IDSX Manuscript (121108) Updated 08212011 With Figs

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Evaluation of the direct IDSX method on urinary tract samples: an accurate and inexpensive

antimicrobial susceptibility test which includes presumptive identification, providing a rapid

diagnostic result for prudent antibiotic prescribing

Running title : Evaluation of the direct IDSX kit

Adam R. Taintor +, Read R. Taintor, Elizabeth L. Frank*

*Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT

+ Corresponding author: Adam R. Taintor M.D.

Address: 9450 S. 1300 E. Sandy, Utah 84094

Telephone: 011-801-906-3186

E-mail address: [email protected]

Authors Note (August 2011): This paper was submitted in 2009 to Diagnostic Microbiology and Infectious

Disease, however it was not accepted for publication for several reasons. Probably the most significant was the lack

of a reference method. One reviewer remarked that: The Vitek 2 is a proprietary instrument and not a reference

method. New AST methods need to be compared to existing reference methods published by CLSI (i.e., broth


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Abstract

We evaluated the IDSX kits novel direct antimicrobial susceptibility test using specimens from

patients with urinary tract infection. The VITEK 2 was the reference method. The IDSX

method performed: isolation with quantitation; presumptive identification with determination of

predominating species; and antimicrobial susceptibilities, all at 12-18 hours from specimen

receipt. Urine specimens evaluated were from 132 patients where antimicrobial agent treatment

information was available. A total of 842 microorganism-antimicrobial agent combinations were

evaluated. Comparison of susceptibility results from the IDSX method with those from the Vitek

2 method showed that 792 of 842 (94.1%) were in category agreement. In regards to antibiotic

usage, 77 of 132 (58%) evaluated patients received an antimicrobial agent prescription on the

day of their visit. Of those, 22% were negative for UTI and 16% received an antibiotic

prescription later shown to be ineffective for treatment. IDSX kit usage would allow for much

needed targeted prescribing.


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1. Introduction

Current guidelines for the management of uncomplicated urinary tract infection (UTI), such

as those published by the Infectious Diseases Society of America (IDSA) (Warren et al., 1999)

have supported empirical antibiotic treatment prescribed before definitive drug sensitivities have

been performed. However, antimicrobial resistance among pathogenic agents of both cystitis and

pyelonephritis is increasing (Gupta et al., 2001; Kahlmeter, 2001). A striking example is the

increase in resistance to trimethoprim-sulfamethoxazole, the drug regimen of choice in the U.S.

for empirical therapy of uncomplicated UTI's in women (Gupta et al., 2001). As a result, many

clinicians prescribe more expensive fluoroquinolones for the treatment of acute uncomplicated

cystitis (Taur et al., 2007). Although fluoroquinolones are effective antimicrobials and have an

important role in treating cystitis, these drugs are not appropriate first line therapy (Hooton et al.,

2004). Increasing resistance to broad-spectrum antibiotics, such as the fluoroquinolones, is a

serious worldwide problem (Goettsch et al., 2000; Iqbal et al., 1997; Srinivasa et al., 1999;

Thompson, 1999). It is essential that indiscriminate use of these broad-spectrum antibiotics is


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best course of action (Morell, 1997). Resistance to antibiotics frequently reduces the fitness of

bacteria in the absence of antibiotics ; this is referred to as the cost of resistance (Spratt , 1996).

Decreased fitness due to a mutation or acquisition of resistance suggests that drug-resistant

organisms might diminish if antibiotic use is decreased. However, increasing evidence indicates

that compensatory mutations act to cause long-term persistence of resistant bacteria (Andersson,

2003; Campos et al., 1996; Schrag et al., 1997; Livermore, 2003). An example of this is the

persistence of chloramphenicol-resistant Escherichia coli many years after the antibiotic ceased

to be commonly used.

Most suspected UTI s are confirmed by the quantitative culture of urine followed by

conventional bacterial isolation, identification, and antimicrobial susceptibility testing (AST).

