BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements.

Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as rapid annotation using subsystem technology (RAST), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net.

Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks.

BACKGROUND: Safety issues of probiotic products have been reported frequently in recent years. Ten bacterial strains isolated from seven commercial probiotic products on market were evaluated for their safety, by whole-genome analysis. RESULTS: We found that the bacterial species of three probiotic products were incorrectly labeled. Furthermore, six probiotic product isolates (PPS) contained genes for the production of toxic metabolites, while another three strains contained virulence genes, which might pose a potential health risk. In addition, three of them have drug-resistance genes, among which two strains potentially displayed multidrug resistance. One isolate has in silico predicted transferable genes responsible for toxic metabolite production, and they could potentially transfer to human gut microflora or environmental bacteria. Isolates of Lactobacillus rhamnosus and Bifidobacterium animalis subsp. lactis are associated with low risk for human consumption. Based on a comparative genome analysis, we found that the isolated Enterococcus faecium TK-P5D clustered with a well-defined probiotic strain, while E. faecalis TK-P4B clustered with a pathogenic strain. CONCLUSIONS: Our work clearly illustrates that whole-genome analysis is a useful method to evaluate the quality and safety of probiotic products. Regulatory quality control and stringent regulations on probiotic products are needed to ensure safe consumption and protect human health.

Application of AngioJet rheolytic thrombectomy in the treatment of acute limb ischemia / 介入放射学杂志

Objective To investigate the effectiveness and safety of AngioJet rheolytic thrombectomy in the treatment of acute limb ischemia (ALI). Methods The clinical data of a total of 19 patients with ALI of lower limbs, who were treated with AngioJet rheolytic thrombectomy, were retrospectively analyzed. The patients included 14 males and 5 females, with a mean age of (77.7±6.8)years old (66-90 years old). The thrombus clearance rate ≥90％ was defined as grade Ⅲ, 50％-90％ as grade Ⅱ, and <50％ as grade I, which was used to evaluate the thrombus clearance effect. The postoperative device-related complication, amputation incidence and the mortality were recorded. Results In all the 19 patients, the technical success rate was 100％. The thrombus clearance rate after initial AngioJet rheolytic thrombectomy was >50％ in all patients, among them grade Ⅲ was obtained in 14 patients (73.7％) and grade Ⅱ in 5 patients (26.3％). The symptoms of lower extremity pain, ischemia, etc. were improved. In 5 patients, macroscopic hemoglobinuria occurred once after the treatment. No serious complications such as bleeding at puncture point, hemorrhage of digestive tract, renal function damage or death occurred. Limb salvage was achieved in17, with a limb salvage rate of 89.5％, the 6-month and one-year limb salvage rates were 84.6％ (11/13) and 80.0％ (8/10) respectively. Conclusion For the treatment of ALI of lower limbs, AngioJet rheolytic thrombectomy is safe and effective, it can rapidly recover arterial blood flow. AngioJet rheolytic thrombectomy is especially suitable for the elderly patients and the patients who have high risk for surgical operation or have contraindications for thrombolysis.

Laparoscopic pancreaticoduodenectomy combined with major vascular resection and reconstruction:an analysis of 7 patients / 中华肝胆外科杂志

Objective To review our experience in laparoscopic pancreaticoduodenectomy combined with major vascular resection and reconstruction.Methods Of 183 patients who underwent laparoscopic pancreaticoduodenectomy in our department from November 2013 to January 2017,major vascular resection and reconstruction using the SMA first approach for total mesopancreas excision was performed in 7 patients.The clinical data of these 7 patients were retrospectively analyzed.Results Total 3D laparoscopic surgery was performed in all these 7 patients.The mean operation time,mean blood loss and blood flow occlusion time were (551.4 ± 83.8) min,(671.3 ± 256.3) ml and (45.8 ± 6.7) min,respectively.Six out of 7 patients were pathologically diagnosed to have pancreatic adenocarcinoma with negative surgical margins.Two patients had lymphatic metastasis (the number of metastatic lymph node was 1 in each patient).The mean number of lymph nodes resected was (12.7 ± 5.8).The portal vein-superior mesenteric vein (PV-SMV) was segmentally resected and reconstructed using an end to end anastomosis following the preoperative plan in 4 patients.These included 2 patients who underwent total pancreatectomy.The portal vein was wedge-resected and reconstructed by venorrhaphy in 2 patients.The remaining 1 patient was histopathologically diagnosed to have a mass-type chronic pancreatitis.Only 1 patient was treated in the ICU for 1 day after surgery.Post-operative complications occurred in 2 patients and they were managed with nonsurgical treatment (PV-SMV thrombosis and gastric emptying disorder in 1 and a pancreatic leakage (level A) in 1).The mean length of post-operative hospital stay was (13.7 ± 3.2) days with no in-hospital mortality.Seven patients were alive by April 2017.The mean follow-up for the 6 patients with pancreatic adenocarcinoma was 4.5 (3.5 ～9) months.Conclusions Based on our experience in skillful and masterly major vascular resection and reconstruction in open surgery and on our experience in standard laparoscopic pancreaticoduodenectomy,laparoscopic pancreatieoduodenectomy combined with major vascular resection and reconstruction was feasible and safe.This surgery requires very mature skills in laparoscopic surgery.

