Building an antimicrobial stewardship model for a public-sector hospital: a pre-implementation study.

Antimicrobial resistance (AMR) is recognized as an important global health risk, associated with increased mortality, morbidity and healthcare costs. Antimicrobial stewardship (AMS) involves a coherent set of processes that promote the rational use of antimicrobials. An AMS programme should be adapted and developed according to the available resources of a facility.

Genomic characterization of multi drug resistant ESBL-producing Escherichia coli isolates from patients and patient environments in a teaching hospital in Ghana.

Background: ESBL-producing Escherichia coli pose a growing health risk in community and healthcare settings. We investigated the resistome, virulome, mobilome, and genetic relatedness of multidrug-resistant (MDR) E. coli isolates from patients and their environment in a Ghanaian teaching hospital.

Genome analysis of multidrug resistant Enterococcus faecium and Enterococcus faecalis circulating among hospitalized patients in uMgungundlovu District, KwaZulu-Natal, South Africa.

Background: Vancomycin-resistant enterococci (VRE) are important pathogens categorized as high-priority bacteria in the Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics published by the World Health Organization. The aim of this study was to determine the risk factors, resistance, virulence, mobilomes associated with multidrug-resistant and clonal lineages of Enterococcus faecium and faecalis circulating among hospitalized patients following the health system in South Africa, using whole genome sequencing (WGS).

Methods: A cross-sectional study was conducted during a two-month periods among hospitalized patients in 2017.

Multidrug-resistant Gram-negative bacterial colonization in patients, carriage by healthcare workers and contamination of hospital environments in Ghana.

Background: Patients already colonized with multidrug-resistant (MDR) Gram-negative bacteria (GNB) on admission to critical care units may be an important source of transmission of these bacteria in hospitals. We sought to determine the prevalence of MDR GNB colonization in patients, staff and the ward environment and to assess the risk factors for colonization of patients in wards.

Methods: The study was conducted from April 2021 to July 2021 in a teaching hospital in Ghana.

Evaluation of intermittent antimicrobial infusion documentation practices in intensive care units: A cross-sectional study.

Objective: To observe nurse administration of carbapenem antibiotics, in the context of medication safety measures, in intensive care units.

Research Methodology/design: A quantitative study was conducted using observation principles.

Setting: Three adult private and public Intensive Care Units in the health district of a capital city in KwaZulu-Natal, South Africa.

Antibiotic prescribing amongst South African general practitioners in private practice: an analysis of a health insurance database.

Objectives: To investigate the appropriateness of antibiotic prescribing among GPs in the private primary healthcare sector in South Africa.

Methods: An anonymized national database of claims for antibiotic prescriptions was obtained from a large medical insurer. Antibiotic prescriptions were categorized based on International Classification of Diseases (ICD-10) codes as 'appropriate', 'potentially appropriate' and 'inappropriate' using a classification scheme developed by Chua ( 2019; 364: k5092).

Molecular Epidemiological Characterisation of ESBL- and Plasmid-Mediated AmpC-Producing and at Kamuzu Central Hospital, Lilongwe, Malawi.

The global rise in infections caused by multidrug resistant (MDR) Enterobacterales poses a public health problem. We have performed a molecular epidemiological characterisation of representative plasmid-mediated AmpC (pAmpC) and ESBL-positive clinical isolates of (n = 38) and (n = 17) from a tertiary hospital in Malawi collected in 2017. was the most prevalent ESBL-determinant in (n = 30/38) and (n = 17/17), whereas was detected in nearly all AmpC-phenotype (n = 15/17).

Genome Analysis of ESBL-Producing Isolated from Pigs.

The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)-producing (ESBL-Ec) isolated from pigs in Cameroon and South Africa were assessed using whole genome sequencing (WGS). Eleven clonally related phenotypic ESBL- isolates were subjected to WGS. The prediction of antibiotic resistance genes, virulence factors (VFs) and plasmids was performed using ResFinder, VirulenceFinder and PlasmidFinder, respectively.

