PAM-free diagnostics with diverse type V CRISPR-Cas systems

Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.

Retraction: Dealcoholized muscadine wine was partially effective in preventing and treating dextran sulfate sodium-induced colitis and restoring gut dysbiosis in mice

Retraction of 'Dealcoholized muscadine wine was partially effective in preventing and treating dextran sulfate sodium-induced colitis and restoring gut dysbiosis in mice' by Hao Li et al., Food Funct., 2023, 14, 5994-6011, https://doi.org/10.1039/D3FO00047H.

Effects of Carboxymethylcellulose Artificial Tears on Ocular Surface Microbiome Diversity and Composition, A Randomized Controlled Trial

Purpose

Carboxymethylcellulose is an artificial tear ingredient known to decrease gut microbiome diversity when ingested. This study examines the effect of carboxymethylcellulose on ocular surface microbiome diversity and composition.

Methods

Healthy adult participants without significant ophthalmic disease or concurrent carboxymethylcellulose artificial tear use were allocated randomly to take carboxymethylcellulose or control polyethylene glycol artificial tears for seven days. Conjunctival swabs were collected before and after artificial tear treatment. This trial is registered at clinicaltrials.gov (NCT05292755). Primary outcomes included abundance of bacterial taxa and microbiome diversity as measured by the Chao-1 richness estimate, Shannon's phylogenetic diversity index, and UniFrac analysis. Secondary outcomes included Ocular Surface Disease Index scores and artificial tear compliance.

Results

Of the 80 enrolled participants, 66 completed the trial. Neither intervention affected Chao-1 richness (analysis of variance [ANOVA], P = 0.231) or Shannon's diversity index (ANOVA, P = 0.224). Microbiome samples did not separate by time point (permutation multivariate analysis of variance [PERMANOVA], P = 0.223) or intervention group (PERMANOVA, P = 0.668). LEfSe taxonomic analysis revealed that carboxymethylcellulose depleted several taxa including Bacteroides and Lachnoclostridium, but enriched Enterobacteriaceae, Citrobacter, and Gordonia. Both interventions decreased OSDI scores (Wilcoxon signed rank test, P < 0.05), but there was no significant difference between interventions (Mann-Whitney U, P = 0.54).

Conclusions

Carboxymethylcellulose artificial tears increased Actinobacteriota but decreased Bacteroides and Firmicutes bacteria. Carboxymethylcellulose artificial tears do not affect ocular surface microbiome diversity and are not significantly more effective than polyethylene glycol artificial tears for dry eye treatment.

Translational Relevance

The 16S microbiome analysis has revealed small changes in the ocular surface microbiome associated with artificial tear use.

Pneumocystis jirovecii pneumonia presenting as a large pulmonary mass in a patient with AIDS

Pneumocystis jirovecii pneumonia typically presents with diffuse bilateral infiltrates or ground-glass opacities. However, the radiographic pattern may be atypical. We report a case of a woman in her 40s who presented with multiple pulmonary masses and prolonged symptoms of non-productive cough, generalised weakness and fatigue. Serial chest CT performed prior to her presentation showed a large right lower lobe lung mass with multiple additional bilateral pulmonary nodules. Her workup revealed a new diagnosis of AIDS. Pathology of several CT-guided needle biopsies was consistent with Pneumocystis which was confirmed by microbial DNA sequencing. No additional pathogens were identified. Her clinical symptoms and radiographs improved significantly with trimethoprim-sulfamethoxazole and treatment of her HIV infection. Clinicians should evaluate for underlying immunodeficiency and seek infectious disease and pulmonary consultation early for consideration of alternative diagnoses when patients present with cough, dyspnoea and atypical chest radiographs, and initial pathological examination is unrevealing.

Dealcoholized muscadine wine was partially effective in preventing and treating dextran sulfate sodium-induced colitis and restoring gut dysbiosis in mice

Muscadine wine has a unique polyphenol profile consisting of anthocyanins, ellagic acids, and flavonols. This study aims to compare the prevention, treatment, and combined activity (P + T) of dealcoholized muscadine wine (DMW) on DSS-induced colitis in mice and its impact on the gut microbiome. Male C57BL/6 mice in the healthy and colitis group received an AIN-93M diet for 28 days. In the prevention, treatment, and P + T (prevention + treatment) groups, mice received an AIN-93M diet containing 2.79% (v/w) DMW on days 1-14, 15-28, and 1-28, respectively. Except for mice in the healthy group, all mice were given water with 2.5% (w/v) DSS on days 8-14 to induce colitis. DMW in all three receiving groups reduced myeloperoxidase activity, histology scores, and phosphorylation of Iκb-α in the colon. Colon shortening, serum IL-6, and colonic mRNA of TNF-α were blunted only in the P + T group. Gut permeability was reduced in the treatment and P + T groups. DMW in P + T group showed higher activity to increase microbiome evenness, modulate β-diversity, elevate the cecal content of SCFAs, and enrich SCFA-producing bacteria, including Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Peptococcaceae. This was accompanied by a decrease in pathogenic Burkholderiaceae in mice. This study suggests that muscadine wine has partial preventive and therapeutic effects against inflammatory bowel disease. The combination of prevention and treatment using DMW showed better activities than either prevention or treatment.

Smoking-induced subgingival dysbiosis precedes clinical signs of periodontal disease

Smoking accelerates periodontal disease and alters the subgingival microbiome. However, the relationship between smoking-associated subgingival dysbiosis and progression of periodontal disease is not well understood. Here, we sampled 233 subgingival sites longitudinally from 8 smokers and 9 non-smokers over 6-12 months, analyzing 804 subgingival plaque samples using 16 rRNA sequencing. At equal probing depths, the microbial richness and diversity of the subgingival microbiome was higher in smokers compared to non-smokers, but these differences decreased as probing depths increased. The overall subgingival microbiome of smokers differed significantly from non-smokers at equal probing depths, which was characterized by colonization of novel minority microbes and a shift in abundant members of the microbiome to resemble periodontally diseased communities enriched with pathogenic bacteria. Temporal analysis showed that microbiome in shallow sites were less stable than deeper sites, but temporal stability of the microbiome was not significantly affected by smoking status or scaling and root planing. We identified 7 taxa-Olsenella sp., Streptococcus cristatus, Streptococcus pneumoniae, Streptococcus parasanguinis, Prevotella sp., Alloprevotella sp., and a Bacteroidales sp. that were significantly associated with progression of periodontal disease. Taken together, these results suggest that subgingival dysbiosis in smokers precedes clinical signs of periodontal disease, and support the hypothesis that smoking accelerates subgingival dysbiosis to facilitate periodontal disease progression.

A randomized controlled trial to evaluate the effectiveness of a novel mouth rinse in patients with gingivitis

Background

This single-center, randomized controlled trial aimed to determine the effectiveness of a novel, biofilm-disrupting, mouth rinse that combines Cetylpyridinium chloride (CPC) and essential oils in preventing re-accumulation of supragingival plaque and supragingival microbiome in patients with gingivitis after dental prophylaxis.

Methods

One hundred eighteen participants were randomly assigned in a 1:1 ratio to receive twice-daily test mouth rinse (59) or carrier rinse control (59) for 12 weeks after dental prophylaxis.

Results

In a per-protocol analysis that included patients who completed the intervention, the treatment group (39) had significantly lower supragingival plaque scores at 6 and 12 weeks compared to the control group (41; p = 0.022). Both groups showed similar improvement in gingivitis score, but neither group had improvement in bleeding score or probing depth. Thirty-eight (29%) patients did not complete the study due to loss of follow-up (17) or early discontinuation of the assigned intervention (21). Microbiome sequencing showed that the treatment rinse significantly depleted abundant and prevalent members of the supragingival plaque microbiome consortium.

Conclusions

Among patients with gingivitis, the novel mouth rinse significantly reduced re-accumulation of supragingival plaque following dental prophylaxis by depleting supragingival plaque microbiome. However, long-term adherence to the rinse may be limited by adverse effects (ClinicalTrials.gov number, NCT03154021).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-022-02518-2.

