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The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had severe consequences for health and the global economy. To control the transmission, there is an urgent demand for early diagnosis and treatment in the general population. In the present study, an automatic system for SARS-CoV-2 diagnosis is designed and built to deliver high specification, high sensitivity, and high throughput with minimal workforce involvement. The system, set up with cross-priming amplification (CPA) rather than conventional reverse transcription-polymerase chain reaction (RT-PCR), was evaluated using more than 1000 real-world samples for direct comparison. This fully automated robotic system performed SARS‐CoV‐2 nucleic acid-based diagnosis with 192 samples in under 180 min at 100 copies per reaction in a “specimen in data out” manner. This throughput translates to a daily screening capacity of 800–1000 in an assembly-line manner with limited workforce involvement. The sensitivity of this device could be further improved using a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based assay, which opens the door to mixed samples, potentially include SARS-CoV-2 variants screening in extensively scaled testing for fighting COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s00449-021-02674-9.

Non-specific symptoms and low viremia levels make early diagnosis of dengue virus (DENV) infection challenging. This study aimed to i) identify laboratory markers that can be used to predict a DENV-positive diagnosis and ii) perform a molecular characterization of DENVs from the 2014 Guangdong epidemic. This retrospective study analyzed 1,044 patients from the Guangdong epidemic who were clinically suspected cases of dengue. Viral RNA was detected by real-time RT-PCR, and viral-specific NS1 antigen was detected using enzyme-linked immuno sorbent assay. A molecular phylogenetic analysis was performed for the with the DENV C-prM gene junction. Patients with dengue infection had leukopenia (2.8 × 109/L), thrombocytopenia (109.0 × 109/L), elevated aspartate aminotransferase (56.0 IU/L) and alanine aminotransferase (43.5 IU/L), and prolonged activated partial thromboplastin time (APTT, 33.5 s) (all P ＜ 0.001) compared to patients without dengue. The positive predictive value of leukopenia and thrombocytopenia for DENV infection were 96.9% and 93.0%, respectively. Leukopenia, thrombocytopenia, elevated aminotransferases, and prolonged APTT were useful predictive markers for an early diagnosis of DENV infection. Phylogenetic analysis indicated that the DENVs from the 2014 epidemic were closely related to a 2010 New Delhi strain and a 2013 Guangzhou strain. The 2014 epidemic consisted of co-circulating DENV-1 genotypes I and V from multiple origins. Efficient dengue surveillance can facilitate rapid response to future outbreaks.

Background Hepatocellular carcinoma (HCC) is the fifth most prevalent cancer and the second leading cause of cancer-related deaths worldwide. The poor prognosis of HCC is mainly because of its discovery at advanced stages. Because chronic hepatitis B (CHB) accounts for 50–80% HCC occurrence worldwide, and immunity is regarded as an emerging hallmark of cancer, we investigated the predictive role of peripheral immune cells in HCC incidence in CHB patients. Methods This investigation collected and analyzed data from 89 CHB patients, 94 primary HCC patients with hepatitis B virus (HBV), 81 primary HCC patients without HBV, 69 normal healthy patients, and 257 CHB patients with at least 3-year regular followup. Results The results demonstrated that CHB and primary HCC patients had different concentrations of lymphocytes, neutrophils, and monocytes in their peripheral circulation. Further study showed that the peripheral lymphocyte concentration was an independent prognostic factor for HCC incidence in CHB patients during the 3 years of followup. Finally, a predictive HCC incidence model with an AUROC (area under the receiver operating characteristic) of 0.832 was constructed based on the peripheral lymphocyte concentration, serum alpha-fetoprotein (AFP) concentration, and cirrhosis status of CHB patients. Conclusions The peripheral lymphocyte concentration was an independent prognostic factor for HCC incidence in CHB patients, and a more accurate predictive model based on peripheral lymphocytes, serum AFP, and cirrhosis status was constructed.

Background: Helicobacter pylori (H. pylori) infection is one of the most risk factors for gastric cancer. More than 80 % of H. pylori infection was demonstrated as asymptomatic infection. Vitamin D was recently found to play important roles in many diseases including infectious disease and cancer. While the level of vitamin D in asymptomatic H. pylori infection was rarely reported, so we investigated serum vitamin D concentration in asymptomatic H. pylori infection in this study. Methods: Data for 3567 people were collected and analyzed, 182 of whom were identified as asymptomatic H. pylori infection without any other disease. H. pylori infectionstatus was determined by carbon-13 urea breath test. Serum 25-hydroxyvitamin D, was detected with ELISA. Periphery leukocyte, neutrophile and lymphocyte frequencies were detected with standard automated clinical methodologies. Results: No significant different serum 25-hydroxyvitamin D concentration was found between asymptomatic H .pylori infection patients and normal healthy control. Asymptomatic H. pylori infection patients had significantly higher periphery leukocyte and neutrophile frequencies than those in normal healthy control. Conclusion: Asymptomatic H. pylori infection status did not influence the concentration of circulating vitamin D.

