Cluster analysis and geospatial mapping of antibiotic resistant Escherichia coli O157 in southwest Nigerian communities.

Geospatial spread and antibiotic-resistant relatedness of Escherichia coli O157, which are important virulent serotypes causing severe complications leading to high intestinal morbidity and occasional mortality in several communities in southwest Nigeria, were evaluated. Biotyped Escherichia coli strains (n = 508) from subjects with diarrhea and related intestinal infections, various domestic water sources and food animal products were evaluated for antibiotic resistance relatedness, conjugative activity, virulence factor and biofilm production. Antibiotic resistance of Escherichia coli O157 encoded with stx was mapped for geospatial spread. Detected stx-encoded Escherichia coli O157 (7.56%) of human strains were significantly higher compared to water and food animal strains (p = 0.001) with high conjugative and transformative activity (OR(95%CI) = 34.65(94.5); p = 0.023). Water- Escherichia coli O157 reveal significant median resistance to ciprofloxacin, gentamycin (p < 0.05) and human diarrheagenic strains showed >60% resistance to doxycycline (MIC50 8 µg/mL and MIC90 128 µg/mL; p = 0.018), tetracycline (MIC50 4 µg/mL and MIC90 64 µg/mL), ciprofloxacin (MIC50 2 µg/mL and MIC90 128 µg/mL) and gentamycin (MIC50 4 µg/mL and MIC90 256 µg/mL). Strains from human diarrhea, UTI, colitis, cattle, fish, sheep, ground waters, streams, and rivers characterized with biofilm, hemolysin, protease productions, R-plasmid (≈14.30kbp) and MARI (0.84) were highly related. Principal component analysis (score plot) revealed a significant association between resistant human diarrheic strains with cattle and poultry strains. A high population of heterogeneous stx-encoded diarrheagenic and colitis strains was predominant in urban settings spreading with food animal and water Escherichia coli O157 strains. Human diarrheagenic Escherichia coli O157 were highly related to antibiotic resistance and virulence pattern with water and animal products strains. Strategic interventions through the implementation of One Health approach and population-target antimicrobial stewardship are needed to mitigate the increasing intestinal morbidity and reduction of mortality impact. Regular application of spatial data on clonal dissemination is important for monitoring, surveillance of antimicrobial resistance and transmission of zoonotic food-borne Escherichia coli O157 pathogens.

Bioaccumulation of organochlorine pesticides in the parasite Cosmocerca sp. (Nematoda: Cosmocercidae) and the amphibian host Amietophrynus regularis (Reuss, 1833) within Lagos metropolis, Nigeria.

BACKGROUND: Amphibian species are being threatened worldwide and chemical pollution is one of the leading causes of this decline. The use of agrochemicals such as organochlorine pesticides (OCPs) among the several health and ecological challenges it causes, the sharp amphibian population decline is most pressing.Toad specimens Amietophrynus regularis were sampled from three (3) selected areas; each comprising of natural habitat and dumpsites within Lagos metropolis. METHODS: The congeners of organochlorine pesticides were tested in the liver, intestine, and parasite (Cosmocerca sp.) of the toads and soil samples from the respective locations using gas chromatography-mass spectrometer (GC-MS). Histopathological analyses were conducted on the intestines and liver of the toads using hematoxylin and eosin (H&E) stain and then examined under the binocular dissecting microscope. RESULTS: The concentration of aldrin in the intestine of A. regularis sampled at the dumpsites was higher than the concentrations in the intestines of A. regularis in the natural habitat. The concentrations of dieldrin in the uninfected A. regularis at both dumpsite and natural habitat were higher than the concentrations in the infected A. regularis at both environments. This indicated that the parasite Cosmocerca sp. may have played a depurative role in sequestering the concentration of dieldrin in the toads irrespective of the location. The parasites exhibited marked sequestration capacity characterized by the notably high total bioaccumulation rate both in the liver and the intestine at the dumpsite. The stunted villi being the common histological alteration in the infected and uninfected toads at the dumpsite but missing in the uninfected counterparts at the natural habitat may be attributed to the differences in the background concentration of the OCP congeners. CONCLUSIONS: The parasite- Cosmocerca sp. has been shown to be a potential tool in the biomonitoring of these OCP congeners which persists in the environment. Continuous research on these congeners is a searchlight to checkmate the environment to see how compliant industries and the consumers are in terms of regulation of these chemicals.

