Reducing Time To Result For Urinary Tract Pathogen .

Reducing Time to Result for Urinary Tract Pathogen DetectionUtilizing Real-Time PCR TechnologyDavid A. Baunoch, Ph.DChief Scientific OfficerPathnostics

Evolving Picture of Urinary Tract Infections The Scope of the Problem Evaluating the Tools Available Refining the Definition Moving from a Monocentric Thought Process Understanding the Prevalence and Nature of Polymicrobial Infections Development of New Tools for the Diagnosis and Management ofUrinary Tract Infections

Objectives At the conclusion of the presentations participants will be able to :Understand the Impact of UTI’s in Patient CareEvaluate the Technical Challenges Associated with Urine CultureIdentify the Different Classes of UropathogensExplain the Role of the Urinary Microbiome and Polymicrobial Infectionsin the Management of Urinary Tract Infections.– Assess the Use of qPCR in the Diagnosis of Urinary Tract Infections– Compare the Clinical Utility of Genotypic and Phenotypic Methods inTreatment of Urinary Tract Infections––––

THE SCOPE OF THE PROBLEMMARKET SIZE AND INCIDENCE

Symptoms of Urinary Tract Infections Pressure in Lower PelvisDysuriaFrequencyUrgencyNocturiaAbnormal Color or OdorHematuriaFlank PainFever/ChillsMental Changes/Confusion

The Impact Cost to SystemUTI complicationsresult inResponsible for 10.5MILLIONoffice visits/year19-11DAYSlonger for eachhospital stay2 Cost to HumanityUp to 1/3 of infectionsillustrate resistance toan antibiotic3Health carecost exceed 13BILLIONin the US1According to the CDC, antibioticresistance gives rise to at least2MILLIONINFECTIONSand23,000DEATHS/YEAR4

UTIs Segmentation (US)AsymptomaticUrinary Tract Infections (UTIs)Symptomatic 10-15% of adultwomen/year1,2; 2-3MPregnant women 12MER visitsCystitisMajority are uncomplicated4Uncomplicated UTIsComplicated UTIsPyelonephritisPatient who will undergoinvasive urologic procedure(eg, prostate biopsy)Majority are uncomplicated4Recurrent UTIRenal transplant recipient 3M25% of UTIs in women will recur within 6 months of initial infection 1Low riskCatheter-associated UTI1MIncidence: 449,334 CAUTI events (2002)5; 35,600 CAUTI events (2011)6 in acute care hospitalsUTI in men 1.1MIncidence: 0.1% in 30-65 years old; 5% in 65-85 years old2Urosepsis400K 4MAsymptomatic bacteriuria (ABU): 2-10% of pregnant women10(2013)3High riskPatient with urinary catheter 1M

Long Term Care Facilities– 1.5M under care in 16,700 NursingHomes with a total of 5.3M forecastedfor 2030 US Market Up1.2 Million infections per year withpatients averaging 3-4 courses ofantibiotics annuallyUp to 120,000 Hospital admissionsannually which make up 30-50% of allMedicare Hospital admissions annually Average Cost of Treating UTI in NursingHome of 150 Per Patient– Total Cost of 180M Up to 120,000 Hospitalization– from Average Hospital stay per admissioncosts an average of 1947 per nightTotal Cost of Long Term CareDerived UTI – 647M Total Cost of Hospital Admission fromLong Term Care Facilities - 467M

Hospital Acquired Urinary Tract Infections– 25% of patients in the US have catheters. US MarketCatheter-acquired urinary infection is thesource for about 20% of episodes of healthcare acquired bacteremia in acute carefacilities, and over 50% in long-term carefacilities– 561,667 infections per year with a patient– Average 2 additional nights based on UTI Average Hospital stay per admission costsan average of 1947 per nightTypeTotal Cost of Hospital AcquiredUTI 2.2 BillionNumberCost per NightState/Local1053 1,974.00Non-Profit1003 2,346.00For Profit2870 1,798.004926 1,947

