scholarly journals Genomic content typifying a prevalent clade of bovine mastitis-associated Escherichia coli

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Robert J. Goldstone ◽  
Susan Harris ◽  
David G. E. Smith
Keyword(s):  
Bovine Mastitis ◽  
Genomic Analysis ◽  
Population Level ◽  
Mammary Tissue ◽  
Specific Gene ◽  
The European Union ◽  
Dairy Farmers ◽  
E Coli ◽  
Genomic Signatures ◽  
Causative Agents

AbstractE. colirepresents a heterogeneous population with capabilities to cause disease in several anatomical sites. Among sites that can be colonised is the bovine mammary gland (udder) and a distinct class of mammary pathogenicE. coli(MPEC) has been proposed. MPEC are the principle causative agents of bovine mastitis in well-managed dairy farms, costing producers in the European Union an estimated €2 billion per year. Despite the economic impact, and the threat this disease presents to small and medium sized dairy farmers, the factors which mediate the ability forE. colito thrive in bovine mammary tissue remain poorly elucidated. Strains belonging toE. coliphylogroup A are most frequently isolated from mastitis. In this paper, we apply a population level genomic analysis to this group ofE. colito uncover genomic signatures of mammary infectivity. Through a robust statistical analysis, we show that not all strains ofE. coliare equally likely to cause mastitis, and those that do possess specific gene content that may promote their adaptation and survival in the bovine udder. Through a pan-genomic analysis, we identify just three genetic loci which are ubiquitous in MPEC, but appear dispensable forE. colifrom other niches.

scholarly journals Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers

2022 ◽  
Vol 11 ◽  
Author(s):  
Xiaomei Zhang ◽  
Michael Payne ◽  
Sandeep Kaur ◽  
Ruiting Lan
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
In Silico ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Metagenomic Sequencing ◽  
Accurate Identification ◽  
Gene Markers ◽  
E Coli

Shiga toxin-producing Escherichia coli (STEC) have more than 470 serotypes. The well-known STEC O157:H7 serotype is a leading cause of STEC infections in humans. However, the incidence of non-O157:H7 STEC serotypes associated with foodborne outbreaks and human infections has increased in recent years. Current detection and serotyping assays are focusing on O157 and top six (“Big six”) non-O157 STEC serogroups. In this study, we performed phylogenetic analysis of nearly 41,000 publicly available STEC genomes representing 460 different STEC serotypes and identified 19 major and 229 minor STEC clusters. STEC cluster-specific gene markers were then identified through comparative genomic analysis. We further identified serotype-specific gene markers for the top 10 most frequent non-O157:H7 STEC serotypes. The cluster or serotype specific gene markers had 99.54% accuracy and more than 97.25% specificity when tested using 38,534 STEC and 14,216 non-STEC E. coli genomes, respectively. In addition, we developed a freely available in silico serotyping pipeline named STECFinder that combined these robust gene markers with established E. coli serotype specific O and H antigen genes and stx genes for accurate identification, cluster determination and serotyping of STEC. STECFinder can assign 99.85% and 99.83% of 38,534 STEC isolates to STEC clusters using assembled genomes and Illumina reads respectively and can simultaneously predict stx subtypes and STEC serotypes. Using shotgun metagenomic sequencing reads of STEC spiked food samples from a published study, we demonstrated that STECFinder can detect the spiked STEC serotypes, accurately. The cluster/serotype-specific gene markers could also be adapted for culture independent typing, facilitating rapid STEC typing. STECFinder is available as an installable package (https://github.com/LanLab/STECFinder) and will be useful for in silico STEC cluster identification and serotyping using genome data.

scholarly journals Th17-related mammary immunity, but not a high systemic Th1 immune response is associated with protection against E. coli mastitis

npj Vaccines ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Nathan Cebron ◽  
Sarah Maman ◽  
Sarah Walachowski ◽  
Blandine Gausserès ◽  
Patricia Cunha ◽  
...  
Keyword(s):  
T Cells ◽  
Cd4 T Cells ◽  
Bovine Mastitis ◽  
Lymphocyte Activation ◽  
Mammary Tissue ◽  
Protective Mechanisms ◽  
E Coli ◽  
Activation Profile ◽  
Type 3 ◽  
And Control

