New Vaccine Introductions in WHO African Region between 2000 and 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.

Systematic Mapping of Research on Vaccine-Preventable Diseases in Children in Sub-Saharan Africa: A Decennial Scientometric Analysis.

Vaccine-preventable diseases (VPDs) remain a significant public health challenge, particularly in sub-Saharan Africa. The high burden of VPDs in this region necessitates the need for continued investigation and intervention. This paper presents a bibliometric analysis of research on VPDs in children in sub-Saharan Africa in the last 10 years to capture the current state of research in the field. This study used a systematic search for articles published between 2013 and 2022 in the Web of Science Core Collection database and, subsequently, scientometric techniques for data analyses and interpretation. Annual scientific production of publications on the research of VPDs in children in sub-Saharan Africa increased from 2013 to 2019 and then gradually declined. South Africa had the most VPD studies (n = 148; 16.2%), followed by Nigeria, Ghana, Kenya, The Gambia, Malawi, Ethiopia, and the Republic of Congo. The Vaccine journal published the most. The Pan African Medical Journal was the most frequent destination journal based in Africa. The commonly studied pathogens were Streptococcus pneumoniae and Haemophilus influenzae. Research productivity increased exponentially in the pre-COVID era and declined in the past two years, so more VPD research in this region is needed.

Spatial diarrheal disease risks and antibiogram diversity of diarrheagenic Escherichia coli in selected access points of the Buffalo River, South Africa.

Freshwater sources, often used for domestic and agricultural purposes in low- and middle-income countries are repositories of clinically significant bacterial pathogens. These pathogens are usually diversified in their antibiogram profiles posing public health threats. This study evaluated the spatial diarrhoeal disease risk and antibiogram diversity of diarrheagenic Escherichia coli (DEC) in four access points of the Buffalo River, Eastern Cape Province, South Africa using standard epidemiological, culture, and molecular methods. The diarrhoeal disease risk was characterised using the Monte Carlo simulation, while the antibiogram diversity was assessed using the species observed Whittaker's single alpha-diversity modelling. E. coli mean count was highest in King William's Town dam [16.0 × 102 CFU/100ml (SD: 100.0, 95% CI: 13.5 × 102 to 18.5 × 102)]. Enterohemorrhagic E. coli (stx1/stx2) was the most prevalent DEC pathotype across the study sites. A high diarrhoeal disease risk of 25.0 ×10-2 exceeding the World Health Organization's standard was recorded across the study sites. The average single and multiple antimicrobial resistance indices of the DEC to test antimicrobials were highest in the Eluxolzweni dam [0.52 (SD: 0.25, 95% CI: 0.37 to 0.67)] and King William's Town dam [0.42 (SD: 0.25, 95% CI: 0.27 to 0.57)] respectively. The prevalent antibiotic resistance genes detected were tetA, blaFOX and blaMOX plasmid-mediated AmpC, blaTEM and blaSHV extended-spectrum ß-lactamases, which co-occurred across the study sites on network analysis. The phenotypic and genotypic resistance characteristics of the DEC in Maden dam (r = 0.93, p<0.00), Rooikrantz dam (r = 0.91, p<0.00), King William's Town dam (r = 0.83, p = 0.0), and Eluxolzweni dam (r = 0.91, p<0.00) were strongly correlated. At least, three phylogenetic clades of the DEC with initial steep descent alpha-diversity curves for most of the test antimicrobials were observed across the study sites, indicating high diversity. The occurrence of diversified multi drug resistant DEC with diarrhoeal disease risks in the Buffalo River substantiates the role surface water bodies play in the dissemination of drug-resistant bacterial pathogens with public health implications.

Methods for early characterisation of the severity and dynamics of SARS-CoV-2 variants: a population-based time series analysis in South Africa.

