Thesis (MSc (Med)(Microbiology))--University of Limpopo (Medunsa Campus), 2010. / Mycoplasma genitalium, a human mycoplasma species has been established as a cause of nongonococcal urethritis (NGU) in men, particularly in Chlamydia trachomatis-negative patients. It was also shown to play a role in cervicitis and pelvic inflammatory disease (PID) in women. Due to difficulty in culturing, and the lack of routine molecular diagnostic tests, many M. genitalium infections are undetected. The purpose of this study was to evaluate three nucleic acid amplification tests (NAATs) i.e. a recently developed Gen-Probe research only transcription mediated amplification (TMA) assay, a conventional polymerase chain reaction (PCR) assay and a real-time PCR (q-PCR) assay for the detection of M. genitalium in urine specimens of men with symptoms of urethritis. To evaluate the three assays, 300 urine specimens were collected between June 2007 and July 2008 from sexually active male patients presenting with discharge (N=94) and/or burning on micturition (N=206) to a private medical practitioner in Silverton, Pretoria. A specimen was considered positive by extension of the gold standard i.e. if any two of the three assays were positive. This was used to calculate the sensitivity and specificity of each method. TMA detected M. genitalium in 62 (21%), PCR in 43 (14%) and q-PCR in 48 (16%) of the 300 patients. The sensitivities of the assays were 100% (TMA), 92% (q-PCR) and 78% (PCR), with specificities of 90% (TMA), 95% (q-PCR) and 97% (PCR). The sensitivity of the TMA assay was higher than that of the q-PCR and PCR assays. The lower sensitivity obtained by the q-PCR assay might have been due to inhibition and limitations in the amount of the DNA template. However, the q-PCR assay was easy to perform as it combines amplification and detection thus eliminating further handling of PCR products. The PCR, although with a higher specificity, was the least desirable in terms of testing time and problems with subjectivity when reading agarose gels. v We concluded that the Gen-Probe TMA assay is a highly sensitive method for detection of M. genitalium in urine specimens of men. The use of Gen-Probe TMA and the q-PCR assay, will increase the detection of M. genitalium in clinical specimens at this catchment area.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Mycoplasma nasistruthionis sp. nov. str. Ms03 (Ms03) is one of three Mycoplasma species that were identified from ostriches. Mycoplasmas infections have been implicated in ostrich chick mortalities, growth retardation and downgrading of ostrich carcasses. Currently there is no vaccine available for the treatment of mycoplasmosis in ostriches. This study investigated the development of DNA vaccines against Ms03 infections in ostriches. To this end, the Ms03 genome was sequenced and annotated. The vaccine candidate gene, oppA, was identified within the genome sequence and characterized before DNA vaccines containing the oppA were developed and tested. The genome of Ms03 was sequenced and the resulting 172 contigs were annotated. This dissertation presents the first Ms03 draft genome and annotation which contributed to the understanding of Ms03 as a miniature genetically independent organism. In Ms03, genome replication, cell division, RNA transcription, protein translation and glycolysis resemble that of the closely related Mycoplasma synoviae 53. Purine and pyrimidine metabolism was incomplete and de novo synthesis thereof was not possible. Amino acid synthesis in Ms03 was mostly absent and only the genes that convert aspartate to asparagine and glycine to serine were found. More importers than exporters were annotated owing to the lack of synthesis pathways in Ms03, which is typical for mycoplasmas that have parasitic life styles. Two oligopeptide permease (opp) operons were annotated within the Ms03 genome. The potential of the oppA as a vaccine candidate gene was evaluated by investigating the need for a substrate-binding domain (OppA) as part of the OppBCDF transporter within Mycoplasma species. An oppA homologue could be identified for each oppBCDF operon