AbstractVaccination against bovine mastitis lags behind despite high demand from the dairy industry and margin for efficacy improvement. We previously compared two immunization protocols against E. coli using either only the intramuscular route or a combination of intramuscular and mammary ductal routes, also known as ‘prime and pull’ strategy. A homologous mammary challenge during the memory phase showed that immunization favorably modified the mastitis course, notably in locally immunized cows in comparison to intramuscular and control adjuvant-only groups. Here, we performed whole-blood profiling through RNA-seq transcriptome and plasma cytokine 15-plex analyses at time points of the E. coli mastitis that showed significant clinical and laboratory differences among the groups. Diminished production of inflammatory cytokines and increased IFNγ were detected in the blood of immunized cows, where a T lymphocyte activation profile was evidenced at 12-h post infection. Acute phase neutropenia was less severe in these cows, and pathways related to neutrophil diapedesis and monocyte activation were also present. Furthermore, three intramammary-immunized cows showing faster healing and shorter mastitis duration had gene profiles that differed from their counterparts, but without any clue for the mastitis susceptibility difference. Inasmuch, when gene expression of CD4 T cells was assessed in mammary tissue, enrichment of IL-17-associated pathways was identified in the quarters of intramammary-immunized cows not only after challenge but also in the control quarters that were not infected. These findings indicate that local immunization mobilizes protective mechanisms that rely on the settlement of type 3 immunity-related CD4 T cells prior to infection.

scholarly journals Distribution and Epidemiological Aspects Associated with Enteric Bacterial Infections in Bulgaria

2020 ◽  
Vol 47 (1) ◽  
pp. 17-23
Author(s):  
Y. Mitova ◽  
V. Doicheva ◽  
S. Angelova ◽  
N. Chumak
Keyword(s):  
Incidence Rate ◽  
Bacterial Infections ◽  
The European Union ◽  
Salmonella Spp ◽  
Notification Rate ◽  
E Coli ◽  
Shigella Spp ◽  
Causative Agents ◽  
Campylobacter Infection ◽  
The Eu

AbstractEnteric bacterial infections are characterized by the location of causative agents in the intestine and their distribution in the environment with excrements. Intestinal bacterial infections in Bulgaria are caused by Salmonella spp., Shigella spp., E. coli, Campilobacter spp., Yesinia enterocolitica. For the period 2016-2018, the incidence rate of salmonellosis in Bulgaria was close to that of the European Union (EU). It was 11,21 per 100 000 population in 2017 (14,6%ooo in the EU). The incidence rate of typhoid fever in Bulgaria was lower than that in the EU for the period 2016-2018 – 0.01-0.03 per 100 000 population. Bulgaria had the highest rate of shigellosis in the EU. For the period 2016-2018 it was between 3,33%ooo and 4,07 per 100 000. The incidence of Campylobacter infection in Bulgaria during the period 2016-2018 was between 2,72%ooo and 2,88%ooo and was lower than the EU average. Data on yersiniosis in Bulgaria is incomplete. For the period 2016-2018, 36 cases were reported. E. coli enteritis had a higher average annual notification rate in the 0 to 1 age group (142,65 cases per 100 000 population). The main means of controlling intestinal infection are sanitary measures that prevent the transmission of pathogenic microorganisms with food, water, insects, contaminated hands, etc.

Antimicrobial activity of Romanian propolis ethanolic extracts against E. coli isolated from bovine mastitis

Planta Medica ◽  
2013 ◽  
Vol 79 (13) ◽  
Author(s):  
M Niculae ◽  
CD Sandru ◽  
E Pall ◽  
S Popescu ◽  
L Stan ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Bovine Mastitis ◽  
E Coli ◽  
Ethanolic Extracts

Use of gene probes for the detection of quiescent enteric bacteria in marine and fresh waters

1995 ◽  
Vol 31 (5-6) ◽  
pp. 291-298
Author(s):  
Sally A. Anderson ◽  
Gillian D. Lewis ◽  
Michael N. Pearson
Keyword(s):  
Membrane Filtration ◽  
Enteric Bacteria ◽  
Probe Method ◽  
Detection Methods ◽  
23S Rrna ◽  
Specific Gene ◽  
Gene Probe ◽  
Selective Media ◽  
Selective Enrichment ◽  
E Coli

