Gonorrhea is caused by the human pathogen Neisseria gonorrhoeae. More than 106 million new cases of N. gonorrhoeae infections occur each year worldwide. There is no vaccine available against gonococcal infections and treatment of gonorrhea with antibiotics is the only way to eradicate infection. The high prevalence of antibiotic resistance (AMR) in this microorganism makes the effective treatment of gonococcal infections increasingly problematic. The emergence of AMR, especially to extended spectrum cephalosporins (i.e. cefixime and ceftriaxone) which are the last possibilities for single dose treatment options for gonococcal infections, is a serious concern. Gonorrhea may become an untreatable infection in the near future. Saskatchewan (SK) has one of the highest rates of gonorrhea in Canada. In order to better characterize the gonorrhea epidemic in SK, the objectives of the present research were to determine the prevalence and trends of AMR and emerging AMR mechanisms in N. gonorrhoeae isolates. AMR mechanisms were ascertained for the first time in SK in order to identify genetic causes of resistance. This was completed by determining and analyzing the DNA sequences of various genes - penA, mtrR, porB ponA, gyrA, parC mtrR, 23S rRNA alleles and erm –implicated in gonococcal AMR. The population dynamics of the N. gonorrhoeae isolates in SK was investigated by DNA based molecular methods to determine strain distribution, evolution of AMR phenotypes, and association between strain types (STs) and AMR genotypes and phenotypes. N. gonorrhoeae isolates (n=427) from Saskatchewan (2003-2011) were susceptible to antibiotics now recommended for treatment - cefixime, ceftriaxone and spectinomycin. Over 95% of the isolates tested were also susceptible to penicillin (96%) and ciprofloxacin (95.5%), antibiotics no longer recommended for treatment, and azithromycin (99.4%). Tetracycline resistance was also high (50.1%). N. gonorrhoeae isolates that were resistant to the antibiotics tested and also those isolates with MICs ≥0.003 mg/L to cefixime and ceftriaxone were analyzed (n=146) to determine their resistance mechanisms. This analysis revealed that reduced susceptibility to ceftriaxone and cefixime and resistance to penicillin is mediated by specific mutations in penicillin binding protein 2 (PBP2), in the promoter and dimerization domains of MtrR and porin protein (PorB). Novel mutations and combinations of mutations were noted. Ciprofloxacin resistant N. gonorrhoeae isolates carried double mutations in GyrA (S91F and D95G/N) and a S87R or S88P substitution in ParC. Isolates resistant to azithromycin had specific mutations in all the four alleles of 23S rRNA as well as in the DNA binding domain of MtrR. Most resistance was chromosomally mediated while plasmid-mediated resistance to penicillin (0.93% of penicillin resistant isolates) and tetracycline (3.3%) was low. DNA based strain typing methods such as porB-DNA sequencing, N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and multilocus sequence typing (MLST) showed that the gonococcal population in SK differs appreciably from both other Canadian provinces and from strains reported internationally. MLST analysis, which ascertains the evolution of isolates over time, demonstrated that penicillin and tetracycline resistant isolates in SK evolved through spontaneous mutations in established lineages. Ciprofloxacin and azithromycin resistant N. gonorrhoeae isolates, on the other hand, were introduced into SK from outside the province. Significant associations between particular mutation pattern combinations in resistance determining genes and specific NG-MAST STs were identified e.g. NG-MAST ST 25 was associated with specific combined mutation patterns in PBP2, MtrR and PorB and antibiotic susceptibility; and, NG-MAST ST 3654 was associated with another PBP2/MtrR/PorB mutation pattern, chromosomal resistance to penicillin and tetracycline and elevated MICs to cefixime. This research shows the importance of regional antimicrobial susceptibility monitoring. In the context of SK, this means that local surveillance of gonococcal AMR may be used to develop policies for regional treatment guidelines which promote the prudent use of antimicrobials for treatment, including those antibiotics which may no longer be used in other regions due to higher AMR rates. Further, the significant association between particular AMR mutation pattern combinations and specific STs indicates that AMR might be predicted. These results should assist in the development of non-culture-based tests for the diagnosis of gonococcal AMR similar to nucleic acid amplification tests used to diagnose N. gonorrhoeae infections.

