Transcriptome Analysis of Peripheral Blood Mononuclear Cells in SARS-CoV-2 Naïve and Recovered Individuals Vaccinated With Inactivated Vaccine

The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. Herein, we performed serum IgG antibody detection and transcriptomics analysis on 20 SARS-CoV-2 naïve individuals who received multiple doses of inactivated vaccine and 5 SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. Our research revealed the important role of many innate immune pathways after vaccination, identified a significant correlation with the third dose of booster vaccine and proteasome-related genes, and found that SARS-CoV-2 recovered individuals can produces a strong immune response to a single dose of inactivated vaccine. These results help us understand the reaction mechanism of the host's molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.

Genomic diversity of human papillomavirus type 6 from patients with condyloma acuminatum in Eastern China

OBJECTIVE

Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts both men and women. However, there is limited data on its genomic characterization in mainland China. The aim of this study was to understand the complete genomic diversity of HPV6 from patients with condyloma acuminatum (CA) and to explore the prevalence of different variant lineages/sublineages in eastern China.

METHODS

CA samples were collected in 3 hospitals in Shandong Province, China from January 2020 to March 2021. DNA extraction, PCR amplification, Sanger sequencing and sequence assembly were performed on HPV6-positive samples. The complete genomes obtained in this study were analyzed phylogenetically with global HPV6 sequences in GenBank database using MEGA 11.

RESULTS

A total of 55 complete genomic sequences of HPV6 were obtained in this study. They were classified as HPV6 variant lineage A (n = 20), sublineage B1 (n = 34) and sublineage B3 (n = 1) by phylogenetic analysis. Sequence alignment showed E1, E5A, E5B, L1, L2, LCR were relatively highly variable regions for sublineage B1 whereas E1, E5A, L2 for lineage A. Both phylogenetic trees of lineage A and sublineage B1 composed of two main branches. Chinese sequences of lineage A segregated into the major branch while those in sublineage B1 belonged to both branches. Genomic divergence between sequences from China and other countries was 0.00% - 0.33% in lineage A and 0.00% - 0.40% in sublineage B1.

CONCLUSIONS

This is the first study on HPV variant lineages circulating in mainland China. The results revealed that lineage A and sublineage B1 were prevalent and they had different highly variable regions. Further surveillance is needed to understand the dynamic change of different variants in the population.

Prevalence and transmission of mobilized colistin resistance (mcr-1) gene positive Escherichia coli in healthy rural residents in Shandong province, China

This study was conducted to explore the prevalence and transmission of mcr-1 Escherichia coli among healthy rural residents in Shandong, China, and to provide theoretical basis for the prevention and control of spread and treatment of multi-drug resistant Escherichia coli. A total of 218 healthy residents from 3 villages in Guan County, Shandong Province, China were included in this study, and their fecal samples were collected. Colistin-resistant Escherichia coli were selected, and their drug sensitivity and plasmids' transferability were measured. After analysis, some conclusions can be drawn. The colistin-resistant Escherichia coli, most strains of which are MDROs, is common and highly transmissible in healthy residents in rural areas in China. Interventions should be implemented to prevent the spread of colistin-resistant Escherichia coli through health education and tighter regulation of antibiotics.

SARS-CoV-2 Variant of Concern 202 012/01 (B.1.1.7) in a traveller from the UK to China

We report the complete genome of SARS-CoV-2 VOC 202012/01 in a traveler from the United Kingdom to China, representing the first such case in North China. This study highlights that intensive genomic sequencing enables early identification and rapid characterization of the SARS-CoV-2 importing to China.

Epidemiological characteristics and spatial-temporal clusters of hand, foot, and mouth disease in Qingdao City, China, 2013-2018

Background

Hand, foot, and mouth disease (HFMD) has become one of the most important infectious diseases recent years. Qingdao City has suffered from serious HFMD epidemic. This study aimed to describe epidemiological characteristics and investigate spatial-temporal distribution at town level in Qingdao City.