Specific gene probe detection methods that utilise a non-selective culturing step were tested for the ability to recognise the presence of quiescent enteric bacteria (Escherichia coli and Enterococcus faecalis ) within illuminated freshwater and seawater microcosms. An E. coli specific uidA gene probe and a 23S rRNA oligonucleotide probe for Enterococci were compared with recoveries using membrane filtration and incubation on selective media (mTEC and mE respectively). From these microcosm experiments a greater initial detection (from 4 hours to 1 day) of E. coli and Ent. faecalis using gene probe methods was observed. Additionally, a comparison of E. coli direct viable counts (DVC) in sunlight exposed microcosms with recoveries by selective media and gene probe methods revealed a large number of viable non-culturable cells. This suggests that enumeration of E. coli by a gene probe method is limited by the replication of the bacteria during the initial non-selective enrichment step. The detection of stressed Ent. faecalis by the oligonucleotide gene probe method was significantly greater than recovery on selective mE agar, indicating an Enterococci non-growth phase.

scholarly journals Can Family Farms Depend on Price Information? Testing Butter and Curd Price Integration in Poland

Agriculture ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 434
Author(s):  
Anna M. Klepacka ◽  
Wojciech J. Florkowski ◽  
Cesar Revoredo-Giha
Keyword(s):  
World Market ◽  
Response Analysis ◽  
The European Union ◽  
Family Farms ◽  
Quota System ◽  
Dairy Farmers ◽  
Vector Error Correction ◽  
Vector Error ◽  
Vec Model ◽  
Dairy Markets

This study examines the integration of regional dairy markets in Poland, which is a major European dairy producing country. The analysis of prices is important, as many dairy farmers are members of dairy processing cooperatives, and their incomes are affected by the prices of two popular products: butter and curd. Moreover, the period of study included significant fluctuations in the world market and the termination of the milk quota system in the European Union (EU). The price records used in this study are from the two main milk-producing regions in the country: Northern and Central. The data were tested for stationarity and Granger causality before estimating a Vector Error Correction (VEC) model. Estimation results show that the removal of the milk quota lowered prices of butter and curd in the two regions. The relationships of the prices in both regions for butter markets were nearly perfect during the period January 2010–November 2017, but curd prices were found unintegrated. Impulse response analysis showed that the effect of shocks was mostly absorbed in a two-week period and prices returned to full equilibrium in about four to five weeks. This fast price adjustment indicates that both markets operate properly and no market participant can obtain gains above those offered at equilibrium.

scholarly journals Influence of nutrient availability on in vitro growth of major bovine mastitis pathogens

2021 ◽  
Vol 88 (1) ◽  
pp. 80-88
Author(s):  
Remo Stürmlin ◽  
Josef J. Gross ◽  
Olga Wellnitz ◽  
Lea A. Wagner ◽  
Camille Monney ◽  
...  
Keyword(s):  
Bacterial Growth ◽  
Nutrient Availability ◽  
Bovine Mastitis ◽  
Milk Composition ◽  
B Vitamins ◽  
E Coli ◽  
Streptococcus Uberis ◽  
Whole Milk ◽  
Mastitis Pathogens

AbstractThe aim of the present study was to investigate the effects of milk composition changes on the in vitro growth of bovine mastitis pathogens. Nutritional requirements of three major bovine mastitis pathogens Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Streptococcus uberis (S. uberis) were investigated in vitro. We used ultra-high temperature (UHT) treated milk with different contents of fat, protein, and carbohydrates to test the influence of the availability of various milk constituents on pathogen growth characteristics. Additionally, the bacterial growth was investigated under experimentally modified nutrient availability by dilution and subsequent supplementation with individual nutrients (carbohydrates, different nitrogen sources, minerals, and different types of B vitamins) either to milk or to a conventional medium (thioglycolate broth, TB). Varying contents of fat, protein or lactose did not affect bacterial growth with the exception of growth of S. uberis being promoted in protein-enriched milk. The addition of nutrients to diluted whole milk and TB partly revealed different effects, indicating that there are media-specific growth limiting factors after dilution. Supplementation of minerals to diluted milk did not affect growth rates of all studied bacteria. Bacterial growth in diluted whole milk was decreased by the addition of high concentrations of amino acids in S. aureus, and by urea and additional B vitamins in E. coli and S. aureus. The growth rate of S. uberis was increased by the addition of B vitamins to diluted whole milk. The present results demonstrate that growth-limiting nutrients differ among pathogen types. Because reduced bacterial growth was only shown in diluted milk or TB, it is unlikely that alterations in nutrient availability occurring as a consequence of physiological changes of milk composition in the cow's udder would directly affect the susceptibility or course of bovine mastitis.