Genomic Investigation of Carbapenem-Resistant Colonization in an Intensive Care Unit in South Africa.

The study investigated carbapenemase-producing   (CPKP) isolates of patients in an intensive care unit (ICU) in a public hospital in the KwaZulu-Natal province, South Africa using whole-genome sequencing (WGS). Ninety-seven rectal swabs, collected from all consenting adult patients ( = 31) on days 1, 3, and 7 and then weekly, were screened for carbapenemase-production using Chrome-ID selective media. Antibiotic susceptibility was determined for the fourteen positive CPKP isolates obtained using the VITEK 2 automated system.

Carbapenem Resistance Determinants Acquired through Novel Chromosomal Integrations in Extensively Drug-Resistant Pseudomonas aeruginosa.

Two novel - or -containing genomic islands (GIs) were discovered by whole-genome sequence analyses in four extensively drug-resistant (XDR) Pseudomonas aeruginosa isolates from inpatients at a tertiary hospital in Ghana. The strains were of sequence type 234 (ST234) and formed a phylogenetic clade together with ST111, which is recognized as a global high-risk clone. Their carbapenem resistance was encoded by two Tn-type integrons, In1592 () and In1595 (), both carrying complete mobilization modules.

β-lactam and fluoroquinolone resistance in Enterobacteriaceae from imported and locally-produced chicken in Mozambique.

Introduction: Plasmid-mediated resistance to β-lactam and fluoroquinolone antibiotics was investigated in Enterobacteriaceae isolated from retailed frozen chickens from Brazil, South Africa and Mozambique.

Methodology: Carcass swabs and the liquid thaw of 33 chickens from each of the three countries constituted the total sample size of 198. Isolates were identified by biochemical tests, antibiotic susceptibility was ascertained by the disc diffusion assay and β-lactamases were detected using the double-disk synergy test.

Bacterial diversity and functional profile of microbial populations on surfaces in public hospital environments in South Africa: A high throughput metagenomic analysis.

With the introduction of the One Health approach to global health advocated by the World Health Organization, the role of the environment as a reservoir and transmission route for diverse microorganisms is increasingly being recognised globally. This study investigated the diversity and functional profiles of bacterial communities using high-throughput metagenomics of the 16S rRNA gene in samples collected from environmental surfaces in different levels of healthcare in South Africa. A total of 150 samples were collected in three public hospitals [District (A), Regional (C) and Central (B)] from intensive care and paediatric wards.

Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa.

Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. Forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period.

Publisher Correction: The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa.

Antibiotic-resistant Escherichia coli is a common occurrence in food, clinical, community and environmental settings worldwide. The resistome, mobilome, virulome and phylogenomics of 20 multidrug resistant (MDR) clinical E. coli isolates collected in 2013 from Pretoria, South Africa, were characterised.

Draft genome sequence of a clinical Acinetobacter haemolyticus isolate from South Africa.

Objectives: Here we describe the draft genome sequence of a clinical Acinetobacter haemolyticus isolate (A109R1B4) from a rectal swab of a hospitalised patient in South Africa.

Methods: Genomic DNA from the isolate was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using Qiagen CLC Genomics Workbench.

Genomic analysis of a multidrug-resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln1483 and an A/C plasmid replicon.

Whole-genome sequence analysis was performed on a multidrug-resistant Providencia rettgeri PR002 clinical strain isolated from the urine of a hospitalized patient in Pretoria, South Africa, in 2013. The resistome, mobilome, pathogenicity island(s), as well as virulence and heavy-metal resistance genes of the isolate, were characterized using whole-genome sequencing and bioinformatic analysis. PR002 had a genome assembly size of 4,832,624 bp with a GC content of 40.

Genome analysis of methicillin-resistant Staphylococcus aureus isolated from pigs: Detection of the clonal lineage ST398 in Cameroon and South Africa.

