scholarly journals StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11884
Author(s):  
Kévin Da Silva ◽  
Nicolas Pons ◽  
Magali Berland ◽  
Florian Plaza Oñate ◽  
Mathieu Almeida ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Simulated Data ◽  
Strain Level ◽  
Complex Configuration ◽  
Graph Representation ◽  
Genomic Sequences ◽  
Major Step ◽  
Real Dataset ◽  
Multiple Genomes

Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes. We developed StrainFLAIR with the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph. On simulated data composed of mixtures of strains from the same bacterial species Escherichia coli, results show that StrainFLAIR was able to distinguish and estimate the abundances of close strains, as well as to highlight the presence of a new strain close to a referenced one and to estimate its abundance. On a real dataset composed of a mix of several bacterial species and several strains for the same species, results show that in a more complex configuration StrainFLAIR correctly estimates the abundance of each strain. Hence, results demonstrated how graph representation of multiple close genomes can be used as a reference to characterize a sample at the strain level.

scholarly journals StrainFLAIR: Strain-level profiling of metagenomic samples using variation graphs

2021 ◽  
Author(s):  
Kévin Da Silva ◽  
Nicolas Pons ◽  
Magali Berland ◽  
Florian Plaza Oñate ◽  
Mathieu Almeida ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Simulated Data ◽  
Strain Level ◽  
Complex Configuration ◽  
Graph Representation ◽  
Genomic Sequences ◽  
Major Step ◽  
Real Dataset ◽  
Link Type

ABSTRACTCurrent studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes.We developed StrainFLAIR with the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph.On simulated data composed of mixtures of strains from the same bacterial species Escherichia coli, results show that StrainFLAIR was able to distinguish and estimate the abundances of close strains, as well as to highlight the presence of a new strain close to a referenced one and to estimate its abundance. On a real dataset composed of a mix of several bacterial species and several strains for the same species, results show that in a more complex configuration StrainFLAIR correctly estimates the abundance of each strain. Hence, results demonstrated how graph representation of multiple close genomes can be used as a reference to characterize a sample at the strain level.Availabilityhttp://github.com/kevsilva/StrainFLAIR

scholarly journals An Understanding of the Global Status of Major Bacterial Pathogens of Milk Concerning Bovine Mastitis: A Systematic Review and Meta-Analysis (Scientometrics)

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 545
Author(s):  
Paramanandham Krishnamoorthy ◽  
Kuralayanapalya P. Suresh ◽  
Kavitha S. Jayamma ◽  
Bibek R. Shome ◽  
Sharanagouda S. Patil ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Management Practices ◽  
Meta Analysis ◽  
Bacterial Species ◽  
Clinical Mastitis ◽  
Therapeutic Interventions ◽  
Coagulase Negative Staphylococcus ◽  
Prevalence Studies ◽  
The World ◽  
Pathogen Prevalence

In this study, the major mastitis pathogen prevalence in the cattle and buffalo of the world was estimated by a meta-analysis. Staphylococcus (S) species, Streptococcus (St) species, and Escherichia coli (Ec) prevalence studies reported during 1979–2019 were collected using online databases, and offline resources. A meta-analysis of these data was done with the meta package in R-Software. The Staphylococcus aureus was the major mastitis pathogen, mostly causing subclinical mastitis, Ec causing clinical mastitis and St causing subclinical and clinical mastitis. The pooled prevalence estimates of S, St, and Ec were 28%, 12%, and 11% in the world from 156, 129, and 92 studies, respectively. The S, St, and Ec prevalences were high in Latin America (51%), Oceania (25%), and Oceania (28%), respectively. Higher S, St, and Ec prevalences were observed by molecular methods, signifying high sensitivity and usefulness for future studies. Among bacterial species, S. aureus (25%) followed by coagulase-negative Staphylococcus species (20%), Escherichia coli (11%), St. agalactiae (9%), St. uberis (9%) were the important pathogens present in the milk of the world. We hypothesize that there is a urgent need to reduce mastitis pathogen prevalence by ensuring scientific farm management practices, proper feeding, therapeutic interventions to augment profits in dairying, and improving animal and human health.

scholarly journals Characterization of Escherichia coli Strains Derived from Cow Milk of Subclinical and Clinical Cases of Mastitis

