Assessment and clinical utility of metagenomic next-generation sequencing for suspected lower respiratory tract infections.

OBJECTIVES: This study aims to compare the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) to traditional diagnostic methods in patients with lower respiratory tract infections (LRTIs), elucidate the etiological spectrum of these infections, and explore the impact of mNGS on guiding antimicrobial therapy. METHODS: We retrospectively analyzed data from 128 patients admitted to the Respiratory Department of Anqing 116 Hospital between July 2022 and July 2023. All patients had undergone both mNGS and conventional microbiological techniques (CMT) for LRTI diagnosis. We assessed the diagnostic performance of these methods and examined the influence of mNGS on antimicrobial decision-making. RESULTS: Overall, mNGS demonstrated superior sensitivity (96.8%) and accuracy (96.8%) compared to CMT. For Mycobacterium tuberculosis detection, the accuracy and sensitivity of mNGS was 88.8% and 77.6%, which was lower than the 94.7% sensitivity of the T-spot test and the 79.6% sensitivity of CMT. In fungal pathogen detection, mNGS showed excellent sensitivity (90.5%), specificity (86.7%), and accuracy (88.0%). Bacteria were the predominant pathogens detected (75.34%), with Mycobacterium tuberculosis (41.74%), Streptococcus pneumoniae (21.74%), and Haemophilus influenzae (16.52%) being most prevalent. Bacterial infections were most common (62.10%), followed by fungal and mixed infections (17.74%). Of the 118 patients whose treatment regimens were adjusted based on mNGS results, 102 (86.5%) improved, 7 (5.9%) did not respond favorably, and follow-up was lost for 9 patients (7.6%). CONCLUSIONS: mNGS offers rapid and precise pathogen detection for patients with suspected LRTIs and shows considerable promise in diagnosing Mycobacterium tuberculosis and fungal infections. By broadening the pathogen spectrum and identifying polymicrobial infections, mNGS can significantly inform and refine antibiotic therapy.

Quantitative risk assessment of Bacillus cereus in wet rice noodles from raw material to marketing phase.

From 2018, several foodborne diseases caused by the consumption of wet rice noodles contaminated with microorganisms have attracted the attention of consumers and surveillance departments. We explored the crucial risk factors for the contamination of Bacillus cereus during the various steps of the wet rice noodles production chain (from raw material to marketing phase). A total of 273 samples were collected in each corresponding production phase. The contamination level was quantitatively detected in the samples, and the corresponding temperature and time were recorded and analyzed using @Risk software. The quantitative detection results of raw material were determined as the initial contamination level in the model to predict the final contamination level and assess the key risk factors for B. cereus contamination in wet rice noodles. The model predicted that the final contamination level of B. cereus was in the range of -3.55 to 4.34 log CFU/g in 95% wet rice noodles at the marketing phase. The highest predicted contamination level was 6.28 log CFU/g, and the risk of exceeding the threshold was 0.80%. The model was verified to be valid for R2 > 0.96, and the predicted results could be used for reference. Moreover, the sensitivity analysis revealed that in addition to raw material, the key control factors were buffering temperature in the packaging delivery phase, transporting temperature and time from factory to marketing phase; their correlation coefficients (r) were 0.18, 0.16, and 0.15, respectively. Therefore, manufacturers need to adjust the current predelivery buffering and transporting mode. It is recommended to reduce the predelivery buffering temperature, and refrigerated trucks are preferred to control the proliferation of B. cereus in transported food, thus reducing the occurrence of foodborne diseases and improving the safety of food.

MRG Chip: A High-Throughput qPCR-Based Tool for Assessment of the Heavy Metal(loid) Resistome.

Bacterial metal detoxification mechanisms have been well studied for centuries in pure culture systems. However, profiling metal resistance determinants at the community level is still a challenge due to the lack of comprehensive and reliable quantification tools. Here, a novel high-throughput quantitative polymerase chain reaction (HT-qPCR) chip, termed the metal resistance gene (MRG) chip, has been developed for the quantification of genes involved in the homeostasis of 9 metals. The MRG chip contains 77 newly designed degenerate primer sets and 9 published primer sets covering 56 metal resistance genes. Computational evaluation of the taxonomic coverage indicated that the MRG chip had a broad coverage matching 2 kingdoms, 29 phyla, 64 classes, 130 orders, 226 families, and 382 genera. Temperature gradient PCR and HT-qPCR verified that 57 °C was the optimal annealing temperature, with amplification efficiencies of over 94% primer sets achieving 80-110%, with R2 > 0.993. Both computational evaluation and the melting curve analysis of HT-qPCR validated a high specificity. The MRG chip has been successfully applied to characterize the distribution of diverse metal resistance determinants in natural and human-related environments, confirming its wide scope of application. Collectively, the MRG chip is a powerful and efficient high-throughput quantification tool for exploring the microbial metal resistome.

Nontyphoidal Salmonella Infection, Guangdong Province, China, 2012.

We used active and passive surveillance to estimate nontyphoidal Salmonella (NTS) infection during 2012 in Guangdong Province, China. Under passive surveillance, for every reported NTS infection, an estimated 414.8 cases occurred annually. Under active surveillance, an estimated 35.8 cases occurred. Active surveillance provides remarkable advantages in incidence estimate.

Can HPV vaccine have other health benefits more than cancer prevention? A systematic review of association between cervical HPV infection and preterm birth.

