Seven Bacteriophages Isolated from the Female Urinary Microbiota

Malki, Kema; Sible, Emily; Cooper, Alexandria; Garretto, Andrea; Bruder, Katherine; Watkins, Siobhan C.; Putonti, Catherine

doi:10.1128/genomea.01003-16

Cited by 26 publications

(28 citation statements)

References 8 publications

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“…Several recent genomic sequencing based studies of human urine demonstrate that the urinary tract is not sterile even when urine cultures are negative; instead, the healthy urinary tract is host to a unique community of bacteria and viruses [29–31]. The bladder microbiome of patients with asymptomatic bacteriuria is ecologically distinct from that of healthy patients with negative cultures [32].…”

Section: Epidemiology Microbiology and Pathogenesis Of Utismentioning

confidence: 99%

Urinary Tract Infection and Asymptomatic Bacteriuria in Older Adults

Cortés-Penfield

Trautner

Jump

2017

Infectious Disease Clinics of North America

163

105

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Synopsis Urinary tract infections (UTIs) are a significant cause of morbidity among older adults; however, antibiotic prescriptions for clinically suspected UTIs are often inappropriate. Healthcare providers frequently struggle to differentiate UTI from asymptomatic bacteriuria, particularly in patients presenting with nonspecific symptoms. Patients with baseline cognitive impairments that limit history-taking can be particularly challenging. Here, we review the epidemiology and pathogenesis of UTI in older adults. We also discuss an approach to the diagnosis and treatment of UTIs, focusing on recognizing patients who would likely benefit from antibiotic treatment and on identifying patients for whom empiric antibiotic therapy should not be given.

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Section: Epidemiology Microbiology and Pathogenesis Of Utismentioning

confidence: 99%

Urinary Tract Infection and Asymptomatic Bacteriuria in Older Adults

Cortés-Penfield

Trautner

Jump

2017

Infectious Disease Clinics of North America

163

105

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“…Coliphages in general are one of the most sequenced phage types with ~450 complete phage genomes within Genbank, isolated from a variety of sources including animal faeces (Niu et al, ; Smith et al, ; Sazinas et al, ; Golomidova et al, ), human faeces (Dalmasso et al, ), urine (Malki et al, ), river water (Alijošius et al, ), agricultural surface waters (Liao et al, ), lagoons (Ngazoa‐Kakou et al, ), sewage (Trotereau et al, ) and animal slurries (Sazinas et al, ). However, much less is known about the genetic diversity of coliphages in seawater.…”

Section: Introductionmentioning

confidence: 99%

Riding the wave of genomics to investigate aquatic coliphage diversity and activity

Michniewski

Redgwell

Grigonyte

et al. 2019

Environmental Microbiology

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Summary Bacteriophages infecting Escherichia coli (coliphages) have been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that is present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterized coliphages from three coastal locations in the United Kingdom and Poland. Comparative genomics and phylogenetic analysis of phage isolates facilitated the identification of putative new species within the genera Rb69virus and T5virus and a putative new genus within the subfamily Tunavirinae. Furthermore, genomic and proteomic analysis combined with host range analysis allowed the identification of a putative tail fibre that is likely responsible for the observed differences in host range of phages vB_Eco_mar003J3 and vB_Eco_mar004NP2.

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“…While new urinary microbiome research has primarily focused on the bacterial constituents of this community (5), a few studies have shown that the urinary microbiota also includes viruses. First, viruses have been isolated from urine, including several eukaryotic viruses (15)(16)(17)(18)(19)(20)(21) and phages (22,23). Second, two metagenomic sequencing studies of the urinary virome (eukaryotic viruses and phages in the lytic cycle) have been conducted (24,25).…”

mentioning

confidence: 99%

Bacteriophages of the Urinary Microbiome

et al. 2018

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Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions. Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic "healthy" individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.

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Seven Bacteriophages Isolated from the Female Urinary Microbiota

Cited by 26 publications

References 8 publications

Urinary Tract Infection and Asymptomatic Bacteriuria in Older Adults

Urinary Tract Infection and Asymptomatic Bacteriuria in Older Adults

Riding the wave of genomics to investigate aquatic coliphage diversity and activity

Bacteriophages of the Urinary Microbiome

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