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1.
Artigo em Inglês | MEDLINE | ID: mdl-34379583

RESUMO

This study describes JE7A12T (=ATCC TSD-225T=NCTC 14479T), an isolate from the ruminal content of a dairy cow. Phenotypic and genotypic traits of the isolate were explored. JE7A12T was found to be a strictly anaerobic, catalase-negative, oxidase-negative, coccoid bacterium that grows in chains. The API 50 CH carbon source assay detected fermentation of d-glucose, d-fructose, d-galactose, glycogen and starch. HPLC showed acetate to be the major fermentation product as a result of carbohydrate fermentation. Phylogenetic analysis of JE7A12T based on 16S rRNA nucleotide sequence and amino acid sequences from the whole genome indicated a divergent lineage from the closest neighbours in the genus Ruminococcus. The results of 16S rRNA sequence comparison, whole genome average nucleotide identity (ANI) and DNA G+C content data indicate that JE7A12T represents a novel species which we propose the name Ruminococcus bovis with JE7A12T as the type strain.


Assuntos
Bovinos/microbiologia , Filogenia , Rúmen , Ruminococcus , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Indústria de Laticínios , Ácidos Graxos/química , RNA Ribossômico 16S/genética , Rúmen/microbiologia , Ruminococcus/classificação , Ruminococcus/isolamento & purificação , Análise de Sequência de DNA
2.
Genet Sel Evol ; 53(1): 65, 2021 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-34362312

RESUMO

BACKGROUND: Analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: how useful can the microbiome be for complex trait prediction? Are estimates of microbiability reliable? Can the underlying biological links between the host's genome, microbiome, and phenome be recovered? METHODS: Here, we address these issues by (i) developing a novel simulation strategy that uses real microbiome and genotype data as inputs, and (ii) using variance-component approaches (Bayesian Reproducing Kernel Hilbert Space (RKHS) and Bayesian variable selection methods (Bayes C)) to quantify the proportion of phenotypic variance explained by the genome and the microbiome. The proposed simulation approach can mimic genetic links between the microbiome and genotype data by a permutation procedure that retains the distributional properties of the data. RESULTS: Using real genotype and rumen microbiota abundances from dairy cattle, simulation results suggest that microbiome data can significantly improve the accuracy of phenotype predictions, regardless of whether some microbiota abundances are under direct genetic control by the host or not. This improvement depends logically on the microbiome being stable over time. Overall, random-effects linear methods appear robust for variance components estimation, in spite of the typically highly leptokurtic distribution of microbiota abundances. The predictive performance of Bayes C was higher but more sensitive to the number of causative effects than RKHS. Accuracy with Bayes C depended, in part, on the number of microorganisms' taxa that influence the phenotype. CONCLUSIONS: While we conclude that, overall, genome-microbiome-links can be characterized using variance component estimates, we are less optimistic about the possibility of identifying the causative host genetic effects that affect microbiota abundances, which would require much larger sample sizes than are typically available for genome-microbiome-phenome studies. The R code to replicate the analyses is in https://github.com/miguelperezenciso/simubiome .


Assuntos
Bovinos/genética , Microbioma Gastrointestinal , Estudo de Associação Genômica Ampla/métodos , Genoma , Herança Multifatorial , Animais , Teorema de Bayes , Bovinos/microbiologia , Simulação por Computador , Fenótipo
3.
PLoS One ; 16(7): e0253754, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34288928

RESUMO

Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d-1), or BCA (6 g d-1). The basal diet consisted of corn silage and dried distiller's grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1-4: 40% corn; d 5-8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.


Assuntos
Acidose/tratamento farmacológico , Ração Animal , Doenças dos Bovinos/tratamento farmacológico , Bovinos/microbiologia , Fibras na Dieta , Conteúdo Gastrointestinal/microbiologia , Microbioma Gastrointestinal/efeitos dos fármacos , Genisteína/uso terapêutico , Rúmen/microbiologia , Acidose/microbiologia , Animais , Bactérias/efeitos dos fármacos , Bactérias/isolamento & purificação , Carga Bacteriana , Doenças dos Bovinos/microbiologia , Celulose/metabolismo , Desoxiglucose/farmacologia , Carboidratos da Dieta/metabolismo , Fibras na Dieta/metabolismo , Proteínas na Dieta/metabolismo , Fermentação , Genisteína/farmacologia , Concentração de Íons de Hidrogênio , Ionóforos/farmacologia , Masculino , Distribuição Aleatória , Silagem , Amido/metabolismo
4.
Sci Rep ; 11(1): 13725, 2021 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-34215807

