Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer.

Molecular typing is an essential tool that has been extensively applied in laboratories as well as in clinical settings. Next-generation sequencing technologies promise high-throughput and cost-effective molecular applications; however, the accessibility of these technologies is limited due to the high capital cost. Oxford Nanopore Technologies (ONT) offers a MinION device with the advantages of real-time data analysis, rapid library preparation, and low cost per test.

Genotypic Diversity of Ciprofloxacin Nonsusceptibility and Its Relationship with Minimum Inhibitory Concentrations in Nontyphoidal Clinical Isolates in Taiwan.

This study analyzed the genetic diversity of ciprofloxacin (CIP) nonsusceptibility and the relationship between two major mechanisms and minimum inhibitory concentrations (MICs) of CIP in nontyphoidal (NTS). Chromosomal mutations in quinolone resistance-determining regions (QRDRs) and plasmid-mediated quinolone resistance (PMQR) genes were searched from ResFinder, ARG-ANNOT, and PubMed for designing the sequencing regions in , , , and , and the 13 polymerase chain reactions for PMQR genes. We found that QRDR mutations were detected in (82.

Evolution and Population Structures of Prevalent Methicillin-Resistant in Taiwan.

Global methicillin-resistant (MRSA) strains were dominated by few genetic lineages, suggesting their inherent advantage of competitive fitness. The information of genome evolution and population structures of prevalent MRSA strains can help gain a better understanding of the success of the pandemic clones. Whole-genome sequencing was performed in 340 MRSA isolates belonging to three prevalent lineages, including ST59 (129 isolates), ST239/241 (140 isolates), and ST5 (71 isolates), collected from 1996 to 2016 in Taiwan.

Temporal Trend of ST131 Clone among Urinary Isolates in the Community: A Taiwan National Surveillance from 2002 to 2016.

Sequence type (ST) 131 is a multidrug-resistant pandemic lineage of responsible for extraintestinal infections. Few surveillance data of ST131 included all antimicrobial-susceptible and -resistant isolates or focused on community-acquired urinary tract infection (UTI). From a population-based surveillance pool of 2997 outpatient urine isolates, 542 were selected for detection of ST131 based on ciprofloxacin and/or cefotaxime resistance.

Detection, spread and phylogeny of meticillin-resistant sequence type 45 in Taiwan.

Meticillin-resistant (MRSA) sequence type (ST) 45 was reported in the literature to have been first identified in 2006 in Taiwan. The present study was carried out to explore and trace the emergence, transmission and evolutional dynamics of MRSA ST45 in Taiwan. We identified MRSA ST45 isolates retrospectively from two collections of MRSA isolates, namely TSAR (Taiwan Surveillance of Antimicrobial Resistance) surveys and the CGMH (Chang Gung Memorial Hospital)-based laboratory collection.

nanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples.

Multilocus sequence typing (MLST) is one of the most commonly used methods for studying microbial lineage worldwide. However, the traditional MLST process using Sanger sequencing is time-consuming and expensive. We have designed a workflow that simultaneously sequenced seven full-length housekeeping genes of 96 meticillin-resistant isolates with dual-barcode multiplexing using just a single flow cell of an Oxford Nanopore Technologies MinION system, and then we performed bioinformatic analysis for strain typing.

Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding.

The Oxford Nanopore MinION is an affordable and portable DNA sequencer that can produce very long reads (tens of kilobase pairs), which enable bacterial genome assembly. Although many algorithms and tools have been developed for base calling, read mapping, assembly, and polishing, an automated pipeline is not available for one-stop analysis for circular bacterial genome reconstruction. In this paper, we present the pipeline CCBGpipe for completing circular bacterial genomes.

Policy-driven revolution of prescription record in outpatient use of fluoroquinolones.

Objective: A policy initiated in 2001 by Taiwan's National Health Insurance (NHI) Administration has effectively reduced outpatient antibiotic use except fluoroquinolones (FQs). The influence of differential regulation policy of narrow-spectrum versus broad-spectrum FQs on the prescriptions is unknown.

Methods: This study analyzed the claim records of oral FQs prescription at outpatient visits during 2000-2010 using the NHI Research Database and compared prescriptions for narrow-spectrum FQs, which are inactive against Streptococcus pneumoniae and lack formulary restriction, with those for broad-spectrum FQs.

Total Synthesis of Tetarimycin A, (±)-Naphthacemycin A, and (±)-Fasamycin A: Structure-Activity Relationship Studies against Drug-Resistant Bacteria.

Making use of a reductive olefin coupling reaction and Michael-Dieckmann condensation as two key operations, we have completed a concise total synthesis of tetarimycin A, (±)-naphthacemycin A, and (±)-fasamycin A in a highly convergent and practical protocol. Synthetic procedures thus developed have also been applied to provide related analogues for structure-activity relationship studies, thereby coming to the conclusion that the free hydroxyl group at C-10 is essential for exerting inhibitory activities against a panel of Gram-positive bacteria, including drug-resistant strains VRE and MRSA.

Clinical and molecular features of MDR livestock-associated MRSA ST9 with staphylococcal cassette chromosome mecXII in humans.

Objectives: Clonal complex (CC) 9 is a prevalent livestock-associated (LA) MRSA clone in Asia whose pathogenicity in humans remains unknown.

Methods: In 2012, we identified a patient with CC9-MRSA infection linked to livestock. After screening 3328 clinical MRSA isolates from a national database, eight isolates (0.

Bromomethylthioindole Inspired Carbazole Hybrids as Promising Class of Anti-MRSA Agents.