Method

The surveillance data of HFMD during 2013–2018 were collected from the National Notifiable Disease Surveillance System. The global Moran’s I statistic was used to detect the spatial autocorrelation of HFMD cases by ArcGis 10.0 software. Purely spatial and spatial-temporal analysis was used to detect epidemic clusters by SatScan^TM v9.6 software.

Results

The annual average incidence of HFMD cases in Qingdao City from 2013 to 2018 was 123.16 per 100000, while the incidence rate of children≤5years old was 2879.80 per 100000. The majority (88.97%) of HFMD cases were aged within 0–5 years old and the males were 60.20%. Other enterovirus (EV), enteriovirus 71(EV71), and Coxsackievirus A16 (CA16) accounted for 48.75%, 30.91% and 20.34%. The seasonal peak was between May and October. HFMD had positive spatial autocorrelation at town level with global Moran’s I from 0.19 to 0.31(P<0.001). Spatial-temporal cluster analysis detected six most likely clusters and three secondary clusters from 2013 to 2018. The most likely cluster was located in urban and urban-rural fringe areas.

Conclusions

Urban and urban-rural fringe areas were the major locations of the clusters with other EV as the dominant pathogen between May and October. The findings suggested that the prevention and control of HFMD in Qingdao City should be focus on these high-risk periods and locations which had important public health significance for the allocation of public health resources.

Highly sensitive and specific detection of hepatitis B virus DNA and drug resistance mutations utilizing the PCR-based CRISPR-Cas13a system

OBJECTIVES

Undetectable or low-level hepatitis B virus (HBV) DNA and drug resistance mutations in patients may increase the risk of HBV transmission or cause active viral replication and other clinical problems. Here, we established a highly sensitive and practical method for HBV and drug resistance detection using a polymerase chain reaction (PCR) -based CRISPR-Cas13a detection system (referred to as PCR-CRISPR) and evaluated its detection capability using clinical samples.

METHODS

Specific CRISPR RNAs (crRNAs) are designed for HBV DNA detection and YMDD (tyrosine-methionine-aspartate-aspartate) variant identification. The HBV DNA was detected in 312 serum samples for HBV diagnosis using quantification PCR (qPCR) and PCR-CRISPR. Additionally, 424 serum samples for YMDD testing were detected by qPCR, direct sequencing, and our assay.

RESULTS

Using PCR-CRISPR, one copy per test of HBV DNA was detected with HBV-1 crRNA in 15 min after PCR amplification. Consistent results with qPCR were observed for 302 samples, while the remaining 10 samples with low-level HBV DNA were detectable by PCR-CRISPR and droplet digital PCR but not by qPCR. PCR-CRISPR diagnosed all 412 drug-resistant samples detected by the YMDD detection qPCR kit and direct sequencing, as well as the other 12 drug-resistant samples with low-level HBV DNA undetectable by qPCR and direct sequencing.

CONCLUSIONS

We developed a novel PCR-CRISPR method for highly sensitive and specific detection of HBV DNA and drug resistance mutations. One copy per test for HBV DNA and YMDD drug resistance mutations could be detected. This method has wide application prospects for the early detection of HBV infection, drug resistance monitoring and treatment guidance.

Emergence of NDM-1- and CTX-M-3-Producing Raoultella ornithinolytica in Human Gut Microbiota

Raoultella ornithinolytica is an opportunistic pathogen of the Enterobacteriaceae family and has been implicated in nosocomial infections in recent years. The aim of this study was to characterize a carbapenemase-producing R. ornithinolytica isolate and three extended-spectrum β-lactamase (ESBL)-producing R. ornithinolytica isolates from stool samples of adults in a rural area of Shandong Province, China. The species were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequence analysis. Antimicrobial susceptibility test showed that all four isolates were multidrug-resistant (MDR). The whole genome sequence (WGS) of these isolates was determined using an Illumina HiSeq platform, which revealed MDR-related genes. The S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) was used to characterize the plasmids carried by the R. ornithinolytica isolates. The bla_NDM-1 and bla_CTX-M-3 genes were probed using Southern blotting, which confirmed the location of both genes on the same plasmid with molecular weight of 336.5–398.4 kb. The transferability of bla_NDM-1 and bla_CTX-M was also confirmed by conjugation assays. Finally, BLAST analysis of both genes showed that mobile genetic elements were associated with the spread of drug resistance genes. Taken together, we report the presence of conjugative bla_NDM-1 and bla_CTX-M plasmids in R. ornithinolytica isolates from healthy humans, which indicate the possibility of inter-species transfer of drug resistance genes. To the best of our knowledge, this is the first study to isolate and characterize carbapenemase-producing R. ornithinolytica and ESBL-producing R. ornithinolytica isolates from healthy human hosts.

