Murine models of neonatal susceptibility to a clinical strain of enterovirus A71.

Enterovirus A71 (EV-A71) is neurotropic and one of the primary enteric pathogens responsible for severe central nervous system infection in infants and young children. Neonatal mice are ideal models for studying the pathogenesis of infection caused by EV-A71. In this study, we assessed the susceptibility of neonatal BALB/c, C57BL/6, ICR, Kunming, and NIH mice to a clinically isolated EV-A71 strain. One-day-old mice were challenged with a clinical isolate of EV-A71 via intraperitoneal injection, then observed for 13 days for mortality, body-weight changes, and limb paralysis. RT-qPCR was performed to quantify viral RNA in the brain, spinal cord, skeletal muscle, and lungs of BALB/c and C57BL/6 mice. The expression of murine scavenger receptor class B member 2 (mSCARB2) was measured by western blotting. Finally, lesions were assessed by histological examination. We found that neonatal BALB/c and C57BL/6 mice were both susceptible to EV-A71, leading to decreased survival rate, greater body weight loss, and prominent hind-limb paralysis. Tissue viral loads of C57BL/6J mice were markedly higher than those of BALB/c mice, indicating that EV-A71 replicated more efficiently in C57BL/6 mice. Increased expression of mSCARB2 was observed 5 days after infection in C57BL/6 mice, which coincided with the peak in EV-A71 replication. Histological examination indicated that infection caused obvious pathogenic lesions. In conclusion, C57BL/6 are most susceptible to infection caused by EV-A71 and can be used as a model for studying its pathogenesis and test therapeutic options.

Comparison of reverse-transcription qPCR and droplet digital PCR for the detection of SARS-CoV-2 in clinical specimens of hospitalized patients.

Accurate detection of severe acute respiratory syndrome coronavirus 2 is not only necessary for viral load monitoring to optimize treatment in hospitalized coronavirus disease 2019 patients, but also critical for deciding whether the patient could be discharged without any risk of viral shedding. Digital droplet PCR (ddPCR) is more sensitive than reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and is usually considered the superior choice. In the current study, we compared the clinical performance of RT-qPCR and ddPCR using oropharyngeal swab samples from patients hospitalized in the temporary Huoshenshan Hospital, Wuhan, Hubei, China. Results demonstrated that ddPCR was indeed more sensitive than RT-qPCR. Negative results might be caused by poor sampling technique or recovered patients, as the range of viral load in these patients varied significantly. In addition, both methods were highly correlated in terms of their ability to detect all three target genes as well as the ratio of copies of viral genes to that of the IC gene. Furthermore, our results evidenced that both methods detected the N gene more easily than the ORF gene. Taken together, these findings imply that the use of ddPCR, as an alternative to RT-qPCR, is necessary for the accurate diagnosis of hospitalized coronavirus disease 2019 patients.

Endogenous ethanol produced by intestinal bacteria induces mitochondrial dysfunction in non-alcoholic fatty liver disease.

BACKGROUND AND AIM: A causal relationship between changes of the gut microbiome and non-alcoholic fatty liver disease (NAFLD) remains unclear. We demonstrated that endogenous ethanol (EnEth) produced by intestinal microbiota is likely a causative agent of NAFLD. METHODS: Two mutants with different alcohol-producing abilities, namely, W14-adh and W14Δadh, were constructed using the clinical high alcohol-producing (HiAlc) Klebsiella pneumoniae strain W14 as a parent. Damage to hepatocytes caused by bacteria with different alcohol-producing capacities was evaluated (EtOH group as positive control). The ultrastructural changes of mitochondria were assessed via transmission electron microscopy (TEM). Hepatic levels of mitochondrial reactive oxygen species (ROS), DNA damage, and adenosine triphosphate were examined. RESULTS: The results illustrated that steatosis was most severe in the W14-adh group, followed by the W14 group, whereas the W14Δadh group had few fatty droplets. TEM and examination of related protein expression revealed that the mitochondrial integrity of HepG2 hepatocytes was considerably damaged in the EtOH and bacteria treatment groups. The impaired mitochondrial function in HepG2 hepatocytes was evidenced by reduced adenosine triphosphate content and increased mitochondrial ROS accumulation and DNA damage in the EtOH and bacteria treatment groups, especially the W14-adh group. Meanwhile, liver injury and mitochondrial damage were observed in the hepatocytes of mice. The livers of mice in the W14-adh group, which had the highest ethanol production, exhibited the most serious damage, similar to that in the EtOH group. CONCLUSIONS: EnEth produced by HiAlc bacteria induces mitochondrial dysfunction in NAFLD.

