Genetic diversity and drug resistance pattern of Mycobacterium tuberculosis strains isolated from pulmonary tuberculosis patients in the Benishangul Gumuz region and its surroundings, Northwest Ethiopia.

INTRODUCTION: Tuberculosis (TB) remains a major global public health problem and is the leading cause of death from a single bacterium, Mycobacterium tuberculosis (MTB) complex. The emergence and spread of drug-resistant strains aggravate the problem, especially in tuberculosis high burden countries such as Ethiopia. The supposedly high initial cost of laboratory diagnosis coupled with scarce financial resources has limited collection of information about drug resistance patterns and circulating strains in peripheral and emerging regions of Ethiopia. Here, we investigated drug susceptibility and genetic diversity of mycobacterial isolates among pulmonary tuberculosis patients in the Benishangul Gumuz region and its surroundings in northwest Ethiopia. METHODS AND MATERIAL: In a cross-sectional study, 107 consecutive sputum smear-positive pulmonary tuberculosis (PTB) patients diagnosed at two hospitals and seven health centers were enrolled between October 2013 and June 2014. Sputum samples were cultured at Armauer Hansen Research Institute (AHRI) TB laboratory, and drug susceptibility testing (DST) was performed against Isoniazid, Rifampicin, Ethambutol, and Streptomycin using the indirect proportion method. Isolates were characterized using polymerase chain reaction (PCR)based Region of Difference 9 (RD9) testing and spoligotyping. Statistical analysis was performed using Statistical Package for the Social Sciences (SPSS) for Windows version 24.0. RESULTS: Of 107 acid-fast-bacilli (AFB) smear-positive sputum samples collected, 81.3% (87/107) were culture positive. A PCR based RD9 testing revealed that all the 87 isolates were M. tuberculosis. Of these isolates, 16.1% (14/87) resistance to one or more drugs was observed. Isoniazid monoresistance occurred in 6.9% (6/87). Multidrug resistance (MDR) was observed in two isolates (2.3%), one of which was resistant to all the four drugs tested. Spoligotyping revealed that the majority, 61.3% (46/75) of strains could be grouped into ten spoligotype patterns containing two to 11 isolates each while the remaining 38.7% (29/75) were unique. SIT289 (11 isolates) and SIT53 (nine isolates) constituted 43.5% (20/46) among clustered isolates while 29.3% (22/75) were ''New" to the database. The dominant families were T, 37% (28/75), CAS, 16.0% (12/75), and H, 8% (6/75), adding up to 51.3% (46/75) of all isolates identified. CONCLUSION AND RECOMMENDATIONS: The current study indicates a moderate prevalence of MDR TB. However, the observed high monoresistance to Isoniazid, one of the two proxy drugs for MDR-TB, reveals the hidden potential threat fora sudden increase in MDR-TB if resistance to Rifampicin would increase. Clustered spoligotype patterns suggest ongoing active tuberculosis transmission in the area. The results underscore the need for enhanced monitoring of TB drug resistance and epidemiological studies in this and other peripheral regions of the country using robust molecular tools with high discriminatory power such as the Mycobacterial Interspersed Repetitive Units -Variable Number of Tandem Repeats (MIRU-VNTR) typing and whole-genome sequencing (WGS).

Line-probe assay and molecular typing reveal a potential drug resistant clone of Mycobacterium tuberculosis in Ethiopia.

