Indications, types, and diagnostic implications of prenatal genetic testing in Sub-Saharan Africa: A descriptive study.

OBJECTIVE: To describe indications, test types, and results of prenatal diagnostic genetic amniocentesis among Ethiopian pregnant women. METHODS: This study was a descriptive study on prenatal diagnostic genetic testing among Ethiopian pregnant women with certain indications and it was conducted at St. Paul's Hospital Millennium Medical College (Addis Ababa, Ethiopia) from January 2017 to April 2023. Data on sociodemographic characteristics, genetic testing indications, types, and results were collected electronically. Data were analysed using SPSS version 23. RESULTS: A total of 159 cases were analysed. The commonest indication for genetic testing among the study subjects was major fetal structural anomalies identified on specialized prenatal anatomic scanning of the index pregnancy detected in 71(44.7%) cases. Down syndrome and Edward syndrome were the commonest genetic aberrations detected accounting for 6.3% (10/159) and 4.4% (7/159), respectively. Among the rare genetic aberration detected were Di-George syndrome (0.6%) and Duchenne muscular dystrophy (0.6%). CONCLUSION: Findings of our study underscore the importance of diagnostic prenatal testing in a Sub-Saharan Africa setting, as common (trisomy 21&18) and rare genetic defects were identified using this important prenatal diagnostic testing. Considering the implications of detecting chromosomal abnormalities for future counselling and care, carrier state in parents for some chromosomal anomalies, and planning post-natal management of some abnormalities that are associated with aneuploidies (notably cardiac anomalies), initiation of diagnostic prenatal genetic testing service at tertiary public health facilities should be acted up on.

Assessing the diagnostic performance of a novel RT-PCR fluorescence method for the detection of human plasmodium species.

BACKGROUND: Malaria elimination effort is hampered not only by the lack of effective medication but also due to the lack of sensitive diagnostic tools to detect infections with low levels of parasitemia. Therefore, more sensitive and specific high-throughput molecular diagnostic approaches are needed for accurate malaria diagnosis. METHODS: In the present study, the performance of a novel single-tube MC004 real-time polymerase chain reaction (PCR) assay (MRC-Holland, Amsterdam, the Netherlands) was assessed for the detection of infection and discrimination of Plasmodium species. Blood samples (n = 150) were collected from malaria suspected patients at Adama malaria diagnosis and treatment centre, Adama, central Ethiopia. The positive predictive value (PPV), negative predictive value (NPV), analytical sensitivity and specificity of the assay were assessed against the conventional microscopic method. RESULTS: Plasmodium species were detected in 59 (39.3%) of the samples by microscopy and in 62 (41.3%) by the novel MC004 RT-PCR. Plasmodium vivax, Plasmodium falciparum and mixed infections with Plasmodium falciparum & Plasmodium vivax accounted for 47.5%, 40.6% and 11.9% respectively as detected by microscopy. The MC004 RT-PCR assay identified 59.7% and 40.3% of the samples positive for Plasmodium vivax and Plasmodium falciparum respectively. The sensitivity, specificity, PPV, and NPV of the MC004 RT-PCR assay were 95.8%, 97.8%, 92%, and 98.9%, respectively. No mixed infections were detected using the MC004 assay. CONCLUSION: The MC004 RT-PCR assay is a useful tool for the early detection of malaria and identification of Plasmodium species with a high degree of sensitivity and specificity. Due to its high sensitivity, and simplicity (being a single-tube assay), the MC004 is suitable for use in clinical settings and epidemiological studies.

A rare case of 46,XX gonadal dysgenesis, Mayer-Rokitansky-Kuster-Hauser syndrome, pituitary and thyroid hypoplasia.

