Prevalence and antibiotic susceptibility patterns of enteric bacterial pathogens in human and non-human sources in an urban informal settlement in Cape Town, South Africa

Prevalence and risk factors of seafood-borne Vibrio vulnificus in Asia: a systematic review with meta-analysis and meta-regression

Vibrio vulnificus is a free-living marine bacterium associated with the contamination of fish and shellfish-the most consumed seafood in Asia. Owing to its potentially lethal clinical consequences, the consumption of seafood contaminated with V. vulnificus has become a growing public health concern. This systematic review with meta-analysis and meta-regression aimed to integrate data on the prevalence of seafood-borne V. vulnificus specifically in Asia and assess the potential risk factors that can influence the outcomes. A comprehensive literature search of four electronic databases yielded 279 relevant studies, among which 38 fulfilled the inclusion criteria. These selected studies were subjected to risk-of-bias assessment and data extraction by three independent researchers. A meta-analysis of the eligible studies estimated the overall prevalence of seafood-borne V. vulnificus in Asia to be 10.47% [95% confidence interval (CI): 6.8-15.8%], with bivalve shellfish, such as oysters, mussels, clams, and cockles being the most contaminated seafood. The highest prevalence was reported in Japan, where 47.6% of the seafood samples tested positive for V. vulnificus. The subgroup and meta-regression analyses identified three potential covariates-detection method, publication year, and country-associated with between-study heterogeneity. Furthermore, data visualization displayed the variations in V. vulnificus prevalence across the studies, associated with differences in sample type, sample size, and sampling stage. This study provides valuable insights into the prevalence of V. vulnificus in fish and shellfish across the entire Asian continent and highlights the potential factors that cause variation in the prevalence rates among the studies. These findings underscore the importance of enhancing hygiene measures throughout the seafood supply chain to mitigate V. vulnificus infection risks and ensure the safety of consumers.

The genomic epidemiology of shigellosis in South Africa

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.

A South African Perspective on the Microbiological and Chemical Quality of Meat: Plausible Public Health Implications

Meat comprises proteins, fats, vitamins, and trace elements, essential nutrients for the growth and development of the body. The increased demand for meat necessitates the use of antibiotics in intensive farming to sustain and raise productivity. However, the high water activity, the neutral pH, and the high protein content of meat create a favourable milieu for the growth and the persistence of bacteria. Meat serves as a portal for the spread of foodborne diseases. This occurs because of contamination. This review presents information on animal farming in South Africa, the microbial and chemical contamination of meat, and the consequential effects on public health. In South Africa, the sales of meat can be operated both formally and informally. Meat becomes exposed to contamination with different categories of microbes, originating from varying sources during preparation, processing, packaging, storage, and serving to consumers. Apparently, meat harbours diverse pathogenic microorganisms and antibiotic residues alongside the occurrence of drug resistance in zoonotic pathogens, due to the improper use of antibiotics during farming. Different findings obtained across the country showed variations in prevalence of bacteria and multidrug-resistant bacteria studied, which could be explained by the differences in the manufacturer practices, handling processes from producers to consumers, and the success of the hygienic measures employed during production. Furthermore, variation in the socioeconomic and political factors and differences in bacterial strains, geographical area, time, climatic factors, etc. could be responsible for the discrepancy in the level of antibiotic resistance between the provinces. Bacteria identified in meat including Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, Campylobacter spp., Salmonella spp., etc. are incriminated as pathogenic agents causing serious infections in human and their drug-resistant counterparts can cause prolonged infection plus long hospital stays, increased mortality and morbidity as well as huge socioeconomic burden and even death. Therefore, uncooked meat or improperly cooked meat consumed by the population serves as a risk to human health.