Efficacy and safety of the combined oral contraceptive ethinylestradiol/drospirenone (Yasmin) in healthy Chinese women: a randomized, open-label, controlled, multicentre trial.

To evaluate and compare the contraceptive efficacy, bleeding pattern, side effects and other positive effects of a combined oral contraceptive (COC) containing drospirenone (DRSP) [Yasmin] with those of a COC containing desogestrel (DSG) in healthy Chinese women. This was a randomized, open-label, controlled, multicentre study of 768 healthy Chinese women requiring contraception. The subjects were randomized to ethinylestradiol (EE) 30 microg/DRSP 3 mg (n = 573) or EE 30 microg/ DSG 150 microg (n = 195), at a ratio of 3 : 1. Each individual was treated for 13 cycles. Further visits were required at cycle 4, cycle 7, cycle 10 and cycle 13 of treatment. Weight, height and body mass index were evaluated at each visit. The Menstrual Distress Questionnaire (MDQ) was administered at baseline, visit 3 (cycle 7) and visit 5 (after cycle 13). Baseline characteristics were similar between the two groups (p > 0.05). The Pearl Index (method failure) for EE/DRSP was 0.208 per 100 women-years, which was lower than that for EE/DSG (0.601 per 100 women-years). There were no significant differences between the treatment groups with regard to bleeding patterns. According to the MDQ subscale, improvements in water retention and increases in appetite during the intermenstrual period and in water retention and general well-being during the menstrual period in the EE/DRSP group (-0.297, -0.057, 0.033 and 0.150, respectively) were significantly improved compared with the EE/DSG group (-0.108, 0.023, 0.231 and -0.023, respectively) [all p < 0.05]. Other values that improved in both groups, particularly improvement in breast pain and tenderness and skin condition, were more evident in the EE/DRSP group (18.0%, 89/494; 12.6%, 62/494) than in the EE/DSG group (11.3%, 19/168; 5.4%, 9/168). Mean weight increased in the EE/DSG group (0.57 kg) while there was a significant decrease in mean weight (-0.28 kg) in the EE/DRSP group (p < 0.01). Both EE/DRSP and EE/DSG have good contraceptive efficacy and a comparable bleeding pattern. EE/DRSP had a more favourable effect on weight and premenstrual symptoms than EE/DSG.

Human papillomavirus type 16 intratypic variant infection and risk for cervical neoplasia / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To study the distribution of human papillomavirus type 16 (HPV16) variants and their clinical significance in Han women with Cervical Intraepithelial Neoplasia (CIN).</p><p><b>METHODS</b>Randomly making a collection of DNA samples of cervical cells from 77 Han out-patients infected with HPV16, PCR amplification of HPV16 DNA fragments containing E6 and E7 genes and sequenced. To study the HPV16 variants types in these out-patients and explore the relationship between the HPV16 variants and CIN by comparing the E6 genes sequenced with the reference strains downloaded from the GenBank. RESULTS Among 77 patients, the minimum age is 21 years old, the maximum age is 56 years old, and the average age is 36.39 +/- 6.86 years old. 61 patients (accounting for 79.2%) were diagnosed as CIN II and higher grade lesions while 16 patients (accounting for 20.8%) as CIN I. In this research, only European variant and Asian variant were found by Parsimony analyses of the sequences. There are 38 Asian variants and 39 European variants. With Chi2 test, Chi2 = 0.0034, P = 0.9535 > 0.05, it suggested that there was no enough evidence to support Asian- and European-variants had the different risk in the cause of cervical intraepithelial neoplasia and cervical cancer.</p><p><b>CONCLUSION</b>It was not found Asian- and European-variants of HPV16 had different effect on the cervical cancer, but found only two major variants-Asian- and European-variants in Han people in this research. So we have reason to speculate that there are two major HPV16 variants (Asian- and European-variants) in China's Han women, while other variants, especially high cancer-causing Asian/American variant are not common.</p>