[The association of high-sensitivity C-reactive protein with new-onset hypertension in different age groups]

Objective: To investigate the association between high sensitivity C-reactive protein (hsCRP) level and new-onset hypertension in different age groups. Methods: This was a prospective cohort study involving non-hypertensive population in Kailuan Group community who participated in health examination between 2006 and 2007.Follow-up was conducted every 2 years, and the time of new onset of hypertension was used as the endpoint of follow-up. The endtime of follow-up for patients without hypertension was the time of death or the last follow-up (December 31, 2017).According to the baseline hsCRP level, the participants were divided into low-risk group (hsCRP<1.0 mg/L), medium-risk group (hsCRP ≥1.0 and ≤3.0 mg/L), and high-risk group (hsCRP>3.0 mg/L), and further stratified by age. Kaplan-Meier method was used to calculate the cumulative incidence of hypertension in each group. Multivariate Cox regression model was used to analyze the association between hsCRP level and new-onset hypertension. Results: A total of 51 179 participants were included in this study, including 38 606 males (75.43%) with an average age of (48.1±12.2) years. The baseline hsCRP was 0.64 (0.25, 1.60) mg/L. The baseline hsCRP was 0.30 (0.16, 0.59), 1.57 (1.20, 2.10), 5.17 (3.80, 7.10) mg/L respectively in low-, medium- and high-risk groups. During the follow-up of (8.1±2.2) years, a total of 9 523 (18.60%) patients developed hypertension, and the cumulative incidence rates of low-, medium- and high-risk groups were 17.41%, 20.48% and 20.73%, respectively. The cumulative incidence of hypertension in low-, medium- and high-risk groups of<45, 45-54, 55-64, ≥65 years old were 13.53%, 15.82%, 16.76%; 19.27%, 22.84%, 21.62%; 21.55%, 24.19%, 24.88%;20.20%, 22.35%, 19.11%, respectively. Except for people aged ≥65 years, there were significant differences in the cumulative incidence of hypertension in low-, medium- and high-risk groups (all P<0.05).Multivariate Cox regression analysis showed that the risk of new-onset hypertension in the high risk group was 1.11 times higher than that in the low risk group (HR=1.11, 95%CI 1.05-1.18). The risk of new-onset hypertension in the high-risk group was 1.22 times (HR=1.22, 95%CI 1.08-1.38), 1.14 times (HR=1.14, 95%CI 1.04-1.26), 1.16 times (HR=1.16, 95%CI 1.04-1.30), and 1.02 times (HR=1.02, 95%CI 0.86-1.20) of the low-risk group, in the<45, 45-54, 55-64, and ≥65 years old groups, respectively. Conclusion: Higher hsCRP level is a risk factor for new-onset hypertension, and the risk of developing hypertension caused by elevated hsCRP is age-dependent.

Efficacy and Safety of RBX2660 in PUNCH CD3, a Phase III, Randomized, Double-Blind, Placebo-Controlled Trial with a Bayesian Primary Analysis for the Prevention of Recurrent Clostridioides difficile Infection

BACKGROUND

Recurrent Clostridioides difficile infection, associated with dysbiosis of gut microbiota, has substantial disease burden in the USA. RBX2660 is a live biotherapeutic product consisting of a broad consortium of microbes prepared from human stool that is under investigation for the reduction of recurrent C. difficile infection.

METHODS

A randomized, double-blind, placebo-controlled, phase III study, with a Bayesian primary analysis integrating data from a previous phase IIb study, was conducted. Adults who had one or more C. difficile infection recurrences with a positive stool assay for C. difficile and who were previously treated with standard-of-care antibiotics were randomly assigned 2:1 to receive a subsequent blinded, single-dose enema of RBX2660 or placebo. The primary endpoint was treatment success, defined as the absence of C. difficile infection diarrhea within 8 weeks of study treatment.

RESULTS

Of the 320 patients screened, 289 were randomly assigned and 267 received blinded treatment (n = 180, RBX2660; n = 87, placebo). Original model estimates of treatment success were 70.4% versus 58.1% with RBX2660 and placebo, respectively. However, after aligning the data to improve the exchangeability and interpretability of the Bayesian analysis, the model-estimated treatment success rate was 70.6% with RBX2660 versus 57.5% with placebo, with an estimated treatment effect of 13.1% and a posterior probability of superiority of 0.991. More than 90% of the participants who achieved treatment success at 8 weeks had sustained response through 6 months in both the RBX2660 and the placebo groups. Overall, RBX2660 was well tolerated, with manageable adverse events. The incidence of treatment-emergent adverse events was higher in RBX2660 recipients compared with placebo and was mostly driven by a higher incidence of mild gastrointestinal events.

CONCLUSIONS

RBX2660 is a safe and effective treatment to reduce recurrent C. difficile infection following standard-of-care antibiotics with a sustained response through 6 months.

CLINICAL TRIAL REGISTRATION

NCT03244644; 9 August, 2017.

Microbiome Resilience despite a Profound Loss of Minority Microbiota following Clindamycin Challenge in Humanized Gnotobiotic Mice

Antibiotics are known to induce gut dysbiosis and increase the risk of antibiotic resistance. While antibiotic exposure is a known risk factor leading to compromised colonization resistance against enteric pathogens such as Clostridioides difficile, the extent and consequences of antibiotic perturbation on the human gut microbiome remain poorly understood. Human studies on impacts of antibiotics are complicated by the tremendous variability of gut microbiome among individuals, even between identical twins. Furthermore, antibiotic challenge experiments cannot be replicated in human subjects for a given gut microbiome. Here, we transplanted feces from three unrelated human donors into groups of identical germfree (GF) Swiss-Webster mice, and examined the temporal responses of the transplanted microbiome to oral clindamycin challenge in gnotobiotic isolators over 7 weeks. Analysis of 177 longitudinal fecal samples revealed that 59% to 81% of human microbiota established a stable configuration rapidly and stably in GF mice. Microbiome responses to clindamycin challenge was highly reproducible and microbiome-dependent. A short course of clindamycin was sufficient to induce a profound loss (∼one third) of the microbiota by disproportionally eliminating minority members of the transplanted microbiota. However, it was inadequate to disrupt the global microbial community structure or function, which rebounded rapidly to resemble its pre-treatment state after clindamycin discontinuation. Furthermore, the response of individual microbes was community-dependent. Taken together, these results suggest that the overall gut microbiome structure is resilient to antibiotic perturbation, the functional consequences of which warrant further investigation. IMPORTANCE Antibiotics cause imbalance of gut microbiota, which in turn increase our susceptibility to gastrointestinal infections. However, how antibiotics disrupt gut bacterial communities is not well understood, and exposing healthy volunteers to unnecessary antibiotics for research purposes carries clinical and ethical concerns. In this study, we used genetically identical mice transplanted with the same human gut microbiota to control for both genetic and environmental variables. We found that a short course of oral clindamycin was sufficient to eliminate one third of the gut bacteria by disproportionally eliminating minority members of the transplanted microbiota, but it was inadequate to disrupt the overall microbial community structure and function, which rebounded rapidly to its pre-treatment state. These results suggest that gut microbiome is highly resilient to antibiotic challenge and degradation of the human gut ecosystem may require repeated or prolonged antibiotic exposure.

Emulsification by vitamin E TPGS or Quillaja extract enhanced absorption of berberine without affecting its metabolism in humans

Berberine is widely used for the prevention of cancers and diabetes.

Linkage of resistance-associated substitutions in GT1 sofosbuvir + NS5A inhibitor failures treated with glecaprevir/pibrentasvir

BACKGROUND & AIMS

Retreatment with glecaprevir/pibrentasvir (G/P) resulted in a rate of sustained virologic response 12 weeks after treatment completion (SVR12) of >90% in HCV genotype 1 (GT1) patients who previously failed a regimen of sofosbuvir plus an NS5A inhibitor (NS5Ai). This study investigated the prevalence and impact of baseline NS3 and NS5A resistance-associated substitutions (RASs) on the efficacy of G/P in prior GT1 sofosbuvir+NS5Ai failures and the persistence of treatment-emergent RASs.

METHODS

Longitudinal samples from 177 patients enrolled in a phase IIIb, randomized pragmatic clinical trial were analyzed. Patients without cirrhosis were randomized to 12 or 16 weeks of G/P, and patients with compensated cirrhosis were randomized to G/P and ribavirin for 12 weeks or G/P for 16 weeks. Linkage of RAS was identified using Primer-ID next-generation sequencing at a 15% cut-off.

RESULTS

Of 177 patients, 169 (95.5%) were PI-naïve. All 33 GT1b-infected patients achieved SVR12. In GT1a-infected patients, baseline NS5A RASs were prevalent (74.5%, 105/141) but NS3 RASs were uncommon. Baseline NS3 RASs had no impact on G/P efficacy and patients with baseline NS5A RASs showed a numerically but not statistically significantly lower SVR12 rate compared to those without NS5A RASs (89% vs. 97%). SVR12 was achieved in 34 of 35 (97%) patients without NS5A baseline substitution, and 53 of 57 (93%), 35 of 40 (88%), 5 of 8 (63%) with single, double-linked, and triple-linked NS5A substitutions, respectively. Among 13 patients with virologic failure, 4 acquired treatment-emergent NS3 RASs and 10 acquired NS5A RASs.

CONCLUSION

Baseline NS5A RASs were highly prevalent. The presence of an increasing number of linked NS5A RASs in GT1a showed a trend in decreasing SVR12 rates, although no specific NS5A RASs or their linkage pattern were associated with lower SVR12 rates.

LAY SUMMARY

Direct-acting antivirals have revolutionized the treatment of chronic hepatitis C infection, but treatment failure occurs in some patients. Retreatment of patients who previously failed a regimen consisting of sofosbuvir and an NS5A inhibitor with a regimen of glecaprevir and pibrentasvir (G/P) is >90% effective. Herein, we analyzed samples from these patients and showed that retreatment efficacy with G/P is lower in patients with double- or triple-linked NS5A resistance mutations than in patients with single or no NS5A resistance mutations.

CLINICAL TRIAL NUMBER

NCT03092375.

