Abstract:
BACKGROUND:Drug resistance in Mycobacterium tuberculosis (MTB) is a major health issue worldwide. Recently, next-generation sequencing (NGS) technology has begun to be used to detect resistance genes of MTB. We aimed to assess the clinical usefulness of Ion S5 NGS TB research panel for detecting MTB resistance in Korean tuberculosis patients. METHODS:Mycobacterium tuberculosis with various drug resistance profiles including susceptible strains (N = 36) were isolated from clinical specimens. Nucleic acids were extracted from inactivated culture medium and underwent amplicon-based NGS to detect resistance variants in eight genes (gyrA, rpoB, pncA, katG, eis, rpsL, embB, and inhA). Data from previous studies using the same panel were merged to yield pooled sensitivity and specificity values for detecting drug resistance compared to phenotype-based methods. RESULTS:The sequencing reactions were successful for all samples. A total of 24 variants were considered to be related to resistance, and 6 of them were novel. Agreement between the phenotypic and genotypic results was excellent for isoniazid, rifampicin, and ethambutol, and was poor for streptomycin, amikacin, and kanamycin. The negative predictive values were greater than 97% for all drug classes, while the positive predictive values varied (44% to 100%). There was a possibility that common mutations could not be detected owing to the low coverage. CONCLUSIONS:We successfully applied NGS for genetic analysis of drug resistances in MTB, as well as for susceptible strains. We obtained lists of polymorphisms and possible polymorphisms, which could be used as a guide for future tests applying NGS in mycobacteriology laboratories. When analyzing the results of NGS, coverage analysis of each samples for each gene and benign polymorphisms not related to drug resistance should be considered.
journal_name
Ann Clin Microbiol Antimicrobjournal_title
Annals of clinical microbiology and antimicrobialsauthors
Ko DH,Lee EJ,Lee SK,Kim HS,Shin SY,Hyun J,Kim JS,Song W,Kim HSdoi
10.1186/s12941-018-0300-ysubject
Has Abstractpub_date
2019-01-03 00:00:00pages
2issue
1issn
1476-0711pii
10.1186/s12941-018-0300-yjournal_volume
18pub_type
杂志文章abstract:BACKGROUND:Persistent bacteremia occurs in at least 30% of patients with Staphylococcus aureus bloodstream infection (SAB) and may be attributable to a dysregulated host immune response. Neutrophils interact with a variety of S. aureus microbial factors, including lipoteichoic acid (LTA), to activate phagocytic functio...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-020-00392-w
更新日期:2020-11-03 00:00:00
abstract:BACKGROUND:Leishmaniasis and malaria are the two most common parasitic diseases and responsible for large number of deaths per year particularly in developing countries like Pakistan. Majority of Pakistan population rely on medicinal plants due to their low socio-economic status. The present review was designed to gath...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章,评审
doi:10.1186/s12941-016-0170-0
更新日期:2016-09-20 00:00:00
abstract:BACKGROUND:Previous studies report high prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) colonization among imprisoned populations. However, there are no data on that prevalence in Brazilian correctional institutions. FINDINGS:We tested 302 male prisoners for nasopharyngeal colonization with Staphyloco...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-13-25
更新日期:2014-07-02 00:00:00
abstract:BACKGROUND:Aquilaria crassna Pierre ex Lecomte has been traditionally used in Thailand for treatment of infectious diseases such as diarrhoea and skin diseases for a long time. The main objectives of this study were to examine antibacterial activity of the Aquilaria crassna leaf extract against Staphylococcus epidermid...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-12-20
更新日期:2013-08-20 00:00:00
abstract::For centuries, plants have been used in traditional medicines and there has been recent interest in the chemopreventive properties of compounds derived from plants. In the present study, we investigated the antibutyrylcholinestrasic (anti-BuChE) and antioxidant (against some free radicals) activities of extracts from ...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-10-32
更新日期:2011-08-31 00:00:00
abstract:BACKGROUND:Accurate measurement of the incidence of diarrhoeagenic E. coli in patients with diarrhoea is hindered by the current methods of detection and varies from country to country. In order to improve the diagnosis of diarrhoeagenic E. coli (DEC), we developed a set of multiplex TaqMan real-time PCRs designed to d...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-9-5
更新日期:2010-01-22 00:00:00
abstract:BACKGROUND:The consumption of carbapenems has increased worldwide, together with the increase in resistant gram negative bacilli. Subsequently, the prevalence of carbapenem-resistant Acinetobacter infections has increased rapidly and become a significant problem particularly in intensive care unit patients. The aim of ...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-13-7
