Whole-genome Based Investigation of Streptococcus pneumoniae Infections

Streptococcus pneumoniae is a common resident of the human throat, yet is also a major cause of community-acquired pneumonia, septicemia, meningitis and otitis media. In recent years, whole-genome sequencing (WGS) has been extensively used in research laboratories to study infectious pathogens. However, to date, the application of WGS in clinical laboratories is limited, especially for S. pneumoniae-associated diseases. We hypothesize that variations between the genome sequence of pneumococcal isolates can be used to monitor epidemiological spread and to reveal unique traits that define clinical disease outcome. In this thesis, I used WGS in a public health laboratory setting for rapid prediction of multi-locus sequence typing (MLST) and antimicrobial resistance, establishing good sensitivity and specificity in this context. I also used WGS to delineate outbreaks of pneumococcal diseases caused by 12F that occurred in Manitoba, Canada, which was the first reported use of WGS for tracing a pneumococcal epidemic. Through genomic comparisons of Canadian and U.S.A. 12F isolates, I was able to pinpoint the source of the outbreak, and monitor transmission and evolution of an emerging 12F outbreak strain. Finally, I performed a large-scale genome comparison of pneumococcal isolates associated with different clinical manifestations to gain insight into genomic landscape of S. pneumoniae, with a goal to reveal genetic differences between strains with a propensity to cause different types of disease. From this work, I have identified a handful of candidate genes that tend to differentiate pathogenic versus commensal strains When considered together, this thesis demonstrates the power of WGS in clinical epidemiology. Once routinely applied, WGS will allow high resolution mapping of epidemics, helpful predictions of antimicrobial resistance, and the presence of factors indicating a predisposition to cause different types of pneumococcal disease. When given the rapid turnaround of state-of-the-art sequencers, this will provide a profound benefit for clinical care and public health interventions against this incessant pathogen.Ph.D

A Systematic Review and Meta-Analysis of Combined Antibiotic Spacer with Ilizarov Methods in the Treatment of Infected Nonunion of Tibia

Background. The objective of this systematic review was to evaluate current studies available reporting the antibiotic spacer combined with Ilizarov methods in the treatment of infected nonunion of tibia and to perform meta-analysis of bone results and infection recurrence to assess the efficacy of an antibiotic spacer combined with Ilizarov methods. Methods. The MEDLINE, Embase, Cochrane Library, CNKI, and CBM (Chinese Biological Medicine) databases were searched for articles published between January 2000 and July 2020. Assessment of study quality was performed using a modified version of the Newcastle-Ottawa scale. Effect size and 95% confidence intervals were calculated for the main outcome. Heterogeneity was assessed. Fixed-effect modeling and Stata version 15.1 were used to analyze the data. Sensitivity analyses were conducted with the evidence of heterogeneity. Results. 11 studies involving 210 patients with infected nonunion of tibia were finally included in our meta-analysis. Bone results and infection recurrence were analyzed based on the single-arm meta-analysis. The average of external fixation index (EFI) was 46.88 days/cm in all studies included. The excellent rate in bone results and the rate of infection recurrence was 65% (95% CI: [0.22, 0.97], I2=0.0%, P=0.932) and 6.99% (95% CI: [0.052, 0.325], I2=0.0%, P=1.000) in patients with infected nonunion of tibia treated with an antibiotic spacer combined with Ilizarov methods. Conclusions. Our meta-analysis revealed that the patients with infected nonunion of tibia treated with an antibiotic spacer combined with Ilizarov methods had a high rate of excellent bone results and a low rate of infection recurrence. Therefore, combining the antibiotic spacer with Ilizarov methods may be an applicable choice for repairing and reconstructing infected nonunion of tibia

Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel.

In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel related. Cases were significantly associated with travel to either Europe (odds ratio, 6.1) or New York (odds ratio, 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe

Adeno-Associated Virus-Mediated RNAi against Mutant Alleles Attenuates Abnormal Calvarial Phenotypes in an Apert Syndrome Mouse Model

Apert syndrome (AS), the most severe form of craniosynostosis, is caused by missense mutations including Pro253Arg(P253R) of fibroblast growth factor receptor 2 (FGFR2), which leads to enhanced FGF/FGFR2-signaling activity. Surgical correction of the deformed skull is the typical treatment for AS. Because of constant maldevelopment of sutures, the corrective surgery is often executed several times, resulting in increased patient challenge and complications. Biological therapies targeting the signaling of mutant FGFR2 allele, in combination with surgery, may bring better outcome. Here we screened and found a small interfering RNA (siRNA) specifically targeting the Fgfr2-P253R allele, and we revealed that it inhibited osteoblastic differentiation and matrix mineralization by reducing the signaling of ERK1/2 and P38 in cultured primary calvarial cells and calvarial explants from Apert mice (Fgfr2+/P253R). Furthermore, AAV9 carrying short hairpin RNA (shRNA) (AAV9-Fgfr2-shRNA) against mutant Fgfr2 was delivered to the skulls of AS mice. Results demonstrate that AAV9-Fgfr2-shRNA attenuated the premature closure of coronal suture and the decreased calvarial bone volume of AS mice. Our study provides a novel practical biological approach, which will, in combination with other therapies, including surgeries, help treat patients with AS while providing experimental clues for the biological therapies of other genetic skeletal diseases. Keywords: craniosynostosis, Apert syndrome, Fgfr2, adeno-associated virus, RNAi, molecular therap