scholarly journals StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3353 ◽  
Author(s):  
Märt Roosaare ◽  
Mihkel Vaher ◽  
Lauris Kaplinski ◽  
Märt Möls ◽  
Reidar Andreson ◽  
...  
Keyword(s):  
Bacterial Isolates ◽  
Web Interface ◽  
Bacterial Strains ◽  
Illumina Hiseq ◽  
Guide Tree ◽  
E Coli ◽  
Custom Made ◽  
Tree Branch ◽  
Correct Tree ◽  
Guide Trees

Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. Results A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1–2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. Conclusion StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.

scholarly journals Antibiotic Resistance Bacteria Associated in Waters Discharges of a Hospital in Patna

2017 ◽  
Vol 7 (1) ◽  
pp. 9
Author(s):  
Vyomesh Vibhaw ◽  
Kumar Pranay ◽  
Krishnadutt Pratihast ◽  
Bipin Bihari Mishra ◽  
S. R. Padmadeo
Keyword(s):  
Antibiotic Resistance ◽  
Group Iv ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Antibiotic Resistant ◽  
Group Iii ◽  
E Coli ◽  
Group I ◽  
Three Samples ◽  
A Site

The isolation and screening of antibiotic resistance strains from three samples sites present in and around hospital of Patna resulted in isolation of 300 bacterial isolates. Out of which maximum number of isolates were obtained from site B while site A gave least number of isolates. 89 bacterial strains showed antibiotic resistance. Among these 89 isolates Site B had maximum number of antibiotic resistant isolates (51) followed by site C with 33 isolates. Among the four groups of antibiotic selected for investigation, the isolates showed highest antibiotic resistance against fluoroquinolones with 1, 20 and 14 isolates from site A, site B and site C respectively showing antibiotic resistance. Site B isolates showed significant resistance against group III (aminoglycosides) antibiotic. Site C isolates also showed maximum resistance against Group IV antibiotics followed by Group II, III and Group I. Site A sample showed resistance against Ciprofloxacin, however it showed sensitivity against all other antibiotics. Study showed that there was a dynamic flux in the response of E. coli strains against antibiotic. Antibiotic resistant E. coli was present in wastewater. Key words: bacterial isolates, antibiotic resistance, E. coli.

scholarly journals StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees.

2016 ◽  
Author(s):  
Mart Roosaare ◽  
Mihkel Vaher ◽  
Lauris Kaplinski ◽  
Mart Mols ◽  
Reidar Andreson ◽  
...  
Keyword(s):  
Rapid Identification ◽  
Clinical Diagnostics ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Newick Format ◽  
Novel Approach ◽  
Custom Made ◽  
High Throughput Detection ◽  
Generation Sequencing ◽  
Guide Trees

Background Fast, accurate and high-throughput detection of bacteria is in great demand. The present work was conducted to investigate the possibility of identifying both known and unknown bacterial strains from unassembled next-generation sequencing reads using custom-made guide trees. Results A program named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables rapid identification of bacterial genomes within minutes. StrainSeeker has been tested and shown to successfully identify Escherichia coli strains from mixed samples in less than 5 minutes. StrainSeeker can also identify bacterial strains from highly diverse metagenomics samples. StrainSeeker is available at http://bioinfo.ut.ee/strainseeker. Conclusions Our novel approach can be useful for both clinical diagnostics and research laboratories because novel bacterial strains are constantly emerging and their fast and accurate detection is very important.

scholarly journals Antibiotic Resistance of Bacteria Isolated from Water Supplies Used in Poultry Production in Ashanti Region of Ghana

2021 ◽  
Vol 15 (1) ◽  
pp. 7-15
Author(s):  
Frank B. Osei ◽  
Vivian E. Boamah ◽  
Yaw D. Boakye ◽  
Christian Agyare ◽  
Robert C. Abaidoo
Keyword(s):  
Culture Media ◽  
Resistance Pattern ◽  
Poultry Production ◽  
Drug Resistant ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
E Coli ◽  
Ashanti Region ◽  
Quality Of Water