[Rare thalassemia caused by novel nucleotide variants in the globin gene: four case reports and literature review]

目的

分析4例少见地中海贫血（地贫）患者的DNA序列、临床表型，提高对地贫的认识。

方法

对2014年5月至2019年12月4例少见地贫患者的临床及DNA序列特征进行回顾性分析并复习相关文献。

结果

地贫基因常规检测显示，例1～3均未检测到常见的3种α株蛋白1/2（HBA1/A2）基因缺失及其3种点突变和16种β株蛋白（HBB）基因点突变，例4检测到αα^--SEA缺失。HBA1/A2和HBB基因全序列Sanger测序示：例1～4分别存在HBB:c.347C>A、HBB:c.1A>G、HBB:c.393T>G及HBA2:c.301-1G>A（IVS-II-142 G>A）突变。同时，例2的祖父、父亲和姑姑均为HBB:c.1A>G杂合突变。

结论

本研究发现了新的珠蛋白基因突变，HBB:c.347C>A、HBB:c.1A>G和HBB:c.393T>G以及HBA2:c.301-1 G>A（IVS-II-142 G>A）突变在中国地贫患者中为首次报道，HBB:c.393T>G突变为全球首次报道，丰富了地贫基因突变数据库。

Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study

Background

Subgingival microbiome in disease-associated subgingival sites is known to be dysbiotic and significantly altered. In patients with rheumatoid arthritis (RA), the extent of dysbiosis in disease- and health-associated subgingival sites is not clear.

Methods

8 RA and 10 non-RA subjects were recruited for this pilot study. All subjects received full oral examination and underwent collection of subgingival plaque samples from both shallow (periodontal health-associated, probing depth ≤ 3mm) and deep subgingival sites (periodontal disease-associated, probing depth ≥ 4 mm). RA subjects also had rheumatological evaluation. Plaque community profiles were analyzed using 16 S rRNA sequencing.

Results

The phylogenetic diversity of microbial communities in both RA and non-RA controls was significantly higher in deep subgingival sites compared to shallow sites (p = 0.022), and the overall subgingival microbiome clustered primarily according to probing depth (i.e. shallow versus deep sites), and not separated by RA status. While a large number of differentially abundant taxa and gene functions was observed between deep and shallow sites as expected in non-RA controls, we found very few differentially abundant taxa and gene functions between deep and shallow sites in RA subjects. In addition, compared to non-RA controls, the UniFrac distances between deep and shallow sites in RA subjects were smaller, suggesting increased similarity between deep and shallow subgingival microbiome in RA. Streptococcus parasanguinis and Actinomyces meyeri were overabundant in RA subjects, while Gemella morbillorum, Kingella denitrificans, Prevotella melaninogenica and Leptotrichia spp. were more abundant in non-RA subjects.

Conclusions

The aggregate subgingival microbiome was not significantly different between individuals with and without rheumatoid arthritis. Although the differences in the overall subgingival microbiome was driven primarily by probing depth, in contrast to the substantial microbiome differences typically seen between deep and shallow sites in non-RA patients, the microbiome of deep and shallow sites in RA patients were more similar to each other. These results suggest that factors associated with RA may modulate the ecology of subgingival microbiome and its relationship to periodontal disease, the basis of which remains unknown but warrants further investigation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-021-01597-x.

[Clinical characteristics of "classical" and "non-classical" paraneoplastic neurological syndrome]

Objective: To explore the clinical features of classical and non-classical paraneoplastic neurological syndrome (PNS). Methods: From 2015 to 2020, 48 cases of definite PNS admitted to the First Affiliated Hospital of University of Science and Technology of China were retrospectively collected, and classification, clinical characteristics, onconeural antibodies and primary tumors were analyzed. The included cases were divided into classical and non-classical groups according to Graus criteria, and the differences of clinical characteristics, onconeural antibodies, combined tumors, time of diagnosis and mortality were compared between the two groups. Results: Among the 48 confirmed patients, 21 (43.8%) were positive for well-characterized onconeural antibodies. There were 28 cases (58.3%) and 20 cases (41.7%) in classic and non-classical PNS groups, respectively. No significant differences of age, sex, clinical involvement site, characteristic positive antibody type, tumor diagnosis rate and follow-up mortality were found between the two groups (all P>0.05). The time of diagnosis in the non-classical PNS group was 3.0 (2.0, 6.5) months, which was significantly longer than that in the classical PNS group 1.0(0.6, 3.0) months (P<0.05). Meanwhile, the combination rate of non-characteristic antibodies in the classical PNS group (10 cases, 35.7%) was significantly higher than that in the non-classical PNS group (1 case, 5.0%) (P=0.016). During the follow-up, 39 patients (81.3%) with tumor were confirmed, and 29 patients (60.4%) were diagnosed with PNS before the tumor was found. Conclusions: The"non-classical"PNSs are common in clinical settings. Diagnosis may be delayed due to the nonclassical symptoms of the patients. When patients have clinical symptoms related to PNS, onconeural antibodies should be detected and the relevant tumors should also be screened. Patients have positive antibodies but with no tumors should be closely followed up for more than 5 years.

Baseline Gut Microbiota Composition Is Associated with Major Infections Early after Hematopoietic Cell Transplantation

Infection is a major cause of morbidity and mortality after hematopoietic cell transplantation (HCT). Gut microbiota (GM) composition and metabolites provide colonization resistance against dominance of potential pathogens, and GM dysbiosis following HCT can be deleterious to immune reconstitution. Little is known about the composition, diversity, and evolution of GM communities in HCT patients and their association with subsequent febrile neutropenia (FN) and infection. Identification of markers before HCT that predict subsequent infection could be useful in developing individualized antimicrobial strategies. Fecal samples were collected prospectively from 33 HCT recipients at serial time points: baseline, post-conditioning regimen, neutropenia onset, FN onset (if present), and hematologic recovery. GM was assessed by 16S rRNA sequencing. FN and major infections (ie, bloodstream infection, typhlitis, invasive fungal infection, pneumonia, and Clostridium difficile enterocolitis) were identified. Significant shifts in GM composition and diversity were observed during HCT, with the largest alterations occurring after initiation of antibiotics. Loss of diversity persisted without a return to baseline at hematologic recovery. GM in patients with FN was enriched in Mogibacterium, Bacteroides fragilis, and Parabacteroides distasonis, whereas increased abundance of Prevotella, Ruminococcus, Dorea, Blautia, and Collinsella was observed in patients without fever. A baseline protective GM profile (BPGMP) was predictive of protection from major infection. The BPGMP was associated with subsequent major infections with 77% accuracy and an area under the curve of 79%, with sensitivity, specificity, and positive and negative predictive values of 0.71, 0.91, 0.77, and 0.87, respectively. Our data show that large shifts in GM composition occur early after HCT, and differences in baseline GM composition are associated with the development of subsequent major infections.

[Consideration of surgeons participating in 2019 coronavirus disease emergency medical rescue]

As a newly epidemic, 2019 coronavirus disease (COVID-19) with a concentrated outbreak poses a great challenge to medical treatment. The severe and critical patients are complex complicatied with the psychological problems, and the medical staff are overworked and under tremendous psychological pressure. The surgeon participated in emergency medical rescue could provide professional treatment for the patients combined with surgical diseases, as well as specialized training for the non-surgeon crew, to reduce surgical-related mortality. With the advantages of good team consciousness, strong aseptic concept and good psychological quality, the surgeons can quickly adapt to and carry out rescue work under the premise of good self-protection. Surgeons need to develop critical care management concepts and focus on the critical care support equipment. Some suggestions are put forward for the standardized training of resident surgeons to cultivate compound talents. It is hoped that this article can lead to the thinking of how to participate in the emergency medical rescue of infectious diseases among surgeons and provide some enlightenment for future surgical education.

A single variant sequencing method for sensitive and quantitative detection of HIV-1 minority variants

HIV drug resistance is a major threat to achieving long-term viral suppression in HIV-positive individuals. Drug resistant HIV variants, including minority variants, can compromise response to antiretroviral therapy. Many studies have investigated the clinical relevance of drug resistant minority variants, but the level at which minority variants become clinically relevant remains unclear. A combination of Primer-ID and deep sequencing is a promising approach that may quantify minority variants more accurately compared to standard deep sequencing. However, most studies that used the Primer-ID method have analyzed clinical samples directly. Thus, its sensitivity and quantitative accuracy have not been adequately validated using known controls. Here, we constructed defined proportions of artificial RNA and virus quasispecies and measured their relative proportions using the Primer-ID based, quantitative single-variant sequencing (qSVS) assay. Our results showed that minority variants present at 1% of quasispecies were detected reproducibly with minimal variations between technical replicates. In addition, the measured frequencies were comparable to the expected frequencies. These data validate the accuracy and reproducibility of the qSVS assay in quantifying authentic HIV minority variants, and support the use of this approach to examine the impacts of minority HIV variants on virologic response and clinical outcome.

