Performance of Conventional Urine Culture Compared to 16S rRNA Gene Amplicon Sequencing in Children with Suspected Urinary Tract Infection

Concordance between conventional culture and 16S rRNA gene amplicon sequencing appears to be high. In children with equivocal culture results, 16S rRNA gene results may provide information that may help clarify the diagnosis.

Download Full-text

Actinomycetes of rhizosphere soil producing antibacterial compounds against Urinary Tract Infection bacteria

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200504 ◽

2019 ◽

Vol 20 (5) ◽

Author(s):

PRAMESITA PRAWADIKA APSARI ◽

SRI BUDIARTI ◽

ARIS TRI WAHYUDI

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

16S Rrna ◽

16S Rrna Gene ◽

Crude Extract ◽

Rhizosphere Soil ◽

Bioactive Compound ◽

Rrna Gene ◽

Antibacterial Compounds

Abstract. Apsari PP, Budiarti S, Wahyudi AT. 2019. Actinomycetes of rhizosphere soil producing antibacterial compounds against Urinary Tract Infection bacteria. Biodiversitas 20: 1259-1265. Based on the ability of actinomycetes as an antibacterial compounds producer and the need of finding novel antibacterial compounds, this study aims to look for antibacterial compounds from rhizosphere actinomycetes against bacteria in urine of UTI patients (Escherichia coli, Citrobacter braakii, Acinetobacter calcoaceticus, and Klebsiella pneumoniae). The screening of 21 actinomycetes was conducted based on the paper disc method. Potential actinomycetes that inhibited test bacteria were, then cultured in liquid medium and the supernatant was tested to six test bacteria. Then, the supernatant was extracted using ethyl acetate and crude extract from extraction process was tested to test bacteria. Afterward, the crude extract was scanned for bioactive compounds by GC-MS. Potential actinomycetes were identified by 16S rRNA gene to reveal the species. The screening results showed that ARJ 16, 24, and 36 had a wider inhibition zone than others. All of them showed that the supernatant and the crude extract could inhibit UTI's bacteria. The highest abundance of bioactive compound of crude extract was found in Propane, 1,2-dichloro, n-Hexadecanoic acid, and Carbonochloridic acid, 2-chloroethyl ester, respectively. Identification of potential actinomycetes based on 16S rRNA gene showed that ARJ 16 and ARJ 24 were highly similar to Streptomyces sp. in 99% and ARJ 36 was similar to Streptomyces tendae in 98%.

Download Full-text

Diversity of urinary tract infection bacteria in children in Indonesia based on metagenomic approach

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d190425 ◽

2018 ◽

Vol 19 (4) ◽

pp. 1375-1381

Author(s):

GRACE CHRISTINE ◽

SRI BUDIARTI ◽

INDRI ASTUTI

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

16S Rrna ◽

16S Rrna Gene ◽

Denaturing Gradient Gel Electrophoresis ◽

Bacterial Invasion ◽

Rrna Gene ◽

Uncultured Bacterium ◽

Metagenomic Approach

Christine G, Budiarti S, Astuti RI. 2018. Diversity of urinary tract infection bacteria in children in Indonesia based onmetagenomic approach. Biodiversitas 19: 1375-1381. Urinary tract infection (UTI) is a common bacterial infection in childhood in bothmales and females. The infection is usually caused by bacterial invasion of the urinary tract including the lower and the upper urinarytract. In Indonesia, to the best our knowledge, the diversity of urinary tract infection bacteria has not been reported yet. Therefore, theaims of this study were to identify the diversity of both culturable and unculturable bacteria in children diagnosed with UTI. In thisstudy, urine samples were obtained from different age groups ranging 6-17 years. Analysis of 16S rRNA gene sequence showed eightculturable isolates (SBU1, SBU2, SBU3, SBU4, SBU5, SBU6, SBU7, SBU8) are closely related to Escherichia coli, Klebsiella pneumoniae,Enterobacter aerogenes, Citrobacter sp. and Acinetobacter sp. with maximum identity up to 98-99%. Diversity of unculturable bacteriacommunity based on 16S rRNA gene was represented by 9 DGGE (Denaturing Gradient Gel Electrophoresis) bands. The ninerespective bands showed the similarity ranging from 84 up to 96% with Klebsiella sp, Escherichia sp., Lactococcus lactic, Shigellaflexneri and uncultured bacterium. Based on phylogenetic analysis, all culturable isolates belong to phylum Proteobacteria, which isdominated by family of Enterobacteriaceae. Interestingly, by using metagenomic approach, it is observed that bacteria belong to phylumFirmicutes were found in the UTI-diagnosed patients, in addition to those bacterial isolates from phylum Proteobacteria. To ourknowledge, this is the first study to report the occurrence of Firmicutes and Proteobacteria in UTI-diagnosed patients in Indonesia.