Human papillomavirus type 16 E5 sequence evolution analysis / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To investigate the distribution of HPV 16 variants in Han women patients without Cervical intraepithelial neoplasia in the diagnosis and treatment center for cervical disease, department of Obstetrics and Gynecology in China-Japan friendship hospital with HPV 16 E5 sequence phylogenetic analysis.</p><p><b>METHODS</b>PCR amplification of HPV 16 E5 sequences and sequenced. The association between variations types and different cervical lesions was analyzed.</p><p><b>RESULTS</b>In this research, We first found that variant classification based on HPV 16 E5 DNA sequence (236 bp) alone had high rate of accuracy. In addition, for the first time, our research revealed that single-4075T can distinguished the As variant from all other variants.</p><p><b>CONCLUSION</b>If E5 sequence was used for phylogenetic analysis, it will greatly reduce the experimental costs and improve efficiency and cost-effectiveness. For the first time, our research revealed that single 4075T can distinguished the As variant from all other variants.</p>

Clinical evaluation of the xMAP technology in detection of high-risk human papillomavirus / 中国医学科学院学报

<p><b>OBJECTIVE</b>To evaluate the clinical application value of flexible multi-analyte profiling (xMAP) technology in detecting high-risk human papillomavirus (HR-HPV).</p><p><b>METHODS</b>Totally 1 061 women, aged 21-65 years, were randomly enrolled into the study. Cervical exfoliated cells were used in xMAP technology and hybrid capture II (hc2). Pathological diagnosis was used as golden standard. Consistency of these two methods was assessed.</p><p><b>RESULTS</b>The sensitivity and specificity of xMAP technology were 80.31% and 85.83%, respectively. The positive and negative predictive values were 44.5% and 96.9%, respectively. The Kappa value for consistency between xMAP technology and hc2 was 0.58.</p><p><b>CONCLUSIONS</b>The specificity of xMAP technology is similar to hc2 test, but the sensitivity is inferior to hc2. However, these two methods show good consistency in the detection of HR-HPV.</p>

Application of high-risk human papillomavirus testing in women with abnormal cytology / 中国医学科学院学报

<p><b>OBJECTIVE</b>To detect the high-risk human papillomavirus (HPV) infectious condition in women with abnormal cytology and evaluate its values in the screening of high grade squamous intraepithelial lesion.</p><p><b>METHODS</b>We used hybrid capture 2 (hc2) method to examine 949 patients with abnormal cervical cytology results [ > or =atypical squamous cells of undetermined significance (ASC-US) according to the 2001 The Bethesda System diagnosis criteria]. All subjects also received colposcopy for tissue studies.</p><p><b>RESULTS</b>Among 949 patients with abnormal cytology, the diagnoses of atypical squamous cells (ASC), low grade squamous intraepithelial lesion (LSIL), and high grade squamous intraepithelial lesion (HSIL) were made in 432, 310, and 207 patients, respectively. The high-risk HPV positive rate in ASC, LSIL, and HSIL were 40.3%, 44.8%, and 89.4%, respectively. The numbers of patients with pathologically confirmed results of negative intraepithelial lesion or malignancy (NILM), cervical intraepithelial neoplasia 1, 2, 3 (CIN 1, 2, 3), and squamous cell carcinoma (SCC) were 335, 388, 118, 101, and 7, and the high-risk HPV positive rate was 17.3%, 66.2%, 92.4%, 97.0%, and 100%, respectively. Among patients with atypical squamous cells of undetermined significance (ASC-US), rate of HSIL in high-risk HPV positive group and negative group were 10.2% and 0.8%, respectively (P < 0.01). In screening HSIL, the sensitivities of cytology [ > or = ASC cannot exclude HSIL (ASC-H)] and cytology ( > or = ASC-H) plus high-risk HPV testing were 0.925 and 0.991, and the specificities were 0.510 and 0.748, respectively (P < 0.01). Sensitivitives of cytology ( > or = LSIL) and cytology (> or = LSIL) plus high risk HPV in detecting HSIL were 0.898 and 0.982, respectively, while the specificitives were 0. 567 and 0.779, respectively (P < 0.01).</p><p><b>CONCLUSIONS</b>The positive rate of high-risk HPV increases with the gravity of cervical lesions. In patients with abnormal cervical cytology, high-risk HPV testing can improve the sensitivity and specificity in the screening of HSIL.</p>