Objective: Water plays an important role in both domestic and commercial settings. Pathogenic microbial contaminants, however, render water unsafe for use. There are several reports on the quality of water used for drinking purposes in humans but few studies have been conducted on the microbial quality of water used in animal farming. Methods: In this study, the resistance pattern of bacterial isolates from drinking water used in poultry production in the Ashanti region of Ghana from our previously published report was determined. The presence of Escherichia coli, Salmonella typhi, Staphylococcus aureus and coagulase-negative Staphylococci was determined using selective culture media (pour plate method) and confirmed through Gram staining and biochemical reactions. Antibiotic sensitivity of isolates was determined followed by detection of Extended-Spectrum Beta-Lactamase (ESBL) producing Gram-negative isolates. Results: The study revealed that water used in poultry farms contains sources of multi-drug resistant strains of E. coli, S. typhi, S. aureus and coagulase-negative staphylococci. E. coli, S. typhi, S. aureus and coagulase-negative staphylococci were recovered from 31%, 36%, 64% and 19% of samples, respectively. Majority of these isolates were resistant to cephalosporins and penicillins. Almost 95% of the bacterial isolates were multi-drug resistant. None of E. coli and S. typhi isolates produced ESBL. Conclusion: There is a need for stringent regulations and stringent measures should be taken to make these various sources of water safe for use in animal husbandry as these waters are a potential source of pathogenic and resistant bacterial strains which can cause infections to the animals and farm workers.

SYNTHESIS, CHARACTERIZATION AND BIOLOGICAL EVALUATION OF 3-FORMYL INDOLE BASED SCHIFF BASES

2018 ◽  
Vol 7 (6) ◽  
Author(s):  
Singh Gurvinder ◽  
Singh Prabhsimran ◽  
Dhawan R. K.
Keyword(s):  
Antimicrobial Activity ◽  
Spectral Analysis ◽  
Schiff Bases ◽  
Antimicrobial Agents ◽  
Biological Evaluation ◽  
Fungal Strain ◽  
Bacterial Strains ◽  
Standard Drug ◽  
Gram Negative ◽  
E Coli

In order to develop new antimicrobial agents, a series of 3-formyl indole based Schiff bases were synthesized by reacting 3-formyl indole(indole-3-carboxaldehyde) with substituted aniline taking ethanol as solvent. The reaction was carried in the presence of small amount of p-toluene sulphonic acid as catalyst.All the synthesized compounds were characterized by IR, 1H-NMR spectral analysis. All the synthesized compounds were evaluated for antimicrobial activity against two gram positive bacterial strains (B. subtilisand S. aureus) and two gram negative bacterial strains (P. aeruginosaand E. coli) and one fungal strain (C. albicans). All the synthesized compounds were found to have moderate to good antimicrobial activity. The  standard drug amoxicillin, fluconazole were used for antimicrobial activity. Among the synthesized compounds, the maximum antimicrobial activity was shown by compounds GS04, GS07, GS08 and GS10.

STUDIES ON SOME BACTERIAL DISEASES IN OREOCHROMIS NILOTICUS WITH SPECIAL REFERENCES TO TREATMENT

2018 ◽  
pp. 39-47
Author(s):  
Viola Zaki ◽  
Ahmed EL-gamal ◽  
Yasmin Reyad
Keyword(s):  
Oreochromis Niloticus ◽  
Bacterial Infections ◽  
Antimicrobial Agents ◽  
Histopathological Examination ◽  
Klebsiella Oxytoca ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Tissue Samples ◽  
Hydropic Degeneration ◽  
Total Prevalence

he present research carried out to study the common bacterial infections in Oreochromis niloticus (Nile tilapia) in Manzala area at Dakahlia governorate and possible antimicrobial agents used for treatment. A total number of 400 fish were randomly collected from Manzala private farms at Dakahlia governorate and subjected to the clinical, bacteriological and histopathological examination. The highest prevalence of bacterial isolates during the whole period of examination of naturally infected O.niloticus was recorded for A.hydrophila (22.66%), followed by V.alginolyticus (19.01%), V.parahemolyticus (13.80%), Streptococcus spp. (12.24%), A.caviae (11.72%), V.cholera (10.16%), A.salmonicida (7.55%), while the lowest prevalence was recorded for Klebsiella oxytoca (2.86%). The seasonal highest total prevalence of bacterial isolates from examined naturally infected O. niloticus was recorded in spring (30.21%), followed by autumn (28.39%), then summer (22.40%) and the lowest prevalence was recorded in winter (19.01%). Histopathological findings of the tissue samples which collected from different organs of naturally infected O.niloticus revealed that spleen show marked hemosiderosis and sever hemorrhage, gills showsever congestion of lamellar capillaries with marked aneurysm, necrosis and hemorrhage of lamellar epithelium and liver show sever hydropic degeneration and necrosis of hepatocytes, Ciprofloxacin was the most effective antibiotic against all isolated bacterial strains

