Urine polymerase chain reaction tests: stewardship helper or hinderance?

Confusing results

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Escherichia coli causes 75-95% of uncomplicated UTIs, with other common organisms including Klebsiella pneumoniae, Proteus mirabilis, and Staphylococcus saprophyticus. Reference Gupta, Hooton and Naber13 Multiplex urine PCR panels assess samples for between 9 and 31 different bacteria and some Candida spp. (see Supplemental Table 1), arguably more targets than necessary. Reference Lehmann, Hauser and Malinka9,Reference Wojno, Baunoch and Luke15,Reference Cybulski, Schmidt and Grabiec16 Users may be confused with urine PCR results which are reported as organisms per quantity of urine, that is, cells/mL or copies/µL. 10-12 The standard colony-forming units (CFUs)/mL reported with SUC considers only those cells that can actively divide under specified conditions. There is a gap in data to provide guidance on the interpretation of quantitative urine PCR results reported as cells/mL or copies/µL per organism. Reference Xu, Deebel, Casals, Dutta and Mirzazadeh7,Reference Lehmann, Hauser and Malinka9-12

Urine PCR testing is more sensitive than SUC techniques, meaning that it is more likely to generate a positive result for organisms that do not represent the infectious agent. Reference Szlachta-McGinn, Douglass, Chung, Jackson, Nickel and Ackerman6,Reference Xu, Deebel, Casals, Dutta and Mirzazadeh7,Reference Lehmann, Hauser and Malinka9,Reference Wojno, Baunoch and Luke15,Reference Van Der Zee, Roorda, Bosman and Ossewaarde17 It is only minimally superior for the detection of E. coli. Reference Xu, Deebel, Casals, Dutta and Mirzazadeh7,Reference Wojno, Baunoch and Luke15,Reference Cybulski, Schmidt and Grabiec16 In a non-inferiority trial, 29% of PCR samples grew E. coli compared to 34% of the same samples utilizing SUC techniques. Reference Wojno, Baunoch and Luke15 A small prospective study comparing the results of urine samples using both PCR and SUC techniques showed that 64% of PCR samples were positive for E. coli compared to 58% of SUC samples. Reference Cybulski, Schmidt and Grabiec16 A single-site, non-inferiority study performed in the outpatient setting collected urine samples for SUC and PCR testing from participants ≥ 60 years of age. Reference Wojno, Baunoch and Luke15 Of 582 patients sampled, 56% had a positive urine PCR result versus 37% with positive culture result; among the 217 with a positive urine culture, there was 90% agreement with urine PCR, suggesting that clinicians are not missing causative UTI organisms with culture alone. Reference Wojno, Baunoch and Luke15 Many of the discordant results were organisms not commonly thought to be causative UTI organisms, such as Actinobaculum schaalii and coagulase-negative Staphylococci. Reference Wojno, Baunoch and Luke15

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