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Cornish NE, Anderson NL, Arambula DG, Arduino MJ, Bryan A, Burton NC, Chen B, Dickson BA, Giri JG, Griffith NK, Pentella MA, Salerno RM, Sandhu P, Snyder JW, Tormey CA, Wagar EA, Weirich EG, Campbell S. Clinical Laboratory Biosafety Gaps: Lessons Learned from Past Outbreaks Reveal a Path to a Safer Future. Clin Microbiol Rev 2021; 34:e0012618. [PMID: 34105993 PMCID: PMC8262806 DOI: 10.1128/cmr.00126-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Patient care and public health require timely, reliable laboratory testing. However, clinical laboratory professionals rarely know whether patient specimens contain infectious agents, making ensuring biosafety while performing testing procedures challenging. The importance of biosafety in clinical laboratories was highlighted during the 2014 Ebola outbreak, where concerns about biosafety resulted in delayed diagnoses and contributed to patient deaths. This review is a collaboration between subject matter experts from large and small laboratories and the federal government to evaluate the capability of clinical laboratories to manage biosafety risks and safely test patient specimens. We discuss the complexity of clinical laboratories, including anatomic pathology, and describe how applying current biosafety guidance may be difficult as these guidelines, largely based on practices in research laboratories, do not always correspond to the unique clinical laboratory environments and their specialized equipment and processes. We retrospectively describe the biosafety gaps and opportunities for improvement in the areas of risk assessment and management; automated and manual laboratory disciplines; specimen collection, processing, and storage; test utilization; equipment and instrumentation safety; disinfection practices; personal protective equipment; waste management; laboratory personnel training and competency assessment; accreditation processes; and ethical guidance. Also addressed are the unique biosafety challenges successfully handled by a Texas community hospital clinical laboratory that performed testing for patients with Ebola without a formal biocontainment unit. The gaps in knowledge and practices identified in previous and ongoing outbreaks demonstrate the need for collaborative, comprehensive solutions to improve clinical laboratory biosafety and to better combat future emerging infectious disease outbreaks.
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Affiliation(s)
- Nancy E. Cornish
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Nancy L. Anderson
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Diego G. Arambula
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Matthew J. Arduino
- Centers for Disease Control and Prevention, National Center for Emerging & Zoonotic Infectious Diseases (NCEZID), Atlanta, Georgia, USA
| | - Andrew Bryan
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Nancy C. Burton
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio, USA
| | - Bin Chen
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Beverly A. Dickson
- Department of Clinical Pathology, Texas Health Presbyterian Hospital Dallas, Dallas, Texas, USA
| | - Judith G. Giri
- Centers for Disease Control and Prevention, Center for Global Health (CGH), Atlanta, Georgia, USA
| | | | | | - Reynolds M. Salerno
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Paramjit Sandhu
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - James W. Snyder
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Christopher A. Tormey
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Pathology & Laboratory Medicine Service, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Elizabeth A. Wagar
- Department of Laboratory Medicine, University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Elizabeth G. Weirich
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Sheldon Campbell
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Pathology & Laboratory Medicine Service, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
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Bailey AL, Farnsworth C. Inactivation of Blood-Borne Enveloped Viruses with the Nonionic Detergent 2-[4-(2,4,4-Trimethylpentan-2-yl)Phenoxy]Ethanol Does Not Bias Clinical Chemistry Results. J Appl Lab Med 2021; 6:1123-1132. [PMID: 33993264 DOI: 10.1093/jalm/jfab006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/21/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Patients infected with virulent pathogens require the sophisticated diagnostic capabilities of a core laboratory for optimal care. This is especially true in outbreaks that strain healthcare system capacity. However, samples from such patients pose an infection risk for laboratory workers. We evaluated a strategy for mitigating this risk by preincubating specimens with 2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanol, a non-ionic detergent commonly calledTriton X-100. METHODS Lithium-heparinized plasma was mixed with the detergent Triton X-100 at 1%. Inactivation of Ebola virus (EBOV), yellow fever virus (YFV), and chikungunya virus (CHIKV) was assessed using a virus-outgrowth assay. The impact of 1% Triton X-100 dilution on the components of a complete metabolic panel (CMP) was assessed on a Roche Cobas analyzer with 15 specimens that spanned a large portion of the analytical measurement range. RESULTS Incubation with 1% Triton X-100 for 5 min was sufficient to completely inactivate EBOV and YFV spiked into plasma but did not completely inactivate CHIKV infectivity even after 60 min of incubation. This was true only for CHIKV when spiked into plasma; CHIKV was completely inactivated in cell culture medium. A bias of -0.78 mmol/L (95% CI, -2.41 to 0.85) was observed for CO2 and 5.79 U/L (95% CI, -0.05 to 11.63) was observed for aspartate aminotransferase after addition of Triton X-100. No other components of the CMP were affected by the addition of Triton X-100. CONCLUSIONS Detergent-based inactivation of plasma specimens may be a viable approach to mitigating the risk that certain blood-borne pathogens pose to laboratory workers in an outbreak setting. However, the effectiveness of this method for inactivation may depend on the specimen type and pathogen in question.
