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The aim of this study was to investigate the prevalence and genetic environment of the multidrug resistance gene lsa(E) in food-related Staphyloccocus aureus in China.1463 S. aureus from retail food products in 39 Chinese cities were investigated to determine the prevalence of lsa(E). Furthermore, antimicrobial susceptibility testing, whole-genome sequencing (WGS), and complete genetic analysis were performed in lsa(E)-positive isolates.Thirty-five isolates (2.4%) were positive for the lsa(E) gene, which had an extensive multidrug-resistance phenotype. ST9-t899 and ST1-t4792 were the common sequence types in positive strains. The lsa(E) genes were located in two different types of novel multidrug resistance region (MRRlsa[E]) on the chromosome. The Sa-MRRlsa(E)-I were inserted into the lctP gene. The Sa-MRRlsa(E)-II were inserted into the crtP gene, and were comprised of seven antibiotic resistance genes (ARGs) interspersed with varieties of insertion sequences (ISs), transposons, and DNA invertase genes, showing a novel arrangement harboring lsa(E). Part of transposon Tn1546 was inserted downstream of lnu(B) in the novel Sa-MRRlsa(E)-II. Both types of Sa-MRRlsa(E) could be excised from the chromosome, indicating that Sa-MRRlsa(E) may be transferable.Our study is the first systematical investigation of lsa(E)-positive S. aureus in retail foods in China. It indicated that the origin of most food-related lsa(E)-positive S. aureus in China might be associated with livestock or poultry breeding farms, and these strains may be transmitted between animals and food. S. aureus carrying novel Sa-MRRlsa(E), especially, serve as reservoirs of antibiotic resistance traits, and warrant further attention.

Small non-coding RNAs (sRNAs) in bacteria are important regulatory molecules for controlling virulence. In Vibrio spp., Qrr sRNAs are critical for quorum-sensing pathways and regulating the release of some virulence factors. However, the detailed role of Qrr sRNAs in the virulence of Vibrio parahaemolyticus remains poorly understood. In this study, we identified a Vibrio sRNA Qrr5 that positively regulates cytotoxicity and adherence in Caco-2 cells by primarily regulating the T3SS1 gene cluster. A number of 185, 586, 355, and 74 differentially expressed genes (DEGs) detected at 0, 2, 4, and 6 h post-infection, respectively, were mainly associated with ABC transporters and two-component system pathways. The DEGs exhibited a dynamic change in expression at various time points post-infection owing to the deletion of Qrr5. Accordingly, 17 related genes were identified in the co-expression network, and their interaction with Qrr5 was determined based on weighted co-expression network analysis during infection. Taken together, our results provide a comprehensive transcriptome profile of V. parahaemolyticus during infection in Caco-2 cells.

Bacillus cereus, an important foodborne pathogen, poses a risk to food safety and quality. Robust biofilm formation ability is one of the key properties that is responsible for the food contamination and food poisoning caused by B. cereus, especially the emetic strains. To investigate the mechanism of biofilm formation in emetic B. cereus strains, we screened for the mutants that fail to form biofilms by using random mutagenesis toward B. cereus 892-1, an emetic strain with strong biofilm formation ability. When knocking out flgE, a flagellar hook encoding gene, the mutant showed disappearance of flagellar structure and swimming ability. Further analysis revealed that both pellicle and ring presented defects in the null mutant compared with the wild-type and complementary strains. Compared with the flagellar paralytic strains ΔmotA and ΔmotB, the inhibition of biofilm formation by ΔflgE is not only caused by the inhibition of motility. Interestingly, ΔflgE also decreased the synthesis of cereulide. To our knowledge, this is the first report showing that a flagellar component can both affect the biofilm formation and cereulide production in emetic B. cereus, which can be used as the target to control the biohazard of emetic B. cereus.

PurposeTo evaluate the association of gut microbiome signature and disease progression in locally advanced non-small cell lung cancer (LA-NSCLC) patients treated with concurrent chemoradiotherapy (CCRT) by fecal metagenome analysis.MethodsMetagenome-wide association studies on baseline fecal samples from 18 LA-NSCLC patients before CCRT and 13 controls from healthy first-degree relatives were performed. Among the 18 LA-NSCLC patients, six patients were defined as the long progression-free survival (long-PFS) group (PFS≥11 months) while another 12 were in the short-PFS group (PFSResultsThe Firmicutes/Bacteroidetes value of long-PFS group was higher than those of short-PFS (p=0.073) and healthy individual groups (p=0.009). Meanwhile, long-PFS group had significantly higher diversities in Fungi, Archaea, and Viruses than short-PFS group. The KEGG pathways overrepresented in short-PFS group included fructose and mannose metabolism (p=0.028), streptomycin biosynthesis (p=0.028), acarbose and validamycin biosynthesis (p=0.013), ribosome biogenesis in eukaryotes (p=0.035), biosynthesis of vancomycin group antibiotics (p=0.004), apoptosis-fly (p=0.044), and tetracycline biosynthesis (p=0.044), while those overrepresented in long-PFS group included fatty acid biosynthesis (p=0.035), fatty acid metabolism (p=0.008), vancomycin resistance (p=0.008), longevity regulating pathway-worm (p=0.028), type II diabetes mellitus (p=0.004), and viral carcinogenesis (p=0.003). Further analysis of antibiotic resistome demonstrated that the short-PFS group had a trend with more antibiotic resistance genes than healthy control (p=0.070) and long-PFS groups (p=0.218). The vancomycin resistance sequences were significantly enriched in the long-PFS group compared to the short-PFS group (p=0.006).ConclusionsThe baseline gut microbiome composition and functionality might be associated with PFS in LA-NSCLC treated with CCRT. The outcome of CCRT might be modulated through bacterial metabolic pathways. The antibiotic resistance genes might play a role in disease progression and provide potential information on the relationship between the use of antibiotics and treatment efficacy of CCRT in LA-NSCLC.

Although lactic acid bacteria (LAB) were shown to be effective for preventing photoaging, the underlying molecular mechanisms have not been fully elucidated. Accordingly, we examined the anti-photoaging potential of 206 LAB isolates and discovered 32 strains with protective activities against UV-induced injury. All of these 32 LABs exhibited high levels of 2,2-diphenyl-picrylhydrazyl, as well as hydroxyl free radical scavenging ability (46.89–85.13% and 44.29–95.97%, respectively). Genome mining and metabonomic verification of the most effective strain, Limosilactobacillus fermentum XJC60, revealed that the anti-photoaging metabolite of LAB was nicotinamide (NAM; 18.50 mg/L in the cell-free serum of XJC60). Further analysis revealed that LAB-derived NAM could reduce reactive oxygen species levels by 70%, stabilize the mitochondrial membrane potential, and increase the NAD+/NADH ratio in UV-injured skin cells. Furthermore, LAB-derived NAM downregulated the transcript levels of matrix metalloproteinase (MMP)-1, MMP-3, interleukin (IL)-1β, IL-6, and IL-8 in skin cells. In vivo, XJC60 relieved imflammation and protected skin collagen fiber integrity in UV-injured Guinea pigs. Overall, our findings elucidate that LAB-derived NAM might protect skin from photoaging by stabilizing mitochondrial function, establishing a therotical foundation for the use of probiotics in the maintenance of skin health.

Matrix-assisted laser desorption/ionization time-of-flight mass (MALDI-TOF) spectrometry fingerprinting has reduced turnaround times, costs, and labor as conventional procedures in various laboratories. However, some species strains with high genetic correlation have not been directly distinguished using conventional standard procedures. Metabolomes can identify these strains by amplifying the minor differences because they are directly related to the phenotype. The pseudotargeted metabolomics method has the advantages of both non-targeted and targeted metabolomics. It can provide a new semi-quantitative fingerprinting with high coverage. We combined this pseudotargeted metabolomic fingerprinting with deep learning technology for the identification and visualization of the pathogen. A variational autoencoder framework was performed to identify and classify pathogenic bacteria and achieve their visualization, with prediction accuracy exceeding 99%. Therefore, this technology will be a powerful tool for rapidly and accurately identifying pathogens.

