Extended-spectrum β-lactamase, shigatoxin and haemolysis capacity of O157 and non-O157 E. coli serotypes from producer-distributor bulk milk

We investigated for virulence genes (stx1, stx2 and hlyA), serotypes and extended-spectrum β-lactamases (ESBLs) producing capacity in O157 and non-O157 Escherichia coli isolated from producer-distributor bulk milk (PDBM). Fifteen different E. coli O-serogroups were observed from the isolates (n=121). The prevalence of stx1 and stx2 genes among the E. coli isolates was 8.3% and 11.6% (n=121), respectively, while 5.8% harboured both stx1 and stx2. Four E. coli isolates (3.3%) had ESBLs producing capacity, resisted multiple cephalosporins and aztreonam, and carried stx genes. Cluster analysis using GTG5 finger printing revealed a diversity of E. coli seropathotypes in PDBM which are known to be associated with human diarrhoeal diseases. These results highlight a potential risk posed on human health by the consumption of PDBM contaminated with pathogenic E. coli. A further quantitative risk assessment of the impact of pathogenic E. coli contamination in PDBM on human health is therefore recommended.Milk South Africahttp://www.elsevier.com/locate/idairyj2018-03-31hb2017Food Scienc

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

An approach to a patient with infective endocarditis

Although infective endocarditis (IE) is relatively uncommon, it remains an important clinical entity with a high in-hospital and 1-yearmortality. It is most commonly caused by viridans streptococci. Staphylococcus aureus is responsible for a malignant course of IE andoften requires early surgery to eradicate. Other rarer causes are various bacilli, including the HACEK (Haemophilus, Actinobacillus,Cardiobacterium, Eikenella and Kingella spp.) group of organisms and fungi. The clinical presentation varies. Patients may present witha nonspecific illness, valve dysfunction, heart failure (HF) and symptoms due to peripheral embolisation. The diagnosis is traditionallybased on the modified Duke criteria and rests mainly on clinical features and to a lesser extent on certain laboratory findings,microbiological assessment and cardiovascular imaging. Identification of the offending micro-organism is not only important from adiagnostic point of view, but also makes targeted antibiotic treatment possible and provides useful prognostic information. A significantproportion of microbiological cultures are negative, frequently owing to the administration of antibiotics prior to appropriate culture.Blood-culture-negative IE poses significant diagnostic and treatment challenges. The course of the disease is frequently complicated, andsequelae include HF, local intracardiac extension of infection (abscess, fistula, pseudoaneurysm), stroke and intracranial haemorrhagedue to septic emboli or mycotic aneurysm formation as well as renal injury. Management includes prolonged intravenous antibiotics andconsideration for early surgery with removal of infective tissue and valve replacement in patients who have poor prognostic features orcomplications. Antibiotic administration for at-risk patients to prevent bacteraemia during specific procedures (particularly dental) isrecommended to prevent IE. The patient population who would benefit from antibiotic prophylaxis has become increasingly restricted,and guidelines recommend prophylaxis only for patients with cyanotic congenital heart disease, prosthetic heart valves and a previousepisode of IE. The management of a patient with IE is challenging and often requires multidisciplinary input from an IE heart team,which includes cardiologists

Characterization of Escherichia coli and other Enterobacteriaceae in producer-distributor bulk milk

The current study was undertaken to characterize Escherichia coli and other Enterobacteriaceae in raw and pasteurized producer-distributor bulk milk (PDBM). A total of 258 samples were collected from purchase points in 8 provinces in South Africa. The samples were tested for antibiotic residues, phosphatase, total aerobic bacteria, coliforms, and E. coli counts. Matrixassisted laser desorption/ionization time-of-flight mass spectrometry was used for identification of isolates. Escherichia coli isolates were characterized for virulence factors, antimicrobial resistance, serotypes, and presumptive E. coli O157:H7. Antibiotic residues and alkaline phosphatase were detected in 2% of both raw and pasteurized PDBM (n = 258) and 21% pasteurized PDBM (n = 104) samples, respectively. A total of 729 isolates belonging to 21 genera and 59 species were identified. Escherichia coli, Enterobacter cloacae, Klebsiella oxytoca, and Raoultella ornithinolytica were the most abundant species. Spoilage Enterobacteriaceae species exceeded 50% of the total isolates. Escherichia coli was detected and isolated from 36% of the milk samples. Thirty-one E. coli isolates harbored virulence genes stx1/stx2 and 38% (n = 121) were presumptive O157:H7. The prevalence of samples with presumptive shigatoxin producing E. coli was 10%. Antimicrobialresistant E. coli isolates were detected in 70% of the milk samples with 36% of stx1/stx2 positive E. coli showing multi-drug resistance. Information obtained from the study will be used for modeling the public health risk posed by milkborne pathogens in PDBM, which in many cases is consumed by poor and vulnerable members of the population.Milk South Africa (Pretoria, Republic of South Africa)http://www.journals.elsevier.com/journal-of-dairy-sciencehb2017Food Scienc

