Application of high-throughput sequencing for microbial diversity detection in feces of specific-pathogen-free ducks.

High-throughput sequencing technologies play important roles in the study of animal enteric microorganisms. Fecal samples collected from 3 strains (9 samples) of specific-pathogen-free (SPF) ducks raised in an isolator. Duck intestinal bacterial flora were analyzed by sequencing distinct regions of the 16S rRNA genes using an Illumina HiSeq2500 platform. The result showed the most abundant primary enteric microbial phyla of 3 different strains of 70-week-old SPF ducks were Firmicutes, Proteobacteria, and Bacteroidetes, the most abundant primary enteric microbial order were Clostridiales, Lactobacillales, and Aeromonadales, and the most abundant primary enteric microbial genera were Bacteroides, Comamonas, and Enterococcus. In addition, the 3 duck strains harbored different compositions of the microorganisms, but these differences were not significant. Duck intestinal bacterial flora were analyzed using a high-throughput sequencing approach to further understand the distribution of intestinal flora and the biology of SPF ducks to ultimately benefit the purification of SPF ducks.

Correlates of antibiotic use in Taiwan hospitals.

OBJECTIVE: To determine factors that correlate with increased antibiotic use among adult inpatients in Taiwan. DESIGN: Retrospective survey of medical records. SETTING: 14 acute-care hospitals (8 regional hospitals, 6 medical centers) in Taiwan. PARTICIPANTS: A systematic probability sample from each hospital, totaling 663 adult inpatients who were discharged or had died in early 1999. MEASUREMENTS: Infectious disease physicians at the 14 hospitals collected data from medical records regarding patient demographics, hospitalization, discharge diagnosis, and antibiotics received. RESULTS: A total of 447 (67%) patients received antibiotics for an overall rate of 813 antibiotic-days (number of days patients received each antibiotic)/1,000 patient-days. Both the proportion of beds in intensive care units ([ICUs] Pearson correlation coefficient [r], 0.67; 95% confidence interval [CI 95], 0.36-0.89; P<.01) and the proportion of patients admitted to surgical services (r, 0.66; CI 95, 0.20-0.88; P=.01) correlated with the mean patient rate of antibiotic-days/hospital-day (MPAUD). In contrast, we found no correlation between the proportion of patients who received antibiotics and the MPAUD. Using multiple linear regression, medical center status was the only independent predictor for increased MPAUD (regression coefficient [b], 0.15; CI 95, 0.05-0.24; P<.01). There was no correlation between pooled rates of antibiotic-days/hospital-day and any hospital demographic factors. First-generation cephalosporin (39%) and aminoglycoside (24%) use accounted for the majority of antibiotic-days. CONCLUSIONS: Antibiotic use is greater in medical centers than in regional hospitals and appears to be independent of surgical case mix or the proportion of ICU beds. Determination of multiple, independent measures of antibiotic use may be necessary to understand the relation between antibiotic use and resistance in hospital.

Emergence of reduced susceptibility and resistance to fluoroquinolones in Escherichia coli in Taiwan and contributions of distinct selective pressures.

A survey of 1,203 Escherichia coli isolates from 44 hospitals in Taiwan revealed that 136 (11.3%) isolates were resistant to fluoroquinolones and that another 261 (21.7%) isolates had reduced susceptibility. Resistance was more common in isolates responsible for hospital-acquired (mostly in intensive care units) infections (17.5%) than in other adult inpatient (11.4%; P = 0.08) and outpatient isolates (11.9%; P > 0.1). Similarly, reduced susceptibility was more common in isolates responsible for hospital-acquired infections (30.9%) than in other adult inpatient (21.0%; P = 0.04) and outpatient (21.4%; P = 0.06) isolates. Isolates from pediatric patients were less likely to be resistant (1.3 versus 12.0%; P < 0.01) but were nearly as likely to have reduced susceptibility (17.7 versus 21.9%; P > 0.1) as nonpediatric isolates. There was an inverse relationship in the proportion of isolates that were resistant versus the proportion that had reduced susceptibility among isolates from individual hospitals (R = 0.031; P < 0.05). In an analysis of isolates from two hospitals, all 9 resistant strains possessed double point mutations in gyrA and all 19 strains with reduced susceptibility strains had single point mutations; no mutations were found among fully susceptible strains. Risk factors for resistance included underlying cancer (odds ratio [OR], 83; 95% confidence interval [CI(95)], 7.3 to 2,241; P < 0.001), exposure to a quinolone (OR, undefined; P = 0.02), and exposure to a nonquinolone antibiotic (OR, 20; CI(95), 2.2 to 482; P < 0.001); underlying cancer was the only independent risk factor (OR, 83; CI(95), 8.6 to 807; P < 0.001). There were no significant associations between any of these factors and reduced susceptibility. Whereas acute and chronic quinolone use in cancer patients is a major selective pressure for resistance, other undetermined but distinct selective pressures appear to be more responsible for reduced susceptibility to fluoroquinolones in E. coli.

