Travis K. Price

The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms

ABSTRACT Enhanced quantitative urine culture (EQUC) detects live microorganisms in the vast majority of urine specimens reported as “no growth” by the standard urine culture protocol. Here, we evaluated an expanded set of EQUC conditions (expanded-spectrum EQUC) to identify an optimal version that provides a more complete description of uropathogens in women experiencing urinary tract infection (UTI)-like symptoms. One hundred fifty adult urogynecology patient-participants were characterized using a self-completed validated UTI symptom assessment (UTISA) questionnaire and asked “Do you feel you have a UTI?” Women responding negatively were recruited into the no-UTI cohort, while women responding affirmatively were recruited into the UTI cohort; the latter cohort was reassessed with the UTISA questionnaire 3 to 7 days later. Baseline catheterized urine samples were plated using both standard urine culture and expanded-spectrum EQUC protocols: standard urine culture inoculated at 1 μl onto 2 agars incubated aerobically; expanded-spectrum EQUC inoculated at three different volumes of urine onto 7 combinations of agars and environments. Compared to expanded-spectrum EQUC, standard urine culture missed 67% of uropathogens overall and 50% in participants with severe urinary symptoms. Thirty-six percent of participants with missed uropathogens reported no symptom resolution after treatment by standard urine culture results. Optimal detection of uropathogens could be achieved using the following: 100 μl of urine plated onto blood (blood agar plate [BAP]), colistin-nalidixic acid (CNA), and MacConkey agars in 5% CO2 for 48 h. This streamlined EQUC protocol achieved 84% uropathogen detection relative to 33% detection by standard urine culture. The streamlined EQUC protocol improves detection of uropathogens that are likely relevant for symptomatic women, giving clinicians the opportunity to receive additional information not currently reported using standard urine culture techniques.

Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome

Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species’ evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts.

Urine trouble: should we think differently about UTI?

Urinary tract infection (UTI) is clinically important, given that it is one of the most common bacterial infections in adult women. However, the current understanding of UTI remains based on a now disproven concept that the urinary bladder is sterile. Thus, current standards for UTI diagnosis have significant limitations that may reduce the opportunity to improve patient care. Using data from our work and numerous other peer-reviewed studies, we identified four major limitations to the contemporary UTI description: the language of UTI, UTI diagnostic testing, the Escherichia coli-centric view of UTI, and the colony-forming units (CFU) threshold-based diagnosis. Contemporary methods and technology, combined with continued rigorous clinical research can be used to correct these limitations.

Culturing of female bladder bacteria reveals an interconnected urogenital microbiota

Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder in the same women identifies highly similar Escherichia coli, Streptococcus anginosus, Lactobacillus iners, and Lactobacillus crispatus, suggesting an interlinked female urogenital microbiota that is not only limited to pathogens but is also characteristic of health-associated commensals.The female bladder seems to harbor a poorly characterized indigenous microbiota. Here, the authors isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women, generating a culture collection representing two thirds of the bacterial diversity within the samples.

Genome sequences and annotation of two urinary isolates of E. coli.

The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not have symptoms of cystitis. Whereas strain E75 is most closely related to an avian extraintestinal pathogen, strain E78 is a member of a clade that includes extraintestinal strains often found in the human bladder. Both genomes are uncommonly rich in prophages.

Draft Genome Sequence of a Urinary Isolate of Lactobacillus crispatus

ABSTRACT While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms.

Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae

ABSTRACT A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N50 of 109,831 bp.