Management of bacteriological specimens of patients suffering from coronavirus disease 2019 (COVID-19)

Abstract

Since 31st December 2019, and as of 29th September 2020, 5 011 669 cases of coronavirus disease 2019 (COVID-19) have been reported in Europe (worldwide 33 423 469, including 1 002 678 deaths). In Germany, 287 421 cases and 9471 deaths have been recorded [[1]https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-casesGoogle Scholar]. COVID-19 presents as a mild to severe disease, and the outcome is potentially fatal [[2]https://www.who.int/csr/don/12-january-2020-novel-coronavirus-china/en/Google Scholar,[3]Wang Y. Li X. Ren L. Zhao J. Hu Y. Zhang L. et al.Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.Lancet. 2020; 395: 497-506https://doi.org/10.1016/S0140-6736(20)30183-5Abstract Full Text Full Text PDF PubMed Scopus (27324) Google Scholar]. The course of infection might be complicated by nosocomial infections (e.g. ventilator-associated pneumonia, sepsis, etc.), eventually caused by multidrug-resistant organisms (MDRO). Timely and coordinated microbiological diagnostics are crucial to ensure the best medical treatment for patients suffering from COVID-19. In contrast to PCR-based virus diagnostics, where samples containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are routinely inactivated (e.g. by heat or detergents), microbiology samples remain untreated to allow subsequent bacterial culture. Therefore, microbiology staff may have a relevant risk of exposure. Specific hands-on protocols are currently not available, as only general biosafety recommendations for the laboratory handling of SARS-CoV-2-positive samples exist [4Iwen P.C. Stiles K.L. Pentella M.A. Safety considerations in the laboratory testing of specimens suspected or known to contain the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).Lab Med. 2020; 51: 239-242https://doi.org/10.1093/labmed/lmaa018Crossref PubMed Scopus (7) Google Scholar, 5World Health OrganizationLaboratory biosafety guidance related to coronavirus disease 2019 (COVID-19): interim guidance. World Health Organization, 2020https://apps.who.int/iris/handle/10665/331138 License: CC BY-NC-SA 3.0 IGOGoogle Scholar, 6https://www.cdc.gov/coronavirus/2019-ncov/lab/lab-biosafety-guidelines.htmlGoogle Scholar, 7https://www.ecdc.europa.eu/en/novel-coronavirus/laboratory-supportGoogle Scholar]. Here, we report on the set-up of a diagnostic approach to provide microbiological algorithms for patients with suspected or confirmed COVID-19. Our experiences are based on 100 patients presenting between 26th March and 4th May 2020. We established a bacteriological workflow that ensures both high throughput and high-quality microbiological diagnostics for COVID-19 patients with maximum staff safety. Microbiology laboratories process a variety of human specimens—such as blood, serum, stool, urine, respiratory secretions, and tissue biopsies—that potentially contain a broad spectrum of infective biological agents. Laboratories should therefore follow standard practices (e.g. decontamination of work surfaces, hand hygiene etc.) and (national) guidelines for laboratory biosafety. Recently, the World Health Organization (WHO), Centers for Disease Control (CDC), and the European Centre for Disease Control (ECDC) released interim recommendations for the laboratory handling of SARS-CoV-2-positive samples [4Iwen P.C. Stiles K.L. Pentella M.A. Safety considerations in the laboratory testing of specimens suspected or known to contain the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).Lab Med. 2020; 51: 239-242https://doi.org/10.1093/labmed/lmaa018Crossref PubMed Scopus (7) Google Scholar, 5World Health OrganizationLaboratory biosafety guidance related to coronavirus disease 2019 (COVID-19): interim guidance. World Health Organization, 2020https://apps.who.int/iris/handle/10665/331138 License: CC BY-NC-SA 3.0 IGOGoogle Scholar, 6https://www.cdc.gov/coronavirus/2019-ncov/lab/lab-biosafety-guidelines.htmlGoogle Scholar, 7https://www.ecdc.europa.eu/en/novel-coronavirus/laboratory-supportGoogle Scholar]. In Germany, the Technical Rules for Biological Agents (TRBA) and the German Quality Standards for the Microbiological Diagnosis of Infectious Diseases (MiQ) reflect the state of technology and occupational hygiene regarding the handling of biological agents [8Technical Rules for Biological Agents (TRBA). 