RESUMO

Enterobacteria that produce extended-spectrum ß-lactamase (ESBL) such as Escherichia coli (E. coli) are common in our environment and known to cause serious health implications in humans and animals. ß-lactam antibiotics such as penicillins, cephalosporins and monobactams are the most commonly used anti-bacterials in both humans and animals, however, Gram negative bacteria (such as E. coli) that produces extended-spectrum ß-lactamases (ESBLs) have the ability to hydrolyze most ß-lactams therefore making them resistant to ß-lactam antibiotics. Recent extensive researches on the epidemiology and genetic characteristics of extended-spectrum ß-lactamase (ESBL)-producing E. coli reported the existence of ESBL-producing E. coli in humans, companion animals and poultry. Therefore, this experiment was performed to investigate the prevalence and genetic characteristics of ß-lactamase producing E. coli isolated from beef cattle farms in the Sichuan-Chongqing circle of China. Phenotypic confirmation of ESBL-producing E. coli was performed using the double disk synergy test. Polymerase Chain Reaction (PCR) was used to detect blaCTX-M, blaSHV and blaTEM gene codes, then after, isolates were divided into different phylogenetic groups and multi-locus sequence typing (MLST). The results showed that out of the 222 E. coli strains isolated from the beef cattle, 102 strains showed ESBL phenotypes. The PCR results showed that blaCTX-M was the predominant ESBL gene identified among the E. coli strains with 21 (9.5%) isolates having this gene, followed by blaSHV which was found in 18 (8.1%) isolates. The majority of these ESBL positive isolates were assigned to phylogroup A (19.8%) followed by phylogroup B1 (13.5%). In addition, from the MLST results on ESBL positive isolates (n = 30) we identified 19 STs, ST398 (ST398cplx) and ST7130 which were the prevalent population (20%). In conclusion, the high prevalence of CTX-M, and SHV in the study confirmed its association with E. coli infection; therefore, this calls for health concerns on ESBL-producing E. coli. As far as we know, this is the first comprehensive research report relating to ESBL-producing E. coli incidence in Chinese beef cattle.


Assuntos
Bovinos/microbiologia , Escherichia coli/enzimologia , beta-Lactamases/genética , Animais , China , Escherichia coli/genética , Carne Vermelha/microbiologia
5.
J Antibiot (Tokyo) ; 74(8): 508-518, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34103703

RESUMO

Drug resistance has been partly driven by the overuse of antimicrobials in agricultural animal feed. Better understanding of antibiotic resistance in bovine gut is needed to assess its potential effects based on metagenomic approach and analysis. In this study, we collected 40 fecal samples to explore drug resistance derived from antibiotic use in the bacterial community by an analysis of the diversities and differences of antibiotic-resistant genes (ARGs) in the gut microbiota from yak, beef, and dairy cattle. Overall, 1688 genes were annotated, including 734 ARG subtypes. The ARGs were related to tetracyclines, quinolones, ß-lactam, and aminoglycosides, in accordance with the antibiotics widely used in the clinic for humans or animals. The emergence, prevalence, and differences in resistance genes in the intestines of yaks, beef, and dairy cattle may be caused by the selective pressure of different feeding patterns, where yaks were raised without antibiotics for growth promotion. In addition, the abundance of ARGs in yak was lower than in beef and dairy cattle, whereas the abundance of integron, a kind of mobile genetic elements (MGEs) was higher in yaks than those in beef and dairy cattle. Furthermore, the results of this study could provide the basis for a comprehensive profile of various ARGs among yak, beef, and dairy cattle in future.


Assuntos
Bovinos/microbiologia , Farmacorresistência Bacteriana/genética , Metagenômica/métodos , Microbiota/genética , Ração Animal , Animais , Laticínios , Fezes/microbiologia , Humanos , Integrons/genética , Sequências Repetitivas Dispersas/genética , Carne , Microbiologia do Solo , Especificidade da Espécie
6.
BMC Vet Res ; 17(1): 224, 2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34172061

RESUMO

BACKGROUND: The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and "host" individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and "host". The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability. RESULTS: The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions - rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the "host effect" showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups. CONCLUSION: The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.


