Characterization and identification of some indigenous Rhizobia using 16S rDNA sequence analysis

ENGLISH : The use of different characteristics (the polyphasic approach) to describe bacterial taxa is a prerequisite for a stable classification. The taxonomy of root- and stem-nodulating rhizobia is in a state of transition. As more legumes are studied, new species and genera of rhizobia are described. It is important to study the indigenous South African rhizobia, as without them a complete rhizobial taxonomy is not possible. Furthermore, strains with superior nitrogen fixation abilities may be discovered. Indigenous strains better adapted to the harsh South African environment are possible candidates for commercial inoculants for cropped legumes.Only two local studies have been done on the diversity of the indigenous rhizobia. These studies revealed the diversity of rhizobia existing in the South African context. As part of a polyphasic approach used to identify and determine the diversity of the indigenous rhizobia, 16S rDNA sequencing analysis was performed on some selected rhizobial and putative rhizobial isolates. The aim of the study was to characterise and identify the indigenous isolates by 16S rDNA sequencing analysis and compare our data with those available in the GenBank database. Results showed that most of the indigenous isolates were slow-growers belonging to the genus Bradyrhizobium. Two isolates from supposedly non-nodulating legume genera (Cassia and Senna) were found to belong to the genus Bradyrhizobium. Some of the isolates were shown to belong to the genera Mesorhizobium, Rhizobium and Sinorhizobium. The identity of five isolates was not clear and further studies need to be performed to unequivocally determine their taxonomic position. Partial sequence analysis of 16S rDNA proved a valuable tool to characterise and identify the indigenous isolates. However, the method was unable to clearly distinguish between closely related species and strains. AFRIKAANS : 'n Stabiele klassifikasiesisteem vir die beskrywing van bakteriese taksa is slegs moontlik deur verskillende eienskappe (die poli-fasiese benadering) te gebruik. Die taksonomie van die wortel- en stamnodulerende rhizobiums verander gedurig. 'n Volledige rhizobiumtaksonomie is slegs moontlik indien die inheemse Suid-Afrikaanse rhizobiums bestudeer word. Geharde inheemse rasse met voortreflike stikstofbindende vermoens kan ontdek word. Hierdie rasse is kandidate vir kommersiele inokulums vir verboude peulplante. Net twee plaaslike studies is gedoen om die diversiteit van die inheemse rhizobiums te bepaal. Die studies het bewys dat die inheemse rhizobiums baie divers is. As deel van die polifasiese benadering om die diversiteit van die inheemse rhizobiums te identifiseer en te bepaal, is 16S rDNS volgordebepaling gedoen op uitgesoekte rhizobia en sogenaamde rhizobia isolate. Die doel van die studie was die karakterisering en identifisering van die inheemse isolate deur 16S rDNS volgordebepaling en die vergelyking van die data met die beskikbaar in die GenBank databasis. Die resultate wys dat die meeste inheemse isolate stadige groeiers is en dus behoort aan die genus Bradyrhizobium. Twee isolate vanaf sogenaamde nie-nodulerende peulplantgenusse (Cassia en Senna) behoort ook tot die genus Bradyrhizobium. Sommige isolate behoort tot die genusse Mesorhizobium, Rhizobium en Sinorhizobium. Die identiteit van vyf isolate was nie duidelik nie en verdere studies is nodig om hul taksonomiese posisie ondubbelsinnig te bepaal. Die gedeeltelike volgordebepaling van die 16S rDNS was 'n waardevolle hulpmiddel om die inheemse isolate mee te karakteriseer en te identifiseer, alhoewel die metode nie tussen nabyverwante spesies en rasse kon onderskei nie. CopyrightDissertation (MSc (Microbiology))--University of Pretoria, 1999.Microbiology and Plant Pathologyunrestricte

