Characterization and antibiogram fingerprints of Enterobacteriaceae and Listeria monocytogenes in irrigation water and agricultural soil samples collected from Amathole and Chris Hani District Municipalities in the Eastern Cape Province, South Africa

Characterization and antibiogram fingerprints of Enterobacteriaceae and Listeria monocytogenes in irrigation water and agricultural soil samples collected from Amathole and Chris Hani District Municipalities in the Eastern Cape Province, South Afric

The occurrence of long COVID : a rapid review

The long-term effects of the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) are not well understood. This rapid review was aimed at synthesizing evidence on the long-term effects of the SARS-CoV-2 infection among survivors. We considered both randomised controlled trials and non-randomised studies eligible for inclusion in this review. The following databases were searched: PubMed, Scopus, Cochrane library, Google Scholar, and the World Health Organization (WHO) COVID-19 database. The reference lists of all the included studies were also searched. Two authors independently screened the search outputs and reviewed full texts of potentially eligible articles. Data extraction was done by one author and checked by a second author. A meta-analysis was not conducted due to heterogeneity among the included studies. Results are presented narratively. Eleven studies met our inclusion criteria. All these studies were conducted in high-income countries. Study findings demonstrate that COVID-19 survivors can experience persistent symptoms after recovering from their initial illness, especially among previously hospitalized persons. The majority of symptoms reported were fatigue, shortness of breath, cough, and sleep disorders. Mental conditions, such as depression and anxiety disorders, were also reported. In conclusion, this study showed that COVID-19 survivors can experience persistent symptoms after recovering from their initial illness. Therefore, there is a need for a long-term follow-up of COVID-19 patients and rehabilitation services for survivors. More research is needed in this area, especially in Africa.https://www.panafrican-med-journal.compm2022School of Health Systems and Public Health (SHSPH

The incidence of antibiotic resistance within and beyond the agricultural ecosystem : a concern for public health

The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of antibiotics in the veterinary, agricultural, and medical sectors. This results in the selective pressure for the intrinsic and extrinsic development of the antimicrobial resistance phenomenon, especially within the aquaculture-animal-manure-soil-water-plant nexus. The existence of antimicrobial resistance in the environment has been well documented in the literature. However, the possible transmission routes of antimicrobial agents, their resistance genes, and naturally selected antibiotic-resistant bacteria within and between the various niches of the agricultural environment and humans remain poorly understood. This study, therefore, outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; transmission routes of antimicrobial resistance in the agro-ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro-ecosystem; and possible ways to curtail the menace of antimicrobial resistance.The South African Medical Research Council (SAMRC), National Research Foundation (NRF), and the United States Agency for International Development (USAID).www.MicrobiologyOpen.comam2021Plant Production and Soil Scienc