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae.

The underlying etiology of nonalcoholic fatty liver disease (NAFLD) is believed to be quite varied. Changes in the gut microbiota have been investigated and are believed to contribute to at least some cases of the disease, though a causal relationship remains unclear. Here, we show that high-alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) is associated with up to 60% of individuals with NAFLD in a Chinese cohort. Transfer of clinical isolates of HiAlc Kpn by oral gavage into mice induced NAFLD. Likewise, fecal microbiota transplant (FMT) into mice using a HiAlc-Kpn-strain-containing microbiota isolated from an individual with NASH induced NAFLD. However, selective elimination of the HiAlc Kpn strain before FMT prevented NAFLD in the recipient mice. These results suggest that at least in some cases of NAFLD an alteration in the gut microbiome drives the condition due to excess endogenous alcohol production.

Synergistic effect of magnetite and zero-valent iron on anaerobic degradation and methanogenesis of phenol.

Anaerobic digestion is widely employed for treating phenol-containing wastewater, but there are still some drawbacks such as slow phenol degradation rate and vulnerable acetoclastic methanogens. Coupling of magnetite (Fe3O4) and zero valent iron (ZVI) was firstly used to enhance anaerobic digestion of phenol. The results indicated an obvious synergistic effect was generated with coupling of Fe3O4 and ZVI during the whole anaerobic digestion of phenol. The phenol degradation rate and methane production of Fe3O4/ZVI-added group were increased by 8.8-23.1% and 11.9-31.6%, respectively compared with Fe3O4-added group, and enhanced by 5.9-17.1% and 4.4-18.3%, respectively compared with ZVI-added group. ZVI improved the growth of hydrogenotrophic methanogens and Fe3O4 enhanced the growth of syntrophic acetate-oxidizing bacteria. Finally, the syntrophic interaction between acetate-oxidizing bacterium and hydrogenotrophic methanogens played a vital role on the synergistic effect of Fe3O4 and ZVI on the whole anaerobic phenol digestion.

Effects of a Lactulose-Rich Diet on Fecal Microbiome and Metabolome in Pregnant Mice.

Lactulose, a safe and beneficial molecule, can be used in food as a prebiotic and as an osmotic laxative during pregnancy. This work evaluated the effects of dietary lactulose on the gut microenvironment of pregnant mice using the fecal microbiota and metabolomic profiling. After 2 weeks of feeding, the Bifidobacterium and Bacteroides abundances in the mouse feces were significantly increased in the LAC-high (the diet supplemented with 15% lactulose) group. A total of 15 metabolites, including 1-monoolein, glucose-6-phosphate, and short-chain fatty acids, were increased significantly in the LAC-high group. The serum glucose and total cholesterol concentrations were significantly decreased, while the progesterone level was significantly increased in the lactulose-fed mice. In the LAC-high group, the colonic pH and intestinal permeability were decreased, while the immunoglobulins in the colonic epithelial cells and the small intestinal absorption capacity were significantly increased. These findings indicated that lactulose supplementation benefitted pregnancy performance in mice.

Characterizing the Biology of Lytic Bacteriophage vB_EaeM_φEap-3 Infecting Multidrug-Resistant Enterobacter aerogenes.

Carbapenem-resistant Enterobacter aerogenes strains are a major clinical problem because of the lack of effective alternative antibiotics. However, viruses that lyze bacteria, called bacteriophages, have potential therapeutic applications in the control of antibiotic-resistant bacteria. In the present study, a lytic bacteriophage specific for E. aerogenes isolates, designated vB_EaeM_φEap-3, was characterized. Based on transmission electron microscopy analysis, phage vB_EaeM_φEap-3 was classified as a member of the family Myoviridae (order, Caudovirales). Host range determination revealed that vB_EaeM_φEap-3 lyzed 18 of the 28 E. aerogenes strains tested, while a one-step growth curve showed a short latent period and a moderate burst size. The stability of vB_EaeM_φEap-3 at various temperatures and pH levels was also examined. Genomic sequencing and bioinformatics analysis revealed that vB_EaeM_φEap-3 has a 175,814-bp double-stranded DNA genome that does not contain any genes considered undesirable for the development of therapeutics (e.g., antibiotic resistance genes, toxin-encoding genes, integrase). The phage genome contained 278 putative protein-coding genes and one tRNA gene, tRNA-Met (AUG). Phylogenetic analysis based on large terminase subunit and major capsid protein sequences suggested that vB_EaeM_φEap-3 belongs to novel genus "Kp15 virus" within the T4-like virus subfamily. Based on host range, genomic, and physiological parameters, we propose that phage vB_EaeM_φEap-3 is a suitable candidate for phage therapy applications.

