Molecular epidemiology of clinical Mycobacterium tuberculosis complex isolates in South Omo, Southern Ethiopia
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SUBMITTER: Wondale B
PROVIDER: S-EPMC7557052 | biostudies-literature | 2020 Jan
REPOSITORIES: biostudies-literature
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Project description:BackgroundPrevious studies suggest the burden of pulmonary tuberculosis (PTB) in Ethiopia may be greater in university students relative to the overall population. However, little is known about the transmission dynamics of PTB among students and members of the communities surrounding university campuses in Eastern Ethiopia.MethodsA cross sectional study was conducted in Eastern Ethiopia among prevalent culture-confirmed PTB cases from university students (n = 36) and community members diagnosed at one of four hospitals (n = 152) serving the surrounding area. Drug susceptibility testing (DST) was performed on Mycobacterium tuberculosis complex (MTBC) isolates using BD Bactec MGIT 960 and molecular genotyping was performed using spoligotyping and 24-loci MIRU-VNTR. MTBC strains with Identical genotyping patterns were assigned to molecular clusters as surrogate marker for recent transmission and further contact tracing was initiated among clustered patients.ResultsAmong all study participants, four MTBC lineages and 11 sub-lineages were identified, with Ethiopia_3 (Euro-American lineage) being most common sub-lineage (29.4%) in both cohorts and associated with strain clustering (P = 0.016). We further identified 13 (8.1%) strains phylogenetically closely related to Ethiopia_3 but with a distinct Spoligotyping pattern and designated as Ethiopia_4. The clustering rate of MTBC strains was 52.9% for university students and 66.7% for community members with a Recent Transmission Index (RTI) of 17.6% and 48.4%, respectively. Female gender, urban residence, and new TB cases were significantly associated with strain clustering (P<0.05). Forty-eight (30%) of the study participants were resistant to one or more first line anti TB drugs, three patients were classified as multidrug resistant (MDR).ConclusionWe found evidence for recent transmission of PTB among Ethiopian university students and the local community in Eastern Ethiopia, mainly linked to strains classified as Ethiopia_3 sub lineage. Drug resistance didn't have a major impact on recent transmission but comprehensive molecular surveillance in combination with drug resistance profiling of MTBC strains is desirable to better characterize TB transmission dynamics in high risk congregate living environments such as university campuses and guide regional TB control programs.
| S-EPMC6141063 | biostudies-literature
Project description:Yellow fever (Yf) outbreak was recently reported in South Omo of Southern Ethiopia. This area was also highly affected by Yf outbreak in the 1960s. However, there is no reliable information on the level of community knowledge attitudes and practices about the disease in the area. The objective of the current study was to assess level of community knowledge, attitudes and practices about Yf.Between March and May 2017, a community-based cross-sectional survey was conducted in two districts of the South Omo area. During the survey, 612 randomly selected adults were interviewed about Yf using structured questionnaire.Out of the 612 study participants, 508 (83.0%) reported that they heard about Yf which is locally known as "a disease that causes vomiting blood". Most (90.4%) of the study participants also said that Yf is different from malaria. Two hundred thirteen (41.9%) participants said that Yf can be transmitted from a patient to another person, while only 80 (37.6%) mentioned that the disease is transmitted through mosquitoes bite. Out of 333 (65.7%) study participants who believed that Yf is a preventable disease, 280 (84.1%) mentioned vaccine as a preventive method. The majority believed that the disease is a killer (97.2%) and a newly emerging (69.4%). Among the total of 612 study participants, 221(36.1%) were considered as having a high level of overall knowledge of Yf. Having educational level above 7th grade (AOR = 3.25, 95% CI: 1.39, 7.57, p = 0.006) and being resident of Bena-Tsemay district (AOR = 1.77, 95% CI: 1.12, 2.78, P = 0.014) were significantly associated with having a high level of overall knowledge of Yf. Agro-pastoralism as an occupation compared to farming was associated with having a low level of overall knowledge of Yf (AOR = 0.51, 95% CI, 0.33, 0.79, P = 0.003).The findings indicate that most of the study community members had a low level of overall knowledge of Yf, especially about its cause, mode of transmission and preventive methods. Thus, there is a need to increase people's knowledge and practices regarding the cause, mode of transmission and preventive methods like avoiding mosquitoe breeding sites beside vaccination through various strategies like disseminating information through community health extension workers and community leaders in the study area.
