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Objectives: Antimicrobial drugs are frequently administered in veal calves, but investigations on associations with antimicrobial susceptibility of bacteria are scarce and convey partly contradictory findings. The aim of this study was to investigate associations of antimicrobial use (AMU) during the fattening period with antimicrobial susceptibility shortly before slaughter.Methods: Detailed treatment data of 1905 veal calves from 38 farms were collected prospectively during monthly farm visits for 1 year (n = 1864 treatments, n = 535 visits); 1582 Escherichia coli, 1059 Pasteurella multocida and 315 Mannheimia haemolytica were isolated from rectal and nasopharyngeal swabs collected before slaughter and subjected to antimicrobial susceptibility testing by microdilution. Associations of antimicrobial treatments with resistant isolates were investigated at the calf level.Results: Associations of AMU with antimicrobial resistance were observed using generalized linear models. For E. coli, the odds of being resistant were increased with increased AMU (OR 1.36 when number of treatments >1, P = 0.066). Use of tetracyclines was associated with resistance to tetracycline (OR 1.86, P < 0.001) and use of penicillins was associated with resistance to ampicillin (OR 1.66, P = 0.014). No significant associations were observed for P. multocida (use of aminoglycosides: OR 3.66 for resistance to spectinomycin, P = 0.074). For M. haemolytica, the odds of being resistant were increased with increased AMU (OR 4.63, P < 0.001), and use of tetracyclines was associated with resistance to tetracycline (OR 6.49, P < 0.001).Conclusions: Occurrence of resistant bacteria shortly before slaughter was associated with AMU in veal calves. Prudent and appropriate use may contribute to limit the selection of resistant bacteria on veal farms. [ABSTRACT FROM AUTHOR]

This study aimed to determine the taxonomic status of a new group of bovine strains of the genus Acinetobacter characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and rpoB gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome de novo sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known Acinetobacter species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05-3.28 Mb) and 1-6 extrachromosomal elements (1.43-122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37-46 °C differed from that of Acinetobacter baumannii. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of strA/strB, tet(Y), and sul2 genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name Acinetobacter thermotolerans sp. nov. The type strain is ANC 7454 T (= CCM 9356 T  = CCUG 77195 T  = CNCTC 8200 T )., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Background: The addition of wine lees to diets can make up for the deficiencies caused by traditional forages in beef cattle farming. However, the effects of different wine lees ratios on average daily weight, gastrointestinal microbial community structure and metabolites in Guanling crossbred cattle have been rarely studied. This study assessed the effects of feeds containing wine lees on weight gain, gastrointestinal microbial community structure, and metabolites in Guanling crossbred cattle and elucidated the metabolic responses induced by wine lees. Eighteen cows were randomly assigned to receive fed concentrate (C group), feed containing 15% wine lees (group A), or feed containing 30% wine lees (group B) for 60 days., Results: The average daily weight gain of group A and group B increased by 76.75% and 57.65%, respectively, compared with group C. Microbial community analysis showed that wine lees increased the abundance of Prevotella&#95;1 in the rumen, decreased the abundance of Ruminococcaceae UCG 011 and Lachnospiraceae&#95;FCS020&#95;group in the rumen, and increased the abundance of Tyzzerella&#95;4, Family&#95;Xlll&#95;AD3011&#95;group, Granulicella, and Eisenbergiella in the cecum. Metabolomics analyses showed that wine lees decreased the concentrations of indole-3-ethanol in the rumen, and complexity cecal metabolism. Notably, linoleic acid metabolism was significantly enriched in both the rumen and cecum. Mantel test analyses indicated that the adverse effects of WL were reduced by stimulating the metabolism of linoleic acid, α-linolenic acid, and tryptophan, and these changes were mediated by intestinal microorganisms. The Guanling cattle cecum was enriched for several unfavorable metabolic pathways when wine lees concentrations reached 30%, which increased the likelihood of intestinal lesions., Conclusion: This study shows that WL supplementation alters gut microbiota and metabolic pathways, improving cattle growth and health. Moderate WL levels (15%) enhance gut health and beneficial pathways (e.g., linoleic and alpha-linolenic acid metabolism). However, higher WL inclusion (30%) may activate adverse pathways, raising the risk of intestinal damage. To maximize benefits and minimize risks, WL levels should be carefully managed., (© 2024. The Author(s).)

Ruminants play an important part in the food supply chain, and manipulating rumen microbiota is important to maximising ruminants' production. Rumen microbiota through rumen fermentation produces as major end products volatile fatty acids that provide animal's energy requirements, and microbial CP. Diet is a key factor that can manipulate rumen microbiota, and each variation of the physical and chemical composition creates a specific niche that selects specific microbes. Alteration in the chemical composition of forage, the addition of concentrates in the diet, or the inclusion of plant extract and probiotics, can induce a change in rumen microbiota. High-throughput sequencing technologies are the approaches utilised to investigate the microbial system. Also, the application of omics technologies allows us to understand rumen microbiota composition and these approaches are useful to improve selection programmes. The aim of this review was to summarise the knowledge about rumen microbiota, its role in nutrient metabolism, and how diet can influence its composition., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Achromobacter marplatensis strain YKS2 isolated from the yak rumen has the feature of producing cellulose. This study aims to analyze the genome and safety of strain YKS2 in vivo, considering its future research and application prospects. The genome of strain YKS2 was sequenced and used for genomic in silico studies. The administration of strain YKS2 in three doses was carried out on mice for 3 days of oral and 7 days of clinical observation tests. The BW, FI, organ indices, gut microbiota, and histological appearances of organs and intestines, along with hematological parameters and serum biochemistry, were measured in mice. The chromosome size of strain YKS2 was 6,588,568 bp, with a GC content of 65.27%. The 6058 coding sequences of strain YKS2 without plasmid were predicted and annotated and have multiple functions. The mice in all groups were alive, with good mental states and functional activities. Compared with the control group, there was no significant difference in the three dose groups on BW, FI, hematological parameters (WBC, LYM, etc.), and serum biochemistry (ALB, ALT, etc.). No abnormalities were observed in the main visceral organs, intestinal tissue, and V/C value in groups. However, the IEL number of duodenum and gut microbiota diversity (Shannon's index) in the high-dose group was significantly higher than in the control group (p < 0.05). Besides, the low dose of strain YKS2 also significantly affected the bacterial abundance of Firmicutes, Actinobacteria, and desulphurizing Bacteroidetes at the phylum level. There was no significant effect at genus levels in groups. In conclusion, the study revealed the genome and potential functional genes of strain YKS2, which is beneficial to understanding the features of the A. marplatensis strain and proved strain YKS2 to be without acute toxicity to mice. However, a long-term feeding toxicity experiment in vivo should be performed to further ensure its potential application value strain in the animal industry., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Toxoplasma gondii is the agent of toxoplasmosis, which is common to both humans and cattle. That is why the goal of work was to study the spreading of the agent of toxoplasmosis among cattle in certain regions of Ukraine, which in turn will make it possible to predict the appearance of the disease among people and prevent the development of its clinical signs. Whole blood or serum samples of cattle of different ages and sexes from farms in Kyiv, Zhytomyr, Khmelnytskyi and Lviv regions of Ukraine were sent to the laboratory for research. The presence of total antibodies to T. gondii was determined in the serum of the animals. To do this, we used the method of enzyme-linked immunosorbent assay using test kits from different manufacturers in accordance with the guidelines. In general, the prevalence of T. gondii among cattle in Kyiv, Zhytomyr, Khmelnytskyi and Lviv regions of Ukraine according to the results of studies was 10.3% (95% confidence interval: 6.7-15.1). At the same time, the study of animals was carried out in two stages, in 2014 and 2018, and the prevalence did not differ significantly. Thus, in 2014, according to the results of research, a positive reaction to the agent of toxoplasmosis was detected in 10 samples or 13.9% (95% confidence interval: 7.3-23.4), while in 2018 this figure was 11 samples or 8.4% (95% confidence interval: 4.5-14.1) of the studied animals. Also, in 2014 and 2018 studies found that the highest level of seroprevalence of the agent of toxoplasmosis in both years of research was registered in cattle from farms of Zhytomyr and Kyiv regions was 11.9% (95% confidence interval: 4.5-24.4) and 11% (95% confidence interval: 5.9-18.3), respectively. During the conducted research, an increase in the prevalence of T. gondii with the age of animals was statistically significant. Among animals under six months of age, of the 65 serum samples tested, 3 tested positively to the agent (4.6; 95% confidence interval: 1.2-12.1), while in the group of animals older than three years (49 cows) 10 samples were positively responded (20.4; 95% confidence interval: 10.9-33.4) compared to the previous group of animals, the P-value was 0.0114. So, the data obtained indicate the presence of the agent of toxoplasmosis among cattle in Ukraine, which requires further study and development of approaches to prevent human infection when eating meat and dairy products of positively reacting animals [ABSTRACT FROM AUTHOR]

