Dataset Information

Mass spectrometry data from identification of host-defense related proteins using label-free quantitative proteomic analysis of milk whey from cows with Staphylococcus aureus subclinical mastitis.

ABSTRACT: This dataset is associated with our research article 'Identification of host-defence related proteins using label-free quantitative proteomic analysis of milk whey from cows with Staphylococcus aureus Subclinical mastitis' published in International Journal of Molecular Sciences. Milk samples were collected from cows suffering from S. aureus-associated subclinical mastitis and the proteins abundance were identified in comparison with samples collected from the control cows using liquid chromatography-mass spectrometry (LC-MS)-based label free proteomics analysis. Following the MS measurements, the raw spectra were processed using MaxQuant-Andromeda software and the protein identification was carried out through a search against Uniprot FASTA files of the Bos taurus reference proteome. Perseus software analysis was applied for computation of protein abundance. The raw file presented in this DiB was deposition at PRIDE repository in the PRIDE repository with the dataset identifier PXD007516.

SUBMITTER: Abdelmegid S

PROVIDER: S-EPMC6354741 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Mass spectrometry data from identification of host-defense related proteins using label-free quantitative proteomic analysis of milk whey from cows with Staphylococcus aureus subclinical mastitis.

Abdelmegid Shaimaa S Murugaiyan Jayaseelan J Abo-Ismail Mohamed M Caswell Jeff J Kelton David D Kirby Gordon G

Data in brief 20190110

This dataset is associated with our research article 'Identification of host-defence related proteins using label-free quantitative proteomic analysis of milk whey from cows with Staphylococcus aureus Subclinical mastitis' published in International Journal of Molecular Sciences. Milk samples were collected from cows suffering from S. aureus-associated subclinical mastitis and the proteins abundance were identified in comparison with samples collected from the control cows using li ...[more]

PMID: 30733978

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Project description:The microbial ecosystem in the udders of dairy cows directly influences the flavor and quality of milk. However, to our knowledge, no published research has analyzed the complex relationship between the udder microbiome and its associated metabolism in animals with subclinical mastitis. We identified the bacterial species and measured relative population numbers in the milk of cows with subclinical Streptococcus agalactiae mastitis (GBS) and compared this information to that from the milk of healthy cows. Metabolite profiles were determined to investigate correlations between the milk microbiota and metabolic factors in healthy vs. GBS dairy cows. Six milk samples from GBS cows and six from healthy cows were subjected to 16S rRNA gene sequencing to identify the microbial species using a MiSeq high-throughput sequencing apparatus. The metabolites present in the milk were identified by gas chromatography time-of-flight mass spectrometry. Both principal component analysis and orthogonal partial least squares discriminant analysis indicated that the metabolites were well-separated from each other in the milk samples from the two groups. GBS dramatically altered microbial diversity, and the GBS group had significantly fewer Proteobacteria, Actinobacteria, and Acidobacteria than the CON group, with greater relative abundance of Firmicutes (p < 0.01). Several bacterial genera, such as Streptococcus, were significantly more abundant in milk from the GBS group than in milk from the CON group, and there was a tendency for greater abundance of Turicibacter (p = 0.07) and Enterococcus spp. (p = 0.07) in the GBS group. The levels of five milk metabolites were significantly higher in the GBS group than in the CON group: phenylpyruvic acid, the homogentisic acid: 4-hydroxyphenylpyruvic acid ratio, the xanthine: guanine ratio, uridine and glycerol. Metabolic pathway analysis of the different metabolites revealed that the following were enriched in both groups: galactose metabolism; pentose and glucuronate interconversion; starch and sucrose metabolism; alanine, aspartate and glutamate metabolism; arginine biosynthesis; citrate cycle (TCA cycle); D-glutamine and D-glutamate metabolism; and the neomycin, kanamycin, and gentamicin biosynthesis pathways. Several typical metabolites were highly correlated with specific ruminal bacteria, such as Streptococcaceae, Lachnospiraceae, Lactobacillaceae and Corynebacteriaceae, demonstrating the functional correlations between the milk microbiome and associated metabolites. These findings revealed that the milk microbiota and metabolite profiles were significantly different between the two groups of cows, raising the question of whether the microbiota associated with the bovine mammary gland could be related to mammary gland health. There was also a relationship between milk quality and the presence of spoilage bacteria. Other bacterial taxa should be investigated, as related information may provide insights into how perturbations in milk metabolomics profiles relate to differences in milk synthesis between healthy cows and those with subclinical mastitis.