Quantitative Risk Assessment of Hemolytic Uremic Syndrome Associated with Consumption of Bulk Milk Sold Directly from Producer to Consumer in South Africa

This study was conducted to estimate the hemolytic uremic syndrome (HUS) risk associated with consumption of producer-distributor bulk milk (PDBM) contaminated with Shiga toxin-producing Escherichia coli (STEC) in South Africa. Data were obtained from recently completed studies in South Africa taking into account prior collected prevalence data of STEC in raw and pasteurized PDBM and survey information from producer-distributor outlets and households. Inputs for the models were complemented with data from published and unpublished literature. A probabilistic exposure model was developed with Monte Carlo simulation in Excel add-in software using @Risk software. Hazard characterization was based on an exponential dose-response model to calculate the probability of illness from STEC infection in individuals 5 years and younger and individuals older than 5 years. The estimated mean STEC level was 0.12 CFU/mL (95% confidence interval [CI]: 0 to 1.2; \u3c3 = 0.34) for raw PDBM and 0.08 CFU/mL (95% CI: 0 to 1; \u3c3 = 0.27) for pasteurized PDBM. A higher risk of HUS cases per year was recorded in raw than in pasteurized PDBM and also in individuals younger than 5 years of age. For every 100,000 servings consumed, the expected median numbers of HUS cases per year from raw PDBM were 52 for 5 years and younger and 3.2 for older than 5 years. The median numbers of cases per year for pasteurized PDBM were 47 for 5 years and younger and 2.9 for older than 5 years. Sensitivity analysis revealed that serving volume and time taken to sell PDBM at producer-distributor outlets were the factors with the greatest impact on probability of illness. The models developed in this study are an example of risk assessments for milk produced and marketed from similar scenarios across the globe

Potential Influence of Regulation of the Food Value Chain on Prevalence and Patterns of Antimicrobial Resistance: the Case of Tilapia (Oreochromis niloticus)

The current study was designed to evaluate the potential impact of the level of regulation on the prevalence and patterns of antimicrobial agent resistance in bacteria isolated from fish. The study sites included two large lakes and both semiregulated and unregulated fish value chains. A total of 328 bacterial isolates belonging to 11 genera were evaluated for antimicrobial susceptibility testing using the disk diffusion method. The bacterial species were tested against 12 different antibiotics (trimethoprim-sulfamethoxazole, tetracycline, ampicillin, cefotaxime, chloramphenicol, nalidixic acid, amoxicillin, meropenem, ciprofloxacin, nitrofurantoin, cefuroxime, and kanamycin). Data analysis was done to assess the heterogeneity in proportion of resistant bacterial species within and between the two value chains using a random-effects model proposed by DerSimonian and Laird (Control Clin Trials 7:177–188, 1986). Statistical heterogeneity within and between groups was estimated using the Cochran chi-square test and the Cochrane I2 index. The overall proportion of bacterial species resistant to antimicrobial agents in semiregulated and unregulated value chains ranged from 0.00 to 0.88 and 0.09 to 0.95, respectively. Shigella spp. had the highest proportion of bacteria that were resistant to most of the antimicrobial agents used. The bacterial species were highly resistant to ampicillin and amoxicillin, and the highest multidrug resistance capacity was observed in Shigella spp. (18.3%, n = 328), Vibrio spp. (18.3%), and Listeria monocytogenes (12.2%). We observed strong heterogeneity within and between the two value chains regarding proportion of resistant bacterial species. Sun-dried fish in both value chains had significantly high proportions of resistant bacterial species. Comparing the two value chains, the unregulated value chain had a significantly higher proportion of bacterial species that were resistant. In order to mitigate the risk of transmitting antimicrobial-resistant bacteria to consumers along the fish value chain, good manufacturing practices coupled with identification and management of possible sources of contamination are recommended for fish and potentially other foods distributed along the less regulated value chains. IMPORTANCE In order to mitigate the risk of transmitting antimicrobial-resistant bacteria to consumers along the fish value chain, good manufacturing practices coupled with identification and management of possible sources of contamination are recommended for fish and potentially other foods distributed along the less regulated value chains