Clonal diversity and spatial dissemination of multi-antibiotics resistant Staphylococcus aureus pathotypes in Southwest Nigeria.

Spread of genetically diverse Staphylococcus aureus characterized with multi-antibiotic resistance and regulated by high level agr functionalities in several communities in southwest Nigeria was investigated and evaluated for infection control. Staphylococcus aureus pathotypes recovered from 256 cases including purulent pus from skin infections, soft tissue aspirates, wounds, otorrhea, eye, throat and endocervical infections were assayed for biofilm and antibiogram. Further genotyped with micro-array, mapped for geospatial distribution and evaluated for clonal diversity and functional accessory gene regulators (agr). Significant Staphylococci infection among the ages (OR:0.021, CI:0.545-1.914) and female gender with prevalence rate of MSSA (53.0%) and MRSA (1.5%) (OR:1.021, CI:0.374-1.785) were observed. More than 52.5% resistance rates to tetracycline and amoxicillin with significant median resistance were observed in all the infection cases (p = 0.001). Resistance rate of 78.8% at MIC50 32µg/ml and MIC90 128µg/ml to amoxicillin-clavulanate, and more than 40% resistance to ceftazidime, ciprofloxacin and tetracycline of MIC90 and MIC50 at 32 µg/ml were observed. Strains with multi-antibiotic resistance index above 0.83, high beta-lactamase and strong biofilm clustered into separate phylo-group. Heterogeneous t442 (wound and pus), t657 (wound), t091 (ear) and t657 (ear and wound) revealed high phylogenetic diversity. Only 4.6% pvl+ MSSA-CC1 agrI, pvl+ MSSA-CC5 (13.6%) and pvl+ MRSA-CC7 agrII (4.6%), expressed enterotoxin, leukocidins, proteases and resistance gene determinants. Livestock clonal types clustered with identified community-associated strains. Clonal dissemination of resistant pvl+ MSSA-CC1 and MRSA-CC5 encoding agr were predominant in several peri-urban communities where adequate geno-surveillance, population-target antimicrobial stewardship, extensive community structured infection control programs are needed to prevent further focal dissemination.

Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences.

BACKGROUND: The ongoing SARS-CoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing a severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months, between 14th February to 24th April 2020, using whole genome sequences. METHODS: We performed recombination analysis against closely related CoV strains, Bayesian time scaled phylogeny, and investigation of spike protein amino acid mutations. RESULTS: Recombination signals were observed between the Afr-SARS-CoV-2 sequences and reference sequences within the RdRPs and S genes. The evolutionary rate of the Afr-SARS-CoV-2 was 4.133 × 10-4 Highest Posterior Density (HPD 4.132 × 10-4 to 4.134 × 10-4) substitutions/site/year. The time to most recent common ancestor (TMRCA) of the African strains was December 7th 2019, (95% HPD November 12th 2019-December 29th 2019). The Afr-SARCoV-2 sequences diversified into two lineages A and B, with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility (MCC) tree and PANGOLIN software. There was a high prevalence of the D614G spike protein amino acid mutation 59/69 (82.61%) among the African strains. CONCLUSION: This study has revealed a rapidly diversifying viral population with the G614G spike protein variant dominatinge advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARS-CoV-2 in Africa.

Nilonema gymnarchi (Nematoda: Philometridae) and trace metals in Gymnarchus niloticus of Epe lagoon in Lagos State, Nigeria.