Analysis of epidemiological characteristics of four natural-focal diseases in Shandong Province, China in 2009-2017: A descriptive analysis

Background

Natural-focal diseases are serious diseases that endanger human health. They threaten about 100 million people in Shandong Province, and cause illness in thousands of people each year. However, information on the epidemiological characteristics of natural-focal diseases in Shandong Province has been limited. The purpose of the study was to describe and analyze the epidemiological characteristics of natural-focal diseases in Shandong Province, 2009–2017.

Methods

We describe the incidence and distribution of four natural-focal diseases in Shandong Province using surveillance data from 2009–2017.

Results

From 2009–2017, 11123 cases of four natural-focal diseases including 257 deaths were reported in Shandong Province, China. The four natural-focal diseases were severe fever with thrombocytopenia syndrome (SFTS), human granulocytic anaplasmosis (HGA), typhus, and scrub typhus. The high-risk groups of the four diseases were farmers and the elderly. The incidence rate of scrub typhus was significantly higher in females. However, this difference was not seen in the other three diseases. The four diseases were mainly clustered in the middle-southern part of Shandong Province and the Shandong Peninsula. The annual incidence of SFTS and scrub typhus increased, typhus was relatively stable, and HGA declined. However, the range of SFTS expanded, while HGA shrunk, and typhus and scrub typhus were unchanged. The epidemic period of SFTS and HGA was from May to October, typhus was from October to November, and scrub typhus was from September to November. The fatality rates of SFTS, typhus, scrub typhus, and HGA were 9.19%, 0%, 0.01%, and 2.24%, respectively.

Conclusions

Our study described and analyzed the prevalence of natural-focal diseases in Shandong Province, and confirmed that age was closely related to the SFTS fatality rate. This study may help to improve the understanding of the prevalence of natural-focal diseases in Shandong Province in recent years and to better develop accurate prevention and control strategies for natural-focal diseases.

Novel Yersinia enterocolitica Prophages and a Comparative Analysis of Genomic Diversity

Yersinia enterocolitica is a major agent of foodborne diseases worldwide. Prophage plays an important role in the genetic evolution of the bacterial genome. Little is known about the genetic information about prophages in the genome of Y. enterocolitica, and no pathogenic Y. enterocolitica prophages have been described. In this study, we induced and described the genomes of six prophages from pathogenic Y. enterocolitica for the first time. Phylogenetic analysis based on whole genome sequencing revealed that these novel Yersinia phages are genetically distinct from the previously reported phages, showing considerable genetic diversity. Interestingly, the prophages induced from O:3 and O:9 Y. enterocolitica showed different genomic sequences and morphology but highly conserved among the same serotype strains, which classified into two diverse clusters. The three long-tailed Myoviridae prophages induced from serotype O:3 Y. enterocolitica were highly conserved, shared ≥99.99% identity and forming genotypic cluster A; the three Podoviridae prophages induced from the serotype O:9 strains formed cluster B, also shared more than 99.90% identity with one another. Cluster A was most closely related to O:5 non-pathogenic Y. enterocolitica prophage PY54 (61.72% identity). The genetic polymorphism of these two kinds of prophages and highly conserved among the same serotype strains, suggested a possible shared evolutionary past for these phages: originated from distinct ancestors, and entered pathogenic Y. enterocolitica as extrachromosomal genetic components during evolution when facing selective pressure. These results are critically important for further understanding of phage roles in host physiology and the pathology of disease.