Assuntos
Bovinos/microbiologia , Microbioma Gastrointestinal , Carneiro Doméstico/microbiologia , Animais , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Dieta/veterinária , Fezes/microbiologia , Firmicutes/genética , Firmicutes/isolamento & purificação , Masculino , Polônia , Reação em Cadeia da Polimerase em Tempo Real
7.
Artigo em Inglês | MEDLINE | ID: mdl-34161222

RESUMO

A novel Gram-stain-positive bacterium was isolated from a purulent bovine milk sample, the bovine placenta from an abortion, the udder secretion of a heifer and the lung of a pig that had succumbed from suppurative bronchopneumonia in Switzerland from 2015 to 2019. The strains grew best under aerobic conditions with 5 % CO2 and colonies were non-haemolytic and greyish-white. They were non-motile and negative for catalase and oxidase. The genomes of the four strains 19M2397T, 15A0121, 15IMD0307 and 19OD0592 were obtained by sequencing. The results of phylogenetic analyses based on the 16S rRNA gene grouped them within the genus Trueperella in the family Arcanobacteriaceae. The genomes had DNA G+C contents of 61.2-62.2 mol% and showed digital DNA-DNA hybridization (dDDH) values of 21.4-22.8 % and average nucleotide identity (ANI) values of approximately 77 % to their closest relatives Trueperella pyogenes and Trueperella bernardiae. With respect to the presence in different livestock species we propose the name Trueperella pecoris sp. nov. The type strain is 19M2397T (=CCOS 1952T=DSM 111392T), isolated from the udder secretion of a heifer diagnosed with summer mastitis in 2019.


Assuntos
Actinomycetaceae/classificação , Bovinos/microbiologia , Leite/microbiologia , Filogenia , Placenta/microbiologia , Suínos/microbiologia , Actinomycetaceae/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Feminino , Hibridização de Ácido Nucleico , Gravidez , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Suíça
8.
Gut Microbes ; 13(1): 1-13, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34060426

RESUMO

It has been hypothesized that both genetics and diet influence the composition of the human cecal microbiota. However, it remains unclear whether and how occupational exposure to microbes impacts the microbial communities in human guts. Using a One Health approach, we visited pig farms (n = 26) and collected stool specimens from pig workers (n = 59), pig barn air samples (n = 19), and rectal swabs from pigs at three different growth stages (n = 144). Stool samples from cattle workers were included as a control group (n = 22). Each sample's microbiota was characterized using 16S rRNA gene sequencing and the DADA2 pipeline.We obtained a significantly different clustering of the microbial compositions of pig and cattle workers by permutational multivariate analysis of variance (PERMANOVA; P < .001). Workers primarily exposed to pigs had higher relative abundances of Prevotellaceae and less Bacteroidaceae than workers exposed to cattle. We also found that the microbial compositions of pig workers' stool samples shared extensive fractions with the samples from their pigs. We also identified amplicon sequencing variants (ASVs) in the airborne microbiota which were likely involved in zoonotic transmission events.We hypothesize that ASVs originating from pig feces are aerosolized and, through breathing, get trapped in the pig farm workers' upper respiratory tract from where they can get swallowed. Consequently, some of the animal associated ASVs are transferred into the gastrointestinal tracts (GITs) which leads to changes in the composition of the human gut microbiota. The importance of this finding for human health must be investigated further.


Assuntos
Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Exposição Ocupacional/análise , Ar/análise , Microbiologia do Ar , Animais , Bactérias/classificação , Bactérias/genética , Bovinos/crescimento & desenvolvimento , Bovinos/microbiologia , Fazendeiros , Fazendas , Fezes/microbiologia , Trato Gastrointestinal/microbiologia , Humanos , Estudos Prospectivos , Reto/microbiologia , Suínos/crescimento & desenvolvimento , Suínos/microbiologia
9.
J Dairy Res ; 88(2): 210-216, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33934726

RESUMO

This paper reveals the technological properties of lactic acid bacteria isolated from raw milk (colostrum and mature milk) of Wagyu cattle raised in Okayama Prefecture, Japan. Isolates were identified based on their physiological and biochemical characteristics as well as 16S rDNA sequence analysis. Streptococcus lutetiensis and Lactobacillus plantarum showed high acid and diacetyl-acetoin production in milk after 24 h of incubation at 40 and 30°C, respectively. These strains are thought to have potential for use as starter cultures and adjunct cultures for fermented dairy products.


Assuntos
Bovinos/microbiologia , Lactobacillales/fisiologia , Leite/microbiologia , Animais , Carga Bacteriana , Colostro/microbiologia , Produtos Fermentados do Leite/microbiologia , DNA/análise , Fermentação , Japão , Ácido Láctico/biossíntese , Lactobacillales/genética , Lactobacillus plantarum/isolamento & purificação , Lactobacillus plantarum/fisiologia , RNA Ribossômico 16S/genética , Streptococcus/isolamento & purificação , Streptococcus/fisiologia
10.
PLoS One ; 16(5): e0243681, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33951039