| S-EPMC5908197 | biostudies-literature
Project description:BackgroundTuberculosis remains common in Singapore, increasing in incidence since 2008. We attempted to determine the molecular epidemiology of Mycobacterium tuberculosis complex (MTC) isolates locally, identifying major circulating genotypes and obtaining a glimpse of transmission dynamics.MethodologyNon-duplicate MTC isolates archived between 2006 and 2012 at the larger clinical tuberculosis laboratory in Singapore were sampled for spoligotyping and MIRU-VNTR typing, with case data obtained from the Singapore Tuberculosis Elimination Program registry database. Isolates between 2008 and 2012 were selected because of either multidrug-resistance or potential epidemiological linkage, whereas earlier isolates were randomly selected. Separate analyses were performed for the early (2006-2007) and later (2008-2012) study phases in view of potential selection bias.Principal findingsA total of 1,612 MTC isolates were typed, constituting 13.1% of all culture-positive tuberculosis cases during this period. Multidrug-resistance was present in 91 (5.6%) isolates - higher than the national prevalence in view of selection bias. The majority of isolates belonged to the Beijing (45.8%) and EAI (22.8%) lineages. There were 347 (30.7%) and 133 (27.5%) cases clustered by combined spoligotyping and MIRU-VNTR typing from the earlier and later phases respectively. Patients within these clusters tended to be of Chinese ethnicity, Singapore resident, and have isolates belonging to the Beijing lineage. A review of prior contact investigation results for all patients with clustered isolates failed to reveal epidemiological links for the majority, suggesting either unknown transmission networks or inadequate specificity of the molecular typing methods in a country with a moderate incidence of tuberculosis.ConclusionOur work demonstrates that Singapore has a large and heterogeneous distribution of MTC strains, and with possible cross-transmission over the past few years based on our molecular typing results. A universal MTC typing program coupled with enhanced contact investigations may be useful in further understanding the transmission dynamics of tuberculosis locally.
| S-EPMC3867517 | biostudies-literature
Project description:The tuberculosis (TB) incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010-2013 was conducted. TB strains isolated from 945 patients were submitted to genotyping by standardized 24-locus-MIRU-VNTR typing and spoligotyping. The phylogenetic analysis showed that the LAM (16.7%) and Haarlem (15.7%) branches are the two most prevalent TB lineages circulating in Brussels. Analysis of the MDR subgroup showed an association with Beijing strains (39.9%) and patients native of Eastern Europe (40.7%). Genotyping detected 113 clusters involving 321 patients, giving a recent transmission index of 22.9%. Molecular-guided epidemiological investigations and routine surveillance activities revealed family transmission or social contact for patients distributed over 34 clusters. Most of the patients were foreign-born (75.7%). However, cluster analysis revealed only limited trans-national transmission. Comparison with the previous study shows a stable epidemiological situation except for the mean age difference between Belgian-born and foreign-born patients which has disappeared. This study confirms that molecular epidemiology has become an important determinant for TB control programs. However, sufficient financial means need to be available to perform all required epidemiological investigations.
| S-EPMC5319770 | biostudies-literature
Project description:BACKGROUND:Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) are the leading causes of liver-related morbidity and mortality throughout the world. The magnitude of HBV and HCV infections in Ethiopia has not been well studied at community level. This study aimed at investigating the sero-prevalence and associated risk factors of HBV and HCV among HBV unvaccinated community members in South Omo Zone, Southern Ethiopia. METHODS:A community-based cross-sectional study was conducted in three districts from March to May 2018. Structured questionnaire was used to collect relevant clinical and socio-demographic data. Three milliliter of blood sample was collected from each study participant and screened for HBV and HCV using one step hepatitis B surface antigen (HBsAg) test strip and one step HCV test strip, respectively. Samples found positive for HBsAg were further tested using immunoassay of Alere DetermineTM HBsAg (Alere Inc., USA). Data were analyzed using SPSS version 25.0. RESULTS:A total of 625 (51.4% males, age 6-80 years, mean age ± SD = 30.83 ± 13.51 years) individuals participated in the study. The sero-prevalence for HBV infection was 8.0% as detected using one step HBsAg test strip, while it was 7.2% using Alere DetermineTM HBsAg test. The sero-prevalence for HCV infection was 1.9%. Two (0.3%) of the participants were seropositive for both HBV and HCV infections. High sero-prevalence for HBV infection was associated with weakness and fatigue (AOR = 5.20; 95% CI: 1.58, 17.15), while high sero-prevalence of HCV infection was associated with age group between 46 and 65 years (AOR = 13.02; 95% CI: 1.11, 152.41). CONCLUSION:This study revealed higher-intermediate endemicity level of HBV infection and low to intermediate endemicity level of HCV infection in the study area. Clinical symptoms like weakness and fatigue were found to be indictors for HBV infection, while individuals in the age group between 46 and 65 years were at higher risk for HCV infection. Provision of community- based health education; vaccination, mass screening and providing treatment would have utmost importance in reducing the transmission of these diseases in the present study area.
