Carbapenem-resistant among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization.

Background: The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown.

Objectives: This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices.

Methods: Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa.

Carbapenem-resistant Enterobacterales among hospitalized patients in Cape Town, South Africa: clinical and microbiological epidemiology.

Background: Carbapenem-resistant Enterobacterales (CRE) are a substantial problem in Cape Town. CRE epidemiology is largely unknown and mortality remains high.

Objectives: To describe and characterize the clinical and microbiological epidemiology of CRE within Cape Town hospitals to better inform therapy with regard to current and novel antibiotics, as well as improve antimicrobial stewardship (AMS), and infection prevention and control (IPC).

Microbe Mail: A microbiology and infectious diseases podcast for clinicians and students.

Unlabelled: Microbe Mail medical podcast is an audio-only informal educational platform, which addresses widespread topics in medical microbiology and infectious diseases (ID), with a particular focus on low- and middle-income settings. Podcasting has become a common form of informal learning in healthcare education and for continual professional development (CPD).

Contribution: In this article, we discuss the development of the Microbe Mail podcast, its informal microbiology and ID education impact in the 2 years since commencement and future directions to improve uptake in Africa and low- and middle-income countries.

Changing character and waning impact of COVID-19 at a tertiary centre in Cape Town, South Africa.

Background: The emergence of genetic variants of SARS-CoV-2 was associated with changing epidemiological characteristics throughout coronavirus disease 2019 (COVID-19) pandemic in population-based studies. Individual-level data on the clinical characteristics of infection with different SARS-CoV-2 variants in African countries is less well documented.

Objectives: To describe the evolving clinical differences observed with the various SARS-CoV-2 variants of concern and compare the Omicron-driven wave in infections to the previous Delta-driven wave.

Random amplified microsatellites (RAMS) analysis ascertains genetic variation of causing black spot disease on in South Africa.

Limited information regarding the occurrence of black spot disease of pecan (), caused by , in South Africa is known. The pecan industry is growing rapidly, so it is essential to understand the impact of the fungal pathogen to pecan health. In this study, the genetic variation of 364 isolates was investigated by two RAMS primers (CCA and CGA).

In Vitro Evaluation of Azoxystrobin, Boscalid, Fentin-Hydroxide, Propiconazole, Pyraclostrobin Fungicides against Pathogen Isolated from in South Africa.

Black spot disease or Alternaria black spot (ABS) of pecan () in South Africa is caused by . This fungal pathogen impedes the development of pecan trees and leads to low yield in pecan nut production. The present study investigated the in vitro effect of six fungicides against the mycelial growth of isolates from ABS symptoms.

Multigene Phylogeny and Pathogenicity Trials Revealed as the Causal Agent of Black Spot Disease and Seedling Wilt of Pecan () in South Africa.

The pecan () industry in South Africa is growing rapidly, and it is becoming increasingly crucial to understand the risks posed to pecans by fungal pathogens. Black spots on leaves, shoots, and nuts in shucks caused by species have been observed since 2014 in the Hartswater region of the Northern Cape Province of South Africa. Species of include some of the most ubiquitous plant pathogens on earth.

Differential Detection of Haplotypes Isolated from Using PCR-RFLP Analysis of Gene Region.

Alternaria black spot disease on pecan is caused by the opportunistic pathogen and poses a serious threat to the local South African and global pecan industry. Several diagnostic molecular marker applications have been established and used in the screening of various fungal diseases worldwide. The present study investigated the potential for polymorphism within samples of isolates obtained from eight different geographical locations in South Africa.

A case for investment in clinical metagenomics in low-income and middle-income countries.

Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology.

Systemically targeted cancer immunotherapy and gene delivery using transmorphic particles.

Immunotherapy is a powerful tool for cancer treatment, but the pleiotropic nature of cytokines and immunological agents strongly limits clinical translation and safety. To address this unmet need, we designed and characterised a systemically targeted cytokine gene delivery system through transmorphic encapsidation of human recombinant adeno-associated virus DNA using coat proteins from a tumour-targeted bacteriophage (phage). We show that Transmorphic Phage/AAV (TPA) particles provide superior delivery of transgenes over current phage-derived vectors through greater diffusion across the extracellular space and improved intracellular trafficking.

Improved oral detection is a characteristic of Omicron infection and has implications for clinical sampling and tissue tropism.