scholarly journals Family history assessment significantly enhances delivery of precision medicine in the genomics era

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Yasmin Bylstra ◽  
Weng Khong Lim ◽  
Sylvia Kam ◽  
Koei Wan Tham ◽  
R. Ryanne Wu ◽  
...  
Keyword(s):  
Family History ◽  
Cancer Risk ◽  
Clinical Care ◽  
Genomic Analysis ◽  
Population Level ◽  
Cancer Genes ◽  
Family History Information ◽  
Screening Programs ◽  
Family History Assessment ◽  
Risk Of Cancer

Abstract Background Family history has traditionally been an essential part of clinical care to assess health risks. However, declining sequencing costs have precipitated a shift towards genomics-first approaches in population screening programs rendering the value of family history unknown. We evaluated the utility of incorporating family history information for genomic sequencing selection. Methods To ascertain the relationship between family histories on such population-level initiatives, we analysed whole genome sequences of 1750 research participants with no known pre-existing conditions, of which half received comprehensive family history assessment of up to four generations, focusing on 95 cancer genes. Results Amongst the 1750 participants, 866 (49.5%) had high-quality standardised family history available. Within this group, 73 (8.4%) participants had an increased family history risk of cancer (increased FH risk cohort) and 1 in 7 participants (n = 10/73) carried a clinically actionable variant inferring a sixfold increase compared with 1 in 47 participants (n = 17/793) assessed at average family history cancer risk (average FH risk cohort) (p = 0.00001) and a sevenfold increase compared to 1 in 52 participants (n = 17/884) where family history was not available (FH not available cohort) (p = 0.00001). The enrichment was further pronounced (up to 18-fold) when assessing only the 25 cancer genes in the American College of Medical Genetics (ACMG) Secondary Findings (SF) genes. Furthermore, 63 (7.3%) participants had an increased family history cancer risk in the absence of an apparent clinically actionable variant. Conclusions These findings demonstrate that the collection and analysis of comprehensive family history and genomic data are complementary and in combination can prioritise individuals for genomic analysis. Thus, family history remains a critical component of health risk assessment, providing important actionable data when implementing genomics screening programs. Trial registration ClinicalTrials.gov NCT02791152. Retrospectively registered on May 31, 2016.

scholarly journals Characterization of Anti-Bacterial Effect of the Two New Phages against Uropathogenic Escherichia coli

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1348
Author(s):  
Lívia Slobodníková ◽  
Barbora Markusková ◽  
Michal Kajsík ◽  
Michal Andrezál ◽  
Marek Straka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Therapeutic Potential ◽  
Medical Intervention ◽  
Uropathogenic Escherichia Coli ◽  
E Coli ◽  
Phage Cocktail ◽  
Causative Agents ◽  
Tract Infections

Urinary tract infections (UTIs) are among the events that most frequently need medical intervention. Uropathogenic Escherichia coli are frequently their causative agents and the infections are sometimes complicated by the presence of polyresistant nosocomial strains. Phage therapy is a tool that has good prospects for the treatment of these infections. In the present study, we isolated and characterized two bacteriophages with broad host specificity against a panel of local uropathogenic E. coli strains and combined them into a phage cocktail. According to genome sequencing, these phages were closely related and belonged to the Tequatrovirus genus. The newly isolated phages showed very good activity on a panel of local clinical E. coli strains from urinary tract infections. In the form of a two-phage cocktail, they were active on E. coli strains belonging to phylogroups B2 and D, with relatively lower activity in B1 and no response in phylogroup A. Our study is a preliminary step toward the establishment of a national phage bank containing local, well-characterized phages with therapeutic potential for patients in Slovakia.

Sign in / Sign up

Export Citation Format

Share Document