The contamination of antibiotic resistance genes (ARGs) may directly threaten human health. This study used a metagenomic approach to investigate the ARG profile in a drinking water treatment system (DWTS) in south China. In total, 317 ARG subtypes were detected; specifically, genes encoding bacitracin, multidrug, and sulfonamide were widely detected in the DWTS. Putative ARG hosts included Acidovorax (6.0%), Polynucleobacter (4.3%), Pseudomonas (3.4%), Escherichia (1.7%), and Klebsiella (1.5%) as the enriched biomarkers in the DWTS, which mainly carried bacitracin, beta-lactam, and aminoglycoside ARGs. From a further analysis of ARG-carrying contigs (ACCs), Stenotrophomonas maltophilia and Pseudomonas aeruginosa were the most common pathogens among the 49 ACC pathogens in the DWTS. The metagenomic binning results demonstrated that 33 high-quality metagenome-assembled genomes (MAGs) were discovered in the DWTS; particularly, the MAG identified as S. maltophilia-like (bin.195) harbored the greatest number of ARG subtypes (n = 8), namely, multidrug (n = 6; smeD, semE, multidrug_transporter, mexE, semB, and smeC), beta-lactam (n = 1; metallo-beta-lactamase), and aminoglycoside [n = 1; aph(3’)-IIb]. The strong positive correlation between MGEs and ARG subtypes revealed a high ARG dissemination risk in the DWTS. Based on the pure-culture method, 93 isolates that belong to 30 genera were recovered from the DWTS. Specifically, multidrug-resistant pathogens and opportunistic pathogens such as P. aeruginosa, Bacillus cereus, and S. maltophilia were detected in the DWTS. These insights into the DWTS’s antibiotic resistome indicated the need for more comprehensive ARG monitoring and management in the DWTS. Furthermore, more effective disinfection methods need to be developed to remove ARGs in DWTSs, and these findings could assist governing bodies in the surveillance of antibiotic resistance in DWTSs.

This study investigated the molecular characteristics of rifampin-resistant (RIF-R) Staphylococcus aureus isolates recovered from 4300 retail food samples covering most provincial capitals in China, from 2011 to 2016. Of the 1463 S. aureus enrolled, 149 isolates (142 MSSA and 7 MRSA) were identified as rifampicin-resistant, including 20 high-level (MICs ≥ 8 μg/mL) and 129 low-level (MICs between 2 and 4 μg/mL) rifampicin-resistant strains. Most of the RIF-R S. aureus isolates were resistant to more than three antibiotics. The mutations in the rifampicin resistance-determining region of the rpoB gene were studied in all RIF-R strains. All of the strains presented the mutational change 481 His/Asn and five isolates presented an additional mutation, including 477 Asp/Tyr, 527 Ile/Met, and 466 Leu/Ser, respectively. Thirteen STs and twenty-one spa types were represented, in which five MRSA showed non-type SCCmec and the remaining MRSA belonged to SCCmec type IV—where, ST1-t127 was the predominant type from all of the isolates, while ST398-t034 was the predominant type for the MRSA isolates. In this study, we found that the food-related RIF-R S. aureus may have a unique genetic background selection. However, the scenario regarding the presence of RIF-R S. aureus, especially MRSA, in retail food in China is not favorable and warrants public attention.

Currently, invasive infections caused by Staphylococcus argenteus, which is a recently named staphylococcal species, are increasingly reported worldwide. However, only a few genomic studies of S. argenteus have offered comprehensive information regarding its genetic diversity, epidemiological characteristics, antimicrobial resistance genes (ARGs), virulence genes and other profiles. Here, we describe a comparative genomic analysis by population structure, pangenome, panmobilome, region-specific accessory genes confer an adaptive advantage in 153 S. argenteus strains which comprised 24 strains sequenced in this study and 129 strains whose genome sequences were available from GenBank. As a result, the population of S. argenteus comprised seven genetically distinct clades, including two major clades (C1 and C2), with distinct isolation source patterns. Pangenome analysis revealed that S. argenteus has an open pangenome composed of 7,319 genes and a core genome composed of 1,508 genes. We further determined the distributions of 75 virulence factors (VFs) and 30 known ARGs and identified at least four types of plasmids and 93 complete or partial putative prophages. It indicate that S. argenteus may show a similar level of pathogenicity to that of S. aureus. This study also provides insights into the evolutionary divergence of this pathogen, indicating that the geographical distribution was a potential driving force behind the evolutionary divergence of S. argenteus. The preferential horizontal acquisition of particular elements, such as staphylococcal cassette chromosome mec elements and plasmids, was observed in specific regions, revealing potential gene exchange between S. argenteus strains and local S. aureus strains. Moreover, multiple specific genes related to environmental adaptation were identified in strains isolated from East Asia. However, these findings may help promote our understanding of the evolutionary divergence of this bacterium at a high genetic resolution by providing insights into the epidemiology of S. argenteus and may help combat its spread.

The commensal microbiome influences skin immunity, but its function in toenail health remains unclear. Paronychia is one of the most common inflammatory toenail diseases, but antibiotic treatment is seldom effective in clinical cases. In this study, we performed 16S rRNA sequencing to investigate the characteristics of microbes associated with paronychia in order to identify the key microorganisms involved in inflammation. Seventy dermic samples were collected from patients with paronychia and the differences in dermic microbiota were analyzed in patients with different inflammation severities. Distinct clustering of dermal microbiota was observed in the dermis with different inflammation severities. A higher relative abundance of anaerobic microorganisms such as Parvimona, Prevotella, and Peptoniphilus was observed in severe paronychia, whereas Lactobacillus disappeared with disease progression. Co-occurring network analysis suggested that the disturbance of the dermic microbiome and attenuation of antagonism by Lactobacillus against anaerobic pathogens may aggravate inflammation in paronychia. Functional analysis showed that dermic microbiome disturbance may worsen microbial metabolism and tissue repair in the skin. In conclusion, we revealed that an increased abundance of anaerobic microorganisms and loss of Lactobacillus in the dermis may promote paronychia progression and microbiological imbalance may aggravate inflammation in patients with paronychia.

Foodbone norovirus (NoV) is the leading cause of acute gastroenteritis worldwide. Candidate vaccines are being developed, however, no licensed vaccines are currently available for managing NoV infections. Screening for stimulated antibodies with broad-spectrum binding activities can be performed for the development of NoV polyvalent vaccines. In this study, we aimed to develop an indirect enzyme-linked immunosorbent assay (ELISA) for testing the broad spectrum of anti-NoV antibodies. Capsid P proteins from 28 representative NoV strains (GI.1–GI.9 and GII.1–GII.22 except GII.11, GII.18, and GII.19) were selected, prepared, and used as coating antigens on one microplate. Combined with incubation and the horseradish peroxidase chromogenic reaction, the entire process for testing the spectrum of unknown antibodies required 2 h for completion. The intra-assay and inter-assay coefficients of variation were less than 10%. The new method was successfully performed with monoclonal antibodies and polyclonal antibodies induced by multiple antigens. In conclusion, the indirect ELISA assay developed in this study had a good performance of reliability, convenience, and high-throughput screening for broad-spectrum antibodies.

The process of soybean fermentation has been practiced for more than 3,000 years. Although Dajiang and Sufu are two popular fermented soybean products consumed in North China, limited information is available regarding their microbial composition. Hence, the current study sought to investigate, and compare, the physicochemical indicators and microbial communities of traditional Dajiang and Sufu. Results showed that the titratable acidity (TA), and salinity, as well as the lactic acid, and malic acid contents were significantly higher in Sufu samples compared to Dajiang. Furthermore, Sufu samples contain abundant sucrose and fructose, while the acetic acid content was lower in Sufu compared to Dajiang samples. Moreover, the predominant bacterial phyla in Dajiang and Sufu samples were Firmicutes and Proteobacteria, while the major genera comprise Bacillus, Lactobacillus, Tetragenococcus, and Weissella. Moreover, Dajiang samples also contained abundant Pseudomonas, and Brevundimonas spp., while Halomonas, Staphylococcus, Lysinibacillus, Enterobacter, Streptococcus, Acinetobacter, and Halanaerobium spp. were abundant in Sufu samples. At the species level, Bacillus velezensis, Tetragenococcus halophilus, Lactobacillus rennini, Weissella cibaria, Weissella viridescens, Pseudomonas brenneri, and Lactobacillus acidipiscis represented the major species in Dajiang, while Halomonas sp., Staphylococcus equorum, and Halanaerobium praevalens were the predominant species in Sufu. Acetic acid and sucrose were found to be the primary major physicochemical factor influencing the bacterial communities in Dajiang and Sufu, respectively. Furthermore, Bacillus subtilis is strongly correlated with lactic acid levels, L. acidipiscis is positively correlated with acetic acid levels, while Staphylococcus sciuri and S. equorum are strongly, and positively, correlated with malic acid. Following analysis of carbohydrate and amino acid metabolism in all samples, cysteine and methionine metabolism, as well as fatty acid biosynthesis-related genes are upregulated in Dajiang compared to Sufu samples. However, such as the Staphylococcus, W. viridescens, and P. brenneri, as potentially foodborne pathogens, existed in Dajang and Sufu samples. Cumulatively, these results suggested that Dajiang and Sufu have unique bacterial communities that influence their specific characteristics. Hence, the current study provides insights into the microbial community composition in Dajiang and Sufu samples, which may facilitate the isolation of functional bacterial species suitable for Dajiang and Sufu production, thus improving their production efficiency.

