Metagenome-Assembled Genome Sequence of a Strain of Burkholderia cepacia Isolated from the Gut of Macrotermes bellicosus in Nigeria.

The efficiency of the termite Macrotermes bellicosus at digesting lignocellulose is due to its gut bacterial symbionts. We report the metagenome-assembled genome sequence of Burkholderia cepacia UJ_SKK_1.2, reconstructed from metagenomes produced from Macrotermes bellicosus gut microbiota. The 7,460,271-bp genome obtained consists of 6,763 protein-coding sequences, with 6,719 functionally assigned genes and 59 RNA genes.

Metagenome-Assembled Genome Sequence of Stenotrophomonas maltophilia Strain UJ_SKK_5.5, Obtained from the Gut Microbiome of a Macrotermes bellicosus Termite Collected from Hot, Arid Nigeria.

The metagenome-assembled genome (MAG) sequence of Stenotrophomonas maltophilia strain UJ_SKK_5.5 was obtained from the gut microbiome of Macrotermes bellicosus (termite) from hot, arid Nigeria. The assembled genome (4,313,335 bp) contains 157 contigs, the N50 is 41,072 bp, the GC content is 66.57%, and there are 3,925 protein coding sequences, 3,886 proteins with functional assignments, 39 pseudogenes, and 67 RNA genes.

Assembly of Olivibacter sp. Strain UJ_SKK_5.1 Genome Sequence, Isolated from Metagenomes of Macrotermes bellicosus Guts Collected from Hot, Arid Nigeria.

The metagenome-assembled genome sequence of Olivibacter sp. strain UJ_SKK_5.1 was generated from the metagenome of a Macrotermes bellicosus (termites) gut collected from Nigeria's hot, arid environment. The assembled genome (6,135,249 bp) contains 432 contigs, with an N50 value of 22,779 bp, GC content of 41.1%, 5,043 protein-coding sequences, 5,034 proteins with functional assignments, and 9 pseudogenes and 48 RNA genes.

High-Complexity Plasmodium falciparum Infections, North Central Nigeria, 2015-2018.

The mass migration that occurred during 2009-2013 and after the insurgency in northeastern Nigeria could have increased malaria incidence and Plasmodium falciparum genetic diversity in North Central Nigeria. To determine P. falciparum sequence diversity in this region, we screened 282 samples collected in regional clinics during 2015-2018 for Plasmodium spp. and, with positive samples, determined P. falciparum infection complexity and allele diversity using PCR. Of 34 P. falciparum-positive samples, 39 msp1, 31 msp2, and 13 glurp alleles were detected, and 88% of infections were polyclonal. We identified trimorphic and dimorphic allele combinations in a high percentage of samples, indicative of a high infection complexity in the study population. High genetic diversity is a catalyst for the evolution of drug-resistant alleles. Improved measures (e.g., better drug quality, diagnostics) are needed to control P. falciparum transmission and reduce the potential for the emergence of drug resistance in Nigeria.

Molecular characterization of dermatophytes isolated from cattle in Plateau State, Nigeria.

Dermatophytes from cattle were successfully characterized to species and strain levels for the first time in Nigeria. This study was undertaken to isolate and characterize dermatophytes from cattle in Plateau State, Nigeria. Two molecular techniques were utilized. The first was the use of polymerase chain reaction (PCR) to amplify the internal transcribed spacer regions of the ribosomal DNA using ITS-1 and ITS-4 as primers. This was followed by restriction fragment length polymorphism analysis of the amplified ITS regions using the enzyme MvaI to identify dermatophyte species. The second technique was a PCR using the short oligonucleotide 5'-GACAGACAGACAGACA-3' as primer for the RAPD typing of the isolates for identification of dermatophytes based on species specific profiles. Profiles of dermatophytes and their correlation with location, site of infection and severity of disease were also investigated. Both PCR-RFLP and RAPD analysis identified 26 Trichophyton verrucosum and 22 Trichophyton mentagrophytes. The PCR-RFLP analysis of the ITS regions produced two distinct profiles for both T. mentagrophytes and T. verrucosum. The first Profile for T. mentagrophytes consisted of two fragments of approximately 320 bp and 280 bp in length while the second was approximately 350 bp and 250 bp in length. The first profile for T. verrucosum consisted of two fragments having bands of approximately 380 bp and 220 bp. The second profile had a single band of undigested fragment of approximately 600 bp in length. Both T. mentagrophytes and T. verrucosum yielded identifiable fragments by RAPD analysis. Six profiles were produced for T. mentagrophytes and the PCR finger prints ranged from 1 to 9 bands with sizes ranging from approximately 350 to 5000 base pairs in size. Amplification of T. verrucosum isolates produced four Profiles. The PCR fingerprints ranged from 5 to 7 bands with sizes ranging from 500 bp-5000 bp. The results indicate that differences in location could contribute to variations in PCR amplicons of dermatophytes and strain differences in dermatophytes may be responsible for variation in clinical dermatophytosis but no significant association was observed between profiles of dermatophytes and the site of infection. The PCR-RFLP analysis of the internal transcribed spacer regions using the primer set ITS1/ITS4 and RAPD analysis using (GACA)4 as primer were successfully used to accurately identify dermatophytes from cattle to species and strain levels. Few molecular studies targeting dermatophytes of cattle are available in the literature. As far as we know, this may be the first report of molecular characterization of cattle dermatophytes from Africa.