in all species and therefore must play an essential role in oligopeptide transport. All mycoplasmas (except for hemoplasma) had one, two or three opp operons that could be divided into three types (Type A, B and C). Each type had unique InterPro and MEME domains and motifs which together with the phylogenetic analysis suggest unique roles in their survival under different conditions. Ms03 had a Type A and a Type B opp operon, the Type A oppA was used as vaccine candidate gene. The Type A oppA was cloned and site-directed mutagenesis was used for codon correction before the mutated gene was sub-cloned into three DNA vaccine vectors. The three DNA vaccines (pCI-neo_oppA, VR1012_oppA and VR1020_oppA) were used to vaccinate ostriches and the OppA-antibody response was analysed by ELISA. The VR1020_oppA and pCI-neo_oppA constructs elicited a primary immune response in ostriches, indicating that the OppA protein was expressed in vivo and was immunogenic. This can therefore be viewed as the first step in the development of a DNA vaccine for the control of mycoplasma infections in ostriches. / AFRIKAANSE OPSOMMING: Mycoplasma nasistruthionis sp. nov. str. Ms03 (Ms03) is een van drie mikoplasma spesies wat volstruise infekteer. Mikoplasma-infeksies in volstruise veroorsaak kuiken vrektes, vertraagde groei en afgradering van volstruis karkasse. Daar is tans geen geregistreerde mikoplasma entstof beskikbaar vir gebruik in volstruise nie. Hierdie studie het die ontwikkeling van DNS-entstowwe teen Ms03-infeksies in volstruise ondersoek. Vir hierdie doel was die Ms03-genoomvolgorde bepaal en geannoteer. Die entstofkandidaat-geen, oppA, was geïdentifiseer in die genoomvolgorde en gekarakteriseer voordat DNS-entstowwe (wat die oppA-geen bevat) ontwikkel en getoets is. Die Ms03-genoomvolgorde was bepaal en die gegenereerde 172 aaneenlopende volgordes was geannoteer. Hierdie proefskrif bied die eerste voorlopige volgorde en annotering van die Ms03-genoom wat bygedra het tot die kennis van Ms03 as 'n miniatuur geneties onafhanklike organisme. Genoom-replikasie, seldeling, RNS-transkripsie, proteïen-translasie en glikolise in Ms03 stem ooreen met dié prosesse in die naverwante Mycoplasma synoviae 53. Die purien en pirimidien metabolisme was onvolledig en de novo sintese daarvan was nie moontlik in Ms03 nie. Aminosuursintese in Ms03 was meestal afwesig en net die gene wat aspartaat omskep na asparagien en glisien na serien was gevind in die annoteerde genoom. Meer invoerders as uitvoerders was geannoteer, wat dui op die gebrek aan sintesepadweë in Ms03. Dit is tipies van mikoplasmas wat ‘n parasitiese lewensstyle het. Twee oligopeptied-permeases (opp) operons was gevind in die Ms03-genoom. Die potensiaal van die oppA-geen as 'n entstofkandidaat-geen was geëvalueer deur die behoefte van 'n substraatbindingsdomein (OppA) as deel van die OppBCDF-vervoerder binne mikoplasma spesies te ondersoek. 'n Homoloog van die oppA-geen kon geïdentifiseer word vir elke oppBCDF-operon in al die spesies en behoort daarom 'n noodsaaklike rol te speel in die vervoer van oligopeptiede. Alle mikoplasmas (behalwe vir hemoplasmas) het een, twee of drie opp-operons, wat verdeel kan word in drie tipes (Tipe A, B en C). Elke tipe het unieke InterPro en MEME domeine en motiewe wat saam met die filogenetiese ontleding daarop dui dat hulle unieke rolle in oorlewing onder verskillende omstandighede speel. Ms03 het 'n Tipe A en Tipe B opp-operon, die Tipe A oppA is gebruik as entstofkandidaat-geen. Die Tipe A oppA-geen was gekloneer en teikengerigte-mutagenese was gebruik vir kodonregstellings voordat die gemuteerde geen in drie DNS-entstof vektore gesubkloneer was. Die drie DNS-entstowwe (pCI-neo_oppA, VR1012_oppA en VR1020_oppA) was gebruik om volstruise in te ent en die OppA-teenliggaamsreaksie was geanaliseer deur ELISA. Inenting met die VR1020_oppA en pCI-neo_oppA entstowwe het tot 'n primêre immuniteitsreaksie in volstruise gelei. Dit dui daarop dat die OppA proteïen in vivo uitgedruk en immunogenies was. Dit kan beskou word as die eerste stap in die ontwikkeling van 'n DNS-entstof vir die beheer van mikoplasma-infeksies in volstruise.