Human norovirus is a common cause of acute gastroenteritis worldwide, and oysters have been found to be the main carriers for its spread. The lack of efficient pre-treatment methods has been a major bottleneck limiting the detection of viruses in oysters. In this study, we established a novel immunomagnetic enrichment method using polyamidoamine (PAMAM) dendrimer/SA-biotin-mediated cascade amplification for reverse transcriptase quantitative real-time polymerase chain reaction (RT-qPCR) detection. We compared the capture efficiency of traditional immunomagnetic enrichment, biotin-amplified immunomagnetic enrichment, and PAMAM dendrimer/SA-biotin-mediated cascade-amplification immunomagnetic enrichment. The optimal capture efficiency of the novel method was 44.26 ± 1.45%, which increased by 183.17% (P < 0.01) and 18.09% (P < 0.05) compared with the first two methods, respectively. Three methods were all applied in detecting norovirus in 44 retail oysters, the detection rate of the PAMAM dendrimer/SA-biotin-mediated method was 25.0%, which was higher than those of traditional IME (15.90%) and SA-biotin-amplified IME (18.80%) by 9.1 and 6.2%, respectively. In conclusion, the novel method can be applied for the rapid detection of norovirus in oysters, which can help reduce the cost and time of detection and improve detection rates.

Phenol is a toxic organic molecule that is widely detected in the natural environment, even in drinking water sources. Biological methods were considered to be a good tool for phenol removal, especially microbial immobilized technology. However, research on the “seed” bacteria along with microbial community analysis in oligotrophic environment such as drinking water system has not been addressed. In this study, Acinetobacter sp. DW-1 with high phenol degradation ability had been isolated from a drinking water biofilter was used as seeded bacteria to treat phenol micro-polluted drinking water source. Meanwhile, the whole genome of strain DW-1 was sequenced using nanopore technology. The genomic analysis suggests that Acinetobacter sp. DW-1 could utilize phenol via the β-ketoadipate pathway, including the catechol and protocatechuate branches. Subsequently, a bio-enhanced polyhedral hollow polypropylene sphere (BEPHPS) filter was constructed to investigate the stability of the seeded bacteria during the water treatment process. The denatured gradient gel electrophoresis (DGGE) profile and the quantification of phenol hydroxylase gene results indicate that when the BEPHPS filter was operated for 56 days, Acinetobacter sp. was still a persistent and competitive bacterium in the treatment group. In addition, 16S rRNA gene amplicon sequencing results indicate that Acinetobacter sp., as well as Pseudomonas sp., Nitrospira sp., Rubrivivax sp. were the predominant bacteria in the treatment group, which were different from that in the CK group. This study provides a better understanding of the mechanisms of phenol degradation by Acinetobacter sp. DW-1 at the gene level, and provides new insights into the stability of seeded bacteria and its effects on microbial ecology during drinking water treatment.

Vibrio parahaemolyticus is a common foodborne pathogen causing gastroenteritis worldwide. Determining the prevalence and genetic diversity of this pathogen can contribute to the minimization of the risk of infection and of the economic burden. Multilocus sequence typing (MLST) is an important tool for molecular epidemiology and population genetic studies of bacterial pathogens. In this study, we analysed the genetic and evolutionary relationships of 162 V.parahaemolyticus strains isolated in the Guangdong province, China, using MLST, a total of 120 strains were isolated from food samples, while 42 strains were isolated from clinical samples. The 162 strains were divided into 100 sequence types (STs), of which 58 were new. ST415 was the most prevalent ST in food isolates, but in clinical isolates the most prevalent one was ST3. Among these new STs, 48 (55.81%) referred to food isolates, while 10 (66.67%) referred to clinical isolates; therefore, the clinical isolates showed a higher proportion of novel STs. Moreover, there were 12 clonal complexes (CCs), 14 doublets, and 73 singletons obtained from all ST clusters, showing high genetic diversity. At the concatenated sequence level, the nonsynonymous sites of both food and clinical isolates were associated with purifying selection. Of note, in both food and clinical isolates, dN/dS >1 for some housekeeping genes. It was found for the first time that some loci were under positive selection. Our results confirmed that recombination frequently occured in V.parahaemolyticus and had a much greater effect than mutation events in the generation of genetic heterogeneity in food isolates, but the probabilities of recombination and mutations were almost equal in clinical isolates. Phylogenetic analysis showed that clinical isolates were concentrated in the maximum likelihood tree, while food isolates were heterogeneously distributed. In conclusion, this study reviewed the population and genetic diversity of food and clinical V.parahaemolyticus, using MLST. The results suggest that the food and clinical V.parahaemolyticus isolates from Guangdong province are similar, but differ in their evolutionary trends, which may help prevent the large-scale spreading of highly virulent strains and provide a genetic basis for the disclosure of the microevolutionary relationships of V.parahaemolyticus populations.

Salmonella is a widely distributed foodborne pathogen. The use of Salmonella phages as biocontrol agents has recently gained significant interest. Because the Salmonella genus has high diversity, efforts are necessary to identify lytic Salmonella phages focusing on different serovars. Here, five Salmonella phages were isolated from soil samples, and vB_SalP_TR2 was selected as a novel phage with high lytic potential against the host Salmonella serovar Albany, as well as other tested serovars, including Corvallis, Newport, Kottbus, and Istanbul. Morphological analyses demonstrated that phage vB_SalP_TR2 belongs to the Podoviridae family, with an icosahedral head (62 ± 0.5 nm in diameter and 60 ± 1 nm in length) and a short tail (35 ± 1 nm in length). The latent period and burst size of phage vB_SalP_TR2 was 15 min and 211 PFU/cell, respectively. It contained a linear dsDNA of 71,453 bp, and G + C content was 40.64%. Among 96 putative open reading frames detected, only 35 gene products were found in database searches, with no virulence or antibiotic resistance genes being identified. As a biological control agent, phage vB_SalP_TR2 exhibited a high temperature and pH tolerance. In vitro, it lysed most S. Albany after 24 h at 37°C with multiplicities of infection of 0.0001, 0.001, 0.01, 0.1, 1, 10, and 100. In food matrices (milk and chicken meat), treatment with phage vB_SalP_TR2 also reduced the number of S. Albany compared with that in controls. These findings highlighted phage vB_SalP_TR2 as a potential antibacterial agent for the control of Salmonella in food samples.

Vibrio parahaemolyticus is an important foodborne pathogen and its biofilm formation ability facilitates its colonization and persistence in foods by protecting it from stresses including environmental variation and antibiotic exposure. Several important proteins are involved in biofilm formation; however, the identity and function of many remain unknown. In this study, we discovered a hypothetical protein, VP0610 that negatively regulates biofilm formation in Vibrio parahaemolyticus, and we found that the loss of vp0610 typically results in pleiotropic phenotypes that contribute toward promoting biofilm formation, including significantly increased insoluble exopolysaccharide production and swimming motility, decreased soluble exopolysaccharide production, and decreased bis-(3′-5′)-cyclic dimeric guanosine monophosphate production. Pull-down assays revealed that VP0610 can interact with 180 proteins, some of which (Hfq, VP0710, VP0793, and CyaA) participate in biofilm formation. Moreover, deleting vp0610 enhanced the expression of genes responsible for biofilm component (flaE), the sugar phosphotransferase system (PTS) EIIA component (vp0710 and vp0793), and a high-density regulator of quorum sensing (opaR), while reducing the expression of the bis-(3′-5′)-cyclic dimeric guanosine monophosphate degradation protein (CdgC), resulting in faster biofilm formation. Taken together, our results indicate that vp0610 is an integral member of the key biofilm regulatory network of V. parahaemolyticus that functions as a repressor of biofilm formation.

Human norovirus is regarded as the leading cause of epidemic acute gastroenteritis with GII.4 being the predominant genotype during the past decades. In the winter of 2014/2015, the GII.17 Kawasaki 2014 emerged as the predominant genotype, surpassing GII.4 in several East Asian countries. Hence, the influence of host immunity response on the continuous evolution of different GII.17 variants needs to be studied in depth. Here, we relate the inferences of evolutionary mechanisms of different GII.17 variants with the investigation of cross-reactivity and cross-protection of their respective antisera using the expression of norovirus P particles in Escherichia coli. The cross-reactivity assay showed that the antisera of previous strains (GII.17 A and GII.17 B) reacted with recent variants (GII.17 C and GII.17 D) at high OD values from 0.8 to 1.16, while recent variant antisera cross-reacting with previous strains were weak with OD values between 0.26 and 0.56. The cross-protection assay indicated that the antisera of previous strains had no inhibitory effect on recent variants. Finally, mutations at amino acids 353–363, 373–384, 394–404, and 444–454 had the greatest impact on cross-reactivity. These data indicate that the recent pandemic variants GII.17 C and GII.17 D avoided the herd immunity effect of previous GII.17 A and GII.17 B strains through antigenic variation.

Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S. delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.

Listeria spp. is an important foodborne disease agent, often found in the fresh mushroom (Flammulina velutipes) and its production environment. The aim of this study was to develop multiplex PCR for rapid identification of Listeria monocytogenes and Listeria ivanovii, and nonpathogenic Listeria in F. velutipes plants. Pan-genome analysis was first used to identify five novel Listeria-specific targets: one for the Listeria genus, one for L. monocytogenes, and three for L. ivanovii. Primers for the novel targets were highly specific in individual reactions. The detection limits were 103–104 CFU/mL, meeting the requirements of molecular detection. A mPCR assay for the identification of pathogenic Listeria, with primers targeting the novel genes specific for Listeria genus (LMOSLCC2755_0944), L. monocytogenes (LMOSLCC2755_0090), and L. ivanovii (queT_1) was then designed. The assay specificity was robustly verified by analyzing nonpathogenic Listeria and non-Listeria spp. strains. The determined detection limits were 2.0 × 103 CFU/mL for L. monocytogenes and 3.4 × 103 CFU/mL for L. ivanovii, for pure culture analysis. Further, the assay detected 7.6 × 104 to 7.6 × 100 CFU/10 g of pathogenic Listeria spiked into F. velutipes samples following 4–12 h enrichment. The assay feasibility was evaluated by comparing with a traditional culture-based method, by analyzing 129 samples collected from different F. velutipes plants. The prevalence of Listeria spp. and L. monocytogenes was 58.1% and 41.1%, respectively. The calculated κ factors for Listeria spp., L. monocytogenes, and L. ivanovii were 0.97, 0.97, and 1, respectively. The results of the novel mPCR assay were highly consistent with those of the culture-based method. The new assay thus will allow rapid, specific, and accurate detection and monitoring of pathogenic Listeria in food and its production environment.

Infection with Vibrio vulnificus is notorious for its atypical clinical manifestations and irreversible disease progression. Lysine acetylation is a conserved post-translational modification (PTM) that plays a critical regulatory role in diverse cellular processes. However, little is known about the role of lysine acetylation on the pathogenesis of V. vulnificus. Here, we report the complete genome sequence and a global profile for protein lysine acetylation of V. vulnificus Vv180806, a highly cefoxitin resistant strain isolated from a mortality case. The assembled genome comprised two circular chromosomes and one circular plasmid; it contained 4,770 protein-coding genes and 153 RNA genes. Phylogenetic analysis revealed genetic homology of this strain with other V. vulnificus strains from food sources. Of all the proteins in this strain, 1,924 (40.34%) were identified to be acetylated at 6,626 sites. The acetylated proteins were enriched in metabolic processes, binding functions, cytoplasm, and multiple central metabolic pathways. Moreover, the acetylation was found in most identified virulence factors of this strain, suggesting its potentially important role in bacterial virulence. Our work provides insights into the genomic and acetylomic features responsible for the virulence and antibiotic resistance of V. vulnificus, which will facilitate future investigations on the pathogenesis of this bacterium.

Vibrio parahaemolyticus is a marine and estuarine bacterium that leads to damage of aquatic industry by foodborne outbreaks and possesses an enormous threat to food safety as well as human health worldwide. In the current study, we investigated 905 food samples (ready-to-eat foods, fish, and shrimp) from 15 provinces in China, and aimed to determine prevalence, biological characteristics and genetic diversity of presumptive V. parahaemolyticus isolates. Firstly, 14.17% of 240 fish samples, 15.34% of 365 shrimp samples and 3.67% of 300 RTE food samples were positive for potential V. parahaemolyticus. Secondly, 69 food samples (14.87%) collected in summer were positive for target isolates, while the rate of positive sample of 441 food samples in winter reached 7.26%. Thirdly, we purified 202 V. parahaemolyticus strains for further research. And antimicrobial susceptibility results of strains tested revealed that the highest resistance rate was observed for ampicillin (79.20%). At the same time, 148 (73.27%) of all isolates were classified and defined as multi-drug resistant foodborne bacteria. The results of PCR assay showed that the isolates being positive for the tdh, trh or both genes, were up to 9.90%, 19.80% or 3.96%. Besides, multiplex PCR test showed that the isolates carrying O2 serogroup were the most prevalent. Furthermore, sequence types (STs) of 108 isolates were obtained via multi-locus sequence typing. Not only 82 STs were detected, but also 41 of which were updated in the MLST database. Thus, our findings significantly demonstrated the high contamination rates of V. parahaemolyticus in fish and shrimp and it may possess potential threat for consumer health. We also provided up-to-date dissemination of antibiotic-resistant V. parahaemolyticus which is important to ensure the high efficacy in the treatment of human and aquatic products infections. Lastly, with the identification of 82 STs including 41 novel STs, this study significantly revealed the high genetic diversity among V. parahaemolyticus. All of our research improved our understanding on microbiological risk assessment in ready-to-eat foods, fish, and shrimp.

Sequence type 59 (ST59) is a predominant clonal lineage of community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) in Asia. Despite its increasing clinical relevance in China, the evolution and geographic expansion of ST59 has been relatively uncared for. Previous study has shown that ST59 was the predominant clone in food-related MRSA in China. This study compared the genomes of 87 clonal complex (CC) 59 S. aureus isolates sourced from food chain and infection cases to reconstruct the molecular evolution and geographical spread of ST59. Accordingly, three major sub-clades of ST59 were identified and these did not correlate with isolation source or location. Phylogenetic analysis estimated that ST59 in mainland China diverged from a most common recent ancestor around 1974, and most of the cases of cross-country transmission occurred between 1987 and 2000. Notably, two recent events of cross-country transmission through the food chain were observed, the isolates from these events diverged within relatively short time intervals. These isolates also showed high similarity in terms of their core genome, accessory genes, and antibiotic resistance patterns. These findings provide a valuable insight into the potential route of ST59 expansion in China and indicate a need for robust food chain surveillance to prevent the spread of this pathogen.

Campylobacter jejuni is a major foodborne pathogen worldwide. As it forms biofilms, it can become a persistent contaminant in the food and pharmaceutical industries. In this study, it was demonstrated that C. jejuni could make more biofilm in aerobic conditions than in microaerobic conditions, and only 13.9% C. jejuni entered coccus (a VBNC state) under microaerobic conditions; however, the rate increased to 95.5% under aerobic conditions. C. jejuni could form more biofilm in mixed culture with Escherichia coli or Pseudomonas aeruginosa than in pure culture. Scanning electron microscope results showed that C. jejuni retained its normal spiral shape under aerobic conditions for 48 h by forming crosslinks with the aerobic and facultative anaerobic bacteria. Additionally, culture medium containing 0.5 mg/ml ZnO nanoparticles inhibited biofilm formation. Our results provide information on a new approach to controlling contamination via C. jejuni.

Bacillus cereus is widely distributed in different food products and can cause a variety of symptoms associated with food poisoning. Since ready-to-eat (RTE) foods are not commonly sterilized by heat treatment before consumption, B. cereus contamination may cause severe food safety problems. In this study, we investigated the prevalence of B. cereus in RTE food samples from different regions of China and evaluated the levels of bacterial contamination, antibiotic resistance, virulence gene distribution, and genetic polymorphisms of these isolates. Of the tested retail RTE foods, 35% were positive for B. cereus, with 39 and 83% of the isolated strains harboring the enterotoxin-encoding hblACD and nheABC gene clusters, respectively. The entFM gene was detected in all B. cereus strains. The cytK gene was present in 68% of isolates, but only 7% harbored the emetic toxin-encoding gene cesB. Antimicrobial susceptibility testing revealed that the majority of the isolates were resistant not only to most β-lactam antibiotics, but also to rifamycin. Multilocus sequence typing (MLST) revealed that the 368 isolates belonged to 192 different sequence types (STs) including 93 new STs, the most prevalent of which was ST26. Collectively, our study indicates the prevalence, bacterial contamination levels, and biological characteristics of B. cereus isolated from RTE foods in China and demonstrates the potential hazards of B. cereus in RTE foods.

The aim of this study was to develop a potential microbial preservative to prevent the growth of fungi in food. The isolate ZC-G-5 showed strong antifungal activity against food spoilage fungi and Streptomyces albulus was identified on the basis of morphologic, culture, and 16S rDNA sequence analyses. The active metabolite was elucidated as tetramycin A (TMA) through spectroscopic techniques, including HR-ESI-MS, 1D-NMR, and 2D-NMR. An antifungal activity assay revealed that the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of TMA were 1.50-2.50 and 3.00-5.00 μg/ml, respectively. In situ antifungal activity analyses demonstrated that 90.0 μg/ml of TMA could inhibit the growth of fungi for over 14 days. In order to enhance TMA production, the high-yield mutant strain YB101 was screened, based on the isolate ZC-G-5, using a high-throughput screening method. The best metabolic precursor was selected during fermentation, when the concentration of glycerol was 8% (v/v) in Gauze's broth medium to cultivate the mutant strain YB101; the concentration of TMA could be increased to 960.0 μg/ml, compared with the original isolate ZC-G-5, where the concentration of the TMA was only 225.0 μg/ml. Our study may contribute to the application of S. albulus and its active metabolite as a potential bio-preservative in the food industry.