Molecular Detection of Torque Teno Sus Virus and Coinfection with African Swine Fever Virus in Blood Samples of Pigs from Some Slaughterhouses in Nigeria.

Torque teno sus virus 1 (TTSuV1a/TTSuV1b) infection is present in pig herds worldwide. This study investigated the prevalence of TTSuV1a/TTSuV1b infections in domestic pigs from some slaughterhouses in Nigeria as well as coinfection with African swine fever virus (ASFV) and described the phylogeny in relation to global strains. One hundred and eighty-one (181) blood samples from four slaughterhouses were used for the study and viral nucleic acid detection was carried out by PCR. Comparative sequence analysis was carried out to infer phylogeny. The overall prevalence of TTSuV1a/b was 17.7%. Prevalence of individual genotypes was 10.5% and 7.2% for TTSuV1a and TTSuV1b, respectively. Coinfection of ASFV/TTSuV1a/b was 7.7% while that of TTSuV1a and TTSuV1b was 1.7%. ASFV alone was detected in 11.91% of the total samples. The Nigerian TTSuV1a and TTSuV1b shared a sequence identity of 91-100% and 95-100%, respectively, among each other. The ASFV sequences were 100% identical to members of genotype 1. This is the first report on the presence of TTSuV1a/b in domestic pigs in Nigeria and coinfection with ASFV. Although the prevalence of TTSuV1a/b in Nigeria was low, we recommend further studies to establish the trend and possible role in the pathogenesis of ASFV.

Further evidence for very virulent infectious bursal disease virus in vaccinated chickens in Nigeria.

Reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of the VP2 hypervariable region was performed on clinical samples from two infectious bursal disease (IBD) outbreaks in Plateau state, Nigeria. IBD virus RNA was detected in all four bursa of Fabricius samples. Nucleotide sequencing and analysis of the four samples revealed high similarity to previous IBDV sequences from northern and southern Nigeria. The deduced amino acid sequences were compared to reference IBDV strains retrieved from the GenBank; virulence markers A222, I256, and I294 were conserved in both outbreak and reference sequences. Amino acid residue S254 was conserved in the outbreak viruses and previous viruses from northern Nigeria. Phylogenetic analysis revealed that all four viruses were very virulent IBDVs. These viruses clustered with vv2-1 variant viruses from Oyo and Ogun states and less closely with vv2-2 isolates from Tanzania. The nucleotide identity of the sequences in this study ranged from 99.6 to 100 % with each other. These findings are further evidence of IBD outbreaks in vaccinated chicken flocks in Nigeria.

Investigation of African swine fever in slaughtered pigs, Plateau state, Nigeria, 2004-2006.

The occurrence of African swine fever (ASF) DNA in slaughtered pigs in the major pig producing areas of Plateau state over a 2-year period was investigated. Three hundred fifty-nine pig tissue samples from five local government councils (LGCs) were analyzed by clinical signs (C/S), postmortem (PM) lesions and polymerase chain reaction (PCR). The results of diagnosis made by C/S and PM were compared to results obtained by PCR. Out of the 359 abattoir samples, 13 (3.62%) were positive by examination of C/S and PM lesions while 346 (96.38%) were negative. Jos-north LGC had the highest occurrence of PCR positive samples (31 samples); Panyam in Mangu LGC had no positive result. PCR analysis identified 53 positive samples (14.76%); more than 40 were identified on the field. Of the samples, 306 were PCR negative, thus giving a true ASF status of pigs in Plateau state. Analysis of the results, variables involved in the ASF spread and predictable effects of such findings in the pig industry in Plateau state and Nigeria as a whole is discussed.

