The COVID-19 pandemic has caused an unprecedented global public health and economy crisis. The origin and emergence of its causal agent, SARS-CoV-2, in the human population remains mysterious, although bat and pangolin were proposed to be the natural reservoirs. Strikingly, comparing to the SARS-CoV-2-like CoVs identified in bats and pangolins, SARS-CoV-2 harbors a polybasic furin cleavage site in its spike (S) glycoprotein. SARS-CoV-2 uses human ACE2 as its receptor to infect cells. Receptor recognition by the S protein is the major determinant of host range, tissue tropism, and pathogenesis of coronaviruses. In an effort to search for the potential intermediate or amplifying animal hosts of SARS-CoV-2, we examined receptor activity of ACE2 from 14 mammal species and found that ACE2 from multiple species can support the infectious entry of lentiviral particles pseudotyped with the wild-type or furin cleavage site deficient S protein of SARS-CoV-2. ACE2 of human/rhesus monkey and rat/mouse exhibited the highest and lowest receptor activity, respectively. Among the remaining species, ACE2 from rabbit and pangolin strongly bound to the S1 subunit of SARS-CoV-2 S protein and efficiently supported the pseudotyped virus infection. These findings have important implications for understanding potential natural reservoirs, zoonotic transmission, human-to-animal transmission, and use of animal models. IMPORTANCE SARS-CoV-2 uses human ACE2 as primary receptor for host cell entry. Viral entry mediated by the interaction of ACE2 with spike protein largely determines host range and is the major constraint to interspecies transmission. We examined the receptor activity of 14 ACE2 orthologues and found that wild type and mutant SARS-CoV-2 lacking the furin cleavage site in S protein could utilize ACE2 from a broad range of animal species to enter host cells. These results have important implications in the natural hosts, interspecies transmission, animal models and molecular basis of receptor binding for SARS-CoV-2.

Bacterial pathogens impose a heavy health burden worldwide. In the new era of high-throughput sequencing and online bioinformatics, real-time genome typing of infecting agents, and in particular those with potential severe clinical outcomes, holds promise for guiding clinical care to limit the detrimental effects of infections and to prevent potential local or global outbreaks. Here, we sequenced and compared 85 isolates of Streptococcus suis, a zoonotic human and swine pathogen, wherein we analyzed 32 recognized serotypes and 75 sequence types representing the diversity of the species and the human clinical isolates with high public health significance. We found that 1,077 of the 2,469 genes are shared by all isolates. Excluding 201 common but mobile genes, 876 genes were defined as the minimum core genome (MCG) of the species. Of 190,894 single-nucleotide polymorphisms (SNPs) identified, 58,501 were located in the MCG genes and were referred to as MCG SNPs. A population structure analysis of these MCG SNPs classified the 85 isolates into seven MCG groups, of which MCG group 1 includes all isolates from human infections and outbreaks. Our MCG typing system for S. suis provided a clear separation of groups containing human-associated isolates from those containing animal-associated isolates. It also separated the group containing outbreak isolates, including those causing life-threatening streptococcal toxic shock-like syndrome, from sporadic or less severe meningitis or bacteremia-only isolates. The typing system facilitates the application of genome data to the fields of clinical medicine and epidemiology and to the surveillance of S. suis. The MCG groups may also be used as the taxonomical units of S. suis to define bacterial subpopulations with the potential to cause severe clinical infections and large-scale outbreaks.

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BackgroundAlthough the Bacillus Calmette-Guérin (BCG) vaccine against tuberculosis (TB) has been available for more than 75 years, one third of the world's population is still infected with Mycobacterium tuberculosis and approximately 2 million people die of TB every year. To reduce this immense TB burden, a clearer understanding of the functional genes underlying the action of BCG and the development of new vaccines are urgently needed.Methods and FindingsComparative genomic analysis of 19 M. tuberculosis complex strains showed that BCG strains underwent repeated human manipulation, had higher region of deletion rates than those of natural M. tuberculosis strains, and lost several essential components such as T-cell epitopes. A total of 188 BCG strain T-cell epitopes were lost to various degrees. The non-virulent BCG Tokyo strain, which has the largest number of T-cell epitopes (359), lost 124. Here we propose that BCG strain protection variability results from different epitopes. This study is the first to present BCG as a model organism for genetics research. BCG strains have a very well-documented history and now detailed genome information. Genome comparison revealed the selection process of BCG strains under human manipulation (1908–1966).ConclusionsOur results revealed the cause of BCG vaccine strain protection variability at the genome level and supported the hypothesis that the restoration of lost BCG Tokyo epitopes is a useful future vaccine development strategy. Furthermore, these detailed BCG vaccine genome investigation results will be useful in microbial genetics, microbial engineering and other research fields.