During this process, which takes 48 to 72 hours or longer, the patient is often treated empirically

with a broad-spectrum antimicrobial agent. Automated methods for identifying bacterial isolates

and testing antimicrobial susceptibility have become the norm in most clinical laboratories and

may shorten the process. However, an overnight pre-isolation step is still required in current


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IDSX set-up, incubation and analysis. Briefly, specimens were applied directly to the IDSX kit

or diluted and applied, antimicrobial-impregnated papers were then applied, and the plate was

incubated at 35C overnight. The IDSX plate was divided into four quadrants. Two of the

chambers contained media for bacterial isolation. The media were Columbia CNA agar with 5%

sheep bred blood cells and MacConkey agar. The remaining chambers contained Mueller-Hinton

agar and Mueller-Hinton agar with 5% sheep red blood cells. These chambers were used for

antimicrobial susceptibility testing. Amikacin(AN), amoxicillin/clavulenate(AMC),

ampicillin(AM), cefazolin(CZ), cefotetan(CTT), ciprofloxacin(CIP), gentamicin(GM),

levofloxacin(LVX), nitrofurantoin(F/M), piperacillin/tazobactam(TZP), and

trimethoprim/sulfamethoxazole(SXT) were the antimicrobial agents primarily evaluated. Other

antimicrobial agents used include cephalothin(CF), doxycycline(D), ceftriaxone(CRO),

tetracycline (TE) and cefdinir(CDR).

The decision to perform a dilution or not was based on results from a urine dipstick.

Leukocyte esterase, nitrite, blood or protein in the specimen may indicate bacteria in the urine. A


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with additional spot testing, such as the catalase test for gram-positive organisms and the

cytochrome oxidase test for gram-negative organisms, when necessary. E. coli American Type

Culture Collection (ATCC) 25922, Staphylococcus aureus ATCC 25923, and Pseudomonas

aeruginosa ATCC 27853 were used as control strains. These are species with known zones of

inhibition values used in control testing to assure that antimicrobial susceptibility systems are

operating correctly.

2.4 Standard VITEK 2 quantitative cultures

All samples were processed by the standard quantitative culture method using a calibrated 2.5

milliliter loop onto Columbia agar with 5% sheep blood and MacConkey agar plates. After 18 to

24 hours of incubation, the colonies were counted. Colony counts of greater than or equal to

104cfu/ml were considered significant. Identification (ID) and susceptibility testing of the

microorganisms that were isolated were performed on the VITEK 2 system using cards ID-GNB

(identification- Gram negative bacilli) and AST (antimicrobial susceptibility testing) N029 for

gram-negative rods, and ID-GPC (identification Gram positive cocci) and AST-P524 for


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possible combinations. The categories are: (1) agreement, (2) minor error, (3) major error, or (4)

very major error. These designations are displayed in Table 1.

2.6 Prescription information

The medical record database was searched to obtain data concerning treatment during the

period of the study. De-identified sample result information was linked to the patient record

using HIPAA approved methods. The IRB protocol insured that appropriate measures were in

place for the data extraction.

3. Results

3.1 Time to result

During the study period, 132 comparable samples were processed concurrently by the IDSX

and VITEK 2 methods. Eighty-one of the samples revealed a significant infection for which

antibiotic treatment was indicated. Of these, the IDSX method produced a result within 1 day

following receipt of specimen 78 of 81 times (96%). The remaining three specimens (4%)

required an additional culture to speciate the predominant species; results were available on day


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There were 132 patients seen at the community clinic where therapy prescription information

was available. Seventy-seven patients received empirical treatment (a prescription was written)

on the day of their visit (see Table 2). However, microbiology culture results for 17 of the

77(22%) were negative for a urinary tract infection. Forty-eight of the 77(62%) tested culture-

positive for a UTI and were treated with an antimicrobial agent that was subsequently

bactericidal for the uropathogens. Twelve of the 77(16%) tested positive for a UTI but were

treated with an agent that was not effective treatment for their uropathogens. Antimicrobial agent

choices, diagnostic results, and treatment outcomes, for the day of visit empirical therapies, are

shown in Table 2.

Fifty-five patients did not receive empirical treatment on the day of the office visit.

Microbiology results for 27 of the 55 were negative for a urinary tract infection and no treatment

was given within a 30-day period. Five of the 55 were culture positive for a UTI but were not

treated within the 30-day period. Four of the 55 were prescribed an antimicrobial agent by

telephone from thirteen days to one day prior to their clinic visit. All 4 of these patients were


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Selected results comparing the IDSX and VITEK 2 are shown in Table 3 and Figures 3,4,5,6,

and 7. Shown are the days to result (DTR), presumptive (IDSX) versus definitive (VITEK 2)

identifications, AST results for each antimicrobial agent and the prescription medication history

during the time period plus or minus 30 days from the day the patient was seen by the doctor and

a specimen was collected and sent to the lab.