RESUMO

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is a public health concern globally. This study reports the phenotypic and genotypic antimicrobial resistance (AMR) profiles of NTS isolates from bovine lymph nodes (n = 48) and ground beef (n = 29). Furthermore, we compared genotypic AMR data of our isolates with those of publicly available NTS genomes from Mexico (n = 2400). The probability of finding MDR isolates was higher in ground beef than in lymph nodes:χ2 = 12.0, P = 0.0005. The most common resistant phenotypes involved tetracycline (40.3%), carbenicillin (26.0%), amoxicillin-clavulanic acid (20.8%), chloramphenicol (19.5%) and trimethoprim-sulfamethoxazole (16.9%), while more than 55% of the isolates showed decreased susceptibility to ciprofloxacin and 26% were MDR. Conversely, resistance to cephalosporins and carbapenems was infrequent (0-9%). MDR phenotypes were strongly associated with NTS serovar (χ2 = 24.5, P<0.0001), with Typhimurium accounting for 40% of MDR strains. Most of these (9/10), carried Salmonella genomic island 1, which harbors a class-1 integron with multiple AMR genes (aadA2, blaCARB-2, floR, sul1, tetG) that confer a penta-resistant phenotype. MDR phenotypes were also associated with mutations in the ramR gene (χ2 = 17.7, P<0.0001). Among public NTS isolates from Mexico, those from cattle and poultry had the highest proportion of MDR genotypes. Our results suggest that attaining significant improvements in AMR meat safety requires the identification and removal (or treatment) of product harboring MDR NTS, instead of screening for Salmonella spp. or for isolates showing resistance to individual antibiotics. In that sense, massive integration of whole genome sequencing (WGS) technologies in AMR surveillance provides the shortest path to accomplish these goals.


Assuntos
Bovinos/microbiologia , Farmacorresistência Bacteriana , Farmacorresistência Bacteriana Múltipla , Genômica , Aves Domésticas/microbiologia , Salmonella/fisiologia , Animais , México , Salmonella/efeitos dos fármacos
11.
Artigo em Inglês | MEDLINE | ID: mdl-33999792

RESUMO

Four novel independent strains of Streptococcus spp. were isolated from faeces of alpaca (SL1232T), cattle (KCJ4950), and from respiratory tract of wild California sea lions (CSL7508T, CSL7591T). The strains were indole-, oxidase- and catalase-negative, non-spore-forming, non-motile Gram-positive cocci in short and long chains, facultative anaerobes. The 16S rRNA gene of SL1232T and KCJ4950 shared 99.40-99.60% nucleotide similarity to strains of S. equinus, S. lutetiensis, S. infantarius, and the 16S rRNA gene of CSL7508T and CSL7591T demonstrated 98.72 and 98.92% similarity, respectively, to S. marimammalium. All other known Streptococcus species had the 16S rRNA gene sequence similarities of ≤95%. The genomes were sequenced for the novel strains. Average nucleotide identity (ANI) analysis for strains SL1232T and KCJ4950, showed the highest similarity to S. equinus, S. lutetiensis, and S. infantarius with 85.21, 87.17, 88.47, 85.54, 87.47 and 88.89%, respectively, and strains CSL7508T and CSL7591T to S. marimammalium with 87.16 and 83.97%, respectively. Results of ANI were confirmed by pairwise digital DNA-DNA hybridization and phylogeny, which also revealed that the strains belong to three novel species of the genus Streptococcus. Phenotypical features of the novel species were in congruence with closely related members of the genus Streptococcus and gave negative reactions with the tested Lancefield serological groups (A-D, F and G). MALDI-TOF mass spectrometry supported identification of the species. Based on these data, we propose three novel species of the genus Streptococcus, for which the name Streptococcus vicugnae sp. nov. is proposed with the type strain SL1232T (=NCTC 14341T=DSM 110741T=CCUG 74371T), Streptococcus zalophi sp. nov. is proposed with the type strain CSL7508T (=NCTC 14410T=DSM 110742T=CCUG 74374T) and Streptococcus pacificus sp. nov. is proposed with the type strain CSL7591T (=NCTC 14455T=DSM 111148T=CCUG 74655T). The genome G+C content is 36.89, 34.85, and 35.34 % and draft genome sizes are 1906993, 1581094 and 1656080 bp for strains SL1232T, CSL7508T, and CSL7591T, respectively.