BACKGROUND: Assessment of disease severity associated with a novel pathogen or variant provides crucial information needed by public health agencies and governments to develop appropriate responses. The SARS-CoV-2 omicron variant of concern (VOC) spread rapidly through populations worldwide before robust epidemiological and laboratory data were available to investigate its relative severity. Here we develop a set of methods that make use of non-linked, aggregate data to promptly estimate the severity of a novel variant, compare its characteristics with those of previous VOCs, and inform data-driven public health responses. METHODS: Using daily population-level surveillance data from the National Institute for Communicable Diseases in South Africa (March 2, 2020, to Jan 28, 2022), we determined lag intervals most consistent with time from case ascertainment to hospital admission and within-hospital death through optimisation of the distance correlation coefficient in a time series analysis. We then used these intervals to estimate and compare age-stratified case-hospitalisation and case-fatality ratios across the four epidemic waves that South Africa has faced, each dominated by a different variant. FINDINGS: A total of 3 569 621 cases, 494 186 hospitalisations, and 99 954 deaths attributable to COVID-19 were included in the analyses. We found that lag intervals and disease severity were dependent on age and variant. At an aggregate level, fluctuations in cases were generally followed by a similar trend in hospitalisations within 7 days and deaths within 15 days. We noted a marked reduction in disease severity throughout the omicron period relative to previous waves (age-standardised case-fatality ratios were consistently reduced by >50%), most substantial for age strata with individuals 50 years or older. INTERPRETATION: This population-level time series analysis method, which calculates an optimal lag interval that is then used to inform the numerator of severity metrics including the case-hospitalisation and case-fatality ratio, provides useful and timely estimates of the relative effects of novel SARS-CoV-2 VOCs, especially for application in settings where resources are limited. FUNDING: National Institute for Communicable Diseases of South Africa, South African National Government.

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.

Modelling the Potential Risk of Infection Associated with Listeria monocytogenes in Irrigation Water and Agricultural Soil in Two District Municipalities in South Africa.

Listeria monocytogenes (L. monocytogenes) is the etiologic agent of listeriosis which significantly affects immunocompromised individuals. The potential risk of infection attributed to L. monocytogenes in irrigation water and agricultural soil, which are key transmission pathways of microbial hazards to the human population, was evaluated using the quantitative microbial risk assessment modelling. A Monte Carlo simulation with 10,000 iterations was used to characterize the risks. High counts of L. monocytogenes in irrigation water (mean: 11.96 × 102 CFU/100 mL; range: 0.00 to 56.67 × 102 CFU/100 mL) and agricultural soil samples (mean: 19.64 × 102 CFU/g; range: 1.33 × 102 to 62.33 × 102 CFU/g) were documented. Consequently, a high annual infection risk of 5.50 × 10-2 (0.00 to 48.30 × 10-2), 54.50 × 10-2 (9.10 × 10-3 to 1.00) and 70.50 × 10-2 (3.60 × 10-2 to 1.00) was observed for adults exposed to contaminated irrigation water, adults exposed to contaminated agricultural soil and children exposed to agricultural soil, respectively. This study, therefore, documents a huge public health threat attributed to the high probability of infection in humans exposed to L. monocytogenes in irrigation water and agricultural soil in Amathole and Chris Hani District Municipalities in the Eastern Cape province of South Africa.

A Systematic Analysis of Research on Arcobacter: Public Health Implications from a Food-Environment Interphase Perspective.

This review maps the global research landscape of the public health implications of Arcobacter from the food-environment interphase using content analytics and integrated science mapping. The search term "Arcobacter" was used to retrieve relevant articles published in Web of Science and Scopus between 1991 to 2019. The number of articles included in the review was 524, with 1304 authors, 172 journal sources, and a collaborative index of 2.55. The annual growth rate of the publications was 9.74%. The most contributing author in the field was Houf K., with 40 publications, 26 h-index, and 2020 total citations. The most productive country was the USA (13.33%). The majority of the articles were published in English (96%) and in the Journal of Food Protection (8.02%). The highest research outputs were in the field of Microbiology (264). The frequently occurred keywords were Arcobacter, poultry, shellfish, cattle, and chicken. This study revealed a fair increase in the growth rate of Arcobacter-related research-especially in the area of isolation and detection of the pathogen in foods and food environments, as well as the pathogenesis and genetic diversity of the pathogen. Research themes in the area of prevalence and epidemiology seem to be underexplored.

An insight into the implementation of the global action plan on antimicrobial resistance in the WHO African region: A roadmap for action.

