19 research outputs found
Prevalence and patterns of antimicrobial resistance of respiratory pathogens isolated from patients attending the cystic fibrosis clinic at Charlotte Maxeke Johannesburg academic hospital, 2006-2010
MBBCh(Wits) DCH (SA) DipHIVMan (SA) FCPath (SA) Micro
Degree: MMed (Micro)
Department: Clinical Microbiology and Infectious Diseases
NHLS MicrobiologyMT201
Molecular characterisation of Acinetobacter baumannii isolates from bloodstream infections in a tertiary-level hospital in South Africa
Acinetobacter baumannii is an opportunistic pathogen and causes
various infections in patients. This study aimed to describe the clinical,
epidemiological and molecular characteristics of A. baumannii isolated
from BCs in patients at a tertiary-level hospital in South Africa. Ninety-six
isolates from bloodstream infections were collected. Clinical characteristics
of patients were recorded from patient files. Organism identification and
AST was performed using automated systems. PCR screening for the mcr-1
to mcr-5 genes was done. To infer genetic relatedness, a dendrogram
was constructed using MALDI-TOF MS. All colistin-resistant isolates (n = 9)
were selected for WGS. The patients were divided into three groups, infants
(<1 year; n = 54), paediatrics (1â18 years; n = 6) and adults (â„19 years;
n = 36) with a median age of 13 days, 1 and 41 years respectively. Of the 96
A. baumannii bacteraemia cases, 96.9% (93/96) were healthcare-associated.
The crude mortality rate at 30 days was 52.2% (48/92). The majority of the
isolates were multidrug-resistant (MDR). All isolates were PCR-negative for
the mcr-1 to mcr-5 genes. The majority of the isolates belonged to cluster
1 (62/96) according to the MALDI-TOF MS dendrogram. Colistin resistance
was confirmed in nine A. baumannii isolates (9.4%). The colistin-resistant
isolates belonged to sequence type (ST) 1 (5/6) and ST2 (1/6). The majority
of ST1 isolates showed low SNP diversity (â€4 SNPs). All the colistin-resistant
isolates were resistant to carbapenems, exhibited an XDR phenotype and
harboured the blaOXAâ23 gene. The blaNDM gene was only detected in ST1 colistin-resistant isolates (n = 5). The lpsB gene was detected in all colistinresistant isolates as well as various efflux pump genes belonging to the RND,
the MFS and the SMR families. The lipooligosaccharide OCL1 was detected in
all colistin-resistant ST1 and ST2 isolates and the capsular polysaccharide KL3
and KL17 were detected in ST2 and ST1 respectively. This study demonstrated
a 9.4% prevalence of colistin-resistant ST1 and ST2 A. baumannii in BC isolates.
The detection of the lpsB gene indicates a potential threat and requires close
prospective monitoring.National Health Laboratory Service (NHLS) Research Trust.https://www.frontiersin.org/journals/microbiologydm2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog
Appropriate use of colistin in neonates, infants and children : interim guidance
DATA AVAILABILITY : No raw data are available for this guidance document.No abstract available.http://www.sajid.co.zaam2024Paediatrics and Child HealthSDG-03:Good heatlh and well-bein
Acinetobacter baumannii complex, national laboratory-based surveillance in South Africa, 2017 to 2019
OBJECTIVE :
We aimed to provide an analysis of A. baumannii complex (ABC) isolated from blood cultures in South Africa.
MATERIALS AND METHODS :
ABC surveillance was conducted from 1 April 2017 to 30 September 2019 at 19 hospital
sites from blood cultures of any age and sex. Organism identification was performed using
the MALDI-TOF MS and antimicrobial susceptibility testing (AST), MicroScan Walkaway
System. We confirmed colistin resistance with Sensititre, FRCOL panel, and selected for
whole-genome sequencing.
RESULTS :
During the study period, we identified 4822 cases of ABC, of which 2152 cases were from
19 enhanced surveillance sites were reported during the enhanced surveillance period (1
August 2018 to 30 September 2019). Males accounted for 54% (2611/4822). Of the cases
with known age, 41% (1968/4822) were infants (< 1-year-old). Seventy-eight percent (1688/
2152) of cases had a known hospital outcome, of which 36% (602/1688) died. HIV status
was known for 69% (1168/1688) of cases, and 14% (238/1688) were positive. Eighty-two percent (1389/1688) received antimicrobial treatment in admission. Three percent (35/
1389) of cases received single colistin. Four percent (75/2033) were resistant to colistin. At
least 75% of the isolates (1530/2033) can be classified as extensively drug-resistant (XDR),
with resistance to most antibiotics except for colistin. The majority, 83% (20/24), of the colistin-resistant isolates were of the sequence type (ST) 1. Resistance genes, both plasmidand chromosomal- mediated were not observed. Although all isolates had, nine efflux pump
genes related to antimicrobial resistance.
