National sentinel site surveillance for antimicrobial resistance in Klebsiella pneumoniae isolates in South Africa, 2010-2012

PKBackground: The increasing rates of antimicrobial resistance observed in the nosocomial pathogen Klebsiella pneumoniae are of major public health concern worldwide. Objectives: To describe the antibiotic susceptibility profiles of K. pneumoniae isolates from bacteraemic patients submitted by sentinel laboratories in five regions of South Africa from mid-2010 to mid-2012. Molecular methods were used to detect the most commonly found extended-spectrum beta-lactamase (ESBL) and carbapenemase resistance genes. Methods: Thirteen academic centres serving the public healthcare sector in Gauteng, KwaZulu-Natal, Free State, Limpopo and Western Cape provinces submitted K. pneumoniae isolates from patients with bloodstream infections. Vitek 2 and MicroScan instruments were used for organism identification and susceptibility testing. Multiplex polymerase chain reactions (PCRs) were used to detect blaCTX-M, blaSHV and blaTEM genes in a proportion of the ESBL isolates. All isolates exhibiting reduced susceptibility to carbapenems were PCR tested for blaKPC and blaNDM-1 resistance genes. Results: Overall, 68.3% of the 2 774 isolates were ESBL-positive, showing resistance to cefotaxime, ceftazidime and cefepime. Furthermore, 46.5% of all isolates were resistant to ciprofloxacin and 33.1% to piperacillin-tazobactam. The major ESBL genes were abundantly present in the sample analysed. Most isolates (95.5%) were susceptible to the carbapenems tested, and no isolates were positive for blaKPC or blaNDM-1. There was a trend towards a decrease in susceptibility to most antibiotics. Conclusion: The high proportion of ESBL-producing K. pneumoniae isolates observed, and the prevalence of ESBL genes, are of great concern. Our findings represent a baseline for further surveillance in SA, and can be used for policy and treatment decisions

Molecular detection of carbapenemase-producing genes in referral Enterobacteriaceae in South Africa: A short report

Molecular confirmation of carbapenemase-producing Enterobacteriaceae (CPE) was introduced in South Africa (SA) at the end of 2011. We report on the detection of these resistance genes based on referral isolates. Enterobacteriaceae with non-susceptibility to any of the carbapenems according to defined criteria for antimicrobial susceptibility testing results were sent to a reference laboratory. A proportion of isolates had limited demographic, epidemiological and clinical data available. Organism identification was reconfirmed using reference laboratory methods, and the presence of carbapenemases was confirmed with a real-time polymerase chain reaction. We analysed 1 503 significant isolates received for confirmation from the National Health Laboratory Service and some private laboratories during 2012 - 2015 and confirmed one or more carbapenemase-producing genes in 68% of isolates, the most common organism being Klebsiella pneumoniae (60%). The most common carbapenemase genes were blaNDM, followed by blaOXA-48 and its variants. BlaOXA-48 and its variants demonstrated non-susceptibility to ertapenem in 89% of the isolates when analysed by the phenotypic method, and to ceftazidime in 34%. Overall, the detection rate for carbapenemases in K. pneumoniae blood isolates in the public sector was 1.9% during the 4-year period. This report indicates the presence of CPE in SA, and it is important for all healthcare workers to be aware of this major public health threat so that infection prevention and control measures can be implemented to prevent the spread of CPE in healthcare facilities

Removal of nickel from wastewater using an agricultural adsorbent

Chemical wastewater streams may contain toxic compounds which are non-biodegradable, and therefore require advanced treatment techniques such as adsorption. However, application of adsorption processes is often limited by the cost of adsorbents. In this study, the adsorption capacity of a low-cost adsorbent (pine sawdust) was investigated by treating wastewater containing nickel (II) and other heavy metal ions. Results were analysed using response surface methodology and a factorial design was employed to determine the interactive effects of the various factors on the adsorption capacity. Furthermore, Langmuir and Freundlich adsorption isotherms were fitted to experimental data to characterise the adsorption of the nickel ions by the pine sawdust. As a result, the highest adsorption capacity was attained at the combined effect of low adsorbent dose, high pH and high initial concentration. On the other hand, the Freundlich isotherm fitted the experimental data better than the Langmuir isotherm. Results of this study indicate that the use of pine sawdust could be a promising solution to the elimination of nickel ions from multi-component aqueous solutions.Keywords: sawdust, adsorption, nickel ions, wastewater, isother