| S-EPMC6936792 | biostudies-literature
Project description:Prothionamide (PTH) has been widely used in the treatment of tuberculosis (TB), especially multidrug resistant tuberculosis (MDR-TB), while data regarding prevalence of resistance-causing mutation is limited. In this study, we aimed to investigate the molecular characteristics of PTH-resistant MTB isolates, and also analyzed the risk factors for PTH resistance among Mycobacterium tuberculosis (MTB) isolates in southern China. A total of 282 MTB isolates were enrolled in from Guangzhou Chest Hospital. Among these isolates, 46 (16.3%) were resistant to PTH. Statistical analysis revealed that PTH resistance was more likely to be associated with resistance to levofloxacin (LFX; OR: 2.18, 95% CI: 1.02-4.63; P = 0.04). Of the 46 PTH-resistant MTB isolates, 37 (80.4%) isolates harbored 19 different mutation types, including 10 (21.7%) isolates with double nucleotide substitutions and 27 (58.7%) with single nucleotide substitution. The mutations in ethA (51.4%, 19/37) were most frequently observed among PTH-resistant isolates, followed by 16 (43.2%) in the promoter of inhA and 6 (16.2%) in inhA. In addition, no significant difference was found in the distribution of isolates with different mutation types between Beijing and non-Beijing genotypes (P > 0.05). In conclusion, our data demonstrate that high diversity of genetic mutations conferring PTH resistance is identified among MTB isolates from southern China. Mutations in inhA, ethA, mshA, and ndh genes confer increased resistance of MTB to PTH. Ancient Beijing genotype strains have higher proportion of drug resistance compared with modern Beijing strains. In addition, PTH resistance is more likely to be observed in the LFX-resistant MTB isolates.
| S-EPMC5714880 | biostudies-literature
Project description:BackgroundChikungunya (CHIK) and yellow fever (YF) are becoming major public health threats in East African countries including Ethiopia. In Ethiopia, there is no reliable information about the epidemiology of CHIK. This study aimed to assess a community-based sero-prevalence of CHIK and YF in the South Omo Valley, an endemic area for YF.MethodsBetween February and June 2018, blood samples were collected from study participants and screened for IgG antibody against CHIK virus (CHIKV) and YF virus (YFV) infections using ELISA. Data were computerized using Epi Data Software v.3.1 and analyzed using SPSS.ResultsA total of 360 participants (51.7% males, age range from 6 to 80, mean age ± SD = 31.95 ± 14.05 years) participated in this study. The overall sero-prevalence of IgG antibody was 43.6% (157/360) against CHIKV, while it was 49.5% (155/313) against YFV. Out of 155 samples which were positive for IgG antibody to YFV, 93 (60.0%) were positive for IgG antibody to CHIKV. Out of 158 samples which were negative for IgG antibody to YFV, 64(40.5%) were positive for IgG antibody to CHIKV. There was a significant positive correlation between IgG antibodies to CHIKV and YFV (sr = 0.82; P<0.01). Residency in the Debub Ari district (AOR = 8.47; 95% CI: 1.50, 47.74) and travel history to sylvatic areas (AOR = 2.21; 95% CI: 1.02, 4.81) were significantly and positively associated with high sero-prevalence of IgG antibody to CHIKV and YFV, respectively.ConclusionHigh sero-prevalence of IgG antibody to CHIKV shows the circulation of the virus in the present study area. A low sero-prevalence of IgG antibody to YFV in YF vaccine received individuals is highly concerning from a public health point of view as waning of immune response to YFV infection could result in a periodic outbreaks of YF in endemic areas.Nevertheless, the present study has not investigated for possible cross-reactivity of antibody to CHIKV with other alphaviruses like O'nyong-nyong virus and antibody to YFV with other flaviviruses like Dengue fever virus and this warrants further studies in the present study area.