Series of -substituted carbazole analogues bearing an indole ring were synthesized as anti-methicillin-resistant (MRSA) agents from a molecular hybridization approach. The representative compound showed an MIC = 1 μg/mL against a panel of MRSA clinical isolates as it possessed comparable activities to that of vancomycin. Moreover, compound also exhibited MIC = 1 μg/mL activities against a recent identified Z172 MRSA strain (vancomycin-intermediate and daptomycin-nonsusceptible phenotype) and the vancomycin-resistant (VRE) strain.

In Vivo and In Vitro Efficacy of Minocycline-Based Combination Therapy for Minocycline-Resistant Acinetobacter baumannii.

Minocycline-based combination therapy has been suggested to be a possible choice for the treatment of infections caused by minocycline-susceptible Acinetobacter baumannii, but its use for the treatment of infections caused by minocycline-resistant A. baumannii is not well established. In this study, we compared the efficacy of minocycline-based combination therapy (with colistin, cefoperazone-sulbactam, or meropenem) to that of colistin in combination with meropenem for the treatment of minocycline-resistant A.

Antimicrobial Non-Susceptibility of Escherichia coli from Outpatients and Patients Visiting Emergency Rooms in Taiwan.

Longitudinal nationwide surveillance data on antimicrobial non-susceptibility and prevalence of extended-spectrum β-lactamases (ESBLs) as well as AmpC β-lactamases producers among Escherichia coli from different sources in the community settings are limited. Such data may impact treatment practice. The present study investigated E.

Contribution of Acinetobacter-derived cephalosporinase-30 to sulbactam resistance in Acinetobacter baumannii.

The sulbactam resistance rate in Acinetobacter baumannii has increased worldwide. Previous reports have shown that the β-lactamase bla TEM-1 confers resistance to sulbactam in A. baumannii.

Studies on Antibiotics Active against Resistant Bacteria. Total Synthesis of MRSA-Active Tetarimycin A and Its Analogues.

Making use of the Hauser-Kraus annulation as a key step, the first total synthesis of tetarimycin A has been accomplished in a highly convergent and operationally simple manner. Preliminary SAR not only validated that tetarimycin A exhibited potent activity against MRSA and VRE at a low MIC value but also identified that the hydroxyl group at C-10 was essential for antibacterial activities.

Carbapenem-nonsusceptible Enterobacteriaceae in Taiwan.

A total of 1135 carbapenem-resistant (nonsusceptible) Enterobacteriaceae (CRE) isolates were recovered between November 2010 and July 2012 (517 from 2010-2011 and 618 from 2012) from 4 hospitals in Taiwan. Carbapenemase-producing Enterobacteriaceae (CPE) comprised 5.0% (57 isolates), including 17 KPC-2 (16 Klebsiella pneumoniae and 1 Escherichia coli), 1 NDM-1 (K.

Antimicrobial susceptibilities of Proteus mirabilis: a longitudinal nationwide study from the Taiwan surveillance of antimicrobial resistance (TSAR) program.

Background: Longitudinal nationwide data on antimicrobial susceptibility in Proteus mirabilis from different sources are rare. The effects of the revised Clinical and Laboratory Standards Institute (CLSI) β-lactam breakpoints on susceptibility rates and on detecting extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase-producers in this species are also seldom evaluated. The present study analyzed data from the Taiwan Surveillance of Antimicrobial Resistance program to address these issues.

Levofloxacin-resistant haemophilus influenzae, Taiwan, 2004-2010.

Levofloxacin resistance in Haemophilus influenzae has increased significantly in Taiwan, from 2.0% in 2004 to 24.3% in 2010 (p<0.

Epidemiology and molecular characterization of macrolide-resistant Streptococcus pyogenes in Taiwan.

Our multicenter nationwide surveillance data indicated that erythromycin (ERY) resistance among group A Streptococcus (GAS) isolates in Taiwan declined from 53.1% in 1998 and 2000 to 14.6% in 2002 and 2004 and 10.

A multicenter surveillance of antimicrobial resistance in Serratia marcescens in Taiwan.

Background: Serratia marcescens is an important nosocomial pathogen and the characteristic property of resistance conferred by extended-spectrum beta-lactamase or a novel AmpC cephalosporinase was not unusual in Taiwan. This study investigated the trends in antimicrobial resistance in S. marcescens from a nationwide surveillance in Taiwan.

Metastatic complications of pericarditis and cardiac tamponade as a result of Staphylococcus aureus bacteremia developing during antimicrobial therapy.

Acute bacterial pericarditis is a rare but devastating complication of Staphylococcus aureus bacteremia (SAB). We herein describe the case of a previously healthy 81-year-old woman with SAB complicated by pericarditis that evolved into cardiac tamponade despite the administration of optimal antimicrobial therapy for 11 days. Three adhesion factor genes, fnbA, clfA and clfB, were identified in the causative isolate.

Emergence of extensively drug-resistant Acinetobacter baumannii complex over 10 years: nationwide data from the Taiwan Surveillance of Antimicrobial Resistance (TSAR) program.

Background: Acinetobacter baumannii complex (ABC) has emerged as an important pathogen causing a variety of infections. Longitudinal multicenter surveillance data on ABC from different sources in Taiwan have not been published. Using data from the Taiwan Surveillance of Antimicrobial Resistance (TSAR) conducted biennially, we investigated the secular change in resistance of 1640 ABC from 2002 to 2010 (TSAR period III to VII) to different antimicrobial agents and identified factors associated with imipenem-resistant and extensively drug-resistant ABC (IRABC and XDRABC).