METAGENOMIC ANALYSIS TO IDENTIFY THE CAUSATIVE AGENTS OF ATYPICAL UROGENITAL TRACT INFECTIONS

Russian Journal of Infection and Immunity ◽

10.15789/2220-7619-mat-1713 ◽

2021 ◽

Author(s):

D. Kutilin

Keyword(s):

Chronic Inflammation ◽

High Throughput ◽

High Throughput Sequencing ◽

Urogenital Tract ◽

Metagenomic Analysis ◽

Healthy Individuals ◽

Microbiological Methods ◽

Wide Range ◽

Tract Infections ◽

Apparently Healthy

Importance. Research in recent decades has shown that classical microbiological methods can only detect a small, cultivable portion of microorganisms. One of the modern approaches to detect a wide range of bacteria and archaea is presented as a type of metagenomic analysis performed by high-throughput sequencing of ribosomal operon fragment libraries.Objective. Metagenomic analysis of samples from the urogenital tract of patients with chronic inflammation to identify pathogens not detected by other methods.Methods. Taxonomic analysis of the bacterial community was performed by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by using the Illumina HiSeq 3000 platform.Results. The study allowed to identify the taxonomic diversity of microorganisms in samples from the urogenital tract (from 197 to 794 different microorganisms belonging to the Bacteria were identified), as well as to establish differential differences concerning members of the genera Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phobormidium, Sphing Temperatibacter, Oxobacter, Georgenia, Actinobaculum, Varibaculum, Mycobacterium, Rhodococcus, Sediminihabitans, Actinobacter, Actinoplanes, Spirochaeta, Enhydrobacter, Thermacetogenium, Bdellovibrio, Oleibacter, Porphyrom, Klebsiella, Lachnoclostridium, Caulobacter, Xanthomonas, Novispirillum, Marvinbryantia, afipia, Shinella, Tepidimonas, Faecalibacterium, Paludibacterium, Aerococcus, Campylobacter, Pasteurella, Rumen, Psychrobacter, Haemophilus, Brevibacillus, Sporosarcina, Yaniella and Lactobacillus between samples from patients with chronic inflammation and apparently healthy individuals.Conclusion. Differential differences were found in the composition of the microbiome from the samples of patients with chronic inflammation and apparently healthy individuals, concerning members of 44 genera, including Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phormidium and Lactobacillus. The inflammatory processes observed in the patient urogenital tract can be associated with imbalanced microflora such as decreased level of typical members of the genera Staphylococcus, Streptococcus and Lactobacillus, but increased number of members from of the genera Klebsiella and Citrobacter.

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Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

Nucleic Acids Research ◽

10.1093/nar/gkw471 ◽

2016 ◽

Vol 44 (14) ◽

pp. e123-e123 ◽

Cited By ~ 24

Author(s):

Yun Zheng ◽

Bo Ji ◽

Renhua Song ◽

Shengpeng Wang ◽

Ting Li ◽

...

Keyword(s):

High Throughput ◽

Small Rna ◽

High Throughput Sequencing ◽

Accurate Detection ◽

Wide Range

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Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis , and Ixodes scapularis Ticks

mSphere ◽

10.1128/msphere.00614-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 35

Author(s):

Rafal Tokarz ◽

Stephen Sameroff ◽

Teresa Tagliafierro ◽

Komal Jain ◽

Simon H. Williams ◽

...

Keyword(s):

New York ◽

High Throughput ◽

High Throughput Sequencing ◽

Ixodes Scapularis ◽

The United States ◽

Dermacentor Variabilis ◽

Amblyomma Americanum ◽

Animal Pathogens ◽

Wide Range ◽

Sequencing Platforms

ABSTRACT Ticks carry a wide range of known human and animal pathogens and are postulated to carry others with the potential to cause disease. Here we report a discovery effort wherein unbiased high-throughput sequencing was used to characterize the virome of 2,021 ticks, including Ixodes scapularis ( n = 1,138), Amblyomma americanum ( n = 720), and Dermacentor variabilis ( n = 163), collected in New York, Connecticut, and Virginia in 2015 and 2016. We identified 33 viruses, including 24 putative novel viral species. The most frequently detected viruses were phylogenetically related to members of the Bunyaviridae and Rhabdoviridae families, as well as the recently proposed Chuviridae . Our work expands our understanding of tick viromes and underscores the high viral diversity that is present in ticks. IMPORTANCE The incidence of tick-borne disease is increasing, driven by rapid geographical expansion of ticks and the discovery of new tick-associated pathogens. The examination of the tick microbiome is essential in order to understand the relationship between microbes and their tick hosts and to facilitate the identification of new tick-borne pathogens. Genomic analyses using unbiased high-throughput sequencing platforms have proven valuable for investigations of tick bacterial diversity, but the examination of tick viromes has historically not been well explored. By performing a comprehensive virome analysis of the three primary tick species associated with human disease in the United States, we gained substantial insight into tick virome diversity and can begin to assess a potential role of these viruses in the tick life cycle.