| S-EPMC7470273 | biostudies-literature
Project description:ContextAvailable molecular epidemiological data from recent studies suggest significant genetic variation between the different lineages of Mycobacterium tuberculosis complex (MTBC) and the MTBC lineages might have adapted to different human populations.AimThis study sought to determine the population structure of clinical MTBC isolates from the Volta Region of Ghana.MethodsThe MTBC isolates obtained from collected sputum samples were identified by PCR detecting of IS6110 and genotyped using spoligotyping. Non-tuberculous mycobacterial isolates were characterized by amplification of the heat shock protein 65 (hsp65) gene and sequencing. The drug susceptibility profiles of the MTBCs determined using GenoType MTBDRplus.ResultsOne hundred and seventeen (117, 93.6%) out of 125 mycobacterial positive isolates were characterized as members of the MTBC of which M. tuberculosis sensu stricto (MTBss) and M. africanum (MAF) were respectively 94 (80.3%) and 23 (19.7%). In all, 39 distinct spoligotype patterns were obtained; 26 for MTBss and 13 for MAF lineages. Spoligotyping identified 89 (76%) Lineage 4, 16 (13.6%) Lineage 5, 7 (6.0%) Lineage 6, 3 (2.6%) Lineage 2, 1(0.9%) Lineage 3 and 1 (0.9%) Lineage 1. Among the Lineage 4 isolates, 62/89 (69.7%) belonged to Cameroon sub-lineage, 13 (14.7%) Ghana, 8 (9.0%) Haarlem, 2 (2.2%) LAM, 1 (1.1%) Uganda I, 1 (1.1%) X and the remaining two (2.2%) were orphan. Significant localization of MAF was found within the Ho municipality (n = 13, 29.5%) compared to the more cosmopolitan Ketu-South/Aflao (n = 3, 8.3%) (p-value = 0.017). Eight (8) non-tuberculous mycobacteria were characterized as M. abscessus (7) and M. fortuitum (1).ConclusionWe confirmed the importance of M. africanum lineages as a cause of TB in the Volta region of Ghana.
| S-EPMC7968653 | biostudies-literature
Project description:BackgroundAlthough Ethiopia ranks seventh among the world's 22 high-burden tuberculosis (TB) countries, little is known about strain diversity and transmission. In this study, we present the first in-depth analysis of the population structure and transmission dynamics of Mycobacterium tuberculosis strains from Northwest Ethiopia.MethodsIn the present study, 244 M. tuberculosis isolates where analysed by mycobacterial interspersed repetitive unit - variable number tandem repeat 24-loci typing and spoligotyping methods to determine phylogenetic lineages and perform cluster analysis. Clusters of strains with identical genotyping patterns were considered as an indicator for the recent transmission.ResultsOf 244 isolates, 59.0% were classified into nine previously described lineages: Dehli/CAS (38.9%), Haarlem (8.6%), Ural (3.3%), LAM (3.3%), TUR (2.0%), X-type (1.2%), S-type (0.8%), Beijing (0.4%) and Uganda II (0.4%). Interestingly, 31.6% of the strains were grouped into four new lineages and were named as Ethiopia_3 (13.1%), Ethiopia_1 (7.8%), Ethiopia_H37Rv like (7.0%) and Ethiopia_2 (3.7%) lineages. The remaining 9.4% of the isolates could not be assigned to the known or new lineages. Overall, 45.1% of the isolates were grouped in clusters, indicating a high rate of recent transmission.ConclusionsThis study confirms a highly diverse M. tuberculosis population structure, the presence of new phylogenetic lineages and a predominance of the Dehli/CAS lineage in Northwest Ethiopia. The high rate of recent transmission indicates defects of the TB control program in Northwest Ethiopia. This emphasizes the importance of strengthening laboratory diagnosis of TB, intensified case finding and treatment of TB patients to interrupt the chain of transmission.
| S-EPMC3605317 | biostudies-literature
Project description:Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n?=?6), 2.0% (n?=?3) and 1.3% (n?=?2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n?=?1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n?=?2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.
| S-EPMC7393130 | biostudies-literature