Analysis of Tryptophan Metabolites in Serum Using Wide-Isolation Strategies for UHPLC-HRMS/MS

Current targeted metabolomic workflows are limited by design and thus sacrifice crucial information from a profiling standpoint that could lead to a more fundamental understanding of the metabolic processes of interest. One drawback to performing targeted analysis on ion trapping instruments is the potential for increased variability in analysis when analytes and standards are isolated and trapped individually for fragmentation. In addition, this sequential isolation process increases the duty cycle of the mass spectrometer and reduces the number of points collected across a chromatographic peak. To address this, the use of a wide-isolation window (12 Da) to encompass the target analyte and the isotope standard within a single fragmentation window ensures that fragmentation is consistent when quantitation relies on the ratio of the target to the internal standard. Additionally, the preservation of a faster scan rate ensures that optimal representation of chromatographic peaks is preserved for the purposes of both quantitative and qualitative analyses that require peak integration for statistical analysis. The use of this flexible method is promising in the investigation of pathways that require multiple targets and are highly integrated within the system. Here, we demonstrate the application of this method in a fast ultra-high performance liquid chromatography (UHPLC) analysis to integrate wide-isolation quantitative strategies for high-resolution mass spectrometry (HRMS) combined with profiling qualitative metabolomics for the analysis of tryptophan degradation metabolites in mouse serum. Analysis of tryptophan-deficient states as compared to control in both germ-free or E. coli gut microbiota states was used to quantitate pathway-specific metabolites as well as obtain full profiling information. The quantitative and qualitative results revealed the preservation of the primary pathways of degradation in the kynurenine pathway to potentially produce primary products such as nicotinamide during stress-induced dietary states.

Efficacy of Glecaprevir and Pibrentasvir in Patients With Genotype 1 Hepatitis C Virus Infection With Treatment Failure After NS5A Inhibitor Plus Sofosbuvir Therapy

BACKGROUND & AIMS

Treatment options are limited for patients with hepatitis C (HCV) infection with treatment failure after sofosbuvir plus an NS5A inhibitor. There are some data for the efficacy of glecaprevir/pibrentasvir (G/P) in these patients. We performed a randomized trial of the safety and efficacy of 12 and 16 weeks of G/P, with or without ribavirin, in patients with HCV genotype 1 infection with treatment failure after sofosbuvir and an NS5A inhibitor.

METHODS

We performed a phase 3b, open-label study of patients with chronic HCV genotype 1 infection who received previous treatment with sofosbuvir plus an NS5A inhibitor. Patients without cirrhosis were randomly assigned to groups that received G/P for 12 weeks (n = 78, group A) or 16 weeks (n = 49, group B). Patients with compensated cirrhosis were randomly assigned to groups that received G/P and ribavirin for 12 weeks (n = 21, group C) or G/P for 16 weeks (n = 29, group D). The primary end point was a sustained virologic response 12 weeks after treatment. Samples collected at baseline and at time of treatment failure were sequenced for resistance-associated substitutions in NS3 and NS5A.

RESULTS

Of the 177 patients in the 4 groups, 81% were men, 79% had HCV genotype 1a infection, and 44% were black. Proportions of patients with sustained virologic response 12 weeks after treatment in groups A, B, C, and D were 90%, 94%, 86%, and 97%, respectively. The treatment failed in 13 (7.3%) patients with HCV genotype 1a infection, 6 (7.9%) in group A, 3 (6.1%) in group B, 3 (6.1%) in group C (6.1%), and 1 (3.4%) in group D. Most patients had baseline resistance-associated substitutions in NS5A. Treatment-emergent resistance-associated substitutions in NS3 and NS5A were observed in 9 and 10 patients with treatment failure, respectively. G/P was well tolerated. Ribavirin increased adverse events but did not increase efficacy.

CONCLUSIONS

In a randomized study of patients with chronic HCV genotype 1 infection who received previous treatment with sofosbuvir plus an NS5A inhibitor, 16 weeks treatment with G/P produced sustained virologic response 12 weeks after treatment in >90% of patients, including those with compensated cirrhosis. ClinicalTrials.gov, Number: NCT03092375.

Decreased ω-6:ω-3 PUFA ratio attenuates ethanol-induced alterations in intestinal homeostasis, microbiota, and liver injury

Ethanol (EtOH)-induced alterations in intestinal homeostasis lead to multi-system pathologies, including liver injury. ω-6 PUFAs exert pro-inflammatory activity, while ω-3 PUFAs promote anti-inflammatory activity that is mediated, in part, through specialized pro-resolving mediators [e.g., resolvin D1 (RvD1)]. We tested the hypothesis that a decrease in the ω-6:ω-3 PUFA ratio would attenuate EtOH-mediated alterations in the gut-liver axis. ω-3 FA desaturase-1 (fat-1) mice, which endogenously increase ω-3 PUFA levels, were protected against EtOH-mediated downregulation of intestinal tight junction proteins in organoid cultures and in vivo. EtOH- and lipopolysaccharide-induced expression of INF-γ, Il-6, and Cxcl1 was attenuated in fat-1 and WT RvD1-treated mice. RNA-seq of ileum tissue revealed upregulation of several genes involved in cell proliferation, stem cell renewal, and antimicrobial defense (including Alpi and Leap2) in fat-1 versus WT mice fed EtOH. fat-1 mice were also resistant to EtOH-mediated downregulation of genes important for xenobiotic/bile acid detoxification. Further, gut microbiome and plasma metabolomics revealed several changes in fat-1 versus WT mice that may contribute to a reduced inflammatory response. Finally, these data correlated with a significant reduction in liver injury. Our study suggests that ω-3 PUFA enrichment or treatment with resolvins can attenuate the disruption in intestinal homeostasis caused by EtOH consumption and systemic inflammation with a concomitant reduction in liver injury.

[Nephrogenic clear cell carcinoma of nasal cavity：a case report]

SummaryRenal clear cell carcinoma（RCCC） is the most common type of renal cell carcinoma, but metastasis to the nasal cavity is extremely rare. A case of RCCC to the nasal cavity and paranasal sinuses was reported. The early clinical manifestations of this case were intermittent epistaxis and subsequent massive epistaxis. Imaging examination revealed that there were masses in the nasal cavity and paranasal sinus, accompanied by bleeding and destruction of the skull base. Renal CT examination showed a tumor in the right kidney, and considered the patient suffering from renal cell carcinoma. The patient underwent a nasal side incision to remove the tumor, the patient's pathological return; nasal nephrogenic clear-cell carcinoma.

Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation

Objective

Airways of children with cystic fibrosis (CF) harbor complex polymicrobial communities which correlates with pulmonary disease progression and use of antibiotics. Throat swabs are widely used in young CF children as a surrogate to detect potentially pathogenic microorganisms in lower airways. However, the relationship between upper and lower airway microbial communities remains poorly understood. This study aims to determine (1) to what extent oropharyngeal microbiome resembles the lung microbiome in CF children and (2) if lung microbiome composition correlates with airway inflammation.

Method

Throat swabs and bronchoalveolar lavage (BAL) were obtained concurrently from 21 CF children and 26 disease controls. Oropharyngeal and lung microbiota were analyzed using 16S rRNA deep sequencing and correlated with neutrophil counts in BAL and antibiotic exposure.

Results

Oropharyngeal microbial communities clustered separately from lung communities and had higher microbial diversity (p < 0.001). CF microbiome differed significantly from non-CF controls, with a higher abundance of Proteobacteria in both upper and lower CF airways. Neutrophil count in the BAL correlated negatively with the diversity but not richness of the lung microbiome. In CF children, microbial genes involved in bacterial motility proteins, two-component system, flagella assembly, and secretion system were enriched in both oropharyngeal and lung microbiome, whereas genes associated with synthesis and metabolism of nucleic acids and protein dominated the non-CF controls.

Conclusions

This study identified a unique microbial profile with altered microbial diversity and metabolic functions in CF airways which is significantly affected by airway inflammation. These results highlight the limitations of using throat swabs as a surrogate to study lower airway microbiome and metagenome in CF children.

[The value of acoustic parameters in the voice therapy for patients with unilateral vocal cord paralysis]

Objective: To investigate the value of acoustic parameters in the voice therapy for patients with unilateral vocal cord paralysis (UVCP). Methods: From May 2015 to April 2018, 51 patients with UVCP and 59 healthy controls in Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, were involved in this research retrospectively. The UVCP patients were diagnosed with stroboscopic laryngoscopy. The minimum glottal area (MGA) was calculated by KIPS software when the people were pronouncing/i:/. The fundamental frequency (F0), Jitter, Shimmer and NHR were detected by CSL4500 multiple acoustic voice analyzer. Results: MGA of UVCP patients was much higher than that of healthy control (male: 433.68±64.52 vs. 294.41±51.82, t=9.23, P=0.000; female: 498.80±73.42 vs. 302.03±76.54, t=13.21, P=0.000), which meaned vocal cord insufficiency.After voice therapy, MGA reduced significantly (male: 288.48±55.09, female: 258.22±57.17, t=24.41 and 31.22, P=0.000 vs. pre-therapy). MGA of untreated patients decreased in varying degrees. Compared with the voice therapy group, the MGA decreased in a significantly lower extent (24.25±22.91 vs. 188.31±54.37, t=8.97, P=0.000). The F0, Jitter, Shimmer and NHR raised significantly in UVCP patients group (P=0.000 vs. healthy control group), and they were reduced by voice therapy (all P<0.05). Each of the four acoustic parameters was relative with MGA, r=0.551, 0.867, 0.853 and 0.875 in turn, P=0.001, 0.000, 0.000, and 0.000. Conclusion: MGA and acoustic parameters can reflect the acoustic features of UVCP patients, which are useful tools in the UVCP assessment and voice therapy.