Patient #48 (Figure 3, Table 3), was treated with SXT on the day of the medical visit.

Category agreement was assigned as R-R for both SXT and AM. The patient waited 14 days

for CIP therapy, which was effective against the infecting organism. AMC, F/M and TE would

have been effective therapy also.

Patient #91 (Figure 4, Table 3) was treated with CIP 11 days before an office visit. Results of

AST showed category agreement (CA) of R-R for CIP, and the patient was prescribed with the

effective agent F/M (CA S -S) 3 days post-visit. SXT would have worked equally well ( CA S -

S).

Patient #100 (Figure 5, Table 3,) was treated on the day of the visit with SXT. IDSX showed


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that the infecting organism was S to F/M. (It is instructive to note that CIP and SXT were both

Resistant. Therefore empirically F/M was a good guess.)

Patient #115 (Figure 7, Table 3) was treated for 13 days before the office visit with a

combination of AM and F/M. Both methods showed these agents to be ineffective in treating the

organism. No treatment was prescribed on the day of the visit. CIP was used as therapy two days

post visit. The uropathogen was a very resistant P. aeruginosa with few effective oral treatment

options. LVX, another fluoroquinolone, would have been effective as well.

4. Discussion

The IDSX s DAST method and the VITEK 2s AST method were considered to be in total

agreement when both methods presented the same susceptibility category (susceptible,

intermediate, or resistant) by both methods. When the results from the methods were not in

agreement the severity of the discrepancy is ranked (from least severe to most severe): Minor-

error (the IDSX method indicated intermediate and the VITEK 2 method indicated

susceptible or resistant; the IDSX indicated resistant and the VITEK 2 indicated


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(15%)for piperacillin-tazobactam when using the VITEK (15.0%) and VITEK 2 (20.0 to 21.7%)

systems (Juretschko et al., 2007).

Four of the discrepancies concerned the microorganism-SXT couple. With trimethoprim and

the sulfonamides, antagonists in the medium allowed some slight growth which was not

disregarded although CLSI guidelines recommend disregarding slight growth (20% or less of the

lawn growth) and measurement of the more obvious margin to determine the zone diameter

(CLSI M2-A9, 2006).

Several other observations concerning the discrepancies were: 1) Seventeen of the errors were

within 0.5 mm of being in category agreement. 2) Twenty-five of the 37 minor errors were either

intermediate for IDSX and susceptible for VITEK 2 or r esistant for IDSX and

intermediate for VITEK 2. These errors fall on the side of a safer (less chance for treatment

failure) therapeutic approach to the infection. 3) Discrepancy resolution if validated by digital

image could have reduced the major errors from 13 to 2. See for example the IDSX TZP result

for patient #91 in Table 3, and Figure 4, TZP disk- quarter for a visual: the result was E.coli -


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cultures from 13 of the 21 patients were susceptible to the oral antimicrobial agent ampicillin,

cultures from 18 of the 21 patients were susceptible to amoxicillin/clavuanic acid, cultures from

19 of the 21 patients were susceptible to nitrofurantoin, and cultures from 16 of the 21 patients

were susceptible to trimethoprim/sulfamethoxizole.

Simple DAST of urine specimens by a disc diffusion assay have been shown in the past to

offer a means of rapidly and inexpensively guiding antimicrobial therapy for patients with

urinary tract infections when used selectively and interpreted carefully (Johnson et al., 1995;

Bronnestam 1999; Blue et al., 1991; Gillenwater et al., 1996). However, the DAST of these

former studies did not have the benefit of a concurrent isolation for presumptive identification or

a means to quantitate the concentration of pathogens in the specimen as the IDSX kit does. The

DAST portion of the IDSX method operates on the principle of a disc diffusion assay. It is

important to note that the DAST portion of the IDSX method produces results that are equivalent

to a standardized disc diffusion assay such as the Kirby-Bauer assay, only when the antibiotic

papers are placed so that they are against the walls or into the corners of the test chambers.


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in mixed culture, and yields bacterial cell concentration, all concurrently performed with the

DAST.