INTRODUCTION: The Global Action Plan (GAP) on antimicrobial resistance (AMR) delivers a 'One Health' strategy for the development of the national action plan. It encourages the optimal use of antimicrobials and strengthens the evidence base through surveillance and research. METHODS: This study evaluated the current status of implementation of the GAP on AMR in World Health Organization (WHO) African countries via a retrospective, cross-sectional analysis of routinely collected data on AMR. A SWOT analysis was used to identify the strengths, weaknesses, opportunities and threats involved in the GAP implementation. A roadmap for action was proposed. RESULTS: The overall mean GAP performance score across all the countries that were assessed was 32% ± SD12 (95% CI 27-36%). The mean thematic scores were 59% ± 12 (53-65%) for multi-sector and One Health collaboration; 50% ± 22 (42-58%) for developing national AMR action plans; 38% ± 12 (33-42%) for awareness and training; 18% ± 13 (13-23%) for surveillance; 33% ± 13 (29-38%) for infection prevention and control; and 28% ± 23 (20-37%) for optimal use of antimicrobial medicines in human, animal and plant health. The difference in GAP performance scores between African sub-regions and between income categories was not statistically significant (P > 0.05). While seven countries exhibited strengths in two themes, 25 countries exhibited weaknesses across all themes. Six threats and six opportunities were identified to inform a practical roadmap for AMR action. CONCLUSION: The findings from this study indicate that the overall GAP implementation on AMR in the WHO African region is inadequate. Some thematic GAP scores appeared to be relatively good, but on closer inspection, individual indicators revealed a lack of progress and implementation, requiring action.

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.

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.

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.

Treatment of COVID-19: implications for antimicrobial resistance in Africa.

There is currently no approved pharmaceutical product for the treatment of COVID-19. However, antibiotics are currently being used for the management of COVID-19 patients in many settings either treat to co-infections or for the treatment of COVID-19 itself. In this commentary, we highlight that the increased rates of antimicrobial prescribing for COVID-19 patients could further worsen the burden of antimicrobial resistance (AMR). We also highlight that though AMR is a global threat, Africa tends to suffer most from the consequences. We, therefore, call on African countries not to lose sight of the possible implications of the treatment of COVID-19 on AMR and a need to redouble efforts towards the fight against AMR while dealing with the pandemic.

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.

Characterization of antibiogram fingerprints in Listeria monocytogenes recovered from irrigation water and agricultural soil samples.

Listeria monocytogenes (L. monocytogenes) is a foodborne pathogen and the etiologic agent of listeriosis, which can be disseminated within the agricultural environment particularly soil and irrigation water, contaminate farm produce and cause high mortality and morbidity among vulnerable individuals. This study assessed the incidence and antibiogram of L. monocytogenes recovered from irrigation water and agricultural soil samples collected from Chris Hani and Amathole District Municipalities (DMs) in Eastern Cape Province, South Africa. The distribution of presumptive L. monocytogenes in irrigation water and agricultural soil samples was done using the standard plate count method, while polymerase chain reaction (PCR) was used to identify the isolates. The confirmed isolates were screened for 9 key virulence markers using PCR after which they were subjected to antibiotic susceptibility testing against 18 antibiotics used for the alleviation of listeriosis using the disk diffusion method. Relevant putative antibiotic resistance genes in the resistant variants were screened for using PCR. The distribution of L. monocytogenes in irrigation water samples was statistically significant (P ≤ 0.05) and ranged from log10 1.00 CFU/100ml to log10 3.75 CFU/100 ml. In agricultural soil samples, the distribution ranged significantly (P ≤ 0.05) from log10 2.10 CFU/g to log10 3.51 CFU/g. Of the 117 presumptive L. monocytogenes recovered from irrigation water samples and 183 presumptive L. monocytogenes isolated from agricultural soil samples, 8 (6.8%) and 12 (6.6%) isolates were confirmed respectively. Nine virulence genes including inlA, inlB, inlC, inlJ, actA, hlyA, plcA, plcB, and iap were detected in all the isolates. The proportion of the isolates exhibiting phenotypic resistance against the test antimicrobials followed the order: tetracycline (90%), doxycycline (85%), cefotaxime (80%), penicillin (80%), chloramphenicol (70%), linezolid (65%), erythromycin (60%) and trimethoprim/sulfamethoxazole (55%). The isolates exhibited multiple antibiotic resistance against 3 or more antibiotics and the MAR indices of all the multidrug isolates were ≥0.2. The isolates harboured antibiotic resistance genes including tetA, tetB, tetC, sulI, sulII, aadA, aac(3)-IIa and ESBLs including blaTEM, blaCTX-M group 9, blaVEB as well as AmpC. None of the isolates harboured the carbapenemases. We conclude that irrigation water and agricultural soil collected from Chris Hani and Amathole District Municipalities (DMs) in Eastern Cape Province of South Africa are reservoirs and potential transmission routes of multidrug-resistant L. monocytogenes to the food web and consequently threat to public health.