[Epidemiological survey of mental disorders in the rural left behind elderly aged 60 years and older in Gansu]

Objective: To investigate the prevalence, demographic characteristics and social life function of mental disorders in the rural left behind elderly aged 60 years and older in Gansu. Methods: Between November 2017 and June 2018, a multi-stage stratified cluster sampling method was used to randomly select the rural left behind elderly aged 60 years and older in Gansu, and totally 6 000 elderly were enrolled. By using the extended general health questionnaire (GHQ-12) and the American Handbook for Diagnosis and Statistics of Mental Disorders (DSM-Ⅳ) Axis Ⅰ Disorders Formal Clinical Examination Patient Edition, all the included subjects were screened and diagnosed. Functional status was assessed by the Global Assessment Function scale (GAF). Statistical analysis of the prevalence of various mental illnesses, as well as the differences in the prevalence of different gender, marital status and age groups was performed. Results: Totally, 6 000 subjects completed the survey. The adjusted current prevalence of any mental disorder was 20.11% (95%CI 17.70%-22.85%). The six most prevalent specific disorders were major depressive disorder (9.20%), pain disorder (2.71%), mood disorder due to the body condition (2.08%), generalized anxiety disorder (1.99%), anxiety disorder not otherwise specified (1.15%) and dysthymic disorder (0.84%). The lifetime prevalence of mental disorders was 20.54% (95%CI 18.40%-23.39%). The overall current prevalence of mental disorders was higher in women (242.89‰) than in men (119.55‰), and the unmarried (248.37‰) was higher than those married (187.53‰). There was no significant difference in the prevalence of mental disorders among different age groups (P>0.05). The GAF score of mental disorders was 56±11, and 71.82% was moderate to severe functional impairment. Conclusions: The prevalence of mental disorders is high in rural left-behind population aged 60 years and over in Gansu Province. Major depression is a condition that deserves special attention.

The subgingival microbiome in patients with established rheumatoid arthritis

OBJECTIVES

To profile and compare the subgingival microbiome of RA patients with OA controls.

METHODS

RA (n = 260) and OA (n = 296) patients underwent full-mouth examination and subgingival samples were collected. Bacterial DNA was profiled using 16 S rRNA Illumina sequencing. Following data filtering and normalization, hierarchical clustering analysis was used to group samples. Multivariable regression was used to examine associations of patient factors with membership in the two largest clusters. Differential abundance between RA and OA was examined using voom method and linear modelling with empirical Bayes moderation (Linear Models for Microarray Analysis, limma), accounting for the effects of periodontitis, race, marital status and smoking.

RESULTS

Alpha diversity indices were similar in RA and OA after accounting for periodontitis. After filtering, 286 taxa were available for analysis. Samples grouped into one of seven clusters with membership sizes of 324, 223, 3, 2, 2, 1 and 1 patients, respectively. RA-OA status was not associated with cluster membership. Factors associated with cluster 1 (vs 2) membership included periodontitis, smoking, marital status and Caucasian race. Accounting for periodontitis, 10 taxa (3.5% of those examined) were in lower abundance in RA than OA. There were no associations between lower abundance taxa or other select taxa examined with RA autoantibody concentrations.

CONCLUSION

Leveraging data from a large case-control study and accounting for multiple factors known to influence oral health status, results from this study failed to identify a subgingival microbial fingerprint that could reliably discriminate RA from OA patients.

Prevalence and impact of baseline resistance-associated substitutions on the efficacy of ledipasvir/sofosbuvir or simeprevir/sofosbuvir against GT1 HCV infection

Baseline resistance-associated substitutions (RASs) have variable impacts in clinical trials but their prevalence and impact in real-world patients remains unclear. We performed baseline resistance testing using a commercial assay (10% cutoff) for 486 patients treated with LDV/SOF or SMV/SOF, with or without ribavirin, in the multi-center, observational HCV-TARGET cohort. Linkage of RASs was evaluated in selected samples using a novel quantitative single variant sequencing assay. Our results showed that the prevalence of NS3, NS5A, NS5B RASs was 45%, 13%, and 8%, respectively, and 10% of patients harbored RASs in 2 or more drug classes. Baseline LDV RASs in GT1a, TE, and cirrhosis LDV/SOF subgroup was associated with 2–4% lower SVR12 rates. SMV RASs was associated with lower SVR12 rates in GT1a, treatment-experienced, cirrhotics SMV/SOF subgroup. Pooled analysis of all patients with baseline RASs revealed that SVR12 was 100% (19/19) in patients treated for longer than 98 days but was 87% (81/93) in patients treated for shorter than 98 days. These results demonstrate that RASs prevalence and their impact in real world practice are in general agreement with registration trials, and suggest that longer treatment duration may overcome the negative impact of baseline RASs on SVR12 rates in clinical practice.

Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing

Background

Intra-abdominal abscesses are localized collections of pus, which generally arise from a breach in the normal mucosal defense barrier that allows bacteria from gastrointestinal tract, and less commonly from the gynecologic or urinary tract, to induce inflammation, resulting in an infection. The microbiology of these abscesses is usually polymicrobial, associated with the primary disease process. However, the microbial identity, diversity and richness in intra-abdominal abscesses have not been well characterized, due in part to the difficulty in cultivating commensal organisms using standard culture-based techniques.

Methods

We used culture-independent 16S rRNA Illumina sequencing to characterize bacterial communities in intra-abdominal abscesses collected by percutaneous drainage. A total of 43 abscess samples, including 19 (44.2%) Gram stain and culture-negative specimens, were analyzed and compared with results from conventional microbiologic cultures.

Results

Microbial composition was determined in 8 of 19 culture-negative samples and 18 of 24 culture-positive samples, identifying a total of 221 bacterial taxa or operational taxonomic units (OTUs) and averaging 13.1 OTUs per sample (interquartile range, 8-16.5 OTUs). Microbial richness for monomicrobial and polymicrobial samples was significantly higher than culture-negative samples (17 and 15.2 OTUs vs 8 OTUs, respectively), with a trend toward a higher microbial diversity (Shannon diversity index of 0.87 and 1.18 vs 0.58, respectively).

Conclusions

The bacterial consortia identified by cultures correlated poorly with the microbial composition determined by 16S rRNA sequencing, and in most cases, the cultured isolates were minority constituents of the overall abscess microbiome. Intra-abdominal abscesses were generally polymicrobial with a surprisingly high microbial diversity, but standard culture-based techniques failed to reveal this diversity. These data suggest that molecular-based approaches may be helpful for documenting the presence of bacteria in intra-abdominal abscesses where standard cultures are unrevealing, particularly in the setting of prior antibiotic exposure.

Sofosbuvir (SOF) Suppresses Ledipasvir (LDV)-resistant Mutants during SOF/LDV Combination Therapy against Genotype 1b Hepatitis C Virus (HCV)

Our objective was to identify drug interactions between ledipasvir (LDV) and sofosbuvir (SOF) against a genotype 1b replicon to determine optimal exposures for each agent that will maximize antiviral activity against susceptible and drug-resistant subpopulations. LDV and SOF were evaluated using a fully factorial experimental design in the BelloCell system. Replicon levels and drug-resistant variants were quantified at various times post-therapy for 14 days and a high-dimensional mathematical model was fit to the data. Mutations associated with SOF resistance were not detected; but LDV-resistant mutants were selected and mutant subpopulations increased as exposure intensity increased. Combination therapy was additive for the total replicon population and the LDV-resistant population, but a threshold concentration of 100 ng/ml of SOF must be attained to suppress LDV-resistant subpopulations. These novel findings hold important implications for not only improving therapeutic outcomes, but also maximizing the clinical utility of LDV and SOF combination regimens.

Sequencing of hepatitis C virus for detection of resistance to direct-acting antiviral therapy: A systematic review

The significance of the clinical impact of direct‐acting antiviral (DAA) resistance‐associated substitutions (RASs) in hepatitis C virus (HCV) on treatment failure is unclear. No standardized methods or guidelines for detection of DAA RASs in HCV exist. To facilitate further evaluations of the impact of DAA RASs in HCV, we conducted a systematic review of RAS sequencing protocols, compiled a comprehensive public library of sequencing primers, and provided expert guidance on the most appropriate methods to screen and identify RASs. The development of standardized RAS sequencing protocols is complicated due to a high genetic variability and the need for genotype‐ and subtype‐specific protocols for multiple regions. We have identified several limitations of the available methods and have highlighted areas requiring further research and development. The development, validation, and sharing of standardized methods for all genotypes and subtypes should be a priority. (Hepatology Communications 2017;1:379–390)

Locoregional Effects of Microbiota in a Preclinical Model of Colon Carcinogenesis

Inflammation and microbiota are critical components of intestinal tumorigenesis. To dissect how the microbiota contributes to tumor distribution, we generated germ-free (GF) Apc^Min/+ and Apc^Min/+ ;Il10^-/- mice and exposed them to specific-pathogen-free (SPF) or colorectal cancer-associated bacteria. We found that colon tumorigenesis significantly correlated with inflammation in SPF-housed Apc^Min/+ ;Il10^-/- , but not in Apc^Min/+ mice. In contrast, small intestinal neoplasia development significantly correlated with age in both Apc^Min/+ ;Il10^-/- and Apc^Min/+ mice. GF Apc^Min/+ ;Il10^-/- mice conventionalized by an SPF microbiota had significantly more colon tumors compared with GF mice. Gnotobiotic studies revealed that while Fusobacterium nucleatum clinical isolates with FadA and Fap2 adhesins failed to induce inflammation and tumorigenesis, pks⁺Escherichia coli promoted tumorigenesis in the Apc^Min/+ ;Il10^-/- model in a colibactin-dependent manner, suggesting colibactin is a driver of carcinogenesis. Our results suggest a distinct etiology of cancers in different locations of the gut, where colon cancer is primarily driven by inflammation and the microbiome, while age is a driving force for small intestine cancer. Cancer Res; 77(10); 2620-32. ©2017 AACR.