Use and abuse of surgical antibiotic prophylaxis in hospitals in Taiwan.

BACKGROUND AND PURPOSE: A large proportion of antibiotics used in hospitals is for surgical prophylaxis. We determined the prevailing practices and factors associated with the misuse of surgical antibiotic prophylaxis in hospitals in Taiwan. METHODS: In a systematic survey of the medical records of 629 patients from 14 hospitals who underwent clean or clean-contaminated surgery from September 1998 through March 1999, data on the timing and duration of, and reasons for, antibiotic use were collected and analyzed. RESULTS: Overall, 578 (92%) patients received antibiotics perioperatively; in 499 (79%) cases, antibiotics were used for surgical prophylaxis. Only 302 (61%) patients received prophylaxis within 1 hour before surgery. More than 70% of patients received more than 3 days of postoperative antibiotic prophylaxis. The most commonly used antibiotics were first-generation cephalosporins and aminoglycosides. Factors independently associated with inappropriately timed prophylaxis included surgery performed at a hospital with a greater proportion of intensive care unit beds (conditional odds ratio [OR] = 1.14 per 1% increase, 95% confidence interval [CI95%] 1.06-1.23; p < 0.01), surgery duration of at least 1 hour (OR = 0.40, CI95% 0.24-0.67; p < 0.01), orthopedic surgery (OR = 0.59, CI95% 0.36-0.98; p = 0.041), and cardiothoracic surgery (OR = 2.07, CI95% 1.14-3.77; p = 0.02). Risk factors for more than 3 days of prophylaxis included surgical placement of prosthetic material (OR = 2.26, CI95% 1.10-4.64; p = 0.03), the number of antibiotics used (OR = 1.99 per antibiotic, CI95% 1.26-3.13; p < 0.01), surgery duration of at least 1 hour (OR = 3.07, CI95% 1.45-6.51; p < 0.01), neurosurgery (OR = 4.57, CI95% 2.24-9.31; p < 0.01), and the use of oral antibiotics together with intravenous drugs (OR = 20.72, CI95% 10.72-40.07; p < 0.01). CONCLUSIONS: The results of this survey indicate that inappropriate use of surgical antibiotic prophylaxis is common in hospitals in Taiwan. Our results identify several problem areas, including incorrect timing, duration, and use of oral antibiotics for surgical prophylaxis, that require targeted physician education and public health interventions.

[Effect of mm-LDL on NF-kB activation in endothelial cell].

OBJECTIVE: To investigate the signal transduction pathway of NF-kB activated by minimally modified low density lipoprotein (mm-LDL) in endothelial cells and the effect of NF-kB on platelet derived growth factor b (PDGFb) mRNA expression. METHODS: mm-LDL was prepared through iron oxidation by dialyzing the native LDL against FeSO4 in PBS. Endothelial cells were incubated in a medium containing mm-LDL, TNF, and IL-1 respectively and electrophoretic mobility shift assay (EMSA) was displayed to check on the activation of NF-kB. Luciferase reporter gene was analysed to investigate the effect of nuclear factor inducing kinase (NIK), inhibitor of NF-kB kinase alpha (IKK alpha) and inhibitor of NF-kB kinase beta (IKK beta) on NF-kB activation. In addition, endothelial cells were transfected using PDGFb promoter-luciferase for reporter gene analysis or transfected with mut-NIK for slot blot analysis to study the effect of NF-kB on PDGFb mRNA expression. RESULTS: mm-LDL was able to activate NF-kB in endothelial cells. mut-NIK and mut-IKK beta inhibited luciferase activity induced by mm-LDL. mm-LDL could also enhance luciferase activity controlled by upstream sequence of PDGFb promoter which contains element interacting with NF-kB. Result of slot blot showed inhibition of PDGFb mRNA expression by mut-NIK in the endothelial cells stimulated by mm-LDL. CONCLUSION: mm-LDL may activate NF-kB through NIK-IKK beta pathway and promote PDGFb mRNA expression in endothelial cells.