Dataset Information

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.

ABSTRACT: Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 UCD samples categorized as mild (n = 17) or severe (n = 19) and 13 control samples were sequenced using a shotgun metagenomic approach and the reads were taxonomically classified based on their k-mer content. The Wilcoxon rank sum test was used to compare the abundance of different taxa between different sample types, as well as to compare the bacterial diversity between samples. A high proportion of bacteria was seen in all samples. Control samples had a higher proportion of archaeal reads, whereas most samples had low proportions of fungi, protozoa and viruses. The bacterial microbiota differed between controls and mild and severe UCD samples in both composition and diversity. Subgroups of UCD samples were visible, characterized by increased proportion of one or a few bacterial genera or species, e.g. Corynebacterium, Staphylococcus, Brevibacterium luteolum, Trueperella pyogenes and Fusobacterium necrophorum. Bifidobacterium spp. were more common in controls compared to UCD samples. The bacterial diversity was higher in controls compared to UCD samples. Bacteria commonly associated with mastitis were uncommon. In conclusion, a dysbiosis of the microbiota of mild and severe UCD samples was seen, characterized by decreased diversity and an increased proportion of certain bacteria. There was no evidence of a specific pathogen causing UCD or that UCD lesions are important reservoirs for mastitis-causing bacteria.

SUBMITTER: Ekman L

PROVIDER: S-EPMC7710049 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.

Ekman Lisa L Bagge Elisabeth E Nyman Ann A Persson Waller Karin K Pringle Märit M Segerman Bo B

PloS one 20201202 12

Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 ...[more]

PMID: 33264351

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Project description:This study investigated 960 Slovak and Czech spotted cattle from four different conventional (non-organic) dairy herds located in Eastern Slovakia and Czechia during early lactation (14-100 days after calving). Dairy cows were examined clinically; milk from fore-stripping of each udder quarter was subjected to sensory examination and assessed by the California mastitis test (CMT), and laboratory analyses of bacterial pathogens in milk, including virulence factors, were conducted. Positive CMT scores (1-3) for one or more quarters were detected in 271 (28.2%) of the examined animals. Out of 230 infected milk samples, representing 24.0% of all dairy cows, staphylococci (59.1% of positive findings) were the most commonly isolated organisms, followed by E. coli (11.3%), streptococci Str. uberis (9.1%) and Str. agalactiae (3.4%), and enterococci (6.1%). From 136 isolates of S. aureus (38 isolates) and non-aureus staphylococci (NAS; 98 isolates), virulence factors and their resistance to 14 antimicrobials were detected using the disk diffusion method, with PCR detection of the methicillin resistance gene, mecA. An increased incidence of clinical and chronic forms of mastitis has been reported in mastitic cows in which staphylococci, especially S. aureus and NAS (S. chromogenes, S. warneri, and S. xylosus), have been detected and compared to other isolated udder pathogens. From those species, S. aureus and isolates of NAS mentioned above showed multiple virulence factors that are more likely to hydrolyze DNA, hemolysis, produce gelatinase and biofilm, and have multi-drug resistance as compared to other less virulent staphylococci. Generally, the isolated staphylococci showed 77.2% resistance to one or more antimicrobials, in particular to aminoglycosides, β-lactams, macrolides, or cephalosporins. Isolates that showed the ability to form a biofilm were more resistant to more than one antimicrobial than isolates without biofilm production. Multi-drug resistance to three or more antimicrobial classes was recorded in 16 isolates (11.7%), and the presence of the mecA gene was also confirmed in two isolates of S. aureus and two species of NAS.