Molecular characterisation of African swine fever viruses from Nigeria (2003-2006) recovers multiple virus variants and reaffirms CVR epidemiological utility.

Samples collected from wild and domestic suids in Nigeria, over a 3-year period (2003-2006), were evaluated for African swine fever (ASF) virus genome presence by targeting three discrete genome regions, namely the 478-bp C-terminal p72 gene region advocated for genotype assignment, a 780-bp region spanning the 5'-ends of the pB125R and pB646L (p72) genes and the hypervariable central variable region (CVR) encoded within the 9RL ORF (pB602L). ASF virus (ASFV) presence was confirmed in 23 of the 26 wild and domestic pigs evaluated. No evidence of ASF infection was found in two warthogs from Adamawa State; however, one bushpig from Plateau State was positive. Nucleotide sequences of the 478-bp and 780-bp amplicons were identical across all ASFV-positive samples sequenced. However, five discrete CVR variants were recovered, bringing the total number identified to date, from Nigeria, to six. The largest of the CVR variants, termed 'Tet-36' was identical to a virus causing outbreaks in neighbouring Benin in 1997, indicating a prolonged persistence of this virus type in Nigeria. Co-circulation of three tetramer types (Tet-36, Tet-27 and Tet-20) was found in Plateau State in July 2004, whilst in Benue State, two tetramer types (Tet-20 and Tet-21) were present in August 2005. Despite simultaneous field presence, individual co-infection was not observed. This study has reaffirmed the epidemiological utility of the CVR genome region for distinguishing between geographically and temporally constrained genotype I viruses, and has revealed the presence of multiple ASFV variants in Nigeria.

Comparison of a DNA based PCR method with conventional methods for the detection of M. tuberculosis in Jos, Nigeria.

BACKGROUND: To achieve early diagnosis and effective treatment of pulmonary tuberculosis, simple and sensitive methods that enhance the detection of Mycobacterium tuberculosis (M. tuberculosis) from clinical specimens are needed. This study compared the effectiveness and suitability of an insertion sequence (IS 6110) based polymerase chain reaction (PCR) assay with conventional methods for the detection of M. tuberculosis from clinical specimens in a resource-limited setting. METHODS: Sputa from 101 HIV-positive patients and 40 clinical specimens (sputa, gastic wash out, ascitic fluid, pleural fluid and cerebrospinal fluid) collected from children (HIV status unknown), all suspected for pulmonary tuberculosis at the Jos University Teaching Hospital, Jos, (JUTH) Nigeria, were examined by Ziehl Neelsen (ZN) smear microscopy, Lowenstein Jensen's (LJ) egg-based culture, and PCR methods for the detection of M. tuberculosis. RESULTS: Mycobacteria was detected in 45/101 (44.6%) of the specimens from the HIV-positive patients and comprised of 6% ZN(+)culture(+)PCR(+), 4% ZN(-)culture(+)PCR(-), 16% ZN(-)culture(+)PCR(+) and 19% ZN(-)culture(-)PCR(+). Twenty-two of forty (55%) children were positive with 0% smear microscopy; 4/40 (10%) culture(+)PCR(+); and 18/40 (45%) culture(-)PCR(+). The sensitivity and specificity of the PCR for the HIV-positive patients were 85% and 74% respectively against 23% and 100% for ZN smear microscopy. CONCLUSION: The IS6110 PCR is a rapid and sensitive method that is specific for the M. tuberculosis complex group. It is simple in our experience and increased the detection of M. tuberculosis from the specimens examined. We suggest its use for the detection of M. tuberculosis in high TB and HIV burden areas.

Introduction into Nigeria of a distinct genotype of avian influenza virus (H5N1).

Genetic characterization of highly pathogenic avian influenza viruses (H5N1) isolated in July 2008 in Nigeria indicates that a distinct genotype, never before detected in Africa, reached the continent. Phylogenetic analysis showed that the viruses are genetically closely related to European and Middle Eastern influenza A (H5N1) isolates detected in 2007.