Phenotypic and genotypic correlation of carbapenememase-producing Enterobacteriaceae and problems experienced in routine screening

Background. The emergence and transmission of carbapenem-resistant Enterobacteriaceae (CRE) is a concern in both the clinical and public health arenas. Reliable and accurate detection of these organisms is required for patient management and infection prevention and control purposes. In the routine laboratory, phenotypic methods are utilised for identification of CRE.Objectives. To investigate the phenotypic profiles of suspected carbapenemase-producing Enterobacteriaceae (CPE) isolates generated by the automated MicroScan Walkaway system making use of the Clinical and Laboratory Standards Institute (CLSI) guidelines, and correlate these with carbapenemase production by molecular methods.Methods. Antimicrobial susceptibility testing was performed using the MicroScan Walkaway system, and the presence of six carbapenemase genes (blaNDM, blaVIM, blaIMP, blaOXA-48and variants, blaGESand blaKPC) was screened for using a multiplex real-time polymerase chain reaction.Results. A total of 2 678 isolates were evaluated. Klebsiella pneumoniae accounted for 62.9% of the isolates (n=1 685), followed by Enterobacter cloacae (n=361, 13.5%). Carbapenemases accounted for 75.2% of isolates; blaOXA-48 and its variants predominated (n=978, 36.5%), followed by blaNDM (n=904, 33.8%), blaVIM (n=108, 4.0%), blaIMP (n=35, 1.3%), blaGES (n=24, 0.9%) and blaKPC (n=18, 0.7 %).Conclusions. A considerable number of isolates expressing a carbapenemase or carbapenemases (the majority of which were blaOXA-48 producing) were susceptible to third-and fourth-generation cephalosporins and carbapenems, demonstrating that confirmed carbapenemase-producing isolates are not presenting as possible carriers of carbapenemases using routine diagnostic methods. Similar results were obtained when CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST) clinical breakpoints were applied and are suitable for the purpose of patient management. However, since genotyping assays are costly, it is suggested that routine laboratories first perform comprehensive phenotypic screening for CPE

Data sharing governance in sub-Saharan Africa during public health emergencies:gaps and guidance

While the COVID-19 pandemic has captured the attention of the global community since the end of 2019, deadly health pandemics are not new to Africa. Tuberculosis (TB), malaria and human immunodeficiency virus (HIV) count amongst other serious diseases that have had a catastrophic impact on the African continent. Effective responses to such pandemics require high-quality, comprehensive data sets that can inform policymaking and enhance healthcare decision-making. While data is driving the information economy in the 21st century, the scarcity in Africa of carefully curated, large epidemiologic data sources and analytical capacity to rapidly identify and understand emerging infectious diseases poses a major challenge to mounting a time-sensitive response to unfolding pandemics. Data access, sharing and transfer between countries are crucial to effectively managing current and future health pandemics. Data access and sharing, however, raises questions about personal privacy, the adequacy of governance mechanisms to regulate cross-border data flows, and ethical issues relating to the collection and use of personal data in the interests of public health. Sub-Saharan Africa’s most research-intensive countries are characterised by diverse data management and privacy governance frameworks. Such regional variance can impede time-sensitive data sharing and highlights the need for urgent governance reforms to facilitate effective decision-making in response to rapidly evolving public health threats.</p

Data sharing governance in sub-Saharan Africa during public health emergencies: Gaps and guidance