Project description:Background and aimThe term ESKAPE, recognized by the WHO, is an acronym, which refers to the pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., which is extremely virulent and multidrug-resistant. Although the term is used to designate nosocomial pathogens, in a milking environment, strains of Methicillin-resistant S. aureus have been isolated from cattle diagnosed with clinical and subclinical mastitis. Resistant strains may be involved in the transfer of genes conferring resistance to beta-lactam antimicrobials among the species of microorganisms related to mastitis etiology. This study aimed to trace the phenotypic and genotypic profiles of susceptibility to beta-lactams in S. aureus isolated from milk of cattle diagnosed with subclinical mastitis obtained from different rural properties located in the North of Minas Gerais State, Brazil.Materials and methodsSixteen microorganisms previously identified as S. aureus isolated from milk of cattle diagnosed with subclinical mastitis were submitted to matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF), mass spectrometry, and polymerase chain reaction (PCR) analysis for microbial species confirmation. The S. aureus beta-lactams antimicrobial phenotypic resistance profile was investigated by disk diffusion method. PCR methods were also performed to investigate the S. aureus genotypic beta-lactams resistance profile. For this purpose, bla Z, mec A, mec ALGA251, bla Oxa23, and bla KPC genes were screened among S. aureus isolates. The genetic diversity of S. aureus by fingerprint random amplified polymorphic DNA (RAPD)-PCR was also performed in this study.ResultsAll isolates showed phenotypic resistance to at least three beta-lactams, among which was meropenem. None of the isolates tested positive for the genes mec ALGA251, bla Oxa23, and bla KPC; however, the presence of the genes bla Z and mecA was detected among the isolates. The fingerprint analysis divided isolates into two distinct groups and 15 different subgroups. Despite the presence of clonality among the isolates, the PCR-RAPD analysis unveiled a heterogeneous profile with genetic diversity among the S. aureus isolates.ConclusionIn this study, we identified beta-lactams resistant S. aureus strains isolated from the milk of cows diagnosed with subclinical mastitis. The S. aureus beta-lactams resistance was investigated using a phenotypic and genotypic approach. We believe that molecular epidemiology, improved knowledge, and genetic basis of resistance to beta-lactams might assist in asserting guidelines for better management practices of dealing with subclinical mastitis and mapping of origin of resistant pathogens in the studied Brazilian area.

Project description:Whole-genome sequencing was carried out on 30 Staphylococcus (S.) aureus isolates from dairy cows with subclinical mastitis from all five provinces of Rwanda. Twenty-five of the isolates produced enough sequence to be analyzed using core genome multilocus sequence typing (cg-MLST). The isolates group into three main clusters. The largest cluster contain isolates of sequence type (ST) 152 (n = 6) and the closely related ST1633 (n = 2). These sequence types have previously mainly been encountered in humans. The isolates of the second-largest cluster belong to ST5477 (n = 5),so far exclusively isolated from cows in Rwanda. The third cluster consists of isolates of ST97 (n = 4), which is a well-known bovine-adapted sequence type. These three clusters were all widespread over the country. Isolates of the usually human-adapted sequence types 1 (n = 2) and 5 (n= 1) were found and a single isolate of ST2430, previously found among humans in Africa. Finally, four isolates of novel sequence types were found: ST7108 (n = 2), ST7109 (n = 1), and ST7110 (n = 1). The blaZ penicillin resistance gene was found in 84% of the isolates and was in all cases corroborated by phenotypic resistance determination. Five (20%) of the isolates carried a tetracycline resistance gene, tet(K) or tetM, and three of these five also displayed phenotypic resistance while two isolates carried a tetM-gene but were yet tetracycline susceptible. Seven (28%) isolates carried the dfrG gene conferring resistance to trimethoprim. Four of these isolates indeed were resistant to trimethoprim while three isolates were sensitive. The str gene conferring resistance to aminoglycosides was found in three isolates; however, none of these displayed resistance to gentamycin. Our data revealed a high diversity of the sequence types of S. aureus isolates from cows with subclinical mastitis in Rwanda. Two major clusters of ST97 and ST5477 are likely to be bovine adapted and cause mastitis while the third cluster of ST152 usually have been found in humans and may signify a recent transmission of these types from human to cows, for example from hand milking. The high prevalence of this sequence type among dairy cows may pose zoonotic threat. The sequence types were widely distributed without any geographic correlation. Penicillin resistance, the most common type of resistance with a prevalence over 80%, but also tetracycline and trimethoprim resistance were displayed by several isolates.

Dataset Information

Mass spectrometry data from identification of host-defense related proteins using label-free quantitative proteomic analysis of milk whey from cows with Staphylococcus aureus subclinical mastitis.

Publications

Mass spectrometry data from identification of host-defense related proteins using label-free quantitative proteomic analysis of milk whey from cows with <i>Staphylococcus aureus</i> subclinical mastitis.

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