New vaccine introductions in WHO African region between 2000 and 2022

DATA AVAILABILITY STATEMENT : Data used for this study were publicly available.SUPPLEMENTARY MATERIALS : TABLE S1: Summarises the number of Gavi eligible and ineligible countries that have introduced each new vaccine. FIGURE S1: Status of Hepatitis B vaccine introduction in the WHO African region as of May 2022. Figure S2: Status of Hib vaccine introduction in the WHO African region as of May 2022. Figure S3: Status of IPV introduction in the WHO African region as of May 2022. Figure S4: Status of MCV2 introduction in the WHO African region as of May 2022. FIGURE S5: Status of PCV introduction in the WHO African region as of May 2022. FIGURE S6: Status of rotavirus vaccine introduction in the WHO African region as of May 2022. FIGURES7: Status of rubella vaccine introduction in the WHO African region as of May 2022. FIGURE S8: Status of yellow fever vaccine introduction in the WHO African region as of May 2022. FIGURE S9: Status of HPV vaccine introduction in the WHO African region as of May 2022. FIGURE S10: Status of IPV2 introduction in the WHO African region as of May 2022. FIGURE S11: Status of meningococcal meningitis vaccine introduction in the WHO African region as of May 2022. FIGURE S12: Status of HepB birth dose vaccine introduction in the WHO African region as of May 2022. FIGURE S13: Status of seasonal influenza vaccine introduction in the WHO African region as of May 2022. FIGURE S14: Status of mumps vaccine introduction in the WHO African region as of May 2022. FIGURE S15: Status of acellular vaccine introduction in the WHO African region as of May 2022. FIGURE S16: Status of hepatitis A vaccine introduction in the WHO African region as of May 2022.Significant progress has been made in vaccine development worldwide. This study examined the WHO African Region’s vaccine introduction trends from 2000 to 2022, excluding COVID-19 vaccines. We extracted data on vaccine introductions from the WHO/UNICEF joint reporting form for 17 vaccines. We examined the frequency and percentages of vaccine introductions from 2000 to 2022, as well as between two specific time periods (2000–2010 and 2011–2022). We analysed Gavi eligible and ineligible countries separately and used a Chi-squared test to determine if vaccine introductions differed significantly. Three vaccines have been introduced in all 47 countries within the region: hepatitis B (HepB), Haemophilus influenzae type b (Hib), and inactivated polio vaccine (IPV). Between 2011 and 2022, HepB, Hib, IPV, the second dose of measles-containing vaccine (MCV2), and pneumococcal conjugate vaccine (PCV) were the five most frequently introduced vaccines. Hepatitis A vaccine has only been introduced in Mauritius, while Japanese encephalitis vaccine has not been introduced in any African country. Between 2000–2010 and 2011–2022, a statistically significant rise in the number of vaccine introductions was noted (p < 0.001) with a significant positive association between Gavi eligibility and vaccine introductions (p < 0.001). Significant progress has been made in the introduction of new vaccines between 2000 and 2022 in the WHO African Region, with notable introductions between 2011 and 2022. Commitments from countries, and establishing the infrastructure required for effective implementation, remain crucial.https://www.mdpi.com/journal/vaccinesam2024School of Health Systems and Public Health (SHSPH)SDG-03:Good heatlh and well-bein

Polymyxin sensitivity/resistance cosmopolitan status, epidemiology and prevalence among O1/O139 and non-O1/non-O139 Vibrio cholerae : a meta-analysis

DATA AVAILABLE STATEMENT : The datasets/information used for this study are avail- able within the manuscript and the supplementary mate- rials.Resistance/sensitivity to polymyxin-B (PB) antibiotic has been employed as one among other epidemiologically relevant biotyping-scheme for Vibrio cholerae into Classical/El Tor biotypes. However, recent studies have re- vealed some pitfalls bordering on PB-sensitivity/resistance (PBR/S) necessitating study. Current study assesses the PBR/S cosmopolitan prevalence, epidemiology/distribution among O1/O139 and nonO1/nonO139 V. cholerae strains. Relevant databases (Web of Science, Scopus and PubMed) were searched to retrieve data from environ- mental and clinical samples employing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Random-effect-model (REM) and common-effect-model (CEM) of meta-analysis was performed to de- termine prevalence of PBR/S V. cholerae strains, describe the cosmopolitan epidemiological potentials and biotype relevance. Heterogeneity was determined by meta-regression and subgroup analyses. The pooled analyzed iso- lates from articles (7290), with sensitive and resistance are 2219 (30.44%) and 5028 (69.56%). Among these PB- sensitive strains, more than 1944 (26.67%) were O1 strains, 132 (1.81%) were nonO1 strains while mis-reported Classical biotype were 2080 (28.53) respectively indicating potential spread of variant/dual biotype. A significant PB-resistance was observed in the models (CEM = 0.66, 95% CI [0.65; 0.68], p -value = 0.001; REM = 0.83 [0.74; 0.90], p = 0.001) as both models had a high level of heterogeneity ( I2 = 98.0%; 2 =33 = 1755 . 09 , = 2 . 4932 ). Egger test ( z = 5.4017, p < 0.0001) reveal publication bias by funnel plot asymmetry. The subgroup analysis for continents (Asia, Africa) and sources (acute diarrhea) revealed (98% CI (0.73; 0.93); 55% CI (0.20; 0.86)), and 92% CI (0.67; 0.98). The Epidemiological prevalence for El tor/variant/dual biotype showed 88% CI (0.78; 0.94) with O1 strains at 88% CI (0.78; 0.94). Such global prevalence, distribution/spread of phenotypes/genotypes ne- cessitates updating the decades-long biotype classification scheme. An antibiotic stewardship in the post antibiotic era is suggestive/recommended. Also, there is need for holistic monitoring/evaluation of clinical/epidemiological relevance of the disseminating strains in endemic localities.African German Network of Excellence in Science 2022.www.elsevier.com/locate/imjhttp://www.elsevier.com/locate/imjam2024Microbiology and Plant PathologySDG-03:Good heatlh and well-bein