Assuntos
Camelídeos Americanos/microbiologia , Bovinos/microbiologia , Filogenia , Leões-Marinhos/microbiologia , Streptococcus/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Sequência de Bases , California , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Florida , Maryland , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Sistema Respiratório/microbiologia , Análise de Sequência de DNA , Streptococcus/isolamento & purificação
12.
Parasit Vectors ; 14(1): 270, 2021 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-34016174

RESUMO

BACKGROUND: The emergence of tick-borne disease is increasing because of the effects of the temperature rise driven by global warming. In Turkey, 19 pathogens transmitted by ticks to humans and animals have been reported. Based on this, this study aimed to investigate tick-borne pathogens including Hepatozoon spp., Theileria spp., Babesia spp., Anaplasma spp., Borrelia spp., and Bartonella spp. in tick samples (n = 110) collected from different hosts (dogs, cats, cattle, goats, sheep, and turtles) by molecular methods. METHODS: To meet this objective, ticks were identified morphologically at the genus level by microscopy; after DNA isolation, each tick sample was identified at the species level using the molecular method. Involved pathogens were then investigated by PCR method. RESULTS: Seven different tick species were identified including Rhipicephalus sanguineus, R. turanicus, R. bursa, Hyalomma marginatum, H. anatolicum, H. aegyptium, and Haemaphysalis erinacei. Among the analyzed ticks, Hepatozoon spp., Theileria spp., Babesia spp., and Anaplasma spp. were detected at rates of 6.36%, 16.3%, 1.81%, and 6.36%, respectively while Borrelia spp. and Bartonella spp. were not detected. Hepatozoon spp. was detected in R. sanguineus ticks while Theileria spp., Babesia spp., and Anaplasma spp. were detected in R. turanicus and H. marginatum. According to the results of sequence analyses applied for pathogen positive samples, Hepatozoon canis, Theileria ovis, Babesia caballi, and Anaplasma ovis were identified. CONCLUSION: Theileria ovis and Anaplasma ovis were detected for the first time to our knowledge in H. marginatum and R. turanicus collected from Turkey, respectively. Also, B. caballi was detected for the first time to our knowledge in ticks in Turkey.


Assuntos
Ixodidae/microbiologia , Ixodidae/parasitologia , Doenças Transmitidas por Carrapatos/veterinária , Anaplasma/genética , Anaplasma/isolamento & purificação , Animais , Babesia/genética , Babesia/isolamento & purificação , Bartonella/genética , Bartonella/isolamento & purificação , Gatos/microbiologia , Gatos/parasitologia , Bovinos/microbiologia , Bovinos/parasitologia , Cães/microbiologia , Cães/parasitologia , Ixodidae/classificação , Ovinos/microbiologia , Ovinos/parasitologia , Theileria/genética , Theileria/isolamento & purificação , Doenças Transmitidas por Carrapatos/microbiologia , Doenças Transmitidas por Carrapatos/parasitologia , Turquia , Tartarugas/microbiologia , Tartarugas/parasitologia
13.
Vet Microbiol ; 258: 109124, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34058524

RESUMO

Multiple outbreaks of Mycoplasma bovis (M. bovis) have been reported in North American bison (Bison bison) in Alberta, Manitoba, Saskatchewan, Nebraska, New Mexico, Montana, North Dakota, and Kansas. M. bovis is mainly spread through direct contact and disseminated via animal movements thus, reliable genotyping is crucial for epidemiological investigations. The present study describes the genotyping of sixty-one M. bovis strains from cattle and bison isolated from different provinces of Canada by multi locus sequence typing (MLST), and multiple-locus variable-number tandem repeat analysis (MLVA). The sixty M. bovis clinical isolates together with the reference strain PG45 were divided into ten sequence types by MLST. Three novel sequence types were identified. Two isolates, one from cattle and one from bison shared the same sequence type, whereas one strain had the same sequence type as PG45. The cattle isolates could be further subdivided in Clade A with two subclades and bison isolates were grouped in Clade B with two subclades. With the exception of one animal, isolates originating from the same animal had the same sequence type. The sixty-one isolates also formed three main clades with several subclades when analyzed by MLVA. A total of 20 VNTR (Variable number tandem repeats) types were distinguished, 8 in cattle and 12 in bison isolates. The results showed multiple sequence types and genotype populations of M. bovis in bison and cattle. The results may further help to understand the evolution of M. bovis and develop strain specific or sequence type diagnostic tools.


Assuntos
Técnicas de Tipagem Bacteriana/veterinária , Búfalos/microbiologia , Bovinos/microbiologia , Tipagem de Sequências Multilocus/veterinária , Mycoplasma bovis/genética , Filogenia , Animais , Repetições Minissatélites
14.
Toxins (Basel) ; 13(3)2021 03 13.
Artigo em Inglês | MEDLINE | ID: mdl-33805744