Diversity of root nodulating bacteria associated with Cyclopia species

In recent years, the rhizobial taxonomy changed significantly with the discovery of novel symbiotic associations between legumes and nodulating bacteria. This was aided by the focus shift from studying only agricultural crops to legumes indigenous to certain regions, ultimately to discover new inoculant strains and to uncover the secrets of the rhizobium¬legume symbiosis. In previous studies on the diversity of South African rhizobia, it has become clear that our country has a wealth of rhizobia. Cyclopia is a legume genus, which belongs to the fynbos biome of South Africa. Honeybush tea is a herbal infusion manufactured from the leaves and stems of certain Cyclopia spp. Commercial cultivation of this potentially new agricultural crop is now developed to protect the natural Cyclopia spp. populations from harvesting and ultimately extinction. Superior inoculant strains are necessary for these commercial seedlings. The diversity of root-nodulating strains isolated from 14 Cyclopia spp. was determined using 16S-23S IGS-RFLP and partial 16S rDNA base sequencing. Based on 16S-23S IGS-RFLP and partial 16S rDNA base sequencing most of the isolates, with the exception of seven strains, were found to belong to the genus Burkholderia. More extensive phylogenetic, symbiotic and phenotypic studies of selected strains were performed using near full-length 168 rDNA base sequencing, nodA base sequencing and substrate utilisation analysis. In the genus Burkholderia, the isolates belonged to the novel root-nodulating species Burkholderia tuberum and several novel, undescribed Burkholderia genotypes. However, no new Burkholderia species could formally be proposed, since DNA-DNA hybridisation analysis, which is a prerequisite for the description of new species could not be performed in our laboratory. The seven strains not affiliated with the Burkholderia genus belonged to two Bradyrhizobium genospecies, R tropici and a possibly new genus in the a-Proteobacteria. The nodA sequences of all the Cyclopia isolates corresponded to a large extent, indicating that different chromosomal genotypes harbour the same symbiotic genotype. All the isolates of the Cyclopia genus appear to be acid-tolerant, which is in agreement with the acidic nature of the soil from which the strains were isolated.Thesis (PhD(Microbiology))--University of Pretoria, 2004.Microbiology and Plant Pathologyunrestricte

Importance of Candida infection and fluconazole resistance in women with vaginal discharge syndrome in Namibia

BACKGROUND : Vaginal discharge syndrome (VDS) is a common condition. Clinical management targets sexually transmitted infections (STIs) and bacterial vaginosis (BV); there is limited focus on Candida infection as cause of VDS. Lack of Candida treatment coverage and, if present, antifungal resistance may result in VDS treatment failure. This study aimed to determine the prevalence of Candida infection, antifungal resistance, and coinfections in Namibian women with VDS. METHODS : A cross-sectional study was performed using 253 vaginal swabs from women with VDS in Namibia. Demographic data was collected, and phenotypic and molecular detection of Candida species was performed followed by fluconazole susceptibility testing of Candida isolates. BV was diagnosed using Nugent score microscopy; molecular detection of Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis was performed. RESULTS : Candida species was detected in 110/253 women (43%). Ninety women (36%) had Candida albicans and 24 (9.5%) had non-albicans Candida species. The non-albicans species detected were 19 (17%) Candida glabrata, 4.0 (3.5%) Candida krusei, and 1.0 (0.9%) Candida parapsilosis. Candida albicans were more frequently isolated in younger (p = 0.004) and pregnant women (p = 0.04) compared to non-albicans Candida species. Almost all (98%) Candida albicans isolates were susceptible to fluconazole while all non-albicans Candida species were fluconazole resistant. STIs were diagnosed in 92 women (36%): 30 (12%) with C. trachomatis, 11 (4.3%) N. gonorrhoeae, and 70 (28%) T. vaginalis; 98 (39%) women had BV. Candida infection alone was diagnosed in 30 women (12%), combined with STIs in 42 women (17%) and was concurrent with BV in 38 women (15%). Candida infection was more often detected in swabs from women without C. trachomatis detected (6.4% vs. 16%; OR 0.30; 95% CI 0.10–0.77, p = 0.006). CONCLUSIONS : The high prevalence of Candida infection, especially those due to non-albicans Candida species that are resistant to fluconazole, is a great concern in our setting and may lead to poor treatment outcomes. Access to microbiological testing for Candida species in the context of syndromic management is warranted.The University of Pretoria Doctoral Commonwealth Scholarship.http://www.aricjournal.comam2023Medical Microbiolog