Staphylococcus aureus is amongst the most virulent pathogens, causing chronic and life-threatening human infections. Methicillin-resistant S. aureus (MRSA) are multidrug-resistant strains, and the ability of forming a biofilm reduces their sensitivity to antibiotics. Thus, the alternative compounds inhibiting both resistant strains and biofilm formation are in high demand. In our study, the strain FJKB0103 was isolated from the rhizosphere of Garcinia mangostana, showing strong anti-MRSA activity. We performed molecular phylogenic analysis, analyzed average nucleotide identity (ANI), in silico DNA-DNA hybridization (isDDH), and biochemical characteristics to identify strain FJKB0103 as Pseudomonas protegens. Herein, the genome of strain FJKB0103 was sequenced and subjected to antiSMASH platform, mutational, and functional analyses. The FJKB0103 draft genome was 6,776,967 bp with a 63.4% G + C content, and 16 potential secondary compound biosynthetic clusters in P. protegens FJKB0103 were predicted. The deletion mutant and complementary analysis suggested that DAPG was the anti-MRSA compound. Further tests showed that MRSA strains were sensitive to DAPG, and the lysis of bacterial cells was observed at a high concentration of DAPG. Additionally, DAPG inhibited the biofilm formation of MRSA at subinhibitory concentration. These results suggested that DAPG might be a good alternative treatment to control infections caused by MRSA.

Salmonella remains the leading cause of reported bacterial foodborne disease in China. Meat products are recognized as one of the major sources of human salmonellosis; however, there is a lack of comprehensive, quantitative data concerning Salmonella contamination of these foods. Therefore, the objectives of this study were to investigate the prevalence, bacterial load, and antimicrobial resistance profiles of various Salmonella serovars in retail meat across the whole of China. Between July 2011 and June 2016, a total of 807 retail meat samples were collected, covering most provincial capitals in China. Overall, 159 (19.7%) samples tested positive for Salmonella. The highest contamination rate occurred in pork (37.3%, n = 287), followed by beef (16.1%, n = 161), mutton (10.9%, n = 92), dumplings (6.6%, n = 212), and smoked pork (3.6%, n = 55). Most probable number (MPN) analysis revealed that contamination was mainly in the range of 0.3–10 MPN/g among those samples testing positive using this method (n = 83), with eight samples exceeding 110 MPN/g. Among the 456 Salmonella enterica subsp. enterica isolates obtained in this study, 29 serovars and 33 multilocus sequence typing patterns were identified, with S. Derby, S. Typhimurium, S. London, S. Rissen, S. 1,4,[5],12:i:-, S. Weltevreden, and S. Enteritidis being the most prevalent. Among the 218 non-duplicate isolates, 181 (83.0%) were resistant to at least one class of antimicrobials and 128 (58.7%) were resistant to at least three classes. High rates of resistance were observed for tetracycline (65.6%), ampicillin (45.4%), trimethoprim-sulfamethoxazole (40.8%), streptomycin (40.4%), and nalidixic acid (35.8%), with the seven most prevalent serovars, except S. Weltevreden, showing higher rates of resistance and multidrug resistance compared with the less dominant serovars. Of note, all S. Indiana isolates exhibited resistance to extended-spectrum cephalosporins (including ceftriaxone and cefepime), ciprofloxacin, and multiple other classes of antibiotics. Further, two S. 1,4,[5],12:i:- isolates showed resistance to imipenem. This study provides systematic and comprehensive data on the prevalence and antimicrobial resistance profiles of various Salmonella serovars isolated from meat products in China, indicating their potential risk to public health.

Cronobacter strains harboring CRISPR-Cas systems are important foodborne pathogens that cause serious neonatal infections. CRISPR typing is a new molecular subtyping method to track the sources of pathogenic bacterial outbreaks and shows a promise in typing Cronobacter, however, this molecular typing procedure using routine PCR method has not been established. Therefore, the purpose of this study was to establish such methodology, 257 isolates of Cronobacter sakazakii, C. malonaticus, and C. dublinensis were used to verify the feasibility of the method. Results showed that 161 C. sakazakii strains could be divided into 129 CRISPR types (CTs), among which CT15 (n = 7) was the most prevalent CT followed by CT6 (n = 4). Further, 65 C. malonaticus strains were divided into 42 CTs and CT23 (n = 8) was the most prevalent followed by CT2, CT3, and CT13 (n = 4). Finally, 31 C. dublinensis strains belonged to 31 CTs. There was also a relationship among CT, sequence type (ST), food types, and serotype. Compared to multi-locus sequence typing (MLST), this new molecular method has greater power to distinguish similar strains and had better accordance with whole genome sequence typing (WGST). More importantly, some lineages were found to harbor conserved ancestral spacers ahead of their divergent specific spacer sequences; this can be exploited to infer the divergent evolution of Cronobacter and provide phylogenetic information reflecting common origins. Compared to WGST, CRISPR typing method is simpler and more affordable, it could be used to identify sources of Cronobacter food-borne outbreaks, from clinical cases to food sources and the production sites.

Listeria monocytogenes is a foodborne pathogen with a high mortality rate in humans. This study aimed to identify the pathogenic potential of L. monocytogenes isolated from ready-to-eat (RTE) foods and pasteurized milk in China on the basis of its phenotypic and genotypic characteristics. Approximately 7.7% (44/570) samples tested positive for L. monocytogenes among 10.8% (39/360) RTE and 2.4% (5/210) pasteurized milk samples, of which 77.3% (34/44) had < 10 MPN/g, 18.2% (8/44) had 10–110 MPN/g, and 4.5% (2/44) had > 110 MPN/g. A total of 48 strains (43 from RTE foods and five from milk samples) of L. monocytogenes were isolated from 44 positive samples. PCR-serogroup analysis revealed that the most prevalent serogroup was II.2 (1/2b-3b-7), accounting for 52.1% (25/48) of the total, followed by serogroup I.1 (1/2a-3a) accounting for 33.3% (16/48), serogroup I.2 (1/2c-3c) accounting for 12.5% (6/48), and serogroup II.1 (4b-4d-4e) accounting for 2.1%. All isolates were grouped into 11 sequence types (STs) belonging to 10 clonal complexes (CCs) and one singleton (ST619) via multi-locus sequence typing. The most prevalent ST was ST87 (29.2%), followed by ST8 (22.9%), and ST9 (12.5%). Virulence genes determination showed that all isolates harbored eight virulence genes belonging to Listeria pathogenicity islands 1 (LIPI-1) (prfA, actA, hly, mpl, plcA, plcB, and iap) and inlB. Approximately 85.4% isolates carried full-length inlA, whereas seven isolates had premature stop codons in inlA, six of which belonged to ST9 and one to ST5. Furthermore, LLS (encoded by llsX gene, representing LIPI-3) displays bactericidal activity and modifies the host microbiota during infection. LIPI-4 enhances neural and placental tropisms of L. monocytogenes. Results showed that six (12.5%) isolates harbored the llsX gene, and they belonged to ST1/CC1, ST3/CC3, and ST619. Approximately 31.3% (15/48) isolates (belonging to ST87/CC87 and ST619) harbored ptsA (representing LIPI-4), indicating the potential risk of this pathogen. Antimicrobial susceptibility tests revealed that > 95% isolates were susceptible to 16 antimicrobials; however, 60.4 and 22.9% isolates were intermediately resistant to streptomycin and ciprofloxacin, respectively. The results show that several isolates harbor LIPI-3 and LIPI-4 genes, which may be a possible transmission route for Listeria infections in consumers.