CONCLUSION :
Our surveillance data contributed to a better understanding of the natural course of A. baumannii disease, the patient characteristics among infants, and the level of resistance. At
least two-thirds of the isolates were extensively drug-resistant, and four percent of isolates
were resistant to colistin.http://www.plosone.orgdm2022Medical Microbiolog
Federation of Infectious Diseases Societies of Southern Africa guideline : recommendations for the detection, management and prevention of healthcare-associated Candida auris colonisation and disease in South Africa
Candida auris has been detected at almost 100 South African hospitals, causing large
outbreaks in some facilities, and this pathogen now accounts for approximately 1 in 10 cases
of candidaemia. The objective of this guideline is to provide updated, evidence-informed
recommendations outlining a best-practice approach to prevent, diagnose and manage
C. auris disease in public- and private-sector healthcare settings in South Africa. The 18
practical recommendations cover five focus areas: laboratory identification and antifungal
susceptibility testing, surveillance and outbreak response, infection prevention and control,
clinical management and antifungal stewardship.The South African Society for Clinical Microbiology and the Federation of Infectious Diseases Societies of Southern Africa.https://sajid.co.za/index.php/sajidpm2020School of Health Systems and Public Health (SHSPH
Case-fatality and sequelae following acute bacterial meningitis in South Africa, 2016 through 2020
OBJECTIVES : Providing country-specific estimates of case fatality and sequelae from bacterial meningitis (BM) is important to evaluate and monitor progress toward the World Health Organization's roadmap to âdefeating meningitis by 2030â.
METHODS : From 2016-2020, GERMS-SA conducted enhanced surveillance at 26 hospitals across South Africa. Episodes of laboratory-confirmed BM due to Streptococcus pneumoniae, Haemophilus influenzae , and Neisseria meningitidis were included. Risk factors for in-hospital death and sequelae at hospital discharge among survivors were analyzed.
RESULTS : Of 12,717 invasive bacterial infections reported nationally, 39% (4980) were from enhanced surveillance sites, including 4159 pneumococcal, 640 H. influenzae , and 181 meningococcal infections. BM accounted for 32% (1319/4159) of pneumococcal, 21% (136/640) of H. influenzae , and 83% (151/181) of meningococcal invasive diseases. Clinical data were available for 91% (1455/1606) of BM: 26% (376/1455) were aged <5 years, 50% (726/1455) were female, and 62% (723/1171) with known HIV results, were HIV-infected. In-hospital case fatality was 37% (534/1455), and 24% (222/921) of survivors had adverse sequelae. Risk factors for death included altered mental status, HIV infection, and comorbidities. Risk factors for adverse sequelae included altered mental status and antimicrobial nonsusceptibility.
CONCLUSION : BM in South Africa has a high case fatality, and adverse sequelae frequently occur among survivors. Those with comorbidities (including HIV) are at the highest risk.The NICD of the National Health
Laboratory Service.http://www.elsevier.com/locate/ijidhj2023Medical Microbiolog
The potential impact of the COVID-19 pandemic on global antimicrobial and biocide resistance:An AMR Insights global perspective
The COVID-19 pandemic presents a serious public health challenge in all countries. However, repercussions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections on future global health are still being investigated, including the pandemic's potential effect on the emergence and spread of global antimicrobial resistance (AMR). Critically ill COVID-19 patients may develop severe complications, which may predispose patients to infection with nosocomial bacterial and/or fungal pathogens, requiring the extensive use of antibiotics. However, antibiotics may also be inappropriately used in milder cases of COVID-19 infection. Further, concerns such as increased biocide use, antimicrobial stewardship/infection control, AMR awareness, the need for diagnostics (including rapid and point-of-care diagnostics) and the usefulness of vaccination could all be components shaping the influence of the COVID-19 pandemic. In this publication, the authors present a brief overview of the COVID-19 pandemic and associated issues that could influence the pandemic's effect on global AMR.</p
Neonatal invasive candidiasis in low-and-middle-income countries: data from the NeoOBS study