Impact of the Ebola outbreak on routine immunization in western area, Sierra Leone - a field survey from an Ebola epidemic area

Background

Since March 2014, the Ebola Virus Disease (EVD) outbreak in West Africa disrupted health care systems - especially in Guinea, Liberia and Sierra Leone – with a consequential stress on the area’s routine immunization programs. To address perceived decreased vaccination coverage, Sierra Leone conducted a catch-up vaccination campaign during 24–27 April 2015. We conducted a vaccination coverage survey and report coverage estimates surrounding the time of the EVD outbreak and the catch-up campaign.

Methods

We selected 3 villages from each of 3 communities and obtained dates of birth and dates of vaccination with measles vaccine (MV) and the 3rd dose of Pentavalent vaccine (Pentavalent3) of all children under 4 years of age in the 9 selected villages. Vaccination data were obtained from parent-held health cards. We calculated the children’s MV and Pentavalent3 coverage rates at 3 time points, 1 August 2014, 1 April 2015, and 1 May 2015, representing coverage rates before the EVD outbreak, during the EVD outbreak, and after the Maternal and Child Health Week (MCHW) catch-up campaign.

Results

The final sample size was 168 children. MV coverage among age-eligible children was 71.3% (95% confidence interval [CI]: 62.1% - 80.4%) and 45.7% (95% CI: 29.2% - 62.2%) before and during the outbreak of EVD, respectively, and was 56.8% (95% CI: 40.8% - 72.7%) after the campaign. Pentavalent3 coverage among age-eligible children was 79.8% (95% CI: 72.6% - 87.0%) and 40.0% (95% CI: 22.5% - 57.5%) before and during the outbreak of EVD, and was 56.4% (95% CI: 39.1% - 73.4%) after the campaign.

Conclusions

Coverage levels of MV and Pentavalent3 were low before the EVD outbreak and decreased further during the outbreak. Although the MCHW catch-up campaign increased coverage levels, coverage remained below pre-outbreak levels. High-quality supplementary immunization activities should be conducted and routine immunization should be strengthened to address gaps in immunity among children in this EVD-affected area.

Genotype diversity and distribution of Orientia tsutsugamushi in scrub typhus patients and rodents in Shandong, northern China

Orientia tsutsugamushi, the etiologic agent of scrub typhus, is transmitted to humans through the bites of infected chiggers. To identify the genotypes of O.tsutsugamushi and their geographical distribution in Shandong, 236 patient's samples and 1606 captured rodents were collected in major-endemic regions of Shandong Province from June 2013 to December 2014. Sequences were determined for the 56-kDa TSA gene, and the relationship between these sequences and those previously determined was assessed. Two genotypes out of 5 previously reported in Shandong were identified, i.e. Kawasaki-related and STA-07. The Kawasaki-related genotype was predominant (82.1% (23/28) in human and 50% (5/10) in rodents), with wide distribution through the endemic areas of Shandong Province. The STA-07 was confined to Tai'an, Linyi and Qingdao districts. The Fuji-related, Shimikoshi-related and Karp-related genotypes were not found, while identified in previous studies. For prevention and control of scrub typhus in Shandong, more attention should be paid to surveillance of Kawasaki-related and STA-07 genotypes.

[Molecular types of group A Streptococcus isolated from scarlet fever patients and asymptomatic carriers in Shandong province, 2013]

OBJECTIVE

To describe the molecular characteristics of group A Streptococcus (GAS) isolated from patients and asymptomatic carriers of scarlet fever in Shandong province, 2013, and to explore the relationships between emm types and other molecular types.

METHODS

72 strains of GAS were isolated from throat swabs of children with scarlet fever or asymptomatic carriers of GAS. All the strains were typed by emm typing, multilocus sequence typing (MLST), super-antigen (SAg) genes detections and pulsed-field gel electrophoreses (PFGE).