The aim of this study was to gain insight into the bacterial composition and dynamics in a mineral water treatment system (MWTS). The bacterial community of a full-scale mineral water treatment plant in the Maofeng Mountain, South China, was studied using high-throughput sequencing combined with cultivation-based techniques in both the dry and wet season. Overall, adenosine tri-phosphate (ATP) concentration (6.47 × 10-11 – 3.32 × 10-8 M) and heterotrophic plate counts (HPC) (3 – 1.29 × 103 CFU/mL) of water samples in the wet season were lower than those (ATP concentration 5.10 × 10-11 – 6.96 × 10-8 M, HPC 2 – 1.97 × 103 CFU/mL) in the dry season throughout the whole MWTS. The microbial activity and biomass of water samples obviously changed along with treatment process. All 300 isolates obtained using cultivation-based techniques were distributed in 5 phyla, 7 classes, and 19 genera. Proteobacteria accounted for 55.7% (167) of the total isolates, among which predominant genus was Pseudomonas (19.3%). Illumina sequencing analysis of 16s rRNA genes revealed 15 bacterial phyla (relative abundance >0.1%) as being identified in all water samples. Among these, Proteobacteria constituted the dominant bacteria microbiota in all water samples. A large shift in the proportion of Bacteroidetes, Actinobacteria, and Firmicutes was obtained during the treatment process, with the proportion of Bacteroidetes, Actinobacteria decreasing sharply, whereas that of Firmicutes increased and predominated in the final water product. The core microbiome, which was still present in whole MWTS comprised several genera including Pseudomonas, Acinetobacter, Clostridium, and Mycobacterium, that contain species that are opportunistic pathogens, suggesting a potential threat for mineral water microbiology safety. This study is the first to investigate the bacterial community of a full-scale mineral water treatment plant in China. The results provided data regarding the bacteria composition and dynamics in an MWTS, which will contribute to the beneficial manipulation of the mineral water microbiome.

Background Ready-to-eat (RTE) vegetables have become increasingly popular along with the trend of moving towards a healthy lifestyle. However, RTE vegetables are at a higher risk of containing pathogens, maybe owing to lack of rigorous sanitization procedures. To understand the prevalence and potential risk of Listeria monocytogenes in RTE vegetables, we investigated the contamination level and characteristics of L. monocytogenes isolated from fresh vegetables. Results Twenty-three (5.49%) of the 419 vegetables samples were positive for L. monocytogenes. Phylogenetic group I.1 (1/2a-3a) and II.2 (1/2b-3b-7) strains were predominant in 30 isolates, which accounted for 33.3 and 50.0%, respectively. Multilocus sequence typing of the 30 isolates grouped them into nine sequence types (STs). The most common STs were ST87 (36.7%) and ST8 (26.7%). Virulence analysis showed that all 30 isolates harbored eight classical virulence genes, 10.0% isolates harbored the llsX gene (ST3 and ST1 strains), and 36.7% carried the ptsA gene and belonged to ST87. Approximately 83.3% isolates carried full-length inlA, whereas five isolates had premature stop codons in inlA, three of which belonged to ST9 and two to ST8. Antibiotic susceptibility showed the isolates were varyingly resistant to 13 antibiotics, 26.7% of the isolates were multi-drug resistant. Conclusions The fresh vegetables contain some potential hypervirulent L. monocytogenes (ST1 and ST87) in the Chinese markets. In addition, the high rate of L. monocytogenes isolates was multi-drug resistant. Fresh raw vegetables may be a possible transmission route for L. monocytogenes infection in consumers. Therefore, sanitization of raw fresh vegetables should be strengthened to ensure their microbiological safety when used as RTE vegetables. Electronic supplementary material The online version of this article (10.1186/s12866-019-1488-5) contains supplementary material, which is available to authorized users.

Listeria monocytogenes is a globally notorious foodborne pathogen. This study aimed to qualitatively and quantitatively detect L. monocytogenes from meat and meat products in China and to establish their virulence profiles and population diversity. From 1212 meat and meat product samples, 362 (29.9%) were positive for L. monocytogenes. Of these positive samples, 90.6% (328/362) had less than 10 MPN/g, 5.5% (20/364) samples had 10–110 MPN/g, and 3.9% (14/362) of the positive samples had over 110 MPN/g. Serogroup analysis showed that the most prevalent serogroup of L. monocytogenes was I.1 (1/2a-3a), which accounted for 45.0% (123/458) of the total, followed by serogroup I.2 (1/2c-3c) that comprised 26.9%, serogroup II.1 (4b-4d-4e) that comprised 4.8%, and serogroup II.2 (1/2b-3b-7) that comprised 23.3%. A total of 458 isolates were grouped into 35 sequence types (STs) that belonged to 25 clonal complexes (CCs) and one singleton (ST619) by multi-locus sequence typing. The most prevalent ST was ST9 (26.9%), followed by ST8 (17.9%), ST87 (15.3%), ST155 (9.4%), and ST121 (7.6%). Thirty-seven isolates harbored the llsX gene (representing LIPI-3), and they belonged to ST1/CC1, ST3/CC3, ST288/CC288, ST323/CC288, ST330/CC288, ST515/CC1, and ST619, among which ST323/CC288, ST330/CC288, and ST515/CC1 were newly reported to carry LIPI-3. Seventy-five isolates carried ptsA, and they belonged to ST87/CC87, ST88/CC88, and ST619, indicating that consumers may be exposed to potential hypervirulent L. monocytogenes. Antibiotics susceptibility tests revealed that over 90% of the isolates were susceptible to 11 antibiotics; however, 40.0% of the isolates exhibited resistance against ampicillin and 11.8% against tetracycline; further, 45.0 and 4.6% were intermediate resistant and resistant to ciprofloxacin, respectively. The rise of antibiotic resistance in L. monocytogenes suggests that stricter regulations should be formulated to restrict the use of antibiotic agents in human listeriosis treatment and livestock breeding.

Cronobacter spp. are foodborne pathogens that can infect and cause life-threatening diseases in all age groups, particularly in infants and immunocompromised elderly. This study aimed to investigate the prevalence, antibiotic susceptibility, and molecular characteristics of Cronobacter spp. isolates in edible mushrooms collected from 44 cities in China. In total, 668 edible mushrooms were collected from traditional retail markets and supermarkets and were analyzed by quantitative methods, PCR-based serotyping, multilocus sequence typing (MLST), and antibiotic susceptibility testing. Among the 668 samples tested, 89 (13.32%) were positive for Cronobacter spp., and the contamination levels exceeded the 110 most probable number (MPN)/g in 13.48% (12/89) of the samples. Flammulina velutipes samples had the highest contamination rate of 17.54% (37/211), whereas Hypsizygus marmoreus samples had the lowest contamination rate of 3.28% (2/61). Ten serotypes were identified among 115 isolates, of which the C. sakazakii serogroup O1 (n = 32) was the primary serotype. MLST indicated that there was quite high genetic diversity in Cronobacter spp. and 72 sequence types were identified, 17 of which were new. Notably, C. sakazakii ST148 (n = 10) was the most prevalent, followed by C. malonaticus ST7 (n = 5). Antibiotic susceptibility testing revealed that the majority of Cronobacter spp. strains were susceptible to the 16 antibiotics tested. However, a portion of isolates exhibited relatively high resistance to cephalothin, with resistance and intermediate rates of 93.91 and 6.09%, respectively. One isolate (cro300A) was multidrug-resistant, with resistance to five antibiotics. Overall, this large-scale study revealed the relatively high prevalence and high genetic diversity of Cronobacter spp. on edible mushrooms in China, indicating a potential public health concern. To our knowledge, this is the first large-scale and systematic study on the prevalence of Cronobacter spp. on edible mushrooms in China, and the findings can provide valuable information that can guide the establishment of effective measures for the control and precaution of Cronobacter spp on edible mushrooms during production processes.

Methicillin-resistant Staphylococcus aureus (MRSA) is an emerging pathogen that is difficult to treat due to the multiresistance of the bacteria upon infection. From 2011 to 2016, 1581 S. aureus strains were isolated from 4300 samples from retail foods covering most provincial capitals in China. To determine the prevalence of food-related MRSA and its genetic background in China, antibiotic resistance, staphylococcal toxin genes, staphylococcal cassette chromosome mec (SCCmec) typing, spa-typing and MLST were carried out in this study. In total, 108 (7.4%) isolates were confirmed for MRSA by phenotyping (cefoxitin) and genotyping (mecA/mecC gene). A total of 52.8% (57/108) of the MRSA isolates belonged to clonal complex 59 (CC59) (ST59, ST338, and ST3355), which was the predominant clone in this study. These CC59 isolates carried SCCmec elements of type IV, V, or III and exhibited spa type t437, t441, t543, t163, t1785, or t3485, and half of them carried major virulence genes, such as the Panton-Valentine leucocidin (PVL) gene. The secondary clones belonged to ST9 (15.7%, 17/108) with a type of t899-SCCmec III and showed a broader range of antimicrobial resistance. The remaining MRSA isolates (31.5%, 34/108) were distributed in 12 different STs and 18 different spa types. All isolates harbored at least one of the enterotoxin genes, whereas only 4 isolates (3.70%) were positive for the toxic shock syndrome toxin tsst alleles. For antibiotic susceptibility testing, all isolates were resistant to more than three antibiotics, and 79.6% of the isolates were resistant to more than 10 antibiotics. Amoxycillin/clavulanic acid, ampicillin, cefoxitin, penicillin, ceftazidime, kanamycin, streptomycin, clindamycin, and telithromycin was the most common antibiotic resistance profile (55.6%, 60/108) in the study. In summary, the results of this study implied that the major food-related MRSA isolate in China was closer to community-associated MRSA, and some of the remaining isolates (ST9-t899-SCCmec III) were supposed to livestock-associated MRSA. In addition, most MRSA isolates showed resistance to multiple drugs and harbored staphylococcal toxin genes. Thus, the pathogenic potential of these isolates cannot be ignored. In addition, further studies are needed to elucidate the transmission routes of MRSA in relation to retail foods and to determine how to prevent the spread of MRSA.