Relationship between cyclin G1 and human papilloma virus infection in cervical intraepithelial neoplasia and cervical carcinoma / 中国医学科学杂志(英文版)

<p><b>OBJECTIVE</b>To evaluate the overexpression of cyclin G1 in cervical intraepithelial neoplasia (CIN) and cervical carcinoma, and the correlation between cyclin G1 and high-risk human papilloma virus (HPV) infection.</p><p><b>METHODS</b>All of the specimens were obtained from the Department of Pathology of China-Japan Friendship Hospital from January 2000 to August 2004. We detected the expression of cyclin G1 with immunohistochemistry, HPV16/18 infection with in situ hybridization, and high-risk HPV infection with Hybrid capture system II (HC-II) in normal group (25 cases), CIN I (48 cases), CIN II (56 cases), CIN III (54 cases), and invasive cervical squamous-cell carcinoma (SCC, 31 cases).</p><p><b>RESULTS</b>The positive rates of cyclin G1 expression in CIN (77.85%) and SCC cervical tissues (87.10%) were significantly higher than normal (8.00%, P < 0.01), and the intensities of cyclin G1 expression in CIN (40.60%) and SCC cervical tissues (61.51%) were significantly higher than normal (2.72%, P < 0.05). The positive rates and intensities of cyclin G1 expression increased gradually with the grade of cervical lesions. High-risk HPV infection rates were higher in CIN and SCC than normal groups (P < 0.05). There was a positive correlation between cyclin G1 expression and high-risk HPV infection detected with HC-II (Kendall's tau-b = 0.316, 0.269, 0.352, and 0.474 in CIN I, CINII, CIN III, and SCC, respectively, P < 0.05).</p><p><b>CONCLUSIONS</b>Cyclin G1 is overexpressed in CIN and SCC. Cyclin G1 may be a biomarker for detecting CIN and SCC. Cyclin G1 may play an important role in the oncogenesis of CIN and SCC by high-risk HPV infection.</p>

Cervical cytological screening and management in pregnant and postpartum women / 中国医学科学杂志(英文版)

<p><b>OBJECTIVE</b>To examine and follow up cervical cytology of pregnant and postpartum women and study their cytopathologic characteristics, so as to determine screening and managing programs for abnormal cervical cytology.</p><p><b>METHODS</b>Totally 5296 patients in pregnancy and postpartum, in which 3729 by computer-assisted cytology test and 1567 by liquid-based monolayers cytology test, were examined and diagnosed by the Bethesda System made in 2001. Those proven epithelial abnormalities patients were followed up until the lesions regressed to normal. The remaining patients, who exhibited persistent abnormalities or progression, were given further examinations.</p><p><b>RESULTS</b>The positive rate of cervical cytological test was 8.72% (462/5296), including squamous carcinoma (SCA) 1 case (0.02%), high grade squamous intraepithelial lesion (HSIL) 34 cases (0.64%), low grade squamous intraepithelial lesion (LSIL) 145 cases (2.74%), atypical glandular cells (AGC) 5 cases (0.09%), atypical squamous cells cannot exclude HSIL (ASC-H) 14 cases (0.26%), atypical squamous cells of undetermined significance (ASC-US) 263 cases (4.97%). The 419 proven cytological abnormality cases were followed up successfully. The total transnegative rate in three months was 73.74% (309/419), in which 303 cases (72.32%) persisted normal status for more than six months after regression. And the transnegative rate of ASC-US, ASC-H, AGC, LSIL, and HSIL were 79.56%, 64.29%, 100%, 72.14% and 44.12%, respectively. Forty-six cases received biopsy directed by colposcopy. The distribution of coincidence of cytopathologic and histopathologic diagnosis was: SCA 1 case (100%), HSIL 10 cases (76.92%), LSIL 13 cases (65%), ASC-H 2 cases (50%), ASC-US 3 cases (37.50%), total 29 cases (63.04%).</p><p><b>CONCLUSIONS</b>We should cast more attention to screening cervix lesions in pregnant and postpartum women. Their cytopathologic characteristics are liable to make the clinician give a false positive diagnosis. So we propose to follow up them closely and to lower the indication of biopsy.</p>