scholarly journals Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury

2012 ◽  
Vol 10 (1) ◽  
Author(s):  
Derrick E Fouts ◽  
Rembert Pieper ◽  
Sebastian Szpakowski ◽  
Hans Pohl ◽  
Susan Knoblach ◽  
...  
2020 ◽  
Vol 41 (S1) ◽  
pp. s90-s90
Author(s):  
Alison Nelson ◽  
Kalpana Gupta ◽  
Judith Strymish ◽  
Maura Nee ◽  
Katherine Linsenmeyer

Background: Guidelines regarding asymptomatic bacteriuria (ASB) have consistently recommended against screening and treatment in most circumstances. However, screening of patients with spinal cord injury (SCI) is common practice and in some cases is a formal protocol at the organizational level. A previous study found that more than one-third of patients with ASB detected on routine screening cultures performed at annual visits in 2012 received antibiotics. However, the role of antibiotic stewardship has become more prominent over the last decade. We hypothesized that diagnostic and therapeutic stewardship efforts may be impacting the practice of annual urine-culture screening for SCI patients. We evaluated urine culture screening and treatment rates over a 10-year period. Methods: Patients with SCI seen in the VA Boston HCS for an annual exam in 2018 were eligible for inclusion and formed the baseline cohort for this study. Annual visits for the cohort over a 10-year period (January 1, 2009–December 31, 2018) were included in the analysis. Electronic data collection and manual chart review were utilized to capture outcomes of interest including urine culture, antibiotic prescriptions and indication within 15 days, and documentation of urinary or infectious symptoms. The main outcomes were (1) rate of urine cultures performed ±3 days of the visit, (2) rate of antibiotic treatment in asymptomatic patients, and (3) trend over time of urine culturing and treating. The χ2 test for trend was used to compare rates over time. Results: In total, 1,962 annual visits were made by the 344 unique patients over the 10-year period and were available for analysis. Among these, 639 (32.6%) visits had a urine culture performed within 3 days. The proportion of visits with a collected culture decreased from (109 of 127) 85.8% of visits in 2009 to (65 of 338) 19.2% of visits in 2018, P ≤ .001 (Fig. 1). In the treatment analysis, 39 visits were excluded for active symptoms, concern for uncontrolled infection, or prophylaxis as antibiotic indication. Among 600 remaining screening cultures, 328 had a bacterial pathogen or >100,000 mixed colonies consistent with ASB. Overall, 51 patients (17%) received antimicrobials. The rate of antibiotic treatment for ASB did not significantly decrease over time pP = 0.79 (Fig. 2). Conclusions: Over a 10-year period of annual SCI visits, the proportion of visits with a urine culture performed as routine screening significantly and consistently decreased. However, the rate of treatment for positive urine cultures remained consistent. These data support targeted diagnostic stewardship in this population to reduce unnecessary antibiotic use.Funding: NoneDisclosures: None


2020 ◽  
pp. mcs.a005876
Author(s):  
Joshua Lieberman ◽  
Kyoko Kurosawa ◽  
Dhruba J SenGupta ◽  
Brad T Cookson ◽  
Stephen J Salipante ◽  
...  

Spinal Cord ◽  
2004 ◽  
Vol 42 (8) ◽  
pp. 438-442 ◽  
Author(s):  
S Vaidyanathan ◽  
G Singh ◽  
B M Soni ◽  
P L Hughes ◽  
Paul Mansour ◽  
...  

2016 ◽  
Author(s):  
Steven L. Salzberg ◽  
Florian Breitwieser ◽  
Anupama Kumar ◽  
Haiping Hao ◽  
Peter Burger ◽  
...  

Objective: To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected central nervous system (CNS) infections. Methods: In a prospective-pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from ten patients with neurological problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results. Results: Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in three patients, identified possible pathogens in two more, and helped to understand neuropathological processes in three others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Validation techniques confirmed the pathogens identified by NGS in each of the three positive cases. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in eight of ten cases, and were non-contributory in the remaining two. Conclusions: NGS-guided metagenomic studies of brain, spinal cord or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.


2018 ◽  
Vol 9 ◽  
pp. 1-6 ◽  
Author(s):  
Tina Kollannoor Johny ◽  
Bindiya Ellathuparambil Saidumohamed ◽  
Raghul Subin Sasidharan ◽  
Sarita Ganapathy Bhat

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Anna Raguzzini ◽  
Elisabetta Toti ◽  
Tommaso Sciarra ◽  
Anna Lucia Fedullo ◽  
Ilaria Peluso

Background. Urinary tract infection (UTI) is common in individuals with spinal cord injury (SCI) and neurogenic lower urinary tract dysfunction (NLUTD) and in veterans with SCI who use antibiotics improperly for asymptomatic bacteriuria. Cranberry (CB) has been suggested for UTI prevention. Methods. We performed a systematic search up to May 2020 in the following databases: AccessMedicine, BioMed Central, CINAHL, Cochrane Library, ProQuest, and PubMed. Quality assessment was performed using a specifically designed quality score. Risk ratio was calculated with both random effect model analysis (DerSimonian-Laird method) and quality effect model analysis (Doi Thalib method). Results. Six studies on bacteriuria and SCI were reviewed. From the four studies available for meta-analysis, two of which with individuals taking both CB and control, 477 data from 415 participants were analysed (241 CB and 236 control). No significant differences were detected with meta-analysis. However, bias, limitations, and incompleteness were observed in the reviewed studies. Conclusion. Although further studies are needed, we suggest an accurate monitoring of diet and fluid intake, the evaluation of risk for potential food or nutraceutical interactions with drugs, and the inclusion of inflammatory markers among the outcomes in addition to UTI.


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