Improving the availability of vaccines in primary healthcare facilities in South Africa : is the time right for a system redesign process?

An uninterrupted supply of vaccines at different supply chain levels is a basic component of a functional immunization programme and care service. There can be no progress toward achieving universal health coverage and sustainable development without continuous availability of essential medicines and vaccines in healthcare facilities. Shortages of vaccines, particularly at health facility level is an issue of grave concern that requires urgent attention in South Africa. The causes of vaccine stock-outs are multifactorial and may be linked to a broader systems issue. These factors include challenges at higher levels such as delays in the delivery of stock from the pharmaceutical depot; health facility level factors, which include a lack of commitment from healthcare workers and managers; human resource factors, such as, staff shortages, and lack of skilled personnel. Therefore, there is a compelling need to address the factors associated with shortages of vaccines in health facilities. This paper highlights the challenges of vaccine availability in South Africa, the associated factors, the available interventions, and recommended interventions for the expanded programme on immunization in South Africa. We propose a system redesign approach as a potentially useful intervention.World Health Organization Regional Office for Africa (WHO/AFRO) and the Hideyo Noguchi Africa Prize (HNAP).http://www.tandfonline.com/loi/khvi20hj2023School of Health Systems and Public Health (SHSPH

Antibiogram signatures of some enterobacteria recovered from irrigation water and agricultural soil in two district municipalities of South Africa

This study was undertaken to evaluate the antibiogram fingerprints of some Enterobacteria recovered from irrigation water and agricultural soil in two District Municipalities of the Eastern Cape Province, South Africa using standard culture-based and molecular methods. The prevalent resistance patterns in the isolates follow the order: Salmonella enterica serovar Typhimurium [tetracycline (92.3%), ampicillin (69.2%)]; Enterobacter cloacae [amoxicillin/clavulanic acid (77.6%), ampicillin (84.5%), cefuroxime (81.0%), nitrofurantoin (81%), and tetracycline (80.3%)]; Klebsiella pneumoniae [amoxicillin/clavulanic acid (80.6%), ampicillin (88.9%), and cefuroxime (61.1%)]; and Klebsiella oxytoca [chloramphenicol (52.4%), amoxicillin/clavulanic acid (61.9%), ampicillin (61.9%), and nitrofurantoin (61.9%)]. Antibiotic resistance genes detected include tetC (86%), sulII (86%), and blaAmpC (29%) in Salmonella enterica serovar Typhimurium., tetA (23%), tetB (23%), tetC (12%), sulI (54%), sulII (54%), catII (71%), blaAmpC (86%), blaTEM (43%), and blaPER (17%) in Enterobacter cloacae., tetA(20%), tetC (20%), tetD(10%), sulI (9%), sulII (18%), FOX (11%) and CIT (11%)-type plasmid-mediated AmpC, blaTEM (11%), and blaSHV (5%) in Klebsiella pneumoniae and blaAmpC (18%) in Klebsiella oxytoca. Our findings document the occurrence of some antibiotic-resistant Enterobacteria in irrigation water and agricultural soil in Amathole and Chris Hani District Municipalities, Eastern Cape Province of South Africa, thus serving as a potential threat to food safety.Table S1: Description of sampling points, Table S2: Primer sequence and PCR cycling conditions used for the molecular detection of members of Enterobacteriales, Table S3: The primer sequence and expected amplicon size used for the screening of resistance genes in members of Enterobacteriales, Table S4: The primer sequence and expected amplicon size used for the screening of AmpC -lactamase and ESBLs in members of Enterobacteriales [44].The South African Medical Research Council (SAMRC), United States Agency for International Development (USAID) and the National Research Foundation (NRF).http://www.mdpi.com/journal/microorganismsam2021Plant Production and Soil Scienc