Food animals are considered reservoirs of methicillin-resistant Staphylococcus aureus (MRSA) and are implicated in their zoonotic transmission in the farm-to-plate continuum. LA-MRSA has been reported as a zoonotic agent that has the potential to spread to humans and may cause infections in at-risk groups. In this study, whole genome sequencing was used to describe the genetic environment (resistance mechanisms, virulence factors and mobile genetic elements) and investigate the genetic lineages of MRSA isolates from pigs in Cameroonian and South African abattoirs.

Whole Genome Sequencing of Extended Spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae Isolated from Hospitalized Patients in KwaZulu-Natal, South Africa.

Extended spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae remain a critical clinical concern worldwide. The aim of this study was to characterize ESBL-producing K. pneumoniae detected within and between two hospitals in uMgungundlovu district, South Africa, using whole genome sequencing (WGS).

Genomic analysis of methicillin-resistant Staphylococcus aureus isolated from poultry and occupational farm workers in Umgungundlovu District, South Africa.

This study detected methicillin-resistant Staphylococcus aureus (MRSA) isolates circulating in poultry and farm workers at an intensive poultry production system in uMgungundlovu, South Africa and established the genetic relatedness and characteristics of the isolates using whole genome sequencing (WGS). A total of 145 S. aureus were isolated from poultry (120) and occupational workers (25) in the "farm to fork" continuum (farm, transport, slaughterhouse, and retail points).

Emergence and Spread of Extended Spectrum β-Lactamase Producing Enterobacteriaceae (ESBL-PE) in Pigs and Exposed Workers: A Multicentre Comparative Study between Cameroon and South Africa.

Extended spectrum β-lactamase-producing (ESBL-PE) represent a significant public health concern globally and are recognized by the World Health Organization as pathogens of critical priority. However, the prevalence of ESBL-PE in food animals and humans across the farm-to-plate continuum is yet to be elucidated in Sub-Saharan countries including Cameroon and South Africa. This work sought to determine the risk factors, carriage, antimicrobial resistance profiles and genetic relatedness of extended spectrum β-lactamase producing (ESBL-PE) amid pigs and abattoir workers in Cameroon and South Africa.

Extended spectrum beta-lactamase mediated resistance in carriage and clinical gram-negative ESKAPE bacteria: a comparative study between a district and tertiary hospital in South Africa.

Background: Gram-negative ESKAPE bacteria are increasingly implicated in several difficult-to-treat infections in developed and developing countries. They are listed by the World Health Organization as resistant bacteria of critical priority in research.

Objectives: To determine the risk factors, prevalence, phenotypic profiles, genetic diversity and clonal relatedness of extended-spectrum β-lactamase (ESBL)-producing multi-drug resistant (MDR) Gram-negative ESKAPE bacteria in the faecal carriage and clinical samples from patients in an urban, tertiary and a rural, district hospital in uMgungundlovu District, KwaZulu-Natal, South Africa.

Draft genome sequence of a methicillin-resistant Staphylococcus epidermidis isolate from swine.

Objectives: Here we report the draft genome sequence of a methicillin-resistant Staphylococcus epidermidis strain (sequence type 59) isolated from a pooled rectal sample from pigs collected in an abattoir in South Africa.

Methods: Genomic DNA of S. epidermidis PR246B0 was sequenced using an Illumina MiSeq platform.

Mannitol-fermenting methicillin-resistant staphylococci (MRS) in pig abattoirs in Cameroon and South Africa: A serious food safety threat.

Food animals can be reservoirs of methicillin-resistant staphylococci (MRS) and are involved in their zoonotic transmission through the food chain. In Africa, there is a dearth of information about the food safety issues associated with their dissemination in the farm-to-plate continuum. This study sought to determine and compare the carriage, antimicrobial resistance profiles and clonal relatedness of circulating MRS strains among pigs and exposed workers in Cameroon and South Africa.