While the COVID-19 pandemic has captured the attention of the global community since the end of 2019, deadly health pandemics are not new to Africa. Tuberculosis (TB), malaria and human immunodeficiency virus (HIV) count amongst other serious diseases that have had a catastrophic impact on the African continent. Effective responses to such pandemics require high-quality, comprehensive data sets that can inform policymaking and enhance healthcare decision-making. While data is driving the information economy in the 21st century, the scarcity in Africa of carefully curated, large epidemiologic data sources and analytical capacity to rapidly identify and understand emerging infectious diseases poses a major challenge to mounting a time-sensitive response to unfolding pandemics. Data access, sharing and transfer between countries are crucial to effectively managing current and future health pandemics. Data access and sharing, however, raises questions about personal privacy, the adequacy of governance mechanisms to regulate cross-border data flows, and ethical issues relating to the collection and use of personal data in the interests of public health. Sub-Saharan Africa’s most research-intensive countries are characterised by diverse data management and privacy governance frameworks. Such regional variance can impede time-sensitive data sharing and highlights the need for urgent governance reforms to facilitate effective decision-making in response to rapidly evolving public health threats. Significance: We explore governance considerations that ought to apply to the collection, transfer, and use of data in public health emergencies. Specifically, we provide an overview of the prevailing data sharing governance landscape in selected African countries. In doing so, we identify limitations and gaps that impede effective data collation, sharing and analysis. This work could find utility amongst a range of stakeholders, including bioinformaticians, epidemiologists, artificial intelligence coders, and government decision-makers. While this work focuses primarily on an African context, the issues explored are of universal concern and therefore of relevance to a broader international audience

Molecular detection of carbapenemase-producing genes in referral Enterobacteriaceae in South Africa: A short report

Molecular confirmation of carbapenemase-producing Enterobacteriaceae (CPE) was introduced in South Africa (SA) at the end of 2011. We report on the detection of these resistance genes based on referral isolates. Enterobacteriaceae with non-susceptibility to any of the carbapenems according to defined criteria for antimicrobial susceptibility testing results were sent to a reference laboratory. A proportion of isolates had limited demographic, epidemiological and clinical data available. Organism identification was reconfirmed using reference laboratory methods, and the presence of carbapenemases was confirmed with a real-time polymerase chain reaction. We analysed 1 503 significant isolates received for confirmation from the National Health Laboratory Service and some private laboratories during 2012 - 2015 and confirmed one or more carbapenemase-producing genes in 68% of isolates, the most common organism being Klebsiella pneumoniae (60%). The most common carbapenemase genes were blaNDM, followed by blaOXA-48 and its variants. BlaOXA-48 and its variants demonstrated non-susceptibility to ertapenem in 89% of the isolates when analysed by the phenotypic method, and to ceftazidime in 34%. Overall, the detection rate for carbapenemases in K. pneumoniae blood isolates in the public sector was 1.9% during the 4-year period. This report indicates the presence of CPE in SA, and it is important for all healthcare workers to be aware of this major public health threat so that infection prevention and control measures can be implemented to prevent the spread of CPE in healthcare facilities

Myeloid cell interferon responses correlate with clearance of SARS-CoV-2

Emergence of mutant SARS-CoV-2 strains associated with an increased risk of COVID-19-related death necessitates better understanding of the early viral dynamics, host responses and immunopathology. Single cell RNAseq (scRNAseq) allows for the study of individual cells, uncovering heterogeneous and variable responses to environment, infection and inflammation. While studies have reported immune profiling using scRNAseq in terminal human COVID-19 patients, performing longitudinal immune cell dynamics in humans is challenging. Macaques are a suitable model of SARS-CoV-2 infection. Our longitudinal scRNAseq of bronchoalveolar lavage (BAL) cell suspensions from young rhesus macaques infected with SARS-CoV-2 (n = 6) demonstrates dynamic changes in transcriptional landscape 3 days post- SARS-CoV-2-infection (3dpi; peak viremia), relative to 14-17dpi (recovery phase) and pre-infection (baseline) showing accumulation of distinct populations of both macrophages and T-lymphocytes expressing strong interferon-driven inflammatory gene signature at 3dpi. Type I interferon response is induced in the plasmacytoid dendritic cells with appearance of a distinct HLAD