Incidence and Virulence Factor Profiling of Vibrio Species: A Study on Hospital and Community Wastewater Effluents

This study aimed to determine the incidence and virulence factor profiling of Vibrio species from hospital wastewater (HWW) and community wastewater effluents. Wastewater samples from selected sites were collected, processed, and analysed presumptively by the culture dependent methods and molecular techniques. A total of 270 isolates were confirmed as Vibrio genus delineating into V. cholerae (27%), V. parahaemolyticus (9.1%), V. vulnificus (4.1%), and V. fluvialis (3%). The remainder (>50%) may account for other Vibrio species not identified in the study. The four Vibrio species were isolated from secondary hospital wastewater effluent (SHWE), while V. cholerae was the sole specie isolated from Limbede community wastewater effluent (LCWE) and none of the four Vibrio species was recovered from tertiary hospital wastewater effluent (THWE). However, several virulence genes were identified among V. cholerae isolates from SHWE: ToxR (88%), hylA (81%), tcpA (64%), VPI (58%), ctx (44%), and ompU (34%). Virulence genes factors among V. cholerae isolates from LCWE were: ToxR (78%), ctx (67%), tcpA (44%), and hylA (44%). Two different genes (vfh and hupO) were identified in all confirmed V. fluvialis isolates. Among V. vulnificus, vcgA (50%) and vcgB (67%) were detected. In V. parahaemolyticus, tdh (56%) and tlh (100%) were also identified. This finding reveals that the studied aquatic niches pose serious potential health risk with Vibrio species harbouring virulence signatures. The distribution of virulence genes is valuable for ecological site quality, as well as epidemiological marker in the control and management of diseases caused by Vibrio species. Regular monitoring of HWW and communal wastewater effluent would allow relevant establishments to forecast, detect, and mitigate any public health threats in advance.

Understanding diarrhoeal diseases in response to climate variability and drought in Cape Town, South Africa: a mixed methods approach

BACKGROUND

The climate of southern Africa is expected to become hotter and drier with more frequent severe droughts and the incidence of diarrhoea to increase. From 2015 to 2018, Cape Town, South Africa, experienced a severe drought which resulted in extreme water conservation efforts. We aimed to gain a more holistic understanding of the relationship between diarrhoea in young children and climate variability in a system stressed by water scarcity.

METHODS

Using a mixed-methods approach, we explored diarrhoeal disease incidence in children under 5 years between 2010 to 2019 in Cape Town, primarily in the public health system through routinely collected diarrhoeal incidence and weather station data. We developed a negative binomial regression model to understand the relationship between temperature, precipitation, and relative humidity on incidence of diarrhoea with dehydration. We conducted in-depth interviews with stakeholders in the fields of health, environment, and human development on perceptions around diarrhoea and health-related interventions both prior to and over the drought, and analysed them through the framework method.

RESULTS

From diarrhoeal incidence data, the diarrhoea with dehydration incidence decreased over the decade studied, e.g. reduction of 64.7% in 2019 [95% confidence interval (CI): 5.5-7.2%] compared to 2010, with no increase during the severe drought period. Over the hot dry diarrhoeal season (November to May), the monthly diarrhoea with dehydration incidence increased by 7.4% (95% CI: 4.5-10.3%) per 1 °C increase in temperature and 2.6% (95% CI: 1.7-3.5%) per 1% increase in relative humidity in the unlagged model. Stakeholder interviews found that extensive and sustained diarrhoeal interventions were perceived to be responsible for the overall reduction in diarrhoeal incidence and mortality over the prior decade. During the drought, as diarrhoeal interventions were maintained, the expected increase in incidence in the public health sector did not occur.

CONCLUSIONS

We found that that diarrhoeal incidence has decreased over the last decade and that incidence is strongly influenced by local temperature and humidity, particularly over the hot dry season. While climate change and extreme weather events especially stress systems supporting vulnerable populations such as young children, maintaining strong and consistent public health interventions helps to reduce negative health impacts.

A meta-analysis on the distribution of pathogenic Vibrio species in water sources and wastewater in Africa