3% of children per year develop a urinary tractinfection accounting for 1 million officer visitsper year Recurrent infections occur in up to 50% of patientsPediatric UrinaryTract Infections Permanent renal cortical scarring may occur in upto 65% of affected children, especially in recurrentUTI and its long-term complications includehypertension and chronic renal failure which mayresult in end stage renal disease 1.5 million office visits annually– 150M in annual costs 50,000 hospital admissions– Average cost of hospitalization is 10,489 per patient– Annual cost of 520 Million Total cost 670 Million– Does not include costs associated with treatment ofpatients for consequences of renal/cortical scarring

Sepsis 30 million sepsis cases worldwide annually 1.1 million cases in US annually Urosepsis comprises 25% of that total Total US cost for sepsis treatment is 24B annually Total cost for sepsis due to urinary tractinfection is 6B annuallyFig 1. hospital admissions for sepsis have overtaken those for stroke or myocardialinfarction. Adapted from Seymour et al. [16]

Total Cost of UTITreatment in USHealthcare SystemTypeCostPhysician Office Based 3.9BLTC Facility Based 647MHAI Based 2.2BPediatric UTI .67BSepsis (UTI Based) 6B 13 Billion Dollars Annually

The Situation is Complicated by Lack of New Antibiotics andIncreasing Rates of Antibiotic Resistance

Limited Efficacy of Current Testing MethodologiesLimit Treatment OptionsDue to Prolonged Turn around Times (48-72 Hours)and Limited Sensitivity Associated with UrineCulture Clinicians Frequently Treat PatientsEmpirically Resulting in Poor Antibiotic Stewardshipand Increased Rate of Antibiotic Resistance.

EVALUATING THE TOOLS

Urine Culture – The Current Gold Standard for Urinary TractInfections The Method – Developed in the 1950’s, the standard methodinvolves applying 1ul of urine onto Blood and MacConkey Agarplates and incubating them at 35 degrees centigrade for 24 hoursin the presence of oxygen.

What Is theFundamental ProblemWith Culture as aDetection Method? From the composition of the agar, to the pH, gasratio’s, and time of incubation culture is amethodology that has been biased for thedetection of a subset of pathogens – primarily E.Coli– The biased results developed using thismethodology often creates findings that are notconsistent with the clinical symptoms– Is unable to detect slow growing organismsincluding fastidious and non aerobic organisms aswell as most gram positive organisms.– Time consuming process that can take upto 72 hours to complete– Inherent methodology issues limit the number oforganisms reported to no more then 2 with 3 ormore considered indications of contamination

What Has Been Missed by Culture? The Loyola Study followed 150 patients who were splitinto two groups based on the whether they believed theywere symptomatic for UTI– They compared the results obtained when they usedstandard culture to an enhanced version which hadmodified growth conditions including an increasedincubation time In the group who believed they were symptomaticstandard culture detected only 57% of the uropathogenswhere the enhanced methodology detected 91%.Price TK, et al. J Clin Microbiol. 2016;54[5]:1216– 1222

Expanding the Number and Types of UropathogensqPCR Assay ResultsCases with Organism 2400130010101

Frequency of Uropathogens - TypeEnterococcus faecalisEscherichia coliActinobaculum schaaliiStreptococcus anginosusMorganella morganiiAerococcus urinaeKlebsiella pneumoniaeProteus mirabilisStreptococcus agalactiaeAlloscardovia omnicolensCandida albicansCorynebacterium riegeliiStaphylococcus aureusPseudomonas aeruginosaKlebsiella oxytocaAcinetobacter baumanniiNumber of 6%8.6%7.0%6.0%5.6%5.2%5.0%5.0%Common Organisms CultureIdentified PositiveGram Gram -Escherichia coliKlebsiellaEnterococcusProteus

Fungal Uropathogens Fungal Infections most often due to Candida species including– Candida albicans– Candida glabrata– Candida parapsilosis Can cause both UTI’s and Prostatitis Most patients asymptomatic but symptomatic patients areindistinguishable from those with bacterial UTI.