Shifts in the Gut Microbiota Composition Due to Depleted Bone Marrow Beta Adrenergic Signaling Are Associated with Suppressed Inflammatory Transcriptional Networks in the Mouse Colon

The brain-gut axis plays a critical role in the regulation of different diseases, many of which are characterized by sympathetic dysregulation. However, a direct link between sympathetic dysregulation and gut dysbiosis remains to be illustrated. Bone marrow (BM)-derived immune cells continuously interact with the gut microbiota to maintain homeostasis in the host. Their function is largely dependent upon the sympathetic nervous system acting via adrenergic receptors present on the BM immune cells. In this study, we utilized a novel chimera mouse that lacks the expression of BM beta1/2 adrenergic receptors (b1/2-ARs) to investigate the role of the sympathetic drive to the BM in gut and microbiota homeostasis. Fecal analyses demonstrated a shift from a dominance of Firmicutes to Bacteroidetes phylum in the b1/2-ARs KO chimera, resulting in a reduction in Firmicutes/Bacteroidetes ratio. Meanwhile, a significant reduction in Proteobacteria phylum was determined. No changes in the abundance of acetate-, butyrate-, and lactate-producing bacteria, and colon pathology were observed in the b1/2-ARs KO chimera. Transcriptomic profiling in colon identified Killer Cell Lectin-Like Receptor Subfamily D, Member 1 (Klrd1), Membrane-Spanning 4-Domains Subfamily A Member 4A (Ms4a4b), and Casein Kinase 2 Alpha Prime Polypeptide (Csnk2a2) as main transcripts associated with the microbiota shifts in the b1/2-ARs KO chimera. Suppression of leukocyte-related transcriptome networks (i.e., function, differentiation, migration), classical compliment pathway, and networks associated with intestinal function, barrier integrity, and excretion was also observed in the colon of the KO chimera. Moreover, reduced expression of transcriptional networks related to intestinal diseases (i.e., ileitis, enteritis, inflammatory lesions, and stress) was noted. The observed suppressed transcriptome networks were associated with a reduction in NK cells, macrophages, and CD4⁺ T cells in the b1/2-ARs KO chimera colon. Thus, sympathetic regulation of BM-derived immune cells plays a significant role in modifying inflammatory networks in the colon and the gut microbiota composition. To our knowledge, this study is the first to suggest a key role of BM b1/2-ARs signaling in host-microbiota interactions, and reveals specific molecular mechanisms that may lead to generation of novel anti-inflammatory treatments for many immune and autonomic diseases as well as gut dysbiosis across the board.

[Research advances in the damage and regeneration of mammalian vestibular hair cells]

Vertigo is a common symptom in the clinic and impacts life quality of patients. It is closely related to the damage of vestibular hair cells. So far, there is no available approach which can facilitate abundant regeneration of mammalian vestibular hair cells, so as to recover the impaired vestibular function. Illuminating the mechanisms underlying vestibular hair cell damage and developing potential therapeutic strategies for vestibular hair cell regeneration are of great significance for the prevention and treatment of vertigo. In this study, we summarized research advances in the damage and regeneration of mammalian vestibular hair cells.

[SPINK3: A novel growth factor that promotes rat liver regeneration]

Serine peptidase inhibitor, Kazal type 3 (SPINK3) is a trypsin inhibitor, and also a growth factor that has an identical structure to epidermal growth factor (EGF), which could combine with epidermal growth factor receptor (EGFR) to promote cell proliferation. To shed light on the role and regulation mechanism of SPINK3 in rat liver regeneration (LR), Rat Genome 230 2.0 assay was used to detect the expression profiles of LR genes after partial hepatectomy (PH). The results showed that Spink3 was significantly up-regulated at 2-24 h and 72-168 h after PH. In the present study, RT-PCR and immunoblotting were used to validate the assay results. Ingenuity Pathway Analysis 9.0 (IPA) software was used to build the SPINK3 signaling regulating LR and analyze the possible mechanism. And then the expression of cell proliferation-associated gene Ccna2 was examined by RT-PCR in normal rat liver cell line BRL-3A in which Spink3 was overexpressed. The results showed that Ccna2 was significantly up-regulated in BRL-3A in which Spink3 was over-expressed. SPINK3 combining with EGFR accelerated cell proliferation during rat liver regeneration via P38, PKC, JAK-STAT and AKT pathways. Thus, SPINK3 was likely to promote hepatocytes proliferation in LR through P38, PKC, JAK-STAT and AKT.

CD4+ T-cell recovery with suppressive ART-induced rapid sequence evolution in hepatitis C virus envelope but not NS3

OBJECTIVES

CD4 T-cell depletion from HIV infection leads to a global decline in anti-hepatitis C virus (HCV) envelope neutralizing antibody (nAb) response, which may play a role in accelerating liver fibrosis. An increase in anti-HCV nAb titers has been reported during antiretroviral therapy (ART) but its impact on HCV remains poorly understood. The objective of this study is to determine the effects of ART on long-term HCV evolution.

DESIGN AND METHODS

We examined HCV quasispecies structure and long-term evolution in HIV/HCV coinfected patients with ART-induced CD4 T-cell recovery, and compared with patients with CD4 T-cell depletion from delayed ART. We applied a single-variant sequencing (SVS) method to construct authentic viral quasispecies and compared sequence evolution in HCV envelope, the primary target for humoral immune responses, and NS3, a target for cellular immunity, between the two cohorts.

RESULTS

The SVS method corrected biases known to skew the proportions of viral variants, revealing authentic HCV quasispeices structures. We observed higher rates of HCV envelope sequence evolution in patients with ART-induced CD4 T-cell recovery, compared with patients with CD4 T-cell depletion from delayed ART (P = 0.03). Evolutionary rates for NS3 were considerably lower than the rates for envelope (P < 0.01), with no significant difference observed between the two groups.

CONCLUSION

ART-induced CD4 T-cell recovery results in rapid sequence evolution in HCV envelope, but not in NS3. These results suggest that suppressive ART disproportionally enhances HCV-specific humoral responses more than cellular responses, resulting in rapid sequence evolution in HCV envelope but not NS3.

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection

Clostridium difficile infection (CDI) is characterized by dysbiosis of the intestinal microbiota and a profound derangement in the fecal metabolome. However, the contribution of specific gut microbes to fecal metabolites in C. difficile-associated gut microbiome remains poorly understood. Using gas-chromatography mass spectrometry (GC-MS) and 16S rRNA deep sequencing, we analyzed the metabolome and microbiome of fecal samples obtained longitudinally from subjects with Clostridium difficile infection (n = 7) and healthy controls (n = 6). From 155 fecal metabolites, we identified two sterol metabolites at >95% match to cholesterol and coprostanol that significantly discriminated C. difficile-associated gut microbiome from healthy microbiota. By correlating the levels of cholesterol and coprostanol in fecal extracts with 2,395 bacterial operational taxonomic units (OTUs) determined by 16S rRNA sequencing, we identified 63 OTUs associated with high levels of coprostanol and 2 OTUs correlated with low coprostanol levels. Using indicator species analysis (ISA), 31 of the 63 coprostanol-associated bacteria correlated with health, and two Veillonella species were associated with low coprostanol levels that correlated strongly with CDI. These 65 bacterial taxa could be clustered into 12 sub-communities, with each community containing a consortium of organisms that co-occurred with one another. Our studies identified 63 human gut microbes associated with cholesterol-reducing activities. Given the importance of gut bacteria in reducing and eliminating cholesterol from the GI tract, these results support the recent finding that gut microbiome may play an important role in host lipid metabolism.