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Affiliation(s)
- Adam L Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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Farnsworth CW, Wallace MA, Liu A, Gronowski AM, Burnham CAD, Yarbrough ML. Evaluation of the Risk of Laboratory Microbial Contamination during Routine Testing in Automated Clinical Chemistry and Microbiology Laboratories. Clin Chem 2021; 66:1190-1199. [PMID: 32870987 DOI: 10.1093/clinchem/hvaa128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/20/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Every clinical specimen is potentially infectious, but data regarding risk for contamination of the laboratory environment during routine testing are scarce. We assessed contamination during routine sample analysis in automated clinical chemistry and microbiology laboratories. METHODS A fluorescent marker was applied to specimen container exteriors to assess the impact of gross contamination. Nonpathogenic MS2 virus was added to remnant blood, urine, and ESwab matrices as a biomarker of cross-contamination. Samples were processed and analyzed using Roche Cobas 8100 and ISE, c502, e602, and c702 modules (blood) and BD Kiestra total laboratory automation (blood, urine, ESwabs) over 3 experiments. Fluorescence transfer to laboratory surfaces and personnel was visualized using ultraviolet light. Surfaces were swabbed and assessed for MS2 cross-contamination by RT-PCR. Adherence to standard precautions by laboratory staff was assessed by observation. RESULTS Fluorescence was observed on 49 of 165 (30%) laboratory surfaces and personnel and 21 of 93 (23%) total laboratory automation instruments. Fluorescence transferred most frequently to gloves (31/40), computer accessories (9/18), and specimen loading racks (12/12). None of 123 areas swabbed were positive for MS2. Improper personal protective equipment use occurred at a rate of 0.36 and 0.15 events per staff per hour in the chemistry and microbiology laboratories, respectively. Hand-washing compliance was observed for 61 of 132 (46%) staff members evaluated. CONCLUSIONS Analysis of grossly contaminated specimens on automated chemistry and microbiology equipment elicits a low likelihood of instrument contamination. However, handling contaminated specimen containers can result in contamination of environmental laboratory surfaces, representing a source of risk that is heightened by low adherence to appropriate personal protective equipment.