Bovine brucellosis caused by the organism Brucella abortus is a chronic infectious disease of public health and economic significance. Studies on prevalence of bovine brucellosis in Abia State are scarce. Therefore, a cross-sectional study was conducted to determine the prevalence of bovine brucellosis in the State. Blood samples were collected from 212 cattle from various parts of the State and sera subjected to Rose Bengal Plate Test (RBPT) to detect antibodies against Brucella. Overall sero-prevalence of 13.7% was reported. The prevalence was higher in female cattle (24.2%) than in males (11%). Red Bororo showed higher seropositivity (26.7%) than other breeds screened. Sero-prevalence was higher in the semi-intensively managed animals (27.8%) than in extensively reared cattle. Similarly, cattle aged 2 to 3 years recorded a higher prevalence (25%) than others. However, there was no statistically significant association between the seroprevalence of brucellosis and sex (P= 0.05), age (P=0.82), breed (P=0.25), and management system (P=0.07 ). The detection of brucellosis in cattle poses a very significant public health risk in Abia state, and so it is important to carry out awareness campaigns to enlighten cattle handlers and the general public of its public health significance. [ABSTRACT FROM AUTHOR]

Ruminant livestock are major contributors to anthropogenic methane emissions in the United States and worldwide. Enteric methane is generated by methanogenic archaea residing in ruminant digestive tracts. Information on when methanogens colonize the gut and when they begin to interact with bacteria during the early phases of the ruminant life cycle is less explored. The objectives of this study were (i) to investigate the composition of the methanogenic archaeal community at birth and through the weaning transition and (ii) to determine if and when the methanogenic archaea begin to interact with bacteria in the lower gut of neonatal dairy calves. Ten female Holstein calves (approximately 45kg birth weight) were enrolled in the study. Fecal samples were collected every two weeks (Wk 2, 4, 6, 8, 10, and 12) between birth and weaning and analyzed for methanogenic archaeal diversity via 16S rRNA amplicon sequencing and quantitative real-time PCR (RT-qPCR). Estimates of alpha diversity (Observed species, and Shannon diversity index) and beta diversity (weighted and unweighted UniFrac distances) showed significant differences (P < 0.05) between archaeal communities across timepoints. Both 16S rRNA amplicon sequencing and RT-qPCR analyses revealed Methanobrevibacter was the most prevalent genus at Wk2, Wk4, and Wk6, whereas Methanosphaera gradually increased with time and was most abundant at Wk10 and Wk12. Correlation analysis revealed that Methanobrevibacter and Methanosphaera were inversely correlated with each other and formed distinct cohorts with specific bacterial lineages similar to those reported in the mature rumen, thus revealing that these associations are established during the preweaning period. Therefore, the preweaning period presents a window of opportunity to interfere with early-life methanogenic colonization with the ultimate goal of reducing enteric methane emissions without perturbing ruminal function later in the life of dairy cattle., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Indugu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Along bacteria, yeasts are common in forages and forage fermentations as spoilage microbes or as additives, yet few studies exist with species-level data on these fungi's occurrence in feedstuff. Active dry yeast and other yeast-based products are also common feed additives in animal husbandry. Here, we aimed to characterize both fermented and non-fermented milking cow feedstuff samples from Hungary to assess their microbial diversity in the first such study from Central Europe., Results: We applied long-read bacterial metabarcoding to 10 fermented and 25 non-fermented types of samples to assess bacterial communities and their characteristics, surveyed culturable mold and yeast abundance, and identified culturable yeast species. Fermented forages showed the abundance of Aerococcaceae, Bacillaceae, Brucellaceae, Lactobacillaceae, Staphylococcaceae, and Thermoactinomycetaceae, non-fermented ones had Cyanothecaceae, Enterobacteriaceae, Erwiniaceae, Gomontiellaceae, Oxalobacteraceae, Rhodobiaceae, Rickettsiaceae, and Staphylococcaceae. Abundances of bacterial families showed mostly weak correlation with yeast CFU numbers, only Microcoleaceae (positive) and Enterococcaceae and Alcaligenaceae (negative correlation) showed moderate correlation. We identified 14 yeast species, most commonly Diutina rugosa, Pichia fermentans, P. kudriavzevii, and Wickerhahomyces anomalus. We recorded S. cerevisiae isolates only from animal feed mixes with added active dry yeast, while the species was completely absent from fermented forages. The S. cerevisiae isolates showed high genetic uniformity., Conclusion: Our results show that both fermented and non-fermented forages harbor diverse bacterial microbiota, with higher alpha diversity in the latter. The bacterial microbiome had an overall weak correlation with yeast abundance, but yeasts were present in the majority of the samples, including four new records for forages as a habitat for yeasts. Yeasts in forages mostly represented common species including opportunistic pathogens, along with a single strain of Saccharomyces used as a feed mix additive., (© 2024. The Author(s).)

The rumen microbiome is the focus of a growing body of research, mostly based on investigation of rumen fluid samples collected once from each animal. Exploring the temporal stability of rumen microbiome profiles is imperative, as it enables evaluating the reliability of findings obtained through single-timepoint sampling. We explored the temporal stability of rumen microbiomes considering taxonomic and functional aspects across the 7-month growing-finishing phase spanning 6 timepoints. We identified a temporally stable core microbiome, encompassing 515 microbial genera (e.g., Methanobacterium) and 417 microbial KEGG genes (e.g., K00856-adenosine kinase). The temporally stable core microbiome profiles collected from all timepoints were strongly associated with production traits with substantial economic and environmental impact (e.g., average daily gain, daily feed intake, and methane emissions); 515 microbial genera explained 45-83%, and 417 microbial genes explained 44-83% of their phenotypic variation. Microbiome profiles influenced by the bovine genome explained 54-87% of the genetic variation of bovine traits. Overall, our results provide evidence that the temporally stable core microbiome identified can accurately predict host performance traits at phenotypic and genetic level based on a single timepoint sample taken as early as 7 months prior to slaughter., (© 2024. The Author(s).)

This study provides an emended description of Acinetobacter faecalis, a species previously described based on a single isolate (YIM 103518 T ) from elephant feces in China. Our emended description is based on 15 novel isolates conspecific with the A. faecalis type strain, obtained from eight cattle farms in the Czech Republic. The A. faecalis strains have relatively small genomes (≈2.5-2.7 Mbp), with a GC content of 36.3-36.7 mol%. Core genome-based phylogenetic analysis showed that the 15 strains, together with the type strain of A. faecalis, form a distinct and internally coherent phylogroup within the genus. Pairwise genomic ANIb values for the 16 A. faecalis strains were 97.32-99.04 %, while ANIb values between the genomes of the 16 strains and those of the other Acinetobacter spp. were ≤ 86.2 %. Analysis of whole-cell MALDI-TOF mass spectra supported the distinctness and cohesiveness of the taxon. The A. faecalis strains could be differentiated from the other validly named Acinetobacter spp. by the absence of hemolytic activity along with their ability to grow at 37 °C and on L-aspartate, ethanol, and L-glutamate but not at 41 °C or on adipate or 2,3-butanediol. Reduced susceptibility to sulfamethoxazole, trimethoprim and/or streptomycin was shown in eight strains, along with the presence of corresponding antibiotic resistance genes. In conclusion, this study provides a comprehensive description of A. faecalis and demonstrates its occurrence in cattle feces. Though the ecological role of A. faecalis remains unknown, our results show its ability to acquire antibiotic resistance genes, likely as an adaptation to antibiotic selection pressure in livestock farms., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

In ruminants, the rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides through the coordinated activities of a diverse microbial community. Bacteroidota is a major phylum in this bovine rumen microbiota. They contain several clusters of genes called polysaccharide utilization loci (PULs) that encode proteins working in concert to capture, degrade, and transport polysaccharides. Despite the critical role of SusD-like proteins for efficient substrate transport, they remain largely unexplored. Here, we present the biochemical characterization of a SusD-like protein encoded by a β-glucan utilization locus from an Escherichia coli metagenomic clone previously isolated by functional screening of the bovine rumen microbiome. In this study, we show that clone 41O1 can grow on laminaritriose, cellotriose, and a mixture of cellobiosyl-cellobiose and glucosyl-cellotriose as sole carbon sources. Based on this, we used various in vitro analyses to investigate the binding ability of 41O1&#95;SusD-like towards these oligosaccharides and the corresponding polysaccharides. We observed a clear binding affinity for β-1,6 branched β-1,3-glucans (laminarins, yeast β-glucan) and laminaritriose. Comparison of the AlphaFold2 model of 41O1&#95;SusD-like with its closest structural homologs highlights a similar pattern of substrate recognition. In particular, three tryptophan residues are shown to be crucial for laminarin recognition. In the context of the cow rumen, we discuss the possible substrates targeted by the 41O1&#95;PUL, such as the (1,3;1,4)-β-d-glucans present in cereal grains or the β-1,3- and (1,3;1,6)-β-d-glucans that are components of the cell wall of ruminal yeasts.IMPORTANCEThe rumen microbiota can majorly impact overall animal health, feed efficiency, and release of harmful substances into the environment. This microbiota is involved in the fermentation of organic matter to provide the host with valuable and assimilable nutrients. Bacteroidota efficiently captures, breaks down, and imports complex polysaccharides through the concerted action of proteins encoded by polysaccharide utilization loci (PULs). Within this system, SusD-like protein has proven necessary for the active internalization of the substrate. Nevertheless, the vast majority of SusD-like proteins characterized to date originate from cultured bacteria. With regard to the diversity and importance of uncultured bacteria in the rumen, further studies are required to better understand the role of polysaccharide utilization loci in ruminal polysaccharide degradation. Our detailed characterization of the 41O1&#95;SusD-like therefore contributes to a better understanding of the carbohydrate metabolism of an uncultured Bacteroides from the cow rumen., Competing Interests: The authors declare no conflict of interest.