Vibrio fluvialis is an emerging foodborne pathogen of increasing public health concern. The mechanism(s) that contribute to the bacterial survival and disease are still poorly understood. In other bacterial species, type VI secretion systems (T6SSs) are known to contribute to bacterial pathogenicity by exerting toxic effects on host cells or competing bacterial species. In this study, we characterized the genetic organization and prevalence of two T6SS gene clusters (VflT6SS1 and VflT6SS2) in V. fluvialis. VflT6SS2 harbors three “orphan” hcp-vgrG modules and was more prevalent than VflT6SS1 in our isolates. We showed that VflT6SS2 is functionally active under low (25°C) and warm (30°C) temperatures by detecting the secretion of a T6SS substrate, Hcp. This finding suggests that VflT6SS2 may play an important role in the survival of the bacterium in the aquatic environment. The secretion of Hcp is growth phase-dependent and occurs in a narrow range of the growth phase (OD600 from 1.0 to 2.0). Osmolarity also regulates the function of VflT6SS2, as evidenced by our finding that increasing salinity (from 170 to 855 mM of NaCl) and exposure to high osmolarity KCl, sucrose, trehalose, or mannitol (equivalent to 340 mM of NaCl) induced significant secretion of Hcp under growth at 30°C. Furthermore, we found that although VflT6SS2 was inactive at a higher temperature (37°C), it became activated at this temperature if higher salinity conditions were present (from 513 to 855 mM of NaCl), indicating that it may be able to function under certain conditions in the infected host. Finally, we showed that the functional expression of VflT6SS2 is associated with anti-bacterial activity. This activity is Hcp-dependent and requires vasH, a transcriptional regulator of T6SS. In sum, our study demonstrates that VflT6SS2 provides V. fluvialis with an enhanced competitive fitness in the marine environment, and its activity is regulated by environmental signals, such as temperature and osmolarity.

Kinesin family member C1 (KIFC1, also known as HSET) is a minus end-directed motor protein, which is critical in centrosome clustering. The present study investigated the expression of KIFC1 in paired hepatocellular carcinoma (HCC) tissues and adjacent non-cancerous tissues from 91 patients by immunohistochemical analysis; clinical data were concomitantly collected. KIFC1 was expressed at high levels in HCC tissues, compared with that in peritumoral tissues (54.9 vs. 14.3%; P<0.01), and its expression correlated with tumor emboli, metastasis, recurrence and time of recurrence. Kaplan-Meier analysis showed that the expression of KIFC1 was significantly associated with tumor-free survival rates. In addition, multivariate analyses revealed that the overexpression of KIFC1was an independent predictive marker in patients with HCC. Consistently, data derived from GEPIA was in agreement with the results. In vitro, KIFC1 knockdown effectively decreased HCC cell viability, and induced apoptosis and cell death. KIFC1 knockdown also significantly suppressed tumor cell migration and invasion in vitro. Mechanistically, the apoptosis-related protein, B-cell lymphoma-2 (Bcl-2), was downregulated in KIFC1 small interfering RNA-treated groups, whereas thee levels of Bcl-2-associated X protein and p53 were upregulated. In addition, the expression levels of phosphorylated phosphoinositide 3-kinase and phosphorylated AKT were decreased significantly when KIFC1 was silenced. The epithelial-mesenchymal transition-related proteins, N-cadherin, matrix metalloproteinase-2 (MMP-2), β-catenin, Slug, and Zinc finger E-box-binding homeobox 1, were downregulated, whereas the expression of E-cadherin was upregulated. The overexpression of KIFC1 was correlated closely with the progression of HCC and poor prognosis, and suggested that the expression levels of KIFC1 are a potential prognostic biomarker and therapeutic target in HCC.

The plasmid-mediated high-level tigecycline resistance gene, tet (X4), was detected in seven Escherichia coli isolates from pork in two Chinese provinces. Two isolates belonged to the epidemic spreading sequence type ST101. Tet (X4) was adjacent to IS Vsa3 and concurrent with floR in all seven isolates. In addition to IncFIB, the replicon IncFII was found to be linked to tet (X4). This report follows a recent detection of tet (X3)/(X4) in E. coli from animals and humans in China.

Background: The survival benefit of postoperative adjuvant transcatheter arterial chemoembolization (PA-TACE) remained controversial. We aimed to investigate the prognosis effect of PA-TACE on the Barcelona Clinic Liver Cancer (BCLC) early stage multinodular hepatocellular carcinoma (MHCC) patients with/without microvascular invasion (MVI). Methods: Two hundred and seventy-one patients from January 2010 to December 2014 undergoing curative hepatectomy were included in this study. Disease-free survival (DFS) rates and overall survival (OS) rates as well as prognostic factors were analyzed by the Kaplan-Meier method, the log-rank test and the Cox proportional hazard model. Results: Thirty-four point four percent (44/128) MVI positive and 55.2% (79/143) MVI negative patients underwent PA-TACE. Multivariate analysis revealed that HBV DNA load >10 3 copy/mL, >three tumors, MVI, and without PA-TACE were independent risk factors for poor DFS. Higher alkaline phosphatase (ALP), three tumors, MVI, and without PA-TACE were independent risk factors for poor OS. Both DFS and OS were significantly improved in patients with MVI who received PA-TACE as compared to those who underwent hepatic resection alone (5-year DFS, 26.3% vs. 20.7%, P=0.038; 5-year OS, 73.6% vs.