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Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report.

Siddiqui H, Lagesen K, Nederbragt AJ, Eri LM, Jeansson SL, Jakobsen KS - Open Microbiol J (2014)

Bottom Line: A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a suitable subject for a culture-independent 16S rDNA analysis on the patient´s urine.One year later, the subject was still experiencing severe symptoms, and a follow-up analysis was performed.This time the urine-culture was negative, however, the 16S rDNA profile was quite similar to that of the first sample, again displaying a complex bacterial profile.

View Article: PubMed Central - PubMed

Affiliation: University of Oslo, Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, P.O. Box 1066 Blindern, 0316 Oslo, Norway.

ABSTRACT

Introduction: Overactive bladder syndrome (OAB) is described as urgency, with or without urgency incontinence. A range of medical conditions shares the symptoms of OAB, however the diagnosis is contingent on the exclusion of urinary tract infection (UTI). Knowing that urine dipstick and routine culture of bacteria can miss UTI diagnosis caused by low-count bacteriuria or "difficult-to-culture" pathogens, we examined a case of OAB with a culture-independent approach.

Case presentation: A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a suitable subject for a culture-independent 16S rDNA analysis on the patient´s urine. The patient's medical records showed no history of recurrent UTI, however, when the urine specimen was sent to routine culture at the time of study it showed a significant bacteriuria caused by a single bacterium, and the patient was prescribed antibiotics. The 16S rDNA analysis revealed not one, but many different bacteria, including a considerable amount of fastidious bacteria, indicating a polymicrobial state. One year later, the subject was still experiencing severe symptoms, and a follow-up analysis was performed. This time the urine-culture was negative, however, the 16S rDNA profile was quite similar to that of the first sample, again displaying a complex bacterial profile.

Conclusion: The use of 16S rDNA pyrosequencing and sequence analysis to uncover "difficult-to-culture" bacteria should be considered when examining patients with chronic urinary symptoms. These methods may contribute to further elucidation of the etiology of overactive bladder syndrome and other urinary syndromes.

No MeSH data available.


Related in: MedlinePlus

Taxonomical classification of 16S rDNA found in reported samples.A and B: Tree view of 16S rDNA sequences from culture-positive urine (α-hemolytic Streptococcus >105 CFU/ml), assigned at different taxonomy levels (family, genus and species) as computed by MEGAN 3.4 for V1V2 (A) and V6 (B) amplicons. Each circle represents a taxon and is labeled by its name and the number of sequenced reads assigned. Taxonomical assignment was done by comparing the sequences to a curated version of the SSUrdp database, then assigning the sequences to the taxon of the best-matched reference sequence (lowest common ancestor). The size of the circles is scaled logarithmically to the number of reads assigned to the taxon.C and D: Comparison of bacterial communities from culture-positive urine positive for α-hemolytic green Streptococcus (red bars) and culture-negative urine (blue bars) from a case subject diagnosed with overactive bladder syndrome. Sequence analysis is based on V1V2 (C) and V6 (D) amplicons. Only major genera with a sequence abundance ≥10 % for either V1V2 or V6 analysis are shown. The calculation of sequence abundance for each genus was relative to the total number of sequence assigned to Bacteria in each dataset.
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Figure 1: Taxonomical classification of 16S rDNA found in reported samples.A and B: Tree view of 16S rDNA sequences from culture-positive urine (α-hemolytic Streptococcus >105 CFU/ml), assigned at different taxonomy levels (family, genus and species) as computed by MEGAN 3.4 for V1V2 (A) and V6 (B) amplicons. Each circle represents a taxon and is labeled by its name and the number of sequenced reads assigned. Taxonomical assignment was done by comparing the sequences to a curated version of the SSUrdp database, then assigning the sequences to the taxon of the best-matched reference sequence (lowest common ancestor). The size of the circles is scaled logarithmically to the number of reads assigned to the taxon.C and D: Comparison of bacterial communities from culture-positive urine positive for α-hemolytic green Streptococcus (red bars) and culture-negative urine (blue bars) from a case subject diagnosed with overactive bladder syndrome. Sequence analysis is based on V1V2 (C) and V6 (D) amplicons. Only major genera with a sequence abundance ≥10 % for either V1V2 or V6 analysis are shown. The calculation of sequence abundance for each genus was relative to the total number of sequence assigned to Bacteria in each dataset.

Mentions: We performed both a urine dipstick analysis and a routine culture to ensure that the patient, as previously, did not have any traditionally detectable UTI. The urine stick analysis was negative, however she had a positive urine culture; she was reported to be infected with α-hemolytic green Streptococcus > 105 colony-forming unit (CFU/ml) (Streptococcus viridians group) (see Table 1). Antimicrobial susceptibility was determined and she was prescribed Trimethoprim 160 mg x twice a day for a week. In contrast to the clinical reports, the molecular analysis revealed a complex bacterial composition of the urine sample taken (Fig. 1A, 1B). Consistent with the culture report, Streptococcus was observed (sequences assigned to α-hemolytic Streptococci). The abundance of the bacterial sequences assigned to this genus was 23% and 30% for both V1V2 and V6 analysis. Several fastidious bacteria not identifiable by routine culture were also present. Atopobium was the major genus identified, with a total sequence abundance of 24% and 33,5% for V1V2 and V6, respectively. Interestingly, Ureaplasma was also present with a relatively high sequence abundance of 17% for V1V2 analysis, although V6 analysis only gave an abundance of 1.2%. Prevotella was also identified with an abundance of 16% for V1V2 and 8.6% for V6 analysis. The species Bacteroides urealyticus was also detected with abundances of 10.8% and 5.8% for V1V2 and V6, respectively.


Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report.