Background Neutrophil to lymphocyte ratio (NLR) was reported to be an independent easy-to-measure marker for many diseases, while the distribution of NLR in healthy population was not formally studied. So we investigated NLR in healthy people in this study. Methods Data include NLR, systolic pressure, diastolic pressure, and body mass index (BMI), which were collected from 3,262 healthy population. Correlations of NLR with variables were analyzed with SPSS16.0. Results Results demonstrated that NLR was positively associated with age (P < 0.001). The eldest age group possessed the highest NLR and the youngest age group had the lowest NLR. NLR was also slightly positively associated with systolic pressure, diastolic pressure, and BMI (P < 0.001). Conclusion Older people possessed relatively high NLR in healthy population.

Agarose gel image of virulence factor genes of partial positive strains in the 62 MRSA isolates. (A ~ M), Virulence factor genes detected by PCR. Marker refers to DNA marker (100 bp ladder); # numbers, isolate number; Sea ~ seo, staphylococcal enterotoxins A ~ O gene; hla, α-hemolysin gene; hlb, β-hemolysin gene; hlg, γ-hemolysin gene; tsst-1,toxic shock syndrome toxin 1 gene; PVL, Panton-Valentine leukocidin gene ; PCR, polymerase chain reaction. (PDF 280 kb)

Genetic relatedness among the 60 MRSA strains. Phylogenetic relationships were obtained by PFGE. Cluster analysis was performed with the software program BioNumerics 5.0 (Maths, Belgium) using the Dice coefficient and the unweighted pair group method(UPGMA). The isolates with the similarity over 75Â % were clustered in patterns. PFGE, pulsed-field gel electrophoresis; CA/HA, community-acquired MRSA or hospital-acquired MRSA; PVL, Panton-Valentine leukocidin gene; SCCmec, staphylococcal cassette chromosome mec; MLST, multilocus sequence typing; +, positive. (PDF 24Â kb)

The antibiotic resistance of 62 methicillin-resistant S. aureus isolates. Table S2. The SCCmec type distribution of CA-MRSA and HA-MRSA. Table S3. MLST type distribution of CA-MRSA and HA-MRSA. Table S4. SCCmec type and MLST type distribution of 62 MRSA isolates. (PDF 202Â kb)

The main aim of this study was to understand the relationship between the drug-resistant characteristics of Klebsiella pneumoniae and CTX-M-type extended spectrum β-lactamases (ESBLs), and to detect the distributions of CTX-M-type ESBLs in clinically isolated strains. CTX-M ESBL genes isolated from the clinical samples were amplified by polymerase chain reaction and identified by sequence analysis; the antibiotic susceptibility of the samples was determined using the Kirby-Bauer disc-diffusion method. One hundred and five strains among the 246 isolated strains of K. pneumoniae tested positive for ESBL production (42.68%); 92 of these produced CTX-M ESBLs. Of the 92 CTX-M ESBL strains, 81 produced CTX-M-1 ESBLs and 11 produced CTX-M-25 ESBLs. Fifty-seven of the CTX-M-1 ESBL- and six of the CTX-M-25 ESBL-producing bacteria had CTX-M ESBL genes that coexisted in the plasmid and chromosome. The Kirby-Bauer antibiotic susceptibility method revealed that CTX-M ESBL-positive strains showed a higher rate of resistance to cefazolin, cefoxitin, cefuroxime, ceftazidime, cefotaxime, aztreonam, levofloxacin, and cotrimoxazole, compared to the CTX-M ESBL-negative strains (P < 0.05). The CTX-M ESBL genes were commonly observed in the K. pneumoniae isolated from respiratory tract samples; these were significantly associated with the drug-resistant characteristics of K. pneumoniae to β-lactam antibiotics.

