Characterising the urinary microbial community in patients with symptoms of urinary tract infection

Abstract

Background. Every year 250 million individuals develop urinary tract infections (UTI), the diagnosis of which, usually involves the ‘gold standard’ midstream urine culture (MSU) test. Prompt detection aided by sensitive tests may increase the likelihood of successful treatment. However, recent evidence highlights the potential inadequacies of this test. Methods. We assessed the UK’s MSU culture by comparison with enhanced culture techniques and 16S rRNA gene sequencing. With ethical approval, patients attending their first consultation at the Whittington Hospital Clinic and asymptomatic controls provided MSU specimens. Each specimen was submitted to the Hospital Microbiology laboratory for MSU culture. 16S rRNA gene sequencing was performed on 1ml unspun urine and 30ml of centrifuged urine. Results. Urine specimens were analysed for 33 patients (mean age= 49 years, sd=16.5) and 29 controls (mean age=40.7 years, sd=15.7). Comparison of routine MSU cultures between patients and controls indicated that the test failed to discriminate between patients and controls(χ2= 0.539, df = 1, P = 0.674).Bacterial DNA was detected in 97.0% patients and 89.7% controls. Enterobacteriaceae was most abundant in patients, whereas Streptococcus dominated in controls. A higher distribution of the median number of observed taxa (centrifuged and unspun samples combined) was seen in patients (χ2 = 8.0, df = 2, P <0.05). Conclusion. The MSU culture failed to discriminate between patients and controls and missed recognised uropathogens that were detected with bacterial DNA sequencing. Microbial communities characterised by sequencing warrant further investigation to understand the role of each member in UTI.