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.
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.
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DOI：
10.1186/1479-5876-10-174
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发表时间：
2012-08-28
影响因子：
7.4
通讯作者：
Groah SL
中科院分区：
文献类型：
--
作者：
Fouts DE;Pieper R;Szpakowski S;Pohl H;Knoblach S;Suh MJ;Huang ST;Ljungberg I;Sprague BM;Lucas SK;Torralba M;Nelson KE;Groah SL
临床教条认为，健康的尿液是无菌的，存在带有炎症反应的细菌表明尿路感染（UTI）。无症状细菌尿（ABU）是指细菌存在但炎症反应可以忽略不计的状态。在诊断上区分ABU和UTI具有挑战性，但也至关重要，因为ABU的过度治疗可使抗菌素耐药性长期存在，而UTI治疗不足可导致发病率和死亡率增加。在这项研究中，我们利用16S rRNA基因（16S rDNA）测序和宏蛋白质组学描述了健康和ABU尿液微生物组的关键特征，未来的目标是利用这些信息根据关键个体特征个性化UTI治疗。对26名健康对照者和27名因脊髓损伤相关性神经性膀胱（NB）而有ABU风险的健康受试者进行了横断面研究。27例NB患者中，8例正常排尿，8例间歇导尿，11例留置Foley导尿膀胱引流。尿液由排尿者清洁采集，或由使用导尿管的受试者直接从导尿管中采集。对所有样本进行尿液分析、尿液培养和16S rDNA测序，并对亚样本进行元蛋白质组学分析。通过NextGen 16S rDNA分析流水线处理共589454个经过质量过滤的16S rDNA序列读数。尿微生物组因正常膀胱功能与NB、性别、使用的膀胱导管类型和NB持续时间而异。样品中相对丰度和变化最大的前10个细菌类群分别是乳酸杆菌、肠杆菌、放线菌、杆菌、梭菌、拟杆菌、伯克霍尔德菌、假单胞菌、双歧杆菌和Coriobacteriales。宏蛋白质组学证实了16S rDNA的结果，并且在宿主防御启动的受试者中发现了功能性的人类蛋白质-病原体相互作用。与临床观点相反，健康的尿液并非无菌的。健康尿液微生物组的特点是女性以乳酸杆菌为主，男性以棒状杆菌为主。NB的存在和持续时间以及导尿方法会改变健康尿液微生物群。16S rDNA测序与宏蛋白质组学的综合方法提高了我们对健康尿液的理解，并促进了更个性化的预防和治疗感染的方法。
Clinical dogma is that healthy urine is sterile and the presence of bacteria with an inflammatory response is indicative of urinary tract infection (UTI). Asymptomatic bacteriuria (ABU) represents the state in which bacteria are present but the inflammatory response is negligible. Differentiating ABU from UTI is diagnostically challenging, but critical because overtreatment of ABU can perpetuate antimicrobial resistance while undertreatment of UTI can result in increased morbidity and mortality. In this study, we describe key characteristics of the healthy and ABU urine microbiomes utilizing 16S rRNA gene (16S rDNA) sequencing and metaproteomics, with the future goal of utilizing this information to personalize the treatment of UTI based on key individual characteristics. A cross-sectional study of 26 healthy controls and 27 healthy subjects at risk for ABU due to spinal cord injury-related neuropathic bladder (NB) was conducted. Of the 27 subjects with NB, 8 voided normally, 8 utilized intermittent catheterization, and 11 utilized indwelling Foley urethral catheterization for bladder drainage. Urine was obtained by clean catch in voiders, or directly from the catheter in subjects utilizing catheters. Urinalysis, urine culture and 16S rDNA sequencing were performed on all samples, with metaproteomic analysis performed on a subsample. A total of 589454 quality-filtered 16S rDNA sequence reads were processed through a NextGen 16S rDNA analysis pipeline. Urine microbiomes differ by normal bladder function vs. NB, gender, type of bladder catheter utilized, and duration of NB. The top ten bacterial taxa showing the most relative abundance and change among samples were Lactobacillales, Enterobacteriales, Actinomycetales, Bacillales, Clostridiales, Bacteroidales, Burkholderiales, Pseudomonadales, Bifidobacteriales and Coriobacteriales. Metaproteomics confirmed the 16S rDNA results, and functional human protein-pathogen interactions were noted in subjects where host defenses were initiated. Counter to clinical belief, healthy urine is not sterile. The healthy urine microbiome is characterized by a preponderance of Lactobacillales in women and Corynebacterium in men. The presence and duration of NB and method of urinary catheterization alter the healthy urine microbiome. An integrated approach of 16S rDNA sequencing with metaproteomics improves our understanding of healthy urine and facilitates a more personalized approach to prevention and treatment of infection.
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DOI：
10.1073/pnas.0607898104
发表时间：
2007-10-16
影响因子：
11.1
作者：
Lane, M. Chelsea;Alteri, Christopher J.;Mobley, Harry L. T.
通讯作者：
Mobley, Harry L. T.
高度平行的焦索测序者产生的16S rRNA序列的准确分类学分配。
影响因子：
14.9
作者：
Liu Z;DeSantis TZ;Andersen GL;Knight R
通讯作者：
Knight R
DOI：
10.1136/mp.54.5.289
发表时间：
2001-10-01
期刊：
JOURNAL OF CLINICAL PATHOLOGY-MOLECULAR PATHOLOGY
影响因子：
--
作者：
Isaksen, B;Fagerhol, MK
通讯作者：
Fagerhol, MK
影响因子：
9.4
作者：
Domann, E;Hong, G;Chakraborty, T
通讯作者：
Chakraborty, T
影响因子：
14.9
作者：
Cole JR;Wang Q;Cardenas E;Fish J;Chai B;Farris RJ;Kulam-Syed-Mohideen AS;McGarrell DM;Marsh T;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM