A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.
- MeSH
- bachor metabolismus MeSH
- fenotyp MeSH
- fylogeneze MeSH
- kohortové studie MeSH
- krev metabolismus MeSH
- methan metabolismus MeSH
- mléko metabolismus MeSH
- skot genetika mikrobiologie MeSH
- střevní mikroflóra genetika fyziologie MeSH
- zvířata MeSH
- Check Tag
- skot genetika mikrobiologie MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne's disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.
- MeSH
- feces mikrobiologie MeSH
- mlékárenství MeSH
- Mycobacterium avium subsp. paratuberculosis genetika izolace a purifikace fyziologie MeSH
- nemoci skotu mikrobiologie MeSH
- paratuberkulóza mikrobiologie MeSH
- sekvenční analýza DNA veterinární MeSH
- skot mikrobiologie MeSH
- vylučování bakterií z těla MeSH
- zvířata MeSH
- Check Tag
- skot mikrobiologie MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
Cíl práce: Tato studie byla zpracována ve spolupráci se Státní veterinární správou (SVS) s cílem monitorovat výskyt Shiga-toxin produkujících izolátů Escherichia coli ve sterech z jatečně upravených těl prasat a skotu. Materiál a metody: Od června do srpna roku 2013 odebraU pracovníci SVS 168 stěrů ze skotu a 318 z prasat na 157 různých porážkách v ČR Základní zpracování vzorků bylo provedeno ve Státních veterinárních ústavech Praha, Jihlava a Olomouc podle metodického postupu koordinovaného Národní referenční laboratoří (NRL) pro oblast Escherichia coh v rámci rezortu Ministerstva zemědělství. Laboratorní zpracování vzorků vycházelo z normy ISO TS 13136. Výsledky: Z celkem 486 odebraných stěrů bylo detekováno 22 pozitivních vzorků. Získáno bylo 22 izolátů shigatoxigenních E. coli (STEC) a 1 kmen s charakteristikou enterohemoragických E. coli (EHEC). U žádného izolátů nebyly zjištěny geny typické pro enteroagregativní E. coh (EAggEC). Většina získaných kmenů STEC pocházela z prasat (15 kmenů). Gen stx1, byl detekován 2krát (stx1a, stx1d), gen stx2 13krát (12krát stx2e, 1krát Stx2a). Ze vzorků stěrů skotu bylo získáno 8 izolátů STEC. jedenkrát se jednalo o gen stx, (subtyp a), 6krát byl zjištěn gen stx2 (4krát stx2e, 1krát stx2a a 1krát stx2c). Jeden izolát nesl současně geny pro oba typy toxinů stx1a a stx2a. Vždy po jednom izolátů byly detekovány séroskupiny 091,0113,0146 popisované ve spojitosti s onemocněním lidi. U žádného z těchto kmenu ale nebyly detekovány další faktory virulence, typické pro kmeny vyvolávající závažná onemocnění. Závěr: Z výsledků této studie vyplývá celková prevalence výskytu shigatoxigenních E. coli ve sterech z povrchu jatečně upravených těl prasat a skotu 4,5 % a v případě kmenů EHEC pouze 0,2 %. Syrové maso pocházející z tuzemských chovů zřejmě nepředstavuje v souČasnosti významný zdroj STEC pro člověka.
Objectives: This study was performed in cooperation with the State Veterinary Administration (SVA) in order to monitor the occurrence of Shiga toxin-producing Escherichia coli isolates in swabs from the carcasses of pigs and cattle at slaughterhouses. Material and Methods: From June to August 2013, SVA staff took 168 swabs from cattle and 318 from pigs at 157 different slaughters in the Czech Republic. Basic processing of the samples was carried out in the State Veterinary Institutes (SVIs) in Prague, Jihlava and Olomouc according to the methodical process coordinated by the National reference laboratory (NRL) for Escherichia coli (Czech Ministry of Agriculture). The procedure was based on the guideline ISO TS 13136. Results: Out of the 486 swabs, twenty-two positive samples were detected. There were a total of 22 isolates of Shiga toxigenic E. coli (STEC) and 1 strain with the characteristic of enterohemorrhagic E. coli (EHEC). Genes typical for enteroaggregative E. coli (EAggEC) were not found in any of the isolates. Most STEC strains originated from pigs. The stx, gene was detected twice (stxi1a, stx1d) and the stx2 gene 13 times (12 times stx2e, once Stx2a). Seven STEC isolates were detected from samples of cattle origin. One strain was stx1 (stx1a) -positive, the stx2 gene was found 6 times (4 stx2e, 1 stx2a aud 1 stx2c). One isolate carried simultaneously both stxja and stx2a. Each of the serogroups 091,0113 and 0146 described as etiological agents of severe disease in humans were detected only once. None of these strains harbored additional virulence factors typical for strains causing serious illness. Conclusion: Results of this study show the overall prevalence of Shiga toxigenic E. coli of 4.5% and 0.2% of enterohemorrhagic strains in the studied samples. Raw meat originating from local farms does not currently represent an important source of STEC for humans.
- Klíčová slova
- stěry, potravinová zvířata,
- MeSH
- enterohemoragická Escherichia coli * genetika izolace a purifikace MeSH
- epidemiologické monitorování veterinární MeSH
- Escherichia coli izolace a purifikace MeSH
- hospodářská zvířata MeSH
- jatka MeSH
- prasata mikrobiologie MeSH
- prevalence MeSH
- shiga toxin 1 genetika MeSH
- shiga toxin 2 genetika MeSH
- shiga-toxigenní Escherichia coli * genetika izolace a purifikace MeSH
- skot mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- skot mikrobiologie MeSH
- zvířata MeSH
- Publikační typ
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
We previously reported the presence of an OXA-23 carbapenemase in an undescribed species of the genus Acinetobacter isolated from horse dung at the Faculty of Veterinary Medicine, Ghent University, Belgium. Here we include six strains to corroborate the delineation of this taxon by phenotypic characterization, DNA-DNA hybridization, 16S rRNA gene and rpoB sequence analysis, % G+C determination, MALDI-TOF MS and fatty acid analysis. The nearly complete 16S rRNA gene sequence of strain UG 60467(T) showed the highest similarities with those of the type strains of Acinetobacter bouvetii (98.4 %), Acinetobacter haemolyticus (97.7 %), and Acinetobacter schindleri (97.2 %). The partial rpoB sequence of strain UG 60467(T) showed the highest similarities with 'Acinetobacter bohemicus' ANC 3994 (88.6 %), A. bouvetii NIPH 2281 (88.6 %) and A. schindleri CIP 107287T (87.3 %). Whole-cell MALDI-TOF MS analyses supported the distinctness of the group at the protein level. The predominant fatty acids of strain UG 60467(T) were C12 : 0 3-OH, C12 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Strains UG 60467(T) and UG 60716 showed a DNA-DNA relatedness of 84 % with each other and a DNA-DNA relatedness with A. schindleri LMG 19576(T) of 17 % and 20 %, respectively. The DNA G+C content of strain UG 60467(T) was 39.6 mol%. The name Acinetobacter gandensis sp. nov. is proposed for the novel taxon. The type strain is UG 60467(T) ( = ANC 4275(T) = LMG 27960(T) = DSM 28097(T)).
- MeSH
- Acinetobacter klasifikace genetika izolace a purifikace MeSH
- bakteriální geny MeSH
- DNA bakterií genetika MeSH
- feces mikrobiologie MeSH
- fylogeneze * MeSH
- hybridizace nukleových kyselin MeSH
- koně mikrobiologie MeSH
- mastné kyseliny chemie MeSH
- molekulární sekvence - údaje MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- skot mikrobiologie MeSH
- techniky typizace bakterií MeSH
- zastoupení bazí MeSH
- zvířata MeSH
- Check Tag
- skot mikrobiologie MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Belgie MeSH
Resistance of bacteria to antibiotics is a global medical problem requiring close cooperation between veterinary and human physicians. Raw materials and foods of animal origin may be not only a source of pathogenic bacteria causing alimentary tract infections but also a source of bacteria with a dangerous extent of resistance to antibiotics, potentially entering the human food chain. This article presents results of the first study in the Czech Republic detecting the presence of Enterobacteriaceae-producing extended-spectrum b -lactamases (ESBLs) in swabs collected in slaughterhouses from surfaces of healthy animal carcasses. In 2012, swabs taken from pig (n = 166) and cattle (n = 140) carcass surfaces were analyzed. In 17 % of 53 studied slaughterhouses, ESBL-producing Escherichia coli strains were isolated. ESBLs were found in 11 and 4 % of porcine and bovine samples, respectively. Swabs collected from pigs yielded 18 ESBL-producing E. coli strains. The bla genes were found to encode production of CTX-M-1 group enzymes in 16 strains, SHV in one case, and both CTX-M-1-like and TEM in another case. In swabs taken from cattle, five ESBL-producing E. coli strains were isolated. In three cases, the bla genes for CTX-M-1-like production were identified; in two cases, genes for both CTX-M-1-like and TEM production were found. The similarity/identity of ESBL-positive isolates was compared by pulsed-field gel electrophoresis. This is the first report and characterization of the presence and nature of ESBL-producing E. coli in swabs collected from surfaces of healthy pig and cattle carcasses in slaughterhouses in the Czech Republic.
- MeSH
- beta-laktamasy biosyntéza genetika izolace a purifikace MeSH
- Escherichia coli enzymologie genetika izolace a purifikace MeSH
- jatka * MeSH
- lidé MeSH
- potravinářská mikrobiologie MeSH
- prasata mikrobiologie MeSH
- prevalence MeSH
- pulzní gelová elektroforéza MeSH
- skot mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- skot mikrobiologie MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
In our previous experiment, the ten calves originated bifidobacterial strains were administered to calves and re-isolated. Fingerprinting techniques used in this study enabled us to distinguish the surviving and non-surviving strains. Only the species Bifidobacterium animalis ssp. animalis and Bifidobacterium longum ssp. suis were found to survive in the intestine.
- MeSH
- bakteriální proteiny genetika MeSH
- Bifidobacterium klasifikace genetika izolace a purifikace MeSH
- chaperon hsp60 genetika MeSH
- feces mikrobiologie MeSH
- fylogeneze MeSH
- probiotika MeSH
- RNA ribozomální 16S MeSH
- skot mikrobiologie MeSH
- střeva mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- skot mikrobiologie MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The aim of the study was to compare the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli bovine isolates on a conventional dairy cattle farm with high consumption of parenteral and intramammary cephalosporins (farm A) and on an organic dairy farm with no cephalosporin use (farm B). ESBL-producing E. coli were isolated from rectal swabs and milk filters by selective cultivation on MacConkey agar with cefotaxime (2mg/l). ESBL genes were identified by polymerase chain reaction (PCR) and sequencing, and the genetic diversity of the isolates was determined by XbaI pulsed field gel electrophoresis (PFGE). Conjugative transfer, incompatibility group, and restriction fragment length polymorphism (RFLP) profiles of the ESBL-carrying plasmids were studied. Higher prevalence (39%, n(rectal samples in cows)=309) of CTX-M-1-producing E. coli isolates was found on farm A compared to farm B (<1%, n(rectal samples in cows)=154; 0%, n(rectal samples in calves)=46). Using PFGE, the isolates from farm A were divided into nine pulsotypes. In all ESBL-positive isolates, the bla(CTX-M-1) gene was carried on 40 kb IncN conjugative plasmids of three related HincII restriction profiles. Horizontal gene transfer through transmission of IncN plasmids harboring bla(CTX-M-1) as well as clonal dissemination of a particular clone seems to be involved in dissemination of CTX-M-1-producing E. coli isolates in cows on the farm using cephalosporins in treating bacterial infections. The study demonstrates a possible role of cephalosporin use in the widespread occurrence of CTX-M-1-producing E. coli on the conventional dairy cattle farm compared to the organic farm.
- MeSH
- beta-laktamasy genetika MeSH
- cefalosporiny farmakologie MeSH
- DNA bakterií genetika MeSH
- Escherichia coli klasifikace genetika izolace a purifikace MeSH
- infekce vyvolané Escherichia coli mikrobiologie veterinární MeSH
- nemoci skotu mikrobiologie MeSH
- plazmidy genetika MeSH
- polymerázová řetězová reakce MeSH
- polymorfismus délky restrikčních fragmentů MeSH
- přenos genů horizontální MeSH
- proteiny z Escherichia coli genetika MeSH
- pulzní gelová elektroforéza MeSH
- rezistence k cefalosporinům MeSH
- skot mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- skot mikrobiologie MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Geografické názvy
- Česká republika MeSH
- MeSH
- epidemický výskyt choroby MeSH
- Escherichia coli O157 fyziologie izolace a purifikace MeSH
- hemolyticko-uremický syndrom epidemiologie mikrobiologie prevence a kontrola MeSH
- infekce vyvolané Escherichia coli epidemiologie mikrobiologie přenos prevence a kontrola MeSH
- lidé MeSH
- skot mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- skot mikrobiologie MeSH
- zvířata MeSH
- Publikační typ
- souhrny MeSH
Twenty-five bifidobacteria were isolated from feces of calves. Isolates were identified, and their functional properties and antimicrobial activity were determined. From 10 strains with suitable properties rifampicin-resistant mutants (RRBs) were prepared and mixture of RRBs was administered to 2-d-old calves. These strains were identified by sequencing as Bifidobacterium animalis ssp. animalis (6 strains), B. thermophilum (2 strains), B. choerinum (1 strain) and B. longum ssp. suis (1 strain). The control group was without probiotic treatment. Survival ability of administered bifidobacteria was monitored in fecal samples by cultivation on modified TPY agar supplemented with mupirocin, acetic acid, and rifampicin. Administered bifidobacteria survived in gastrointestinal tract of calves for at least 60 d. Other bacteria were also determined after cultivation using fluorescence in situ hybridization (FISH). Bifidobacteria and lactobacilli dominated in fecal microflora. Significantly lower amounts of E. coli and higher amounts of bifidobacteria and total anaerobes were found in the treated group relative to the control group.
- MeSH
- antibakteriální látky farmakologie MeSH
- Bacteria izolace a purifikace klasifikace MeSH
- Bifidobacterium fyziologie metabolismus účinky léků MeSH
- časové faktory MeSH
- DNA bakterií genetika MeSH
- feces mikrobiologie MeSH
- financování organizované MeSH
- fylogeneze MeSH
- gastrointestinální trakt mikrobiologie MeSH
- hybridizace in situ MeSH
- mikrobiální testy citlivosti MeSH
- mikrobiální viabilita MeSH
- počet mikrobiálních kolonií MeSH
- probiotika aplikace a dávkování izolace a purifikace MeSH
- shluková analýza MeSH
- skot mikrobiologie MeSH
- techniky typizace bakterií MeSH
- zvířata MeSH
- Check Tag
- skot mikrobiologie MeSH
- zvířata MeSH