2021 ◽  
Vol 11 (2) ◽  
pp. 541
Author(s):  
Katarzyna Grudlewska-Buda ◽  
Krzysztof Skowron ◽  
Ewa Wałecka-Zacharska ◽  
Natalia Wiktorczyk-Kapischke ◽  
Jarosław Bystroń ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Subclinical Mastitis ◽  
Clinical Mastitis ◽  
Economic Problem ◽  
Cow Milk ◽  
P Value ◽  
Dairy Herds ◽  
E Coli ◽  
Bonferroni Test

Mastitis is a major economic problem in dairy herds, as it might decrease fertility, and negatively affect milk quality and milk yield. Out of over 150 bacterial species responsible for the udder inflammation, Escherichia coli is one of the most notable. This study aimed to assess antimicrobial susceptibility, resistance to dipping agents and biofilm formation of 150 E. coli strains isolated from milk of cows with subclinical and clinical mastitis. The strains came from three dairy herds located in Northern and Central Poland. The statistical analyses were performed with post-hoc Bonferroni test and chi-square test (including Yates correction). The data with a p value of <0.05 were considered significant. We found that the tested strains were mostly sensitive to antimicrobials and dipping agents. It was shown that 37.33% and 4.67% of strains were resistant and moderately resistant to at least one antimicrobial agent, respectively. No extended-spectrum beta-lactamases (ESBL)-producing E. coli were detected. The majority of strains did not possess the ability to form biofilm or formed a weak biofilm. The strong biofilm formers were found only among strains derived from cows with subclinical mastitis. The lowest bacteria number was noted for subclinical mastitis cows’ strains, after stabilization with iodine (3.77 log CFU × cm−2) and chlorhexidine (3.96 log CFU × cm−2) treatment. In the present study, no statistically significant differences in susceptibility to antibiotics and the ability to form biofilm were found among the strains isolated from cows with subclinical and clinical mastitis. Despite this, infections in dairy herds should be monitored. Limiting the spread of bacteria and characterizing the most common etiological factors would allow proper treatment.

scholarly journals The distribution of homologues of the Escherichia coli KefC K+-efflux system in other bacterial species

1991 ◽  
Vol 137 (8) ◽  
pp. 1999-2005 ◽  
Author(s):  
R. M. Douglas ◽  
J. A. Roberts ◽  
A. W. Munro ◽  
G. Y. Ritchie ◽  
A. J. Lamb ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Efflux System

scholarly journals Pathovar Transcriptomes

mSystems ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Amy Platenkamp ◽  
Jay L. Mellies
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Regulatory Networks ◽  
Virulence Gene ◽  
Model System ◽  
Genomic Sequences ◽  
Bacterial Strains ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Link Type

ABSTRACT Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-17 ) used 9 isolates representing 8 lineages and 3 phylogroups to find that isolates with similar genomic sequences exhibit similarities in global transcriptomes under conditions of growth in medium that induces virulence gene expression, and they found variation among individual isolates. Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-17 ) used 9 isolates representing 8 lineages and 3 phylogroups to find that isolates with similar genomic sequences exhibit similarities in global transcriptomes under conditions of growth in medium that induces virulence gene expression. They also found variation among individual isolates. Their work illustrates the importance of moving beyond observing regulatory phenomena of a limited number of regulons in a few archetypal strains, with the possibility of correlating clinical symptoms to key transcriptional pathways across lineages and phylogroups.

scholarly journals Directed Evolution of Ionizing Radiation Resistance in Escherichia coli

2009 ◽  
Vol 191 (16) ◽  
pp. 5240-5252 ◽  
Author(s):  
Dennis R. Harris ◽  
Steve V. Pollock ◽  
Elizabeth A. Wood ◽  
Reece J. Goiffon ◽  
Audrey J. Klingele ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ionizing Radiation ◽  
Directed Evolution ◽  
Radiation Resistance ◽  
Bacterial Species ◽  
Repair System ◽  
Multiple Alleles ◽  
Evolutionary Pathways ◽  
K 12 ◽  
Ionizing Radiation Resistance