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jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator

10.1101/650747 ◽

2019 ◽

Author(s):

Lucas A. Nell

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Population Genomics ◽

R Package ◽

Gene Trees ◽

Sequencing Platform ◽

Genomic Variants ◽

Pacific Biosciences ◽

Wide Range ◽

Reference Genomes

AbstractHigh-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage, and bioinformatic tools. Simulating HTS data better informs these decisions. However, current standalone HTS simulators cannot generate genomic variants under even somewhat complex evolutionary scenarios, which greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. Genomic variants can be simulated using phylogenies, gene trees, coalescent-simulation output, population-genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. It can read reference genomes from FASTA files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows, and Linux systems.

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A Study on Medically Inclined Apparently Healthy Individuals Acquiring Urinary Tract Infections in North-Central, Nigeria

International Journal of Health and Life Sciences ◽

10.5812/ijhls.107634 ◽

2020 ◽

Vol In Press (In Press) ◽

Author(s):

Daniel David Otobo

Keyword(s):

Urinary Tract ◽

Nursing Students ◽

Urinary Tract Infections ◽

University Teaching ◽

Healthy Individuals ◽

Predisposing Factor ◽

Medical College Campus ◽

Tract Infections ◽

Age Range ◽

Apparently Healthy

Background: Urinary tract infections (UTI) simply the symptomatic or asymptomatic colonization of the kidneys, ureters, urinary bladder or/and the urethra by microorganisms, commonly bacteria. When these infections affect the kidneys, it is known as pyelonephritis. Objectives: To calculate the percentile risk of medically inclined apparently healthy individuals acquiring urinary tract infection. Methods: Written consent was sought on every questionnaire. It was carried out within the period of August to November, 2018. The study was done with over 160 persons; 154 questionnaires were accepted as properly filled. The questionnaires were gender specific. Persons cut across doctors, nurses, laboratory scientists, nursing students and medical students. The sampling study used was single blinded method. Areas studied were Plateau state (Jos University Teaching Hospital, Plateau Specialist Hospital and school of Midwifery; Vom), Abuja (University of Abuja Medical College Campus) and Nasarawa state (Bingham University). Data was collected, tabulated and classified into mild, moderate and high risks. (males, N = 71 with an age range of 19 - 45 years; females, N = 83 with an age range of 19 - 44 years). Results: Assessment criteria male/female low risk 42 (59.2%)/10 (12.0%), moderate risk 23 (32.4%)/29 (34.9%) and high risk 6 (08.5%)/44 (53.0%). Conclusions: Hygiene is a crucial factor in predisposition to UTI. Women are at higher risk of acquiring urinary tract infections. Sickle cell may be a predisposing factor to pyelonephritis.

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Learning Sparse Log-Ratios for High-Throughput Sequencing Data

10.1101/2021.02.11.430695 ◽

2021 ◽

Author(s):

Elliott Gordon-Rodriguez ◽

Thomas P. Quinn ◽

John P. Cunningham

Keyword(s):

High Throughput ◽

Latent Variables ◽

High Throughput Sequencing ◽

Compositional Data ◽

Predictive Accuracy ◽

Learning Algorithm ◽

Sequencing Data ◽

Genetic Sequencing ◽

Wide Range ◽

Benchmark Datasets

AbstractThe automatic discovery of interpretable features that are associated to an outcome of interest is a central goal of bioinformatics. In the context of high-throughput genetic sequencing data, and Compositional Data more generally, an important class of features are the log-ratios between subsets of the input variables. However, the space of these log-ratios grows combinatorially with the dimension of the input, and as a result, existing learning algorithms do not scale to increasingly common high-dimensional datasets. Building on recent literature on continuous relaxations of discrete latent variables, we design a novel learning algorithm that identifies sparse log-ratios several orders of magnitude faster than competing methods. As well as dramatically reducing runtime, our method outperforms its competitors in terms of sparsity and predictive accuracy, as measured across a wide range of benchmark datasets.

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Dung beetles as vertebrate samplers – a test of high throughput analysis of dung beetle iDNA

10.1101/2021.02.10.430568 ◽

2021 ◽

Author(s):