Vibrio species are waterborne ubiquitous organisms capable of causing diseases in humans and animals and the occurrence of infections caused by pathogenic Vibrio species among humans have increased globally. This reemergence is attributed to environmental impacts such as global warming and pollution. Africa is most vulnerable to waterborne infections caused by these pathogens because of lack of good water stewardship and management. This study was carried out to provide an in-depth inquiry into the occurrence of pathogenic Vibrio species in water sources and wastewater across Africa. In this regard, a systematic review and meta-analysis was conducted by searching five databases: PubMed, ScienceDirect, Google Scholar, Springer Search and African Journals Online (AJOL). The search yielded 70 articles on pathogenic Vibrio species presence in African aquatic environments that fit our inclusion criteria. Based on the random effects model, the pooled prevalence of pathogenic Vibrio species in various water sources in Africa was 37.6 % (95 % CI: 27.7-48.0). Eighteen countries were represented by the systematically assessed studies and their nationwide prevalence in descending order was: Nigeria (79.82 %), Egypt (47.5 %), Tanzania (45.8 %), Morocco (44.8), South Africa (40.6 %), Uganda (32.1 %), Cameroon (24.5 %), Burkina Faso (18.9 %) and Ghana (5.9 %). Furthermore, 8 pathogenic Vibrio species were identified across water bodies in Africa with the highest detection for V. cholerae (59.5 %), followed by V. parahaemolyticus (10.4 %), V.alginolyticus (9.8 %), V. vulnificus (8.5 %), V. fluvialis (6.6 %), V. mimicus (4.6 %), V. harveyi (0.5 %) and V. metschnikovii (0.1 %). Evidently, pathogenic Vibrio species occurrence in these water sources especially freshwater corroborates the continuous outbreaks observed in Africa. Therefore, there is an urgent need for proactive measures and continuous monitoring of water sources used for various purposes across Africa and proper treatment of wastewater before discharge into water bodies.

Microbiological assessment reveals that Salmonella, Shigella and Campylobacter infections are widespread in HIV infected and uninfected patients with diarrhea in Mozambique

Diarrhea is an important cause of hospitalizations in Mozambique. However, little attention has been paid to the impact HIV infection on the prevalence or clinical manifestations of enteric bacterial infections. This study aimed to determine the prevalence of Salmonella spp., Shigella spp. and Campylobacter spp. in HIV-infected and HIV-uninfected patients with diarrhea, identify risk factors for infection, and explore the association between HIV status, viral load, and bacterial prevalence. We conducted a case-control study at the Centro de Saúde de Mavalane and Centro de Saúde 1° de Maio in Maputo, Mozambique, from November 2021 to May 2022. We recruited 300 patients, including 150 HIV-infected (cases) and 150 HIV-uninfected patients (controls), aged between 0-88 years, presenting with diarrhea. Stool samples were collected for bacterial isolation through culture, and for each HIV-infected patient, 4 ml of venous blood were obtained for viral load detection through PCR. A total of 129 patients (43.0%) had at least one bacterial infection. The prevalence of Salmonella spp., Shigella spp. and Campylobacter spp. was 33.0% (n = 99), 15.0% (n = 45) and 4.3% (n = 13), respectively. The prevalence of any bacterial infection did not differ significantly between HIV-infected (45.3%, n = 68) and HIV-uninfected patients (40.7%, = 61) (p = 0.414). Overall, having 2-3 symptoms of enteric disease (p = 0.008) and a basic education (p = 0.030) were factors associated with bacterial infection. Of the 148 patients for whom HIV-1 RNA levels were available, 115 had copy numbers ≤ 75. Another 13 had levels between 76 and 1,000 and the remaining 20 had an average of 327,218.45 copies/ml. Bivariate logistic regression found that Shigella spp. were associated with HIV (p = 0.038), although no association was found in the multivariate analysis. Enteric infections are common in both HIV-infected and -uninfected patients. Low schooling influences the occurrence of enteric infections, which highlights the need to raise awareness about their prevention.

A review of antibiotic resistance among Campylobacter species in human, animal, and water sources in South Africa: a One Health Approach

Campylobacter species are among the aetiological agents responsible for 400-500 million human diarrhoea cases per annum. The risk of dissemination of antibiotic-resistant Campylobacter species between humans, animals, and the environment is anticipated, given its transmissibility through these sources. The objective of this paper is to present a situation analysis that reports the current patterns and determinants of Campylobacter antibiotic resistance in South Africa. This review applies the One Health (OH) Approach to systematically review and collate the current antibiotic resistance status among Campylobacter spp. in South Africa. The highest level of resistance of Campylobacter in humans is to azithromycin (69.7%), whereas the lowest level of resistance of Campylobacter is to gatifloxacin (8.3%). In animals, high resistance to common antibiotics erythromycin (95.06%), clindamycin (95.68%), doxycycline (87.65%), erythromycin (90%), tetracycline (84.3%), streptomycin (88%), and ampicillin (73%) while 100% resistance of Campylobacter from water samples to tetracycline, imipenem, is recorded. Furthermore, resistance to clarithromycin (95%), azithromycin (92%), clindamycin (84.2%), doxycycline (80%), and ciprofloxacin (77.8%) is reported among Campylobacter spp. from water samples. The genetic similarity results suggest the movement of antibiotic-resistant Campylobacter spp. between humans and the environment. More research on antibiotic resistance among Campylobacter from other sources, outside clinical isolates, is recommended.

