susceptibilities are given in the table; 13% were nonsusceptible to ceftriaxone and five isolates

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carried blaKPC. The eravacycline MIC50 and MIC90 values for all of the isolates were 0.12 and 0.5

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µg/ml, respectively. Of the isolates resistant to ceftriaxone, eravacycline MIC50 and MIC90

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values were 0.25 and 0.5 µg/ml, respectively.

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Among 944 isolates of K. pneumoniae, 33% were resistant to ceftriaxone and 124 isolates

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carried blaKPC. For all of the isolates, the MIC50 and MIC90 values for eravacycline were 0.25 and

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1 µg/ml, respectively, which were one dilution lower than the corresponding values for

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tigecycline. For the tigecycline resistant isolates, eravacycline MIC50 and MIC90 values were 2

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and 8 µg/ml, respectively. For both cephalosporin-resistant isolates and those expressing blaKPC,

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MIC50 and MIC90 values of eravacycline were 0.5 and 1 µg/ml, respectively. Twenty-three

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isolates with blaKPC, from 11 different hospitals, underwent fingerprinting. Eight rep-PCR types

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were identified, including 12 isolates that belonged to one clone (data not shown).

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Eleven isolates of K. pneumoniae with eravacycline MICs of ≥ 4 µg/ml underwent PCR

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analysis of ramR and rpsJ (encoding the S10 ribosomal protein). For ramR, two isolates had a

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nonamplifiable gene, five isolates had mutations leading to premature stop codons, and two

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isolates had deletions leading to frameshift mutations. One isolate had a mutation leading to

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Thr50→Ile50, and one isolate had no mutation. For rpsJ, four isolates had a nonamplifiable

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gene, and only one had the previously described mutation leading to Val57→Leu57 (11).

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There were 216 Enterobacter spp. isolates, including 90 E. aerogenes and 124 E. cloacae.

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Three isolates of E. aerogenes and four isolates of E. cloacae harbored blaKPC. For all 216

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Enterobacter spp., 96% were susceptible to tigecycline (MIC50 and MIC90 values of 0.5 and 2

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µg/ml, respectively). The corresponding MIC50 and MIC90 values for eravacycline were 0.5 and

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1 µg/ml, respectively. For both E. aerogenes and E. cloacae, eravacycline MIC90 values were

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one dilution lower than that of tigecycline (Table). For the tigecycline resistant isolates, the

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eravacycline MICs ranged from 0.5-2 µg/ml. For the three isolates of E. aerogenes with blaKPC,

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two had eravacycline MIC values of 0.25 and one of 0.5 µg/ml. For the four isolates of E.

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cloacae that had blaKPC, two each had eravacycline MIC values of 0.5 and 1 µg/ml.

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Only 31% of the 158 isolates of A. baumannii were susceptible to meropenem. Fifty-eight

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were found to have blaOXA-23-like, two carried blaOXA-24-like, and one harbored blaKPC. For all 158

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isolates, 66% were susceptible to tigecycline (MIC ≤ 2 µg/ml). The MIC50 and MIC90 values of

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eravacycline were 0.5 and 1 µg/ml, which were fourfold lower than the corresponding values for

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tigecycline. Among the tigecycline-resistant isolates, the MIC50 and MIC90 values of

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eravacycline were 1 and 2 µg/ml, respectively. For the 58 isolates that had blaOXA-23-like, the

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MIC90 value for eravacycline was 1 µg/ml. Eighteen isolates, from eight hospitals, with blaOXA-

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23-like

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belonging to a single clone (data not shown).

underwent fingerprinting. A total of 10 rep-PCR types were identified, including six

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A collection of thirty-eight previously characterized isolates of A. baumannii, representing 10

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different strains, were examined (12). Of the 38 isolates, 26 were resistant to meropenem. None

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harbored blaKPC, blaOXA23-type, or blaOXA24-type carbapenemases. The eravacycline MIC values

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ranged from 0.06-4 μg/ml, with MIC50 and MIC90 values of 0.5 and 2 µg/ml, respectively. By

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multiple regression analysis, there was a significant correlation between the eravacycline MICs

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and expression of adeB (P=0.002); there was no correlation with expression of abeM and ompA.

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For five isolates with negligible adeB expression (64

87%

Meropenem

≤ 0.125

≤ 0.125

≤ 0.125 - >8

99.8%

Gentamicin

1

>8

≤ 0.25 - >8

85%

≤ 0.125

>4

≤ 0.125 - >4

69%

≤ 0.5

>4

≤ 0.5 - >4

64%

Tetracycline

4

>16

≤ 0.25 - >16

59%

Eravacycline

0.12

0.5

≤ 0.015 - 4

Ceftriaxone

≤ 0.25

>64

≤ 0.25 - >64

67%

Meropenem

≤ 0.125

4

≤ 0.125 - >8

87%

Gentamicin

0.5

>8

≤ 0.25 - >8

78%

≤ 0.125

>4

≤ 0.125 - >4

67%

≤ 0.5

>4

≤ 0.5 - >4

65%

Ciprofloxacin Trimethoprim sulfamethoxazole

K. pneumoniae (n=944)

Ciprofloxacin Trimethoprim -

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sulfamethoxazole Tetracycline

4

>16

≤ 0.25 - >16

68%

Tigecycline

0.5

2

≤ 0.015 - 16

95%

Eravacycline

0.25

1

0.06 - 4

Ceftriaxone

≤ 0.25

32

≤ 0.25 - >64

78%

Meropenem

≤ 0.125

≤ 0.125

≤ 0.125 - >8

94%

Gentamicin

0.5

1

≤ 0.25 - >8

94%

≤ 0.125

0.5

≤ 0.125 - >4

93%

≤ 0.5

>4

≤ 0.5 - >4

91%

Tetracycline

2

>16

≤ 0.25 - >16

82%

Tigecycline

0.5

2

≤ 0.25 - >16

97%

Eravacycline

0.25

1

0.12 - 2

Ceftriaxone

≤ 0.25

2

≤ 0.25 - >64

77%

Meropenem

≤ 0.125

≤ 0.125

≤ 0.125 - >8

96%

Gentamicin

0.5

2

≤ 0.25 - >8

94%

≤ 0.125

2

≤ 0.125 - >4

89%

≤ 0.5

>4

≤ 0.5 - >4

82%

Tetracycline

2

8

≤ 0.25 - >16

79%

Tigecycline

0.5

2

≤ 0.25 - >16

96%

E. aerogenes (n=90)

Ciprofloxacin Trimethoprim sulfamethoxazole

E. cloacae (n=124)

Ciprofloxacin Trimethoprim sulfamethoxazole

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Eravacycline

0.5

1

0.25 - 2

Ceftazidime

16

>16

≤ 0.25 - >16

33%

Meropenem

>8

>8

≤ 0.125 - >8

31%

Gentamicin

8

>8

≤ 0.25 - >8

45%

Ciprofloxacin

>4

>4

≤ 0.125 - >4

31%

Trimethoprim -

>4

>4

≤ 0.5 - >4

34%

Tetracycline

>16

>16

2 - >16

10%

Tigecycline

2

4

0.06 - 16

66%

Eravacycline

0.5

1

≤ 0.015 - 8

A. baumannii (n=158)

sulfamethoxazole

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Activity of eravacycline against Enterobacteriaceae and Acinetobacter baumannii, including multidrug-resistant isolates, from New York City.

Eravacycline demonstrated in vitro activity against a contemporary collection of more than 4,000 Gram-negative pathogens from New York City hospitals,...
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