Usability application of multiplex polymerase chain reaction in the diagnosis of microorganisms isolated from urine of patients treated in cancer hospital

Abstract

Background. The objective of this study was: i) to compare the results of urine culture with polymerase chain reaction (PCR) -based detection of microorganisms using two commercially available kits, ii) to assess antimicrobial susceptibility of urine isolates from cancer patients to chosen antimicrobial drugs and, if necessary, to update the recommendation of empirical therapy. Materials and methods. A one-year hospital-based prospective study has been conducted in Greater Poland Cancer Centre and Genetic Medicine Laboratory CBDNA Research Centre in 2011. Urine cultures and urine PCR assay from 72 patients were examined Results. Urine cultures and urine PCR assay from 72 patients were examined. Urine samples were positive for 128 strains from which 95 (74%) were identical in both tests. The most frequently isolated bacteria in both culture and PCR assay were coliform organisms and Enterococcus spp. The Gram negative bacilli were most resistant to cotrimoxazol. 77.2% of these bacilli and 100% of E. faecalis and S. agalactiae were sensitive to amoxicillin-clavulanic acid. 4.7% of Gram positive cocci were resistant to nitrofurantoin. Conclusions. The PCR method quickly finds the causative agent of urinary tract infection (UTI) and, therefore, it can help with making the choice of the proper antimicrobial therapy at an early stage. It appears to be a viable alternative to the recommendations made in general treatment guidelines, in cases where diversified sensitivity patterns of microorganisms have been found.

A New Gold Rush: A Review of Current and Developing Diagnostic Tools for Urinary Tract Infections

“…Although PCR can uniformly provide faster identification of pathogens, it is also subject to identifying pathogens that are either present in inconsequential amounts in the urine or a part of the patient’s urinary microbiome [ 38 ]. Additionally, while identification of the causative organism helps tailor antimicrobial treatment, most PCR results are unable to provide information regarding sensitivity of the pathogens to different treatments, unlike the standard urine culture [ 46 ]. Currently, the detection of antibiotic resistance in bacteria present in urine is limited to a handful of known resistance genes [ 46 ], or a more robust investigation of several treatment resistance-associated genes in multiplex PCR testing of a single family of bacteria such as Enterobacteriaceae [ 47 ].…”

“…Additionally, while identification of the causative organism helps tailor antimicrobial treatment, most PCR results are unable to provide information regarding sensitivity of the pathogens to different treatments, unlike the standard urine culture [ 46 ]. Currently, the detection of antibiotic resistance in bacteria present in urine is limited to a handful of known resistance genes [ 46 ], or a more robust investigation of several treatment resistance-associated genes in multiplex PCR testing of a single family of bacteria such as Enterobacteriaceae [ 47 ]. Schmidt et al, suggest that this admittedly limited capability of PCR testing may still offer clinicians the ability to guide treatment decisions early in the disease course by including genes commonly associated with drug-resistance in urinary pathogens.…”

Multiplex PCR Based Urinary Tract Infection (UTI) Analysis Compared to Traditional Urine Culture in Identifying Significant Pathogens in Symptomatic Patients

“…9 Few studies have compared multiplex PCR with urine culture for diagnosis of UTIs and acute cystitis. Although several studies have compared performance of PCR with urine culture for detection of a single pathogen, only 4 have tested multiplex PCR: one against 15 bacteria, 10 a second against 14 bacteria together with 6 fungi, 11 a third against 20, 12 and the fourth against 9 bacteria. 13 Polymicrobial infections may occur in as many of 39% of UTIs 14,15 and can display enhanced virulence and increased antibiotic resistance.…”

The Utility of Real-Time Quantitative Polymerase Chain Reaction Genotype Detection in the Diagnosis of Urinary Tract Infections in Children

“…The presence of multiple strains of bacteria in urine is a recent finding of unknown significance, made possible only by the extreme sensitivity of RT-qPCR. Cybulski et al 17 found a similarly high number of mixed infections in a study evaluating the performance of multiplex PCR on 72 positive urine cultures from adult oncology patients. While E coli and Enterococcus spp were the most common in that study, E coli and P vulgaris were the most commonly identified in the present study.…”

“…Numerous studies have validated the utility of PCR-based methodologies for the rapid identification of uropathogens in adult patients, however there have been no similar investigations in pediatric patients. [12][13][14][15][16][17]…”