Project description:Mastitis is one of the most important infectious diseases and one of the diseases that causes the greatest use of antibiotics in dairy cows. Therefore, updated information on the bacteria that cause mastitis and their antibiotic susceptibility properties is important. Here, for the first time in over 10 years, we updated the bacterial findings in clinical mastitis in Swedish dairy cows together with their antibiotic resistance patterns and risk factors for each bacterial species. During the period 2013-2018, samples from clinical mastitis were collected, together with information on the cows and herds of origin. The samples were cultured, and a total of 664 recovered bacterial isolates were subjected to susceptibility testing. Staphylococcus aureus (S. aureus) was the most common pathogen and accounted for 27.8% of diagnoses, followed by Streptococcus dysgalactiae (S. dysgalactiae) (15.8%), Escherichia coli (E. coli) (15.1%), Streptococcus uberis (S. uberis) (11.4%), Trueperella pyogenes (T. pyogenes) (7.7%), non-aureus staphylococci (NAS) (2.8%), Klebsiella spp. (2.7%), Enterococcus spp. (1.3%), and Streptococcus agalactiae (S. agalactiae) (1.2%). Various other bacteria accounted for 2.6%. Staphylococci were, in general, susceptible to most antibiotics, but 2.6% of S. aureus and 30.4% of NAS were resistant to penicillin. No methicillin-resistant staphylococci were found. All S. agalactiae were susceptible to penicillin. Bimodal and trimodal MIC distributions for penicillin in S. dysgalactiae and S. uberis, respectively, indicate acquired reduced susceptibility in some isolates. The mostly unimodal MIC distributions of T. pyogenes indicate that acquired resistance does usually not occur in this species. Among E. coli, 14.7% were resistant to at least one antibiotic, most often ampicillin (8.7%), streptomycin (7.8%), or sulphamethoxazole (6.9%). Klebsiella spp. had low resistance to tetracycline (9.1%) but is considered intrinsically resistant to ampicillin. Pathogen-specific risk factors were investigated using multivariable models. Staphylococcus aureus, S. dysgalactiae, and T. pyogenes were more common, while E. coli was less common in quarters with more than one pathogen. S. aureus and T. pyogenes were mostly seen in early lactation, while E. coli was more common in peak to mid lactation and S. dysgalactiae in early to peak lactation. Trueperella pyogenes and Klebsiella spp. were associated with a previous case of clinical mastitis in the current lactation. Staphylococcus aureus was associated with tie stalls and T. pyogenes with loose housing. All pathogens except E. coli and S. dysgalactiae had a seasonal distribution. In conclusion, the aetiological agents for clinical bovine mastitis have remained relatively stable over the last 10-15 years, S. aureus, S. dysgalactiae, E. coli and S. uberis being the most important. Resistance to penicillin among Gram-positive agents was low, and in general, antibiotic resistance to other compounds was low among both Gram-positive and Gram-negative agents.

Project description:Biogeography (body site) is known to be one of the main factors influencing the composition of the skin microbial community. However, site-associated microbial variability at a fine-scale level was not well-characterized since there was a lack of high-resolution recognition of facial microbiota across kingdoms by shotgun metagenomic sequencing. To investigate the explicit microbial variance in the human face, 822 shotgun metagenomic sequencing data from Han Chinese recently published by our group, in combination with 97 North American samples from NIH Human Microbiome Project (HMP), were reassessed. Metagenomic profiling of bacteria, fungi, and bacteriophages, as well as enriched function modules from three facial sites (forehead, cheek, and the back of the nose), was analyzed. The results revealed that skin microbial features were more alike in the forehead and cheek while varied from the back of the nose in terms of taxonomy and functionality. Analysis based on biogeographic theories suggested that neutral drift with niche selection from the host could possibly give rise to the variations. Of note, the abundance of porphyrin-producing species, i.e., Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, and Cutibacterium namnetense, was all the highest in the back of the nose compared with the forehead/cheek, which was consistent with the highest porphyrin level on the nose in our population. Sequentially, the site-associated microbiome variance was confirmed in American populations; however, it was not entirely consistent. Furthermore, our data revealed correlation patterns between Propionibacterium acnes bacteriophages with genus Cutibacterium at different facial sites in both populations; however, C. acnes exhibited a distinct correlation with P. acnes bacteriophages in Americans/Chinese. Taken together, in this study, we explored the fine-scale facial site-associated changes in the skin microbiome and provided insight into the ecological processes underlying facial microbial variations.

Dataset Information

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.

Publications

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.

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