RESUMO

Clostridium perfringens is a Gram-positive bacterium that possess seven toxinotypes (A, B, C, D, E, F, and G) that are responsible for the production of six major toxins, i.e., α, ß, ε, ι, CPE, and NetB. The aim of this study is to find out the occurrence of toxinotypes in buffalo and cattle of Punjab province in Pakistan and their corresponding toxin-encoding genes from the isolated toxinotypes. To accomplish this aim, six districts in Punjab province were selected (i.e., Lahore, Sahiwal, Cheecha Watni, Bhakkar, Dera Ghazi Khan, and Bahawalpur) and a total of 240 buffalo and 240 cattle were selected for the collection of samples. From isolation and molecular analysis (16S rRNA), it was observed that out of seven toxinotypes (A-G), two toxinotypes (A and D) were found at most, whereas other toxinotypes, i.e., B, C, E, F, and G, were not found. The most frequently occurring toxinotype was type A (buffalo: 149/240; cattle: 157/240) whereas type D (buffalo: 8/240 cattle: 7/240) was found to occur the least. Genes encoding toxinotypes A and D were cpa and etx, respectively, whereas genes encoding other toxinotypes were not observed. The occurrence of isolated toxinotypes was studied using response surface methodology, which suggested a considerable occurrence of the isolated toxinotypes (A and D) in both buffalo and cattle. Association between type A and type D was found to be significant among the isolated toxinotypes in both buffalo and cattle (p ≤ 0.05). Correlation was also found to be positive and significant between type A and type D. C. perfringens exhibits a range of toxinotypes that can be diagnosed via genotyping, which is more reliable than classical toxinotyping.


Assuntos
Toxinas Bacterianas/genética , Búfalos/microbiologia , Bovinos/microbiologia , Clostridium perfringens/genética , Perfilação da Expressão Gênica , Toxicogenética , Transcriptoma , Animais , Toxinas Bacterianas/metabolismo , Toxinas Bacterianas/toxicidade , Clostridium perfringens/metabolismo , Regulação Bacteriana da Expressão Gênica , Paquistão , Ribotipagem
15.
J Sci Food Agric ; 101(15): 6220-6227, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33913172

RESUMO

BACKGROUND: The effect of live yeast Saccharomyces cerevisiae strain CNCM I-1077 (SC) on the ruminal degradability of different forages commonly found in dairy diets in South America was evaluated. We also assessed if SC supplementation interacts with forage group to affect ruminal fiber degradability. Four non-lactating rumen-cannulated Holstein cows were randomly assigned to two treatment sequences: Control-SC-Control or SC-Control-SC, in a switchback design, with three 30-day periods. Cows in the SC treatment were supplied with 1 × 1010 colony-forming units of yeast daily via rumen cannula. In situ degradability of dry matter (DM) and neutral detergent fiber (aNDF) was measured in 15 forages collected in South America. Forages were assigned to one of three groups: corn silages; tropical grasses (sugarcane silages and tropical grass silages); and temperate grasses and alfalfa (oat silages, ryegrass silages, alfalfa silage, and alfalfa hay). RESULTS: Cows supplemented with SC had higher (P = 0.05) counts of yeasts and lower (P = 0.03) concentration of lactate in rumen fluid. There was no interaction between forage group and yeast supplementation (P > 0.10) on in situ degradability. The SC increased DM (by 4.6%) and aNDF degradation (by 10.3%) at 24 h of incubation (P < 0.05). Metabolomics revealed that a chemical entity (C17 H29 N6 O3 , m/z 365.2284 [M + H]+ ) from the family of lipids and related molecules was suppressed in the rumen fluid of cows supplemented with SC. CONCLUSION: The SC supplementation improved DM and aNDF degradability regardless of the forage group. © 2021 Society of Chemical Industry.


Assuntos
Bovinos/metabolismo , Fibras na Dieta/metabolismo , Probióticos/administração & dosagem , Rúmen/metabolismo , Saccharomyces cerevisiae/metabolismo , Ração Animal/análise , Animais , Bovinos/microbiologia , Suplementos Nutricionais/análise , Fermentação , Medicago sativa/metabolismo , Poaceae/metabolismo , Rúmen/microbiologia , Saccharum/metabolismo , Silagem/análise , Zea mays/metabolismo
16.
Int J Antimicrob Agents ; 57(6): 106350, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33910096

RESUMO

Colistin is a last-resort antimicrobial used to treat infections caused by multidrug-resistant Gram-negative bacilli (MDR-GNB). The emergence of colistin resistance, particularly linked to mobile genetic elements including the mcr genes, is a major threat to the management of MDR-GNB infections. The aim of this study was to assess the presence of mcr genes in a collection of 40 colistin-resistant commensal Escherichia coli isolated from healthy pigs, cattle and poultry in Belgium between 2012 and 2016. All isolates carried at least one mcr gene. The genes mcr-1 to -5 were observed in this collection. Different replicons associated with mcr genes were identified, including IncHI2/IncHI2A associated with mcr-1, IncX4 associated with mcr-1 and mcr-2, and ColE10 associated with mcr-4. While the occurrence of multiple mcr genes in a single isolate has rarely been reported elsewhere, a triple occurrence (mcr-1, -3 and -5) was found in this study. All isolates were MDR and carried between one and nine different replicons. Seventeen different sequence types were observed among the 40 E. coli isolates. In conclusion, this study revealed the presence of a reservoir of mobile colistin resistance genes (mcr-1 to -5) observed during at least 5 years (2012-2016) in the commensal gut flora of pigs, cattle and poultry in Belgium.


