BACKGROUND: Workers in the microbiology laboratories are continuously exposed to the risk of laboratory-associated infections. Tuberculosis (TB) is a frequent laboratory-acquired infection owing to production of cough-generated aerosols with ease and high infectivity of Mycobacterium tuberculosis. This study aims to investigate the current situation of biosafety in Korean TB laboratories. METHODS: We conducted a nationwide survey of laboratories in hospitals conducting TB tests using questionnaires about their facility and management standards. RESULTS: We analyzed data from 52 hospitals nationwide that have a capacity of 100–2,000 beds, of which only two laboratories conduct high risk drug-susceptibility testing on cultured isolates among other test items, whereas six laboratories perform only direct sputum-smear microscopy. The remaining laboratories performed moderate-risk activities/tests, like sample processing for culture. In the majority of these laboratories, there are laboratory medicine specialists who are fully in charge of health checkup programs for laboratorians. The facility and management standards vary widely according to the size of the hospital and risk of TB tests. CONCLUSIONS: Our survey results about the current situation of TB laboratories could be useful as baseline data for preparing biosafety guidelines for all TB laboratories in Korea.
Aerosols ; Korea* ; Microscopy ; Mycobacterium tuberculosis ; Specialization ; Tuberculosis*

BACKGROUND: National surveillance of antimicrobial resistance becomes more important for the control of antimicrobial resistance and determination of treatment guidelines. We analyzed Korean Antimicrobial Resistance Monitoring System (KARMS) data collected from 2013 to 2015. METHODS: Of the KARMS participants, 16 secondary or tertiary hospitals consecutively reported antimicrobial resistance rates from 2013 to 2015. Data from duplicate isolates and institutions with fewer than 20 isolates were excluded. To determine the long-term trends, previous KARMS data from 2004 to 2012 were also considered. RESULTS: The prevalence of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium from 2013 to 2015 was 66–72% and 29–31%, respectively. The resistance rates of Escherichia coli to cefotaxime and cefepime gradually increased to 35% and 31%, respectively, and fluoroquinolone resistance reached 48% in 2015. The resistance rates of Klebsiella pneumoniae to cefotaxime, cefepime, and carbapenem were 38–41%, 33–41%, and <0.1–2%, respectively, from 2013 to 2015. The carbapenem susceptibility rates of E. coli and K. pneumoniae decreased from 100% and 99.3% in 2011 to 99.0% and 97.0% in 2015, respectively. The resistance rate of Pseudomonas aeruginosa to carbapenem increased to 35% and the prevalence of carbapenem-resistant Acinetobacter baumannii increased from 77% in 2013 to 85% in 2015. CONCLUSIONS: Between 2013 and 2015, the resistance rates of E. coli to third- and fourth-generation cephalosporins increased continuously, while carbapenem-susceptibility gradually decreased, particularly in K. pneumoniae. The prevalence of carbapenem-resistant P. aeruginosa and A. baumannii increased significantly; therefore, few treatment options remain for these resistant strains.
Acinetobacter baumannii ; Cefotaxime ; Cephalosporins* ; Drug Resistance, Microbial ; Enterococcus faecium ; Escherichia coli ; Klebsiella pneumoniae* ; Klebsiella* ; Methicillin-Resistant Staphylococcus aureus ; Pneumonia ; Prevalence ; Pseudomonas aeruginosa ; Tertiary Care Centers

