9 research outputs found
Characteristics and outcomes of patients admitted to a tertiary academic hospital in Pretoria with HIV and severe pneumonia : a retrospective cohort study
BACKGROUND : Human immunodeficiency virus (HIV) contributes significantly to morbidity and mortality in South
Africa. Pneumonia and opportunistic infections remain a major cause for hospital admission among those living with
HIV, even in the era of the widespread availability of antiretroviral therapy.
METHODS : In this retrospective cohort study, the records of patients admitted with HIV and severe pneumonia,
requiring high care/intensive care admission, during a period of 12 months (February 2018 to January 2019) were
reviewed. Demographic details, antiretroviral use, HIV viral load, CD4 count, sputum culture results and radiological
imaging of patients were recorded. Data was analysed to determine variables associated with mortality.
RESULTS : One hundred and seventeen patient records were reviewed for this study. The patients were young (mean
age 38.3 years), had advanced disease with low CD4 counts (mean 120.2 cells/mm3) and high HIV viral loads (mean
594,973.7 copies/mL). Only 36.9% (42/117) were on highly active antiretroviral therapy (HAART) on presentation to the
hospital. Mycobacterium tuberculosis (M. tuberculosis) was found to be the cause for pneumonia in 35% (41/117), whilst
Pneumocystis jirovecii (P. jirovecii) was found in 21.4% (25/117). Bacterial pneumonia was the cause in 17.1% (20/117)
of patients while no specific aetiology was found in 26.6% (31/117) of patients in the cohort. Mortality among the
cohort studied was high (40.1%) and the average length of stay in hospital in excess of two weeks. The need for ICU
admission, ventilation and CMV viremia was associated with increased mortality. Chest X-ray findings did not correlate
with the aetiology of pneumonia, but multiple B-lines on lung ultrasound correlated with P. jirovecii as an aetiology
and there was a signal that pleural effusion with fibrin stranding predicts tuberculosis.
CONCLUSIONS : Patients studied presented with advanced HIV and were often naïve to antiretroviral therapy. Mortality
in this cohort of young patients was high, which emphasis the need for earlier diagnosis and treatment of HIV at a
primary care level. Lung ultrasound may have clinical utility in the management of patients with HIV and pneumonia,
particularly to diagnose P. jirovecii as an aetiology.http://www.biomedcentral.com/bmcinfectdisam2023Internal MedicineMedical 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
Diversity of the gut, vaginal and oral microbiome among pregnant women in South Africa with and without pre-eclampsia
The datasets presented in this study can be found in online
repositories. The names of the repository/repositories and accession number(s) can be found below: NCBI SRA database,
accession number PRJNA798597 (BioProjectID).BACKGROUND : Changes in microbial communities are a known characteristic of various inflammatory diseases and have been linked to adverse pregnancy outcomes, such as preterm birth. However, there is a paucity of information regarding the taxonomic composition and/or diversity of microbial communities in pre-eclampsia. The aim of this study was to determine the diversity of the gut, vaginal and oral microbiome in a cohort of South African pregnant women with and without pre-eclampsia. The diversity of the gut, vaginal and oral microbiome was determined by targeted next generation sequencing (NGS) of the V3 and V4 region of the 16S rRNA gene on the Illumina MiSeq platform. RESULTS : In this study population, pre-eclampsia was associated with a significantly higher alpha diversity (P = 0.0472; indicated by the Shannon index) in the vaginal microbiome accompanied with a significant reduction in Lactobacillus spp. (P = 0.0275), compared to normotensive pregnant women. Lactobacillus iners was identified as the predominant species of the vaginal microbiome in both cohorts. High inter-individual variation in alpha diversity was observed in the gut and oral microbiome in both cohorts. Although differences in the relative abundance of bacteria at all phylogenetic levels were observed, overall microbial composition of the gut, oral and vaginalmicrobiome was not significantly different in the pre-eclampsia cohort compared to the normotensive cohort. CONCLUSION : Collectively, a reduction of Lactobacillus spp., and predominance of L. iners in pregnant women with pre-eclampsia could suggest an unstable vaginal microbiome that might predispose pregnant women to develop pre- eclampsia. The lack of significant structural changes in the gut, oral and vaginal microbiome does not suggest that the characterized communities play a role in pre-eclampsia, but could indicate a characteristic unique to the study population. The current study provided novel information on the diversity of the gut, oral and vaginal microbiome among pregnant women in South Africa with and without pre-eclampsia. The current study provides a baseline for further investigations on the potential role of microbial communities in pre-eclampsia.The University of Pretoria and the National Health Laboratory Service (NHLS).https://www.frontiersin.org/journals/global-womens-healtham2023BiochemistryGeneticsMedical MicrobiologyMicrobiology and Plant Patholog
The lung microbiome in HIV‑positive patients with active pulmonary tuberculosis
Tuberculosis poses one of the greatest infectious disease threats of our time, especially when
associated with human immunodeficiency virus (HIV) infection. Very little data is available on the
lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were
studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia
and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a
paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN,
Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for
16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was
performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with
PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria
and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared
to the HIV-positive control cohort. Microbial community structure was also distinct from the control
cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter,
Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe
the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIVpositive
control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the
HIV-positive control cohort without PTB, with an associated loss of microbial diversity.DATA AVAILABILITY : The datasets generated and analysed during the current study are available in the University of Pretoria data
repository and can be accessed at https://doi.org/10.25403/UPresearchdata.19491317.v1.The Infectious diseases Research Fund.http://www.nature.com/scientificreportsam2023BiochemistryGeneticsInternal MedicineMedical MicrobiologyMicrobiology and Plant Patholog
