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Little is known about Subgenomic RNA (sgRNA) dynamics in patients with Coronavirus diseases 2019 (COVID-19). We collected 147 throat swabs, 74 gut swabs and 46 plasma samples from 117 COVID-19 patients recruited in the LOTUS China trial (ChiCTR2000029308) and compared E and orf7a sgRNA load in patients with different illness duration, outcome, and comorbidities. Both sgRNAs were detected in all the three types of samples, with longest duration of 25, 13, and 17 days for E sgRNA, and 32, 28, and 17 days for orf7a sgRNA in throat, gut, and plasma, respectively. A total of 95% (57/60) of patients had no E sgRNA detected after 10 days post treatment, though 86% of them were still E RNA positive. High correlation on titer was observed between sgRNA encoding E and orf7a gene. sgRNA showed similar variation in the standard care and Lopinavir-Ritonavir group. Patients with diabetes and heart diseases showed higher pharyngeal E sgRNA at the first day (P ​= ​0.016 and 0.013, respectively) but no difference at five days after treatment, compared with patients without such commodities. Patients with hypertension and cerebrovascular diseases showed no difference in the pharyngeal sgRNA levels at both one and five days after treatment, compared with patients without these two commodities. E sgRNA levels in the initial infection showed no correlation with the serum antibody against spike, nucleoprotein, and receptor binding domains at ten days later. sgRNA lasted a long period in COVID-19 patients and might have little effect on humoral response.

Nocardia spp. is a pathogen responsible for a variety of clinical infections, ranging from skin and soft tissue infections, to the respiratory tract and central nervous system infections. Its epidemiological characteristics, including species distribution, clinical features, and antimicrobial susceptibility profiles, should be under surveillance for the prevention and treatment of nocardiosis. In the present study, over a 9-year period (from 2009 to 2017), 53 non-repetitive Nocardia isolates were collected from 8 tertiary general hospitals of 7 cities in China. These isolates were identified to species level by multilocus sequence analysis(MLSA). The clinical data were also reviewed. The susceptibilities to 10 commonly-used antibiotics for Nocardia were determined by E-test stripes, and the resistance rates, MIC50 and MIC90 to each antibiotic by different species were analyzed. Of 53 Nocardia isolates, N. farcinica was the most common species (24.5%, 13/53), followed by N. cyriacigeorgica (20.8%, 11/53), N. terpenica (15.1%, 8/53), N. abscessus (9.43%, 5/53), N. otitidiscaviarum (7.55%, 4/53), respectively. Furthermore, 31 Nocardia (58.5%) isolates were recovered from lower respiratory tract (sputum and BALF), 15 (28.3%) from superficial Infection, 3 (5.7%) from pleural effusion, 2 (3.8%) from CSF, and 1 from bone marrow and 1 from synovial fluid, respectively. The antibiotic resistance profiles varied between different Nocardia species. All Nocardia isolates were susceptible to linezolid, followed by imipenem and amikacin (both 92.5% susceptibility rate). N. terpenica, rarely documented elsewhere, showed a different antimicrobial susceptibility profile. In summary, herein, the clinical and antibiotic resistance features of Nocardia species reported would be helpful for understanding the diversity of Nocardia species circulating in China and for decision making in the context of empiric therapy.

Background: The diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming. Methods: We enrolled 292 consecutively hospitalized patients suspected to have LRI between November 2018 and June 2019 in a single-center, prospective cohort study. Rapid clinical metagenomics test was performed on-site, and the results were compared with those of routine microbiology tests and evaluated for potential clinical benefit. Results: 171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRI. The turn around-time (from sample registration to result) for the rapid metagenomics test was 6.4 ± 1.4 hours, compared to 94.8 ± 34.9 hours for routine culture. Compared with culture and real-time PCR tests, rapid metagenomics achieved 96.6% sensitivity and 88.0% specificity and identified pathogens in 63 out of 161 (39.1%) culture-negative samples. Correlation of anaerobes enrichment with lung abscess was demonstrated as 38 anaerobic species failed in culture but identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture. Conclusions: Rapid clinical metagenomics test increased pathogen detection yield in the diagnosis of LRI. Empirical antimicrobial therapy could be de-escalated if rapid metagenomics test results were hypothetically applied to clinical management. Funding: The funder of the study had no role in study design, data collection,data analysis, data interpretation, or writing of the report. The corresponding authors had full access to all the data in the study and had final responsibility for the decision to submit for publication. Declaration of Interest: None to declare Ethical Approval: The study was carried out in China-Japan Friendship Hospital, Beijing, China. Ethical approval was obtained from the China-Japan Friendship Hospital Ethics Committee(2018-145-k102). All subjects provided written consents.