Targeting the Gut Microbiota to Investigate the Mechanism of Lactulose in Negating the Effects of a High-Salt Diet on Hypertension.

SCOPE: High-salt diets (HSDs) are widely considered to cause health problems such as gut microecological imbalances, constipation, and hypertension. This study explores how lactulose as a safe molecule can stimulate bodily responses to alleviate salt-sensitive hypertension by regulating the gut microbiotas of HSD-fed mice. METHODS AND RESULTS: After 4 weeks, the blood pressures of mice fed a high-salt plus lactulose diet (HSLD) are significantly lower than those of the HSD-fed mice. The HSD increases the abundances of Alistipes and Ruminococcaceae_UCG_009 and reduced the abundance of Lactobacillus in the gut, while lactulose supplementation increases the abundances of Bifidobacterium, Alloprevotella, and Subdoligranulum. Fecal metabolic profiling shows significant increases in metabolites involved in ATP-binding cassette transporter pathways, and tryptophan metabolism is significantly reduced in the HSLD group compared with the HSD group. Lactulose maintains the intestinal microenvironmental health in the HSD-fed mice by improving glycolipid metabolism, decreasing the small intestinal interleukin-17a (IL-17a) and interleukin-22 (IL-22) mRNA levels and serum IL-17a and IL-22 levels, relieving constipation, increasing fecal sodium, and reducing intestinal permeability. CONCLUSION: Lactulose negates salt-sensitive hypertension. Regulating the gut microbiota is a potential treatment for salt-sensitive hypertension.

Identification and molecular characterization of Serratia marcescens phages vB_SmaA_2050H1 and vB_SmaM_2050HW.

Serratia marcescens is a rod-shaped, Gram-negative bacterium causing nosocomially acquired infections. Bacteriophages are natural opponents of their pathogenic bacterial hosts and could be an alternative to traditional antibiotic treatments. In this study, two S. marcescens-specific bacteriophages, vB_SmaA_2050H1 and vB_SmaM_2050HW, were isolated from two different waste samples in China. Phage plaque assays, transmission electron microscopy, host-range determination, and one-step growth curve analyses were performed for both phages. vB_SmaA_2050H1 was classified as belonging to the family Ackermannviridae, and vB_SmaM_2050HW was classified as belonging to the family Myoviridae. One-step growth curve analysis showed that the latent and rise period of vB_SmaA_2050H1 were 80 min and 50 min, respectively, with a burst size of approximately 103 phage particles per infected cell. For vB_SmaM_2050HW, latent and rise periods of 40 min and 60 min, respectively, were determined, with a burst size of approximately 110 phage particles per infected cell. vB_SmaA_2050H1 infected 10 of the 15 (66.67%) S. marcescens strains tested, while vB_SmaM_2050HW infected 12 (80%) of the strains. Whole-genome sequencing and annotation of each of the phage genomes revealed genome sizes of 159,631 bp and 276,025 bp for vB_SmaA_2050H1 and vB_SmaM_2050HW, respectively, with the respective genomes containing 213 and 363 putative open reading frames. Sequence analysis of the genomes revealed that vB_SmaA_2050H1 is a member of the ViI-like family, while vB_SmaM_2050HW is a novel virulent bacteriophage. These findings provide further insights into the genomic structures of S. marcescens bacteriophages.

Characterization of Tail Sheath Protein of N4-Like Phage phiAxp-3.

Achromobacter phage phiAxp-3, an N4-like bacteriophage, specifically recognize Achromobacter xylosoxidans lipopolysaccharide (LPS) as its receptor. PhiAxp-3 tail sheath protein (TSP, ORF69) shares 54% amino acid sequence identity with the TSP of phage N4 (gp65); the latter functions as a receptor binding protein and interacts with the outer membrane receptor NfrA of its host bacterium. Thus, we hypothesized that ORF69 is the receptor-binding protein of phiAxp-3. In the present study, a series of ORF69 truncation variants was constructed to identify the part(s) of this protein essential for binding to A. xylosoxidans LPS. Phage adsorption and enzyme-linked immunosorbent assay showed that amino acids 795-1195 of the TSP, i.e., ORF69(795-1195), are sufficient and essential for receptor and binding. The optimum temperature and pH for the functions of ORF69 and ORF69(795-1195) are 4/25°C and 7, respectively. In vitro cytotoxicity assays showed that ORF69 and ORF69(795-1195) were respectively toxic and non-toxic to a human immortalized normal hepatocyte cell line (LO2; doses: 0.375-12 µg). The potential of this non-toxic truncated version of phiASP-3 TSP for clinical applications is discussed.