Microbiota analyses are key to understanding the bacterial communities within dairy cattle, but the impact of different storage conditions on these analyses remains unclear. This study sought to examine the effects of freezing at -80°C immediately after collection, refrigeration at 4°C for three days and seven days and absolute ethanol preservation on the microbiota diversity of pooled fecal samples from dairy cattle. Examining 16S rRNA gene sequences, alpha (Shannon, Pielou evenness, observed features and Faith PD indices) and beta (Bray-Curtis, βw and Weighted UniFrac) diversity were assessed. The effects of storage conditions on these metrics were evaluated using linear mixed models and PERMANOVA, incorporating the farm as a random effect. Our findings reveal that 7d and E significantly altered the Shannon index, suggesting a change in community composition. Changes in Pielou evenness for 3d and 7d storage when compared to 0d were found, indicating a shift in species evenness. Ethanol preservation impacted both observed features and Faith PD indices. Storage conditions significantly influenced Bray-Curtis, βw, and Weighted UniFrac metrics, indicating changes in community structure. PERMANOVA analysis showed that these storage conditions significantly contributed to microbiota differences compared to immediate freezing. In conclusion, our results demonstrate that while refrigeration for three days had minimal impact, seven days of refrigeration and ethanol preservation significantly altered microbiota analyses. These findings highlight the importance of sample storage considerations in microbiota research., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Jaramillo-Jaramillo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The performance of dairy cows is influenced by the microbial communities hosted within their digestive tract. While the rumen microbiota has long been associated with host phenotypes, the impact of the faecal microbiota remains elusive. In this study, we collected 697 faecal samples from commercial Holstein cows and analysed them with 16S rRNA gene analyses. For each animal, routinely recorded data, i.e., milk yield, fat yield, protein yield, fat content, protein content, and an aggregate production trait (pINEL) based on the French economic dairy index, were available to assess the links between the faecal microbiota and host production. Our findings revealed a strong and significant association between the structure of the bacterial and prokaryote community (β-diversity) and dairy production. In addition, differential abundance analyses identified 48 genera whose abundances were significantly associated with pINEL, milk, fat and protein yield. Among these genera, the increased abundance of Bifidobacterium, and particularly an amplicon sequence variant with a 16S rRNA V3-V4 gene region identical to B. globosum and B. pseudolongum, was found to be the most important for high-yielding animals. Bifidobacterium seemed to be a potential key member of the bovine faecal microbiota that should be further investigated. Conversely, the p-1088-a5 gut group genus was found more abundant in low-productive cows. In conclusion, this study demonstrates significant associations between the faecal microbiota and the performance of dairy cows at the whole lactation scale. A better understanding of the physiology of the gut microbiota could help to improve dairy cow production., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

The development and growth of animals coincide with the establishment and maturation of their microbiotas. To evaluate the respiratory and fecal microbiotas of beef calves from birth to weaning, a total of 30 pregnant cows, and their calves at birth, were enrolled in this study. Deep nasal swabs and feces were collected from calves longitudinally, starting on the day of birth and ending on the day of weaning. Nasopharyngeal, vaginal, and fecal samples were also collected from cows, and the microbiotas of all samples were analyzed. The fecal microbiota of calves was enriched with Lactobacillus during the first 8 weeks of life, before being displaced by genera associated with fiber digestion, and then increasing in diversity across time. In contrast, the diversity of calf respiratory microbiota generally decreased with age. At birth, the calf and cow nasal microbiotas were highly similar, indicating colonization from dam contact. This was supported by microbial source-tracking analysis. The structure of the calf nasal microbiota remained similar to that of the cows, until weaning, when it diverged. The changes were driven by a decrease in Lactobacillus and an increase in genera typically associated with bovine respiratory disease, including Mannheimia , Pasteurella , and Mycoplasma . These three genera colonized calves early in life, though Mannheimia was initially transferred from the cow reproductive tract. Path analysis was used to model the interrelationships of calf respiratory and fecal microbiotas. It was observed that respiratory Lactobacillus and fecal Oscillospiraceae UCG-005 negatively affected the abundance of Mannheimia or Pasteurella .IMPORTANCEIn beef cattle production, bovine respiratory disease (BRD) accounts for most of the feedlot morbidities and mortalities. Metaphylaxis is a common management tool to mitigate BRD, however its use has led to increased antimicrobial resistance. Novel methods to mitigate BRD are needed, including microbiota-based strategies. However, information on the respiratory bacteria of beef calves prior to weaning was limited. In this study, it was shown that the microbiota of cows influenced the initial composition of both respiratory and fecal microbiotas in calves. While colonization of the respiratory tract of calves by BRD-associated genera occurred early in life, their relative abundances increased at weaning, and were negatively correlated with respiratory and gut bacteria. Thus, microbiotas of both the respiratory and gastrointestinal tracts have important roles in antagonism of respiratory pathogens and are potential targets for enhancing calf respiratory health. Modulation may be most beneficial, if done prior to weaning, before opportunistic pathogens establish colonization., Competing Interests: The authors declare no conflict of interest.

Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Aim: Cattle is one of the main sources of food supply chain for humans in most countries. The present study aimed to identify the infection rates for Toxoplasma gondii, Neospora caninum, and Sarcocystis spp. by polymerase chain reaction (PCR) method in native slaughtered cattle in Kashan, central Iran. Materials and Methods: Totally, 159 diaphragm, esophagus, and muscle samples (53 samples of each) were collected from native beef cattle from Kashan slaughterhouse, central Iran. The genomic DNA was extracted, and PCR method was used separately for detection of N. caninum, Sarcocystis, and T. gondii species using specific primers. Finding: Sarcocystis was found in 84.9% of muscles, 83% of esophagus, and 84.9% of diaphragm samples. Mixed infection (Sarcocystis cruzi–Sarcocystis hominis) was the most common infection, followed by S. cruzi and S. hominis. Sarcocystis hirsuta was not detected in any samples. T. gondii was detected only in three (5.7%) out of the 53 muscle tissues samples of cattle. N. caninum was found in 18.9% of muscles, 24.5% of esophagus, and 28.3% of diaphragm samples. One of the cattle had coinfection to Neospora, Toxoplasma, and Sarcocystis in muscles simultaneously. There was no statistically significant difference between infection rates and age as well as sex in each organ. Conclusion: This study revealed a low prevalence rate of T. gondii, but a high prevalence of infection to N. caninum and S. cruzi or mixed infection of S. cruzi with S. hominis among slaughtered cattle. Prevention measures such as keeping away dogs from cattle grazing are recommended. [ABSTRACT FROM AUTHOR]

Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces ( n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome ( P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days ( P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella -related ASVs decreased after exposure, while ASVs belonging to Acinetobacter , Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species., Competing Interests: The authors declare no conflict of interest.

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency., (© 2024. The Author(s), under exclusive licence to Microbiological Society of Korea.)

Species of the genus Sarcocystis are recognized as protozoan parasites infecting a wide range of animals, including humans. This study aimed to provide data on the occurrence, genetic characterization, and epidemiological significance of Sarcocystis spp. in cattle destined for human consumption in Romania. A total of 117 heart samples from slaughtered cattle in three southwestern Romanian counties (Dolj, Timiș, and Gorj) were analyzed in order to detect sarcocysts, using fresh examination microscopic techniques. Subsequently, the isolated sarcocysts and/or cyst fragments (5–15 per sample) from each infected animal were molecularly characterized. Overall, 17.9% (21/117) of the tested animals were found to be Sarcocystis spp. positive by microscopy. Genetic characterization of Sarcocystis spp. isolates, based on sequence analysis of the 18S rRNA gene, showed the presence of a single species, namely S. cruzi. No correlation was found (p>0.05) between S. cruzi infection and the origin, age, breed, and gender of cattle, but the grazing farming system was positively associated (p=0.031) with the pathogen prevalence and can be considered a risk factor (OR = 3.6) in acquiring infection. To evaluate the possible public health risk, further investigation focused on the processing of other Sarcocystis-specific tissue matrices and evidence of human infections is recommended. This is the first study of bovine Sarcocystis infection in Romania. [ABSTRACT FROM AUTHOR]

