Interim proposal for collecting and handling of microbiology specimens from patients with COVID‐19 in general hospitals

SARS-CoV-2 infections have an increased risk of developing severe disease and a variety of secondary bacterial or fungal infections, and the types of microbiology testing of specimens vary accordingly. A standardized process of specimen collection and handling contributes to the correct diagnosis and treatment of patients with COVID-19. Accurate pathogenic testing is essential for early diagnosis and precise treatment of COVID-19, and correct specimen collection and handling is vital for accurate diagnosis [1]. With the continuing mutations, the pathogenicity of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gradually decreased, so the management of COVID-19 in China has been downgraded to Class B (http://www.nhc.gov.cn). Infections with different SARS-CoV-2 variants produce variable clinical manifestations, and the types of specimens vary accordingly [2]. The purpose of developing this guideline was to standardize the process of specimen collection and handling for microbiological testing from patients with confirmed or suspected COVID-19 to avoid incorrect diagnosis and treatment. The SARS-CoV-2 Omicron variant has become the predominant variant circulating globally [1, 3-7] and has a strong immune-evasion ability and short incubation period; the Omicron variant is thus more infectious than previous variants but produces less severe infections. Omicron causes clinical symptoms primarily related to the upper respiratory tract, such as cough, throat pain, and fever [8-10]. However, individuals with underlying conditions and advanced age who are infected with Omicron have an increased risk of developing severe disease and secondary bacterial or fungal infections [11-13]. As the number of patients with severe infections admitted to general hospitals increases and the types of specimens become more diverse than those during the past 3 years, standardization of microbiological specimen collection and processing procedures has become crucial for healthcare providers. Biosafety: Clinical specimen collection and initial processing can be handled at biosafety shelter laboratory-2 (BSL2) using Standard Precautions (N95 mask, cap, double-gloving, and disposable gown). Goggles and face shields are recommended during procedures likely to generate splashes or sprays of body fluids. It is vital for the laboratory staff to have a site-specific risk assessment in place. Healthcare workers are recommended to follow the standard precautions for different types of specimen collection. For a diagnosis of COVID-19, it is recommended to obtain an upper respiratory tract sample (e.g., nasopharyngeal or oropharyngeal swabs). A lower sampling of sputum or broncho-alveolar lavage (BAL) is suggested for patients with signs/symptoms of lower respiratory tract infection, such as cough and expectoration. Induced sputum should be avoided because of aerosol generation, potentially putting healthcare providers and others at an increased risk of pathogen exposure and infection [14]. Specimens should be collected before administration of antibiotics. In general, examining cultures of specimens from sterile sites, especially blood cultures, has a higher clinical value for the detection of bacteria and fungi. If only one specimen is collected for multiple microbiological testing, it should be divided into multiple sterile containers and packed into sealed bags to reduce the possibility of contamination caused by sub-packaging operations in the laboratory. If specimens need to be dispensed in the laboratory, a strict aseptic technique should be used in a BSL2 biological safety cabinet to prevent contamination. Specimens must be labeled completely and accurately (e.g., patient name, age, gender, testing purpose, sampling time) to ensure that the laboratory can accurately identify the specimen. If a specimen needs to be transported, it should be triple packed following the transportation requirements of class A or B infectious substances [14]. A respiratory tract specimen is recommended for diagnostic testing of COVID-19. Before sampling, please contact a laboratory to confirm the acceptable type of specimens and follow the manufacturer's instructions for specimen collection. Sterile swabs should be used for the collection of upper respiratory tract specimens. Note that nasopharyngeal and oropharyngeal specimens are unsuitable for self-sampling [15]. Use synthetic fiber swabs with thin plastic shafts designed for sampling the nasopharyngeal mucosa. Although an oropharyngeal specimen is acceptable, a nasopharyngeal specimen is preferred for sampling. If both specimens are collected, place them in one tube to increase test sensitivity [15]. Tilt the head of the patient back at 70° and gently insert a swab through the nostril parallel to the palate until resistance is encountered, indicating contact with the nasopharynx. Then, gently rub and roll the swab and leave the swab in place for several seconds to absorb secretions. Finally, slowly remove the swab while rotating it and then place it into the provided transport tube. Insert the swab into the posterior pharynx and tonsillar areas, and then rub the swab over both the tonsillar pillars and posterior oropharynx. Avoid touching the tongue, teeth, or