Rapid visual detection of binary toxin producing Clostridium difficile by loop-mediated isothermal amplification.

The binary toxin Clostridium difficile transferase (CDT) is frequently observed in C. difficile strains and is associated with an increased severity of C. difficile infection. CDT-producing C. difficile infections cause higher fatality rates than infections with CDT negative isolates. Thus, the rapid and accurate identification of a CDT positive C. difficile infection is critical for effective treatment. The present study demonstrates how loop-mediated isothermal amplification (LAMP) can be used to detect CDT-producing C. difficile based on visual observation. This is a low complexity, rapid molecular method that has the potential to be used within a point of care setting. The specificity and sensitivity of the primers in the LAMP reactions for CDT detection were determined using two different methods, a real-time turbidity monitor and visual detection after the addition of calcein to the reaction tube. The results revealed that target DNA was amplified and visualized by these two detection methods within 60 min at a temperature of 60°C. The sensitivity of the LAMP assay was identified to be 10-fold greater than that of polymerase chain reaction analysis. When 25 alternative bacterial strains lacking CDT were tested, the results of the amplification were negative, confirming the specificity of the primers. In conclusion, the visual LAMP method established in the present study may be a rapid, reliable and cost-effective tool for detecting CDT-producing C. difficile strains at the point of care.

Effect of Functional Oligosaccharides and Ordinary Dietary Fiber on Intestinal Microbiota Diversity.

Functional oligosaccharides, known as prebiotics, and ordinary dietary fiber have important roles in modulating the structure of intestinal microbiota. To investigate their effects on the intestinal microecosystem, three kinds of diets containing different prebiotics were used to feed mice for 3 weeks, as follows: GI (galacto-oligosaccharides and inulin), PF (polydextrose and insoluble dietary fiber from bran), and a GI/PF mixture (GI and PF, 1:1), 16S rRNA gene sequencing and metabolic analysis of mice feces were then conducted. Compared to the control group, the different prebiotics diets had varying effects on the structure and diversity of intestinal microbiota. GI and PF supplementation led to significant changes in intestinal microbiota, including an increase of Bacteroides and a decrease of Alloprevotella in the GI-fed, but those changes were opposite in PF fed group. Intriguing, in the GI/PF mixture-fed group, intestinal microbiota had the similar structure as the control groups, and flora diversity was upregulated. Fecal metabolic profiling showed that the diversity of intestinal microbiota was helpful in maintaining the stability of fecal metabolites. Our results showed that a single type of oligosaccharides or dietary fiber caused the reduction of bacteria species, and selectively promoted the growth of Bacteroides or Alloprevotella bacteria, resulting in an increase in diamine oxidase (DAO) and/or trimethylamine N-oxide (TMAO) values which was detrimental to health. However, the flora diversity was improved and the DAO values was significantly decreased when the addition of nutritionally balanced GI/PF mixture. Thus, we suggested that maintaining microbiota diversity and the abundance of dominant bacteria in the intestine is extremely important for the health, and that the addition of a combination of oligosaccharides and dietary fiber helps maintain the health of the intestinal microecosystem.

Community-Metabolome Correlations of Gut Microbiota from Child-Turcotte-Pugh of A and B Patients.