BACKGROUND: Antimicrobial resistance is a global concern of increasing significance. Multidrug resistant tuberculosis (MDR-TB) is spreading worldwide. It is important to monitor trends of antimycobacterial resistance. This is particularly true for high TB burden countries such as Ethiopia where disproportionally less drug sensitivity data are reported from. METHODS: The prevalence of drug resistance was assessed with the line probe assay GenoType MTBDRplus in a set of 161 M. tuberculosis strains that were selected from four common lineages and sub-lineages previously identified in Ethiopia. Most of the tested M. tuberculosis isolates had been genotyped by established Spoligotyping and MIRU-VNTR typing methods. RESULTS: The proportion of MDR-TB among the isolates was 3.1%. Mono-resistance was 1.2% to rifampicin and 4.3% to isoniazid, and resistance to either of the two first line drugs was 8.7%. Strains of Lineage 4 had the highest resistance rate (13.6%) followed by Lineage 3 (4.9%). None of the isolates representing Lineages 1 and Lineage 7 were drug resistant. Multidrug resistance among pulmonary TB and TB lymphadenitis clinical isolates was 2.8 and 3.7%, respectively. Drug resistance of strains carrying the most prevalent spoligotype in Ethiopia - SIT149 - was further explored. Stratification by MIRU-VNTR identified one genotype with a high rate of drug resistance against Rifampicin and Isoniazid and circulation of a potential MDR-TB clone is proposed. CONCLUSION: Although the strain selection was not fully randomized, the overall M. tuberculosis drug resistance rate in this strain set was 8.7% while the rate of MDR was 3.1%. In parallel, we identified a sub-lineage that showed a high rate of resistance to both rifampicin and isoniazid. These resistant strains may belong to a clone of M. tuberculosis that is circulating in the highlands of Ethiopia.

Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia.

BACKGROUND: Meningococcal colonization is a prerequisite for transmission and disease, but the bacterium only very infrequently causes disease while asymptomatic carriage is common. Carriage is highly dynamic, showing a great variety across time and space within and across populations, but also within individuals. The understanding of genetic changes in the meningococcus during carriage, when the bacteria resides in its natural niche, is important for understanding not only the carriage state, but the dynamics of the entire meningococcal population. RESULTS: Paired meningococcal isolates, obtained from 50 asymptomatic carriers about 2 months apart were analyzed with whole genome sequencing (WGS). Phylogenetic analysis revealed that most paired isolates from the same individual were closely related, and the average and median number of allelic differences between paired isolates defined as the same strain was 35. About twice as many differences were seen between isolates from different individuals within the same sequence type (ST). In 8%, different strains were detected at different time points. A difference in ST was observed in 6%, including an individual who was found to carry three different STs over the course of 9 weeks. One individual carried different strains from the same ST. In total, 566 of 1605 cgMLST genes had undergone within-host genetic changes in one or more pairs. The most frequently changed cgMLST gene was relA that was changed in 47% of pairs. Across the whole genome, pilE, differed mostly, in 85% of the pairs. The most frequent mechanisms of genetic difference between paired isolates were phase variation and recombination, including gene conversion. Different STs showed variation with regard to which genes that were most frequently changed, mostly due to absence/presence of phase variation. CONCLUSIONS: This study revealed within-host genetic differences in meningococcal isolates during short-term asymptomatic carriage. The most frequently changed genes were genes belonging to the pilin family, the restriction/modification system, opacity proteins and genes involved in glycosylation. Higher resolution genome-wide sequence typing is necessary to resolve the diversity of isolates and reveals genetic differences not discovered by traditional typing schemes, and would be the preferred choice of technology.

Prevalence and epidemiology of meningococcal carriage in Southern Ethiopia prior to implementation of MenAfriVac, a conjugate vaccine.

BACKGROUND: Neisseria meningitidis colonizes humans and transmits mainly by asymptomatic carriage. We sought to determine the prevalence and epidemiology of meningococcal carriage in Ethiopia prior to the introduction of MenAfriVac, a serogroup A meningococcal conjugate vaccine. METHODS: A cross-sectional meningococcal carriage study was conducted in Arba Minch, southern Ethiopia. A total of 7479 oropharyngeal samples were collected from 1 to 29 year old volunteers, between March and October, 2014. The swabs were cultured for N. meningitidis and Neisseria lactamica in Ethiopia. N. meningitidis isolates were confirmed and characterized by their serogroup, sequence type (ST) and PorA:FetA profile in Norway. RESULTS: Overall carriage prevalence was 6.6 %. There was no significant difference in overall carriage between male (6.7 %) and female (6.4 %) participants. Highest carriage prevalence (10.9 %) for females was found in the 15-19 years of age, while prevalence among males was highest (11.3 %) in the 20-24 age group. Non-groupable isolates dominated (76.4 %), followed by serogroups X (14.0 %) and W (5.9 %) isolates. No serogroup A was found. Most non-groupable isolates were ST-192. Serogroup W isolates were assigned to the ST-11 clonal complex, and serogroup X isolates to the ST-181 and ST-41/44 clonal complexes. Overall carriage prevalence of N. lactamica was 28.1 %. Carriage of N. meningitidis and N. lactamica varied depending on age and geographic area, but there was no association between carriage of the two species. CONCLUSIONS: Epidemic strains of serogroups W and X were circulating in this area of Ethiopia. As no serogroup A was found among the carriage isolates the immediate impact of mass-vaccination with MenAfriVac on transmission of N. meningitidis in this population is expected to be marginal.