100 Protective measures for specific and non-specific activities involving biological agents in laboratories GMBl. 21. 2007: 434http://www.baua.de/nn_14914/de/Themen-von-A-Z/Biologische-Arbeitsstoffe/TRBA/pdf/TRBA-100.pdfGoogle Scholar, 9Mikrobiologisch-infektiologische Qualitätsstandards (MiQ)MiQ 20: sicherheit im mikrobiologisch-diagnostischem Labor Teil 1.3-437-22616-9 Elsevier GmbH, 2005Google Scholar, 10Mikrobiologisch-infektiologische Qualitätsstandards (MiQ)MiQ 21: sicherheit im mikrobiologisch-diagnostischem Labor Teil 2.3-437-22626-6 Elsevier GmbH, 2005Google Scholar]. Further, the German Committee on Biological Agents (Ausschuss für biologische Arbeitsstoffe, ABAS) establishes several safety rules and adapts them to the current state of development (https://www.baua.de/EN/Home/Home_node.html). The German Biological Agents Ordinance (Biostoffverordnung) governs the classification of biological agents into risk groups 1–4 (in accordance with the EU-wide classification due to directive 2000/54/EC) and the corresponding protection levels 1–4 [[11]Ordinance on safety and health protection at workplaces involving biological agents (biological agents ordinance - BioStoffV) of 15 july 2013 (federal law gazette [BGBl.] Part I p. 2514), last amended by article 146 of the law of 29 March 2017 (federal law gazette I p. 626).Google Scholar,[12]Directive 2000/54/EC of the European Parliament and of the Council of 18 September 2000 on the protection of workers from risks related to exposure to biological agents at work.https://osha.europa.eu/de/legislation/directives/exposure-to-biological-agents/77Google Scholar]. TRBA 100 specifies protective measures for activities involving biological agents in laboratories by differentiating specific and unspecific activities. Examples for specific activities are the handling of a biological agent that is known by species (e.g. propagation of a bacterial culture or a virus by cell culture). The processing of a primary patient specimen in the microbiological laboratory typically falls into the unspecific activity category. TRBA 462 applies to the classification of viruses. The protection levels typically meet the risk group of the biological agent. The Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-1 and SARS-CoV-2 are labelled as biosafety level 3 (BSL-3) agents. They cause disease which may be fatal, are easily transmitted by an airborne route, and consequently require protection level 3 standards. On 27th March 2020 the German ABAS clarified that the unspecific handling of respiratory samples for the detection of SARS-CoV-2 is possible under BSL-2 standards, requiring a BSL-2 cabinet, a laboratory coat and, potentially, gloves, while FFP2 mask and safety glasses are only recommended [[13]Beschluss 1/2020 des ABAS vom 27.3. 2020https://www.baua.de/DE/Aufgaben/Geschaeftsfuehrung-von-Ausschuessen/ABAS/pdf/SARS-CoV-2.pdf?