Quantitative risk assessment of hemolytic uremic syndrome associated with consumption of bulk milk sold directly from producer to consumer in South Africa

This study was conducted to estimate the hemolytic uremic syndrome (HUS) risk associated with consumption of producer-distributor bulk milk (PDBM) contaminated with Shiga toxin-producing Escherichia coli (STEC) in South Africa. Data were obtained from recently completed studies in South Africa taking into account prior collected prevalence data of STEC in raw and pasteurized PDBM and survey information from producer-distributor outlets and households. Inputs for the models were complemented with data from published and unpublished literature. A probabilistic exposure model was developed with Monte Carlo simulation in Excel add-in software using @Risk software. Hazard characterization was based on an exponential dose-response model to calculate the probability of illness from STEC infection in individuals 5 years and younger and individuals older than 5 years. The estimated mean STEC level was 0.12 CFU/mL (95% confidence interval [CI]: 0 to 1.2; σ = 0.34) for raw PDBM and 0.08 CFU/mL (95% CI: 0 to 1; σ = 0.27) for pasteurized PDBM. A higher risk of HUS cases per year was recorded in raw than in pasteurized PDBM and also in individuals younger than 5 years of age. For every 100,000 servings consumed, the expected median numbers of HUS cases per year from raw PDBM were 52 for 5 years and younger and 3.2 for older than 5 years. The median numbers of cases per year for pasteurized PDBM were 47 for 5 years and younger and 2.9 for older than 5 years. Sensitivity analysis revealed that serving volume and time taken to sell PDBM at producer-distributor outlets were the factors with the greatest impact on probability of illness. The models developed in this study are an example of risk assessments for milk produced and marketed from similar scenarios across the globe.https://www.foodprotection.org/publications/journal-of-food-protection2019-02-23hj2018Food Scienc

Structural Investigations and Binding Mechanisms of Oseltamivir Drug Resistance Conferred by the E119V Mutation in Influenza H7N9 Virus

The use of vaccinations and antiviral medications have gained popularity in the therapeutic management of avian influenza H7N9 virus lately. Antiviral medicines are more popular due to being readily available. The presence of the neuraminidase protein in the avian influenza H7N9 virus and its critical role in the cleavage of sialic acid have made it a target drug in the development of influenza virus drugs. Generally, the neuraminidase proteins have common conserved amino acid residues and any mutation that occurs around or within these conserved residues affects the susceptibility and replicability of the influenza H7N9 virus. Herein, we investigated the interatomic and intermolecular dynamic impacts of the experimentally reported E119V mutation on the oseltamivir resistance of the influenza H7N9 virus. We extensively employed molecular dynamic (MD) simulations and subsequent post-MD analyses to investigate the binding mechanisms of oseltamivir-neuraminidase wildtype and E119V mutant complexes. The results revealed that the oseltamivir-wildtype complex was more thermodynamically stable than the oseltamivir-E119V mutant complex. Oseltamivir exhibited a greater binding affinity for wildtype (−15.46 ± 0.23 kcal/mol) relative to the E119V mutant (−11.72 ± 0.21 kcal/mol). The decrease in binding affinity (−3.74 kcal/mol) was consistent with RMSD, RMSF, SASA, PCA, and hydrogen bonding profiles, confirming that the E119V mutation conferred lower conformational stability and weaker protein–ligand interactions. The findings of this oseltamivir-E119V mutation may further assist in the design of compounds to overcome E119V mutation in the treatment of influenza H7N9 virus patients