Systematic and meta-analysis of Mycobacterium avium subsp. paratuberculosis related type 1 and type 2 diabetes mellitus

Global increase in diabetes (DM) prevalence necessitated the need to establish the association between DM and environmental triggers including MAP (Mycobacterium avium subsp. paratuberculosis) that have been postulated to play a role in DM etiopathology for effective management. The present investigation aimed to assess the odds ratio (OR) presenting the association between MAP and DM. MAP-related DM studies were systematically retrieved from 6 databases until 31 September 2021 according to PRISMA principles for data abstraction. The abstracted dataset was fitted to the fixed-effects (FE) and random-effects (RE) models using the Mantel–Haenszel approach. Sixteen studies involving 2072 participants (1152 DM patients (957 type 1 diabetes mellitus (T1DM) & 195 type 2 diabetes mellitus (T2DM)) and 920 healthy controls) met the inclusion criteria. Results revealed a significant association between anti-MAP antibodies (abs) seroprevalence and T1DM (FE: OR 7.47, 95% CI 5.50–10.14, p value < 0.0001; RE: OR 7.92, 95% CI 4.39–14.31, p < 0.0001) and MAP DNA with T1DM (FE: OR 4.70 (95% CI 3.10–7.13, p value < 0.0001), RE: OR 3.90 (95% CI 0.93–16.38, p value = 0.06)). Both anti-MAP abs and MAP DNA based meta-analyses had medium heterogeneity (I2 = 47.2–61.0%). Meanwhile, no significant association between MAP and T2DM (FE: OR 1.13, 95% CI 0.54–2.37, p value = 0.74; RE: OR 1.19; 95% CI 0.34–4.12, p value = 0.69), its OR magnitude exceeded 1 and prediction interval (0.09–15.29) suggest possibility of association between the duo in the future. The leave-one-out sensitivity analysis depicts a robust meta-analysis in all cases. In conclusion, the study manifests a positive association between MAP and T1DM, highlighting that MAP prevention and environmental control would indubitably revolutionize T1DM management. Also, its projects possible link between MAP and T2DM as more data becomes available. However, it remains elusive whether MAP triggers T1/T2DM or a mere comorbidity in T1/T2DM. Epidemiological activities to fill the global/regional data gaps on MAP-related T1DM and T2DM are advocated in order to assess the burden of MAP-related DM and improve their clinical management.https://www.nature.com/srepSchool of Health Systems and Public Health (SHSPH

Preventing and managing antimicrobial resistance in the African region : a scoping review protocol

INTRODUCTION: Antimicrobial resistance (AMR) constitutes a significant threat to global health and food security, typically associated with high morbidity and mortality rate. The high burden of infectious diseases coupled with the weak health systems in most countries of Africa magnifies the risk of increasing AMR and its consequences thereof. This scoping review will be aimed at mapping the evidence on interventions used to prevent and manage antimicrobial resistance in Africa, guided by the “One Health” concept. METHODS: We will consider interventions targeting multiple sectors such as health care systems, the agricultural and veterinary sectors. The outcomes to be considered include reduction of AMR decreased morbidity and mortality due to infectious diseases, increased awareness for rational use of antimicrobials and reduced antibiotic consumption. We will include all types of studies regardless of study designs conducted within the context of the WHO African region. Studies will be excluded if they are not conducted in Africa and if they are literature reviews, only describing the concept of AMR without mentioning interventions. We will include studies identified through a comprehensive search of peer-reviewed and grey literature databases. In addition, we will search the reference lists of included studies and relevant reviews. Finally, we plan to do a citation search for included studies. Findings of this review will be narratively synthesized.http://www.plosone.orgSchool of Health Systems and Public Health (SHSPH

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