Objectives: To explore the dynamics of faecal ESBL/AmpC shedding in dairy cattle and farmers, a study was conducted to examine changes in shedding by individual animals, as well as environmental exposure, and to study the association between antimicrobial use (AMU) and ESBL/AmpC shedding.Methods: The study comprised a cross-sectional survey of 20 farms and a 1 year follow-up of 10 farms. Faecal samples were cultured by both direct inoculation on MacConkey agar + 1 mg/L cefotaxime (MC+) and enrichment in LB-broth + 1 mg/L cefotaxime with subsequent inoculation on MC+. Dust samples were collected using electrostatic dustfall collectors (EDCs). Human faecal samples were collected by the farmers. Presence of ESBL/AmpC genes was screened for by PCR and sequencing. Using mixed effects logistic regression, ORs were determined and population-attributable fractions (PAFs) calculated subsequently.Results: In Phase 1, 8/20 farms were positive for ESBL/AmpC and, with 2 negative farms, were selected for Phase 2. Transient shedding of dominant allele variants was observed in the animals. EDCs and human faecal samples did not reflect what was observed in the animals. AMU was related to shedding of ESBLs in the next sampling moment [OR 14.6 (95% CI 3.0-80.0)] and the PAF of AMU was 0.36 (95% CI 0.08-0.77). Calves fed with colostrum from cows on dry-off therapy was not a risk factor [OR 1.7 (95% CI 0.7-4.9, P = 0.28)].Conclusions: The presence of ESBL/AmpC could only be partly explained by AMU. No link was shown between shedding in cattle and humans or the environment. Interventions should focus on prevention of introduction. [ABSTRACT FROM AUTHOR]

Disease incidence is intimately associated with an animal's commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. An understanding of the animal's resident respiratory pathogens, in the upper nasal cavity prior to weaning, may help us to understand the impact of these pathogens on incidence of respiratory disease. For this research, the overall goal was to characterize bacterial populations associated with calves at an early age and through time periods prior to weaning in 3 herds at the U.S. Meat Animal Research Center. Nasal swabs from the upper nasal cavity were collected at initial vaccination (approximately 40 d of age), preconditioning (approximately 130 d of age), and weaning (approximately 150 d of age) in 2015 and 2016. DNA was extracted from nasal swabs and combined into 2 pools of 10 animals for each sampling time point, in each herd, for a total of 6 pools at each sampling time point and 18 pools for all sampling time points within each year. To evaluate and compare the microbiome of each pooled sample, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Alpha and beta diversity were also measured. Overall, microbial communities were different between combinations of sampling year, herd location, and sampling time prior to weaning as shown by beta diversity. Analysis of these specific respiratory pathogens prior to weaning will present a clearer picture of the distribution of microbial populations in animals prior to weaning and not exhibiting clinical signs of respiratory disease. Therefore, evaluation of the animal's resident bacterial populations in the upper nasal cavity during different phases of the beef production system may help us to understand the impact of the microbiome on incidence of respiratory disease in cattle. [ABSTRACT FROM AUTHOR]

Background: There are few data on the epidemiology of infections caused by Streptococcus bovis (Sb). Some studies suggest that both residence in rural areas and contact with livestock could be potential risk factors. Methods: We performed a retrospective study for the period 2005–2016 of all cases of bacteremia caused by Sb in Galicia (a region in the northwest of Spain). The association between the incidence rate of Sb bacteremia and the number of cattle by province and district was analyzed. Results: 677 cases were included with a median age of 76 years, 69.3% males. The most frequent infections were endocarditis (234 cases, 34.5%), primary bacteremia (213 cases, 31.5%) and biliary infection (119 cases, 17.5%). In 252 patients, colon neoplasms were detected (37.2%). S. gallolyticus subsp. gallolyticus was the predominant species (52.3%). Mortality was 15.5% (105 cases). The annual incidence rate was 20.2 cases/106 inhabitants and was correlated with the density of cattle (p < 0.001), but not with rurality. When comparing the two provinces with a strong predominance of rural population, but with important differences in the number of cattle, such as Orense and Lugo, with 6% and 47.7% of Galician cattle, respectively, the rates were very different: 15.8 and 43.6 cases/106, respectively, with an RR of 2.7 (95% CI, 2.08–3.71). Some districts of the province of Lugo had rates higher than 100 cases/106 inhabitants. Conclusions: Our study shows a significant correlation between the rates of Sb bacteremia and cattle density, suggesting a possible transmission of Sb from cows to people. [ABSTRACT FROM AUTHOR]

This study aimed to molecular investigation the prevalence of Theileriaannulataparasite that isolated from blood samples of cattle. A hundred of blood sampleswascollected randomanly from cattles ofthe middle area of Iraq (Babylon province). Samples were submitted to blood DNA extraction assay. Nano drop spectrophotometer and QRT-PCR with TaqMan methods were involved for the surface antigen Tams1detection of Theileriaannulata. Real- Time PCR results showed only 16 samples were positive out of 50 blood samples with a percentage 32%. The threshold cycle (CT value) of these positive samples were ranged from CT: 24.29 to CT: 35.69. The Real-Time PCRefficiency was validated using standard curve method, and the efficiently was approximately (99.9%).Surprisingly, the overall results from current study showed there were no association between ages, gender. Infectionsdistribution between (1-12month) (28.57%), 1-2 year (31.57%) and 3-10 year (29.4%).Additionally, the ratio of the infected females at age of 1-2yearswere twice more than the ratio of infected males. [ABSTRACT FROM AUTHOR]

Natural transference of maternal microbes to the neonate, especially at birth via the vaginal canal, has recently been recognized in humans and cows; however, its microbial influence on calf health has not yet been documented. We compared the bacterial communities in vaginal and fecal samples from 81 pregnant dairy cows versus those in nasopharyngeal and fecal samples collected at 3, 14 and 35 days of life from their respective progeny. The microbiota of the calf upper respiratory tract (URT), regardless of calf age, was found to be highly similar to the maternal vaginal microbiota. Calf fecal microbiota clustered closely to the maternal fecal microbiota, progressing toward an adult-like state over the first 35 days when relative abundances of taxa were considered. Sixty-four, 65 and 87% of the detected OTUs were shared between cow and calf fecal microbiota at days 3, 14 and 35 respectively, whereas 73, 76 and 87% were shared between maternal vaginal microbiome and calf URT microbiota at days 3, 14 and 35, respectively. Bacteroidetes, Ruminococcus, Clostridium, and Blautia were the top four genera identified in maternal and calf fecal samples. Mannheimia, Moraxella, Bacteroides, Streptococcus and Pseudomonas were the top five genera identified in maternal vaginal and calf URT samples. Mannheimia was relatively more abundant in the vaginal microbiota of cows whose progeny were diagnosed with respiratory and middle ear disease. Our results indicate that maternal vaginal microbiota potentially influences the initial bacterial colonization of the calf URT, and that might have an important impact on the health of the calf respiratory tract and middle ear. [ABSTRACT FROM AUTHOR]

The aim of this study was to explore the effects of saponins on the rumen microbiota and the ruminal metabolome. Alfalfa hay (AH) and soybean hulls (SH) were used as fiber sources for the control diets. The AH and SH diets were supplemented with tea saponins resulting in two additional diets named AHS and SHS, respectively. These 4 diets were fed to 24 young male Holstein cattle (n = 6 per diet). After 28 days of feeding, the rumen fluid from these cattle was collected using an oral stomach tube. Illumina MiSeq sequencing and ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF/MS) were used to investigate the changes in the ruminal microbes and their metabolites. The relative abundance of Prevotellaceae_YAB2003 increased, while Ruminococcaceae_NK4A214 and Lachnospiraceae_NK3A20 decreased in SHS and AHS compared to SH and AHS, respectively. Feeding SHS resulted in higher ruminal concentrations of squalene, lanosterol, 3-phenylpropanoic acid, and citrulline compared to SH. The different microbial genes predicted by Tax4Fun were involved in amino sugar and nucleotide sugar metabolism. The pathways of arginine and proline metabolism, purine metabolism, and pyrimidine metabolism were enriched by different metabolites. Moreover, in the SH group, a positive correlation was observed between Prevotella_1 (Bacteroidetes), Prevotellaceae_YAB2003 (Bacteroidetes), and Christensenellaceae_R.7 (Firmicutes), and the metabolites, including citrulline, lanosterol, and squalene. The increased abundances of Prevotella_1 , Ruminococcaceae_UCG.002 , and Prevotellaceae_YAB2003 might result in increased fiber digestion and nutrient utilization but nutrient digestion was not measured in the current study. In summary, saponins have the ability to modulate the ruminal microbial community and ruminal metabolites and thus affect the rumen environment. However, the response seems to be dependent on the composition of the basal diet. This study provides a comprehensive overview of the microbial and biochemical changes in the rumen of cattle fed saponins. [ABSTRACT FROM AUTHOR]

