Browsing by Author "Naicker, Preneshni"

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    Open Access
    Colonisation with pathogenic drug-resistant bacteria and Clostridioides difficile among residents of residential care facilities in Cape Town, South Africa: a cross-sectional prevalence study
    (2019-11-19) September, Jason; Geffen, Leon; Manning, Kathryn; Naicker, Preneshni; Faro, Cheryl; Mendelson, Marc; Wasserman, Sean
    Abstract Background Residential care facilities (RCFs) act as reservoirs for multidrug-resistant organisms (MDRO). There are scarce data on colonisation with MDROs in Africa. We aimed to determine the prevalence of MDROs and C. difficile and risk factors for carriage amongst residents of RCFs in Cape Town, South Africa. Methods We performed a cross-sectional surveillance study at three RCFs. Chromogenic agar was used to screen skin swabs for methicillin-resistant S. aureus (MRSA) and stool samples for extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E). Antigen testing and PCR was used to detect Clostridiodes difficile. Risk factors for colonisation were determined with logistic regression. Results One hundred fifty-four residents were enrolled, providing 119 stool samples and 152 sets of skin swabs. Twenty-seven (22.7%) stool samples were positive for ESBL-E, and 13 (8.6%) residents had at least one skin swab positive for MRSA. Two (1.6%) stool samples tested positive for C. difficile. Poor functional status (OR 1.3 (95% CI, 1.0–1.6)) and incontinence (OR 2.9 (95% CI, 1.2–6.9)) were significant predictors for ESBL-E colonisation. MRSA colonization appeared higher in frail care areas (8/58 v 5/94, p = 0.07). Conclusions There was a relatively high prevalence of colonisation with MDROs, particularly ESBL-E, but low C. difficile carriage, with implications for antibiotic prescribing and infection control practice.
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    Epidemiology of leptospirosis in Groote Schuur Hospital
    (2021) Mteshana, Ziningi Charity; Dlamini, Sipho; Muloiwa, Rudzani; Naicker, Preneshni
    Background The burden of leptospirosis in sub-Saharan Africa remains unclear although it is accepted that this infection is widely spread in this region. The global estimated number of cases is one million with 58 900 deaths attributable to leptospirosis annually. Objective To describe the profile of patients with suspected leptospirosis and to compare their in hospital outcomes. Methods & Material We performed a retrospective study at a tertiary referral hospital in South Africa. All adults with suspected leptospirosis who had a laboratory request for leptospirosis ELISA IgM testing between 2005 and 2015 were included. Clinical and laboratory findings at presentation were correlated with the patient's subsequent clinical course and ELISA IgM status. Results During the study period 223 patients who had ELISA IgM test requests were enrolled. Leptospirosis ELISA IgM was positive in 45 (20%) patients. Enrolled patients had a median age of 38 (IQR 31 – 53) years, 147/223 (66%) were males and 80/223 (36%) were HIV positive. There were 12/45 (27%) HIV-positive patients in the IgM-positive group compared to 68/178 (38%) in the IgM-negative group, p=0.22. Compared to IgM-negative patients, patients with positive IgM were more likely to present with jaundice 37/45 (82%) vs. 82/178 (46%), p <0.01, and acute kidney injury (AKI) 34/45 (76%) vs.102/178(57%), p=0.06. The median length of hospital stay was 13 days (IQR 8-22 days) for IgM-positive compared to 10 days (IQR 6-21 days) in IgM-negative patients, p= 0.10. A total of 11/45 (24%) IgMpositive patients required ICU admission compared to 41/178 (23%) of IgM-negative patients, p=0.84 and the median length of ICU stay was 7 days (IQR 4-11) for IgM-positive compared to 6 days (IQR 3-9.5) for IgM-negative patients, p=0.51. There were 13/45 (29%) IgM-positive patients who needed dialysis compared to 42/178 (24%) of IgM-negative patients, p= 0.46. The mortality rate was 7/45 (16%) in IgM-positive compared to 52/178 (29%) in IgM-negative patients, p=0.07. Conclusion Patients with positive IgM presented predominantly with jaundice and AKI. There was no statistically significant difference in HIV status and outcomes between the two groups of patients
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    Streptococcus pneumoniae Serotypes and Mortality in Adults and Adolescents in South Africa: Analysis of National Surveillance Data, 2003 - 2008
    (Public Library of Science, 2015) Cohen, Cheryl; Naidoo, Nireshni; Meiring, Susan; de Gouveia, Linda; van Mollendorf, Claire; Walaza, Sibongile; Naicker, Preneshni; Madhi, Shabir A; Feldman, Charles; Klugman, Keith P; Dawood, Halima; von Gottberg, Anne; GERMS-SA
    BACKGROUND: An association between pneumococcal serotypes and mortality has been suggested. We aimed to investigate this among individuals aged ≥15 years with invasive pneumococcal disease (IPD) in South Africa. METHODS: IPD cases were identified through national laboratory-based surveillance at 25 sites, pre-pneumococcal conjugate vaccine (PCV) introduction, from 2003-2008. We assessed the association between the 20 commonest serotypes and in-hospital mortality using logistic regression with serotype 4 (the third commonest serotype with intermediate case-fatality ratio (CFR)) as referent. RESULTS: Among 3953 IPD cases, CFR was 55% (641/1166) for meningitis and 23% (576/2484) for bacteremia (p<0.001). Serotype 19F had the highest CFR (48%, 100/207), followed by serotype 23F (39%, 99/252) and serotype 1 (38%, 246/651). On multivariable analysis, factors independently associated with mortality included serotype 1 (OR 1.9, 95%CI 1.1-3.5) and 19F (OR 2.9, 95%CI 1.4-6.1) vs. serotype 4; increasing age (25-44 years, OR 1.8, 95%CI 1.0-3.0; 45-64 years, OR 3.6, 95%CI 2.0-6.4; ≥65 years, OR 5.2, 95%CI 1.9-14.1; vs. 15-24 years); meningitis (OR 4.1, 95%CI 3.0-5.6) vs. bacteremic pneumonia; and HIV infection (OR1.7, 95%CI 1.0-2.8). On stratified multivariate analysis, serotype 19F was associated with increased mortality amongst bacteremic pneumococcal pneumonia cases, while no serotype was associated with increased mortality in meningitis cases. CONCLUSION: Mortality was increased in HIV-infected individuals, which may be reduced by increased antiretroviral therapy availability. Serotypes associated with increased mortality are included in the 10-and-13-valent PCV and may become less common in adults due to indirect effects following routine infant immunization.