RESULTS

Among the 72 strains, emm1 (41.67%) and emm12 (56.94%) were the most common emm types. Two ST types were found, including ST28 (43.06%) and ST36 (56.94%). Additionally, emm1 was also found correlated to ST28, while emm12 was associated with ST36. Eight super-antigen genes were detected, including smeZ (100.00%), ssa (100.00%), speG (97.22%), speC (95.83%), speL (54.17%), speJ (41.67%), speA (38.89%) and speH (38.89%), while speK, speM, speL were not found (0%). Both speA and speJ genes were detected primarily in emm1 strains (all P < 0.05), while speH and speI genes were not detected in emm 1 strains (all P < 0.05). And emm12 strains were inclined to harbor speH and speL (all P < 0.05) but not speA or speJ (all P < 0.05). Twenty different genotypes were identified by PFGE.

CONCLUSION

All the emm types of GAS isolated from scarlet fever patients and asymptomatic carriers in Shandong province 2013 were mainly emm1 and emm12 and carrying speC, speG and smeZ, ssa. ST types mainly exsited in ST28 and ST36. In addition, there were correlations between emm types and super-antigen genes, ST types, PFGE types.

[Spatial and temporal characteristics of human brucellosis, from 2004 to 2012 in Shandong province]

OBJECTIVE

To explore the spatial and temporal characteristics of human brucellosis in Shandong province and to provide scientific basis for the development of related regional public health strategies.

METHODS

1 802 diagnosed cases of human brucellosis patients were selected based on the data that was collected by Diseases Reporting Information System between year 2004 and 2012 in Shandong province. Methods on spatial thematic mapping, spatial autocorrelation analysis, spatial clustering analysis, and temporal clustering analysis were applied to describe the temporal and spatial distribution on human brucellosis cases.

RESULTS

The incidence rate of human brucellosis increased from 0.038 2/100 000 (35 cases) to 0.620 5/100 000 (598 cases), with annual average incidence rate as 0.211 1/100 000 and the incidence was evidently increased. The value of M (0.375 3) showed that this disease was seasonal, with the epidemic months between March and June, accounting for 56.27% (1 014/1 802). The Global Moran's I index was 0.198 901 (P = 0.000 120), showing that there was a positive correlation between space and the incidence of brucellosis. The incidence rates in 2006, 2007, 2009 and 2012 and the space distribution appeared a positive correlation (P < 0.05) in Shandong province. The local Moran's I index showed that there were 8 "High-High" (HH) clustering areas, which were proved to have statistical significance (P < 0.05). Local indicators of spatial association (LISA) revealed that southwest and north districts of Shandong were highly clustered districts of brucellosis and the areas paralleled to the areas that having higher incidence rates. There were two spatial clustering areas in this study, one as the center of Juanchen with radiation radius at 33.83 km whose RR was 9.78 (P < 0.05) and the other was the center of Binchen with radiation radius at 62.78 km with RR as 4.99 (P < 0.05). All the 8 HH counties (districts) were included in the two cluster regions.

CONCLUSION

Incidence of human brucellosis showed an obvious increase in Shandong during year 2004-2012. Months with epidemics were between March and June. The incidence of brucellosis in counties (districts) was non-randomly distributed. A positive spatial correlation and the feature of clusters was noticed.

Two novel ail-positive biotype 1A strains of Yersinia enterocolitica isolated in China with unequal adhesion and invasion properties

Yersinia enterocolitica is an enteric pathogen having six biotypes: 1A, 1B, 2, 3, 4, and 5. Different bioserotypes have been associated with varying pathogenicity, and the strains of biotype 1A lack the virulence-associated pYV-bearing genes and were once considered to be avirulent. However, there is growing epidemiological, clinical, and experimental evidence to suggest some biotype 1A isolates are virulent and can cause gastrointestinal disease. Here, we describe two biotype 1A strains discovered from 3807 isolates that carry the ail (attachment and invasion locus) gene. The two strains showed unique PFGE patterns compared to all other isolates in the Chinese Y. enterocolitica isolate PFGE database. Strain SDWL-003 isolated from a sheep shared ail sequence identical to A1 pattern, and the foxA (ferrioxamine receptor) sequence was identical to the pathogenic F5 pattern, besides, the PFGE patterns of SDWL-003 was also cluster to pathogenic branch; however it does not attach to or invade Hep-2 cells. The ail sequence of strain 2006RAT isolated from a Microtus fortis showed several mutations compared to other published genomes, and therefore formed an entirely new pathogenic pattern. Though it clustered to non-pathogenic block with foxA sequence polymorphism analysis or PFGE assay, the strain 2006RAT showed adhesion properties. The data here bring new insights into the molecular genetics of Y. enterocolitica biotype 1A, show some isolates of 1A biotype gaining potential pathogenicity using the function of the virulence gene - ail, and indicate the lateral gene transfer of ail virulence genes proceeded between pathogenic and nonpathogenic Y. enterocolitica.