The socioeconomic impact of multidrug resistant tuberculosis on patients: results from Ethiopia, Indonesia and Kazakhstan.

BACKGROUND: One of the main goals of the post-2015 global tuberculosis (TB) strategy is that no families affected by TB face catastrophic costs. We revised an existing TB patient cost measurement tool to specifically also measure multi-drug resistant (MDR) TB patients' costs and applied it in Ethiopia, Indonesia and Kazakhstan. METHODS: Through structured interviews with TB and MDR-TB patients in different stages of treatment, we collected data on the direct (out of pocket) and indirect (loss of income) costs of patients and their families related to the diagnosis and treatment of TB and MDR-TB. Direct costs included costs for hospitalization, follow-up tests, transport costs for health care visits, and food supplements. Calculation of indirect costs was based on time needed for diagnosis and treatment. Costs were extrapolated over the patient's total treatment phase. RESULTS: In total 406 MDR-TB patients and 197 other TB patients were included in the survey: 169 MDR-TB patients and 25 other TB patients in Ethiopia; 143 MDR-TB patients and 118 TB patients in Indonesia; and 94 MDR-TB patients and 54 other TB patients in Kazakhstan. Total costs for diagnosis and current treatment episode for TB patients were estimated to be USD 260 in Ethiopia, USD 169 in Indonesia, and USD 929 in Kazakhstan, compared to USD 1838, USD 2342, and USD 3125 for MDR-TB patients, respectively. These costs represented 0.82-4.6 months of pre-treatment household income for TB patients and 9.3-24.9 months for MDR-TB patients. Importantly, 38-92 % reported income loss and 26-76 % of TB patients lost their jobs due to (MDR) TB illness, further aggravating the financial burden. CONCLUSIONS: The financial burden of MDR-TB is alarming, although all TB patients experienced substantial socioeconomic impact of the disease. If the patient is the breadwinner of the family, the combination of lost income and extra costs is generally catastrophic. Therefore, it should be a priority of the government to relieve the financial burden based on the cost mitigation options identified.

Performance of general health workers in leprosy control activities at public health facilities in Amhara and Oromia States, Ethiopia.

BACKGROUND: Leprosy is a chronic infectious disease of public health importance and one of the leading causes of permanent physical disability. Nevertheless, the drop in prevalence following multidrug therapy has resulted in the neglect of leprosy. The annual incidence of leprosy has remained the same in Ethiopia since decades with more than 76% of the reported new cases coming from Oromia and Amhara Regional States. This study was aimed to assess the knowledge, attitude and skill of general health workers in leprosy control activities at public health facilities in Oromia and Amhara Regional States. METHODS: A cross-sectional study was conducted from September 2011 to February 2012 at different public health facilities in selected eight zones in Oromia and Amhara Regional States. A multistage sampling method was used to obtain representative samples. High and low endemic zones for leprosy were included in the study in both regional states. Data were collected from general health workers through a structured self-administered questionnaire and at on-site assessment of their performance. Baseline socio-demographic data, health workers' attitude towards leprosy and their knowledge and skill in the management of leprosy were assessed. Bloom's cut off point was used to describe the knowledge and practical skills of the respondents while Likert's scale was used for attitude assessment. RESULT: A total of 601 general health workers responsible for leprosy control activities at public health facilities were included in knowledge and attitude assessment and 83 of them were subjected to practical evaluation, with on-site observation of how they handle leprosy patients. These included medical doctors (4%), health officers and nurses with Bachelor degree in Science (27%), clinical nurses with diploma (66%) and health assistants (2.8%). The median age of the respondents was 26.0 years and females made up of 45%. Generally the knowledge and skills of the respondents were found to be poor while attitude towards leprosy was positive for the majority of the respondents. The result showed that 519 (86.3%) had poor knowledge. Overall 155 (25.8%) of the respondents had positive attitude towards leprosy while 205 (34.1%) had intermediate (mixed) attitude and 241 (40.1%) had negative attitude to the disease. Among 83 respondents assessed for diagnosis of leprosy only 15(18.0%) diagnosed leprosy correctly. Variation in knowledge and attitude indicated a significant difference (p < 0.05) among different health institutions, professions, gender, in-service training and years of experience. CONCLUSION: The current finding underlines that although leprosy control activities are integrated to the general health services in the country, the knowledge and skills of leprosy diagnosis, treatment and management by health workers was unsatisfactory. Hence, attention should be given to develop training strategies that can improve health worker knowledge and promote better leprosy management at public health facilities. This could be achieved through pre-service and in-service training and giving adequate emphasis to leprosy related practical work and continuous follow- up.

