Comparative Transcriptomic Analysis of Staphylococcus aureus Reveals the Genes Involved in Survival at Low Temperature

Low temperature storage leads to advanced upregulation of typical virulence regulators, pyk and purR of enterotoxigenic Staphylococcus aureus cultured on chicken meat

Staphylococcal enterotoxins have long been studied due to the food-borne illness caused and complex intracellular virulence regulation involved. Along with the popularized application of cold chain production of meat products, there is important significance to explore the influence of low temperature on enterotoxin genes expression correlated to regulators under meat cultivation. In this study, SEA and SEB type Staphylococcus aureus strains (designated Sa08 and Sa13 respectively) were cultivated on chicken meat at 8 and 25 °C, typical virulence regulators (agrA, saeS, srrB, rot, codY and icaA), enterotoxins (sea and seb) and metabolic factors (pyk and pyruvate, purR and xanthosine monophosphate) were monitored. As a result, cell density remained stable (104-105 CFU/g) at 8 °C with slight increase in 6 day, and there were drastic pyruvate accumulation along with storing days. Significant upregulation of typical virulence regulators, pyk, purR and seb occurred in post exponential phase at 25 °C (p < 0.001). Nevertheless, phenotypic indexes failed to correspond to transcriptional changes. Expression of seb depended on the upregulation of typical virulence regulators at 8 and 25 °C, and sea had independent expression profile different from typical virulence regulators at 8 °C. Comparing with 25 °C, consistent advanced upregulation of typical virulence regulators (except codY of Sa08), pyk and purR were observed both for Sa08 and Sa13 at 8 °C, and different strains exhibited varied early metabolic response but similar later metabolic status at 8 °C. These phenomena highlighted a concern that, enterotoxigenic S. aureus colonizing on chicken meat exhibited advanced upregulation of typical virulence regulators and close-related virulence at low temperature.

BD Vacutainer™ Urine Culture & Sensitivity Preservative PLUS Plastic Tubes Minimize the Harmful Impact of Stressors Dependent on Temperature and Time Storage in Uropathogenic Bacteria

Background: Urinary tract infection is a worldwide health problem. According to the Clinical Laboratory Improvement Amendments and the European Urinalysis Guideline, urine samples should be tested within 2 h of collection. Thus, using chemical preservatives that guarantee the pre-analytical conditions is a practical tool. However, the effects of temperature and storage time as uropathogenic bacteria stressors are unclear. Methods: Gram-negative and -positive ATTC strains, E. coli, P. mirabilis, E. faecalis, and S. aureus, were used in this study. Strains in liquid media were stored at 4, 25, and 37 °C for 0, 2, 12, 24, and 48 h in tubes with and without preservatives. Then, reactive oxygen species (ROS) levels, viable but non-culturable bacteria (VBNC), and bacteria growth were analyzed. Results: A high ROS level was associated with the presence of VBNC and dead bacteria with low CFU counts, but a low ROS level increased the CFU number, depending on temperature and storage time in tubes without preservatives (boric acid, sodium borate, and formate). The BD Vacutainer™ Urine Culture & Sensitivity Preservative PLUS Plastic Tubes (C&S-PP) prevent this ROS increase, maintaining the CFU number for longer. Conclusions: C&S-PP tubes minimize the stressor effects (temperature and time storage) on uropathogenic bacteria when stored, improving the pre-analytical conditions of cultures realized by the clinical laboratory.

Comparative genomic analysis and multilocus sequence typing of Staphylococcus aureus reveals candidate genes for low-temperature tolerance

Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types. The ST352 strains exhibited the greatest tolerance to low temperature, with a mean reduction in survival rate of 10.34 % (p < 0.05). Comparative genomics revealed a total of 1941 core genes in the three S. aureus strains, and BB-1 had 468 specific genes, which were enriched mainly in translation, DNA recombination, DNA repair, metabolic pathways, two-component systems, and quorum sensing. Molecular docking analysis revealed that the binding of the RsbW protein to the SigB protein of BB-1 decreased due to base mutations in rsbW, while the binding to the RsbV protein was enhanced. In addition, the results of real-time quantitative PCR showed that the RsbV-RsbW/SigB system of BB-1 may play a role in the low-temperature survival of S. aureus and the formation of SCVs. These results suggest that genes specific to BB-1 may contribute to the mechanism of adaptation to low temperature and the formation of SCVs. This study helps elucidate the causes of SCV formation by S. aureus at low temperature at the molecular level and provides a basis for exploring the safety control of cold chain food environments.