The Characterization of Antibiotic Resistance of Bacterial Isolates from Intensive Care Unit Patient Samples in a University Affiliated Hospital in Romania

2019 ◽  
Vol 70 (5) ◽  
pp. 1778-1783
Author(s):  
Andreea-Loredana Golli ◽  
Floarea Mimi Nitu ◽  
Maria Balasoiu ◽  
Marina Alina Lungu ◽  
Cristiana Cerasella Dragomirescu ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Bacterial Pathogens ◽  
Resistance Rate ◽  
Resistance Pattern ◽  
Bacterial Isolates ◽  
E Coli ◽  
Acinetobacter Spp ◽  
Almost All ◽  
Klebsiella Spp

To determine the resistance pattern of bacterial pathogens involved in infections of the patients aged between 18-64 years, admitted in a ICU from a 1518-bed university-affiliated hospital. A retrospective study of bacterial pathogens was carried out on 351 patients aged between 18-64 years admitted to the ICU, from January to December 2017. In this study there were analysed 469 samples from 351 patients (18-64 years). A total of 566 bacterial isolates were obtained, of which 120 strains of Klebsiella spp. (35.39%%), followed by Nonfermenting Gram negative bacilli, other than Pseudomonas and Acinetobacter (NFB) (75- 22.12%), Acinetobacter spp. (53 - 15.63%), Pseudomonas aeruginosa and Proteus (51 - 15.04%), and Escherichia coli (49 - 14.45%). The most common isolates were from respiratory tract (394 isolates � 69.61%). High rates of MDR were found for Pseudomonas aeruginosa (64.70%), MRSA (62.65%) and Klebsiella spp. (53.33%), while almost all of the isolated NFB strains were MDR (97.33%). There was statistic difference between the drug resistance rate of Klebsiella and E. coli strains to ceftazidime and ceftriaxone (p[0.001), cefuroxime (p[0.01) and to cefepime (p[0.01). The study revealed an alarming pattern of antibiotic resistance in the majority of ICU isolates.

Biodegradation of organophosphorus Pollutants by Soil Bacteria: Biochemical Aspects and Unsolved Problems

2020 ◽  
Vol 36 (4) ◽  
pp. 126-135
Author(s):  
T.V. Shushkova ◽  
D.O. Epiktetov ◽  
S.V. Tarlachkov ◽  
I.T. Ermakova ◽  
A.A. Leontievskii
Keyword(s):  
Genome Sequencing ◽  
Soil Bacteria ◽  
Activity Regulation ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Russian Science ◽  
Degrading Bacteria ◽  
Phosphorus Source ◽  
Glyphosate Herbicide ◽  
Enzymatic Pathways

The degradation of persistent organophosphorus pollutants have been studied in 6 soil bacterial isolates and in 3 bacterial strains adapted for utilization of glyphosate herbicide (GP) under laboratory conditions. Significant differences in the uptake of organophosphonates were found in taxonomically close strains possessing similar enzymatic pathways of catabolism of these compounds, which indicates the existence of unknown mechanisms of activity regulation of these enzymes. The effect of adaptation for GP utilization as a sole phosphorus source on assimilation rates of several other phosphonates was observed in studied bacteria. The newly found efficient stains provided up to 56% of GP decomposition after application to the soil in the laboratory. The unresolved problems of microbial GP metabolism and the trends for further research on the creation of reliable biologicals capable of decomposing organophosphonates in the environment are discussed. organophosphonates, glyphosate, biodegradation, bioremediation, C-P lyase, phosphonatase, degrading bacteria Investigation of phosphonatase and genome sequencing were supported by Russian Science Foundation Grant no. 18-074-00021.

scholarly journals In Vitro Coliform Resistance to Bioactive Compounds in Urinary Infection, Assessed in a Lab Catheterization Model

2021 ◽  
Vol 11 (9) ◽  
pp. 4315
Author(s):  
Emanuel Vamanu ◽  
Laura Dorina Dinu ◽  
Cristina Mihaela Luntraru ◽  
Alexandru Suciu
Keyword(s):  
Urinary Tract ◽  
Bioactive Compounds ◽  
Urinary Tract Infections ◽  
Antimicrobial Effect ◽  
Biologically Active ◽  
Bacterial Strains ◽  
E Coli ◽  
Functional Product ◽  
Tract Infections