ABSTRACT We have generated extreme ionizing radiation resistance in a relatively sensitive bacterial species, Escherichia coli, by directed evolution. Four populations of Escherichia coli K-12 were derived independently from strain MG1655, with each specifically adapted to survive exposure to high doses of ionizing radiation. D37 values for strains isolated from two of the populations approached that exhibited by Deinococcus radiodurans. Complete genomic sequencing was carried out on nine purified strains derived from these populations. Clear mutational patterns were observed that both pointed to key underlying mechanisms and guided further characterization of the strains. In these evolved populations, passive genomic protection is not in evidence. Instead, enhanced recombinational DNA repair makes a prominent but probably not exclusive contribution to genome reconstitution. Multiple genes, multiple alleles of some genes, multiple mechanisms, and multiple evolutionary pathways all play a role in the evolutionary acquisition of extreme radiation resistance. Several mutations in the recA gene and a deletion of the e14 prophage both demonstrably contribute to and partially explain the new phenotype. Mutations in additional components of the bacterial recombinational repair system and the replication restart primosome are also prominent, as are mutations in genes involved in cell division, protein turnover, and glutamate transport. At least some evolutionary pathways to extreme radiation resistance are constrained by the temporally ordered appearance of specific alleles.

Toxicity of the First Ten MEIC Chemicals to Bacteria

1993 ◽  
Vol 21 (2) ◽  
pp. 151-155
Author(s):  
Gustaw Kerszman
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Linear Regression ◽  
Minimal Inhibitory Concentration ◽  
Blood Concentration ◽  
Inhibitory Concentration ◽  
Human Lymphocytes ◽  
Bacterial Species ◽  
E Coli ◽  
Mild Toxicity

The toxicity of the first ten MEIC chemicals to Escherichia coli and Bacillus subtilis was examined. Nine of the chemicals were toxic to the bacteria, with the minimal inhibitory concentration (MIC) ranging from 10-3 to 4.4M. The sensitivities of both organisms were similar, but the effect on E. coli was often bactericidal, while it was bacteriostatic for B. subtilis. Digoxin was not detectably toxic to either bacterial species. Amitriptyline and FeSO4 were relatively less toxic to the bacteria than to human cells. For seven chemicals, a highly significant linear regression was established between log MIC in bacteria and log of blood concentration, giving lethal and moderate/mild toxicity in humans, as well as with toxicity to human lymphocytes.

scholarly journals Identification and antibiogram study of bacterial species isolated from milk samples of different locations in Bangladesh

2016 ◽  
Vol 1 (3) ◽  
pp. 457-462 ◽  
Author(s):  
Md Nuruzzaman Munsi ◽  
Nathu Ram Sarker ◽  
Razia Khatun ◽  
Mohammed Khorshed Alam
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Salmonella Typhi ◽  
Diffusion Method ◽  
Biochemical Tests ◽  
Public Health Importance ◽  
Milk Samples ◽  
First Choice

Cow’s milk containing pathogenic bacteria is an important threat to the consumers. The objectives of the present study were to identify the bacterial agents of public health importance in milk samples (n=35) of different locations and to determine their sensitivity to different antibiotics. The milk samples were collected and transported aseptically and subsequently allowed for culture in bacteriological media, Gram’s staining and biochemical tests for the identification of bacterial species. The bacteria identified were Staphylococcus aureus, Escherichia coli and Salmonella typhi, and their prevalence, in case of vendor milk specimens (n=28), were 96.43%, 53.57% and 35.71% respectively, and of brand milk specimens (n=7), were 42.86 %, 28.57% and 0%, respectively. This suggests that cautionary measures should be taken for quality milk production and consumption. The antibiotic sensitivity test was done by disc diffusion method and the average inhibition zones, in case of Staphylococcus aureus, were 32 mm for oxytetracycline, 26 mm for amoxicillin, 35 mm for ciprofloxacin, 27 mm for cefotaxime, 30 mm for ceftriaxone, 30 mm for azithromycin, and 26 mm for erythromycin; in case of Escherichia coli, were 5 mm for oxytetracycline, 9 mm for amoxicillin, 22 mm for ciprofloxacin, 30 mm for cefotaxime, 31 mm for ceftriaxone, 15 mm for azithromycin, and 0 mm for erythromycin; in case of Salmonella typhi., were 25 mm for oxytetracycline, 24 mm for amoxicillin, 38 mm for ciprofloxacin, 31 mm for cefotaxime, 34 mm for ceftriaxone, 24 mm for azithromycin, and 0 mm for erythromycin. Therefore, ciprofloxacin and ceftriaxone may be the antibiotics of first choice, and cefotaxime and azithromycin may be the second choice among the test antibiotics for the treatment of illness caused by these bacteria.Asian J. Med. Biol. Res. December 2015, 1(3): 457-462