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Affiliation(s)
| | - Meghan A Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Albert Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Ann M Gronowski
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Melanie L Yarbrough
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
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Genzen JR. Wiping the Slate Clean-Assessing Clinical Laboratory Contamination Risk. Clin Chem 2021; 66:1128-1130. [PMID: 32829408 DOI: 10.1093/clinchem/hvaa161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 11/13/2022]
Affiliation(s)
- Jonathan R Genzen
- Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT.,ARUP Laboratories, Salt Lake City, UT
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Bailey AL, Anderson N. Risks of requiring a dedicated molecular specimen for HIV diagnosis and a potential strategy for mitigation. PLoS One 2020; 15:e0237580. [PMID: 32790740 PMCID: PMC7425950 DOI: 10.1371/journal.pone.0237580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/30/2020] [Indexed: 11/18/2022] Open
Abstract
Background HIV screening (i.e. antigen/antibody) tests are followed by a supplemental (i.e. antibody-only) if the screen is positive. Discrepant results can result from two scenarios: a false-positive screening test or acute HIV infection. These scenarios can be distinguished by a molecular HIV test, but due to contamination concerns, our laboratory recently implemented a policy requiring a second specimen dedicated for molecular HIV testing. Our objective was to (1) characterize the effect of this policy on the time-to-diagnosis for patients with discrepant screening and supplemental test results, and (2) explore “strength of positivity” as an interim predictor of screening test accuracy while awaiting confirmatory test results. Methods Data from our laboratory information system, electronic health record, and instrument logs were used to collate data for all HIV testing performed at Barnes-Jewish Hospital (BJH) between January 1, 2014 and October 18, 2017. Results Requiring a dedicated specimen for molecular testing significantly increased the time-to-diagnosis for patients with discrepant screening and supplemental HIV tests (p = 0.0084). This policy also contributed to loss-to-followup, with 0/35 discrepant cases lost-to-followup prior to policy implementation compared to 2/10 after implementation. However, by optimizing the signal-to-cutoff (S/CO) ratio of the screening test, we were able to more accurately distinguish false-positives from acute-HIV prior to molecular testing (sensitivity of 100%, specificity of 89%). Conclusions We propose utilizing quantitative fourth-generation assay results (S/CO) ratios as a predictor of infection true positivity in situations where the screening assay is reactive but the supplemental test is negative and confirmatory molecular results are not immediately available.
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Affiliation(s)
- Adam L. Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Neil Anderson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
- * E-mail:
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Nolte FS. Distributed Model for Molecular Diagnostics. Clin Chem 2019; 66:clinchem.2019.304634. [PMID: 31719036 DOI: 10.1373/clinchem.2019.304634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/02/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Frederick S Nolte
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC.
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Greninger AL, Naccache SN. Metagenomics to Assist in the Diagnosis of Bloodstream Infection. J Appl Lab Med 2018; 3:643-653. [PMID: 31639732 DOI: 10.1373/jalm.2018.026120] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has emerged as a promising technology that enables pan-pathogen detection from any source. However, clinical utility and practical integration into the clinical microbiology work flow and a bloodstream infection detection algorithm are currently uncharted. In the context of bloodstream infections, the challenges associated with blood culture, including sensitivity, postantibiotic treatment, attaining sufficient volumes sufficient volumes, and turnaround time, are well-known. Molecular assays have helped expedite turnaround time, especially when performed directly from positive culture media bottles. mNGS offers an unbiased but more complex version of molecular testing directly from sample, but it is unclear how and if it should be implemented in the clinical microbiology laboratory today. CONTENT Here we map out the potential utility and application of mNGS tests to infectious disease diagnostics from blood sources, including intrinsic limitations of the methodology in diagnosing bloodstream infections and sepsis vs DNAemia, current barriers to integration into routine workup, and milestones that may need to be met before implementation. SUMMARY Polymerases and pores move faster than bugs divide, so the thermodynamics of mNGS adoption for bloodstream infection is favorable. Nonetheless, considerable activation barriers exist that will slow this likely diagnostic transition. We eagerly await the manufacturer who designs an integrated sample-to-answer box to do for mNGS what has been done for other aspects of molecular detection.