__blob=publicationFile&v=3Google Scholar]. Of note, this resolution by ABAS does not address the spectrum of microbiology laboratories that handle hundreds of specimens of various origins per day, with the majority of samples being processed by culture-based techniques that by nature do not allow sample inactivation. Thus, microbiologists are obliged to independently perform a site-specific (what infrastructure is available?) and activity-specific (what kind of specimen is being handled and which tests are being applied?) risk assessment and to define a detailed workflow applicable 7 days/week for the processing of SARS-CoV-2-positive samples. In this context we reviewed the potential infection risk (reflected by the viral load) by type of specimen according to current knowledge (Table 1). Furthermore, we evaluated the spectrum of microbiological samples of the first 100 patients hospitalized at the University hospital Frankfurt due to confirmed or highly suspected COVID 19 (Fig. 1). MDRO screening samples accounted for 35% of all specimens. The majority of the clinical microbiology samples (n = 337; 27%) were blood cultures with a negligible laboratory risk of SARS-CoV-2 laboratory infection. Frequently, respiratory samples were submitted to the laboratory (n = 205; 17%).Table 1Source-specific risk assessment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity of microbiological samples from patients suffering from coronavirus disease 2019 (COVID-19)Clinical specimenRT-PCRaPercentage of positive samples (total number of tested samples), reference.% (n); referenceVirus load (copies/mL)Bronchoalveolar lavage93% (14), [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]<2.6 × 104 bMean cycle value threshold value of 30 (<2.6 × 104 copies/mL) [16].Sputum72% (104), [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]<2.6 × 104100% (18), [[19]Corman C.M. Rabenau H.F. Adams O. Oberle D. Funk M.B. Keller-Stanislawski B. et al.SARS-CoV-2 asymptomatic and symptomatic patients and risk for transfusion transmission.Transfusion. 2020; https://doi.org/10.1111/trf.15841Crossref PubMed Scopus (64) Google Scholar]2.36 × 102Nasal swab/nasopharyngeal swab100% (1), [[20]Holshue M.L. DeBolt C. Lindquist S. Lofy K.H. Wiesman J. Bruce H. et al.First case of 2019 novel coronavirus in the United States.N Engl J Med. 2020; 382: 929-936Crossref PubMed Scopus (3691) Google Scholar]CT values of 18–2063% (8, nasal), [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]1.4 × 106 cMean cycle value threshold value of 24.3 (1.4 × 106 copies/mL) [16].Oropharyngeal swab100% (1), [[20]Holshue M.L. DeBolt C. Lindquist S. Lofy K.H. Wiesman J. Bruce H. et al.First case of 2019 novel coronavirus in the United States.N Engl J Med. 2020; 382: 929-936Crossref PubMed Scopus (3691) Google Scholar]CT values of 23–2432% (398, pharyngeal), [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]<2.6 × 10478% (9), [[21]Peng L. Liu J. Xu W. Luo Q. Chen D. Lei Z. et al.SARS-CoV-2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens.J Med Virol. 2020; https://doi.org/10.1101/2020.02.21.20026179Crossref Scopus (0) Google Scholar]4.56 × 102 to 6.77 × 10453.3% (15, oral), [[22]Zhang W. Du R.H. Li B. Zheng X.S. Yang X.L. Hu B. et al.Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes.Emerg Microbe. Infect. 2020; 9: 386-389https://doi.org/10.1080/22221751.2020.1729071Crossref PubMed Scopus (1169) Google Scholar]NAUrine0% (72), [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]NA0% (18), [[23]To K.K.-W. Tsang O.T.-Y. Leung W.-S. Tam A.R. Wu T.-C. Lung D.C. et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.Lancet Infect Dis. 2020; https://doi.org/10.1016/S1473-3099(20)30196-1Abstract Full Text Full Text PDF PubMed Scopus (2049) Google Scholar]NA11% (9), [[21]Peng L. Liu J. Xu W. Luo Q. Chen D. Lei Z. et al.SARS-CoV-2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens.J Med Virol. 