Although the association between high-risk human papillomavirus (HPV) infection and cervical dysplasia as well as cervical cancer is well established, studies on the relationship between HPV infection and risk of preterm birth (PTB) have yielded inconclusive and inconsistent results. Therefore, we conducted a meta-analysis to investigate the association between HPV infection and PTB. The electronic database was searched until July 1, 2014. Relevant studies reporting the association between HPV infection and the risk of PTB were included and for further evaluation. Statistical analysis was performed using Revmen 5.3 and Stata 10.0. Six observational cohort studies and 2 case-control studies were included. A significant association between HPV infection and PTB was observed (odds ratio=2.12, 95% CI 1.51-2.98, P<0.001, random effect model). Stratification according to diagnostic methods indicated that both positive HPV DNA status and abnormal cervical cytology were associated with increased risk of PTB. Moreover, our data suggested a higher risk of PTB in Caucasian HPV-infected population, while no significant association was observed in the Asian population. Although the causality remains unclear, findings from our meta-analysis indicate that HPV infection might increase the risk of PTB. In the future, prospective cohorts with larger samples sizes are warranted to ascertain the causality and pathophysiological studies are required to explore the possible biological mechanisms involved.

Assessment of CSF Aß42 as an aid to discriminating Alzheimer's disease from other dementias and mild cognitive impairment: a meta-analysis of 50 studies.

Mild Alzheimer's disease (AD) is usually difficult to differentiate from other dementias or mild cognitive impairment (MCI). The aim of our study is to evaluate the clinical importance of cerebrospinal fluid (CSF) ß-amyloid 42 (Aß42) in MCI, AD and other dementias, more specifically: frontotemporal dementia (FTD), dementia with Lewy bodies (DLB), Parkinson's disease (PD) with dementia (PDD) and vascular dementia (VaD). Fifty eligible articles were identified by search of databases including PubMed, EMBASE, Elsevier, Springer Link and the Cochrane Library, from January 1990 to May 2014. The random effects model was used to calculate the standardized mean difference (SMD) with corresponding 95% CI by STATA 9.0 software. The subgroup analyses were made on the method (ELISA, xMAP). We found that CSF Aß42 concentrations were significantly lower in AD compared to MCI (SMD: -0.68, 95% CI: [-0.80, -0.56], z=11.34, P<0.001), FTD (SMD: -1.09, 95% CI: [-1.41, -0.76], z=6.62, P<0.001), PDD (SMD: -0.75, 95% CI: [-1.39, -0.10], z=2.27, P=0.023), VaD (SMD: -0.95, 95% CI: [-1.30, -0.61], z=5.43, P<0.001). In addition, compared to DLB, Aß42 concentrations are moderately lower in AD (SMD: -0.27, 95% CI: [-0.51, -0.03], z=2.20, P=0.028). Results from this meta-analysis hinted that CSF Aß42 is a good biomarker for discriminating Alzheimer's disease from other dementias and MCI.

[Application of flow cytometry on functional assessment of health food].

OBJECTIVE: To establish flow cytometry (FCM) methods and evaluate their application value for measuring the index for enhancing immune function of health food. METHODS: In mice experiment model, the dosage groups were respectively oral fed with three test substances according to 5, 10, 30 times of the recommended dose for human body; both the negative and positive control groups were fed with equivalence purified water once a day. The positive control was fed with 25 mg/kg body weight levamisole for 3 days before finishing the administration, and the immune two percent of sheep erythrocytes were administrated at the last day. In rats experiment model, the test substance was given by mixing feed according to 25 and 50 times of the recommended dose for human body. At the end of the experiment, indices below were simultaneously detected. (1) The classical indices included: spleen lymphocyte transformation test by using ConA (MTT assay); spleen NK cell activity test (LDH assay); delayed-type hypersensitivity test by using sheep erythrocyte (foot palm thickening) method and phagocytosis activity tested by mice peritoneal macrophages. (2) FCM indices included: T and B lymphocytes quantitating in mice peripheral blood, activated antigen expression level in the surface of T lymphocytes and NK cells and phagocytosis activity for fluospheres in mice peritoneal macrophages. RESULTS: (1) Compared with the negative control group, there were no significant differences in T and B lymphocytes proportion and the number of lymphocytes in mice peripheral blood after given 0.83, 1.67, 5.01 g/kg protein powder; (2) mice peripheral blood T lymphocyte sub-cluster CD(69)(+)/CD(3)(+) of 3.75, 7.50, 15.0 ml/kg bw Cen-Rong Cream groups were all significantly increased (P < 0.05), which were shown a good coherence with the classic test index; (3) mice peripheral blood NK cell sub-cluster CD(69)(+)/NKG2D(+) of 0.83, 1.67 g/kg protein powder groups were both significantly increased (P < 0.05), which was kept in good coherence with those of NK cell activity test (LDH assay); rats peripheral blood NK cell sub-cluster CD(161a+)/CD(25)(+) of 1.50 g/kg ganoderma lucidum and cordycepicmycelia group was significantly increased (P < 0.05); (4) the phagocytosis activity in mice peritoneal macrophages: there were no significant difference found between the controls and the dosage groups in the classic test. However, in the FCM test, the percentage of phagocytic cells of 0.15, 0.30, 0.90 g/kg ganoderma lucidum and cordycepicmycelia groups and the phagocytic index of 0.30, 0.90 g/kg were enhanced. CONCLUSION: It suggests that was shown in detecting and assessing enhancing immune function of health food the results tested by FCM were fairly consistent with those by using traditional methods, most of them would have higher sensitivity. It should be valuable to applying FCM in the measurement and assessment of enhancing immune function of health food and worth while to further study as to enlarging its application.