Additional file 1 of Enhancing indicator condition–guided HIV testing in Taiwan: a nationwide case–control study from 2009 to 2015

Additional file 1. Definition of four baseline comorbidities and 34 selected ICs from NHIRD by ICD-9 codes, eight selected ICs from NDSS, and the categories thereof

The Contribution of Antibiotic Resistance Mechanisms in Clinical <i>Burkholderia cepacia</i> Complex Isolates: An Emphasis on Efflux Pump Activity

<div><p>Due to the limited information of the contribution of various antibiotic resistance mechanisms in clinical <i>Burkholderia cepacia</i> complex isolates, Antibiotic resistance mechanisms, including integron analysis, identification of quinolone resistance-determining region mutations, measurement of efflux pump activity, and sequence analysis of efflux pump regulators, were investigated in 66 clinical <i>B. cepacia</i> complex isolates. Species were identified via <i>recA</i>-RFLP and MALDI-TOF. Four genomovars were identified by <i>recA</i>-RFLP. <i>B. cenocepacia</i> (genomovar III) was the most prevalent genomovar (90.1%). Most isolates (60/66, 90.9%) were correctly identified by MALDI-TOF analysis. Clonal relatedness determined by PFGE analysis revealed 30 pulsotypes, including two major pulsotypes that comprised 22.7% and 18.2% of the isolates, respectively. Seventeen (25.8%) isolates harboured class 1 integron with various combinations of resistance genes. Among six levofloxacin-resistant isolates, five had single-base substitutions in the <i>gyrA</i> gene and three demonstrated efflux pump activities. Among the 42 isolates exhibiting resistance to at least one antimicrobial agent, 94.4% ceftazidime-resistant isolates (17/18) and 72.7% chloramphenicol-resistant isolates (16/22) demonstrated efflux pump activity. Quantitation of efflux pump RNA level and sequence analysis revealed that over-expression of the RND-3 efflux pump was attributable to specific mutations in the RND-3 efflux pump regulator gene. In conclusion, high-level expression of efflux pumps is prevalent in <i>B. cepacia</i> complex isolates. Mutations in the RND-3 efflux pump regulator gene are the major cause of efflux pump activity, resulting in the resistance to antibiotics in clinical <i>B. cepacia</i> complex isolates.</p></div

Association of bacterial genotypes and epidemiological features with treatment failure in hemodialysis patients with methicillin-resistant <i>Staphylococcus aureus</i> bacteremia

<div><p>Objectives</p><p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) infections in the hemodialysis (HD) population are epidemiologically classified as healthcare-associated infections. The data about the clinical impact and bacterial characteristics of hospital-onset (HO)- and community-onset (CO)-MRSA in HD patients are scarce. The current study analyzed the difference in the clinical and molecular characteristics of HO-MRSA and CO-MRSA.</p><p>Methods</p><p>We performed a retrospective review and molecular analysis of clinical isolates from 106 HD patients with MRSA bacteremia from 2009 to 2014. CA genotypes were defined as isolates carrying the SCC<i>mec</i> type IV or V, and HA genotypes were defined as isolates harboring SCC<i>mec</i> type I, II, or III.</p><p>Results</p><p>CO-MRSA infections occurred in 76 patients, and 30 patients had HO-MRSA infections. There was no significant difference in the treatment failure rates between patients with CO-MRSA infections and those with HO-MRSA infections. CA genotypes were associated with less treatment failure (odds ratio [OR]: 0.18; 95% confidence interval [95% CI], 0.07–0.49; <i>p</i> = 0.001). For isolates with a vancomycin minimum inhibitory concentration (MIC) < 1.5 mg/L, the multivariate analysis revealed that HA genotypes and cuffed tunneled catheter use were associated with treatment failure. For isolates with a vancomycin MIC ≥1.5 mg/L, the only risk factor for treatment failure was a higher Pitt score (OR: 1.76; 95% CI, 1.02–3.05; <i>p</i> = 0.043).</p><p>Conclusion</p><p>CA genotypes, but not the epidemiological classification of CO-MRSA, impacted the clinical outcome of MRSA bacteremia in the HD population.</p></div

Molecular Epidemiology and Phylogenetic Analysis of Human Adenovirus Caused an Outbreak in Taiwan during 2011

<div><p>An outbreak of adenovirus has been surveyed in Taiwan in 2011. To better understand the evolution and epidemiology of adenovirus in Taiwan, full-length sequence of hexon and fiber coapsid protein was analyzed using series of phylogenetic and dynamic evolution tools. Six different serotypes were identified in this outbreak and the species B was predominant (HAdV-3, 71.50%; HAdV-7, 15.46%). The most frequent diagnosis was acute tonsillitis (54.59%) and bronchitis (47.83%). Phylogenetic analysis revealed that hexon protein gene sequences were highly conserved for HAdV-3 and HAdV-7 circulation in Taiwan. However, comparison of restriction fragment length polymorphism (RFLP) analysis and phylogenetic trees of fiber gene in HAdV-7 clearly indicated that the predominant genotype in Taiwan has shifted from 7b to 7d. Several positive selection sites were observed in hexon protein. The estimated nucleotide substitution rates of hexon protein of HAdV-3 and HAdV-7 were 0.234×10^-3 substitutions/site/year (95% HPD: 0.387~0.095×10^-3) and 1.107×10^-3 (95% HPD: 0. 541~1.604) respectively; those of the fiber protein of HAdV-3 and HAdV-7 were 1.085×10^-3 (95% HPD: 1.767~0.486) and 0.132×10^-3 (95% HPD: 0.283~0.014) respectively. Phylodynamic analysis by Bayesian skyline plot (BSP) suggested that using individual gene to evaluate the effective population size might possibly cause miscalculation. In summary, the virus evolution is ongoing, and continuous surveillance of this virus evolution will contribute to the control of the epidemic.</p></div

Class 1 integron cassette analysis.

<p>Genes are shown as arrows with the direction of transcription indicated by the arrowheads. <i>Int1</i>: class 1 integrase, <i>qacF</i>: quaternary ammonium compound-resistance protein, <i>qacEΔ1</i>: remnants of quaternary ammonium compound resistance protein, <i>sul1</i>: sulphonamides resistance gene, <i>aacA4</i>: aminoglycoside 6′-acetyltransferase, <i>aacA7</i>: aminoglycoside 6′-acetyltransferase, and <i>catB3</i>: chloramphenicol acetyltransferase.</p

Univariate analyses of the association between potential predictor variables and treatment failure in patients with methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) bacteremia.

<p>Univariate analyses of the association between potential predictor variables and treatment failure in patients with methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) bacteremia.</p

A dendrogram of pulsotype relationships developed via the unweighted pair group method using arithmetic averages (UPGMA) with BioNumerics software version 6.5 (Applied Maths).

<p>Pulsotypes were assigned to the same clusters if they exhibited 80% similarity in the dendrogram. Species identification was performed by <i>recA</i>-RFLP and MALDI-TOF analysis for 66 <i>B. cepacia</i> complex isolates.</p

Multivariate analyses of the association between potential predictor variables and treatment failure in patients with methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) bacteremia.

<p>Multivariate analyses of the association between potential predictor variables and treatment failure in patients with methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) bacteremia.</p

Genetic features of four <i>bla</i>_OXA-48<i>Klebsiella pneumoniae</i>.

<p>Genetic features of four <i>bla</i>_OXA-48<i>Klebsiella pneumoniae</i>.</p

EcoRI-digested plasmid digestion profile of four OXA-48-producing <i>Klebsiella pneumoniae</i> isolates.

<p>M, marker.</p