A Randomized, Placebo-Controlled Trial Evaluating Safety and Immunogenicity of the Killed, Bivalent, Whole-Cell Oral Cholera Vaccine in Ethiopia.

Killed whole-cell oral cholera vaccine (OCV) has been a key component of a comprehensive package including water and sanitation measures for recent cholera epidemics. The vaccine, given in a two-dose regimen, has been evaluated in a large number of human volunteers in India, Vietnam, and Bangladesh, where it has demonstrated safety, immunogenicity, and clinical efficacy. We conducted a double-blind randomized placebo-controlled trial in Ethiopia, where we evaluated the safety and immunogenicity of the vaccine in 216 healthy adults and children. OCV was found to be safe and elicited a robust immunological response against Vibrio cholerae O1, with 81% adults and 77% children demonstrating seroconversion 14 days after the second dose of vaccine. This is the first study to evaluate safety and immunogenicity of the vaccine in a population outside Asia using a placebo-controlled, double-blind, randomized study design.

Identification and Characterization of Mycobacterium Tuberculosis Isolates from Cattle Owners in North Western and North Eastern Parts of Rural Ethiopia.

Tuberculosis (TB) is a major global public health problem resulting in a considerable morbidity and mortality worldwide. Ethiopia ranks 8th among the 22 high TB burden countries. Establishing an appropriate and improved intervention strategy to prevent and control tuberculosis requires the presence of evidence based data on the genetic diversity of its causative agent. The current research work, therefore, was to differentiate strains of Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients who own cattle in North Eastern and North Western parts of Ethiopia using molecular techniques. Sputum samples were collected from Acid Fast Bacilli (AFB) positive pulmonary tuberculosis patients and cultured on Lowenstein-Jensen (LJ) medium containing glycerol and sodium pyruvate. Deoxyribonucleic acid (DNA) was extracted from each positive culture, spoligotyping and single nucleotide polymorphisms were performed to further differentiate strains of M. tuberculosis, after deletion typing PCR confirmed that all the isolates were Mycobacterium tuberculosis. The mean age of study participants was 35.7 years (18-63 years) + 13.24. The majority (55.7%) were from North Gondar zone. Spoligotyping revealed that (47/50) 94% had interpretable patterns and 3 lineages namely; East-Africa-Indian (57.4%), Euro-American-African (EAA lineage-Lineage 4) 38.3% and Ethiopian (lineage-7) 2/50 (4.3%). Lineage 7 was registered in North Wollo zone only. In this study 8 clusters (with cluster size ranging from 2-8), 8 unique and 10 new patters were recorded. Spoligotype International Types (SIT) (21, 25, 26, 35, 53, 109, 149 and 289), were found as clusters and of these SIT 25 (7) and SIT 289 (8) were the predominant ones. Our study proved that 3 Mycobacterium tuberculosis lineages, namely; the ancient, intermediate between the modern lineages as well as modern were identified. Besides, considerable clustering was seen, which indicates the presence of current TB transmission in the study areas.

Immunocytochemical detection of Mycobacterium Tuberculosis complex specific antigen, MPT64, improves diagnosis of tuberculous lymphadenitis and tuberculous pleuritis.