Siddiqui H, Lagesen K, Nederbragt AJ, Eri LM, Jeansson SL, Jakobsen KS - Open Microbiol J (2014)

Taxonomical classification of 16S rDNA found in reported samples.A and B: Tree view of 16S rDNA sequences from culture-positive urine (α-hemolytic Streptococcus >105 CFU/ml), assigned at different taxonomy levels (family, genus and species) as computed by MEGAN 3.4 for V1V2 (A) and V6 (B) amplicons. Each circle represents a taxon and is labeled by its name and the number of sequenced reads assigned. Taxonomical assignment was done by comparing the sequences to a curated version of the SSUrdp database, then assigning the sequences to the taxon of the best-matched reference sequence (lowest common ancestor). The size of the circles is scaled logarithmically to the number of reads assigned to the taxon.C and D: Comparison of bacterial communities from culture-positive urine positive for α-hemolytic green Streptococcus (red bars) and culture-negative urine (blue bars) from a case subject diagnosed with overactive bladder syndrome. Sequence analysis is based on V1V2 (C) and V6 (D) amplicons. Only major genera with a sequence abundance ≥10 % for either V1V2 or V6 analysis are shown. The calculation of sequence abundance for each genus was relative to the total number of sequence assigned to Bacteria in each dataset.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4323767&req=5

Figure 1: Taxonomical classification of 16S rDNA found in reported samples.A and B: Tree view of 16S rDNA sequences from culture-positive urine (α-hemolytic Streptococcus >105 CFU/ml), assigned at different taxonomy levels (family, genus and species) as computed by MEGAN 3.4 for V1V2 (A) and V6 (B) amplicons. Each circle represents a taxon and is labeled by its name and the number of sequenced reads assigned. Taxonomical assignment was done by comparing the sequences to a curated version of the SSUrdp database, then assigning the sequences to the taxon of the best-matched reference sequence (lowest common ancestor). The size of the circles is scaled logarithmically to the number of reads assigned to the taxon.C and D: Comparison of bacterial communities from culture-positive urine positive for α-hemolytic green Streptococcus (red bars) and culture-negative urine (blue bars) from a case subject diagnosed with overactive bladder syndrome. Sequence analysis is based on V1V2 (C) and V6 (D) amplicons. Only major genera with a sequence abundance ≥10 % for either V1V2 or V6 analysis are shown. The calculation of sequence abundance for each genus was relative to the total number of sequence assigned to Bacteria in each dataset.
Mentions: We performed both a urine dipstick analysis and a routine culture to ensure that the patient, as previously, did not have any traditionally detectable UTI. The urine stick analysis was negative, however she had a positive urine culture; she was reported to be infected with α-hemolytic green Streptococcus > 105 colony-forming unit (CFU/ml) (Streptococcus viridians group) (see Table 1). Antimicrobial susceptibility was determined and she was prescribed Trimethoprim 160 mg x twice a day for a week. In contrast to the clinical reports, the molecular analysis revealed a complex bacterial composition of the urine sample taken (Fig. 1A, 1B). Consistent with the culture report, Streptococcus was observed (sequences assigned to α-hemolytic Streptococci). The abundance of the bacterial sequences assigned to this genus was 23% and 30% for both V1V2 and V6 analysis. Several fastidious bacteria not identifiable by routine culture were also present. Atopobium was the major genus identified, with a total sequence abundance of 24% and 33,5% for V1V2 and V6, respectively. Interestingly, Ureaplasma was also present with a relatively high sequence abundance of 17% for V1V2 analysis, although V6 analysis only gave an abundance of 1.2%. Prevotella was also identified with an abundance of 16% for V1V2 and 8.6% for V6 analysis. The species Bacteroides urealyticus was also detected with abundances of 10.8% and 5.8% for V1V2 and V6, respectively.

Bottom Line: A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a suitable subject for a culture-independent 16S rDNA analysis on the patient´s urine.One year later, the subject was still experiencing severe symptoms, and a follow-up analysis was performed.This time the urine-culture was negative, however, the 16S rDNA profile was quite similar to that of the first sample, again displaying a complex bacterial profile.

View Article: PubMed Central - PubMed

Affiliation: University of Oslo, Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, P.O. Box 1066 Blindern, 0316 Oslo, Norway.

ABSTRACT

Introduction: Overactive bladder syndrome (OAB) is described as urgency, with or without urgency incontinence. A range of medical conditions shares the symptoms of OAB, however the diagnosis is contingent on the exclusion of urinary tract infection (UTI). Knowing that urine dipstick and routine culture of bacteria can miss UTI diagnosis caused by low-count bacteriuria or "difficult-to-culture" pathogens, we examined a case of OAB with a culture-independent approach.

Case presentation: A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a suitable subject for a culture-independent 16S rDNA analysis on the patient´s urine. The patient's medical records showed no history of recurrent UTI, however, when the urine specimen was sent to routine culture at the time of study it showed a significant bacteriuria caused by a single bacterium, and the patient was prescribed antibiotics. The 16S rDNA analysis revealed not one, but many different bacteria, including a considerable amount of fastidious bacteria, indicating a polymicrobial state. One year later, the subject was still experiencing severe symptoms, and a follow-up analysis was performed. This time the urine-culture was negative, however, the 16S rDNA profile was quite similar to that of the first sample, again displaying a complex bacterial profile.

Conclusion: The use of 16S rDNA pyrosequencing and sequence analysis to uncover "difficult-to-culture" bacteria should be considered when examining patients with chronic urinary symptoms. These methods may contribute to further elucidation of the etiology of overactive bladder syndrome and other urinary syndromes.

No MeSH data available.


Related in: MedlinePlus