Background The pathogenic potential and commensal nature of Staphylococcus aureus allows for easy transmission both within and outside of the hospital environment, and nasal carriage may be responsible for some serious infections. This study aimed to determine the molecular and epidemiological characteristics of nasal colonization by S. aureus in community residents (CR) and healthcare workers (HW) at Sun Yat-Sen University, Guangzhou, China. Methods A total of 589 volunteers, both CR (n = 297) and HW (n = 292), were recruited. Each subject completed a questionnaire, and specimens were obtained from the anterior nares for S. aureus screening. Genotypic analysis included pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, and virulence gene detection. Results A total of 138 S. aureus isolates were recovered from separate subjects (23.4 %, 138/589), with four isolates showing methicillin resistance (0.7 %, 4/589). The prevalence of S. aureus carriage was 25.3 % (75/297) in CR and 21.6 % (63/292) in HW. Methicillin-resistant S. aureus (MRSA) were isolated from one CR (0.3 %, 1/297) and three HW (1.0 %, 3/292). The most common risk factors for S. aureus carriage in CR were being male, age ≤ 30 years, and nasal cavity cleaning habits. Having a household member in the healthcare profession was associated with increased risk among HW. Sequence type (ST)188 and ST59 were the most prevalent among the 20 observed STs, accounting for 14.6 % and 12.2 % of all isolates, respectively. The four MRSA isolates presented four different STs, with one isolate carrying a type IVa SCCmec element and the other three isolates containing type III SCCmec. PFGE analysis grouped the 129 isolates into 23 pulsotypes, with profiles A, N, E, L, and O the most prevalent. The Panton-Valentine leucocidin gene (pvl) was identified in two of the 138 isolates, while 57.5 % of isolates carried both the Staphylococcus aureus enterotoxin A (sea) and enterotoxin B (seb) genes. Conclusions These data indicate a low prevalence of nasal MRSA carriage but evidence of molecular heterogeneity among S. aureus isolates from CR and HW at Sun Yat-Sen University, Guangzhou. Differences in epidemiological and molecular characteristics of S. aureus between CR and HW populations may be useful for the understanding and prevention of S. aureus infection. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1032-7) contains supplementary material, which is available to authorized users.

BACKGROUND: Hepatocellular carcinoma (HCC) is the fifth most prevalent cancer and the second leading cause of cancer‐related deaths worldwide. The poor prognosis of HCC is mainly because of its discovery at advanced stages. Because chronic hepatitis B (CHB) accounts for 50–80% HCC occurrence worldwide, and immunity is regarded as an emerging hallmark of cancer, we investigated the predictive role of peripheral immune cells in HCC incidence in CHB patients. METHODS: This investigation collected and analyzed data from 89 CHB patients, 94 primary HCC patients with hepatitis B virus (HBV), 81 primary HCC patients without HBV, 69 normal healthy patients, and 257 CHB patients with at least 3‐year regular followup. RESULTS: The results demonstrated that CHB and primary HCC patients had different concentrations of lymphocytes, neutrophils, and monocytes in their peripheral circulation. Further study showed that the peripheral lymphocyte concentration was an independent prognostic factor for HCC incidence in CHB patients during the 3 years of followup. Finally, a predictive HCC incidence model with an AUROC (area under the receiver operating characteristic) of 0.832 was constructed based on the peripheral lymphocyte concentration, serum alpha‐fetoprotein (AFP) concentration, and cirrhosis status of CHB patients. CONCLUSIONS: The peripheral lymphocyte concentration was an independent prognostic factor for HCC incidence in CHB patients, and a more accurate predictive model based on peripheral lymphocytes, serum AFP, and cirrhosis status was constructed.

Background Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of both hospital and community infections globally. It’s important to illuminate the differences between community-acquired MRSA (CA-MRSA) and hospital-acquired MRSA (HA-MRSA), but there have been confusions on the definition, especially for the MRSA isolates identified within 48 h of admission. This study aimed to determine the molecular characteristics and virulence genes profile of CA and HA-MRSA isolates identified less than 48 h after hospital admission in our region. Methods A total 62 MRSA isolates identified within 48 h after admission and the clinical data were collected. Antimicrobial susceptibility test (AST) of collected isolates were performed according to the guidelines of Clinical and Laboratory Standards Institute (CLSI) 2015, and staphylococcal cassette chromosome mec (SCCmec) typing, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and virulence gene profiling were performed to explore the molecular diversity. Results SCCmec III and sequence type (ST) 239 were the most prevalent SCCmec type and ST in both CA and HA-MRSA groups. HA-MRSA group had higher prevalence of SCCmec III (87.2 %) and ST239 (79.5 %) compared with CA-MRSA (60.9 and 43.4 %, both P