scholarly journals Impact of Different Carbon Sources on the in vitro Growth and Viability of Escherichia coli (SUBE01) and Salmonella spp. (SUBS01) Cells

2016 ◽  
pp. 39-44
Author(s):  
Ifra Tun Nur ◽  
Jannatun Tahera ◽  
Md Sakil Munna ◽  
M Majibur Rahman ◽  
Rashed Noor
Keyword(s):  
Escherichia Coli ◽  
Bacterial Growth ◽  
Culture Media ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Growth Dynamics ◽  
Luria Bertani ◽  
Tween 20 ◽  
Salmonella Spp

With a previous observation of Escherichia coli growth cessation along with temperature variation within three different bacteriological culture media (nutrient agar, Luria-Bertani agar and minimal agar), current investigation further depicted on the possible growth dynamics of Escherichia coli (SUBE01) and Salmonella (SUBS01) growth and viability upon supplementation of different carbon sources (dextrose, sucrose, lactose, glycerol and tween 20) at 37°C under the aeration of 100 rpm. Viability of the tested bacterial species was assessed through the enumeration of the colony forming unit (cfu) appeared upon prescribed incubation for 12-24 hours on different agar plates consisting of the above mentioned carbon sources. Besides, to inspect the cellular phenotypic changes, morphological observations were conducted under the light microscope. Variations in bacterial growth (either growth acceleration or cessation) were further noticed through the spot tests on the agar plates. Considerable shortfalls in the culturable cells of E. coli and Salmonella spp. were noted in the minimal media separately consisting of sucrose, lactose, glycerol or tween 20 while an opposite impact of accelerated growth was noticed in the media supplied with dextrose. The data revealed a hierarchy of consequence of carbon sources as nutrient generators whereby the favourable bacterial growth and survival order of the carbon sources was estimated as dextrose > glycerol > lactose > tween 20 > sucrose.Bangladesh J Microbiol, Volume 32, Number 1-2,June-Dec 2015, pp 39-44

scholarly journals Research on reproductive performance of mares in Serbia using bacteriological examination

2011 ◽  
Vol 27 (3) ◽  
pp. 883-892
Author(s):  
M.I. Urosevic ◽  
D. Stojanovic ◽  
B. Lako ◽  
I. Jajic ◽  
Z. Milicic ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Reproductive Performance ◽  
Staphylococcus Epidermidis ◽  
Pasteurella Multocida ◽  
Bacterial Species ◽  
The Other ◽  
Streptococcus Zooepidemicus ◽  
Bacteriological Examination ◽  
Reproductive Disorders ◽  
Bacillus Spp

The research was conducted on 19 stud farms in Serbia, on 80 mares used for breeding, with and without reproductive disorders. During the two years period (from 2009 to 2010) double guarded uterine swabs from 80 mares, aged between 3 and 22 years were collected. Mares belonged to the different breeds: Thoroughbred, Standardbred, Lipizzaner and mixed breeds. It was determined, that bacterial infection of genital organs was found in 24 mares in the examined population, and the bacterial species Streptococcus zooepidemicus was diagnosed in the 11 samples from cervical swabs. In the 5 samples, Escherichia coli was isolated, while Staphylococcus epidermidis and Pasteurella multocida were present in the 2 samples each, while the other causes and simultaneous isolation of two bacterial species are much less present. These species are: Bacillus spp. plus Escherichia coli; Streptococcus zooepidemicus plus Klebsiella pneumoniae and Escherichia coli plus Streptococcus zooepidemicus. In one swab we determinated Arcanobacter pyogenes. In this examination, according to available data after natural mating, we found conception level of 43,10%, which is similar with previous reports in our country.

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