Clinicopathological analysis of idiopathic membranous nephropathy in young adults

The aim of this study was to understand the clinicopathological features and prognosis of idiopathic membranous nephropathy (IMN) in youth. A retrospective analysis of the clinicopathological features and prognoses of pathologically confirmed IMN in 21 patients aged 15-30 years was performed. IMN was mainly characterized as nephrotic syndrome (NS), with stage I as the main pathological stage, and associated with hyperplasia of the glomerular mesangial cells and ground substance. High-intensity immunofluorescence also showed multi-site deposition of a variety of immune complexes, and electron microscopy showed multi-site deposition of electron-condensing substances. In the present study, 4 patients received non-specific treatment. Among 17 NS patients, 12 patients exhibited a preference for glucocorticoid therapy, and of these patients, 7 were sensitive to therapy and 5 were resistant. In the 12 patients who received hormone treatment combined with immunosuppressants (including 5 patients who were treated with the combination from the initial start, 5 patients who were steroid resistant, and 2 patients who were sensitive to the initial hormone treatment but who later showed relapse), complete remission was achieved in 6 patients, partial remission was achieved in 2, the treatment was ineffective in 2, and 2 patients were lost to follow-up. In conclusion, the clinical manifestation of IMN in youth in this study was mainly NS. In most patients, the initial hormone treatment was effective, and in some patients, the combination of hormone and immunosuppressant treatment was effective. As the sample size in this study was small, further clinical validation is still required to determine the efficacy of the treatment.

Dysbiosis and alterations in predicted functions of the subgingival microbiome in chronic periodontitis

Chronic periodontitis is an inflammatory disease of the periodontium affecting nearly 65 million adults in the United States. Changes in subgingival microbiota have long been associated with chronic periodontitis. Recent culture-independent molecular studies have revealed the immense richness and complexity of oral microbial communities. However, data sets across studies have not been directly compared, and whether the observed microbial variations are consistent across different studies is not known. Here, we used 16S rRNA sequencing to survey the subgingival microbiota in 25 subjects with chronic periodontal disease and 25 healthy controls and compared our data sets with those of three previously reported microbiome studies. Consistent with data from previous studies, our results demonstrate a significantly altered microbial community structure with decreased heterogeneity in periodontal disease. Comparison with data from three previously reported studies revealed that subgingival microbiota clustered by study. However, differences between periodontal health and disease were larger than the technical variations across studies. Using a prediction score and applying five different distance metrics, we observed two predominant clusters. One cluster was driven by Fusobacterium and Porphyromonas and was associated with clinically apparent periodontitis, and the second cluster was dominated by Rothia and Streptococcus in the majority of healthy sites. The predicted functional capabilities of the periodontitis microbiome were significantly altered. Genes involved in bacterial motility, energy metabolism, and lipopolysaccharide biosynthesis were overrepresented in periodontal disease, whereas genes associated with transporters, the phosphotransferase system, transcription factors, amino acid biosynthesis, and glycolysis/gluconeogenesis were enriched in healthy controls. These results demonstrate significant alterations in microbial composition and function in periodontitis and suggest genes and metabolic pathways associated with periodontal disease.

Epithelial CaSR deficiency alters intestinal integrity and promotes proinflammatory immune responses

The intestinal epithelium is equipped with sensing receptor mechanisms that interact with luminal microorganisms and nutrients to regulate barrier function and gut immune responses, thereby maintaining intestinal homeostasis. Herein, we clarify the role of the extracellular calcium-sensing receptor (CaSR) using intestinal epithelium-specific Casr(-/-) mice. Epithelial CaSR deficiency diminished intestinal barrier function, altered microbiota composition, and skewed immune responses towards proinflammatory. Consequently, Casr(-/-) mice were significantly more prone to chemically induced intestinal inflammation resulting in colitis. Accordingly, CaSR represents a potential therapeutic target for autoinflammatory disorders, including inflammatory bowel diseases.

First Report of Actinidia virus A and Actinidia virus B on Kiwifruit in China

At present, two viruses affecting kiwifruit (Actinidia spp.), Actinidia virus A (AcVA) and Actinidia virus B (AcVB), both belonging to the genus Vitivirus in the family Betaflexiviridae, have been reported from New Zealand (2). The infected trees showed leaf vein chlorosis, flecking, and ringspots. China is the largest commercial kiwifruit producer. During field investigations in the growing season of 2013, symptoms of leaf chlorosis or ringspots, similar to those caused by AcVA and AcVB (1), were observed on some kiwifruit (Actinidia chinensis) plants in Hubei Province in the central China. Leaf samples were collected from three symptomatic and two symptomless plants of two A. chinensis cultivars. Total nucleic acids were extracted from the samples using a CTAB-based protocol described by Li et al. (3) and used as template in RT-PCR for the detection of AcVA and AcVB. Each virus was detected using two sets of primers reported by Blouin et al. (1). Primer sets AcVA 1F/1R and AcVA5F/5R were used for the AcVA detection, and AcVB1F/1R and AcVB5F/Viti3'R were used for the AcVB detection. AcVA was detected in three symptomatic plants (ID: Ac-HN-1, Ac-HN-3, and Ac-HN-5), and AcVB was detected in two symptomatic plants (ID: Ac-HN-1 and Ac-HN-3) and in one symptomless plant (ID: Ac-HN-2). Neither virus was detected in the second symptomless plant (ID: Ac-HN-4). Samples Ac-HN-1 and Ac-HN-3 had mixed infection of AcVA and AcVB, and sample Ac-HN-2 had the latent infection of AcVB. The sequenced 283-bp RT-PCR amplicons of the replicase-encoding gene from AcVA isolates AC-HN-3 and AC-HN-5 using AcVA1F/1R shared 90.8% nucleotide (nt) identity with the corresponding sequence of the New Zealand AcVA isolate (GenBank Accession No. JN427014.1). The 269-bp fragments of the RNA-binding protein-encoding gene obtained by using AcVA5F/5R shared 85.5 to 85.9% nt identities with the corresponding sequence of JN427014.1. The AcVB5F/Viti3'R products of 365 to 369 bp from three AcVB isolates shared 85.5 to 88.6% nt identities with the corresponding sequence of the New Zealand AcVB isolate. The representative sequences were submitted to GenBank with accession numbers KJ696776 and KJ696777 for the 269-bp fragments of AcVA-HN-1 and AcVA-HN-3, and KJ696778 and KJ696779 for the 365-bp and 369-bp fragments of AcVB-HN-1 and AcVB-HN-2, respectively. In addition, 12 and 14 out of 42 kiwi samples (excluding HN-1 to HN-5) collected randomly were positive for AcVA and AcVB as detected by RT-PCR. Meanwhile, the sample affected by AcVA-HN-5 was subjected to deep sequencing of the small RNAs (sRNAs) for complete survey of the infecting viruses. De novo assembly of sRNAs generated four sequence contigs, with lengths ranging from 161 to 285 nt, matching to ORFs 1 to 3 of the genome of the New Zealand AcVA isolate with significant nucleotide (91 to 95%) and amino acid (80 to 94%) similarities, and some other contigs from a new virus (unpublished). The result further confirmed AcVA infection in the kiwi plant. To our knowledge, this is the first report of both AcVA and AcVB outside of New Zealand. The Chinese isolates of the two viruses are distinct from those reported from New Zealand. The results provide valuable information for improving the viral sanitary status of the kiwifruit germplasm in China. References: (1) A. G. Blouin et al. Arch. Virol. 157:713, 2012. (2) A. G. Blouin et al. J. Plant Pathol. 95:221, 2013. (3) R. Li et al. J. Virol. Methods 154:48, 2008.

Colonic immune suppression, barrier dysfunction, and dysbiosis by gastrointestinal bacillus anthracis Infection

Gastrointestinal (GI) anthrax results from the ingestion of Bacillus anthracis. Herein, we investigated the pathogenesis of GI anthrax in animals orally infected with toxigenic non-encapsulated B. anthracis Sterne strain (pXO1⁺ pXO2⁻) spores that resulted in rapid animal death. B. anthracis Sterne induced significant breakdown of intestinal barrier function and led to gut dysbiosis, resulting in systemic dissemination of not only B. anthracis, but also of commensals. Disease progression significantly correlated with the deterioration of innate and T cell functions. Our studies provide critical immunologic and physiologic insights into the pathogenesis of GI anthrax infection, whereupon cleavage of mitogen-activated protein kinases (MAPKs) in immune cells may play a central role in promoting dysfunctional immune responses against this deadly pathogen.