The beef cattle industry represents a significant portion of the USA's agricultural sect, with beef cattle accounting for the most red meat consumed in the USA. Feed represents the largest input cost in the beef industry, accounting for approximately 70% of total input cost. Given that, novel methods need to be employed to optimize feed efficiency in cattle to reduce monetary cost as well as environmental cost associated with livestock industries, such as methane production and nitrogen release into the environment. The rumen microbiome contributes to feed efficiency by breaking down low-quality feedstuffs into energy substrates that can subsequently be utilized by the host animal. Attempts to manipulate the rumen microbiome have been met with mixed success, though persistent changes have not yet been achieved beyond changing diet. Recent technological advances have made analyzing host-wide effects of the rumen microbiome possible, as well as provided finer resolution of those effects. This manuscript reviews contributing factors to the rumen microbiome establishment or re-establishment following rumen microbiome perturbation, as well as host-microbiome interactions that may be responsible for possible host specificity of the rumen microbiome. Understanding and accounting for the variety of factors contributing to rumen microbiome establishment or re-establishment in cattle will ultimately lead to identification of biomarkers of feed efficiency that will result in improved selection criteria, as well as aid to determine methods for persistent microbiome manipulation to optimize production phenotypes. [ABSTRACT FROM AUTHOR]

Objectives: To investigate the prevalence and molecular characteristics of ESBL-producing Escherichia coli (ESBL-EC) in faecal samples from dairy cows in China.Methods: In total, 651 faecal samples were collected from cows distributed among the 10 provinces of China. Potential ESBL-EC isolates were cultured on selective medium. The clonal relatedness of the ESBL-EC isolates was assessed using MLST. WGS was conducted on 3 mcr-positive isolates and 14 additional randomly selected ESBL-EC isolates. Southern blot, S1-PFGE and conjugation were performed for mcr-1-carrying isolates. The genetic environment of the pMCR-JLF4 plasmid was also analysed.Results: In total, 290 unique ESBL-EC isolates were detected from 284 cows (43.6%). Alleles of CTX-M were observed in 94.1% (273/290) of all isolates. The most prevalent genotypes observed in this study were blaCTX-M-14, blaCTX-M-15, blaCTX-M-17 and blaCTX-M-55. Differentiation of 79 STs with a polyclonal structure was accomplished using MLST. Clonal complex 10 was the most prevalent major complex detected here. Furthermore, the mcr-1 gene was detected in three isolates. The complete sequence of the mcr-1-containing pMCR-JLF4 was determined. The plasmid was 66.7 kb in length, with a genetic structure of nikA-nikB-mcr-1-pap2. Conjugation analysis confirmed that the mcr-1 gene in pMCR-JLF4 was transferable without the assistance of the ISApl1 gene.Conclusions: The data presented here suggest high prevalence of ESBL-EC in Chinese cow farms. Furthermore, it was clearly demonstrated that commensal E. coli strains can be reservoirs of blaCTX-M genes, potentially contributing to the dissemination and transfer of the mcr-1 gene to pathogenic bacteria among cows. [ABSTRACT FROM AUTHOR]

The diverse rumen microbiome converts lowquality feedstuffs into usable energy and provides approximately 70% of the energy required by its ruminant host through fermentation byproducts. Due to microbial impacts on host health and productivity, numerous studies have associated rumen microbiome variation with important sustainability phenotypes, such as feed efficiency and methane emissions. Although diet, genetics, and environment contribute to variation in feed efficiency, selection for feed-efficient beef cattle using genetic improvement technologies has helped to understand and improve the persistence and longevity of such phenotypes within the herd. While diet has been considered to be the primary driver for the composition and structure of the rumen microbiome, recent studies have indicated the microbial communities present in the rumen are under low-to-moderate host genetic control. The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. The ability to interrogate these systems at great depth has permitted a greater understanding of the microbiological and molecular mechanisms involved in ruminant nutrition and health. The work in our group in the field of beef cattle gut microbiology, as it relates to feed efficiency, permits the exploration of these critical microbial community networks. This knowledge will aid researchers seeking to address the grand challenge of maintaining host-efficient gut microbiomes throughout cattle production operations. This work is supported by the Agriculture and Food Research Initiative grant no. 2020-67015-30832 from the USDA National Institute of Food and Agriculture. [ABSTRACT FROM AUTHOR]

The research aimed to identify the bacteria present in the reproductive tract of dairy cattle at follicular and luteal phases of the estrus cycle. Seven samples of cervical mucus were each obtained from the reproductive tract, at follicular and luteal phase, of fourteen healthy cattle, 2-3 years of age, with body condition scores of 2.0-8.3. Sporet, motility, triple sugar iron agar, mannitol and glucose tests were done to obtain gram characteristics and bacterial morphology, which enabled identification at the genus level. Non-specific bacteria isolated at follicular phase were Staphylococcus (50%), Corynebacterium (25%) and Escherichia (25%). At luteal phase, Staphylococcus (45.5%), Escherichia (45.5%) and Corynebacterium (9%) were isolated. The results suggest that a number of bacteria can be found in the reproductive tract of dairy cattle, both at follicular phase and luteal phase. [ABSTRACT FROM AUTHOR]

This research was done to evaluate the characteristics and probiotic potential of lactic acid bacteria (LAB) isolated from the small intestine of ten three year-old male Ongole crossbred cattle. Ten-centimeter samples were obtained from each small intestine, wastes were removed then samples were placed in sterile sample bottles, and immediately taken to the laboratory for bacterial isolation. The LAB isolates were subjected to low pH tolerance (pH 2 and 4), bile salt resistance, and antimicrobial activity against enteric pathogens Staphylococcus aureus and Eschericia coli. Biochemical assay indicated that isolate was gram positive, rodshaped, catalase negative, and capable of fermenting glucose, mannitol, xylose, rhamnose, sucrose, lactose, arabinose, raffinose and sorbitol. Biochemical and morphological identification suggests that the isolate was Lactobacillus plantarum WPL 117 (strain number of control indicator organisms was Lactobacillus plantarum ATCC 14917). This isolate was able to survive at low pH (2 and 4), tolerated 0.3% bile salts, and capable of inhibiting S. aureus and E. coli. Thus, this isolate can be considered a probiotic candidate for further study. [ABSTRACT FROM AUTHOR]

Highlights • PCR and culture performance was evaluated for Staph. aureus and Strep. agalactiae. • The sensitivity was higher for PCR than bacterial culture for milk and teat skin. • The specificity of PCR and bacterial culture was generally high. • Different target conditions of culture and PCR probably affected the results. Abstract Streptococcus agalactiae (Strep. agalactiae) and Staphylococcus aureus (Staph. aureus) are originally regarded as contagious mastitis pathogens, however, both pathogens have recently been isolated from extramammary and environmental sites, indicating that other sites than the udder might contribute to the spread of these pathogens potentially causing intramammary infections. Diagnostic tools to identify pathogens at extramammary sites are available but still needs to be validated. The objective of this cross-sectional field study was to estimate the diagnostic sensitivity (Se) and specificity (Sp) of the commercially available Mastit4 qPCR assay and bacterial culture (BC) in identifying Strep. agalactiae and Staph. aureus from milk and teat skin samples. We randomly selected 30–40 cows with high somatic cell counts from eight Danish Strep. agalactiae- positive dairy herds with automatic milking systems. Teat skin samples and aseptic milk samples were collected from right rear quarters (n = 287) for BC and PCR analysis. Se and Sp were estimated in a Bayesian latent class analysis. For milk samples, the Se and Sp of qPCR for Strep. agalactiae were estimated to 0.97 and 0.99, respectively, whereas the Se and Sp of BC were 0.41 and 1.00, respectively. The Se and Sp of qPCR for Staph. aureus were estimated to 0.95 and 0.99, respectively, whereas the Se and Sp of BC were 0.54 and 0.77, respectively. For teat skin samples, the Se and Sp of qPCR for Strep. agalactiae were estimated to be 0.97 and 0.96, respectively, whereas the Se and Sp of BC were 0.33 and 1.00, respectively. The Se and Sp of qPCR for Staph. aureus were estimated to 0.94 and 0.98, respectively, whereas the Se and Sp of BC were 0.44 and 0.74, respectively. In conclusion, the Se for diagnosing Strep. agalactiae and Staph. aureus IMI was higher for qPCR than BC, suggesting that qPCR is a valuable method for detecting both pathogens from quarter-level milk samples. The performance of BC in the detection of Strep. agalactiae and Staph. aureus on teat skin was poor compared to qPCR, indicating that differences in the target condition of the two methods should be considered when implementing them as routine diagnostic tests for detecting teat skin colonisers. The low Se of BC may preclude the use of BC for skin testing, and qPCR is better for this task. [ABSTRACT FROM AUTHOR]