Vibrio parahaemolyticus is a major foodborne pathogen associated with the consumption of aquatic products. The presence of this bacterium in ready-to-eat (RTE) foods has recently been reported. However, the genomic features and potential risks of V. parahaemolyticus isolated from RTE foods are poorly understood. To help understand the genome-wide characteristics of RTE food isolates, the complete genomes of 27 RTE food isolates were sequenced and compared to those of 20 clinical and 19 other environmental (e.g., water and aquatic product source) isolates using a comparative genomics approach. Analysis revealed that V. parahaemolyticus RTE food isolates had higher numbers of genes on average and possessed more accessory genes than isolates from other sources. Most RTE food isolates were positive for some known virulence-associated genes and pathogenicity islands (PAIs), and some of these isolates were genetically homologous to clinical isolates. Genome-wide association analysis revealed 79 accessory genes and 78 missense single-nucleotide polymorphisms that affected 11 protein-coding genes were significantly associated with RTE food sources. These genes were mostly involved in defense mechanisms and energy production and conversion according to functional annotation in the COG database. KEGG Pathway analysis showed that these genes mainly affected the biofilm formation of V. parahaemolyticus, and subsequent experiments confirmed that nearly all RTE food isolates possessed the ability to form biofilm. The biofilm formation can facilitate the persistence of V. parahaemolyticus in RTE foods, and the presence of virulence-associated genes poses a pathogenic potential to humans. Our findings highlight the potential risk of V. parahaemolyticus in Chinese RTE foods and illustrate the genomic basis for the persistence of these isolates. This study will aid in re-evaluating the food safety threats conferred by this bacterium.

Vibrio parahaemolyticus is a common foodborne pathogen found in seafood, and represents a major threat to human health worldwide. Low-temperature storage is an important seafood processing method, but is not sufficient to completely eliminate the bacteria and avoid foodborne illness. To determine the mechanisms behind such cold tolerance, RNA-seq and iTRAQ analyses were first performed to obtain the global transcriptomic and proteomic patterns of frozen squid and clinical V. parahaemolyticus isolates under cold conditions. The integrated analysis revealed the modulation of multiple pathways such as the co-occurrence of down-regulated pyruvate metabolism and up-regulated fatty acid biosynthesis, which likely contribute to V. parahaemolyticus cold tolerance. Furthermore, we found that increasing concentrations of pyruvate can reduce the fatty acid content to influence V. parahaemolyticus growth in cold conditions. Thus, regulation of pyruvate concentration may be an effective method to control this seafood-borne pathogen.

This study was to estimate the prevalence and characteristics of Staphylococcus aureus from 1,850 retail meat and meat products in China during July 2011 to June 2016. The samples were collected covering most provincial capitals in China, including 604 raw meat, 601 quick-frozen meat, and 645 ready-to-eat meat. Using the qualitative and quantitative methods, all 39 cities had S. aureus-positive samples, and S. aureus was detected in 35.0% (647/1,850) of the samples. The levels of S. aureus in retail meat showed that the MPN value of the majority of the positive samples ranged from 0.3 to 100 MPN/g. Twenty-four antibiotics were used to test all 868 S. aureus isolates for antibiotic susceptibility. Only 11 isolates (1.26%) were susceptible to all antibiotics, whereas most isolates (821/868, 94.6%) showed resistance or intermediary resistance to more than three or more antibiotics. Of these strains, 104 (12.0%) were resistant to more than 10 antibiotics. However, the most frequent resistance was observed to ampicillin (85.4%), followed by penicillin (84.6%), erythromycin (52.7%), tetracycline (49.3%), kanamycin (45.3%), telithromycin (30.1%), clindamycin (29.6%), streptomycin (21.1%), norfloxacin (20.4%), gentamicin (19.4%), fusidic acid (18.4%), ciprofloxacin (16.9%), chloramphenicol (13.1%), amoxycillin/clavulanic acid (11.0%), and others (

Listeria monocytogenes is an important Gram-positive foodborne pathogen. However, limited information is available on the comprehensive investigation and potential risk of L. monocytogenes in fresh aquatic products, which are popular to consumers in China. This study aimed to determine the occurrence, virulence profiles, and population diversity of L. monocytogenes isolated from aquatic products in China. In total, 846 aquatic product samples were collected between July 2011 and April 2016 from 43 cities in China. Approximately 7.92% (67/846) aquatic product samples were positive for L. monocytogenes, 86.57% positive samples ranged from 0.3 to 10 MPN/g, whereas 5.97% showed over 110 MPN/g by the Most Probable Number method, which included two samples of products intended to be eaten raw. Serogroups I.1 (serotype 1/2a), I.2 (serotype 1/2b), and III (serotype 4c) were the predominant serogroups isolated, whereas serogroup II.1 (serotype 4b) was detected at much lower frequencies. Examination of antibacterial resistance showed that nine antibacterial resistance profiles were exhibited in 72 isolates, a high level susceptibility of 16 tested antibiotics against L. monocytogenes were observed, indicating these common antibacterial agents are still effective for treating L. monocytogenes infection. Multilocus sequence typing revealed that ST299, ST87, and ST8 are predominant in aquatic products, indicating that the rare ST299 (serotype 4c) may have a special ecological niche in aquatic products and associated environments. Except llsX and ptsA, the 72 isolates harbor nine virulence genes (prfA, actA, hly, plcA, plcB, iap, mpl, inlA, and inlB), premature stop codons (PMSCs) in inlA were found in four isolates, three of which belonged to ST9. A novel PMSC was found in 2929-1LM with a nonsense mutation at position 1605 (TGG→TGA). All ST87 isolates harbored the ptsA gene, whereas 8 isolates (11.11%) carried the llsX gene, and mainly belonged to ST1, ST3, ST308, ST323, ST330, and ST619. Taken together, these results first reported potential virulent L. monocytogenes isolates (ST8 and ST87) were predominant in aquatic products which may have implications for public health in China. It is thus necessary to perform continuous surveillance for L. monocytogenes in aquatic products in China.

In this study, we characterized the β-lactamase genes and phenotypic resistance of cephalosporin-resistant Enterobacteriaceae isolated from retail foods in China. Of 1,024 Enterobacteriaceae isolates recovered from raw meat products, aquatic products, raw vegetables, retail-level ready-to-eat (RTE) foods, frozen foods, and mushrooms from 2011 to 2014, 164 (16.0%) showed cefotaxime (CTX) and/or ceftazidime (CAZ) cephalosporin resistance, and 96 (9.4%) showed the extended-spectrum β-lactamase (ESBL) phenotype. More than 30% isolates were resistant to all antimicrobial agents except carbapenems (MEM 3.1% and IPM 5.2%), cefoxitin (FOX 6.3%), and amoxicillin/clavulanic acid (AMC 26%), and 94.8% of the strains were resistant to up to seven antibiotics. Polymerase chain reaction analysis showed that blaTEM (81.9%) was the most common gene, followed by blaCTX-M (68.1%) and blaSHV (38.9%). Moreover, 16.8% (72/429) of food samples contained ESBL-positive Enterobacteriaceae, with the following patterns: 32.9% (23/70) in frozen foods, 27.2% (5/29) in mushrooms, 17.6% (24/131) in raw meats, 13.3% (4/30) in fresh vegetables, 11.1% (8/72) in RTE foods, and 9.3% (9/97) in aquatic products. In addition, 24 of 217 foods collected in South China (11.1%), 25 of 131 foods collected in North of the Yangtze River region (19.1%), and 23 of 81 foods collected in South of the Yangtze River region (28.4%) were positive for ESBL- Enterobacteriaceae. Conjugation experiments demonstrated that the 22 of 72 isolates were transconjugants that had received the β-lactamase gene and were resistant to β-lactam antibiotics as well as some non-β-lactam antibiotics. These findings demonstrated that retail foods may be reservoirs for the dissemination of β-lactam antibiotics and that resistance genes could be transmitted to humans through the food chain; and the predominant ESBL-producing Enterobacteriaceae in China was isolated from in frozen chicken-meat, followed by frozen pork, cold noodles in sauce, cucumber, raw chicken meat, frozen pasta, brine-soaked chicken and tomato.