Virus in the Urinary Tract Virus typically difficult to detect in the bladder or prostate. Most common viral causes of urinary tract infections include -BK virus, JC virus,Adenovirus, CMV and HSV Impacts those with low immunity, for example:– Bone marrow or organ transplantation– Blood cancers/malignancies (e.g.leukemia)– HIV infection– Pregnancy– Diabetes, alcoholism, malnutrition, liver cirrhosis In UTI, high viral load is associated with high mortality in patients with lowimmunity

UNDERSTANDING THE IMPACT OF THEMICROBIOME AND POLYMICROBIALINFECTIONSREFINING THE DEFINITION – MOVING FROM A MONO-CENTRIC THOUGHTPROCESS

Evolving Picture of the Microbiomeof the Bladder and Urethra Urine is not sterile The bladder contains a microbiome thathas been overlooked primarily becauseof our limited capacity to culturemicroorganismsCompared Samples Obtained From Voided Urine, andTransurethral Catheters to Specimens Obtained bySuprapubic Aspiration – and They Were Very Similar The net result has been anunderstatement of the frequency andscope of bacterial infections

The Female and Male Microbiome The characterization of the male and female urinarymicrobiome are in their infancy but recent studies havebegun to define the basic parameters associated with them. In Females, the FUM Tend to be at lower colony counts as compared toother human microbiomes with counts in the 103to 105 range. They are dominated by Lactobacillus, Gardnerella,Sneathia, Staphylococcus and Enterbacteriaceaeas well as other diverse species. They consist of genital and urinary tractorganisms.

The Female and Male Microbiome In Males, the MUM They are dominated by Lactobacillus, Sneathia,Veillonella, Corynebacterium Prevotelloa,Streptococcus, and Ureaplasma. They consist of genital and urinary tractorganisms.

Asymptomatic Bacteriuria and Dysbiosis Asymptomatic bacteriuria is thepresence of a high number of bacteria 100,000/ml without symptoms. Not treated unless patient is has renaldisease, is immunocompromised orpregnant (to prevent pyelonephritis) May represent an ecological balancebetween pathogenic bacteria and theurinary microbiome.

Dysbiosis in the Urinary Tract Antibiotic UseImmune SuppressionDietStressLack of ExercisePathogenicBacteriaHealthyMicrobiome

Evolving From an Monocentric View of Urinary TractInfections Wolfe and Brubaker have proposed moving from a E.colicentric view of urinary tract infections – As importantly with an increasing number of studies demonstrating thatthe majority of urinary tract infections have multiple urinary pathogenspresent in the same sample, we should begin to shift our thinking awayfrom a monocentric view of urinary tract infections. A simple truth – Polymicrobial Infections may be the norm rather then theexception.

Bacteria Share Metabolic Products inPolymicrobial Infections The sharing of metabolicproducts providespolymicrobial infections anadvantage–In the presence ofantibiotics the sharing ofmetabolic products plays aprotective role increasingresistance and virulence Brings into question thecurrent practice of isolatingorganisms prior todetermining the antibioticresistance

It is becoming increasingly clear that a significant number of urinary tract infections arepolymicrobial in nature. Because of the polymicrobial nature of infections, efficacy oftreatment is dropping significantly.

Polymicrobial Interactions Change MIC Levels

Prevalence of Polymicrobial Infections Requirethe Development of New Methodologies Using current culture guidelines polymicrobial infections would most often be classedas mixed flora—probable contamination and not be worked up – In that there are a number of studies showing polymicrobial infections in the the bloodwith corresponding UTI findings – this supports the clinical importance of propercharacterization of samples This lack of sensitiviy seen with traditional culture coupled with this guidanceunderlys the growing incidence of patients presenting with symtopms of UTI and nodiagnosis—resulting in ineffective treatment

DEVELOPING NEXT GENERATION TOOLSFOR THE EVALUATION OF URINARYTRACT INFECTIONS