Assuntos
Antibacterianos/farmacologia , Colistina/farmacologia , Farmacorresistência Bacteriana Múltipla , Proteínas de Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Animais , Bélgica/epidemiologia , Bovinos/microbiologia , DNA Bacteriano , Escherichia coli/isolamento & purificação , Fezes/microbiologia , Genótipo , Proteínas de Membrana/genética , Testes de Sensibilidade Microbiana , Aves Domésticas/microbiologia , Suínos/microbiologia , Transferases (Outros Grupos de Fosfato Substituídos)/genética , Sequenciamento Completo do Genoma
17.
PLoS One ; 16(4): e0245655, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33848298

RESUMO

The ability to accurately identify infected hosts is the cornerstone of effective disease control and eradication programs. In the case of bovine tuberculosis, accurately identifying infected individual animals has been challenging as all available tests exhibit limited discriminatory ability. Here we assess the utility of two serological tests (IDEXX Mycobacterium bovis Ab test and Enfer multiplex antibody assay) and assess their performance relative to skin test (Single Intradermal Comparative Cervical Tuberculin; SICCT), gamma-interferon (IFNγ) and post-mortem results in a Northern Ireland setting. Furthermore, we describe a case-study where one test was used in conjunction with statutory testing. Serological tests using samples taken prior to SICCT disclosed low proportions of animals as test positive (mean 3% positive), despite the cohort having high proportions with positive SICCT test under standard interpretation (121/921; 13%) or IFNγ (365/922; 40%) results. Furthermore, for animals with a post-mortem record (n = 286), there was a high proportion with TB visible lesions (27%) or with laboratory confirmed infection (25%). As a result, apparent sensitivities within this cohort was very low (≤15%), however the tests succeeded in achieving very high specificities (96-100%). During the case-study, 7/670 (1.04%) samples from SICCT negative animals from a large chronically infected herd were serology positive, with a further 17 animals being borderline positive (17/670; 2.54%). Nine of the borderline animals were voluntarily removed, none of which were found to be infected post-mortem (no lesions/bacteriology negative). One serology test negative animal was subsequently found to have lesions at slaughter with M. bovis confirmed in the laboratory.


Assuntos
Bovinos/sangue , Mycobacterium bovis/isolamento & purificação , Tuberculose Bovina/sangue , Tuberculose Bovina/diagnóstico , Animais , Bovinos/microbiologia , Feminino , Masculino , Irlanda do Norte/epidemiologia , Testes Sorológicos , Teste Tuberculínico , Tuberculose Bovina/epidemiologia , Tuberculose Bovina/microbiologia
18.
Appl Environ Microbiol ; 87(12): e0048521, 2021 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-33863705

RESUMO

Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as one of the primary sources of Salmonella-related outbreaks. Pathogenicity and antibiotic resistance of Salmonella are highly serotype and subpopulation specific, which makes it essential to understand high-resolution Salmonella population dynamics in cattle. Time of year, source of cattle, pen, and sample type (i.e., feces, hide, or lymph nodes) have previously been identified as important factors influencing the serotype distribution of Salmonella (e.g., Anatum, Lubbock, Cerro, Montevideo, Kentucky, Newport, and Norwich) that were isolated from a longitudinal sampling design in a research feedlot. In this study, we performed high-resolution genomic comparisons of Salmonella isolates within each serotype using both single-nucleotide polymorphism-based maximum-likelihood phylogeny and hierarchical clustering of core-genome multilocus sequence typing. The importance of the aforementioned features in clonal Salmonella expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each subpopulation. Our findings indicate that clonal expansion of Salmonella strains in cattle was mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle, i.e., regardless of sampling time and sample type (i.e., feces, lymph node, or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carryover contributions of existing strains of Salmonella and their bacteriophages. IMPORTANCE Salmonella serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of Salmonella, and are often associated with clonal expansion. This makes understanding the subpopulation dynamics of Salmonella in cattle critical for effective mitigation. There remains a gap in the literature concerning subpopulation dynamics within Salmonella serotypes in feedlot cattle from the beginning of feeding up until slaughter. Here, we explore Salmonella population dynamics within each serotype using core-genome phylogeny and hierarchical classifications. We used machine learning to quantitatively parse the relative importance of both hierarchical and longitudinal clustering among cattle host samples. Our results reveal that Salmonella populations in cattle are highly clonal over a 6-month study period and that clonal dissemination of Salmonella in cattle is mainly influenced spatially by experimental block and pen, as well by the geographical origin of the cattle.