Abstract: Cattle are a major reservoir of Shiga toxin‐producing Escherichia coli. This study investigated the occurrence of seven major STEC serogroups including O157, O145, O103, O121, O111, O45 and O26 among 578 STEC isolates previously recovered from 559 cattle. The isolates were characterized for serotype and major virulence genes. Polymerase chain reaction revealed that 41.7% (241/578) of isolates belonged to STEC O157, O145, O103, O121, O45 and O26, and 33 distinct serotypes. The 241 isolates corresponded to 16.5% (92/559) of cattle that were STEC positive. The prevalence of cattle that tested positive for at least one of the six serogroups across the five farms was variable ranging from 2.9% to 43.4%. Occurrence rates for individual serogroups were as follows: STEC O26 was found in 10.2% (57/559); O45 in 2.9% (16/559); O145 in 2.5% (14/559); O157 in 1.4% (8/559); O121 in 1.1% (6/559); and O103 in 0.4% (2/559). The following proportions of virulence genes were observed: stx1, 69.3% (167/241); stx2, 96.3% (232/241); eaeA, 7.1% (17/241); ehxA, 92.5% (223/241); and both stx1 and stx2, 62.2% (150/241) of isolates. These findings are evidence that cattle in South Africa carry STEC that belong to six major STEC serogroups commonly incriminated in human disease. However, only a subset of serotypes associated with these serogroups were clinically relevant in human disease. Most STEC isolates carried stx1, stx2 and ehxA but lacked eaeA, a major STEC virulence factor in human disease. [ABSTRACT FROM AUTHOR]

Dairy cattle manure serves as a potential source of contamination and infection of animals, humans and the environment. Manure samples withdrawn from a balloon-type digester during anaerobic digestion were evaluated for the presence of antibiotic-resistant bacterial pathogens. The bacterial load of the samples was determined via a viable plate count method and the recovered isolates were subjected to characterisation and identification. These isolates were employed in antibiotic susceptibility testing using a disc diffusion method against a suite of 10 conventional antibiotics. The multiple antibiotic resistance (MAR) index was calculated and MAR phenotypes were generated. Although all the bacterial pathogens showed a certain degree of resistance to the studied antibiotics, a marked resistance was demonstrated by Campylobacter sp. to co-trimoxazole (87.5%) and nalidixic acid (81.5%). Remarkably, a high resistance (82.42%) was demonstrated against the antibiotic class, macrolide, followed by beta-lactams (40.44%), suggesting that bacterial resistance depended on the chemical structure of the antibiotics. However, individual bacterial isolates varied in resistance to particular antibiotics. Of the 83 bacterial isolates, 40(48.19%) observed MAR > 0.2 and, thus, were described as multidrug-resistant isolates. A total of 28 MAR phenotypes were revealed with the highest frequency of MAR phenotypes (37.5%) expressed against 3 antibiotics. Results indicated a high risk of exposure to various antibiotics and wide diversity of antibiotic resistance. [ABSTRACT FROM AUTHOR]

Objectives: To elucidate the phylogenetic relationships among ST9-MRSA-XII isolates from different sources and their genetic features in colonization of different hosts.Methods: We obtained whole-genome sequences of two ST9-MRSA-XII isolates from nasal swabs associated with live pigs in China, and compared them with 135 previously sequenced genomes of 78 human-associated, 39 bovine and 18 porcine Staphylococcus aureus consisting of 11 MRSA of SCCmecXII, 62 MRSA of other SCCmec types and 62 MSSA. The distribution of diverse mobile genetic elements (MGEs), resistance genes and virulence determinants was investigated in relation to isolate phylogeny. Comparisons of SNPs and small insertion/deletions (indels) were conducted to examine genome-level variation between porcine and bovine ST9-MRSA-XII.Results: Phylogenetic analysis revealed that both of our porcine ST9-MRSA-XII isolates clustered with porcine, bovine and human-associated ST9-MRSA-XII. All of these isolates possessed a novel type V pathogenicity island, νSaα, carrying the von Willebrand-binding protein gene vwb, the immune evasion complex gene scn, the aminoglycoside resistance gene aadE, staphylococcal superantigen-like genes (ssl1-ssl11) and lpl tandem genes. Compared with bovine ST9-MRSA-XII BA01611, our porcine isolates contain non-synonymous nucleotide substitutions in genes encoding adhesins and an indel located in a phosphonate ABC transporter pseudogene.Conclusions: The data suggest transmission of ST9-MRSA-XII among swine, cattle and humans. The extraordinary success of the ST9-MRSA-XII group in colonization of various hosts is likely due to acquisition of many MGEs harbouring functional antimicrobial resistance and virulence genes. Transmission of ST9-MRSA-XII between porcine and bovine hosts was accompanied by changes in binding profile and function in genes involved in metabolism. [ABSTRACT FROM AUTHOR]

The goal of this study was to compare the molecular features of bovine- and human community-acquired extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Israel. Bovine ESBL-producing E. coli were isolated during a point-prevalence study from the main farming locations throughout Israel. Human ESBL-producing E. coli isolates were collected from community-acquired urinary tract infection cases. Molecular typing was done initially by repetitive extragenic palindromic-PCR. Representative isolates were subjected to next-generation sequencing (NGS) and analyzed for multilocus sequence typing (MLST), core genome MLST (cgMLST), bla CTX-M gene allele, and mobile genetic elements (MGEs) surrounding it. Out of the 287 bovine- and 104 community-derived ESBL-producing E. coli isolates, 44 and 26 isolates were subjected to NGS, respectively. Both populations exhibited a diverse but distinct clonal structure with predominance of several sequence types (STs); two clones, ST-10/167 ( n  = 13) and ST-38 ( n  = 8), were present. cgMLST analysis of these clones revealed that the majority of isolates exhibited phylogenetic distance (PD) of >178 gene difference from their closest isolate, with the exception of five isolates that exhibited PD of <24 gene difference, including two bovine- to three community-derived isolates. Hence, clonal transmission of ESBL-producing E. coli between cattle and the community, although uncommon, is likely to have occurred. The bla CTX-M-15 gene was identified in 52/70 (74%) isolates from both cattle and the community and was surrounded by MGEs that were composed mostly of either the Tn 3 or IS 1380 families. Thus, MGEs are likely to play an important role in the exchange of resistance genes. [ABSTRACT FROM AUTHOR]

The aim of this study was to compare the antimicrobial resistance profiles of top five enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) to E. coli isolated from the fecal flora of the same adult cattle. Previous prevalence studies had led to the isolation by immunomagnetic separation (IMS) of 39 EHEC and 80 EPEC. Seven EHEC were resistant (17.9%), and six were multidrug resistant (MDR) (15.4%). None of the top five EHEC was resistant to azithromycin. Nine EPEC O26:H11 (11.3%) were resistant. They were all resistant to tetracycline, and four were MDR (5.0%). An E. coli strain was isolated from the feces (without preselection by IMS) of 97 bovine carriers of top 5 strains. All these strains were susceptible to antibiotics. Comparative analyses did not reveal any differences between the cytotoxic activities of resistant EHEC and their susceptible counterparts or in the production of attachment and effacement lesions. These results highlighted the higher percentage of resistance of EHEC and EPEC strains compared to other E. coli. They also showed that resistance traits did not have any impact on the expression of virulence phenotypes in EHEC strains. [ABSTRACT FROM AUTHOR]

Livestock microbiota is becoming a focus of interest for veterinaries, animal nutritionists and microbiologists in view to select beneficial bacteria with impact in health and animal productivity. As resident adapted microorganisms, lactic acid bacteria (LAB) were isolated, identified and characterized from the homologous host to promote their permanence/efficiency acting as additives in feedlot cattle feeding. Cultivable LAB numbers from cattle feces (CF), pens soil (PS) and feed rations (FR) ranged from 5 to 6 log CFU/g during feedlot permanence. Isolates (500) were identified by (GTG) 5 -PCR and sequence analysis of 16S rRNA, being represented by Enterococcus, Lactobacillus, Leuconostoc, Pediococcus and Weissella genera and 20 different species. Genetic mapping showed that predominant LAB species in CF and PS samples were Lactobacillus (Lb) mucosae (34%), Enterococcus (E) hirae (26%) and E. faecium-durans (20%), while in FR E. faecium-durans (46%), Pediococcus (P). pentosaceous, P. acidilactici (17%) and Lb. acidophilus (11%) were mainly isolated. Surface characterization showed most of LAB as high hydrophilic, however several strains from CF and PS revealed strong hydrophobic and auto-aggregative character with a positive correlation between both superficial properties. Adhesion to polystyrene displayed variable biofilm formation patterns for Enterococcus and Lactobacillus strains depending on the presence of Tween in MRS medium. When antagonistic activity of isolated LAB against bovine relevant pathogens was evaluated, organic acids and hydrogen peroxide production were mostly responsible for inhibition; bacteriocin production was shown only by a Lb. mucosae strain. In addition, tolerance to acid and bile salts showed lactobacilli to withstand GIT conditions, while enterococci were more sensitive to low acid environment. On these bases, several Lactobacillus strains may be selected to explore their potential use as direct fed bacteria in feedlot cattle. [ABSTRACT FROM AUTHOR]