Prevalence and antimicrobial resistance profiles of Campylobacter species in South Africa: a "One Health" approach using systematic review and meta-analysis

OBJECTIVES

This study investigated the prevalence and antibiotic resistance (AR) profiles of Campylobacter spp. isolated from animals, humans, and the environment in South Africa based on available published data.

METHODS

Original articles published from January 1, 1990 to January 1, 2021 were searched from PubMed, ScienceDirect, Google Scholar, Africa Index Medicus, Scopus, and African Journal Online databases. Data were analyzed with Comprehensive Meta-Analysis (version 3.0).

RESULTS

After screening, articles on animals (n = 25), humans (n = 7), environment (n = 3), animals/environment (n = 2), and a (n = 1) study on animals, humans, and the environment were included in this review. The pooled prevalence estimates (PPEs) were 28.8%, 16.4%, and 28.4% in animals, humans, and the environment, respectively. The Campylobacter jejuni and Campylobacter coli species were commonly isolated from humans, animals, and the environment in South Africa. The AR profiles were screened from 2032 Campylobacter spp., with the highest PPE of AR observed against clindamycin (76.9%) and clarithromycin (76.5%). Campylobacter isolates tested with the disk diffusion assay and minimum inhibitory concentration methods recorded an overall AR prevalence of 35.3% and 37.1%, respectively, whereas multidrug resistance PPE was 35.3%.

CONCLUSION

Regular surveillance of Campylobacter spp. prevalence and its antimicrobial resistance strains is recommended, as well as the formulation of a "One Health" approach for better management and control of Campylobacter spp. infection in South Africa.

Diarrhea-Causing Bacteria and Their Antibiotic Resistance Patterns Among Diarrhea Patients From Ghana

Diarrheal disease remains a major global health problem particularly in children under 5 years and the emergence of antibiotic-resistant strains of causative pathogens could slow control efforts, particularly in settings where treatment options are limited. This surveillance study conducted in Ghana aimed to determine the prevalence and antimicrobial susceptibility profile of diarrhea-causing bacteria. This was a cross-sectional study carried out in five health facilities in the Ga West Municipality of Ghana between 2017 and 2021. Diarrheic stool samples from patients were collected and cultured on standard differential/selective media and isolates identified by standard biochemical tests, MALDI-TOF assay, and serological analysis. The antibiogram was determined using Kirby-Bauer disk diffusion and Microscan autoScan4 MIC panels which were used for extended-spectrum beta-lactamase (ESBL) detection. Bacteria were isolated from 97.5% (772/792) of stool samples, and 167 of the isolates were diarrheagenic and met our inclusion criteria for antimicrobial resistance (AMR) analysis. These included Escherichia coli (49.1%, 82/167), Salmonella species (23.9%, 40/167), Vibrio species (16.8%, 28/167), and Shigella species (10.2%, 17/167). Among 24 Vibrio species, we observed resistances to cefotaxime (21/24, 87.5%), ceftriaxone (20/24, 83.3%), and ciprofloxacin (6/24, 25%), including four multi-drug resistant isolates. All 13 Vibrio parahaemolyticus isolates were resistant to cefazolin. All 17 Shigella isolates were resistant to tetracycline with resistance to shigellosis drugs such as norfloxacin and ciprofloxacin. Salmonella isolates were highly susceptible to norfloxacin (40/40, 100%) and tetracycline (12/34, 35%). Two ESBL-producing E. coli were also identified with marked susceptibility to gentamicin (66/72, 91.7%) and amikacin (57/72, 79.2%) prescribed in the treatment of E. coli infections. This study showed the different bacteria implicated in diarrhea cases in Ghana and the need for differential diagnoses for better treatment outcomes. Escherichia coli, Shigella, Salmonella, and Vibrio have all been implicated in diarrhea cases in Ghana. The highest prevalence was E. coli and Salmonella with Shigella the least prevalent. Resistance to commonly used drugs found in these isolates may render bacteria infection treatment in the near future nearly impossible. Routine antimicrobial susceptibility testing, effective monitoring, and nationwide surveillance of AMR pathogens should be implemented to curb the increase of antimicrobial resistance in Ghana.