First Report of Cucumber mosaic virus in Taro Plants in China

Taro (Colocasia esculenta L. Schott) is an important crop worldwide. In China, the growing area and productivity of taro increased greatly in recent years. During the 2010 to 2013 growing seasons (from May to July), the incidence of Cucumber mosaic virus (CMV) in taro was determined. Leaf samples from 91 taro plants, including 26 plants of cv. Hongyayu grown in Jiangxi Province in eastern China, 33 plants of cv. Eyu no.1 grown in Hubei Province in central China, and 32 plants of cv. Baiyu grown in Guangxi Province in southwest China were collected randomly and tested for the presence of CMV by reverse transcription (RT)-PCR. Some sampled plants of cv. Hongyayu and Eyu no.1 showed leaf chlorosis or chlorotic spots, and most of the plants of these three cultivars showed feather-like mosaic symptom on their leaves, which was confirmed to be associated with the infection of Dasheen mosaic virus (DsMV) in our previous studies (3). Total RNA was extracted from leaves using CTAB protocol reported by Li et al. (1). Primer set forward 5'-ATGGACAAATCTGAATCAACC-3'/reverse 5'-TAAGCTGGATGGACAACCCGT-3' (4) was used for the amplification of a 777-bp fragment, which contains the complete capsid protein (CP) gene of 657 bp. PCR products of the expected size were identified from 11 taro samples, including two samples of Hongyayu, three Eyu no.1, and six Baiyu plants. The result did not show any specific association between the symptoms observed and CMV infection. The obtained PCR products were cloned individually into the vector pMD18-T (TaKaRa, Dalian, China). Three independent clones derived from each product were sequenced by Genscript Corp., Nanjing, China. Pairwise comparison of CP gene sequences (Accession No. of one representation CP sequence: KF564789) showed 99.7 to 99.8% nucleotide (nt) and 99.1 to 99.5% deduced amino acid (aa) sequence identity among themselves, and 92.0 to 94.3% and 76.5 to 77.7% nt identities with corresponding sequences of CMV isolates in subgroup I and subgroup II (2), respectively. The maximum likelihood phylogenetic trees of nt and aa sequences generated by Clustal X v1.8 revealed that all these CMV isolates from taro in China fell into subgroup I. To further confirm the CMV infection, leaf saps of CMV infected taro plants of cv. Eyu no.1 were mechanically inoculated onto Pinellia ternate and Cucumis sativus. Plants of P. ternate showed local chlorotic lesions on the inoculated leaves and downward curl of newly grown leaves, and C. sativus showed local chlorotic lesions on the inoculated leaves and crinkle of newly grown leaves at 10 to 15 days post inoculation. The RT-PCR detection confirmed the CMV infection in those inoculated plants, and that the plants of P. ternate were also positive to DsMV, further complementing the results obtained above. To our knowledge, this is the first report of CMV occurrence in taro plants grown in China. Our results indicated that taro plants were widely infected by CMV isolates in subgroup I. This study provides important information for further evaluating the viral sanitary status of taro germplasm and improving the certification program of taro propagation materials in China. References: (1) R. Li et al. J. Virol. Methods 154:48, 2008. (2) P. Palukaitis et al. Adv. Virus. Res. 62:241, 2003. (3) S. M. Shi et al. Acta Hortic. Sin. 39:509, 2012. (4) P. D. Xu et al. Chinese J. Virol. 15:164, 1999.

First Report of Valsa leucostoma Causing Valsa Canker of Pyrus communis (cv. Duchess de' Angouleme) in China

Pear is a popular fruit in the world market, and has been widely cultivated in China. Since 2008, a severe canker disease has consistently been observed on 20-year-old pear trees (Pyrus communis cv. Duchess de' Angouleme) grown in a nursery in Xingcheng, Liaoning Province, China. Observed symptoms include brown elongated ulcerative lesions (more than 20 cm in length in general), with red brown conidia produced on wet lesions. Reductions in tree vigor and yield were observed for infected trees. Tree mortality was observed for severe infections. To diagnose the pathogen, 15 canker samples were collected from five pear trees in April, 2012. Bark pieces (3 to 5 mm) taken from the border of healthy and diseased tissue were surface-disinfected with 0.1% mercury bichloride and 75% ethanol for 45 s, and placed on potato dextrose agar (PDA) medium at 25°C in darkness. Fungal colonies with a common colony morphology were consistently recovered from three samples. These fungal colonies were initially white, becoming olive green in 3 days. Conidia produced on colonies were hyaline, allantoid, and single-celled with average length × width of 6.04 (5.43 to 6.59) × 0.65 (0.51 to 0.73) μm, which were consistent with descriptions of Valsa leucostoma (1). Genomic DNA was extracted from a representative isolate F-LN-32b, and subjected to PCR amplification of the internal transcribed spacer region (ITS), β-tubulin gene, and EF1 gene using the primer pairs ITS1/ITS4, Bt2a/Bt2b and EF1-728F/EF1-986R (3), respectively. Sequence alignment of the amplified fragments with the deposited data in NCBI showed that sequences of EF1, ITS, and β-tubulin (GenBank Accession No. KF293296 to KF293298, respectively) of isolate F-LN-32b had the highest similarity of 99% to those of V. leucostoma strain 32-2w (JQ900340, JN584644, and JQ900374), and suggested that isolate F-LN-32b is a V. leucostoma strain. Pathogenicity tests was carried out by placing a 5-mm-diameter, 2-day-old mycelium agar plug of isolate F-LN-32b onto a punched bark hole of a detached 1-year-old pear shoot after it was surface disinfested with ethanol. Inoculated shoots were incubated at 25°C in plastic containers covered with plastic film. Pathogenicity assays were conducted on 18 pear varieties (cvs. Qiuyue, Jinshui 2, Hohsui, Huali 1, Cuiguan, Shinseiki, Xuehua, Dangshansu, Zaosu, Hongxiangsu, Yuluxiang, Nanguoli, Xizilv, Bartlett, Huanghua, Huashan, Duchess de' Angouleme, and Packham's) collected from a nursery in Wuhan, Hubei Province, China. Six shoots were inoculated for each variety and the assay was conducted three times. All inoculated shoots developed the typical canker symptoms after 6 days post inoculation (dpi) and sporulated at 25 dpi while the control shoots inoculated with non-colonized PDA plugs remained asymptomatic. Isolates recovered from inoculated samples were of the same morphology and ITS sequence as F-LN-32b. Based on these results, V. leucostoma was determined as the pathogen responsible for the Valsa canker disease on pear. Valsa mali var. pyri was identified as the only pathogen causing Valsa canker disease on pear in China (2). To our knowledge, this is the first report of V. leucostoma causing a canker disease on pear in China. References: (1) G. C. Adams et al. Australas. Plant Pathol. 35:521, 2006. (2) X. L. Wang et al. Mycologia 103:317, 2011. (3) T. J. White et al. Pages 315-322 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990.

The First Report of Cucumber Mosaic Virus Infecting Water Chestnut in China

Water chestnut (Eleocharis dulcis), which is cultivated worldwide today, first originated in India and China. It is a popular seasonal aquatic vegetable valuable to people for its sweet crisp taste and rich nutrition. In October 2012, field-grown water chestnut seedlings (E. dulcis) showing mosaic, chlorotic, dwarfing, and malformed symptoms were observed in Fanggaoping Town, Tuanfeng County, Hubei Province, China. Sap from leaf-like stems of two symptomatic seedlings (BQ6 and BQ7) were mechanically inoculated onto Nicotiana glutinosa plants using 0.01 M phosphate buffer (pH 7.4) to investigate whether viral etiology was responsible for the disease. Typical symptoms of chlorosis and systemic mosaic similar to that inflicted by Cucumber mosaic virus (CMV) were observed on inoculated N. glutinosa leaves 13 days post inoculation, whereas mock inoculated seedlings remained symptomless. Three naturally field-grown symptomatic water chestnut and the inoculated N. glutinosa seedlings, together with a healthy water chestnut plant as negative control, were sampled. Double-antibody sandwich (DAS)-ELISA with antisera against CMV using commercial kits (Agdia, Elkhart, IN) was carried out to detect and confirm the presence of CMV. The symptomic water chestnut and inoculated N. glutinosa seedlings tested positive for CMV. Total RNAs were extracted using the SDS column isolation method from leaves of the inoculated N. glutinosa and stems of 13 field-grown symptomatic water chestnuts. The extracted RNAs were subjected to reverse transcription. The first-round PCR was carried out using the obtained cDNAs as template with the CMV specific primer set CMV-3F (5'-GCGATGYCGTGTTGAGAAG-3') and CMV-3R (5'-TTTAGCCGTAAGCTGGATGGA-3') targeting a 983-bp fragment covering 657 nt of the whole CP and partial flanking sequence within RNA3 referred as 'Fny' strain in GenBank (Accession No. D10538). The resulting amplicons were diluted 1:20 and further amplified with the nested-primer set CMV-P1 (5'-ATGGACAAATCTGAATCAACC-3') and CMV-P2 (5'-TAAGCTGGATGGACAACCCGT-3') targeting a fragment of 777 bp corresponding to the complete CP followed by part of 3'-UTRs of RNA3 (1). The amplicons of the expected size of ~777-bp were consistently amplified from 13 naturally infected water chestnuts and inoculated N. glutinosa. The PCR product derived from BQ6 isolate was cloned and three clones sequenced in both directions. The sequence (GenBank Accession No. KF268463) was analyzed by MEGA5 software (3). Sequence comparison of the complete CP gene of BQ6 isolate showed 98% nt and 99% amino acid (aa) identity with CMV isolate RP6 from South Korea (GenBank Accession No. KC527735) in subgroup I and had low similarities of 76% nt and 80% aa to that of CMV isolate infecting Trifolium from Hungary (GenBank Accession No. L15336) belonging to subgroup II of CMV. Phylogenetic analysis showed BQ6 isolate was more closely related to the isolates belonging to IB subgroup of CMV (GenBank Accession Nos. EF153739, DQ302715, and KC576805) (2). To our knowledge, this is the first report of CMV infecting water chestnut (E. dulcis) in China. CMV infection may pose a significant threat to water chestnut production. This result provide information to the producer that the CMV-free seedlings should be chosen for cultivation of water chestnut. References: (1) P. Palukaifis et al. Adv. Virus Res. 41:281, 1992. (2) S. K. Raj et al. Plant Dis. 92:171, 2008. (3) K. Tamura et al. Mol. Biol. Evol. 28:2731, 2011.