Cochrane corner: personal protective equipment for preventing highly infectious diseases such as COVID-19 in healthcare staff.

As coronavirus disease (COVID-19) cases continue to increase in Africa, healthcare workers (HCWs) have a high risk of being infected and the risks may be higher among those who work closely with patients. The risks of HCW infections can be mitigated with adequate precautions within healthcare facilities, especially with the use of personal protective equipment (PPE). We highlight and contextualise the findings of a Cochrane review on the type of PPE that protects best, the best way to put PPE on (donning) or to remove PPE (doffing) and how to train HCWs to use PPE. The review found low-certainty of evidence that full body PPE offer more protection, but HCWs may be faced with difficulty during donning and doffing. Following standard guidelines may be helpful in reducing infection and increasing compliance among HCWs. Video training and simulations may be better methods for training on the correct use of PPE than traditional methods of teaching. Countries must, therefore, ensure that HCWs undergo compulsory training on the correct use of PPE; regardless of their professional category. Of the 24 studies included in this review, none was conducted on the African continent. There is thus an urgent need for well conducted studies on the experiences of HCWs using full-body covering PPE within the African context. Such studies could lead to tailored interventions that will improve the proper use of PPE among HCWs.

Preharvest Transmission Routes of Fresh Produce Associated Bacterial Pathogens with Outbreak Potentials: A Review.

Disease outbreaks caused by the ingestion of contaminated vegetables and fruits pose a significant problem to human health. The sources of contamination of these food products at the preharvest level of agricultural production, most importantly, agricultural soil and irrigation water, serve as potential reservoirs of some clinically significant foodborne pathogenic bacteria. These clinically important bacteria include: Klebsiella spp., Salmonella spp., Citrobacter spp., Shigella spp., Enterobacter spp., Listeria monocytogenes and pathogenic E. coli (and E. coli O157:H7) all of which have the potential to cause disease outbreaks. Most of these pathogens acquire antimicrobial resistance (AR) determinants due to AR selective pressure within the agroecosystem and become resistant against most available treatment options, further aggravating risks to human and environmental health, and food safety. This review critically outlines the following issues with regards to fresh produce; the global burden of fresh produce-related foodborne diseases, contamination between the continuum of farm to table, preharvest transmission routes, AR profiles, and possible interventions to minimize the preharvest contamination of fresh produce. This review reveals that the primary production niches of the agro-ecosystem play a significant role in the transmission of fresh produce associated pathogens as well as their resistant variants, thus detrimental to food safety and public health.

Pandemic influenza preparedness in the WHO African region: are we ready yet?

BACKGROUND: Prior to the 2009 pandemic H1N1, and the unprecedented outbreak of Highly Pathogenic Avian Influenza (HPAI) caused by the H5N1 virus, the World Health Organization (WHO) called upon its Member States to develop preparedness plans in response to a new pandemic in humans. The WHO Member States responded to this call by developing national pandemic plans in accordance with the International Health Regulations (IHR) to strengthen the capabilities of Member States to respond to different pandemic scenarios. In this study, we aim to evaluate the quality of the preparedness plans in the WHO African region since their inception in 2005. METHODS: A standard checklist with 61 binary indicators ("yes" or "no") was used to assess the quality of the preparedness plans. The checklist was categorised across seven thematic areas of preparedness: preparation (16 indicators); coordination and partnership (5 indicators); risk communication (8 indicators); surveillance and monitoring (7 indicators); prevention and containment (10 indicators); case investigation and treatment (10 indicators) and ethical consideration (5 indicators). Four assessors independently scored the plans against the checklist. RESULTS: Of the 47 countries in the WHO African region, a total of 35 national pandemic plans were evaluated. The composite score for the completeness of the pandemic plans across the 35 countries was 36%. Country-specific scores on each of the thematic indicators for pandemic plan completeness varied, ranging from 5% in Côte d'Ivoire to 79% in South Africa. On average, preparation and risk communication scored 48%, respectively, while coordination and partnership scored the highest with an aggregate score of 49%. Surveillance and monitoring scored 34%, while prevention and containment scored 35%. Case investigation and treatment scored 25%, and ethical consideration scored the lowest of 14% across 35 countries. Overall, our assessment shows that pandemic preparedness plans across the WHO African region are inadequate. CONCLUSIONS: Moving forward, these plans must address the gaps identified in this study and demonstrate clarity in their goals that are achievable through drills, simulations and tabletop exercises.