Pharmacological properties and radical scavenging potential of 5-demethyl sinensetin obtained from Loxostylis alata
Please read abstract in the article.The National Research Foundation (NRF), South Africa, the South African Medical Research Council (SIR) and the University of Pretoria for a Postdoctoral Fellowship.http://www.elsevier.com/locate/sajb2024-03-29hj2023Medical MicrobiologyParaclinical Science
Etiology of bacterial vaginosis and polymicrobial biofilm formation
Microorganisms in nature rarely exist in a planktonic form, but in the form of biofilms. Biofilms have been identified as the cause of many chronic and persistent infections and have been implicated in the etiology of bacterial vaginosis (BV). Bacterial vaginosis is the most common form of vaginal infection in women of reproductive age. Similar to other biofilm infections, BV biofilms protect the BV-related bacteria against antibiotics and cause recurrent BV. In this review, an overview of BV-related bacteria, conceptual models and the stages involved in the polymicrobial BV biofilm formation will be discussed.The South African Medical Research Council (MRC)http://www.tandfonline.com/loi/imby202018-03-30hj2017Medical Microbiolog
In vitro anti-biofilm effects of Loxostylis alata extracts and isolated 5-demethyl sinensetin on selected foodborne bacteria
Bacterial biofilms pose health challenges both in clinical environments and the food industry. Major foodborne bacterial pathogens form biofilms on surfaces and persist, causing infections in humans that may be difficult to treat. Conventional use of antibiotics is fast becoming ineffective due to emerging resistance of pathogens to antibiotics. Previous studies have demonstrated the antimicrobial potential of Loxostylis alata A. Spreng. ex Rchb. extracts against a range of bacterial pathogens. The inhibitory effects of methanol and aqueous extracts of L. alata and an antibacterial compound (5-demethyl sinensetin) isolated from the leaves on the growth and development of microbial biofilms was investigated against clinical isolates of Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis and reference strains of Bacillus cereus, Salmonella Enteritidis and Salmonella Typhimurium using the crystal violet (CV) assay. The Kirby-Bauer disk diffusion method was utilized to determine antibiotic susceptibility and resistance profiles of the four clinical and three reference isolates. E. cloacae was resistant to tetracycline and doxycycline and P. mirabilis was resistant to colistin while E. coli and K. pneumoniae were pan-susceptible to all the antibiotics screened. The hot water extract reduced biofilm adhesion from 7% to >50% for the clinical isolates and the ATCC strains, except for S. Typhimurium. The methanol extract inhibited the growth of preformed biofilms of S. Enteritidis and S. Typhimurium by >50% and also reduced the biofilm biomass in S. Enteritidis and E. coli by >50%. The plant extracts and compound were able to reduce initial cell attachment and biofilm biomass, although inhibition of growth in a preformed biofilm was not attained.The National Research Foundation (NRF), South Africa, the South African Medical Research Council (SIR) and the University of Pretoria is thanked for Postdoctoral Fellowships.http://www.elsevier.com/locate/sajb2024-03-07hj2023Medical MicrobiologyParaclinical Science
Evaluation of the rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test for rapid colistin resistance detection in lactose non-fermenting Gram-negative bacteria
INTRODUCTION : Colistin is one of the last-resort antibiotics for treating multidrug-resistant (MDR) or extensively drug-resistant (XDR) lactose non-fermenting Gram-negative bacteria such as Pseudomonas aeruginosa and Acinetobacter baumannii.
GAP STATEMENT : As the rate of colistin resistance is steadily rising, there is a need for rapid and accurate antimicrobial susceptibility testing methods for colistin. The Rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test has recently been developed for rapid detection of colistin resistance in P. aeruginosa and A. baumannii.
AIM : The present study aimed to evaluate the performance of the Rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test in comparison with the reference broth microdilution (BMD) method.
METHODOLOGY : The Rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test was performed using a total of 135 P. aeruginosa (17 colistin-resistant and 118 colistin-susceptible) and 66 A. baumannii isolates (32 colistin-resistant and 34 colistin-susceptible), in comparison with the reference BMD method.
RESULTS : The categorical agreement of the Rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test with the reference BMD method was 97.5 % with a major error rate of 0 % (0/152) and a very major error (VME) rate of 10.2 %. The VME rate was higher (23.5 %) when calculated separately for P. aeruginosa isolates. The overall sensitivity and specificity were 89.8 and 100 %, respectively.
CONCLUSION : The Rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test performed better for A. baumannii than for P. aeruginosa.TABLE S1: The Rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test results in
comparison with the reference broth microdilution (BMD).The National Health Laboratory Service
Research trust.https://www.microbiologyresearch.org/content/journal/jmmhj2022Medical Microbiolog
Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations
triggered by infections. The aim of this study was to determine the composition of the lung
microbiome and lung virome in patients with COPD in an African setting and to compare their
composition between the stable and exacerbated states. Twenty-four adult COPD patients were
recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted
metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were
extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing
was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes
and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There
were no considerable diferences for alpha and beta diversity measures between the disease states.
However, a diference in the abundances between disease states was observed for: (i) Serratia (3%
lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated
state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5%
higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058
virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the frst
to report lung microbiome composition in COPD patients from Africa. In this small sample set, no
diferences in alpha or beta diversity between stable and exacerbated disease state was observed, but
an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the
need for further research of the lung microbiome of COPD patients in African settings.National Health Laboratory Service of South Africa (NHLS) Research Trusthttp://www.nature.com/srep/index.htmlpm2022Internal MedicineMedical Oncolog