gums. Place the swab into the transport tube provided. Saliva specimens (1–5 mL) should be self-collected into a sterile container by patients according to the healthcare provider's instructions. The collection of specimens other than sputum from the lower respiratory tract may be limited to patients presenting with more severe disease, including those admitted to the hospital and/or fatal cases. A physician should generally collect specimens using professional equipment and precautions at BSL2. Specimens (2–3 mL) should be placed in a sterile container. Nonrespiratory specimens include blood, peritoneal fluid, pleural fluid, cerebrospinal fluid, and other sterile body fluids, for example, urine and feces. PPE should be used following BSL2 recommendations. After the antisepsis of the sampling site, blood or sterile body fluid specimens were taken into a vacutainer, blood culture vial, or sterile cup. If an injection is needed, it should be performed slowly and carefully to avoid generating aerosols. The surface of the container should be disinfected by spraying with 75% alcohol. Under the guidance of medical staff, the patient should wash the vulva thoroughly and then collect the clean-voided midstream urine into a sterile cup. The surface of the container should be disinfected by spraying with 75%. The container should be placed in a sealed bag for transport. Under the guidance of medical staff, the patient should place feces specimens into a sterile cup with a specimen size of at least the size of soybeans. The surface of the container should be disinfected by spraying with 75% alcohol. The container should be placed in a sealed bag for transport. Upon collection, specimens should be packed in a Biosafety Transport Box and delivered to the microbiology laboratory as promptly as possible. In principle, all specimens should be delivered within 2 h of being collected. Moreover, appropriate transport temperatures should be used depending on the purpose of testing. If a delay in testing or storage is expected, the specimens can generally be stored at 2–8°C. The blood culture vials should be stored at room temperature. However, specimens for Streptococcus pneumoniae and Neisseria gonorrhoeae detection should be kept at warmer temperatures. Any specimen sent to the laboratory should be free of external contamination, tightly sealed, and placed in a biohazard bag for transportation. According to the management of Class II highly pathogenic microorganisms, the biosafety and biosecurity of such specimens should follow the Regulations on the Bio-safety Management of Pathogenic Microbe Labs and the Regulations on Transport Management for Bacterial (Viral) Strains of Highly Pathogenic Microorganisms or Specimens Capable of Infecting Human (MOH Decree No. 45) and other relevant requirements. The specimen carrier should use a 75% alcohol spray on the surface of the specimen transport box. Opening the specimen transport box is prohibited during transportation. Before receiving the specimen, the surface of the biosafety transport box should be disinfected by spraying with 75% alcohol. A qualified specimen is critical for testing. Any specimens unacceptable for processing should be rejected, and new specimens should be collected whenever possible. When specimens are rejected, the patient's caregiver should be contacted to explain the reason for rejection and request a replacement specimen of acceptable quality (Table 1). In specimen processing, it is essential to pay attention to biosafety and formulate the corresponding processing process according to the type of specimen and diagnostic procedures (Table 2, Figure 1). Flow diagram showing the process of microbiology specimen collection and handling in COVID-19 patients. Collected specimens should be stored in an appropriate environment if they cannot be processed on time (Table 3). The correct collection and processing of specimens is key to clinical testing, and timely and accurate testing reports can assist clinical diagnosis of diseases and provide adequate guidance to precise treatment and rational drug use [ [1, 16]]. More importantly, during the COVID-19 pandemic, efficient and accurate testing results are helpful for accurate prognosis of the disease, and early intervention can prevent the disease from developing from mild cases to severe and critical cases, thus protecting the lives and health of patients [17-19]. Therefore, healthcare providers in general hospitals at all levels should understand and follow specimen collection and processing guidance, follow standard precautions and perform testing in strict accordance with the guidelines. Zhaofang Jiang and Shan Chen: writing the original draft; Jiayao Qu and Houming Liu: information retrieval; Siyuan Liu and Tao Hong: English writing and polishing; Yi-Wei Tang: making writing suggestions; Jiuxin Qu and Hongzhou Lu: providing writing ideas as corresponding authors. None. Professor Hongzhou Lu and Yi-wei Tang are the members of the iLABMED Editorial Board. To minimize bias, they were excluded from all editorial decision-making related to the acceptance of this article for publication. The remaining authors declare no conflicts of interest. Not applicable. Not applicable. Data sharing is not applicable to this article as no data sets were generated or analyzed during the current study.