SUMMARY: Mayer-Rokitansky-Kuster-Hauser syndrome is characterized by congenital absence or hypoplasia of the uterus and upper two-thirds of the vagina in both phenotypically and karyotypically normal females with functional ovaries, whereas gonadal dysgenesis is a primary ovarian defect in otherwise normal 46,XX females. An association between these two conditions is extremely rare. We report a 21-year-old female presented with primary amenorrhea and undeveloped secondary sexual characteristics. The karyotype was 46,XX and the hormonal profile revealed hypothyroidism and hypogonadotropic hypogonadism. Pelvic MRI showed class I Mullerian duct anomaly with ovarian dysgenesis. Ultrasound showed bilateral thyroid hypoplasia and brain MRI suggested anterior pituitary hypoplasia. Levothyroxine and hormone replacement therapy were started. LEARNING POINTS: The simultaneous presentation of 46,XX gonadal dysgenesis, Mayer-Rokitansky-Kuster-Hauser syndrome, hypothyroidism, and pituitary hypoplasia is a Possibility. Extensive evaluation should be made when a patient presents with one or more of these features. The diagnosis imposes a significant psychological burden on patients and adequate counseling should be provided. Hormone replacement therapy remains the only therapeutic option for the development of secondary sexual characteristics and the prevention of osteoporosis.

A 1-year and 4-month-old child with mucopolysaccharidoses type II: A clinical case report from Ethiopia.

Mucopolysaccharidoses (MPSs) are a class of lysosomal storage disorders resulting in progressive disease manifestations and are caused by pathogenic variants in genes coding for enzymes needed to degrade glycosaminoglycans. While most of the seven MPSs are autosomal recessive disorders, MPS II, also known as Hunter syndrome, is inherited in an X-linked recessive manner and is the most common MPS. Here, we report a 1-year and 4-month-old boy who presented with delayed developmental milestones, back deformity, and left scrotal swelling noticed by parents at one year of age. He has coarse facial appearance with macrocephaly, widened wrists, congenital dermal melanocytosis on his back, kyphotic deformity in the thoracolumbar area and left-sided inguinal hernia all consistent with a suspected MPS II diagnosis. The MPS II diagnosis was subsequently confirmed with genetic testing of the IDS gene. To our knowledge, this is the first case of MPS II reported from Ethiopia. This case shows the importance of early clinical recognition of genetic conditions and the utility of genetic testing for confirmation. The diagnosis provided important surveillance and natural history information for the patient's providers and family.

The introduction of clinical genetic testing in Ethiopia: Experiences and lessons learned.

Limited data are available on genetic testing laboratories in low- and middle-income countries including those in sub-Saharan Africa (SSA). To characterize the need for genetic testing in SSA we describe the experience of MRC-ET Advanced Laboratory, a genetic testing laboratory in Ethiopia. Test results were analyzed based on indication(s) for testing, referral category, and diagnostic yield. A total of 1311 tests were run using the full MRC-Holland catalogue of Multiplex-Ligation Probe Amplification assays. Of all samples, 77% were postnatal samples, 15% products of conception (POC), and 8% amniotic samples. Of postnatal samples, the most common testing categories were multiple congenital anomalies (32%), disorders of sex development (17%), and Obstetrics/Gynecology (16%). Forty-three percent of postnatal samples were diagnostic, 11% were variants of uncertain significance (VUS), and 46% were normal with Trisomy 21 the most common diagnosis. Of POC samples, 10% were diagnostic, 34% revealed VUSs, and 55% were normal with Trisomy 18 the most common diagnosis. Of amniotic samples 17.5% were diagnostic, 3% revealed VUSs, and 79% were normal with Trisomy 18 the most common diagnosis. There is increasing demand for genetic testing in Ethiopia. Diagnostic genetic testing in SSA deserves increased attention as testing platforms become more affordable.

Isolation and Molecular Identification of Lactic Acid Bacteria Using 16s rRNA Genes from Fermented Teff (Eragrostis tef (Zucc.)) Dough.

Injera is soft fermented baked product, which is commonly prepared from teff (Eragrostis tef (Zucc.)) flour and believed to be consumed on daily basis by two-thirds of Ethiopians. As it is a product of naturally fermented dough, the course of fermentation is done by consortia of microorganisms. The study was aimed at isolating and identifying some dominant bacteria from fermenting teff (Eragrostis tef) dough. A total of 97 dough samples were collected from households, microenterprises, and hotels with different fermentation stage from Addis Ababa. The bacterial isolates obtained from the fermenting teff dough samples were selected on the basis of their acid production potentials. A total of 24 purified bacterial isolates were found to be Gram-positive (they are coccus and rod under microscope) and were good acid producers. Genomic DNA of bacterial isolates were extracted using Invisorb® Spin DNA Extraction kit. 16S rRNA of bacterial isolates were amplified using the bacteria universal primers (rD1 and fD1). The amplified product was sequenced at Genewiz, USA. Sequence analysis and comparison with the resources at the database were conducted to identify the isolated microbes into species and strain levels. The bacterial isolates were identified as Lactobacillus paracasei, Lactobacillus brevis, Enterococcus durans, Enterococcus hirae, Enterococcus avium, and Enterococcus faecium. All identified lactic acid bacteria were able to produce acid at 12 h time of incubation. This study has confirmed the presence of different bacterial species in the fermenting teff dough and also supports the involvement of various groups of bacterial species in the course of the fermentation.

