Since the outbreak of coronavirus disease 2019, hospital laboratories have become an important place for testing all kinds of specimens of patients with suspected or confirmed coronavirus disease 2019. There may be a high load of severe acute respiratory syndrome coronavirus 2 in clinical specimens of confirmed patients, and the biosafety risk is high, so it poses a challenge to the hospital laboratory testing process. This paper compares the microbial pre-processing, culture, identification and drug sensitivity analysis of the traditional clinical microbial detection process and the fully automated microbial pipeline, expounds the biosafety risks of the traditional manual detection process of pathogenic microorganisms in the epidemic situation, and discusses the role and dilemma of the fully automated microbial pipeline in the biosafety assurance of the epidemic situation. The purpose is to provide a basis for the promotion of fully automated microbial pipeline in the future.
Whipple’s disease is a multisystemic disease caused by Tropheryma (T.) whipplei that primarily affects the gastrointestinal tract. In literature, T. whipplei can also cause pulmonary infections. The detection of T. whipplei depends on nucleic acid-based test. With the application of next-generation sequencing (NGS), cases with T. whipplei detected from respiratory tract samples by NGS are increasingly found but there is lack of recognized diagnostic criteria for these cases. Within the context, we propose a grading diagnostic scheme for the situation that T. whipplei is detected from respiratory tract samples, based on clinical experience and diagnostic thinking, and referring to the international classifications of invasive fungal infections. The scheme comprises five levels: confirmed, probable, possible, impossible, and excluded. There were 26 such cases from West China Hospital of Sichuan University and we used our diagnostic scheme to define probable in 6 cases, possible in 9 cases, impossible in 8 cases, and excluded in 3 cases. Based on this, we also propose specific suggestions for sample collection and testing, patient management, and further research directions. These recommendations are preliminary based on the existing cases from West China Hospital of Sichuan University and therefore needs to be verified, modified, optimized, and even reconstructed when more clinical evidence and further clinical studies become available.
Objective To investigate antimicrobial resistance profiles of carbapenem-resistant Enterobacter spp. (CREn) and the bactericidal effects of aztreonam combined with avibactam. Methods The CREn strains isolated from the West China Hospital of Sichuan University between 2016 and 2021 were identified by gyrB gene amplification and subsequent sequencing. The drug sensitivity results, sample types and distribution of relevant patient departments of these strains were summarized. Colistin-resistant and -intermediate strains were selected to carry out the bactericidal test of colistin and aztreonam combined with avibactam. Results A total of 110 clinical strains of CREn were included. The most common strain was Enterobacter xiangfangensis (91 strains), the highest proportion was in the intensive care unit (27.27%), and the proportion of respiratory tract samples was more than 40%. The antimicrobial sensitivity results showed that CREns were all resistant to carbapenems, the resistance rate to colistin was 23.64%, and the resistance rate to aztreonam combined with avibactam was 0. Among other antimicrobial agents, the antimicrobial resistance rate of amikacin and tigecycline were less than 10%. The time-kill curve showed that for colistin-intermediate strains, colistin could achieve bactericidal effect in a shorter time than aztreonam combined with avibactam. However, whether the strain was resistant to colistin or not, the bactericidal rate of 2 μg/mL aztreonam combined with avibactam in 24 hours could exceed 99%. Conclusion CREn is resistant to most commonly used clinical antibacterial drugs, but remains sensitive to aztreonam combined with avibactam, and aztreonam combined with avibactam has bactericidal effect on it.