【病毒外文文献】2016 Survey of Clinical Laboratory Practices for 2015 Middle East Respiratory Syndrome Coronavirus Outbreak in the Repub

ISSN 2234 3806 eISSN 2234 3814 154 www annlabmed org http dx doi org 10 3343 alm 2016 36 2 154 Ann Lab Med 2016 36 154 161 http dx doi org 10 3343 alm 2016 36 2 154 Original Article General Laboratory Medicine Survey of Clinical Laboratory Practices for 2015 Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea Mi Kyung Lee M D 1 Sinyoung Kim M D 2 Mi Na Kim M D 3 Oh Joo Kweon M D 1 Yong Kwan Lim M D 1 Chang Seok Ki M D 4 Jae Seok Kim M D 5 Moon Woo Seong M D 6 Heungsup Sung M D 4 Dongeun Yong M D 2 Hyukmin Lee M D 7 Jong Rak Choi M D 2 Jeong Ho Kim M D 2 MERS CoV Laboratory Response Task Force of The Korean Society for Laboratory Medicine Department of Laboratory Medicine 1 Chung Ang University College of Medicine Seoul Department of Laboratory Medicine 2 Yonsei University College of Medicine Seoul Department of Laboratory Medicine 3 Asan Medical Center University of Ulsan College of Medicine Seoul Department of Laboratory Medicine and Genetics 4 Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Department of Laboratory Medicine 5 Kangdong Sacred Heart Hospital Hallym University College of Medicine Seoul Department of Laboratory Medicine 6 Seoul National University College of Medicine Seoul Department of Laboratory Medicine 7 Catholic Kwandong University College of Medicine Incheon Korea 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 infec tions 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 re ferral medical laboratories A short questionnaire to survey clinical laboratory practices re lating to MERS CoV diagnostic testing was sent by email to the directors and clinical pa thologists 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 in cluded 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 prepa ration for future emerging infections Key Words Middle East respiratory syndrome coronavirus MERS CoV Korea Outbreak Clinical laboratory Preparedness Survey Received August 11 2015 Revision received September 3 2015 Accepted November 10 2015 Corresponding author Jeong Ho Kim Department of Laboratory Medicine Yonsei University College of Medicine 50 1 Yonsei ro Seodaemun gu Seoul 03722 Korea Tel 82 2 2228 2448 Fax 82 2 364 1583 E mail jeongho yuhs ac The Korean Society for Laboratory Medicine This is an Open Access article distributed under the terms of the Creative Commons Attribution Non Commercial License http creativecom mons org licenses by nc 3 0 which permits unrestricted non commercial use distribution and reproduction in any medium provided the original work is properly cited INTRODUCTION On May 20 2015 Middle East respiratory syndrome coronavirus MERS CoV was confirmed for the first time in an infected pa tient in the Republic of Korea Although the primary case trav eled to the United Arab Emirates and Saudi Arabia the patient Lee M K et al Lab practices for 2015 MERS CoV outbreak in Korea http dx doi org 10 3343 alm 2016 36 2 154 www annlabmed org 155 did not initially report his recent travel in those countries 1 This case led to transmission of MERS CoV both within a hospital and between hospitals and eventually resulted in the largest outbreak of MERS CoV infections outside the Arabian Peninsula At that time we had limited information on MERS CoV and only a few clinical laboratories were prepared to perform molec ular diagnostic testing for the virus During the longer than two months of the outbreak 186 confirmed cases were diagnosed by real time reverse transcription PCR rRT PCR of MERS CoV and specimens from tens of thousands of suspected cases in cluding individuals who contacted the confirmed cases were submitted for this testing Many clinical laboratories were in structed to set up facilities to perform MERS CoV rRT PCR on site in a short time to fight against the transmission of this virus in their own institutes An earlier outbreak in 2009 of a novel strain of H1N1 influ enza virus A H1N1 influenza affected laboratories worldwide with a potentially tremendous impact on the practices of clinical laboratories 2 The outbreak of H1N1 influenza also had a great influence in the Republic of Korea The field of molecular testing for pathogens has been expanded in clinical laborato ries and the molecular testing industry has responded quickly with the production of new molecular test kits Numerous stud ies including viral etiology epidemiology risk factors clinical and laboratory characteristics and diagnostic tests have been reported 3 Despite the fact that clinical laboratory practice was a critical element in the response to the H1N1 influenza outbreak there are only a