Dellaglioa spp. an underestimated genus isolated from high-oxygen modified-atmosphere packaged meat

The genus Dellaglioa (D.) actually comprises two species, i.e., D. algida and the recently described species D. carnosa. Both species are adapted to cold and have been typically recovered from meat products. However, their importance has thus far been underestimated, since routine culture-based analysis failed to support their growth. Furthermore, their occurrence on meat packed under high-oxygen MA conditions (HiOx-MAP) is controversial because they have been described as being oxygen-sensitive. In this study, we focused on the targeted isolation of Dellaglioa spp. from HiOx-MAP meat samples and the characterization of our isolates regarding their adaption to HiOx-MAP conditions, their spoilage potential, as well as food safety aspects. We used a medium recently developed specifically for strains of this genus and investigated ten meat batches from seven different suppliers. Our study confirms that the occurrence of Dellaglioa spp. on HiOx-MAP meat is non-sporadic, reaching cell counts ranging from log10 5.8-7.1 CFU/cm2 at a late stage of chilled storage. Autochthonous Dellaglioa spp. and Leuconostoc (L.) gasicomitatum dominated the microbiota of the beef steaks with similar growth behavior. Our results suggest that Dellaglioa spp. benefits from the heme-dependent respiration of oxygen by L. gasicomitatum. Furthermore, whole genome analysis revealed the presence of genes predictively involved in oxidative stress defense, survival, and adaptation in meat environments. Moreover, we predict a weak aminogenic potential of D. algida strains. Tyramine production from tyrosine seems to be a species-specific characteristic of D. carnosa. The extent to which D. algida and D. carnosa occurrence is influenced by or even dependent on the composition of the entire microbiota remains to be investigated.

Comparison of microbial molecular diagnosis efficiency within unstable template metagenomic DNA samples between qRT-PCR and chip-based digital PCR platforms

Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.

Integrative analysis of the effects of organic and conventional farming methods on peanut based on transcriptome and metabolomics

To elucidate the nutritional quality of peanut under different farming methods, we selected two cultivars, "jihua13" and "jihua4", to grow in organic and conventional environments, respectively. After harvest, we measured physiological parameters and differential metabolites. Metabolomics showed that most of the amino acids, carbohydrates, and secondary metabolites in organically grown jihua4 were downregulated, which was completely the opposite in jihua13. Fatty acids associated with heart disease and hypertension are reduced in organically grown peanuts. In particular, the highly statistically significant tryptophan betaine seems to be used as a reference to distinguish between organic and conventional cultivation. Mechanisms leading to differences in crop chemical composition are explained by transcriptome analysis. The results of the transcriptome analysis indicated that organic cultivation largely affects the synthesis of amino acids and carbohydrates in jihua13. Combined analysis of transcriptome and metabolomics found that variety jihua13 is more sensitive to farming methods and produces more unsaturated fatty acids than jihua4.

ArcR contributes to tolerance to fluoroquinolone antibiotics by regulating katA in Staphylococcus aureus

Staphylococcus aureus is an opportunistic pathogen that shows a unique ability to quickly respond to a variety of antibiotics. The Crp/Fnr family transcriptional regulator ArcR controls expression of arginine deiminase pathway genes arcABDC, which enable the utilization of arginine as an energy source for cell growth under anaerobic conditions. However, ArcR shares low overall similarity with other Crp/Fnr family proteins, suggesting that they differ in the response to environmental stress. In this study, MIC and survival assays were performed to determine the role of ArcR in antibiotic resistance and tolerance. The results showed that deletion of arcR reduced tolerance of S.aureus to fluoroquinolone antibiotics, mainly through a defect in the response to oxidative stress. In ΔarcR mutant, the expression of the major catalase gene katA was downregulated, and katA overexpression restored bacterial resistance to oxidative stress and antibiotics. We showed that ArcR directly regulated katA transcription by binding to the promoter region of katA. Therefore, our results revealed the contribution of ArcR in bacterial tolerance to oxidative stress and subsequently to fluoroquinolones antibiotics. This study added our understanding on the role of Crp/Fnr family in bacterial susceptibility to antibiotics.