One family cluster of avian influenza A(H7N9) virus infection in Shandong, China

BACKGROUND

The first case of human infection with avian influenza A (H7N9) virus was identified in March, 2013 and the new H7N9 virus infected 134 patients and killed 45 people in China as of September 30, 2013. Family clusters with confirmed or suspected the new H7N9 virus infection were previously reported, but the family cluster of H7N9 virus infection in Shandong Province was first reported.

CASE PRESENTATION

A 36-year-old man was admitted to Zaozhuang City Hospital with progressive respiratory distress and suspicion of impending acute respiratory distress syndrome on April 21. The chest radiography revealed bilateral ground-glass opacities and pulmonary lesions. The second case, the first case's 4 year old son, was admitted to the same hospital on April 28 with fever and multiple patchy shadows in the bilateral lungs. Both of the two cases were confirmed to infect with H7N9 virus by the results of real-time reverse transcriptase-polymerase-chain reaction (rRT-PCR), virus isolation and serum antibody titer. At the same time, one environment samples was detected positive for H7N9 virus in the living poultry market in Zaozhuang. The homologous analysis of the full genome sequence indicated that both viruses from the patients were almost genetically identical. The field epidemiology investigation showed that the two cases had no recognized exposure to poultry, but had the exposure to the environment. The second case had substantial unprotected close exposure to his ill father and developed symptoms seven days after his last contact with his father. After surgery, the index case and his son were discharged on May 16 and May 6, respectively. 11 close contacts of both patients were identified and tested negative both the throat swabs and the serum antibody.

CONCLUSION

The infection of the index case probably resulted from contact with environmentally contaminated material. For the son, the probable infection source was from the index case during unprotected exposure, but the possibility from the environment or other sources could not be completely ruled out.

Clinical correlates of white matter blood flow perfusion changes in Sturge-Weber syndrome: a dynamic MR perfusion-weighted imaging study

BACKGROUND AND PURPOSE

Low brain tissue perfusion due to abnormal venous drainage is thought to be a central mechanism of brain damage in SWS. Here, HR-PWI was used to quantify WM perfusion abnormalities and to correlate these with brain atrophy and clinical variables.

MATERIALS AND METHODS

Fourteen children (age range, 0.8-10.0 years) with unilateral SWS underwent MR imaging examinations, including HR-PWI. rCBV, rCBF, and MTT in the affected WM and in contralateral homotopic WM were measured. AI for each perfusion parameter was correlated with age, brain atrophy, and motor and seizure variables as well as IQ.

RESULTS

Increased perfusion was seen in the affected hemisphere in 5 children and decreased perfusion in 9 children. Brain atrophy was more severe in the low-perfusion group (P = .01) and was related to both CBF-AI and CBV-AI (r = -0.69, P = .007; r = -0.64, P = .014, respectively). Older children had lower CBV values on the affected side (r = -0.62, P = .02). Longer duration of epilepsy was related to lower CBF (more negative CBF-AI, r = -0.58, P = .03) and low CBV (r = -0.55, P = .04) on the affected side. Lower perfusion was associated with more frequent seizures (rCBF-AI: r = -0.56, P = .04; rCBV-AI: r = -0.63, P = .02).

CONCLUSIONS

Increased perfusion in the affected cerebral WM may indicate an early stage of SWS without severe brain atrophy. Decreased perfusion is associated with frequent seizures, long duration of epilepsy, and brain atrophy.