BACKGROUND: Real-time reverse transcription PCR (rRT-PCR) of sputum samples is commonly used to diagnose Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Owing to the difficulty of extracting RNA from sputum containing mucus, sputum homogenization is desirable prior to nucleic acid isolation. We determined optimal homogenization methods for isolating viral nucleic acids from sputum. METHODS: We evaluated the following three sputum-homogenization methods: proteinase K and DNase I (PK-DNase) treatment, phosphate-buffered saline (PBS) treatment, and N-acetyl-L-cysteine and sodium citrate (NALC) treatment. Sputum samples were spiked with inactivated MERS-CoV culture isolates. RNA was extracted from pretreated, spiked samples using the easyMAG system (bioMérieux, France). Extracted RNAs were then subjected to rRT-PCR for MERS-CoV diagnosis (DiaPlex Q MERS-coronavirus, SolGent, Korea). RESULTS: While analyzing 15 spiked sputum samples prepared in technical duplicate, false-negative results were obtained with five (16.7%) and four samples (13.3%), respectively, by using the PBS and NALC methods. The range of threshold cycle (Ct) values observed when detecting upE in sputum samples was 31.1-35.4 with the PK-DNase method, 34.7-39.0 with the PBS method, and 33.9-38.6 with the NALC method. Compared with the control, which were prepared by adding a one-tenth volume of 1:1,000 diluted viral culture to PBS solution, the ranges of Ct values obtained by the PBS and NALC methods differed significantly from the mean control Ct of 33.2 (both P<0.0001). CONCLUSIONS: The PK-DNase method is suitable for homogenizing sputum samples prior to RNA extraction.
Acetylcysteine/chemistry ; Citrates/chemistry ; Coronavirus Infections/diagnosis ; Deoxyribonuclease I/metabolism ; Endopeptidase K/metabolism ; Humans ; Middle East Respiratory Syndrome Coronavirus/genetics/*isolation & purification ; RNA, Viral/analysis/*isolation & purification/metabolism ; Real-Time Polymerase Chain Reaction ; Sputum/*virology

For two months between May and July 2015, a nationwide outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) occurred in Korea. On June 3, 2015, the Korean Society for Laboratory Medicine (KSLM) launched a MERS-CoV Laboratory Response Task Force (LR-TF) to facilitate clinical laboratories to set up the diagnosis of MERS-CoV infection. Based on the WHO interim recommendations, the Centers for Disease Control and Prevention of United States guidelines for MERS-CoV laboratory testing, and other available resources, the KSLM MERS-CoV LR-TF provided the first version of the laboratory practice guidelines for the molecular diagnosis of MERS-CoV to the clinical laboratories on June 12, 2015. The guidelines described here are an updated version that includes case definition, indications for testing, specimen type and protocols for specimen collection, specimen packing and transport, specimen handling and nucleic acid extraction, molecular detection of MERS-CoV, interpretation of results and reporting, and laboratory safety. The KSLM guidelines mainly focus on the molecular diagnosis of MERS-CoV, reflecting the unique situation in Korea and the state of knowledge at the time of publication.
Coronavirus Infections/*diagnosis/epidemiology/virology ; Disease Outbreaks ; Humans ; Laboratories/*standards ; Middle East Respiratory Syndrome Coronavirus/*genetics/isolation & purification ; Product Packaging/standards ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction ; Republic of Korea/epidemiology ; Societies, Scientific ; Specimen Handling/standards

BACKGROUND: It is crucial to understand the current status of clinical laboratory practices for the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in the Republic of Korea to be well prepared for future emerging infectious diseases. METHODS: We conducted a survey of 49 clinical laboratories in medical institutions and referral medical laboratories. A short questionnaire to survey clinical laboratory practices relating to MERS-CoV diagnostic testing was sent by email to the directors and clinical pathologists in charge of the clinical laboratories performing MERS-CoV testing. The survey focused on testing volume, reporting of results, resources, and laboratory safety. RESULTS: A total of 40 clinical laboratories responded to the survey. A total of 27,009 MERS-CoV real-time reverse transcription PCR (rRT-PCR) tests were performed. Most of the specimens were sputum (73.5%). The median turnaround time (TAT) was 5.29 hr (first and third quartile, 4.11 and 7.48 hr) in 26 medical institutions. The median TAT of more than a half of the laboratories (57.7%) was less than 6 hr. Many laboratories were able to perform tests throughout the whole week. Laboratory biosafety preparedness included class II biosafety cabinets (100%); separated pre-PCR, PCR, and post-PCR rooms (88.6%); negative pressure pretreatment rooms (48.6%); and negative pressure sputum collection rooms (20.0%). CONCLUSIONS: Clinical laboratories were able to quickly expand their diagnostic capacity in response to the 2015 MERS-CoV outbreak. Our results show that clinical laboratories play an important role in the maintenance and enhancement of laboratory response in preparation for future emerging infections.
Clinical Laboratory Services/*standards ; Clinical Laboratory Techniques/instrumentation/methods ; Coronavirus Infections/*diagnosis/epidemiology/virology ; Disease Outbreaks ; Humans ; Middle East Respiratory Syndrome Coronavirus/genetics/isolation & purification ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction ; Republic of Korea/epidemiology ; Sputum/virology ; Surveys and Questionnaires