Divergent genes in potential inoculant Sinorhizobium strains are related to DNA replication, recombination, and repair.

To serve as inoculants of legumes, nitrogen-fixing rhizobium strains should be competitive and tolerant of diverse environments. We hybridized the genomes of symbiotically efficient and salt tolerant Sinorhizobium inoculant strains onto the Sinorhizobium meliloti Rm1021 microarray. The number of variable genes, that is, divergent or putatively multiplied genes, ranged from 503 to 1556 for S. meliloti AK23, S. meliloti STM 1064 and S. arboris HAMBI 1552. The numbers of divergent genes affiliated with the symbiosis plasmid pSymA and related to DNA replication, recombination and repair were significantly higher than expected. The variation was mainly in the accessory genome, implying that it was important in shaping the adaptability of the strains.

THREE SIBLINGS WITH ANDROGEN INSENSITIVITY SYNDROME.

Genetic, gonadal, phenotypic and psychological genderis the basis for gender assignment to an individual. Derangement in genetic makeup, under or over exposure to sex hormones and problems related to sex hormone receptors will lead to abnormal development of the external and internal genitalia. Failure to respond for the endogenous androgen, Androgen Insensitivity Syndrome is one of the common causes of genital ambiguity and intersex. In this case series we have presented three girls from a family of seven children visited Tikur Anbassa Specialized Hospital (TASH) with a complaint of primary amenorrhea and diagnosed to have androgen insensitivity syndrome. Their clinical presentation, relevant laboratory and histopathologic findings, karyotype and genetic analysis results are summarized. Potential causes and treatment options are discussed.

Effects of Lactobacillus rhamnosus GG on saliva-derived microcosms.

OBJECTIVE: The probiotic strain Lactobacillus rhamnosus GG (LGG) is shown to hamper the presence of mutans streptococci in saliva and may have positive effects on oral health. We investigated the effects of LGG on the cariogenic potential and microbial composition of saliva-derived microcosms. DESIGN: Single and dual species biofilms of LGG and Streptococcus mutans, and saliva-derived microcosms with or without LGG were grown in an Active Attachment Biofilm model. The microcosms were grown on bovine dentin/enamel discs in the presence or absence of sucrose (suc+/suc-). The presence of LGG was determined by multiplex ligation-dependent probe amplification (MLPA) and real-time PCR. Mutans streptococci (MS) and total viable counts, pH of the spent medium, capacity of lactate formation and integrated mineral loss in dentin was assessed. MLPA was used for identification and relative quantification of 20 oral microorganisms in the microcosms. Principal Component Analysis was applied to MLPA data. RESULTS: LGG inhibited the growth of S. mutans in dual species biofilms and did not affect the pH. LGG established in saliva-derived microcosms and reduced MS counts significantly, but did not affect pH or dentin demineralization. Simultaneous growth of the microcosms with LGG under heavy cariogenic conditions (suc+) introduced a compositional shift in the microbial community. The CFU, real-time PCR and MLPA data correlated significantly. CONCLUSION: We conclude that LGG established into and inhibited the growth of MS in complex saliva-derived biofilms, but this had no significant effect on cariogenic potential of the microcosms. This suggests that other microorganisms besides MS were responsible for increased cariogenicity of sucrose-exposed biofilms.

Effects of probiotic Lactobacillus salivarius W24 on the compositional stability of oral microbial communities.