Listeria monocytogenes, an intracellular foodborne pathogen, is capable of causing listeriosis, such as meningitis, meningoencephalitis, and abortion. In recent years, the occurrence of Listeria monocytogenes in edible mushroom products has been reported in several countries. There are no guidelines for qualitative and quantitative detection of L. monocytogenes in mushroom products in China. Therefore, this study aimed to investigate the prevalence and contamination level of L. monocytogenes in edible mushrooms in Chinese markets and to determine the antibiotic resistance and sequence types (STs) of these isolates to provide data for risk assessments. Approximately 21.20% (141/665) of edible mushroom samples were positive for L. monocytogenes, while 57.44% (81/141) of positive samples contained contamination levels of less than 10 MPN/g. The 180 isolates derived from positive samples belonged to serogroup I.1 (1/2a-3a, n = 111), followed by serogroup II.2 (1/2b-3b-7, n = 66), and serogroup III (4a-4c, n = 3). Antibiotic susceptibility testing showed that over 95% of L. monocytogenes isolates were resistant to penicillin, ampicillin, oxacillin, and clindamycin, while over 90% were susceptible to 16 antibiotic agents, the mechanisms of resistance remain to be elucidated. According to multilocus sequencing typing, the 180 isolates represented 21 STs, one of which was identified for the first time. Interestingly, ST8 and ST87 were predominant in edible mushroom products, indicating that specific STs may have distinct ecological niches. Potential virulence profiles showed that most of the isolates contained full-length inlA genes, with novel premature stop codons found in isolate 2035-1LM (position 1380, TGG→TGA) and 3419-1LM (position 1474, CAG→TAG). Five isolates belonging to serogroup II.2 carried the llsX gene from Listeria pathogenicity island (LIPI)-3, present in ST224, ST3, and ST619; 53 (29.44%) harbored the ptsA gene from LIPI-4, presenting in ST3, ST5, ST87, ST310, ST1166, and ST619. Five potential hypervirulent isolates carrying all three of these virulence factors were identified, suggesting edible mushrooms may serve as possible transmission routes of potential hypervirulent L. monocytogenes, which may be of great public health concern to consumers. Based on our findings, the exploration of novel approaches to control L. monocytogenes contamination is necessary to ensure the microbiological safety of edible mushroom products.

Cronobacter spp. is a foodborne pathogen that causes life-threatening and invasive diseases, such as necrotizing enterocolitis, meningitis, and sepsis. In this study, we aimed to investigate the prevalence, molecular characteristics and antimicrobial resistance of Cronobacter spp. in raw vegetables marketed in China. Based on dietary habits in China, 403 raw vegetables that could be eaten without additional cooking were collected. Of the 403 samples tested, 122 (30.27%) were positive for Cronobacter spp., and the contamination levels exceeded 110 most probable number (MPN)/g for 16.39% (20/122) of the samples. Coriander samples had the highest contamination rate of 52.81%, and the MPN values of 19.15% of positive coriander samples exceeded 100 MPN/g. Eleven serotypes were identified among 171 isolates, with Cronobacter sakazakii serogroup O1 (41 isolates) being the dominant serotype. Molecular characterization indicated that there was quite high genetic diversity in Cronobacter spp., and multilocus sequence typing analyses yielded 106 sequence types (STs), 55 of which were newly identified. Notably, the most prevalent ST (eight isolates) was C. malonaticus ST60, which appeared in a recent clinical infectious disease study in China. Five C. sakazakii ST4, seven C. malonaticus ST7, and three C. sakazakii ST8 confirmed as pathogenic sequence types in other countries were also detected in this study. Furthermore, all isolates were susceptible to amikacin, amoxicillin-clavulanic, cefepime, ciprofloxacin, and imipenem, but some isolates exhibited a high ratio of resistance to cephalothin (59.65%). In this study, the high contamination rate and the detection of pathogenic and new sequence types in raw vegetables indicated potential hazards to customers. To the best of our knowledge, this is the first report to provide valuable information on the contamination status of Cronobacter spp. in vegetables that can be eaten raw in China.

Staphylococcus aureus is a pathogen associated with serious community and hospital-acquired diseases. The aim of this study was to investigate the prevalence of S. aureus from retail vegetables in China and then characterized S. aureus isolates by antibiotic resistance, staphylococcal enterotoxin genes, spa-typing and multi-locus sequence typing. Of 419 retail vegetable samples from 39 cities in China during 2011–2016, 24 (5.73%) samples were positive for S. aureus and the geometric mean was 3.85 MPN/g. The prevalence of S. aureus was highest in lettuce (13/84, 15.48%) followed by tomato (7/110, 6.36%), caraway (2/87, 2.30%), and cucumber (2/128, 1.56%), whereas other vegetables were free of S. aureus. A total of 30 isolates were analyzed. For antibiotics susceptibility test, most isolates (93.3%) were resistant to ampicillin and penicillin, whereas all isolates were susceptible to linezolid, trimethoprim/sulphamethoxazole 1:19, nitrofurantoin, rifampicin, and teicoplanin. All isolates (30/30, 100%) were resistant or intermediate resistant to more than three tested antibiotics, including 9 isolates (30%) were resisted more than 10 antibiotics. Five isolates were resistant to cefoxitin and carried mecA genes which confirmed as MRSA. Of the 18 investigated SE genes, the sem gene was the most frequently detected (86.7%) followed by the sec (83.3%), sep (70.0%), seg (56.7%), sel (53.3%), seh (50.0%), seq (50.0%), sej (46.7%), seb (36.7%), sen (36.7%), and ser (33.3%) genes were harbored by more than one third of the isolates, whereas the seo and seu were detected in only 6.75% of the isolates. MLST and spa typing observed high genetic diversity in S. aureus isolated from retail vegetable in China. ST59-t437 was the predominant types (3/5, 60%) of MRSA isolates, whereas ST188-t189 was the predominant types (7/25, 28%) of MSSA isolates. Our study reflects that the retail vegetable in China could be contaminated with S. aureus but the levels of S. aureus were not very excessive. In addition, these isolates had virulence potential, most of them were enterotoxigenic and multiple antimicrobial resistance, should be draw public attention. These data have signification implications for epidemiological and public health studies of this pathogen.

Bacillus cereus is a common and important food-borne pathogen that can be found in various food products. Due to low-temperature sterilization for a short period of time, pasteurization is not sufficient for complete elimination of B. cereus in milk, thereby cause severe economic loss and food safety problems. It is therefore of paramount importance to perform risk assessment of B. cereus in pasteurized milk. In this study, we isolated B. cereus from pasteurized milk samples in different regions of China, and evaluated the contamination situation, existence of virulence genes, antibiotic resistance profile and genetic polymorphism of B. cereus isolates. Intriguingly, 70 samples (27%) were found to be contaminated by B. cereus and the average contamination level was 111 MPN/g. The distribution of virulence genes was assessed toward 10 enterotoxigenic genes (hblA, hblC, hblD, nheA, nheB, nheC, cytK, entFM, bceT, and hlyII) and one emetic gene (cesB). Forty five percent strains harbored enterotoxigenic genes hblACD and 93% isolates contained nheABC gene cluster. The positive rate of cytK, entFM, bceT, hlyII, and cesB genes were 73, 96, 75, 54, and 5%, respectively. Antibiotic susceptibility assessment showed that most of the isolates were resistant to β-lactam antibiotics and rifampicin, but susceptible to other antibiotics such as ciprofloxacin, gentamicin and chloramphenicol. Total multidrug-resistant population was about 34%. In addition, B. cereus isolates in pasteurized milk showed a high genetic diversity. In conclusion, our findings provide the first reference on the prevalence, contamination level and characteristics of B. cereus isolated from pasteurized milk in China, suggesting a potential high risk of B. cereus to public health and dairy industry.

Enterococcus faecalis is an important opportunistic pathogen which is frequently detected in mineral water and spring water for human consumption and causes human urinary tract infections, endocarditis and neonatal sepsis. The aim of this study was to determine the prevalence, virulence genes, antimicrobial resistance and genetic diversity of E. faecalis from mineral water and spring water in China. Of 314 water samples collected from January 2013 to January 2014, 48 samples (15.3%) were contaminated E. faecalis. The highest contamination rate occurred in activated carbon filtered water of spring water (34.5%), followed by source water of spring water (32.3%) and source water of mineral water (6.4%). The virulence gene test of 58 E. faecalis isolates showed that the detection rates of asa1, ace, cylA, gelE and hyl were 79.3, 39.7, 0, 100, 0%, respectively. All 58 E. faecalis isolates were not resistant to 12 kinds of antibiotics (penicillin, ampicillin, linezolid, quinupristin/dalfopristin, vancomycin, gentamicin, streptomycin, ciprofloxacin, levofloxacin, norfloxacin, nitrofurantoin, and tetracycline). Enterobacterial repetitive intergenic consensus-PCR classified 58 isolates and three reference strains into nine clusters with a similarity of 75%. This study is the first to investigate the prevalence of E. faecalis in mineral water and spring water in China. The results of this study suggested that spring water could be potential vehicles for transmission of E. faecalis.