Bioactive compounds and phenolic compounds are viable alternatives to antibiotics in recurrent urinary tract infections. This study aimed to use a natural functional product, based on the bioactive compounds’ composition, to inhibit the uropathogenic strains of Escherichia coli. E. coli ATCC 25922 was used to characterize the IVCM (new in vitro catheterization model). As support for reducing bacterial proliferation, the cytotoxicity against a strain of Candida albicans was also determined (over 75% at 1 mg/mL). The results were correlated with the analysis of the distribution of biologically active compounds (trans-ferulic acid-268.44 ± 0.001 mg/100 g extract and an equal quantity of Trans-p-coumaric acid and rosmarinic acid). A pronounced inhibitory effect against the uropathogenic strain E. coli 317 (4 log copy no./mL after 72 h) was determined. The results showed a targeted response to the product for tested bacterial strains. The importance of research resulted from the easy and fast characterization of the functional product with antimicrobial effect against uropathogenic strains of E. coli. This study demonstrated that the proposed in vitro model was a valuable tool for assessing urinary tract infections with E. coli.

scholarly journals Design, Synthesis and Biological Evaluation of Novel Benzothiazole Based [1,2,4]Triazolo[4,3-c]quinazoline Derivatives

2020 ◽  
Vol 32 (3) ◽  
pp. 580-586
Author(s):  
Ranjit V. Gadhave ◽  
Bhanudas S. Kuchekar
Keyword(s):  
Biological Evaluation ◽  
Bacterial Strains ◽  
Active Compounds ◽  
Design Synthesis ◽  
Structural Modifications ◽  
E Coli ◽  
Chemical Structures ◽  
Ft Ir ◽  
Antioxidant Agent

A new series of N-(benzo[d]thiazol-2-yl)-[1,2,4]triazolo[4,3-c]quinazoline-5-carboxamide derivatives were synthesized by condensation of [1,2,4]triazolo[4,3-c]quinazoline-5-carboxylate derivatives with substituted benzothiazoles. The chemical structures of the synthesized compounds were confirmed by FT-IR, MS and 1H NMR spectra. Designed triazoloquinazoline derivatives were docked with oxido-reductase enzyme (PDB Code 4h1j) and DNA gyrase enzyme (PDB Code 3g75). Based on high binding affinity score, the best compound were selected for synthesis and subjected to in vitro antioxidant and antibacterial activity. Compounds 7a and 7d were found to be most active compounds as antioxidant agent among this series when compared with ascorbic acid. Compounds 7a, 7d and 7f were found to be most active compounds as an antibacterial agents among this series when compared with ciprofloxacin against bacterial strains such as S. aureus (ATCC 25923), E. coli (ATCC 25922) and P. aeruginosa (ATCC 27853). Study revealed that the most active compounds after structural modifications can be exploited as lead molecules for other pharmacological activities such as anti-inflammatory, anticancer and antidepressant activities.

scholarly journals Epidemiological and phylogenetic analysis reveals Flavobacteriaceae as potential ancestral source of tigecycline resistance gene tet(X)

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Rong Zhang ◽  
Ning Dong ◽  
Zhangqi Shen ◽  
Yu Zeng ◽  
Jiauyue Lu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Resistance Gene ◽  
Gc Content ◽  
Zhejiang Province ◽  
Bacterial Strains ◽  
Gram Negative ◽  
E Coli ◽  
Transmission Mechanisms ◽  
Low Prevalence ◽  
Potential Origin

Abstract Emergence of tigecycline-resistance tet(X) gene orthologues rendered tigecycline ineffective as last-resort antibiotic. To understand the potential origin and transmission mechanisms of these genes, we survey the prevalence of tet(X) and its orthologues in 2997 clinical E. coli and K. pneumoniae isolates collected nationwide in China with results showing very low prevalence on these two types of strains, 0.32% and 0%, respectively. Further surveillance of tet(X) orthologues in 3692 different clinical Gram-negative bacterial strains collected during 1994–2019 in hospitals in Zhejiang province, China reveals 106 (2.7%) tet(X)-bearing strains with Flavobacteriaceae being the dominant (97/376, 25.8%) bacteria. In addition, tet(X)s are found to be predominantly located on the chromosomes of Flavobacteriaceae and share similar GC-content as Flavobacteriaceae. It also further evolves into different orthologues and transmits among different species. Data from this work suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance gene tet(X).

Sign in / Sign up

Export Citation Format

Share Document