Rosie Drinkwater ◽

Elizabeth L. Clare ◽

Arthur Y. C. Chung ◽

Stephen J. Rossiter ◽

Eleanor M. Slade

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Dung Beetle ◽

Blood Feeding ◽

Preliminary Evidence ◽

Dung Beetles ◽

High Throughput Analysis ◽

Humid Forest ◽

Terrestrial Vertebrates ◽

Wide Range

AbstractThe application of environmental DNA (eDNA) sampling in biodiversity surveys has gained widespread acceptance, especially in aquatic systems where free eDNA can be readily collected by filtering water. In terrestrial systems, eDNA-based approaches for assaying vertebrate biodiversity have tended to rely on blood-feeding invertebrates, including leeches and mosquitoes (termed invertebrate-derived DNA or iDNA). However, a key limitation of using blood-feeding taxa as samplers is that they are difficult to trap, and, in the case of leeches, are highly restricted to humid forest ecosystems. Dung beetles (superfamily Scarabaeoidea) feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps; are globally distributed; and also occur in a wide range of biomes, allowing mammal diversity to be compared across habitats. In this exploratory study, we test the potential utility of dung beetles as vertebrate samplers by sequencing the mammal DNA contained within their guts. First, using a controlled feeding experiment, we show that mammalian DNA can be retrieved from the guts of large dung beetles (Catharsius renaudpauliani) for up to 10 hours after feeding. Second, by combining high-throughput sequencing of a multi-species assemblage of dung beetles with PCR replicates, we show that multiple mammal taxa can be identified with high confidence. By providing preliminary evidence that dung beetles can be used as a source of mammal DNA, our study highlights the potential for this widespread group to be used in future biodiversity monitoring surveys.

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High-throughput sequencing reveals dietary segregation in Malaysian babblers

Current Zoology ◽

10.1093/cz/zoab074 ◽

2021 ◽

Author(s):

Mohammad Saiful Mansor ◽

Fasihah Zarifah Rozali ◽

Sian Davies ◽

Shukor Md Nor ◽

Rosli Ramli

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Prey Selection ◽

Niche Partitioning ◽

Peninsular Malaysia ◽

Similar Species ◽

Insectivorous Birds ◽

Dietary Overlap ◽

Dietary Flexibility ◽

Wide Range

Abstract The coexistence of numerous species within a community results from how those species use available resources. Babblers are one of the major groups of Malaysian insectivorous birds, which frequently forage in dense vegetation cover and have a high level of sympatry. Therefore, examining the diet, prey selection and niche segregation of babblers can be challenging. In this study, we used high-throughput sequencing to investigate potential dietary overlap or segregation among 10 babbler species of the four genera of the family Pellorneidae and Timaliidae: Pellorneum, Malacopteron, Stachyris and Cyanoderma in central peninsular Malaysia. We tested the hypothesis that trophically similar species may differ in resource use to avoid competitive exclusion. We identified 81 distinct arthropod taxa from fecal samples, belonging to 71 families representing 13 orders, which were predominantly from 16 dipteran, 13 lepidopteran and 10 coleopteran families. Of all the prey taxa consumed, 45% were found to be distinct across the 10 babbler species, and less than 35% were shared simultaneously by three or more babbler species, indicating minimal dietary overlap. The black-throated babbler Stachyris nigricollis and moustached babbler Malacopteron magnirostre had the most generalist tendencies because they consumed a greater variety of prey taxa. Small dietary overlap values (Ojk) and a relatively wide range of food resources suggest that dietary segregation occurred among the studied babblers. The great diversity of prey consumed revealed the presence of dietary flexibility among the sympatric insectivorous birds, thus reducing any active dietary competition and facilitating the coexistence through niche partitioning.

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Urinary Tract Infections among Bladder Outlet Obstruction Patients in Accra, Ghana: Aetiology, Antibiotic Resistance, and Risk Factors

Diseases ◽

10.3390/diseases6030065 ◽

2018 ◽

Vol 6 (3) ◽

pp. 65

Author(s):

Karikari Asafo-Adjei ◽

James Mensah ◽

Appiah-Korang Labi ◽

Nicholas Dayie ◽

Eric Donkor

Keyword(s):

Risk Factors ◽

Urinary Tract ◽

Urinary Tract Infections ◽

Bladder Outlet Obstruction ◽

Outlet Obstruction ◽

Bacterial Isolates ◽

Microbiological Methods ◽

Wide Range ◽

Tract Infections ◽

Urine Specimens

The aim of this study was to investigate urinary tract infections among patients with Bladder Outlet Obstruction (BOO) at the Korle Bu Teaching Hospital (KBTH) in Accra, Ghana, including the prevalence, risk factors, aetiological agents and their antibiogram. Urine specimens were collected from 188 male patients presenting with BOO and cultured for bacteria. The bacterial isolates were identified using standard microbiological methods and tested against a spectrum of antimicrobial agents using the Kirby Bauer method. Demographic information and the clinical history of study participants were also recorded. The prevalence of urinary tract infection among the BOO patients was 76.6% and the main risk factor identified was catheterization (p < 0.0001). A wide range of bacterial organisms was isolated from urine specimens and they were predominantly, Enterobacteriaceae; Escherichia coli was the most frequent cause of bacteriuria (33.3%), followed by Klebsiella (17.3%). Bacterial isolates were most resistant to Augmentin (97.8%) followed by tetracycline (85.8%), nalidixic acid (82.8%) and ciprofloxacin (75%) while 93.6% were multi-drug resistant. The highest susceptibility was observed with amikacin, which had a resistance prevalence of 4.4% resistance. These findings have important implications in the treatment of urinary tract infections among the BOO patients in Ghana.

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