Normal flora and bacterial vaginosis in pregnancy : an overview

The female genital tract is an intricate, yet balanced ecosystem that hosts a variety of different residential microflora. The physiological changes that occur during pregnancy may disrupt this balanced ecosystem and predispose women to a potentially pathogenic microbiota. Bacteria that are associated with bacterial vaginosis (BV) are opportunistic pathogens that frequently form part of this microbiota. The overgrowth of and infections with these bacteria are linked to poor obstetric outcomes and increased transmission of other reproductive tract infections (RTIs). These infections increase women’s susceptibility of acquiring HIV, the rates of HIV shedding and the development of Acquired Immune Deficiency Syndrome (AIDS) in HIV infected patients. It is unknown how the plethora of bacterial species associated with BV contributes to the dynamics of this condition. The use of high-throughput methods have led to the in-depth investigation of different BV-related bacterial species and the functional capabilities of these species. However, the pathogenesis of BV is still poorly defined and the role of individual BV-related bacterial species in specific pregnancy complications is unclear and controversial. The majority of BV infections are asymptomatic and successful diagnosis is complicated by the lack of reliable and standardized diagnostic tests.University of Pretoria, the Medical Research Council (South Africa) and the National Health Laboratory Service (NHLS).http://www.tandfonline.com/loi/imby202017-05-31hb2016Medical Microbiolog

Comparison of the new Mycofast Revolution assay with a molecular assay for the detection of genital mycoplasmas from clinical specimens

BACKGROUND: Genital mycoplasmas are opportunistic bacteria that are associated with undesirable gynaecologic and reproductive events. Mycoplasmas are fastidious bacteria with increasing resistance to routine antimicrobials and often fail to grow on conventional culture methods. The commercial Mycofast Revolution assay permits the phenotypic detection and identification of genital mycoplasmas. Antimicrobial susceptibility testing against five antimicrobial agents with MICs corresponding to the CLSI guidelines can also be performed. This study aimed to compare the new commercially available Mycofast Revolution assay with a multiplex PCR assay. METHODS: Self-collected swabs were obtained from pregnant women attending the antenatal clinic of a tertiary academic hospital in Pretoria, South Africa from October 2012 to November 2012. These swabs were used to seed UMMt and modified Amies transport media. The seeded UMMt transported medium was used to inoculate the Mycofast Revolution assay for the identification, enumeration and antimicrobial susceptibility testing of genital mycoplasmas. Following DNA extraction from the modified Amies transport medium, specimens were subjected to a multiplex PCR assay for the detection of genital mycoplasmas. RESULTS: The Mycofast Revolution kit had a sensitivity and specificity of 77.3% (95% CI: 62.15% to 88.51%) and 80% (95% CI: 28.81% to 96.70%), respectively, against the PCR assay. The positive and negative predictive values were 97.1% (95% CI: 85.03% to 99.52%) and 28.6% (95% CI: 8.57% to 58.08%). Genital mycoplasmas were detected in 71.4% (35/49) of samples with the Mycofast Revolution assay with 49% (24/49) being Ureaplasma spp. and 22.4% (11/49) mixed strains. The multiplex PCR assay had a positivity rate of 89.8% (44/49) for genital mycoplasmas; mixed strains were present in 51% (25/49) of samples, Ureaplasma spp. in 16.3% (8/49) and M. hominis in 22.4% (11/49) of samples. CONCLUSIONS: There was a fair agreement (κ = 0.319) between the Mycofast Revolution assay and the mPCR assay. With the high prevalence rates of genital mycoplasmas, fast and efficient diagnostic methods are imperative to treat infections and minimise complications. The Mycofast Revolution assay is simple to use, has a short turnaround time and interpretation of results are straightforward. This assay circumvents common problems experienced with conventional culture and molecular methods in diagnostic laboratories where skilled personnel are limited and can be used as an alternative diagnostic assay.http://www.biomedcentral.com/1471-2334/13/453am201

Surveillance of catheter-related infections : the supplementary role of the microbiology laboratory

BACKGROUND : The burden of catheter-related infections (CRIs) in developing countries is severe. In South Africa, a standardised surveillance definition does not exist and the collection of catheter days is challenging. The aim of the study was to provide baseline data on the prevalence of CRIs and to describe the epidemiology of CRI events within a tertiary academic hospital. METHODS : Surveillance was laboratory-based and conducted for a six month period. A microbiologically confirmed CRBSI (MC-CRBSI) event was defined as the isolation of the same microorganism from the catheter and concomitant blood cultures (BCs), within 48 h of catheter removal, which were not related to an infection at another site. RESULTS : A total of 508 catheters, removed from 332 patients, were processed by the laboratory, of which only 50% (253/508 removed from 143/332 patients) of the catheters were accompanied by BCs within 48 h. Sixty-five episodes of MC-CRBSI in 57 patients were detected, involving 71 catheters and 195 microbial isolates. The institutional prevalence rate was 3.7 episodes per 1 000 admissions and 5.8 episodes per 10 000 in-patient days. Catheter day data was collected in only six wards of the hospital. The pooled laboratory incidence was 10.1 MC-CRBSI episodes per 1 000 catheter days, whereas the hospital-based central line-associated bloodstream infection (CLABSI) rate was pooled at 5.7 episodes per 1 000 catheter days. The majority of patients had an underlying gastro-intestinal condition (33%; 19/56) with a non-tunnelled, triple-lumen central venous catheter, placed in the subclavian vein (38%; 27/71). The most predominant pathogen was methicillin-resistant Staphylococcus epidermidis (28%; 55/195), followed by extensively-drug resistant Acinetobacter baumannii (18%; 35/195). CONCLUSIONS : Catheter-related infection prevention and control efforts require urgent attention, not only to keep patients safe from preventable harm, but to prevent the spread of multidrug resistant microorganisms.RESCOM,Faculty of Health Science, UP, National Health Laboratory Service (NHLS) and the National Research Foundation (NRF).http://www.biomedcentral.com/bmcinfectdis/hb201

