Metagenomics reveals differences in the composition of bacterial antimicrobial resistance and antibiotic resistance genes in pasteurized yogurt and probiotic bacteria yogurt from China.

Antimicrobial resistance has become a global public health concern, and antibiotic resistance genes (ARG) in food are a research focus. In China, probiotics and pasteurized yogurts are the 2 main types of commercially available yogurt, but the distribution and differences of antibiotic-resistant bacteria and gene types in these products are not well known. This study used a shotgun metagenomic approach to analyze 22 different types of yogurt collected from 9 main yogurt-producing areas in China; each type of yogurt included 8 different batches of samples. The abundance and diversity of bacteria identified in probiotic yogurt were significantly higher than those in pasteurized yogurt, with Acetobacter, Raoultella, and Burkholderia identified as unique and highly abundant genera in probiotic yogurt. Similarly, the abundance of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. was higher than that in pasteurized yogurt. A total of 1,149 ARG subtypes belonging to 16 ARG types were identified, with the highest abundance of rifampicin, multidrug efflux pumps, and quinolone resistance genes detected. Network analysis revealed significant nonrandom co-occurrence relationships between different types and subtypes of ARG in yogurt samples. A total of 44 ARG subtypes in pasteurized yogurt were potentially hosted by 36 bacterial genera, and in probiotic yogurt, 63 ARG were expected to be hosted by 86 bacterial species from 37 genera. These findings indicate potential safety issues in fermented dairy products and emphasize the need for a more hygienic environment when processing probiotic yogurt.

Single-molecule real-time sequencing reveals differences in bacterial diversity in raw milk in different regions and seasons in China.

The quality of raw milk is a key factor influencing the whole dairy processing chain. The richness and diversity of bacteria in raw milk affect its quality and safety. However, traditional microbial detection methods mainly depend on the known microbe culture and are often time consuming. Thus, the development of efficient ways for supervising any possible microbiological contamination is desiderated. In the current work, single-molecule real-time (SMRT) sequencing, developed by Pacific Biosciences (PacBio), was applied to acquire long reads and applied for discrimination of bacteria at species level. Forty samples of raw milk obtained from Beijing, Hebei, Inner Mongolia, Shanghai, and Guangdong in China during summer, autumn, and winter were investigated. Among 35 bacteria species identified in these samples, Acinetobacter albensis, Pseudomonas gessardii, Pseudomonas weihenstephanensis, and Rahnella inusitata were the bacteria with the highest relative abundance in the overall sample, whereas the bacteria with the highest relative abundance in raw milk samples of different origins and seasons are different. Significant differences in bacterial richness and bacterial community diversity in raw milk grouped according to different production areas and different sampling seasons were confirmed by Welch's t-test. Interestingly, the transport distance and transport time positively correlated with the relative abundance of Pseudomonas weihenstephanensis, suggesting that the content of this bacteria was expected to be a standard for evaluating the freshness of raw milk. Pathogens Bacillus cereus and Klebsiella pneumoniae were detected in most samples, indicating that the raw milk was at risk of contamination by pathogenic bacteria. Moreover, the findings of this study provide important evidence for quality and safety monitoring and biological control of raw milk.

Metagenomic profiles of the antimicrobial resistance in traditional Chinese fermented meat products: Core resistome and co-occurrence patterns.

Antimicrobial resistance (AMR) poses a significant challenge to global health, and the presence of antibiotic resistance genes (ARGs) in food poses a potential threat to public health. Traditional Chinese fermented meat products (FMPs) are highly favored because of their unique flavors and cultural value. However, microbial safety and the potential distribution and composition of AMR in these products remain unclear. In this study, a comprehensive analysis of bacterial composition and antibiotic-resistant populations in 216 samples of traditional fermented meat products from different regions of China was conducted using a metagenomic approach. Staphylococcus was the most abundant genus in the samples, accounting for an average abundance of 29.9 %, followed by Tetragenococcus (17.1 %), and Latilactobacillus (3.6 %). A core resistome of FMP samples was constructed for the first time using co-occurrence network analysis, which revealed the distribution and interrelationships of ARGs and bio/metal-resistant genes (BMRGs). Random forest analysis identified the lincosamide nucleotidyltransferase lnuA and the multidrug and toxic compound extrusion (MATE) transporter abeM as potential indicators for assessing the overall abundance of the core resistome. Additionally, Staphylococcus, Acinetobacter, and Pseudomonas were identified as hosts constituting the core resistome. Despite their low abundance, the latter two still serve as major reservoirs of antibiotic resistance genes. Notably, Lactococcus cremoris was identified as the key host for tetracycline resistance genes in the samples, highlighting the need for enhanced resistance monitoring in lactic acid bacteria. Based on our findings, in the microbial safety assessment of fermented meat products, beyond common foodborne pathogens, attention should be focused on detecting and controlling coagulase-negative Staphylococcus, Acinetobacter, and Pseudomonas, and addressing bacterial resistance. The quantitative detection of lnuA and abeM could provide a convenient and rapid method for assessing the overall abundance of the core resistome. Our findings have important implications for the control of bacterial resistance and prevention of pathogenic bacteria in fermented meat products.