Since the IDSX kit provides overnight results, it is prudent for the healthcare provider to

delay prescription of antimicrobial therapy for 12-18 hours when results of DAST are available

to guide patient care. Patients can be given an analgesic such as phenazopyridine to minimize

symptoms and provided with literature explaining antibiotic resistance. A prescription can be

telephoned to the pharmacy the next morning. This would allow the healthcare provider to

prescribe the most appropriate antibiotic instead of using empirical treatment. Antimicrobial

therapy that is evidence-based is prudent use of our antibiotic armamentarium.

Acknowledgements

The authors thank the microbiology staff at Central Laboratory, the Utah Health Research

Network (study sponsor), and Atoosa Kourosh MD, MPH.


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References

Andersson DI (2003) Persistence of antibiotic resistant bacteria. Curr Opin Microbiol 6:452-456

Antibiotic/antimicrobial resistance: action plan. Atlanta (1999): US Department of Health and

Human Services Centers for Disease Control and Prevention. Available at

http://www.cdc.gov/drug- resistance/action plan

Blue AP, Gordon DL (1991) Is primary testing on urine samples valid? Pathology 23:149-152.

Bronnestam R (1999) Direct antimicrobial susceptibility testing in bacteriuria. APMIS

107(4):437-444.

Campos J, Roman F, Georgiou M, Garcia C, Gomez-Lus R, Canton R, Escobar H, Baquero F

(1996) Long-term persistence of ciprofloxacin-resistant Haemophilus influenzae in patients

with cystic fibrosis. J Infect Dis 174(6):1345-1347

Clinical and Laboratory Standards Institute. Performance Standards for Antimicrobial Disk

Susceptibility Tests; Approved Standard-Ninth Edition. Clinical and Laboratory Standards

Institute document M2-A9. Clinical and Laboratory Standards Institute (CLSI). Wayne, PA,


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Gupta K, Hooton TM, Stamm WE (2001) Increasing antimicrobial resistance and the

management of uncomplicated community-acquired urinary tract infections. Ann Intern Med

135:41-50

Gupta K, Sahm DF, Mayfield D, Stamm WE (2001) Antimicrobial resistance among

uropathogens causing community-acquired UTI in women: a nationwide analysis. Clin Infect

Dis 33:89-94.

Hooton TM, Besser R, Foxman B, Fritsche TR, Nicolle LE (2004) Acute uncomplicated cystitis

in an era of increasing antibiotic resistance: a proposed approach to empirical therapy. Clin

Infect Dis 39:75-80

Infectious Diseases Society of America (2004) Bad bugs, no drugs: as antibiotic discovery

stagnates, a public health crisis brews. Alexandria, VA: Infectious Diseases Society of

America

Iqbal J, Rahman M, Kabir MS, Rahman M (1997) Increasing ciprofloxacin resistance among

prevalent urinary tract bacterial isolates in Bangladesh. Jpn J Med Sci Biol 50(6):241-250


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Levy S (2002) Factors impacting on the problem of antibiotic resistance. J Antimicrob Chemoth

49:25-30.

Livermore DM (2003) Bacterial resistance: origins, epidemiology, and impact. Clin Infect Dis

36(Suppl 1): S11-S23.

Morell V (1997) Antibiotic resistance: road of no return. Science 278(5338):575-576.

Schrag SJ, Perrot V, Levin BR (1977) Adaptation to the fitness costs of antibiotic resistance in

Escherichia coli. Proc R Soc Lond B Biol Sci 264(1386): 1287-1291

Smolinski MS, Hamburg MA, Lederberg J (2003) Microbial threats to health: emergence,

detection, and response. Washington, DC: Institute of Medicine

Spratt BG (1996) Antibiotic resistance: counting the cost. Curr Biol 6:1219-1221

Srinivasa H, Parija SC, Bhattacharya S, Sehgal R (1999) A high incidence of ciprofloxacin

resistance in urinary isolates in eastern Nepal. J Commun Dis 31(1):45-47

Taur Y, Smith MA (2007) Adherence to the Infectious Diseases Society of America guidelines

in the treatment of uncomplicated urinary tract infection. Clin Infect Dis 44:769-774


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Table 1. Possible combinations of category results with agreement category(agreeement ordiscrepancy)

Reference method (VITEK-2) Test Method (IDSX) Agreement category

Resistant

Intermediate

Susceptible

Resistant

Intermediate

Intermediate

Susceptible

Susceptible

Resistant

Resistant

Intermediate

Susceptible

Intermediate

Resistant

Susceptible

Intermediate

Resistant

Susceptible

Agreement

Agreement

Agreement

Minor error

Minor error

Minor error

Minor error

Major error

Very major error


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Table 2. Empirical treatment on the day of visit. 77 of 132 (58%