Assuntos
Doenças dos Bovinos/microbiologia , Bovinos/microbiologia , Farmacorresistência Bacteriana/genética , Salmonelose Animal/microbiologia , Salmonella enterica/genética , Criação de Animais Domésticos , Animais , Antibacterianos/farmacologia , Cefalosporinas/farmacologia , Dissacarídeos/farmacologia , Fezes/microbiologia , Genômica , Compostos Heterocíclicos/farmacologia , Aprendizado de Máquina , Filogenia , Polimorfismo de Nucleotídeo Único , Sorogrupo
19.
J Biol Chem ; 296: 100497, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33675752

RESUMO

The CRISPR/Cas9 system has been used in a wide range of applications in the production of gene-edited animals and plants. Most efforts to insert genes have relied on homology-directed repair (HDR)-mediated integration, but this strategy remains inefficient for the production of gene-edited livestock, especially monotocous species such as cattle. Although efforts have been made to improve HDR efficiency, other strategies have also been proposed to circumvent these challenges. Here we demonstrate that a homology-mediated end-joining (HMEJ)-based method can be used to create gene-edited cattle that displays precise integration of a functional gene at the ROSA26 locus. We found that the HMEJ-based method increased the knock-in efficiency of reporter genes by eightfold relative to the traditional HDR-based method in bovine fetal fibroblasts. Moreover, we identified the bovine homology of the mouse Rosa26 locus that is an accepted genomic safe harbor and produced three live-born gene-edited cattle with higher rates of pregnancy and birth, compared with previous work. These gene-edited cattle exhibited predictable expression of the functional gene natural resistance-associated macrophage protein-1 (NRAMP1), a metal ion transporter that should and, in our experiments does, increase resistance to bovine tuberculosis, one of the most detrimental zoonotic diseases. This research contributes to the establishment of a safe and efficient genome editing system and provides insights for gene-edited animal breeding.


Assuntos
Bovinos/genética , Clonagem de Organismos , Resistência à Doença , Edição de Genes , Loci Gênicos , Tuberculose Bovina/genética , Animais , Bovinos/microbiologia , Reparo do DNA por Junção de Extremidades , Tuberculose Bovina/metabolismo
20.
BMC Vet Res ; 17(1): 116, 2021 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-33685450

RESUMO

BACKGROUND: Selection pressure exerted by use of antibiotics in both human and veterinary medicine is responsible for increasing antimicrobial resistance (AMR). The objectives of this study were to better understand antimicrobial use in pigs, beef cattle, and poultry on farms on Guadeloupe, French West Indies, and to acquire data on AMR in Escherichia coli in these food-producing animals. A cross-sectional survey was conducted at 45 farms on Guadeloupe, and practical use of antimicrobials was documented in declarative interviews between March and July 2018. A total of 216 fecal samples were collected between January 2018 and May 2019, comprising 124 from pigs, 75 from beef cattle, and 17 from poultry litter. E. coli isolates were obtained for further testing by isolation and identification from field samples. Antimicrobial susceptibility testing and screening for blaCTX-M, blaTEM, tetA, and tetB resistance genes by polymerase chain reaction on extracted genomic DNA were performed. RESULTS: The study showed rational use of antimicrobials, consisting of occasional use for curative treatment by veterinary prescription. Tetracycline was the most commonly used antimicrobial, but its use was not correlated to E. coli resistance. Extended-spectrum ß-lactamase (ESBL) E. coli isolates were detected in 7.3% of pigs, 14.7% of beef cattle, and 35.3% of poultry. blaCTX-M-1 was the predominant gene found in ESBL-E. coli isolates (68.8%), followed by blaCTX-M-15 (31.3%). CONCLUSION: Despite rational use of antimicrobials, the rate of ESBL-E. coli in food-producing animals in Guadeloupe, although moderate, is a concern. Further studies are in progress to better define the genetic background of the ESBL-E. coli isolates.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Escherichia coli/genética , Animais , Antibacterianos/administração & dosagem , Bovinos/microbiologia , Estudos Transversais , Escherichia coli/efeitos dos fármacos , Infecções por Escherichia coli/veterinária , Fezes/microbiologia , Guadalupe , Aves Domésticas/microbiologia , Suínos/microbiologia , beta-Lactamases/metabolismo
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