Insight into Bacillus cereus Associated with Infant Foods in Beijing.

This study was undertaken to investigate the prevalence, antimicrobial resistance, and virulence gene profiles of Bacillus cereus in different brands of infant formula in Beijing supermarkets. Eighty-eight Bacillus cereus isolates were recovered in sixty-eight infant formulas of five domestic brands and fourteen imported brands. The prevalence rate in domestic and imported samples were 70.6% and 52.9%, respectively. Lower mean prevalence level was found in domestic samples (1.17 MPN/g) compared with the imported samples (3.52 MPN/g). Twenty-four virulence gene profiles were found, and most strains carried at least one virulence gene. The prevalence of nheA, nheB, nheC, cytK, bceT, and entFM in domestic and imported brand samples was similar. The occurrence of enterotoxin genes hblA, hblC, and hblD in domestic samples were 22.2%, 27.8%, and 22.2%, respectively, which was significantly higher than imported samples. Antimicrobial drugs-susceptibility analysis showed that all isolates were susceptible to gentamincin, amikacin, and ciprofloxacin; 38%, 7%, and 2.3% were resistant to rifampin, tetracycline, and chloramphenicol, respectively; and only one isolate was resistant to trimethoprim-sulfamethoxazole. Moreover, the cell numbers of Bacillus cereus in prepared infant formula increased rapidly at room temperature. Thus, monitoring guidelines are needed for accepted levels of Bacillus cereus in infant formula.

Reduction of serum cholesterol and its mechanism by Lactobacillus plantarum H6 screened from local fermented food products.

Hypercholesterolemia is the leading cause of cardiovascular disease worldwide. In this study, the lactic acid bacteria (Lactobacillus plantarum H6) screened from homemade fermented foods in northeastern China were used to study their cholesterol-lowering ability and to analyze their degradation mechanism. Results showed that L. plantarum H6 significantly reduced serum cholesterol levels in C57BL/6 mice fed a hypercholesterolemia diet. It mainly promoted the expression of CYP7A1 gene by inhibiting the farnesoid X receptor pathway to increase the in vivo synthesis of bile acids and improved the intestinal microbial community structure of C57BL/6 mice to increase the abundance of bacterial flora containing bile salt hydrolase activity. Hence, L. plantarum H6 played a role in reducing the cholesterol content in mice.

Mixed Lactobacillus plantarum Strains Inhibit Staphylococcus aureus Induced Inflammation and Ameliorate Intestinal Microflora in Mice.

Objective. Staphylococcus aureus is an important pathogen that causes intestinal infection. We examined the immunomodulatory function of single and mixed Lactobacillus plantarum strains, as well as their impacts on the structure of the microbiome in mice infected with Staphylococcus aureus. The experiment was divided into three groups: protection, treatment, and control. Serum IFN-γ and IL-4 levels, as well as intestinal sIgA levels, were measured during and 1 week after infection with Staphylococcus aureus with and without Lactobacillus plantarum treatment. We used 16s rRNA tagged sequencing to analyze microbiome composition. IFN-γ/IL-4 ratio decreased significantly from infection to convalescence, especially in the mixed Lactobacillus plantarum group. In the mixed Lactobacillus plantarum group the secretion of sIgA in the intestine of mice (9.4-9.7 ug/mL) was significantly higher than in the single lactic acid bacteria group. The dominant phyla in mice are Firmicutes, Bacteroidetes, and Proteobacteria. Treatment with mixed lactic acid bacteria increased the anti-inflammatory factor and the secretion of sIgA in the intestine of mice infected with Staphylococcus aureus and inhibited inflammation.

A novel CCM1 gene mutation causes cerebral cavernous malformation in a Chinese family.

Familial cerebral cavernous malformations (CCMs) are characterized by an autosomal dominant transmission with incomplete penetrance. We have previously reported a 1292delAT mutation in the CCM1 gene in a Chinese family with CCM. Here we report a novel deletion of CCM1 that correlates strongly with CCM formation in another family. Ten affected family members were observed among the 25 participants, and multiple CCM lesions were detected in seven individuals. Nucleotide sequencing analysis in the index patient and other affected members showed a CAAA deletion in exon 12 at nucleotide (NT) 1197. We predict this deletion produces a premature stop code (TGA) at NT 1228, resulting in a truncated protein of 409 amino acids.