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    Technical evaluation of a Real-time polymerase chain reaction (PCR) assay for the detection of Bartonella spp for diagnostic purposes
    (2022) Booley, Ghowa; Paul, Lynthia; Moodley, Clinton; Naicker, Preneshni
    Infective endocarditis (IE) is a rare disease affecting heart tissues. The laboratory diagnosis of culture-negative endocarditis is complicated, and largely based on the combination of nucleic acid detection methods and serological investigation. There is a paucity of published data on microbes causing culture-negative endocarditis, but a recent report indicated that the bacterium Bartonella was the commonest cause of culture-negative endocarditis at a tertiary care facility in Cape Town, South Africa. This laboratory-based, non-clinical pilot study, evaluated the utility of a previously published real-time PCR assay for detecting Bartonella spp. on cats. This will be the first time this target will be evaluated in a real-time PCR assay to detect Bartonella spp. in human samples. For this study, we constructed a plasmid vector containing an insert of 83bp, derived from the Bartonella nuoG gene. In this non-clinical, laboratory evaluation, we used one laboratory sample to amplify the nuoG bacterial DNA fragment and cloned it into a plasmid vector. Using this plasmid in a technical validation, we demonstrated that the previously described assay could detect nuoG when using the LightCycler 480 Probes Master Mix. The results indicated that the assay reliably detected as little as 1000 copies of the target DNA, and infrequently also detected 10-100 copies of the target. The study showed no amplification using some commonly encountered organisms found in our clinical setting, thus indicating 100% specificity for Bartonella. We demonstrated that a plasmid construct containing an internal fragment from the nuoG gene successfully detected the target using a real-time PCR assay. Future testing should include further optimisation to improve reaction efficiency of the assay with spiked diagnostic samples, including peripheral blood, and DNA extracted from heart valve samples. The utility of the RT-PCR for diagnostic purposes should be evaluated by comparing assay turnaround time, sensitivity, and specificity of this assay versus the conventional PCR and Sanger sequencing currently in use to detect Bartonella spp. in heart valves. We concluded that the assay exhibited strong potential for use as a diagnostic PCR using the constructed plasmid, but that further optimization to improve PCR efficiency, and work to determine the clinical sensitivity and specificity are needed before the assay can be applied to blood samples.
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    The utility of a real-time PCR to detect Leptospira in a routine diagnostic setting
    (2022) Chanda, Raphael; Paul, Lynthia; Moodley, Clinton; Naicker, Preneshni
    Leptospirosis is a neglected zoonotic infection with world-wide distribution. A paucity of leptospirosis data from the African continent exists, mainly due to limited access to diagnostics. The clinical presentation ranges from mild to severe disease with multi organ involvement, while the mild form mimics another common tropical disease i.e., malaria. The gold standard for diagnostic detection currently is an immunological test discerning the presence of specific antibodies present in the immune phase of the disease. The serological methods are hindered by the inability to distinguish past from current infection and utility limited to only the immune phase of the disease. Due to lack of sensitivity and specificity in serological methods, improved diagnostic methods are needed to aid early identification in the acute phase. Methods should also distinguish saprophyte and pathogenic species. To address this gap, we developed an inhouse PCR assay targeting the microbe's rrs and lipL32 genes, using primer sets previously reported in literature to be both sensitive and specific for pathogenic Leptospira spp. Using inhouse constructed plasmids, we did a non-clinical, technical validation employing probe-based, real time polymerase chain reaction assays and a locally available commercial kit. Although our assay needs further optimization, we demonstrated that the PCR reliably detected 100 copies and 1000 copies of Leptospira rrs and lipL32 targets respectively. To test specificity, we did real-time PCR with pure DNA from a selected set of pathogens known to be prevalent in bacteremia's in local settings and observed that the rrs target was amplified with Group B streptococci as template but no other tested pathogens, while no non-specific amplification for lipL32 was observed. The non-specific amplification had been reported previously in the literature, suggesting the rrs gene is not a good target to use, even when primers are specifically designed to only detect Leptospira rrs. Future work using the assay should include optimizing assay performance using DNA extracted from the ideal clinical samples to detect Leptospira, namely urine and blood of patients clinically suspected to have leptospirosis. However, the assay demonstrated potential for use as a diagnostic PCR using the constructed plasmid, but further optimization to improve PCR efficiency and assessing its performance in clinical setting is required