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Affiliation(s)
| | - Samia N Naccache
- Department of Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
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Frequency of Instrument, Environment, and Laboratory Technologist Contamination during Routine Diagnostic Testing of Infectious Specimens. J Clin Microbiol 2018; 56:JCM.00225-18. [PMID: 29563204 DOI: 10.1128/jcm.00225-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/14/2018] [Indexed: 02/03/2023] Open
Abstract
Laboratory testing to support the care of patients with highly infectious diseases may pose a risk for laboratory workers. However, data on the risk of virus transmission during routine laboratory testing conducted using standard personal protective equipment (PPE) are sparse. Our objective was to measure laboratory contamination during routine analysis of patient specimens. Remnant specimens were spiked with the nonpathogenic bacteriophage MS2 at 1.0 × 107 PFU/ml, and contamination was assessed using reverse transcriptase PCR (RT-PCR) for MS2. Specimen containers were exteriorly coated with a fluorescent powder to enable the visualization of gross contamination using UV light. Testing was performed by two experienced laboratory technologists using standard laboratory PPE and sample-to-answer instrumentation. Fluorescence was noted on the gloves, bare hands, and laboratory coat cuffs of the laboratory technologist in 36/36 (100%), 13/36 (36%), and 4/36 (11%) tests performed, respectively. Fluorescence was observed in the biosafety cabinet (BSC) in 8/36 (22%) tests, on test cartridges/devices in 14/32 (44%) tests, and on testing accessory items in 29/32 (91%) tests. Fluorescence was not observed on or in laboratory instrumentation or adjacent surfaces. In contrast to fluorescence detection, MS2 detection was infrequent (3/286 instances [1%]) and occurred during test setup for the FilmArray instrument and on FilmArray accessory equipment. The information from this study may provide opportunities for the improvement of clinical laboratory safety practices so as to reduce the risk of pathogen transmission to laboratory workers.
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Elmasry S, Wadhwa S, Bang BR, Cook L, Chopra S, Kanel G, Kim B, Harper T, Feng Z, Jerome KR, Kahn JA, Saito T. Detection of Occult Hepatitis C Virus Infection in Patients Who Achieved a Sustained Virologic Response to Direct-Acting Antiviral Agents for Recurrent Infection After Liver Transplantation. Gastroenterology 2017; 152:550-553.e8. [PMID: 27838287 PMCID: PMC5285320 DOI: 10.1053/j.gastro.2016.11.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 12/16/2022]
Abstract
Occult infection with hepatitis C virus (HCV) is defined as the presence of the HCV genome in either liver tissue or peripheral blood monocytes, despite constant negative results from tests for HCV RNA in serum. We investigated whether patients who maintained a sustained virologic response 12 weeks after therapy (SVR12) with direct-acting antiviral (DAA) agents for recurrent HCV infection after liver transplantation had occult HCV infections. We performed a prospective study of 134 patients with recurrent HCV infection after liver transplantation who were treated with DAAs, with or without ribavirin, from 2014 through 2016 (129 patients achieved an SVR12). In >10% of the patients who achieved SVR12 (n = 14), serum levels of aminotransferases did not normalize during or after DAA therapy, or they normalized transiently but then increased sharply after DAA therapy. Of these 14 patients, 9 were assessed for occult HCV infection by reverse transcription quantitative polymerase chain reaction. This analysis revealed that 55% of these patients (n = 5) had an occult infection, with the detection of negative strand viral genome, indicating viral replication. These findings indicate the presence of occult HCV infection in some patients with abnormal levels of serum aminotransferases, despite SVR12 to DAAs for HCV infection after liver transplantation.
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Affiliation(s)
- Sandra Elmasry
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Sanya Wadhwa
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Bo-Ram Bang
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Linda Cook
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, Washington; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Shefali Chopra
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gary Kanel
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Brian Kim
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Tammy Harper
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zongdi Feng
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Keith R Jerome
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, Washington; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jeffrey A Kahn
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California.
| | - Takeshi Saito
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California; Molecular Microbiology and Immunology, University of Southern California, Research Center for Liver Diseases, Los Angeles, California.
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Zakowski J. Bloodborne Pathogen Contamination on Laboratory Automation Systems. Clin Chem 2016; 62:1276-7. [DOI: 10.1373/clinchem.2016.260307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Gonzalez MD, Burnham CAD. Can't Touch This! Contamination of Laboratory Equipment with Bloodborne Pathogens. Clin Chem 2016; 62:910-2. [PMID: 27197678 DOI: 10.1373/clinchem.2016.258715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 04/26/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Mark D Gonzalez
- Department of Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, GA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO.
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