Prevalence of Antibiotic Resistance in Salmonella Serotypes Concurrently Isolated from the Environment, Animals, and Humans in South Africa: A Systematic Review and Meta-Analysis

One of the main global concerns is the usage and spread of antibiotic resistant Salmonella serovars. The animals, humans, and environmental components interact and contribute to the rapid emergence and spread of antimicrobial resistance, directly or indirectly. Therefore, this study aimed to determine antibiotic resistance (AR) profiles of Salmonella serotypes isolated from the environment, animals, and humans in South Africa by a systematic review and meta-analysis. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed to search four databases for studies published from 1980 to 2021, that reported the antibiotic resistance profiles of Salmonella serotypes isolated in South Africa. The AR was screened from 2930 Salmonella serotypes which were isolated from 6842 samples. The Western Cape province had high pooled prevalence estimates (PPE) of Salmonella isolates with AR profiles followed by North West, Gauteng, and Eastern Cape with 94.3%, 75.4%, 59.4%, and 46.2%, respectively. The high PPE and heterogeneity were observed from environmental samples [69.6 (95% CI: 41.7−88.3), Q = 303.643, I² = 98.353, Q-P = 0.045], animals [41.9 (95% CI: 18.5–69.5), Q = 637.355, I² = 98.745, Q-P = 0.577], as well as animals/environment [95.9 (95% CI: 5.4−100), Q = 55.253, I² = 96.380, Q-P = 0.300]. The majority of the salmonella isolates were resistant to sulphonamides (92.0%), enrofloxacin and erythromycin (89.3%), oxytetracycline (77.4%), imipenem (72.6%), tetracycline (67.4%), as well as trimethoprim (52.2%), among the environment, animals, and humans. The level of multidrug-resistance recorded for Salmonella isolates was 28.5% in this review. This study has highlighted the occurrence of AR by Salmonella isolates from animals, humans, and environmental samples in South Africa and this calls for a consolidated “One Health” approach for antimicrobial resistance epidemiological research, as well as the formulation of necessary intervention measures to prevent further spread.

A systematic review and meta-analysis reveal that Campylobacter spp. and antibiotic resistance are widespread in humans in sub-Saharan Africa

INTRODUCTION

Campylobacter spp. are zoonotic bacteria that cause gastroenteritis in humans worldwide, whose main symptom is diarrhea. In certain cases, extra intestinal manifestations may occur, such as Guillain Barré syndrome. The bacteria cause severe diarrhea mostly in children and in immunocompromised individuals. This review aims to address the prevalence of Campylobacter spp. in humans in sub-Saharan Africa. It also aims to understand the impact of HIV in the prevalence, as well as to report data on antibiotic resistance and propose research priorities.

METHODS

We followed PRISMA guidelines to find studies on the occurrence of Campylobacter spp. in humans in all countries from sub-Saharan Africa. Studies published between 2000 and 2020 were searched in PubMed, Cochrane Library, CINAHL, African Index Medicus, African Journals Online, Google Scholar and Science Direct. We have conducted a random-effect meta-analysis and calculated the proportion of resistant isolates to different antibiotics.

RESULTS AND DISCUSSION

We found 77 studies that described such occurrence in humans in 20 out of 53 sub-Saharan African countries. Campylobacter jejuni was the most prevalent species. Pooled prevalence was 9.9% (CI: 8.4%-11.6%). No major variations within the different sub-regions were found. Most studies reported Campylobacter spp. as the cause of diarrhea, mainly in children. Some studies reported the bacteria as a possible etiologic agent of acute flaccid paralysis and urinary tract infection. Campylobacter spp. presented a higher pooled prevalence in HIV infected patients, although not statistically significant. High proportions of resistant strains were reported for many antibiotics, including erythromycin and tetracycline.

CONCLUSION

Campylobacter spp. occur in sub-Saharan Africa, although information is scarce or inexistent for many countries. Research priorities should include investigation of the understudied species; extra intestinal manifestations; the impact of HIV infection and associated risk factors. Control strategies should be reinforced to contain the spread of this pathogen and drug resistance.