Bovine respiratory disease complex (BRD) consists of a largely single clinical entity of bronchopneumonia that is usually associated with the assembly of large numbers of especially weaner cattle into a feedlot environment. It has a multifactorial aetiology and develops as a result of complex interactions between environmental factors, host or animal factors and pathogens. It is often difficult to determine the exact role played by the various pathogens involved in an individual outbreak of disease. None of the many organisms isolated will on their own, reliably reproduce the natural disease in experimental animals. Observations from research studies and clinical experience have indicated that the presence of mycoplasmas increases the severity of respiratory disease. However, the role of Mycoplasma spp. in BRD complex as a primary or secondary pathogen remains controversial. The various stresses associated with the feedlot causes a breakdown of the defense mechanisms that normally hold the nasal infections in check, resulting in a rapid proliferation of virulent Mannheimia haemolytica serotype A1 in particular and the spread to the lower respiratory tract. The various viruses and mycoplasmas have however been shown to have the same effect as stress on the Pasteurella populations of the nasal mucosa. More than 10 species of Mycoplasma have been isolated from the bovine respiratory tract, but not all are pathogenic. They are able to act as a stress-causing agent, leading to a decreased host defense mechanism by altering the immune responsiveness or by causing tissue damage and thereby allowing bacteria to invade and colonise the lung and so causing a severe pneumonia. M. bovis and M. dispar are the more important lung isolates, with M. bovis being the most invasive and destructive and has been shown to increase the severity of calf pneumonias. M. bovis has been isolated from bovine pneumonias, arthritis, mastitis, tendosynovitis, genitalia, keratoconjunctivitis and is considered to be the primary pathogen in endemic pneumonia in younger calves. According to the literature, mycoplasmas are isolated from 25% to 80% of pneumonic lungs in feedlot cattle and the aim of the study was to identify the isolation rates in South African feedlots over a period of 2000 to 2004. To achieve this, 446 transtracheal aspirates (TTA’s) were collected from more than 25 feedlots around South Africa, except for the western Cape. Collection criteria included: pulled for respiratory disease; febrile (≥40ºC); depressed; anorexia and/or lack of rumen fill; nasal discharge or failure to clean muzzle; cough; increased respiratory rate >40 and most importantly, no prior treatment. Samples were also collected from 31 ‘healthy’ animals as controls. Samples collected were used for Mycoplasma isolations, as well as the aerobic bacteria to establish an antibiogram profile of bacteria commonly isolated in cattle feedlots. Mycoplasma spp. were isolated from 52.8% of samples taken from sick animals, with 67 out of 201 isolates (33.3%) being identified as M. bovis. According to the literature, M. bovis, M. haemolytica or P. multocida are isolated from bronchial lavage fluids from healthy calves in only a few cases, with estimates being put at 5 – 10% levels for Mycoplasma. Isolation rates of Mycoplasma spp. from healthy animals in this study was 22.7%, which was considerably higher than anticipated and could possibly be due to problems with the definition of a healthy animal. Although the number of samples from healthy animals was relatively small in this study, it was possible to show that there was a statistically significant association between Mycoplasma isolation and respiratory disease, p = 0,001 and with an odds ratio (OR) of 3,75 in cattle from those feedlots included in the study and thereby proving the hypothesis put forward. / Dissertation (MMedVet (Bovine Medicine))--University of Pretoria, 2007. / Production Animal Studies / MMedVet / Unrestricted

Antimicrobials are commonly used to treat mycoplasmosis in animals. In spite of this and the fact that antimicrobial resistance has been recorded for this group of bacteria there are no universally accepted in vitro means of testing for this resistance, nor is resistance testing for mycoplasmas a routine in most veterinary laboratories. So prior to testing for resistance to a number of mycoplasmas isolated from animals in South Africa it was necessary to compare different tests including broth and agar microdilution tests to find out which one would perform best. Using the field strains M. bovis, M. crocodyli, M. felis, M. gallisepticum and M. synoviae, and the reference strains M. gallisepticum 56USDA, M. gallisepticum VaxSafe MG vaccine strain, M. mycoides T1/44 vaccine strain, and M. mycoides Ygoat (11706) broth- and agar-microdilution minimum inhibitory concentration (MIC)tests were performed using either modified Hayflicks or Mycoplasma synoviae media. Two different metabolism indicator systems were compared in the broth microdilution test (BrMIC) namely sugar fermentation (glucose or pyruvate) with phenol red (SFS) and evidence of reduction with resazurin (AlamurBlue®). It was also tested whether amoxicillin and clavulanic acid (ACA) could be used in the tests to reduce problems associated with contamination. Statistical analyses of the tests (repeatability and linear association) indicated that the BrMIC with SFS was the most reproducible method (pooled standard deviation = 0.14). The antimicrobial ACA was found to not to affect the MIC values (R2= 0.976 to 0.996). Furthermore one hundred forty two field strains including 93 M. bovis, 5 M. synoviae, 21 M. gallisepticum, 13 M. bovirhinis, 8 M. crocodyli and 6 M. felis were tested using the BrMIC+SFS with ACA method. Generally the mycoplasmas originating from poultry were resistant to commonly used antimicrobials and had higher MIC50 and MIC90 values than isolates originating from cattle, crocodiles and cats. It was found that most of the mycoplasmas were susceptible to doxycycline (tetracycline) and enrofloxacin with the exception of M. gallisepticum where 17.9% of strains were resistant to both. Resistance to tiamulin (100%) and tylosin (20 to 64%) was high for the poultry mycoplasmas. Most field isolates tested were resistant to erythromycin, nalidixic acid, florfenicol, norfloxacin, neomycin, sulphamethoxazole, trimethoprim and sulphamethoxazole/ trimethoprim combination, mostly resistant to norfloxacin and florfenicol. It is concluded that BrMIC+SFS with ACA method is a reproducible method that reduces any problems with bacterial contamination. As observed with the poultry strains, it is quite clear that antimicrobial resistance is developing to commonly used antimicrobials such as tylosin, the related pleuromutilins, fluoroquinolones and tetracyclines. In species where antimicrobial therapy is applied routinely such as poultry and possibly feedlot cattle, it is recommended that MIC testing is done prior to any therapeutic interventions. / Dissertation (MSc)--University of Pretoria, 2010. / Veterinary Tropical Diseases / unrestricted