ABSTRACT
Phyloepidemiological approaches have provided specific insight into understanding the emergence and evolution of infection. Knowledge on the outbreak and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Nigeria would assist in provision of preventive measures to reduce transmission among populations at risk. This study aimed to investigate the evolution of SARS-CoV-2 in Nigeria. A total of 39 complete genomes of SARS-CoV-2 were retrieved from the GISAID EpiFlu™ database on 29 March 2020 to investigate its evolution in Nigeria. Sequences were selected based on the travel history of the individual and the collection date. Other sequences were not selected because they were short, contained artefacts, were not from an original source or had insufficient information. Evolutionary history was inferred using the maximum likelihood method based on the general time reversible model. A phylogenetic tree was constructed to determine the common ancestor of each strain. The phylogenetic analysis showed that the strain in Nigeria clustered in a monophyletic clade with a Wuhan sublineage. Nucleotide alignment also showed a 100% similarity indicating a common origin of evolution. Comparative analysis showed 27 972 (93.6%) identical sites and 97.6% pairwise identity with the consensus. The study evidently showed the entire outbreak of SARS-CoV-2 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. Preventive measures that can limit the spread of the infection among populations at risk should be implemented.
ABSTRACT
Background: The development of multi-antibiotic resistant bacteria, especially Gram-negative bacteria which are the major cause of hospital-acquired infections worldwide, had been increasing. Escherichia coli and Klebsiella sp. had become more resistant to different classes of antibiotics, and the treatment of infections caused by these bacteria had developed into a challenge in both developed and developing countries. This study had determined the multi-antibiotic resistance (MAR) patterns of Escherichia coli and Klebsiella sp. isolated from clinical inpatient and outpatient samples. Method: The present study had used 50 E. coli and 48 Klebsiella sp. isolates. Antibiotic susceptibility test had been carried out by using disk diffusion method, and the interpretation of results of the zones of inhibition had accorded with Clinical Laboratory Standards Institute (CLSI). The antibiotics used had included the following: streptomycin, ciprofloxacin, erythromycin, nitrofurantoin, amikacin, gentamicin, ofloxacin, cefepime, oxacillin, colistin sulfate, cefotaxime, ceftazidime, pefloxacine, and cloxacillin. Results: E. coli and K. pneumoniae had shown high-resistance patterns. E. coli had exhibited high resistance against cloxacillin (96%), oxacillin (96%), erythromycin (88%), and most especially streptomycin (98%). Similarly, K. pneumoniae had presented a high resistance to streptomycin (88%), cloxacillin (92%), oxacillin (92%), and colistin (92%). E. coli had presented the highest multidrug resistance with a MAR index of 1.00. A total of 17 E. coli isolates had shown resistance to the 14 antibiotics tested. Conclusion: E. coli and Klebsiella sp. in clinical isolates in outpatients and inpatients in Ibadan, Western Nigeria had demonstrated high antimicrobial resistance. Thus, such condition should be considered a major public health concern, and measures must be taken to establish the sources and drivers of this problem.