2020; https://doi.org/10.1101/2020.02.21.20026179Crossref Scopus (0) Google Scholar]3.22 × 102Stool100% (1), [[20]Holshue M.L. DeBolt C. Lindquist S. Lofy K.H. Wiesman J. Bruce H. et al.First case of 2019 novel coronavirus in the United States.N Engl J Med. 2020; 382: 929-936Crossref PubMed Scopus (3691) Google Scholar]CT values of 36–3829% (153), [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]<2.6 × 10453% (17), [[24]Pan Y. Zhang D. Yang P. Poon L.L.M. Wang Q. Viral load of SARS-CoV-2 in clinical samples.Lancet Infect Dis. 2020; 20: 411-412https://doi.org/10.1016/S1473-3099(20)30113-4Abstract Full Text Full Text PDF PubMed Scopus (1004) Google Scholar]550 to 1.21 × 10553.42% (73), [[25]Xiao F. Meiwen T. Zheng X. Liu Y. Li X. Hong Shan H. Evidence for gastrointestinal infection of SARS-CoV-2.Gastroenterology. 2020; 158: 1831-1833https://doi.org/10.1101/2020.02.17.20023721Abstract Full Text Full Text PDF PubMed Scopus (1685) Google Scholar]NAAnal/rectal swab22% (9), [[21]Peng L. Liu J. Xu W. Luo Q. Chen D. Lei Z. et al.SARS-CoV-2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens.J Med Virol. 2020; https://doi.org/10.1101/2020.02.21.20026179Crossref Scopus (0) Google Scholar]4.47 × 102 to 5.42 × 10438% (8, severe disease), [[23]To K.K.-W. Tsang O.T.-Y. Leung W.-S. Tam A.R. Wu T.-C. Lung D.C. et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.Lancet Infect Dis. 2020; https://doi.org/10.1016/S1473-3099(20)30196-1Abstract Full Text Full Text PDF PubMed Scopus (2049) Google Scholar]NA14% (7, mild disease), [[23]To K.K.-W. Tsang O.T.-Y. Leung W.-S. Tam A.R. Wu T.-C. Lung D.C. et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.Lancet Infect Dis. 2020; https://doi.org/10.1016/S1473-3099(20)30196-1Abstract Full Text Full Text PDF PubMed Scopus (2049) Google Scholar]NA26.7% (15), [[22]Zhang W. Du R.H. Li B. Zheng X.S. Yang X.L. Hu B. et al.Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes.Emerg Microbe. Infect. 2020; 9: 386-389https://doi.org/10.1080/22221751.2020.1729071Crossref PubMed Scopus (1169) Google Scholar]NASerum20% (15), [[22]Zhang W. Du R.H. Li B. Zheng X.S. Yang X.L. Hu B. et al.Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes.Emerg Microbe. Infect. 2020; 9: 386-389https://doi.org/10.1080/22221751.2020.1729071Crossref PubMed Scopus (1169) Google Scholar]NA17% (6), [[26]Chan J.F. Yuan S. Kok K.H. To K.K.W. Chu H. Yang J. et al.A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster.Lancet. 2020; 395: 514-23https://doi.org/10.1016/S0140-6736(20)30154-9Abstract Full Text Full Text PDF Scopus (5402) Google Scholar]NAPlasma15% (41, plasma), [[27]Huang C. Wang Y. Li X. Ren L. Zhao J. Hu Y. et al.Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.Lancet. 2020; 395: 497-506Abstract Full Text Full Text PDF PubMed Scopus (12195) Google Scholar]NA5.6% (18), [[19]Corman C.M. Rabenau H.F. Adams O. Oberle D. Funk M.B. Keller-Stanislawski B. et al.SARS-CoV-2 asymptomatic and symptomatic patients and risk for transfusion transmission.Transfusion. 2020; https://doi.org/10.1111/trf.15841Crossref PubMed Scopus (64) Google Scholar]1.79 × 102Blood1% (307), [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]<2.6 × 10422% (9), [[21]Peng L. Liu J. Xu W. Luo Q. Chen D. Lei Z. et al.SARS-CoV-2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens.J Med Virol. 2020; https://doi.org/10.1101/2020.02.21.20026179Crossref Scopus (0) Google Scholar]9.11 × 10−1 to 8.04 × 10030% (10, severe disease), [[23]To K.K.-W. Tsang O.T.-Y. Leung W.-S. Tam A.R. Wu T.-C. Lung D.C. et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.Lancet Infect Dis. 2020; https://doi.org/10.1016/S1473-3099(20)30196-1Abstract Full Text Full Text PDF PubMed Scopus (2049) Google Scholar]NA15% (13, mild disease), [[23]To K.K.-W. Tsang O.T.-Y. Leung W.-S. Tam A.R. Wu T.-C. Lung D.C. et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.Lancet Infect Dis. 2020; https://doi.org/10.1016/S1473-3099(20)30196-1Abstract Full Text Full Text PDF PubMed Scopus (2049) Google Scholar]NA40% (15), [[22]Zhang W. Du R.H. Li B. Zheng X.S. Yang X.L. Hu B. et al.Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes.Emerg Microbe. Infect. 