更新日期:2014-01-09 00:00:00
abstract:BACKGROUND:Multidrug resistant strains of Acinetobacter baumannii (MDR-AB) have emerged as alarming nosocomial pathogens among patients admitted to Intensive Care Unit and burned patients. The aim of this study was to determine the susceptibility of A. baumannii isolates, the carbapenems resistance patterns bla(OXA-23)...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-014-0038-0
更新日期:2014-09-25 00:00:00
abstract:BACKGROUND:Antibiotic resistance is a defense mechanism, harbored by pathogens to survive under unfavorable conditions. Among several antibiotic resistant microbial consortium, Staphylococcus aureus is one of the most havoc microorganisms. Staphylococcus aureus encodes a unique enzyme 6-hydroxymethyl-7,8-dihydropterin ...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-018-0266-9
更新日期:2018-04-02 00:00:00
abstract:BACKGROUND:Fungal keratitis (FK) has been shown to be a climate-sensitive disease. The differentiation between FK from bacterial keratitis (BK) was difficult. The purpose of this study was to compare the bacteriology and mycology between tropical and subtropical Taiwan and to investigate the independent risk factors fo...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-020-00353-3
更新日期:2020-03-30 00:00:00
abstract:BACKGROUND:Aspergillus is a ubiquitous soil-dwelling fungus known to cause significant pulmonary infection in immunocompromised patients. The incidence of aspergillosis has increased during the past two decades and is a frequently lethal complication of acute leukemia patients that occurs following both chemotherapy an...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-5-17
更新日期:2006-07-27 00:00:00
abstract::Resistance to beta-lactam antibiotics in enteric Gram-negative bacilli may be difficult to detect using standard methods of either Kirby-Bauer disc diffusion (KBDD) or broth dilution for minimal inhibitory concentration (MIC). This difficulty is due to genetic differences in resistance determinants, differences in lev...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-3-13
更新日期:2004-07-15 00:00:00
abstract:BACKGROUND:The emergence of Mycobacterium tuberculosis strains resistant to antituberculosis agents has recently received increased attention owing largely to the dramatic outbreaks of multi drug resistance tuberculosis (MDR-TB). METHODS:Patients residing in Zonguldak and Kayseri provinces of Turkey with, pulmonary tu...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-1-6
更新日期:2002-12-16 00:00:00
abstract:BACKGROUND:Urinary tract infections (UTIs) remain the common infections diagnosed in outpatients as well as hospitalized patients. Current knowledge on antimicrobial susceptibility pattern is essential for appropriate therapy. Extended-Spectrum beta-Lactamase (ESBL) producing bacteria may not be detected by routine dis...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-6-4
更新日期:2007-03-23 00:00:00
abstract:BACKGROUND:Klebsiella pneumoniae is a public health concern because of its ability to develop multidrug resistance and hypervirulent genotypes, of those capsular types K1 and K2 cause community and nosocomial life-threatening infections. This study aimed to determine the antibiotic susceptibility patterns and genotypic...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-020-00349-z
更新日期:2020-03-31 00:00:00
abstract:BACKGROUND:This study aimed to evaluate in vitro susceptibility to ceftobiprole of clinical strains identified from prosthetic joint infections (PJIs) compared to that of the associations currently recommended for post-operative empirical antibiotic therapy (PEAT) (vancomycin with either cefepime, third-generation ceph...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-020-00351-5
更新日期:2020-03-21 00:00:00
abstract:BACKGROUND:Disinfection, antisepsis and sterilization (DAS) practices are of critical importance in hospital practice. This study aims to investigate the daily DAS practices of private hospitals in Istanbul, Turkey. METHODS:The DAS practices of 155 private hospitals in Istanbul province were investigated using a quest...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-015-0073-5
更新日期:2015-03-19 00:00:00
abstract:BACKGROUND:Tuberculous spondylitis (Pott's disease) is an ancient human disease. Because it is rare in high-income, tuberculosis (TB) low incidence countries, misdiagnoses occur as sufficient clinical experience is lacking. CASE PRESENTATION:We describe a fatal case of a patient with spinal TB, who was mistakenly irra...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-8-32
更新日期:2009-11-20 00:00:00