Background: The Omicron variant of concern is characterised by more than 50 distinct mutations, most in the spike protein. The implications of these for disease transmission, tissue tropism and diagnostic testing needs study.

Objectives: We evaluated the performance of RT-PCR on saliva (SA) swabs and antigen testing on mid-turbinate MT samples relative to RT-PCR on MT swabs.

Field performance evaluation of the PanBio rapid SARS-CoV-2 antigen assay in an epidemic driven by the B.1.351 variant in the Eastern Cape, South Africa.

Background: South Africa was the African country with the most recorded cases of SARS-CoV-2 during 2020, experiencing 2 waves of infection. During the first wave, diagnostics were largely based on reverse transcription-linked PCR (RT-PCR). The Abbott PanBio antigen test was deployed during the 2nd wave which may have been driven by emergence of the B.

Varicella-zoster virus reactivation is frequently detected in HIV-infected individuals presenting with stroke.

Infections are an underappreciated cause of stroke, particularly in young and immunocompromised individuals. Varicella-zoster virus (VZV) reactivation, particularly ophthalmic zoster, has been linked to increased risk of stroke but diagnosing VZV-associated cerebral vasculopathy is challenging as neither a recent zoster rash, nor detectable levels of VZV DNA are universally present at stroke presentation. Detection of VZV IgG in cerebrospinal fluid (CSF-VZVG) presents a promising alternative, but requires evaluation of individual blood-CSF dynamics, particularly in the setting of chronic inflammatory states such as HIV infection.

Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests.

Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay from June 2021 when detecting the Delta variant. We investigated whether the reduced amplification efficiency denoted by an increased RT-PCR cycle threshold value (RΔE) can be used as an indirect measure of SARS-CoV-2 Delta variant prevalence. We found a significant increase in the median RΔE for patient samples tested from June 2021, which coincided with the emergence of the SARS-CoV-2 Delta variant within our sample set.

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.

Escape from recognition of SARS-CoV-2 variant spike epitopes but overall preservation of T cell immunity.

SARS-CoV-2 variants that escape neutralization and potentially affect vaccine efficacy have emerged. T cell responses play a role in protection from reinfection and severe disease, but the potential for spike mutations to affect T cell immunity is incompletely understood. We assessed neutralizing antibody and T cell responses in 44 South African COVID-19 patients either infected with the Beta variant (dominant from November 2020 to May 2021) or infected before its emergence (first wave, Wuhan strain) to provide an overall measure of immune evasion.

Detection of a SARS-CoV-2 variant of concern in South Africa.

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.

SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies.

Neutralization escape by SARS-CoV-2 variants, as has been observed in the 501Y.V2 (B.1.

The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa.

The SARS-CoV-2 pandemic has resulted in shortages of both critical reagents for nucleic acid purification and highly trained staff as supply chains are strained by high demand, public health measures and frequent quarantining and isolation of staff. This created the need for alternate workflows with limited reliance on specialised reagents, equipment and staff. We present here the validation and implementation of such a workflow for preparing samples for downstream SARS-CoV-2 RT-PCR using liquid handling robots.

Response to a cluster of Severe Acute Respiratory Syndrome Coronavirus 2 cases at a diagnostic laboratory.

Introduction: We report on the first documented cluster of Coronavirus Disease 2019 cases amongst diagnostic laboratory staff and outline some of the initial and ongoing steps that are being implemented to manage and prevent the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in our laboratory.

Case Presentation: On 24 April 2020, three staff members of a tertiary diagnostic laboratory in Groote Schuur Hospital, Cape Town, South Africa, tested positive for SARS-CoV-2. Within seven days, a further nine cases were identified, which suggested an outbreak and prompted a full investigation.

High positive HIV serology results can still be false positive.

The consequences of falsely reactive HIV test results can be significant, for patients and healthcare providers. This case describes a diagnostic investigation of a patient with pronounced discordant HIV serological results, to determine HIV status. The fourth generation serological screening assay (Roche COBAS Elecsys HIV combiPT) had high positive results but confirmatory testing was negative (Abbott HIV Ag/Ab Combo).

Mycotoxin production by three different toxigenic fungi genera on formulated abalone feed and the effect of an aquatic environment on fumonisins.

Mycotoxins are toxic secondary metabolites produced by various filamentous fungi, of which and are the three main genera. is one of the most dominant toxigenic fungal species, associated with fumonisin contamination in grain-based feeds, such as compound abalone feed. Mycotoxin production is influenced by temperature and available nutrients.