PURPOSE: The detection of high-level tetracycline-resistant strains of Neisseria gonorrhoeae (TRNG) can make important epidemiological contributions that are relevant to controlling infections from this pathogen. In this study, we aimed to determine the incidence of TRNG isolates over time and also to investigate the characteristics and genetic epidemiology of these TRNG isolates in Korea. MATERIALS AND METHODS: The antimicrobial susceptibilities of 601 isolates of N. gonorrhoeae from 2004 to 2011 were tested by standard Clinical and Laboratory Standards Institute methods. To determine the molecular epidemiological relatedness, N. gonorrhoeae multi-antigen sequence typing was performed. RESULTS: The incidence of TRNG increased from 2% in 2004 to 21% in 2011. The minimum inhibitory concentration distributions of ceftriaxone and susceptibility of ciprofloxacin in TRNG were different from non-TRNG and varied according to the year of isolation. Most of the TRNG isolates collected from 2004 to 2007 exhibited genetic relatedness, with sequence type (ST) 1798 being the most common. From 2008 to 2011, the STs of the isolates became more variable and introduction of genetically unrelated TRNG were noted. CONCLUSION: The increased incidence of TRNG strains until 2007 appears to be due, at least in part, to clonal spread. However, we propose that the emergence of various STs since 2008 could be associated with foreign import.
Anti-Bacterial Agents/*pharmacology ; Ceftriaxone/pharmacology ; Ciprofloxacin/pharmacology ; DNA, Bacterial/analysis ; Drug Resistance, Multiple, Bacterial/*genetics ; Gonorrhea/drug therapy/epidemiology/microbiology ; Humans ; Incidence ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Neisseria gonorrhoeae/*drug effects/*genetics/isolation & purification ; Republic of Korea/epidemiology ; Sequence Analysis, DNA ; Tetracycline/pharmacology ; Tetracyclines/*pharmacology

Healthcare-associated infections (HAIs) have increased rapidly, and the wide spread of multidrug resistant (MDR) bacteria has made the control of HAIs a challenging health problem. Transmission of common pathogens from a colonized or infected patient to a susceptible patient has been reported to occur via the hands of healthcare personnel. Therefore, the priority of infection control policy has been allocated in hand hygiene program, contact precautions, and isolation. However, the transmission routes of pathogens are complicated. Furthermore, recent data suggest that the hospital environment could play a role as an important reservoir, and contaminated hospital surfaces, medical equipment, water, and air could be directly or indirectly involved in the transmission pathways. Therefore, we should reconsider the role of hospital environment control in the management of HAIs as well as developing strategies to reduce the contamination of hospital environment.
Bacteria* ; Colon ; Delivery of Health Care ; Hand ; Hand Hygiene ; Humans ; Infection Control*

Quality control (QC) processes are being performed in the majority of clinical microbiology laboratories to ensure the performance of microbial identification and antimicrobial susceptibility testing by using ATCC strains. To obtain these ATCC strains, some inconveniences are encountered concerning the purchase cost of the strains and the shipping time required. This study was focused on constructing a database of reference strains for QC processes using domestic bacterial strains, concentrating primarily on antimicrobial susceptibility testing. Three strains (Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) that showed legible results in preliminary testing were selected. The minimal inhibitory concentrations (MICs) and zone diameters (ZDs) of eight antimicrobials for each strain were determined according to the CLSI M23. All resulting MIC and ZD ranges included at least 95% of the data. The ZD QC ranges obtained by using the CLSI method were less than 12 mm, and the MIC QC ranges extended no more than five dilutions. This study is a preliminary attempt to construct a bank of Korean QC strains. With further studies, a positive outcome toward cost and time reduction can be anticipated.
Anti-Bacterial Agents/*pharmacology ; Asian Continental Ancestry Group ; Escherichia coli/*drug effects ; Humans ; Laboratories ; Microbial Sensitivity Tests/*methods ; Pseudomonas aeruginosa/*drug effects ; Quality Control ; Reference Values ; Republic of Korea ; Staining and Labeling ; Staphylococcus aureus/*drug effects