Probiotics are microorganisms beneficial to gastrointestinal health. Although some strains are also known to possess positive effects on oral health, the effects of most intestinal probiotics on the oral microflora remain unknown. We assessed the ability of the intestinal probiotic Lactobacillus salivarius W24 to incorporate into and to affect the compositional stability and cariogenicity of oral microbial communities. Microtiter plates with hydroxyapatite discs were incubated with W24 ("+W24") or without W24 ("-W24") and saliva from four individuals in plain ("-sucrose") or sucrose-supplemented ("+sucrose") medium. Biofilms were subjected to community profiling by 16S rRNA gene-based Denaturing Gradient Gel Electrophoresis (DGGE) after 72h growth. Diversity (Shannon-Weaver index) and similarities (Pearson correlation) between biofilm communities were calculated. Microcosms "+sucrose" were less diverse and more acidic than "-sucrose" microcosms (p<0.001). The effects of W24 on the community profiles were pH dependent: at pH 4 ("+sucrose"), the respective "+W24" and "-W24" microcosms differed significantly more from each other than if the pH was approximately 7 ("-sucrose"). The pH of "+W24/+sucrose" microcosms was lower (p<0.05) than the pH of the microcosms supplemented with sucrose alone ("-W24/+sucrose"). Although not able to form a monospecies biofilm, L. salivarius W24 established itself into the oral community if inoculated simultaneously with the microcosm. In the presence of sucrose and low pH, W24 further lowered the pH and changed the community profiles of these microcosms. Screening of probiotics for their effects on oral microbial communities allows selecting strains without a potential for oral health hazards.

MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms.

A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts.

Isolation and automated ribotyping of Mycobacterium lentiflavum from drinking water distribution system and clinical specimens.

Automated ribotyping as a tool for identifying of nontuberculous mycobacteria was evaluated. We created a database comprising of riboprints of 60 strains, representing 32 species of nontuberculous mycobacteria. It was shown that combined ribopatterns generated after digestion with EcoRI and PvuII were distinguishable between species of both slow-growing and rapid-growing mycobacteria. The findings were in good agreement with the 16S rRNA gene sequencing results, allowing correct identification of Mycobacterium lentiflavum isolated from clinical specimens and from biofilms growing in public water distribution system. The automated ribotyping was powerful in discriminating between M. lentiflavum and closely related species M. simiae and M. palustre. Mycobacterium lentiflavum strains from drinking water biofilms were resistant to two to four antimycobacterial drugs. The drinking water distribution system may, thus, be a source of nontuberculous mycobacteria resistant to multiple drugs.

Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia.

The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR-RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500-1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR-RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100% similar to those of previously described species and 34 were novel sequences with 94-99% similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.

Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China.

Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species I, II and III, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and II were Mesorhizobium, while candidate species III, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA-DNA relatedness was between 11.3 and 47.1 % among representative strains of candidate species I and II and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4.3 and 25.2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and II, Mesorhizobium septentrionale sp. nov. (type strain, SDW014(T)=CCBAU 11014(T)=HAMBI 2582(T)) and Mesorhizobium temperatum sp. nov. (type strain, SDW018(T)=CCBAU 11018(T)=HAMBI 2583(T)), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species III.

Metabolic and genomic diversity of rhizobia isolated from field standing native and exotic woody legumes in southern Ethiopia.

Eighty-seven rhizobial strains isolated from root nodules of field standing native and exotic woody legumes in southern Ethiopia were characterized using the Biolog method and AFLP fingerprinting technique. Cluster analysis of the metabolic and genomic fingerprints revealed 18 and 25 groups, respectively, demonstrating considerable diversity in rhizobial population indigenous to Ethiopian soils. While 25 strains (29%) were linked to members of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium or Sinorhizobium, the bulk of the strains formed several distinct groups in both methods and did not relate to reference species included in the study. In contrast to exotic species which formed symbiosis with strains of only one specific genomic group, indigenous host species nodulated by metabolically and genomically diverse groups. The results in this study support the view, that long-term association between the symbionts allows gradual differentiation and diversity in compatible rhizobial population resident in native soils. Lack of significant metabolic and genomic relatedness to the reference strains in our results suggested that test strains in our collection probably included 'unique' types, which belong to several yet undefined rhizobial species.

Discordant phylogenies within the rrn loci of Rhizobia.

It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.