A cross-sectional study on the relationship of age, gestational age and HIV infection to bacterial vaginosis and genital mycoplasma infection

OBJECTIVES : Pregnant women are especially at risk of developing complications when infected with reproductive tract infections (RTIs). The objective of this study was to determine the prevalence of bacterial vaginosis (BV) and genital mycoplasmas in pregnant women and investigate the associations between BV, genital mycoplasmas, HIV infection, age and gestational age. DESIGN : Cross-sectional study with descriptive and analytical components. SETTING : Antenatal clinic of a tertiary academic hospital in South Africa. PARTICIPANTS : 220 pregnant women older than 18 were included in the study and provided self-collected vaginal swabs. PRIMARY AND SECONDARY OUTCOMES : BV and genital mycoplasma colonisation and/or infection in women of differing age, gestational period and HIV status. RESULTS : The prevalence of BV was 17.7% (39/220) (95% CI 12.9 to 23.4), intermediate vaginal flora (IVF) 15% (33/220) (95% CI 10.56 to 20.42), and the overall prevalence of genital mycoplasmas was 84% (185/220) (95% CI 78.47 to 88.58). BV was significantly associated with HIV infection with an OR of 2.84 (95% CI 1.08 to 7.46 and p value=0.034). However, BV was inversely associated with gestational age with an OR of 0.08 (95% CI 0.01 to 0.42 and p value=0.003) for second trimester pregnancies and an OR of 0.03 (95% CI 0.01 to 0.17 and p value<0.001) for third trimester pregnancies using the first trimester as reference. IVF was significantly associated with HIV infection with an OR of 2.7 (95% CI 1.07 to 6.79 and p value=0.035) but not with age or gestational age. Genital mycoplasmas were not significantly associated with age, gestational age, HIV status, BV flora or IVF. CONCLUSIONS : The high infection rate of genital mycoplasmas and the association of BV with HIV found in this study reiterate the importance of screening for these RTIs in high-risk groups such as pregnant women.The University of Pretoria and the Medical Research Council (South Africa).http://bmjopen.bmj.comam201

Genetic relatedness of Staphylococcus aureus isolates obtained from cystic fibrosis patients at a tertiary academic hospital in Pretoria, South Africa

Cystic fibrosis (CF) is an inherited recessive disease that affects mucocillary clearance in the lung, allowing it to be colonised with bacteria such as Staphylococcus aureus. To survive in the CF lung S. aureus adapts both phenotypically and genotypically, through various mechanisms. In this study, multiple specimens were collected from the participants and were processed routinely and were additionally cultured in chromogenic media. Multiplex PCR assays were employed to detect methicillin resistance and selected virulence and quaternary ammonium compound (qac) genes. Genetic relatedness of the S. aureus was determined using agr, SCCmec and spa typing as well as pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Thirty-three S. aureus isolates were isolated, of which 51% (17/33) were methicillin resistant S. aureus (MRSA). The virulence and qac genes were more prevalent in MRSA than the methicillin sensitive S. aureus (MSSA) isolates. The PFGE analysis showed nine distinct pulsotypes while MLST showed eight sequence types. All the STs detected in this study, except for ST508 have been previously isolated from CF patients according to the literature. This study showed a genetically diverse S. aureus population with a high prevalence of virulence genes among the MRSA isolates from the CF clinic.The NHLS Research Trust, the NRF and RESCOM.http://www.nature.com/srepam2019Medical Microbiolog