Group B streptococcus (GBS) is an increasing pathogen threat to newborns and adults with immunodepressive diseases. Here, a total of 193 GBS, including 51 invasive and 142 noninvasive isolates, were collected from the patients with infections in 7 tertiary hospitals from 5 cities in China during the year 2008 to 2015. The strains of GBS were characterized by classical and molecular techniques for capsular polysaccharide serotyping, genes for pilus island (PI) and α-like protein (alp), and antibiotic resistance profiling. Of 193 isolates, the predominant serotypes were III (45.6%) and Ia (18.7%). All strains carried at least 1 PI gene. The combination of PI-2b and PI-1 was present in 46.1% isolates, followed by PI-2a alone (80, 41.5%) and PI-2b alone (23, 11.9%). The most prevalent alp gene was rib (87, 45.1%), followed by α-C (47, 24.4%), ε (33, 17.1%), alp2/3 (7, 3.6%) and alp4 (2, 1.0%), respectively. The clonal relationships between strains were investigated using multilocus sequence typing. The strains were distinguished into 26 individual sequence typing, and further clustered into 6 clonal complexes. A significant association was noted between the distributions of alp genes, serotyping and PI profiles, such as serotype III-rib-PI+PI-2a, Ib-α-C, and Ia-ε-PI-2a. No penicillin-resistant strains were detected, and 74.1%, 64.2%, and 68.9% were resistant to erythromycin, clindamycin, and tetracycline, respectively. The infective GBS isolates in China demonstrated epidemical features.

Background: Many unnecessary antibiotics are prescribed to patients with viral lower respiratory tract infections (LRTIs). The FilmArray® Respiratory Panel is a new molecular point-of-care testing (POCT) procedure, which provides faster and comprehensive identification of viruses and atypical pathogens. But whether POCT could potentially help optimize antibiotics use for LRTIs remains a controversial topic. Methods: In this single-center, open-label, randomized controlled study, hospitalized adult patients diagnosed with community-acquired pneumonia, acute exacerbation of chronic obstructive pulmonary disease, or acute exacerbation of bronchiectasis were enrolled in the study. Patients were randomly assigned to the POCT group or the routine real-time PCR assays (control) group. The primary outcome was the duration of intravenous antibiotics used during hospitalization. The secondary outcomes included the length of hospital stay and the total cost of hospitalization. We also evaluated the effects of a combination of viral testing with serum procalcitonin (PCT) levels on the duration of antibiotic use. Findings: Between October 2017 and July 2018, 761 eligible patients were enrolled (383 in the POCT group and 378 in the control group). The positive rates of virus and atypical pathogens in the POCT group was 31·7% (121/383) compared with 17·2% (32/378) in the control group (difference 14·5%, 95% CI 7·3% to 21·6%; P = 0·0003). The median duration of intravenous antibiotics in the POCT group was significantly shorter than that in the control group (7·0 days [IQR, 5·0, 9·0] in the POCT group vs 8·0 [IQR, 6·0, 11·0] days in the control group; mean difference -1·6 days, 95% CI -2·2 to -1·0 days; P < 0·0001). The median length of hospital stay of patients in the POCT group was significantly shorter than that in the control group (8·0 days [IQR, 6·0, 10·0] in the POCT group vs 9·0 days [IQR, 7·0, 12·0] in the control group; mean difference -1·1 days, 95% CI -1·7 to -0·5 days; P < 0·0001). The median cost of hospitalization was significantly lower in the POCT group ($1,761·1 [IQR, 1,261·1, 2581·3] in the POCT group vs $2,017·3 [IQR, 1,442·9, 2,894·3] in the control group). Furthermore, the median duration of intravenous antibiotic treatment was significantly shorter and the median cost of hospitalization was significantly lower in patients with a positive FilmArray Respiratory Panel test result and PCT < 0·25 ng/mL compared with a negative FilmArray test result and PCT ≥ 0·25 ng/mL (6·0 days [IQR, 4·5, 7·5] vs 7·0 days [IQR, 6·0, 10·5]; mean difference 2·3 days, 95% CI 0·6 to 4·0 days; P = 0·0079 and $1,374·6 [IQR, 1,034·2, 1991·7] vs $1,939·6 [IQR, 1,307·6, 2,955·7]). Interpretation: The use of POCT testing for respiratory viruses and atypical pathogens could help to optimize antibiotic use and improve clinical outcomes in hospitalized LRTI patients. Clinical Trial Number: clinicaltrials.gov Identifier: NCT03391076. Funding Statement: National Science Grant for Distinguished Young Scholars (81425001/H0104) Declaration of Interests: We declare that we have no competing interests. Ethics Approval Statement: The study was approved by the Ethics Committee of CJFH. Written informed consent was obtained from each participant before data collection.

SummaryBacteraemia due to non-O1/non-O139 Vibrio cholerae is rarely documented in mainland China. We report such a case in a 70-year-old male with type 2 diabetes mellitus. The clinical features, phenotypic analyses, and presence of a panel of known virulence genes in the isolated strain are described. To the best of our knowledge, this is the first reported case of bacteraemia due to this strain in a T2DM patient without other coexisting underlying diseases in mainland China.