Mycobacterium tuberculosis complex drug-resistance, phylogenetics, and evolution in Nigeria: Comparison with Ghana and Cameroon.

In this article, we provide an in-depth analysis on the drug-resistance phenotypic characteristics of a cohort of 325 tuberculosis and characterize by Whole Genome Sequencing 24 isolates from Nigeria belonging to L4, L5 and L6. Our results suggest an alarming rate of drug-resistance of the L4.6.2.2 Mycobacterium tuberculosis complex (MTBC) lineage and a high diversity of L5. We compiled these new Sequence Read Archives (SRAs) to previously published ones from available Bioprojects run in Nigeria. We performed RAxML phylogenetic reconstructions of larger samples that include public NCBI SRAs from some neighboring countries (Cameroon, Ghana). To confront phylogenetic reconstruction to metadata, we used a new proprietary database named TB-Annotator. We show that L5 genomes in Northern Nigeria belong to new clades as the ones described until now and allow an update of the taxonomy of L5. In addition, we describe the L4.6.2.2 lineage in Nigeria, Cameroon and Ghana. We provide computations on the likely divergence time of L4.6.2.2 and suggest a new hypothesis concerning its origin. Finally we provide a short overview on M. bovis diversity in Nigeria. This study constitutes a baseline knowledge on the global genomic diversity, phylogeography and phylodynamics of MTBC in Nigeria, as well as on the natural history of this largely ignored but densely populated country of Africa. These results highlight the need of sequencing additional MTBC genomes in Nigeria and more generally in West-Africa, both for public health and for academic reasons. The likelihood of replacement of L5-L6 by L4.6.2.2 isolates, leave potentially little time to gather historical knowledge informative on the ancient history of tuberculosis in West-Africa.

Characterization and Antimicrobial Susceptibility Profile of Bacteraemia Causing Pathogens Isolated from Febrile Children with and without Sickle Cell Disease in Kano, Nigeria.

BACKGROUND AND OBJECTIVES: Bacterial infection in sickle cell anaemic patients is a major cause of mortality and requires proper treatment with appropriate antibiotics. However, continue defiant of these infections causing pathogens to many antibiotics and inadequate screening methods in overburden health care facilities such as our in Kano, Nigeria necessitates the conduct of this study. A research was therefore conducted to isolate, characterize and test for antimicrobial susceptibility of bacteraemia-causing pathogens from febrile children with and without sickle cell disease in Kano, Nigeria. METHOD: A total of 225 venous blood samples from suspected sickle cell anaemic children attending three selected hospitals within Kano metropolis were collected and screened for sickle cell disease, followed by blood culture using automated blood culture system. The bacteria isolated from confirmed febrile SCD and non-SCD children were characterized using microscopic, biochemical and serological techniques. Their susceptibility to commonly used antibiotics was tested using disc diffusion method. RESULTS: Of the 225 blood specimens screened, 68 (30.22%) were SCD positive, with the highest percentage (16%) among subjects within 1-2 years of age. A total of 11 genera of bacteria were isolated from both SCD and non SCD positive bloods, with Salmonella typhi having highest occurring rate in SCD positive children 27 (39.71%), followed by Streptococcus pneumoniae 10(14.71%), Salmonella Group B 9(13.24%), Staphylococcus aureus 4 (5.88%), and Escherichia coli 3 (4.41%). Majority of the isolates from SCD children 59 (86.76%) were highly susceptible to ciprofloxacin followed by cefuroxime 45 (66.18%), gentamicin 38 (55.88%), ceftriaxone 30 (44.12%), augmentin 39 (57.35%), ampicillin 25 (36.77%) and co-trimoxazole (22.06%). CONCLUSION: Bacteraemia in SCD confirmed children in the three hospitals are caused by a combination of 11 genera of bacteria. The lesser rate of bacteraemia was found in non-SCD children. Resistance to commonly used antibiotics is on increase, but treatment with ciprofloxacin and some 3rd generation cephalosporin are still promising.