The presence of trace metals in the sediment, water, and biota of the Epe lagoon has been recently linked to oil exploration and municipal perturbations around the lagoon. The study was aimed at assessing the concentrations and associated health risks of Fe, Zn, Cu, Ni, Pb, Cd, Cr, Mn, Co and V in the water, sediment, and Gymnarchus niloticus of Epe lagoon and to evaluate the role of the enteric parasite Nilonema gymnarchi in bioaccumulation of the metals in the fish. The temperature, pH, redox potential, conductivity, turbidity, dissolved oxygen (DO), total dissolved solids (TDS), and salinity were determined in-situ using a handheld multi-parameter probe (Horiba Water Checker Model U-10). The concentrations of Fe, Zn, Cu, Ni, Pb, Cd, Cr, Mn, Co, and V were determined in the surface water, bottom sediment, Gymnarchus niloticus, and its enteric parasites, Nilonema gymnarchi in Epe lagoon using the Flame Atomic Absorption Spectrometer (Philips model PU 9100). The bioaccumulation factors and target hazard quotients of the trace metals in the infected and uninfected fish were estimated and compared. The intestinal tissue sections of the infected and uninfected fish were examined using a binocular dissecting microscope (American Optical Corporation, Model 570) using hematoxylin and eosin (H&E) stain. Biochemical markers such as reduced glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), and lipid peroxidation (MDA) were determined in the liver of the infected and uninfected fish. The SOD level was higher in the uninfected fish than the infected ones supports the indications deduced from the bioaccumulation analysis. Strong positive correlations between SOD and most of the metals- Fe (0.916), Zn (0.919), Cu (0.896), and Ni (0.917) suggests that the metals may have inflicted more toxicity in the uninfected. The histopathological comparisons made between the uninfected and infected fish showed consistency with the outcomes of other comparisons made in this study. These evidence were marked by tissue alterations in the infected fish ranging from no observed changes to mild alterations, while the uninfected exhibited more severe tissue injuries such as hemorrhagic lesions, severe vascular congestion, edema, the increased connective tissue of the submucosa, and vascular congestion. The condition factors of the infected (0.252) and uninfected (0.268) fish indicated slenderness and unfitness possibly due to environmental stressors such as trace metals. The parasitized fish showing better-coping potentials than the uninfected, coupled with the significant bioaccumulation interferences exhibited by the parasite Nilonema gymnarchi is an indication that the parasites may be a good metal sequestration agent for the fish and can be used to forestall the significant health hazard quotient posed by the current level of iron and the synergy of all metals analyzed in the lagoon.

Health risk indices and zooplankton-based assessment of a tropical rainforest river contaminated with iron, lead, cadmium, and chromium.

Oil exploration's devastation on health and the environment may far outweigh its economic benefits. An oil spill occurred at Egbokodo River in Delta State, Nigeria, thereby polluting the land and water bodies. The study was therefore aimed at evaluating the impacts of iron, lead, cadmium, and chromium on the zooplankton community structure of Egbokodo River and the potential health risks. Zooplankton and surface water samples were collected to investigate the concentrations of trace metals and zooplankton abundance. The associated carcinogenic and non-carcinogenic effects of the metals in the water were analyzed. Trace metal concentrations in the surface water were determined using atomic absorption spectroscopy (Philips model PU 9100) and zooplankton samples were collected using a hydrobios plankton net (mesh size 25 µm). Total petroleum hydrocarbons (TPH) and oil and grease (OG) were determined using Agilent 7890B gas chromatography coupled to flame ionization detector (GC-FID) and volumetric analysis respectively. The trend of the abundance of zooplanktons cross the river was 18 individuals (Station A) < 100 individuals (Station B) < 155 individuals (Station C). Cyclopoida proved to be the most resilient to the impacts of the oil spill. On a taxa basis, the order of abundance among Calanoida, Cyclopoida, Cladoceran, and Harpacticoida was Station C > Station B > Station A, except in Amphipoda where Station B > Station C > Station A was observed. Iron and lead posed significant carcinogenic risks that are liable to be inflicted by the ingestion of the water. The cumulative non-carcinogenic health risk in the male was the only significant (> 1) among the age groups. Total petroleum hydrocarbons (TPH), oil and grease (OG), iron, and lead had notable impacts on the general abundance of zooplankton in the aquatic habitat. The dominance of the Cyclopoida in the river buttressed the impact of the oil spill which warrants a prompt remediation measure. The pollution had notable ecological impacts on the zooplankton community structure of the aquatic habitat. The adults in the nearby human populations are liable to elicit carcinogenic health challenges associated with lead and iron ingestion. The males are at risk of non-carcinogenic illnesses which are associated with the combined toxicity effects of all the metals. The study suggests that the pollution in Egbokodo River was validated by the dominance of the Cyclopoida in the aquatic habitat. The study confers bioindicator reputation on the Cyclopoida for future biomonitoring studies.