few reports regarding this aspect of testing 2 4 5 The ability of clinical laboratories to respond appropriately to an outbreak is significant in pathogen control Therefore it is crucial to understand the current status of clinical laboratories in the Republic of Korea in order to be well prepared for any fu ture emerging infectious diseases In this article we present the results of a survey of clinical laboratory practices during the 2015 MERS CoV outbreak METHODS The study population consisted of clinical laboratories perform ing diagnostic testing for MERS CoV in medical institutions hos pitals and medical centers and referral medical laboratories among clinical laboratories accredited by the Korean Laboratory Accreditation Program 6 This survey was an initiative of the MERS CoV Laboratory Re sponse Task Force of the Korean Society for Laboratory Medi cine We conducted a survey of 49 clinical laboratories A short questionnaire to assess clinical laboratory practices related to MERS CoV diagnostic testing was sent by email to the directors and the clinical pathologists laboratory physicians in charge of the clinical laboratories performing MERS CoV tests The survey focused on the number of tests and the number of positive test results for MERS CoV turnaround time TAT request process collection and transportation of specimens testing and report ing communication of results laboratory safety and reagents and equipment RESULTS A total of 40 clinical laboratories 81 6 40 49 including 35 medical institutions and 5 referral medical laboratories re sponded to the survey The number of beds in the medical insti tutions was as follows 1 000 beds 12 34 3 All clinical laboratories used rRT PCR as the detection method for MERS CoV 1 Testing volume and specimen type The number of MERS CoV rRT PCR tests performed was col lected from 32 medical institutions and five referral medical lab oratories Data up to July 15 2015 were collected according to the day and specimen type A total of 27 009 MERS CoV rRT PCR tests were performed at 32 medical institutions N 11 502 and five referral medical laboratories N 15 507 Ta ble 1 and Fig 1 The proportion of medical institutions was sig nificantly underestimated because one tertiary care hospital submitted responses for the survey but not the specimen list and the numbers of MERS CoV rRT PCR tests and positive specimens at this institution would have been predominant in the reporting medical institutions MERS CoV rRT PCR testing at all medical institutions and referral medical laboratories in creased dramatically in early June Fig 1 The number of clini cal laboratories that initiated MERS CoV testing increased in the first two to three weeks Fig 2 Daily test volumes peaked on June 24 1 088 tests and began to decrease thereafter Fig 1 Among the 27 009 MERS CoV rRT PCR specimens 246 0 9 and 91 0 3 specimens were positive and indeterminate re spectively 153 and 71 specimens at medical institutions 93 and 20 specimens at referral medical laboratories Table 1 Most of the specimens for MERS CoV rRT PCR were sputum 73 5 A total of 74 7 of all specimens tested and 82 9 of positive specimens were specimens from the lower respiratory Lee M K et al Lab practices for 2015 MERS CoV outbreak in Korea 156 www annlabmed org http dx doi org 10 3343 alm 2016 36 2 154 tract such as sputum bronchoscopy specimens or tracheal aspirates Table 1 All nasopharyngeal aspirates N 293 were negative for MERS CoV rRT PCR 2 Turnaround time The TAT is defined as the time from the receipt of specimens in the laboratory to the reporting of the results Unfortunately 35 of the laboratories nine medical institutions and five referral medical laboratories were not able to provide or analyze data on TAT The median TAT was 5 29 hr first and third quartile 4 11 and 7 48 hr for 26 medical institutions and the minimum and maximum median TAT first and third quartile were 4 00 hr 3 35 and 5 10 hr and 26 46 hr 19 59 and 31 36 hr respec Table 1 Number of MERS CoV tests and positive and indeterminate results according to the specimen type Specimen type Total Medical institution N 32 Referral medical laboratories N 5 N of tests N of positive tests N of indeterminate tests N of tests N of positive tests N of indeterminate tests N of tests N of positive tests N of indeterminate tests Sputum 19 843 73 5 178 0 90 72 0 36 7 304 63 5 97 1 33 56 0 77 12 539 80 9 81 0 65 16 0 13 Bronchoscopy specimens 202 0 7 11 5 45 0 0 0 69 0 6 11 15 94 0 0 0 133 0 9 0 0 0 0 0 0 Tracheal aspirates 138 0 5 15 10 87 1 0 72 135 1 2 15 11 11 1 0 74 3 0 0 0 0 0 0 0 0 Nasopharyngeal aspirates 293 1 1 0 0 0 0 0 0 233 2 0 0 0 0 0 0 0 60 0 4 0 0 0 0 0 0 Nasopharyngeal Blood Stool Abbreviation