Empiricalantibiotic

Number ofpatients Rxwith theantibiotic

Eventual diagnosis plus pathogensusceptibility

Non-susceptible antibioticswitched with susceptibleantibiotic listed below (daysfrom visit)

No UTI(% oftotal)

UTI--antibioticsusceptible(%)

UTI--antibioticnotsusceptible(%)

SXT 19 5(26%) 9(47%) 5(26%) CIP(14), CIP(4), LVX(4),CDR(22), CIP(2)

CIP 27 6(22%) 19(70%) 2(7%) F/M(23), F/M(2)

F/M 15 2(13%) 11(73%) 2(13%) SXT(3), No replacement

CF 4 2(50%) 2(50%) -

AMC 4 - 3(75%) 1(25%) SXT(13)

AM 2 1(50%) - 1(50%) F/M(6)

D 1 - - 1(100%) No replacement

LVX 3 1(33%) 2(66%) -

CRO+LVX 1 - 1 a -

CDR 1 - 1 b -

77 total 17(22%) 48(62%) 12(16%)


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TABLE 3. Selected results of AST, ID for IDSX and VITEK-2 method. Also includes time to result andantimicrobial agent intervention history. See Figures 3-7.

PRIOR DAY 0 POST

F I G

. #

T E S T

D T R

ID A M

A M C

C Z

C C E

C I P

V A

A N

G M

L V X

F / M

T Z P

T E

S X T

C T T

RX(D) RX RX(D)

3 IDSX 1 1:10dil.,10-6 col/ml gm(-), LF R S S R R S R S S S S S S R SXT CIP(+14)VITEK 2 > 10-5 col/ml Escherichia coli R S S N N S N S S S S S N R

4 IDSX 1 1:10dil.,10-7 col/ml gm(-) LF,w minor gm(+) R R I R R R R S S R S R S S CIP(-11) NONE F/M (+3)VITEK 4 > 10-5 col/ml Escherichia coli R R I N N R N S S R S S N S

5IDSX 1 1:10dil.,5x10-7 col/ml,gm(-),LF R S S S R S S S S S R R S SXT CDR(+22)VITEK 3 > 10-5 col/ml Escherichia coli S S S S N S S S S S N S S

VITEK repeated 1 week later: > 10-5 col/ml E. coli R S S S N S S S S S N R S

6 IDSX 1 1:10dil.,5x10-6 col/ml,gm(-),non-LF,w minor gm(+) R I S R R S R R S S R R S AM(-23) F/MVITEK 2 > 10-5 cfu/ml Escherichia coli R I S R N S R R S S N R S

7 IDSX 1 1:10dil.,10-6 col/ml,gm(-),grn fluorMH,non-LF, ox(+) R R R S R S S S R S R R R AM(-13)NONE

CIP(+2)VITEK 2 pseudomonas aeruginosa, >10-5 col/ml R R R S N N N S N S N R N F/M(-13)

DTR=days to result; ID=identification;1:10 dil=1:10 dilution of specimen; gm(-)=gram negative organism;gm(+)=gram positive organism; LF=lactose fermentor; w minor=minor species present;col=colony,sometimes refered to as colony forming unit or cfu; grn fluorMH=green fluorescence onMueller-Hinton agar; ox(+)=cytochrome oxidase positive colonies;R=resistant,I=intermediate,S=susceptible; See text for the list of antimicrobial agents; CDR=the antibioticCefdinir


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10 cfu/ml4 10 cfu/ml6

10 cfu/ml8

10 cfu/ml5

10 cfu/ml7

Fig.1. Set of incubated IDSX plate images of known bacterial concentration. Test sample resultsare matched for a determination of concentration.


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0

10

20

30

40

50

60

70

80

90

1 2 3 4 5 >=6

number

of

patients

days post receipt of specimen in lab

IDSX result

VITEK 2 result

Fig.2. The IDSX kit antimicrobial susceptibility test result compared to the VITEK 2 result inregards to time from receipt of specimen to result.


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Fig.3. Cultured IDSX plate of specimen from patient #48

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Documents

IDSX Manuscript (121108) Updated 08212011 With Figs