BACKGROUND: A surveillance system for antibiotic resistance is well organized in both Japan and Korea; however, a comparative analysis by microorganism has not previously been conducted. METHODS: We compared the latest antibiotic resistance rates of medically important pathogens, such as Staphylococcus aureus, enterococci, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, between Japan and Korea. Data were collected by JANIS (Japan Nosocomial Infections Surveillance) and KARMS (Korean Antimicrobial Resistance Monitoring System) from 2007-2012. RESULTS: In 2012, the proportions of oxacillin-resistant S. aureus, vancomycin-resistant Enterococcus faecium (VRE), cefotaxime-resistant E. coli, ceftazidime-resistant K. pneumoniae, imipenem-resistant P. aeruginosa, and imipenem-resistant A. baumannii were 53%, 0.4%, 16.6%, 2.9%, 18.5%, and 2% in Japan and 67%, 32%, 29%, 40%, 28%, and 70% in Korea, respectively. CONCLUSION: There were large differences in the frequencies of VRE, ceftazidime-resistant K. pneumoniae, and imipenem-resistant A. baumannii between Japan and Korea. A collaborative study to probe the differences in the antibiotic resistance rates between the two countries should be performed.
Acinetobacter baumannii ; Cross Infection ; Drug Resistance, Microbial* ; Enterococcus faecium ; Escherichia coli ; Japan* ; Klebsiella pneumoniae ; Korea* ; Methicillin-Resistant Staphylococcus aureus ; Pneumonia ; Pseudomonas aeruginosa ; Staphylococcus aureus

BACKGROUND: In this report, we present the annual data of the intensive care unit (ICU) module of the Korean Nosocomial Infections Surveillance System (KONIS) from July 2013 through June 2014. METHODS: We performed a prospective surveillance of nosocomial urinary tract infections (UTIs), bloodstream infections (BSIs), and pneumonia (PNEU) in 166 ICUs of 94 hospitals using the KONIS. Nosocomial infection (NI) rate was defined as the number of infections per 1,000 patient-days or device-days. RESULTS: A total of 2,843 NIs were found during the study period: 861 UTIs (846 were urinary catheter-associated), 1,173 BSIs (1,021 were central line-associated), and 809 PNEUs (498 were ventilator-associated). The rate of urinary catheter-associated UTIs was 1.21 per 1,000 device-days (95% confidence interval [CI]=1.13-1.29), and the urinary catheter utilization ratio was 0.84 (95% CI=0.839-0.841). The rate of central line-associated BSIs was 2.33 per 1,000 device-days (95% CI=2.20-2.48), and the utilization ratio was 0.53 (95% CI=0.529-0.531). The rate of ventilatorassociated PNEUs (VAPs) was 1.46 per 1,000 device-days (95% CI=1.34-1.60), and the utilization ratio was 0.41 (95% CI=0.409-0.411). In hospitals with more than 900 beds, although the ventilator utilization ratio was highest, the rate of VAPs was lower than in hospitals with 300-699 or 700-899 beds. CONCLUSION: BSIs were the most commonly reported nosocomial infections. Although device utilization ratios had increased, nosocomial infection rates did not differ significantly from those during the previous period (July 2012 through June 2013).
Cross Infection* ; Intensive Care Units* ; Critical Care* ; Pneumonia ; Prospective Studies ; Urinary Catheters ; Urinary Tract Infections ; Ventilators, Mechanical