MERS CoV Middle East respiratory syndrome coronavirus Fig 1 Number of Middle East respiratory syndrome coronavirus MERS CoV tests performed in Korea from May 28 to July 15 1 200 1 000 800 600 400 200 0 26 28 30 01 03 05 07 09 11 13 15 17 19 21 23 25 27 29 01 03 05 07 09 11 13 15 May June July N of tests Medical institutions Referral medical laboratories Lee M K et al Lab practices for 2015 MERS CoV outbreak in Korea http dx doi org 10 3343 alm 2016 36 2 154 www annlabmed org 157 tively The median TAT of more than a half of the laboratories 57 7 was less than 6 hr The results were reported within 24 hr in all medical institutions except one Table 2 In the referral medical laboratories the results were reported in less than 6 9 hr during weekday daytime or 9 15 hr during weekday nights and weekends 3 Status of clinical laboratory operation Table 2 shows the current status of clinical laboratories in medi cal institutions with respect to their response to the outbreak of MERS CoV infections Many laboratories were able to perform testing throughout the week 71 4 25 35 and ran tests once or twice per day Specimen was collected mainly by clinicians and all specimens were directly transported person to person In most cases clinicians filled out the specimen request informa tion form and doctors of laboratory medicine completed the test report form Most of the MERS CoV rRT PCR tests were per formed only by clinical laboratory technicians of molecular ge netics divisions 74 3 of 35 laboratories The test results were primarily reported by clinical pathologists via electronic process ing Laboratory biosafety preparedness in response to the MERS CoV outbreak included class II biosafety cabinets 100 35 35 separated pre PCR PCR and post PCR rooms 88 6 31 35 negative pressure pretreatment rooms 48 6 17 35 and neg ative pressure sputum collection rooms 20 0 7 35 As shown in Table 3 the current status of clinical laboratories in referral medical laboratories was similar to that of medical in stitutions in many aspects Specimens were transported twice or three times a day 4 Pretreatment of specimens reagents and equipment Many laboratories 75 30 40 used phosphate buffered sa line for pretreatment of sputum specimens All reagents for the detection of MERS CoV were components of ready made kits and the PowerChek MERS Real time PCR Kit KogeneBiotech Seoul Korea was the most commonly used kit 72 5 29 40 Most laboratories used CFX96 Bio Rad Laboratories Hercules CA USA or ABI7500 or 7800 systems Life Technologies Carls bad CA USA for rRT PCR 85 0 34 40 Table 4 DISCUSSION The emergence of novel viral pathogens and the evolution of pandemics have presented a new and complex challenge to public health care systems at every level 1 3 7 8 The out break of H1N1 influenza eventually turned out to be relatively mild despite the fear it engendered as the potential early stage of a pandemic Breban et al 9 suggested that MERS CoV does not yet have pandemic potential Nevertheless a MERS CoV outbreak recently occurred in the Republic of Korea and its characteristics were very different from those of the outbreak of H1N1 influenza The MERS CoV outbreak was more serious Fig 2 Number of clinical laboratories that started Middle East respiratory syndrome coronavirus MERS CoV testing in Korea from May 28 to July 15 8 7 6 5 4 3 2 1 0 26 28 30 01 03 05 07 09 11 13 15 17 19 21 23 25 27 29 01 03 05 07 09 11 13 15 May June July N of laboratories Medical institutions Referral medical laboratories Lee M K et al Lab practices for 2015 MERS CoV outbreak in Korea 158 www annlabmed org http dx doi org 10 3343 alm 2016 36 2 154 Table 2 Turnaround time and status of clinical laboratories in medical institutions A Median turnaround time TAT for MERS CoV testing N 26 TAT hr N 24 1 3 8 Total 26 100 0 B Status of clinical laboratories in medical institutions N 35 Survey N Specimen request information form input performed by Clinicians 22 62 9 Doctors of laboratory medicine 2 5 7 Infection control nurses 1 2 9 No answer 10 28 6 Test report form input performed by Clinicians 6 17 1 Doctors of laboratory medicine 11 31 4 Technologists of laboratory medicine 4 11 4 Infection control nurses 1 2 9 Medical technologists or doctors of laboratory medicine 3 8 6 No answer 10 28 6 Operating days of MERS CoV test Mon Fri 5 14 3 Mon Sat 5 14 3 Mon Sun 25 71 4 Operating hours of MERS CoV test Regular working hours 20 57 1 Overtime 2 5 7 24 hr 13 37 1 Number of MERS CoV tests run per day One 16 45 7 Two 9 25 7 More than three 5 14 3 Others 5 14 3 Specimen collections performed by Clinicians 18 51 4 Nurses 2 5 7 Clinicians N Number of medical institutions SMS short message service Lee M K et al Lab