Equine arteritis virus (EAV) is the causal agent of equine viral arteritis, a disease of equids. During natural outbreaks of the disease, EAV can cause abortion in pregnant mares and persistent infection in stallions. Understanding how host cellular proteins interact with viral RNA and viral proteins, as well as their role in viral infection, will enable better characterization of the pathogenesis of EAV and establishment of persistent infection in stallions. Accordingly, we hypothesized that both viral factors and host genetically related factors could influence the outcome of EAV infection in horses. To test this hypothesis, we first combined contemporary molecular biology techniques with dual color flow cytometric analysis to characterize the interactions of viral structural proteins and the equine peripheral blood mononuclear cells in vitro. Results from this study demonstrated that interactions between GP2, GP3, GP4, GP5 and M envelope proteins of EAV play a major role in determining the CD14+ monocyte tropism while the tropism of CD3+ T lymphocytes is determined by GP2, GP4, GP5 and M envelope proteins but not the GP3 protein. Secondly, a genome wide association study using SNP genotyping identified a common haplotype associated with the in vitro CD3+ T lymphocyte/resistance to EAV infection among four breeds of horses. Subsequently, these studies were extended to establish a possible correlation between the in vitro susceptibility of CD3+ T lymphocytes to EAV and establishment of persistent infection in stallions. Interestingly, carrier stallions with susceptible CD3+ T lymphocyte phenotype to EAV may represent those at higher risk of becoming persistently infected. Finally, the precise effect of EAV on the immune system of horses, innate and humoral immunity, was studied. Horses were shown to mount a strong humoral antibody response to nonstructural proteins (nsps) 2, 4, 5 and 12 of EAV, whereas nsps 1, 2 and 11 suppressed the type I interferon production. The data presented in this dissertation suggest new directions for future EAV research using genomic and proteomic approaches to study host cell factors involved in EAV attachment and entry and establishment of persistent infection in the stallions.

Gonorrhea, caused by the human pathogen Neisseria gonorrhoeae, is a severe public health problem worldwide with more than 82 million new infections each year. N. gonorrhoeae is transmitted by sexual contact and primarily causes urogenital mucosal infections in men and women. Left untreated, this infection may cause severe complications, especially in females. Eye infections of the newborn can occur. Gonorrhea infections enhance HIV transmission. The highly prevalent antibiotic resistance and the emergence of new drug resistances render treatment of the infections increasingly difficult. Close monitoring of antimicrobial susceptibility of this pathogen is crucial, and enhanced knowledge of molecular mechanisms of gonococcal antimicrobial resistance is urgently needed. There are no vaccines available against N. gonorrhoeae. Control of gonorrhea relies on comprehensive strategies which can be better formulated by understanding, at molecular levels, how N. gonorrhoeae is transmitted in communities. My research aimed to illustrate the severe burden of antimicrobial resistance in N. gonorrhoeae temporally and geographically in China and to reveal the molecular mechanisms of antibiotic resistance particularly the development of reduced susceptibility to ceftriaxone in N. gonorrhoeae isolates. To determine specific strain distributions, N. gonorrhoeae isolates were characterized using molecular typing methods such as a modified porB-based typing scheme and the N. gonorrhoeae Multi-Antigen Typing (NG-MAST) method, compared to traditional epidemiological approaches. The ultimate goal was to provide information for better formulating disease control strategies for gonorrhea. In this research, male patients with gonorrhea and their sex partners were recruited in Shanghai (2005 and 2008) and in Urumchi (2007-2008), China. Epidemiological information pertaining to sexual contacts was collected. N. gonorrhoeae isolates were investigated for their antimicrobial susceptibility. Molecular mechanisms of antimicrobial resistance were explored by analysis of potential resistant determinants (gyrA, parC, porB, mtrR, ponA and penA). The molecular data were combined with bioinformatic analysis and traditional epidemiological data. High percentages of N. gonorrhoeae isolates (11% - 19% in Shanghai, 4.5% in Urumchi) exhibited reduced susceptibility to ceftriaxone (MICs = 0.125-0.25 mg/L), the first line drug recommended for the treatment of gonorrhea in China. The majority of isolates (>98%) were susceptible to spectinomycin, an alternative regimen for gonorrhea treatment; however, the proportion of isolates having intermediate levels of susceptibility increased from 1.9% in 2005 to 9.9% in 2008. The majority of isolates tested were resistant to penicillin (80% - 93%), tetracycline (56% - 65%) and ciprofloxacin (98% - 100%). Plasmid-mediated resistance in N. gonorrhoeae isolates were highly prevalent (51% - 79%) in Shanghai and Urumchi. Analysis of 60 clinical isolates revealed that reduced susceptibility to ceftriaxone is mediated by porB1b allele and is associated with specific mutations in penicillin binding protein 2 and in the DNA binding and dimerization domains of MtrR. Penicillin binding protein 1 is not involved in reduced susceptibility to ceftriaxone. Although mutation patterns in quinolone resistant determinant regions (QRDRs) varied, the majority of ciprofloxacin resistant isolates had double mutations in GyrA (S91F and D95G/A/N) and most isolates also carried a S87R/N mutation in ParC. The presence of mutations in the QRDR of ParC is correlated with elevated ciprofloxacin MICs. A modified porB-based molecular typing scheme was developed and involved ~82% of the DNA sequence of gonococcal porB. This typing method proved to have high discriminatory ability (index of discrimination = 0.93 0.96), and was cost effective and easy to perform as compared to the NG-MAST analysis. Using the modified porB-based typing method, N. gonorrhoeae isolates were reliably differentiated, and transmission clusters were identified. Molecular epidemiology using the porB-based method confirmed direct sexual connections and identified sexual networks otherwise unrevealed by the patient self-reporting or traditional case-tracing methods.

