Biology subjects

Dean, C. J.

Publications and source records attributed to Dean, C. J..

3 recordsLinked to original sources

bioRxiv2024

In vitro antimicrobial activity of non-aureus Staphylococci and Mammaliicocci against Staphylococcus aureus and Streptococcus uberis and their relationship with the presence of intramammary infections in organic dairy cows

Prior studies have suggested that non-aureus staphylococci and mammaliicoci (NASM) possess inhibitory activity against mastitis pathogens. However, their impact on udder health outcomes and the mechanisms underlying this potential protective effect remain poorly understood. Our first objective was to identify NASM species on teat apices of organic dairy cows, assess their within-species phylogeny, and explore associations with presence of intramammary infections (IMI) and genomic features, including antimicrobial peptides (AMPs), virulence, and resistance genes. The second objective was to evaluate the in vitro antimicrobial activity of NASM isolates against mastitis pathogens and examine its associations with taxonomy, phylogeny, AMP genes, and IMI. Milk and teat apex swabs were collected weekly from 114 cows on two organic farms. Milk was cultured to identify Staphylococcus aureus (SAU) or Streptococcus spp. and Streptococcus-like organisms (SSLO) IMI. A case-control was designed to include cows with and without SAU or SSLO IMI. For each selected cow, the teat apex gauze swab collected during the week preceding IMI diagnosis (or corresponding time for controls) was aerobically cultured, and the taxonomy of isolates was determined using mass spectrometry. Isolates classified as NASM were subjected to whole genome sequencing using Illumina MiSeq. The inhibitory activity of NASM isolates was tested against SAU and Streptococcus uberis. Phylogenetic trees were constructed using Snippy and IQ-TREE. Genomes were assembled and annotated to identify species, AMP genes, virulence, and antimicrobial resistance markers. The in vitro antimicrobial activity of NASM varied across species and between cows with and without an IMI. Staphylococcus succinus was the species most frequently associated with highly inhibitory isolates, which were more prevalent in cows without IMI (19.4% vs 5.8%). Organic dairy cow teat apices harbored multiple NASM species and strains. All isolates had at least 1 AMP associated gene in their genome. In vitro antimicrobial activity was generally unrelated to clade membership, except for isolates classified as Staphylococcus succinus. Staphylococcus aureus had high virulence gene prevalence, while NASM species showed lower, species-specific prevalence. This study advances understanding of NASM antimicrobial activity and virulence potential.

microbiology↗

bioRxiv2023

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk

Contaminants can easily outnumber bacteria that originate within the milk itself, milk microbiome research currently suffers from a critical knowledge gap; namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelium, stripped and cisternal milk, used numerous negative controls to identify potential sources of microbial contamination. Two algorithms were used to mathematically remove this contamination and to track potential movement of microbes among our samples. Our results suggest that majority (i.e., >75%) of the sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. The contaminants in milk samples were primarily sourced from the DNA extraction kits and the internal and external skin of the teat, while the teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse and compositionally distinct bacterial profile compared with the teat skin samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in the sequences of milk samples, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during the sample collection and processing workflows. ImportanceObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass, and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows; and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.

microbiology↗

bioRxiv2023

Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infection risk in primiparous cows under organic directives

The primary objective of this study was to identify associations between teat apex microbiome and Staphylococcus aureus intramammary infection (IMI) risk in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on 5 organic dairy farms. We observed a strong association between S. aureus DNA in the metagenomic teat apex data prior to parturition and the odds of S. aureus IMI after parturition (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93) and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Microcin B17 was the most prevalent antibacterial peptide on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of Microcin B17 was also higher in cases compared to controls (LFC 0.26). Cow and farm random effects often explained a large proportion of the observed variability in the teat apex microbiome, suggesting that our results need to be interpreted within the context of the random effects. IMPORTANCEIntramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the organic dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes detection of genomics features such as AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role pre-partum teat apex microbiome dynamics play in IMI risk.

ecology↗