Neonatal invasive candidiasis (NIC) has significant morbidity and mortality. Reports have shown a different profile of those neonates affected with NIC and of fluconazole resistant Candida spp. isolates in low-and-middle-income -countries (LMICs) compared to high-income-countries (HIC). We describe the epidemiology, Candida spp. distribution, treatment and outcomes of neonates with NIC from LMICs enrolled in a global, prospective, longitudinal, observational cohort study (NeoOBS) of hospitalised infants < 60 days postnatal age with sepsis (August 2018-February 2021). 127 neonates from 14 hospitals in 8 countries with Candida spp. isolated from blood culture were included. Median gestational age of affected neonates was 30 weeks (IQR: 28-34) and median birth weight was 1270 g (IQR: 990-1692). Only a minority had high risk criteria, such as being born < 28 weeks, 19% (24/127), or birth weight < 1000 g, 27% (34/127). The most common Candida species were C. albicans (n = 45, 35%), C. parapsilosis (n = 38, 30%) and Candida auris (n = 18, 14%). The majority of C. albicans isolates were fluconazole susceptible, whereas 59% of C. parapsilosis isolates were fluconazole resistant. Amphotericin B was the most common antifungal used [74% (78/105)], followed by fluconazole [22% (23/105)]. Death by day 28 post-enrolment was 22% (28/127). To our knowledge, this is the largest multi-country cohort of NIC in LMICs. Most of the neonates would not have been considered at high risk for NIC in HICs. A substantial proportion of isolates was resistant to first choice fluconazole. Understanding the burden of NIC in LMIC is essential to guide future research and treatment guidelines
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The potential impact of the COVID-19 pandemic on global antimicrobial and biocide resistance : an AMR Insights global perspective
The COVID-19 pandemic presents a serious public health challenge in all countries. However, repercussions of
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections on future global health
are still being investigated, including the pandemicâs potential effect on the emergence and spread of global
antimicrobial resistance (AMR). Critically ill COVID-19 patients may develop severe complications, which may
predispose patients to infection with nosocomial bacterial and/or fungal pathogens, requiring the extensive
use of antibiotics. However, antibiotics may also be inappropriately used in milder cases of COVID-19
infection. Further, concerns such as increased biocide use, antimicrobial stewardship/infection control, AMR
awareness, the need for diagnostics (including rapid and point-of-care diagnostics) and the usefulness of
vaccination could all be components shaping the influence of the COVID-19 pandemic. In this publication, the
authors present a brief overview of the COVID-19 pandemic and associated issues that could influence
the pandemicâs effect on global AMR.This study was supported by internal funding.https://academic.oup.com/jacamram2022School of Health Systems and Public Health (SHSPH
Antimicrobial resistance and antimicrobial stewardship in South Africa: a survey of healthcare workers in academic and nonacademic hospitals
Abstract
Objective:
Antimicrobial stewardship programmes (ASPs) facilitate appropriate antimicrobial use and require contextualization for optimal functioning. We aimed to investigate perceptions of and antimicrobial resistance (AMR) and ASPs among healthcare workers in academic and nonacademic hospitals.
Design:
Cross-sectional survey.
Setting:
Three academic (Charlotte Maxeke Johannesburg Academic, Inkosi Albert Luthuli, Tygerberg) and three nonacademic hospitals (Leratong, Prince Mshiyeni Memorial, and Paarl) in South Africa from January to June 2022.
Participants:
Doctors, nurses, and pharmacists.
Methods:
Voluntary questionnaire using Google Forms, encompassing AMR, ASPs, and selected discipline-specific components.
Results:
Participants comprised 79 doctors (50 academic), 178 nurses (169 academic), and 21 pharmacists (18 academic) and were female predominant. AMR was a problem in academic hospitals (74.7% vs 51.2%, p 0.004); 73.5% overall reported inappropriate antimicrobial use as a major contributor. Adequate education on antimicrobials occurred in only 36.4% overall. Microbiological testing guided therapy more often in nonacademic settings (80.0% vs 50.2%, p <0.001). In both settings, antimicrobial availability drove selection in 48.2%. Overall, ASPs improved patient care (89.8%) and reduced antimicrobial use (86.9%), although felt to override prescriber autonomy in academic settings (29.4% vs 7.5%, p 0.007), mainly among nurses. Only 50.2% reported successful local ASPs. A minority of pharmacists (20.0%) reported sufficient hospital support for ASPs. Education, involvement of infection control staff, and inclusion of nurses in ASPs were most impactful on AMR.
Conclusion:
Selected healthcare worker perspectives differ by category and setting and can be targeted to improve ASPs. Further studies should target a higher number of clinical staff in both settings