2020; 9: 386-389https://doi.org/10.1080/22221751.2020.1729071Crossref PubMed Scopus (1169) Google Scholar]NASaliva (oropharyngeal)50% (8, severe disease), [[23]To K.K.-W. Tsang O.T.-Y. Leung W.-S. Tam A.R. Wu T.-C. Lung D.C. et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.Lancet Infect Dis. 2020; https://doi.org/10.1016/S1473-3099(20)30196-1Abstract Full Text Full Text PDF PubMed Scopus (2049) Google Scholar]5 × 102 (median)23% (13, mild disease), [[23]To K.K.-W. Tsang O.T.-Y. Leung W.-S. Tam A.R. Wu T.-C. Lung D.C. et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.Lancet Infect Dis. 2020; https://doi.org/10.1016/S1473-3099(20)30196-1Abstract Full Text Full Text PDF PubMed Scopus (2049) Google Scholar]Conjunctival swab1.5 % (67), [[28]Zhou Y. Zeng Y. Tong Y. Chen C. Ophthalmologic evidence against the interpersonal transmission of 2019 novel coronavirus through conjunctiva.medRxiv. 2020; 2: 20021956https://doi.org/10.1101/2020.02.11.20021956Crossref Scopus (0) Google Scholar]NANA, not available.a Percentage of positive samples (total number of tested samples), reference.b Mean cycle value threshold value of 30 (<2.6 × 104 copies/mL) [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar].c Mean cycle value threshold value of 24.3 (1.4 × 106 copies/mL) [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]. Open table in a new tab NA, not available. Of note, the available reports on SARS-CoV-2 positivity and the viral load for different specimens are heterogeneous and highly dependent on disease stage. To allow a more precise assessment of specimen infectivity, studies on viral shedding need to be improved [[14]Yang L. Yan L.M. Wan L. Xiang T.X. Le A. Liu J.M. et al.Viral dynamics in mild and severe cases of COVID-19.Lancet Infect Dis. 2020; 20: e79https://doi.org/10.1016/S1473-3099(20)30224-3Abstract Full Text Full Text PDF Scopus (1) Google Scholar]. Most data rely on the detection of viral RNA. Studies determining the level of live virus are very rare, and cover only a very low number of patients, e.g. from throat swabs (n = 2 [[15]Hoehl S. Rabenau H. Berger A. Kortenbusch M. Cinatl J. Bojkova D. et al.Evidence of SARS-CoV-2 infection in returning travelers from Wuhan, China.N Engl J Med. 2020; 382: 1278-1280Crossref PubMed Scopus (373) Google Scholar]) or stool (n = 4 [[16]Wang W. Xu Y. Gao R. Lu R. Han K. Wu G. et al.Detection of SARS-CoV-2 in different types of clinical specimens.JAMA. 2020; 323: 1843-1844PubMed Google Scholar]). However, among available studies there is a clear trend that respiratory secretions contain the highest viral load, while that of serum or plasma [[17]Chang L. Yan Y. Wang L. Coronavirus disease 2019: coronaviruses and blood safety.Transfus Med Rev. 2020; Crossref PubMed Scopus (404) Google Scholar] is very low or even undetectable (Table 1). Respiratory secretions of patients with severe disease are proven to contain significantly higher viral loads than those of patients with mild disease. Viral RNA may also be detected in stool samples (for even longer than in respiratory samples) but typically not from urine [[18]Zheng S. Fan J. Yu F. Feng B. Lou B. Zou Q. et al.Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January–March 2020: retrospective cohort study.BMJ Clin Res. 2020; 369: m1443https://doi.org/10.1136/bmj.m1443Crossref PubMed Scopus (918) Google Scholar]. Thus, respiratory samples from patients with COVID-19 in particular are assessed as potentially infective. Microbiological routine laboratories handle human specimens in a ‘containment level 2 laboratory’ with standard protection measurements. This includes the use of personal protective equipment (PPE) such as laboratory coats, gloves and protective eyewear (both risk-adapted) and safety cabinets for activities with aerosol formation (such as quantitative plating of respiratory secretions). Routine laboratory procedures such as hand disinfection, decontamination