practices for 2015 MERS CoV outbreak in Korea http dx doi org 10 3343 alm 2016 36 2 154 www annlabmed org 159 than expected and numerous problems arose concerning in fection control and prevention in hospitals and among the gen eral public Because clinical laboratories are usually on the front lines for the detection of emerging pathogens the ability of these labora tories to respond to an outbreak is critical for infection control and prevention The elements of clinical laboratory prepared ness and responsiveness include availability of personal protec Table 3 Status of clinical laboratories in referral medical laborato ries N 5 Survey N Operating days of MERS CoV tests Mon Sun 5 100 0 Operating hours of MERS CoV tests 24 hr 5 100 0 Number of MERS CoV tests per day Two 3 60 0 Three 1 20 0 Three on weekdays PBS phosphate buffered saline NALC N acetyl L cysteine DW deionized water KogeneBiotech KogeneBiotech PowerChek MERS CoV real time PCR kit SolGent SolGent DiaPlexQ MERS CoV virus detection kit Bioneer Bioneer AccuPower MERS CoV real time RT PCR kit NANOBIOSYS NANOBIOSYS MERS CoV corona virus detection kit BIO RAD CFX96 BIO RAD CFX96 real time PCR system ABI7500 or 7500 Fast Life Technolo gies ABI7500 or 7800 real time PCR system Bioneer Exicycler Bioneer Exi cycler 96 real time PCR system LG SLAN LG Life Sciences SLAN real time PCR system NANOBIOSYS G2 4 NANOBIOSYS real time PCR G2 4 Lee M K et al Lab practices for 2015 MERS CoV outbreak in Korea 160 www annlabmed org http dx doi org 10 3343 alm 2016 36 2 154 tive equipment and its appropriate use availability and use of appropriate testing supplies adequacy of staffing and infra structure requirements including laboratory space 2 In 2012 and 2013 the European Centre for Disease Prevention and Control ECDC and the WHO Regional Office for Europe con ducted a joint survey 10 Although the number of countries that had laboratory capabilities to detect and confirm MERS CoV increased in 2013 55 8 29 of 52 countries compared with 2012 47 8 22 of 46 countries a half of the countries were still unable to test MERS CoV 10 The present study reveals a snapshot of the current status and capability of clinical laboratories to respond to the MERS CoV outbreak in the Republic of Korea Most clinical laboratories participating in the survey were considered to have sufficient capacity to respond to the outbreak Immediately after the MERS CoV rRT PCR test was approved many laboratories were able to perform testing seven days a week and the number of tests reported increased dramatically The median TAT of more than a half of the laboratories 57 7 was shorter than 6 hr and the minimum median TAT was 4 00 hr The results were re ported within 24 hr in all medical institutions except one One limitation of our study is that even though we obtained re sponses from the majority of medical institutions and referral medical laboratories the results may not be fully representative for a number of reasons Data were collected before the end of the MERS CoV outbreak and did not include some major medi cal institutions and public health laboratories such as the Korea Centers for Disease Control and Prevention In addition our re sults report the number of MERS CoV rRT PCR tests and not the number of MERS CoV cases Previously Sousa et al 11 suggested that the use of upper respiratory specimens e g nasopharyngeal swabs for MERS CoV diagnosis might not be as sensitive as the use of lower re spiratory tract specimens The laboratory diagnostic guidelines for MERS CoV testing of the Korean Society for Laboratory Medi cine recommended using specimens from the lower respiratory tract In the present survey the number of positive results from MERS CoV rRT PCR was significantly higher in specimens ob tained from the lower respiratory tract 1 01 204 20 183 compared with specimens from the upper respiratory tract 0 6 41 6 785 P 0 002 chi square test Therefore the specimen type is expected to have a significant impact on diag nostic sensitivity and should be considered when testing emerg ing pathogens For laboratory biosafety in response to the MERS CoV out break class II biosafety cabinets were adequately supplied but high end engineering facilities such as negative pressure spu tum collection and pretreatment rooms were not readily avail able However no laboratory acquired infections were reported during the outbreak thus standard precautions with droplet precautions appeared to be sufficient for the prevention of labo ratory acquired infection of MERS CoV Nonetheless improve ments in engineering laboratory biosafety are needed for pre paredness to test agents with a higher biosafety level Clinical laboratories have the primary