The gut flora are widely involved in the cometabolism with the host and have evident effects on the metabolic phenotype of host. This study performed a metabolome analysis of the intestinal microbiota specific for liver cirrhosis. The study population included patients with Child-Turcotte-Pugh score of A (AP, n = 5) and B (BP, n = 5), and control subjects (NM, n = 3). Metagenomic DNA from fecal microbiota was extracted followed by metagenomic sequencing through Illumina MiSeq high throughput sequencing of 16S rRNA regions. The detection of metabolites from fecal samples was performed using high-performance liquid phase chromatography and gas chromatography coupled with tandem mass spectrometry. Intestinal microbiota community and metabolite analysis both showed separation of cirrhotic patients from control participants, moreover, the microbiota-metabolite correlations changed in cirrhotic patients. Fecal microbiota from cirrhotic patients, with the reduced diversity, contained a decreased abundance of Bacteroidetes and an increased abundance of Firmicutes and Proteobacteria compared with the normal samples. Analysis of metabolome revealed a remarkable change in the metabolic potential of the microbiota in cirrhotic patients, with specific higher concentrations of amine, unsaturated fatty acid, and short-chain fatty acids, and lower concentrations of sugar alcohol and amino acid, suggesting the initial equilibrium of gut microbiota community and co-metabolism with the host were perturbed by cirrhosis. Our study illustrated the relationship between fecal microbiota composition and metabolome in cirrhotic patients, which may improve the clinical prognosis of cirrhosis.

Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach.

BACKGROUND: Intestinal microbiota operated as a whole and was closely related with human health. Previous studies had suggested close relationship between liver cirrhosis (LC) and gut microbiota. METHODS: To determine the functional characteristic of the intestinal microbiota specific for liver cirrhosis, the fecal metaproteome of three LC patients with Child-Turcotte-Pugh (CTP) score of A, B, and C, and their spouse were first compared using high-throughput approach based on denaturing polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry in our study. RESULTS: A total of 5,020 proteins (88 % from bacteria, 12 % form human) were identified and annotated based on the GO and KEGG classification. Our results indicated that the LC patients possessed a core metaproteome including 119 proteins, among which 14 proteins were enhanced expressed and 7 proteins were unique for LC patients compared with the normal, which were dominant at the function of carbohydrate metabolism. In addition, LC patients have unique biosynthesis of branched chain amino acid (BCAA), pantothenate, and CoA, enhanced as CTP scores increased. Those three substances were all important in a wide array of key and essential biological roles of life. CONCLUSIONS: We observed a highly comparable cirrhosis-specific metaproteome clustering of fecal microbiota and provided the first supportive evidence for the presence of a LC-related substantial functional core mainly involved in carbohydrate, BCAA, pantothenate, and CoA metabolism, suggesting the compensation of intestinal microbiota for the fragile and innutritious body of cirrhotic patients.

Identification and molecular characterization of bacteriophage phiAxp-2 of Achromobacter xylosoxidans.

A novel Achromobacter xylosoxidans bacteriophage, phiAxp-2, was isolated from hospital sewage in China. The phage was morphologically and microbiologically characterized, and its one-step growth curve, host range, genomic sequence, and receptor were determined. Its morphology showed that phiAxp-2 belongs to the family Siphoviridae. Microbiological characterization demonstrated that pH 7 is most suitable for phage phiAxp-2; its titer decreased when the temperature exceeded 50 °C; phiAxp-2 is sensitive to ethanol and isopropanol; and the presence of calcium and magnesium ions is necessary to accelerate cell lysis and improve the formation of phiAxp-2 plaques. Genomic sequencing and a bioinformatic analysis showed that phage phiAxp-2 is a novel bacteriophage, consisting of a circular, double-stranded 62,220-bp DNA molecule with a GC content of 60.11% that encodes 86 putative open reading frames (ORFs). The lipopolysaccharide of A. xylosoxidans is involved in the adsorption of phiAxp-2.

Corrigendum: Survey and Visual Detection of Zaire Ebolavirus in Clinical Samples Targeting the Nucleoprotein Gene in Sierra Leone.

[This corrects the article on p. 1332 in vol. 6, PMID: 26648918.].

Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes.

Enterobacter aerogenes (Enterobacteriaceae) is an important opportunistic pathogen that causes hospital-acquired pneumonia, bacteremia, and urinary tract infections. Recently, multidrug-resistant E. aerogenes have been a public health problem. To develop an effective antimicrobial agent, bacteriophage phiEap-2 was isolated from sewage and its genome was sequenced because of its ability to lyse the multidrug-resistant clinical E. aerogenes strain 3-SP. Morphological observations suggested that the phage belongs to the Siphoviridae family. Comparative genome analysis revealed that phage phiEap-2 is related to the Salmonella phage FSL SP-031 (KC139518). All of the structural gene products (except capsid protein) encoded by phiEap-2 had orthologous gene products in FSL SP-031 and Serratia phage Eta (KC460990). Here, we report the complete genome sequence of phiEap-2 and major findings from the genomic analysis. Knowledge of this phage might be helpful for developing therapeutic strategies against E. aerogenes.