Vaccines in the fight against antimicrobial resistance - perspectives from South Africa.

Antimicrobial resistance (AMR), in which microbes adapt to and resist current therapies, is a well-recognised global problem that threatens to reverse gains made by modern medicine in the last decades. AMR is a complex issue; however, at its core, it is driven by the overuse and inappropriate use of antimicrobials. Socioeconomic factors have been identified as significant contributors to the emergence and exacerbation of AMR, especially in populations facing inadequate access to healthcare, poor sanitation services and high morbidity and mortality rates.

Antimicrobial resistance and antimicrobial stewardship in South Africa: a survey of healthcare workers in academic and nonacademic hospitals.

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.

Potential for Maternally Administered Vaccine for Infant Group B Streptococcus.

Background: Natural history studies have correlated serotype-specific anti-capsular polysaccharide (CPS) IgG in newborns with a reduced risk of group B streptococcal disease. A hexavalent CPS-cross-reactive material 197 glycoconjugate vaccine (GBS6) is being developed as a maternal vaccine to prevent invasive group B streptococcus in young infants.

Methods: In an ongoing phase 2, placebo-controlled trial involving pregnant women, we assessed the safety and immunogenicity of a single dose of various GBS6 formulations and analyzed maternally transferred anti-CPS antibodies.

Antimicrobial Stewardship in Public-Sector Hospitals in KwaZulu-Natal, South Africa.

Antimicrobial resistance (AMR) is a serious global public-health threat. Evidence suggests that antimicrobial stewardship (AMS) is a valuable tool to facilitate rational antibiotic use within healthcare facilities. A cross-sectional situational analysis using a questionnaire was conducted to determine the current status of antimicrobial stewardship (AMS) activities in all public-sector hospitals in KwaZulu-Natal (KZN).

Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study.

We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform.

First genome sequence of Aeromonas hydrophilia novel sequence type 658 strain isolated from livestock in South Africa.

Objectives: The underlying resistance mechanisms, defence systems, mobilome, virulome, clonality and global phylogenetic relationship of a novel sequence type (ST) 658 Aeromonas hydrophilia (A34a) isolated from a pig abattoir in South Africa was determined using whole-genome sequence (WGS) technology.

Methods: Following isolation on chromogenic agar (CHROMID® CARBA SMART), microbial identification and antibiotic susceptibility testing were performed using a VITEK®2 platform. Genotyping involved WGS performed with an Illumina MiSeq platform.

Comparative Pathogenomics of from Pigs in South Africa: Dominance of the Novel ST657 Clone.

The pathogenomics of carbapenem-resistant isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed.

Pathogenomic Analysis of a Novel Extensively Drug-Resistant Isolate Carrying a bla Carbapenemase in South Africa.

Pathogenomic analysis was performed on a novel carbapenem-resistant isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II.

Genomic Analysis of CarbapenemaseProducing Extensively Drug-Resistant Isolates Reveals the Horizontal Spread of p18-43_01 Plasmid Encoding in South Africa.

Whole-genome sequence (WGS) analyses were employed to investigate the genomic epidemiology of extensively drug-resistant strains, focusing on the carbapenem resistance-encoding determinants, mobile genetic support, clonal and epidemiological relationships. A total of ten isolates were obtained from patients admitted to the intensive care unit (ICU) in a public hospital in South Africa. Five isolates were from rectal swabs of colonized patients and five from blood cultures of patients with invasive carbapenem-resistant infections.

Antimicrobial stewardship in South Africa: a scoping review of the published literature.

Objectives: To map published data of antimicrobial stewardship (AMS) interventions that are currently being carried out in hospitals and clinics in the public and private health sectors of South Africa in line with the antimicrobial resistance (AMR) strategy of South Africa.

Methods: A systematic scoping review was conducted to identify AMS initiatives in the public and private health sectors of South Africa for the period 1 January 2000 to 31 March 2019. An electronic search of databases was made including PubMed, Scopus, a key medical journal (), University of KwaZulu-Natal (UKZN) WorldCat iCatalogue and AMR networks: Federation of Infectious Diseases Societies in South Africa (FIDSSA).

Serum Cryptococcal Antigen Testing in Immunosuppressed HIV-positive Children and Adolescents.

Objectives: Describe the epidemiology of immunocompromised HIV-infected pediatric (children and adolescents ≤ 19 years) and adults (> 19 years) with positive serum cryptococcal antigen lateral flow assay (CrAg-LFA) in KwaZulu-Natal.

Design: Retrospective review of laboratory-based database and clinical charts.

Methods: A review of the National Health Laboratory Services database of all serum CrAg-LFA performed in KwaZulu-Natal between June 2015 and December 2016 and comparison of the epidemiology of pediatric and adult patients was conducted.

Whole-Genome Sequence of a Novel Sequence Type 3136 Carbapenem-Resistant Klebsiella pneumoniae Strain Isolated from a Hospitalized Patient in Durban, South Africa.

Here, we describe the genome sequence of a novel sequence type 3136 (ST3136) Klebsiella pneumoniae strain isolated in South Africa. The 5,574,236-bp genome harbored 23 resistance determinants and 12 virulence factors that are of cardinal importance to infections. The genomics of Klebsiella pneumoniae offer valuable insights into its pathogenicity.

Antibiotic resistance trends of ESKAPE pathogens in Kwazulu-Natal, South Africa: A five-year retrospective analysis.

Background: To combat antimicrobial resistance, the World Health Organization developed a global priority pathogen list of antibiotic-resistant bacteria for prioritisation of research and development of new, effective antibiotics.

Objective: This study describes a five-year resistance trend analysis of the ESKAPE pathogens: spp., from Kwazulu-Natal, South Africa.

Surviving Sepsis in the Intensive Care Unit: The Challenge of Antimicrobial Resistance and the Trauma Patient.

Sepsis in the intensive care unit (ICU) presents a great challenge to any critical care clinician. Patients admitted to the ICU are especially vulnerable to sepsis due to the nature of the underlying pathology that warranted admission to the ICU and deranged physiological function coupled with invasive procedures. Nosocomial infections are common in patients admitted to the ICU, and with these infections come the burden of multidrug-resistant organisms.

Empirical antimicrobial therapy for probable v. directed therapy for possible ventilator-associated pneumonia in critically injured patients.

Background: Ventilator-associated pneumonia (VAP) has recently been classified as possible or probable. Although direct attributable mortality has been difficult to prove, delay in instituting appropriate therapy has been reported to increase morbidity and mortality. Recent literature suggests that in possible VAP, instituting directed therapy while awaiting microbiological culture does not prejudice outcome compared with best-guess empirical therapy.

Microbiological surveillance and antimicrobial stewardship minimise the need for ultrabroad-spectrum combination therapy for treatment of nosocomial infections in a trauma intensive care unit: an audit of an evidence-based empiric antimicrobial policy.

Background: Nosocomial infections are a major cause of morbidity in the critically injured, and the incidence of resistant strains of bacteria is increasing. Management requires a strategy that achieves accurate empiric cover without antibiotic overuse - a goal that may be achieved by surveillance and antibiotic stewardship.

Objectives: With the aim of minimising the use of empirical ultrabroad-spectrum combination antimicrobial prescriptions and reducing bacterial resistance, the level I Trauma Intensive Care Unit (TICU) at Inkosi Albert Luthuli Central Hospital (IALCH) in Durban employs stewardship and an antimicrobial policy based on surveillance.