of work surfaces and management of laboratory waste represent additional mandatory laboratory safety aspects. In contrast, containment level 3 represents an increased safety level (e.g. limited access, airlock, air filtration, autoclave on site, negative pressure area, safety cabinets) [[11]Ordinance on safety and health protection at workplaces involving biological agents (biological agents ordinance - BioStoffV) of 15 july 2013 (federal law gazette [BGBl.] Part I p. 2514), last amended by article 146 of the law of 29 March 2017 (federal law gazette I p. 626).Google Scholar]. In the case of SARS-CoV-2, reports on viral kinetics and the positivity rate and viral load of clinical specimens are highly heterogeneous (Table 1). The processing of respiratory secretions (with high numbers of infective SARS-CoV-2 virus particles) poses the highest risk to microbiological staff and needs to be specifically addressed in terms of laboratory safety. Due to the risk of aerosol formation, respiratory secretions are generally handled in safety cabinets in microbiology laboratories, ensuring a high level of protection for staff. However, non-respiratory specimens such as blood/serum or stool cannot simply be categorized as ‘generally non-infectious’ due to the fact that small amounts of virus/RNA may be present (Table 1). The relevance of viral shedding with non-respiratory samples for person-to-person transmission of SARS-CoV-2 is still not known. Examples of routine microbiology laboratory specimens and corresponding procedures are listed in Table 2.Table 2Microbiology laboratory coronavirus disease 2019 (COVID-19) specimens and corresponding procedures (as applied at Frankfurt University Hospital). Sample can be routinely processed under BSL-2 conditions. A site-specific risk analysis should be performed in accordance with available laboratory facilitiesSpecimenTarget test/techniqueRisk assessment aRegarding SARS-CoV-2 exposure.MeasurementsbSafety level can be adjusted to standard safety precautions if robust data on the source specific risk is available (see Table 1).Respiratory secretions-bronchoalveolar lavage (BAL)-bronchial secretion-tracheal secretion-sputumMicroscopy/Gram stain (remark: dispensable procedure)(Quantitative) microbiology culture-inoculation of media-plating of serial dilutionsELISA/immunochromatographic assay target: galactomannan antigenLow (slide preparation) (none after heat or ethanol fixation)High (high viral load/risk of aerosol formation)BSL-3 containment cIf available on site/ensuring room separation of high-risk sample processing and the reduction in laboratory staff to a minimum (laboratory coat, hand disinfection, decontamination of work surfaces included). plus-BSL-2 cabinet-FFP-2 mask, gloves-protective glassesThroat/nasal swabsMicrobiology culture (MDRO screening)Inoculation of mediaLow (very low risk of aerosol formation when using agar-based swabs)Medium (low risk of aerosol formation when using liquid-based swabs)BSL-2 containment plus-BSL-2 cabinet-FFP-2 mask, gloves-protective glasses (optional)BiopsiesTissue aspiratesPuncturesMicrobiology culture-Specimen homogenization-Inoculation of mediaHigh (if specimen originates from the respiratory tract)Low (if specimen does not originate from the respiratory tract)BSL-2 containment plus-BSL-2 cabinet-FFP-2 mask, gloves-protective glasses (optional)Blood culturesMicrobiology culture-Subculture from blood-culture bottlesNone/minimal (no SARS-CoV-2 content)BSL-2 containment plus-BSL-2 cabinet-gloves (standard precautions independent of SARS-CoV-2)Urine(Quantitative) microbiology culture-inoculation/plating of mediaImmunochromatographic assays target:Legionella antigenPneumococcal antigenMinimal (low risk of aerosol formation/no or only very low SARS-CoV-2 content)BSL-2 containment plus-BSL-2 cabinet-FFP-2 mask, gloves-protective glasses (optional)StoolMicrobiology culture-Inoculation of mediaImmunochromatographic assays target:Clostridioides difficile GDHC. difficile toxinLow (low risk of aerosol formation/no or only low SARS-CoV-2 content)BSL-2 containment plus-BSL-2 cabinet-FFP-2 mask, gloves-protective glasses (optional)Rectal swabMicrobiology culture (MDRO screening)-Inoculation of mediaLow(very low risk of aerosol formation when using agar-based swabs)(low risk of aerosol formation when using liquid-based swabs/no or only low SARS-CoV-2 content)BSL-2 containment plus-BSL-2 cabinet-FFP-2 mask, gloves-protective glasses (optional)SerumSpecific antibody detectionELISA target:Legionella spp.Mycoplasma spp.Chlamydia spp.None/minimal (no or very low SARS-CoV-2 content)BSL-2 containment plus-glovesMDRO, multidrug-resistant organism.a Regarding SARS-CoV-2 exposure.b Safety level can be adjusted to standard safety precautions if robust data on the source specific risk is available (see Table 1).c If available on site/ensuring room separation of high-risk sample processing and the reduction in laboratory staff to a minimum (laboratory coat, hand disinfection, decontamination of work surfaces included). Open table in a new tab MDRO, multidrug-resistant organism. While the primary processing of specimens from COVID-19 patients warrants special attention with regard to safety precautions, the processing of bacterial and/or fungal cultures, inactivated specimens, or the handling of extracted DNA requires standard safety precautions. Generally, inoculated agar plates can be processed under routine laboratory conditions (BSL-2). The correct labelling of specimens from COVID-19 patients is of particular importance in order to guide these specimens in the appropriate workflow. Our experience is that adherence of clinical staff in labelling SARS-CoV-2-confirmed samples (e.g. ‘COV+’) in a pandemic situation is limited. Therefore, definite target sample identification in a routine laboratory setting is not practicable. Thus, assessing all samples from wards treating COVID-19 positive patients as ‘COV+’ is the easiest way to identify SARS-CoV-2-positive samples, although there might not be 100% coverage. Given this workflow (Fig. 2), we set up the following measures. First, in order to separate the processing of respiratory COV + secretions with the highest risk of aerosol formation from other specimens we decided to process these samples in our BSL-3 laboratory by defined staff members (‘COV + team’) in accordance with recommendations of the ABAS (room separation of sample procession/reduction of laboratory staff to a minimum; Fig. 3). Second, the use of gloves, a daily-replaced individual coat, and daily-replaced individual FFP-2 mask and eye protection supplemented the processing of all respiratory samples even from COV– wards (performed under a biosafety cabinet in our BSL-2 laboratory). Furthermore, only a defined number of well-trained staff carried out sample work-up. Third, for additional or follow-up diagnostics, SARS-CoV-2-positive respiratory samples were separately stored for 72 h in a sealed safety box in the BSL-3 laboratory to prevent accidental staff exposure. Fourth, the laboratory test repertoire was replaced by easy-to-process (even under a BSL-2 cabinet) point-of-care test (POCT) devices whenever possible. This includes immunochromatographic tests instead of enzyme-linked immunosorbent assays—e.g. for the detection of glutamate dehydrogenase (GDH) antigen and A/B toxins of Clostridioides difficile from faecal specimens or the detection of Legionella pneumophila and Streptococcus pneumoniae antigens from urine samples—to avoid aerosol formation (Table 2). This was established in the light of the high SARS-CoV-2 viral loads in respiratory samples of COVID-19 patients (see above), our function as a regional centre treating a high number