Interactions of trace metals with bacteria and fungi in selected agricultural soils of Egbema Kingdom, Warri North, Delta state, Nigeria.

This study was aimed at investigating the relationship of trace metals with prevalence of bacteria and fungi in polluted farmland of Egbema Kingdom, Delta state. This may contribute to the knowledge on the influence of the microorganism to the arability of agricultural soil from an ecotoxicological viewpoint. Soil samples were analyzed for physico-chemical parameters and trace metals using atomic absorption spectrophotometer (Buck Scientific, 210VGP). The samples were also screened for fungi and bacteria isolates. Trace metals (Fe, Zn, Cd, Ni and Cu) determined in the agricultural soils of Egbema kingdom were below WHO limits. The fungi species with the highest number of occurrence was Aspergillus niger, while the species with the lowest occurrence were Fusarium oxsporium, Penicillium dirty white, and Penicillium sp. The order of abundance of fungi across the stations was Station 2> Station 4> Station 3> Station 1> Station 7> Station 5> Station 6> Station 9> Station 8. The bacteria species with the highest number of occurrence was Proteus sp I, while the species with the lowest occurrence was Alcaligenes sp. which occurred only once at Station 5. The order of abundance of bacteria in the soil samples across the stations was Station 4> Station 3> Stations 5 and 9> Station 2> Station 8> Station 7> Station 6. All trace metals in the agricultural soils of Egbema kingdom were below WHO limits. Fe, Zn, Cd and Ni showed no relationship with the microbial contents of the soil. Various strains of fungi and bacteria (gram positive and gram negative) were observed in the soil samples. An antagonistic relationship was observed between bacteria and fungi. Significant positive correlation occurred between the concentration of copper and bacteria counts indicating that the concentration of copper in the soil might have enhanced the abundance of bacteria in the soil, vice versa. The bacteria might be a promising tool in regulation of soil copper concentration.

Impacts of trace metals on African common toad, Amietophrynus regularis (Reuss, 1833) and depuration effects of the toad's enteric parasite, Amplicaecum africanum (Taylor, 1924) sampled within Lagos metropolis, Nigeria.

The study aimed at assessing the depuration potentials of endoparasite, Amplicaecum africanum on trace metals in its toad host, Amietophrynus regularis at sites of significant anthropogenic perturbations within the Lagos metropolis, in Nigeria. A total of 120 toads of both sexes, alongside 45 soil samples were collected from each of three (3) stations labeled Dumpsite, Lagoon front and Highrise, using hand nets and by hand-picking between February and October, 2018. The intestinal tissues sections of the toads were examined using a binocular dissecting microscope (American Optical Corporation, Model 570) and hematoxylin and eosin (H&E) stain. Oxidative stress in toad intestine was assessed by estimating the levels of glutathione peroxidase (GPx), superoxide dismutase (SOD), catalase (CAT), and lipid peroxidation (MDA). Trace metals in the water, soil, toad liver, intestine and parasite, Amplicaecum africanum were tested using Atomic Absorption Spectrophotometry (Philips model PU 9100). Lead (Pb), copper (Cu), nickel (Ni), cadmium (Cd), and chromium (Cr) were detected in the toads, with the infected toads having lower concentrations of most trace metals than the uninfected toads, irrespective of the locations and sex. Strong negative correlations between parasitological indices and concentrations of trace metals in the toads suggest that the parasites might have taken up significant amounts of trace metals from the host. The study demonstrated the potentials of parasite, A. africanum to depurate trace metal burden in Amietophrynus regularis. When the dominant factor impacting the toad is the parasitic infection, parasite intensity determines the trade-off between parasitological harm and depuration benefit to the host. Hence, under controlled conditions, parasites may serve as bioremediation agent in the event of pollution. Depuration potential of A. africanum in the study was supported by the mild tissue alterations observed in the intestine of infected toads, compared to the uninfected counterparts, which exhibited severe glandular hyperplasia, increased connective tissue, and severely stunted villi. Consistently lower activities of biochemical biomarkers which characterize the uninfected toads compared to the infected, irrespective of the sex and stations, further corroborate drawn inferences.