abstract:BACKGROUND:Cat-scratch disease (CSD) is a zoonotic infection caused by Bartonella henselae and B. clarridgeiae. The typical manifestations of CSD include regional lymphadenitis and fever. However, CSD can have a wide variety of clinical manifestations that can lead to incorrect diagnoses and prolonged hospital stays. ...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-019-0322-0
更新日期:2019-07-15 00:00:00
abstract:BACKGROUND:Malaria and HIV/AIDS are the two most common infections in sub-Sahara Africa. There are hypotheses and study reports on the possible association between these two infections, hence the prevalence and outcome of their co-infection in an endemic population will be important in defining healthcare strategies. A...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-015-0064-6
更新日期:2015-03-07 00:00:00
abstract::An 87 -year-old female who was undergoing peritoneal dialysis presented with peritonitis caused by Alcaligenes faecalis and Pantoea agglomerans in consecutive years. With the following report we discuss the importance of these unusual microorganisms in peritoneal dialysis patients. ...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-10-12
更新日期:2011-04-10 00:00:00
abstract::Ebola virus disease (EVD) is a potentially fatal haemorrhagic disease of humans. The last and most serious outbreak of Ebola virus (EBOV) started in December 2013 in West Africa and also affected other continents. Animals such as fruit bats and non-human primates are potential sources of EBOV. This review highlights t...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章,评审
doi:10.1186/s12941-015-0089-x
更新日期:2015-05-28 00:00:00
abstract:BACKGROUND:Diarrheal diseases continue to be the major cause of morbidity and mortality among children under 5 years. Salmonella and Shigella specious are the major enteric pathogen causing diarrhea among children worldwide. Examination of stool sample is the most sensitive method to diagnose diarrheal disease in child...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-018-0253-1
更新日期:2018-02-01 00:00:00
abstract:BACKGROUND:Training of infectious disease (ID) specialists is structured on classical clinical microbiology training in Turkey and ID specialists work as clinical microbiologists at the same time. Hence, this study aimed to determine the clinical skills and knowledge required by clinical microbiologists. METHODS:A cro...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-10-38
更新日期:2011-12-16 00:00:00
abstract::Multi-Drug Resistant (MDR) Pseudomonas aeruginosa is one of the most important bacterial pathogens that causes infection with a high mortality rate due to resistance to different antibiotics. This bacterium prompts extensive tissue damage with varying factors of virulence, and its biofilm production causes chronic and...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章,评审
doi:10.1186/s12941-020-00389-5
更新日期:2020-09-30 00:00:00
abstract:BACKGROUND:Escherichia coli is the commonest cause of community and nosocomial urinary tract infection (UTI). Antibiotic treatment is usually empirical relying on susceptibility data from local surveillance studies. We therefore set out to determine levels of resistance to 8 commonly used antimicrobial agents amongst a...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-7-13
更新日期:2008-06-18 00:00:00
abstract::Stenotrophomonas maltophilia (S. maltophilia) has recently emerged as an important nosocomial pathogen. Treatment of invasive infections caused by this organism is difficult as the bacterium is frequently resistant to a wide range of commonly used antimicrobials. Trimethoprim-sulfamethoxazole (TMP - SXT) is recommende...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/1476-0711-5-23
更新日期:2006-09-18 00:00:00
abstract:INTRODUCTION:The aim of this study was to show the emergence of the qnrD gene among fluoroquinolone-resistant Morganella morganii isolate. The occurrence of mutations in DNA gyrase (gyrA and gyrB) and topoisomerase IV (parC,parE) genes was also investigated in this strain. METHODOLOGY:95 clinical Enterobacteria were s...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-014-0034-4
更新日期:2014-08-09 00:00:00
abstract:BACKGROUND:Carbapenemase-producing Klebsiella pneumoniae (CPKP) strains have emerged as a major problem for healthcare systems. The aim of this study was to determine the circulating clones and analyze the clinical and molecular characteristics of CPKP in our hospital. METHODS:A total of 74 carbapenemase producers col...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章
doi:10.1186/s12941-015-0109-x
更新日期:2016-01-19 00:00:00
abstract:INTRODUCTION:Antibiotic resistance decreases success of Helicobacter pylori (Hp) eradication. Recently published results show low rate of resistance and better compliance with moxifloxacin based regiments. AIMS&METHODS: Whether 7 days moxifloxacin with lansoprasole and amoxycillin can be compared with 10 days moxifloxa...
journal_title:Annals of clinical microbiology and antimicrobials
pub_type: 杂志文章,随机对照试验
doi:10.1186/1476-0711-9-13
更新日期:2010-04-15 00:00:00