Between 2009 and 2016, 317 and 529 swabs from cattle and pig carcasses, respectively, were collected all over Poland and tested for the presence of Campylobacter. Among 37 (11.7%) and 161 (30.4%) positive samples, 44 Campylobacter jejuni isolates were detected. A total of 29 different sequence types (STs) and 12 various clonal complexes were identified. Antimicrobial resistance revealed that 17 (38.6%) C. jejuni (10 from cattle and 7 from pig carcasses, respectively) were susceptible to all antimicrobials used in the study, whereas the remaining 27 (61.4%) isolates (12 from cattle and 15 from pigs, respectively) were resistant to at least one antimicrobial agent, mainly to quinolones (23 out of 44 isolates; 52.3%) and tetracyclines (14 strains; 31.8%). Only one isolate from cattle and two from pigs displayed resistance to streptomycin, and none of C. jejuni tested was resistant to erythromycin and gentamicin. All isolates with STs, ST356, ST443, ST464, ST658, ST2036, and ST6411, as well as some isolates belonging to ST257 and ST1947, were resistant to quinolones and tetracyclines. The results show that cattle and pigs may be a reservoir of quinolone and tetracycline resistant C. jejuni with STs which were previously isolated from humans with campylobacteriosis. [ABSTRACT FROM AUTHOR]

The effect of different pathogens was studied by evaluating the contralateral (healthy and infected) mammary quarters of 146 lactating cows. The impact of SM on economic return (quarter milk yield × milk price) was determined by applying milk payment estimates on milk collected from healthy vs. infected glands. Cows were considered infected when they had at least 2 out of 3 weekly composite SCC results > 200 × 10 3 cells/mL and a microbiological culture ( MC ) positive result from composite foremilk samples, collected in the third week of sampling. Infected cows were evaluated a second time within 15 days and had milk yield measured at the quarter level and foremilk samples collected by aseptic technique for analysis of MC, milk composition and SCC. Of the 611-composite milk samples, 397 (65%) were culture-negative, and 214 (35%) were culture-positive and the most frequent isolated bacteria were Corynebacterium spp. (7.9%), coagulase negative staphylococci (5.8%), Staphylococcus aureus (5.3%), Streptococcus uberis (4.6%), Streptococcus agalactiae (3.9%), other environmental streptococci (2.4%), Gram-negative isolates (2.4%), Enterococcus spp. (1.4%) and Streptococcus dysgalactiae (0.7%). A total of 55 pairs of healthy contralateral quarters (control) were compared, and no difference was observed between them when evaluating SCC, milk yield, fat and protein concentration and economic return. A total of 124 pairs of healthy had lower SCC (274.9 × 10 3 cells/mL) than infected contralateral quarters (SCC of 1038.5 × 10 3 cells/mL). At the quarter level, IMI caused by minor pathogens had no effect on SCC, milk yield and economic return. Subclinical mastitis caused by contagious and environmental pathogens increased SCC and decreased milk yield when compared with healthy contralateral quarters. Moreover, quarters infected by contagious pathogens had increased concentrations of milk protein and fat when compared with healthy contralateral quarters. Therefore, the milk economic return was lower in quarters with SM caused by environmental pathogens (US$ 0.18/quarter.milking) and contagious (US$ 0.22/quarter.milking) when compared with healthy contralateral quarters. The milk losses ranged from 0.07 kg/quarter.milking to 1.4 kg/quarter.milking and the economic losses ranged from US$ 0.02–0.4/quarter.milking according to the pathogen causing SM. [ABSTRACT FROM AUTHOR]

Urea has been used in diets of cattle as a non-protein nitrogen source. It is hydrolyzed to ammonia, which can be used for microbial protein synthesis. Use of metabolomics methodologies to study the rumen microbial and host blood metabolic profiles induced by urea nitrogen has not been previously characterized. The objective of this study was to identify changes in rumen microbial and plasma metabolite profiles in dairy cows after urea supplementation using a nuclear magnetic resonance (NMR)-based untargeted quantitative metabolomic approach. Six dairy cows with rumen fistulas were randomly assigned to two groups used in a two period cross-over trial and each experimental period lasted 21 days. All the cows were fed the same total mixed rations, but were intraruminally supplemented with 180 g urea per cow daily or not during the experimental period. Rumen fluid and blood samples were collected and analyzed using nuclear magnetic resonance spectroscopy and multivariate analysis of variance. Differences in rumen and plasma metabolite concentrations in cows from the two groups were assessed using orthogonal partial least-squares discriminant analysis and identified by searching against related databases. Concentrations of valine, aspartate, glutamate, and uracil in the rumen, and urea and pyroglutamate in the plasma, were higher ( P  < 0.05) in the urea-supplemented group than in the control group. Metabolic pathway analysis of the affected metabolites revealed that pantothenate and CoA biosynthesis, beta-alanine metabolism, valine, leucine, and isoleucine metabolism in the rumen, and urea and glutathione metabolism in the plasma were significantly increased by urea nitrogen. The levels of aspartate and glutamate in the rumen correlated strongly ( P  < 0.01) with the level of urea in plasma. These findings provided novel information to aid understanding of the metabolic pathways affected by urea nitrogen in dairy cows, and could potentially help to guide efforts directed at improving the efficiency of urea utilization in the rumen. [ABSTRACT FROM AUTHOR]

Several multiple-media culture systems have become commercially available for on-farm identification of mastitis-associated pathogens. However, the accuracy of these systems has not been thoroughly and independently validated against microbiological evaluations performed by referral laboratories. Therefore, the purpose of the present study was to evaluate the performance of commercially available culture plates (Accumast, Minnesota Easy System, SSGN and SSGNC Quad plates) to identify pathogens associated with clinical mastitis in dairy cows. Milk samples from the affected quarter with clinical mastitis were aerobically cultured with the on-farm culture systems and by two additional reference laboratories. Agreeing results from both standard laboratories were denoted as the reference standard (RS). Accuracy (Ac), sensitivity (Se), specificity (Sp), positive and negative predictive values (PPV and NPV, respectively) and Cohen’s kappa coefficient (k) of on-farm plates were determined based on the RS culture of 211 milk samples. All four plate-systems correctly identified ≥ 84.9% of milk samples with no bacterial growth. Accumast had greater values for all overall predictive factors (Ac, Se, Sp, PPV and NPV) and a substantial agreement (k = 0.79) with RS. The inter-rater agreements of Minnesota, SSGN, and SSGNC with RS were moderate (0.45 ≤ k ≤ 0.55). The effectiveness to categorize bacterial colonies at the genus and species was numerically different amongst the commercial plates. Our findings suggest that Accumast was the most accurate on-farm culture system for identification of mastitis-associated pathogens of the four systems included in the analysis. [ABSTRACT FROM AUTHOR]

The emergence of simultaneous resistance to multiple classes of antibiotics presents an increasing threat. Plasmid-borne multiresistance and integrative conjugative elements have been reported in Pasteurella multocida. We report an alternative strategy for the development of multiresistance observed in a P. multocida strain (Pm238) isolated from calf pneumonia. We identified genes integrated into the chromosomal DNA without known integrative and conjugative elements. These genes conferred resistance to streptomycin (strA), tetracycline (tetB), chloramphenicol (catAIII), and sulphonamides (sulII). We also detected mutation in the quinolone-resistance-determining regions of parC. No plasmids could be isolated from strain Pm238. These results suggest that P. multocida can accumulate multiple resistance determinants on the chromosome as single genes. [ABSTRACT FROM AUTHOR]

Emergence and spread of antimicrobial resistance is a major concern for the dairy industry worldwide. Objectives were to determine: (1) phenotypic and genotypic prevalence of drug-specific resistance for 25 species of non-aureus staphylococci, and (2) associations between presence of resistance determinants and antimicrobial resistance. Broth micro-dilution was used to determine resistance profiles for 1,702 isolates from 89 dairy herds. Additionally, 405 isolates were sequenced to screen for resistance determinants. Antimicrobial resistance was clearly species-dependent. Resistance to quinupristin/dalfopristin was common in Staphylococcus gallinarum (prevalence of 98%), whereas S. cohnii and S. arlettae were frequently resistant to erythromycin (prevalence of 63 and 100%, respectively). Prevalence of resistance was 10% against b-lactams and tetracyclines. In contrast, resistance to antimicrobials critically important for human medicine, namely vancomycin, fluoroquinolones, linezolid and daptomycin, was uncommon (<1%). Genes encoding multidrug-resistance efflux pumps and resistance-associated residues in deducted amino acid sequences of the folP gene were the most frequent mechanisms of resistance, regardless of species. The estimated prevalence of the mecA gene was 17% for S. epidermidis. Several genes, including blaZ, mecA, fexA, erm, mphC, msrA, and tet were associated with drug-specific resistance, whereas other elements were not. There were specific residues in gyrB for all isolates of species intrinsically resistant to novobiocin. This study provided consensus protein sequences of key elements previously associated with resistance for 25 species of non-aureus staphylococci from dairy cattle. These results will be important for evaluating effects of interventions in antimicrobial use in Canadian dairy herds. [ABSTRACT FROM AUTHOR]