of patients, and the imminent risk of a ‘routine-related’ reduction in attentiveness. No procedure resulted in a significantly increased workload. In conclusion, due to the non-inactivated nature of clinical specimens, the emergence of SARS-CoV-2 results in a number of laboratory safety challenges to a clinical microbiology laboratory. Risk assessment of the laboratory work and implementation of appropriate risk control measures are important to guarantee the safety of the laboratory staff as well as the optimal processing of diagnostic specimens. Although we decided to process samples of COVID-19 patients under BSL-3 conditions, this is not a general recommendation from us. In our setting, this algorithm proved to be practicable and increased the staff's attention. A dedicated room for processing respiratory samples under BSL-2 conditions might also improve staff safety. BSL-3 safety standards are only recommended for specific handling procedures such as viral cultures. Moreover, we are not aware of any reports on laboratory infections or contaminations with SARS-CoV-2 due to the handling of positive samples under BSL-2 conditions. It has to be realized that an outbreak scenario in a diagnostic laboratory leads to severe constraints in a hospital's diagnostic capacity, as described recently [[29]Opperman C.J. Marais G.J.K. Naidoo M. Hsiao M. Samodien N. Response to a cluster of severe acute respiratory syndrome coronavirus 2 cases at a diagnostic laboratory.Afr J Lab Med. 2020; 9: 1307https://doi.org/10.4102/ajlm.v9i1.1307.eCollection2020Crossref PubMed Google Scholar], even if the primary source of the infection (staff, patient sample) might not be identified. Therefore, and in addition to the laboratory safety procedures given above, several other measures should be implemented to avoid interpersonal laboratory-associated infections. We decided that all staff must (a) wear surgical masks all through the day, and (b) indicate illness or contact with known COVID-19 patients resulting in quarantine (under the responsibility of the occupational health physicians). Moreover, the space between the laboratory working stations was increased to >1.5 meters, and finally (and perhaps most importantly) social behaviour (breakfast break, lunch break, coffee break etc.) was restructured to minimize interpersonal contact (e.g. non-overlapping breaks, etc.). The COVID-19 pandemic is a global threat and poses a particular challenge to diagnostic laboratories. During treatment of hospitalized COVID-19 patients, clinical microbiology laboratories are faced with the processing of diverse specimens confirmed or at least suspected to contain SARS-CoV-2. Based on the high infectivity of SARS-CoV-2, its interim classification as a biosafety level 3 pathogen, and the fact that inactivation procedures are not feasible in microbiology, precise algorithms for the performance of microbiological diagnostics need to be set up. As SARS-CoV-2 specimens can be handled in BSL-2 facilities, laboratories may individually adapt their workflow. Our approach may represent a blueprint for clinical microbiology diagnostic laboratories to examine their workflow in the presence of emerging highly virulent pathogens. No ethics approval is needed for this description of a laboratory workflow. Conceptualization: MH and VAJK. Data analysis: SB, LV, SG, TW, DV, DH, JS, VI. Writing original draft: MH, SB, TW, VK. Writing, review and editing: MH, VK. The authors have no competing interests to disclose. This work was partially funded by the state of Hesse, Germany (Hessisches Universitäres Kompetenzzentrum Krankenhaushygiene (HuKKH; VAJK)). We thank all clinical and laboratory staff involved in the care of SARS-CoV-2-positive patients. We also thank in particular the following technicians and doctors: R. Raeder, C. Joly, C. Manten, K. Krauß, and H. Juling.