Download Full-text

Third Human Isolate of a Desulfovibriosp. Identical to the Provisionally Named Desulfovibrio fairfieldensis

Journal of Clinical Microbiology ◽

10.1128/jcm.37.9.3076-3077.1999 ◽

1999 ◽

Vol 37 (9) ◽

pp. 3076-3077 ◽

Cited By ~ 10

Author(s):

Bernard La Scola ◽

Didier Raoult

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Amplification ◽

Urine Sample ◽

Human Isolate ◽

Rrna Gene

Desulfovibrio fairfieldensis was isolated from the urine sample of a patient with a urinary tract infection and meningoencephalitis. It was identified by 16S rRNA gene amplification and sequencing.

Download Full-text

Enhanced quantitative urine culture technique, a slight modification, in detecting under-diagnosed pediatric urinary tract infection

BMC Research Notes ◽

10.1186/s13104-019-4875-y ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Januka Thapaliya ◽

Priyatam Khadka ◽

Shovana Thapa ◽

Chenu Gongal

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Urine Culture ◽

Slight Modification ◽

Multidrug Resistant ◽

Culture Technique ◽

Simple Modification ◽

E Coli ◽

Conventional Culture

Abstract Objectives The pediatric urinary tract infection (UTI) often remains under-diagnosed or neglected owing to non-specific clinical presentations, patients failing to describe the actual situation and of clinical practice in diagnosis. The study was aimed to determine the etiologies of UTI in children with enhanced quantitative urine culture (EQUC) technique. Results Of enrolled 570 pediatric urine samples, the significant growth positivity was higher in EQUC 92 (16.15%) compared to standard urine culture (SUC) 73 (12.80%) technique. 20.6% of the significant isolates as detected with EQUC were missed on the SUC technique. The age group, in range 1–4 years, was more prone to the infection, where E. coli was the commonest pathogen. EQUC detected, probably all isolates, contributing UTI i.e. multidrug-resistant (MDR), extensive drug-resistant (XDR), and extended-spectrum β-lactamase (ESBL) producers, as some of them skipped on the SUC technique. Of total organisms isolated from EQUC, 46% were ESBL producer, 56.5% were MDR, and 1.4% were XDR. However, 40.5% ESBL, 44% MDR but no XDR detected on SUC. Hence a simple modification on conventional culture protocol could be a crucial modification for the detection of etiologies, contributing UTI, and hence to reduce inapt antimicrobial burden.

Download Full-text

Paraoxonase and acylated homoserine lactones in urine from patients with urinary tract infections--relationship to microbial diversity by 16S rRNA gene sequencing

10.1101/2021.06.10.447923 ◽

2021 ◽

Author(s):

John E Lafleur ◽

Jacquelyn S Meisel ◽

Seth Commichaux ◽

Richard L. E Amdur ◽

Mihai Pop ◽

...

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

16S Rrna ◽

Biofilm Formation ◽

Rrna Gene ◽

Western Blots ◽

Homoserine Lactones ◽

Tract Infections ◽

Acylated Homoserine Lactones

Paraoxonase (PON) comprises a trio of mammalian enzymes that have been reported to have a number of roles including the inhibition of bacterial virulence and biofilm formation by microorganisms that quorum sense with acylated homoserine lactones (AHLs). PON have previously been reported to inhibit P. aeruginosa biofilm formation in mammalian airways and skin. An innate immune role for PON in urinary tract infection has not previously been reported. We performed western blots for PON1 in urine from patients with urinary tract infection (UTI), and also tested UTI urine for the presence of AHLs using a cellular reporter system. Urine sample microbiota was assessed through sequencing of the 16S rRNA marker gene. We report here that PON1 was not found in the urine of control subjects, however, in patients with UTI, PON1 was associated with the presence of E. coli in urine. AHLs, but not PON, were found in the bulk urine of those with P. aeruginosa UTI. Microbial consortia of PON positive UTI urine was found to be distinct from PON negative UTI urine; differentially over-represented bacteria in PON positive samples included a number of environmental opportunists. We hypothesize that PON may inhibit the quorum sensing activity of AHLs in UTI, as has previously described in skin and airways.

Download Full-text

Assessment of Urine Gram Stain and Urine Culture in the Diagnosis of Urinary Tract Infection

International Journal of Scientific Research ◽

10.15373/22778179/feb2014/156 ◽

2012 ◽

Vol 3 (2) ◽

pp. 472-473

Author(s):

Dr G Sucilathangam Dr G Sucilathangam ◽

◽

Dr G Velvizhi Dr G Velvizhi

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Urine Culture ◽

Gram Stain

Download Full-text

URINARY INFECTION AT DEPARTMENT OF UROLOGY OF HUE UNIVERSITY OF MEDICINE AND PHARMACY HOSPITAL

Journal of Medicine and Pharmacy ◽

10.34071/jmp.2018.3.16 ◽

2018 ◽

pp. 100-108

Author(s):

Dinh Khanh Le ◽

Dinh Dam Le ◽

Khoa Hung Nguyen ◽

Xuan My Nguyen ◽

Minh Nhat Vo ◽

...