Two experiments were carried out to evaluate the bactericidal impacts of Bacillus amyloliquefaciens CECT 5940 on the shedding of faecal pathogenic bacteria in dairy calves (Experiment 1) and in adults dogs (experiment 2). In the calves experiment, a completely randomized design was used to investigate the faecal bacteria profile of Holstein dairy calves fed with either pasteurized waste milk (PWM; n = 9) or a formulated non-medicated milk replacer (NMR; n = 9) for 60 d. The NMR containing sodium-butyrate and the active probiotic B. amyloliquefaciens CECT 5940. In the dogs experiment, addition of same probiotic (i.e., B. amyloliquefaciens CECT 5940) was carried out in two stages. The first stage started from day 7–37, and the second from day 44–71. The assessment of faecal score measured on day 22, 37, 42, 57, 71 and 77 to determine the texture of the stools. Calves received PWM consumed (P < 0.05) more starter feed between day 16 and day 45. The calves fed NMR had more moisture faeces and less cough reflux than the PWM-calves. Feeding NMR to calves increased faecal Klebsiella oxytoca and Proteus vulgaris counts in comparison to PWM-calves. The administration of B. amyloliquefaciens CECT 5940 to the dog diet has no significant effect on the hardness of the stool. Meanwhile, the bacillus count increases while the coliforms count decreases upon B. amyloliquefaciens CECT 5940 administration. This reveals that B. amyloliquefaciens CECT 5940 survived the gastrointestinal passage and rapidly colonized the dog intestine, which could positively affect the metabolism and composition of the intestinal microflora. These results show that B. amyloliquefaciens are a promising probiotic with an antimicrobial and bactericidal activities against the intestinal pathogenic bacteria for dairy calves and adult dogs. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the efficacy of the association of the nematophagous fungi (Duddingtonia flagrans-AC001); (Pochonia chlamydosporia-VC4) and (Arthrobotrys robusta-I31) in a pelletised formulation of a sodium alginate matrix. The viability and activity of pellet germination and fungal activity (after encapsulation) were evaluated usingin vitroandin vivotests. Next, 12 heads of cattle, Dutch mestizo x zebu, with an average age of 12 months were dewormed with an anthelmintic. Next, 20 days after treatment with the anthelmintic, the animals were randomly divided into two groups of six animals each, and placed in two paddocks with 7.0 ha each ofBrachiaria decumbenswith historical grazing by animals naturally infected by gastrointestinal nematode parasites. At first, each animal was treated with 2 g of pellets per 10 kg of animal, containing the associated fungi (AC001 + VC4 + I31) administered twice a week in conjunction with commercial feed. Each animal in the control group received 2 g of pellets without mycelia added to the feed. The percentage reduction of infective larvae in thein vitrotest was 94% (p < .01). In thein vivotest, the treated animals with fungal association had lower egg counts per gram of faeces (p < .01) compared to the control group animals – a reduction of 91.8%. The reduction in the number of infective larvae recovered from the pasture was 27.5% at a distance of 0–20 cm from the stool bulk, and 26.7% at a distance of 20–40 cm. This association (AC001 + VC4 + I31) of nematophagous fungi was effective in nematode control. [ABSTRACT FROM AUTHOR]

The paper presents the study of the habitat of mycobacteria in various natural and climatic zones of the Karaganda region, which showed that out of all the isolated cultures, 307 (94.5%) were atypical mycobacteria (M. scrofulaceum, M. avium). At that, 64.5% of atypical mycobacteria cultures (M.scrofulaceum, M. avium) were isolated from the diagnostic material and objects of the external environment of the steppe zone.Thesensitinsfrom epizootic strains of mycobacteria were tested in terms of such criteria as sterility, safety, reactogenicity, lack of sensitizing properties, activity, and specificity. The sensitinswere administered to guinea pigs and cattle using an intradermal needless syringe. Preliminary experiments on guinea pigs found that sensitins had biological and specific activity, identical to avian purified protein derivative tuberculin. The tests of developed sensitinsM. Scrofulaceumand M. avium on 59 cattle showed that the sensitins were highly effective in differentiating nonspecific reactions and demonstrated the expedience of their application.Using sensitins for lifetime differentiation of nonspecific reactions to tuberculin mammalian in healthy animals and cattle recovering from tuberculosis prevents the premature slaughtering of commercially valuable animals of a reproductive age. [ABSTRACT FROM AUTHOR]

Current information on prevalence and antimicrobial resistance (AMR) of bacterial respiratory pathogens is crucial to guide antimicrobial choice for control and treatment of bovine respiratory disease (BRD). The objectives were to describe the prevalence of three BRD-associated bacteria ( Mannheimia haemolytica , Pasteurella multocida , and Histophilus somni ) in the lower airways of feedlot cattle, and to analyze AMR in these bacteria. Cattle with (n = 210) and without (n = 107) BRD were sampled by trans-tracheal aspiration at four feedlots (Nov. 15–Jan. 16). These cattle had received 2.5 mg/kg of tulathromycin on arrival at the feedlot for BRD control and two in-feed pulses of chlortetracycline (5 g/animal/day for 5 days) within the first 21 days on feed to prevent histophilosis. Bacteria were detected by culture and AMR was tested by microdilution. Pasteurella multocida was the most frequent bacterium isolated in cattle with BRD (54.8%), followed by M. haemolytica (30.5%) and H. somni (22.9%). Compared to those with BRD, healthy cattle were less likely to be positive for P. multocida (OR = 0.27), M. haemolytica (OR = 0.32), or H. somni (OR = 0.25). There were high levels of resistance (>70%) against tulathromycin and oxytetracycline in M. haemolytica and P. multocida isolates and high levels of resistance against oxytetracycline (67%) and penicillin (52%) in H. somni isolates. None or few isolates were resistant to florfenicol, enrofloxacin and ceftiofur. The high prevalence of resistance against tulathromycin and oxytetracycline suggests that these antimicrobials should not be repeatedly used for both control and treatment of BRD and/or histophilosis. [ABSTRACT FROM AUTHOR]

Problem addressed Shiga toxin-producing Escherichia coli (STEC) are a group of bacteria responsible for food-associated diseases. Clinical features include a wide range of symptoms such as diarrhea, hemorrhagic colitis and the hemolytic uremic syndrome (HUS), a life-threatening condition. Objective Our group has observed that animals naturally colonized with STEC strains of unknown serotype were not efficiently colonized with E. coli O157:H7 after experimental infection. In order to assess the basis of the interference, three STEC strains were isolated from STEC persistently-colonized healthy cattle from a dairy farm in Buenos Aires, Argentina. Methods and results The three isolated strains are E. coli O22:H8 and carry the stx1 and stx2d genes. The activatable activity of Stx2d was demonstrated in vitro . The three strains carry the adhesins iha , ehaA and lpf O113 . E. coli O22:H8 formed stronger biofilms in abiotic surface than E. coli O157:H7 ( eae+, stx2+ ) and displayed a more adherent phenotype in vitro towards HeLa cells. Furthermore, when both serotypes were cultured together O22:H8 could reduce O157:H7 adherence in vitro . When calves were intragastrically pre-challenged with 10 8 CFU of a mixture of the three STEC strains and two days later challenged with the same dose of the strain E. coli O157:H7 438/99, the shedding of the pathogen was significantly reduced. Conclusions These results suggest that E. coli O22:H8, a serotype rarely associated with human illness, might compete with O157:H7 at the bovine recto-anal junction, making non-O157 carrying-calves less susceptible to O157:H7 colonization and shedding of the bacteria to the environment. [ABSTRACT FROM AUTHOR]

Bovine respiratory disease (BRD) is one of the most serious causes of health and economic problems in the beef production industry, especially in recently weaned, intensely raised and newly transported feedlot cattle. While the importance of upper airway structure and function in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established, the role of the mucosal microbiota in respirtatory health is less well defined. The objective of this study was to characterize the nasopharyngeal microbiota of feedlot cattle at entry into a commercial feedlot, during initial management processing, and to compare the dynamics of change in these microbial communities between clinically healthy calves and those that develop BRD within the first month after entry. Deep nasopharyngeal swabs were collected from randomly selected healthy calves (n = 66) during initial handling and processing at the feedlot, and again at the initial diagnosis of BRD (n = 22). Clinically healthy pen matched controls calves (n = 10) were sampled at the same time as the BRD affected animals. Genomic DNA was extracted from each sample, and the 16S rRNA gene V1-V3 hypervariable region was amplified and sequenced using the Illumina MiSeq platform. Across all the samples, the predominant bacterial phyla were Proteobacteria , Firmicutes and Actinobacteria. While the predominant genera were Moraxella , Mycoplasma and Acinetobacter . Linear discriminant analysis (LDA) effect size (LEfSe) revealed significant differences in bacterial taxa between healthy and BRD affected calves. Discriminant analysis revealed that the nasopharyngeal microbiota in feedlot calves at entry and in BRD affected calves were distinct from pen matched healthy calves. While the temporal dynamics of this shift were not examined in this study, it is possible that the observed changes in mucosal microbiota are linked to the increased susceptibility of calves to BRD during the first month after entry in to the feedlot. Additional studies are needed to examine the trajectory of change in nasopharyngeal microbial communities from entry to disease onset, and to explore the impact of other factors such as diet transition, commingling, vaccination and housing on the nasopharyngeal microbiota of growing cattle. [ABSTRACT FROM AUTHOR]