Gonorrhea, caused by the human pathogen Neisseria gonorrhoeae, is a severe public health problem worldwide with more than 82 million new infections each year. N. gonorrhoeae is transmitted by sexual contact and primarily causes urogenital mucosal infections in men and women. Left untreated, this infection may cause severe complications, especially in females. Eye infections of the newborn can occur. Gonorrhea infections enhance HIV transmission. The highly prevalent antibiotic resistance and the emergence of new drug resistances render treatment of the infections increasingly difficult. Close monitoring of antimicrobial susceptibility of this pathogen is crucial, and enhanced knowledge of molecular mechanisms of gonococcal antimicrobial resistance is urgently needed. There are no vaccines available against N. gonorrhoeae. Control of gonorrhea relies on comprehensive strategies which can be better formulated by understanding, at molecular levels, how N. gonorrhoeae is transmitted in communities. My research aimed to illustrate the severe burden of antimicrobial resistance in N. gonorrhoeae temporally and geographically in China and to reveal the molecular mechanisms of antibiotic resistance particularly the development of reduced susceptibility to ceftriaxone in N. gonorrhoeae isolates. To determine specific strain distributions, N. gonorrhoeae isolates were characterized using molecular typing methods such as a modified porB-based typing scheme and the N. gonorrhoeae Multi-Antigen Typing (NG-MAST) method, compared to traditional epidemiological approaches. The ultimate goal was to provide information for better formulating disease control strategies for gonorrhea. In this research, male patients with gonorrhea and their sex partners were recruited in Shanghai (2005 and 2008) and in Urumchi (2007-2008), China. Epidemiological information pertaining to sexual contacts was collected. N. gonorrhoeae isolates were investigated for their antimicrobial susceptibility. Molecular mechanisms of antimicrobial resistance were explored by analysis of potential resistant determinants (gyrA, parC, porB, mtrR, ponA and penA). The molecular data were combined with bioinformatic analysis and traditional epidemiological data. High percentages of N. gonorrhoeae isolates (11% - 19% in Shanghai, 4.5% in Urumchi) exhibited reduced susceptibility to ceftriaxone (MICs = 0.125-0.25 mg/L), the first line drug recommended for the treatment of gonorrhea in China. The majority of isolates (>98%) were susceptible to spectinomycin, an alternative regimen for gonorrhea treatment; however, the proportion of isolates having intermediate levels of susceptibility increased from 1.9% in 2005 to 9.9% in 2008. The majority of isolates tested were resistant to penicillin (80% - 93%), tetracycline (56% - 65%) and ciprofloxacin (98% - 100%). Plasmid-mediated resistance in N. gonorrhoeae isolates were highly prevalent (51% - 79%) in Shanghai and Urumchi. Analysis of 60 clinical isolates revealed that reduced susceptibility to ceftriaxone is mediated by porB1b allele and is associated with specific mutations in penicillin binding protein 2 and in the DNA binding and dimerization domains of MtrR. Penicillin binding protein 1 is not involved in reduced susceptibility to ceftriaxone. Although mutation patterns in quinolone resistant determinant regions (QRDRs) varied, the majority of ciprofloxacin resistant isolates had double mutations in GyrA (S91F and D95G/A/N) and most isolates also carried a S87R/N mutation in ParC. The presence of mutations in the QRDR of ParC is correlated with elevated ciprofloxacin MICs. A modified porB-based molecular typing scheme was developed and involved ~82% of the DNA sequence of gonococcal porB. This typing method proved to have high discriminatory ability (index of discrimination = 0.93 0.96), and was cost effective and easy to perform as compared to the NG-MAST analysis. Using the modified porB-based typing method, N. gonorrhoeae isolates were reliably differentiated, and transmission clusters were identified. Molecular epidemiology using the porB-based method confirmed direct sexual connections and identified sexual networks otherwise unrevealed by the patient self-reporting or traditional case-tracing methods.