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Urinary Tract Infections ◽

Urine Culture ◽

Clinical Manifestations ◽

University Hospital ◽

E Coli ◽

Positive Urine ◽

Tract Infections

Objectives: To investigate clinical characteristics, bacterial characteristics, drug resistance status in patients with urinary tract infections treated at Department of Urology, Hue University Hospital. Materials and Method: The study was conducted in 474 patients with urological disease treated at Department of Urology, Hue Universiry Hospital from July 2017 to April 2018. Urine culture was done in the patients with urine > 25 Leu/ul who have symptoms of urinary tract disease or infection symptoms. Patients with positive urine cultures were analyzed for clinical and bacterial characteristics. Results: 187/474 (39.5%) patients had symptoms associated with urinary tract infections. 85/474 (17.9%) patients were diagnosed with urinary tract infection. The positive urine culture rate was 45.5%. Symptoms of UTI were varied, and no prominent symptoms. E. coli accounts for the highest proportion (46.67%), followed by, Staphycoccus aureus (10.67%), Pseudomonas aeruginsa (8,0%), Streptococcus faecali and Proteus (2.67%). ESBL - producing E. coli was 69.23%, ESBL producing Enterobacter spp was 33.33%. Gram-negative bacteria are susceptible to meropenem, imipenem, amikacin while gram positive are vancomycin-sensitive. Conclusions: Clinical manifestations of urinary tract infections varied and its typical symptoms are unclear. E.coli is a common bacterium (46.67%). Isolated bacteria have a high rate of resistance to some common antibiotics especially the third generation cephalosporins and quinolones. Most bacteria are resistant to multiple antibiotics at the same time. Gram (+) bacteria are susceptible to vancomycin, and gram (-) bacteria are susceptible to cefoxitin, amikacin, and carbapenem. Key words: urinary tract infection

Download Full-text

Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽

10.1186/s40168-021-01012-1 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Janis R. Bedarf ◽

Naiara Beraza ◽

Hassan Khazneh ◽

Ezgi Özkurt ◽

David Baker ◽

...

Keyword(s):

Parkinson’S Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

False Positive ◽

Gene Sequencing ◽

Bacterial Biomass ◽

16S Rrna Gene Sequencing ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

Download Full-text

Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

ISME Communications ◽

10.1038/s43705-021-00033-z ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Sandra Reitmeier ◽

Thomas C. A. Hitch ◽

Nicole Treichel ◽

Nikolaos Fikas ◽

Bela Hausmann ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Diversity Analysis ◽

Careful Attention ◽

Operational Taxonomic Units ◽

Basic Concepts ◽

Gnotobiotic Mice ◽

Mock Communities

Abstract16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.

Download Full-text

Detection of Legionella species, the influence of precipitation on the amount of Legionella DNA, and bacterial microbiome in aerosols from outdoor sites near asphalt roads in Toyama Prefecture, Japan

BMC Microbiology ◽

10.1186/s12866-021-02275-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jun-ichi Kanatani ◽

Masanori Watahiki ◽

Keiko Kimata ◽

Tomoko Kato ◽

Kaoru Uchida ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Indoor Environment ◽

Geometric Mean ◽

Amplicon Sequencing ◽

Positive Sample ◽

Outdoor Environment ◽

Rrna Gene ◽

Total Precipitation ◽

Monthly Total Precipitation

Abstract Background Legionellosis is caused by the inhalation of aerosolized water contaminated with Legionella bacteria. In this study, we investigated the prevalence of Legionella species in aerosols collected from outdoor sites near asphalt roads, bathrooms in public bath facilities, and other indoor sites, such as buildings and private homes, using amoebic co-culture, quantitative PCR, and 16S rRNA gene amplicon sequencing. Results Legionella species were not detected by amoebic co-culture. However, Legionella DNA was detected in 114/151 (75.5%) air samples collected near roads (geometric mean ± standard deviation: 1.80 ± 0.52 log10 copies/m3), which was comparable to the numbers collected from bathrooms [15/21 (71.4%), 1.82 ± 0.50] but higher than those collected from other indoor sites [11/30 (36.7%), 0.88 ± 0.56] (P < 0.05). The amount of Legionella DNA was correlated with the monthly total precipitation (r = 0.56, P < 0.01). It was also directly and inversely correlated with the daily total precipitation for seven days (r = 0.21, P = 0.01) and one day (r = − 0.29, P < 0.01) before the sampling day, respectively. 16S rRNA gene amplicon sequencing revealed that Legionella species were detected in 9/30 samples collected near roads (mean proportion of reads, 0.11%). At the species level, L. pneumophila was detected in 2/30 samples collected near roads (the proportion of reads, 0.09 and 0.11% of the total reads number in each positive sample). The three most abundant bacterial genera in the samples collected near roads were Sphingomonas, Streptococcus, and Methylobacterium (mean proportion of reads; 21.1%, 14.6%, and 1.6%, respectively). In addition, the bacterial diversity in outdoor environment was comparable to that in indoor environment which contains aerosol-generating features and higher than that in indoor environment without the features. Conclusions DNA from Legionella species was widely present in aerosols collected from outdoor sites near asphalt roads, especially during the rainy season. Our findings suggest that there may be a risk of exposure to Legionella species not only in bathrooms but also in the areas surrounding asphalt roads. Therefore, the possibility of contracting legionellosis in daily life should be considered.

Download Full-text