Principal Components and Hierarchical Cluster Analyses of Trace Metals and Total Hydrocarbons in Gills, Intestines and Muscles of Clarias gariepinus (Burchell, 1822).

The aim of the study was to comparatively analyze the interrelationships among iron (Fe), manganese (Mn), zinc (Zn), copper (Cu), lead (Pb), cadmium (Cd), chromium (Cr) and total hydrocarbons (THCs) in the gills, intestines and muscles of Clarias gariepinus collected from Osse River, Nigeria, between the periods of April, 2013 to September, 2014. The trace metals in the fish tissues were analyzed using Atomic Absorption Spectrophotometer (AAS, Philips model PU 9100), while total hydrocarbons were analyzed using High Performance Liquid Chromatograph (HPLC,Prominence Dual brand from HGE) equipped with a detector Shimadzu UV-Visible (UV-Vis Prominence SPD 20 A). The concentrations of trace metals and THCs in the tissues were subjected to principal component analysis (PCA), in conjunction with hierarchical cluster analysis (HCA), backed up by correlation analysis (CA). In the most prioritized component among the hierarchies of contaminants, characterized as principal component 1, results of communality extractions and rotated component matrices revealed the order of contaminants was Mn > Cu > Zn > Fe > Cr in the intestines, Cr > Cu > THCs > Mn > Fe in the muscle, while Pb > Cr > Fe > Mn was the order in the gills of the fish. Iron inhibited accumulation of the other trace metals in the gills, where its threshold of essentiality was maximal. Noteworthy is the fact that Mn and Cu were the most active components in the muscle and concurrently of excess concentrations in the tissue, which is the major edible part of fish, and constitutes its main body weight, hence holds its nutritional and economic values. High level of variability which occurred in the toxicant profile across the tissues of C. gariepinus is a function of uptake route, varied organ functions and specificity of tissue permeability of the compared organs. The study demonstrated variability in organ accumulation capacity and toxicant's competitiveness irrespective of bioavailability. The study provides data useful for future ecotoxicological studies and safety of consumers of the fish.

Isolation of Polygalacturonase-Producing Bacterial Strain from Tomatoes (Lycopersicon esculentum Mill.).

BACKGROUND: Polygalacturonase (EC 3.2.1.15) enzyme aids in microbial spoilage of fruits and vegetables. It is very important to find economical ways to producing the enzyme so as to achieve maximum yield in industries due to its use at different areas of production process. METHODS: Isolation of polygalacturonase-producing bacterial strain from tomatoes (Lycopersicon esculentum Mill.) was studied. Polygalacturonase-producing bacterial strains were isolated and screened from tomatoes stored at normal laboratory temperature (25 ± 2°C). They were identified based on their morphological, biochemical, and molecular characteristics. The enzyme produced was partially purified by the ammonium sulphate precipitation method. Molecular weights and optimum conditions for best enzyme activity were obtained by SDS PAGE technique. RESULTS: Five bacterial isolates resulted after screening. Bacterial strain code B5 showed highest polygalacturonase activity. Optimum conditions for polygalacturonase PEC B5 were maintained at pH 4.5; temperature 35°C; substrate concentration 0.3 mg/ml, and best activity at less than 5 min of heating. The enzyme PEC B5 was found to weigh 65 kDa and 50 kDa for crude and partially purified aliquots, respectively. The result of 16S rRNA gene sequencing revealed bacterial strain code B5 as Enterobacter tabaci NR146667 having 79% similarity with the NCBI GenBank. CONCLUSION: Microorganisms should be developed for large-scale production of enzymes in developing countries.