BACKGROUND: A rapid, sensitive and accurate laboratory diagnosis is of prime importance in suspected extrapulmonary tuberculosis (EPTB) cases. However, traditional techniques for the detection of acid-fast bacilli have limitations. The aim of the study was to evaluate the diagnostic value of immunocytochemical staining for detection of Mycobacterium tuberculosis complex specific antigen, MPT64, in aspirates from pleural effusions and lymph nodes, the most common presentations of EPTB. METHOD: A cross-sectional study was conducted by including patients at Tikur Anbessa Specialized Hospital and the United Vision Medical Services from December 2011 to June 2012. Lymph node aspirates and pleural fluid samples were collected and analyzed from a total of 51 cases (26 tuberculous (TB) pleuritis and 25 TB lymphadenitis) and 67 non-TB controls. Each specimen was subjected to Ziehl-Neelsen (ZN) staining, culture on Lowenstein- Jensen (LJ) medium, cytological examination, Polymerase Chain Reaction (PCR) using IS1081gene sequence as a primer and immunocytochemistry (ICC) with polyclonal anti-MPT64 antibody. All patients were screened for HIV. RESULT: ICC was positive in 38 of 51 cases and in the 7 of 67 controls giving an overall sensitivity and specificity of 74.5% and 89.5%, respectively. Using IS1081-PCR as a reference method, the sensitivity and specificity, positive and negative predictive value of ICC was 88.1%, 89.5%, 82.2% and 93.2%, respectively. The case detection rate increased from 13.7% by ZN stain to 19.6% by LJ culture, to 66.7% by cytology and 74.5% by ICC. CONCLUSION: Immunocytochemistry with anti-MPT64 antigen improved detection of TB in pleural effusion and lymph node aspirates. Further studies using monoclonal antibodies on samples from other sites of EPTB is recommended to validate this relatively simple diagnostic method for EPTB.

Serodiagnosis of tuberculous lymphadenitis using a combination of antigens.

BACKGROUND: The diagnosis of extra-pulmonary tuberculosis (EPTB) by conventional methods such as culture and microscopy has low sensitivity and requires an invasive procedure. A simple rapid serological test would be of great value. METHODS: Six antigens (ESAT-6, Ag85A, TB10.4, Rv3881c, lipoarabinomannan (LAM) and Ara6-BSA) were tested in an ELISA to detect antigen specific IgG and IgM antibodies in sera from 54 culture and histology-confirmed tuberculous lymphadenitis (TBLN) patients, among whom four were HIV seropositive, sera from 25 smear positive pulmonary tuberculosis (PTB) patients, 15 culture and histology-negative lymphadenitis (non-TBLN) patients (n=15) and 22 healthy controls (HCs). RESULTS: The sensitivities of the antigens for the detection of IgG in sera of TBLN patients ranged from 4 to 30 %. Specificities ranged from 91 to 100 % with sera from HCs. Sensitivities of the antigens for detection of IgM ranged from 0 to 15 % and specificities ranged from 91 to 100 %. LAM was the most potent antigen followed by ESAT-6 and Rv3881c for detection of IgG. However, the sensitivity for antigen specific IgG antibody detection was improved when LAM was combined with ESAT-6 and Rv3881c.The sensitivity was 54 % and the specificity 91 %. CONCLUSIONS: The study suggests that the combined use of LAM, ESAT-6 and Rv3881c for the detection of IgG in sera of TBLN patients could be a supplement to microscopy of fine- needle aspirate (FNA) to diagnose EPTB.

Identification and genotyping of the etiological agent of tuberculous lymphadenitis in Ethiopia.

BACKGROUND: In Ethiopia, little has been done to assess how Mycobacterium bovis has contributed to human tuberculosis, though the population routinely consumes unpasteurized milk and raw meat. The aim of this study was to determine the proportion of M. tuberculosis and M. bovis as etiological agents of tuberculous lymphadenitis (TBLN). METHODS: Patients with lymphadenopathy (n = 171) were included in a cross-sectional study at Butajira Hospital, Southern Ethiopia. Lymph node biopsies were cultured. Patients' HIV status was identified. DNA from positive cultures was tested by PCR to identify M. bovis and M. tuberculosis. Isolates were genotyped by multiplex ligation-dependent probe amplification (MLPA) assay. RESULTS: Among 171 patients, 156 had culture results. Of these, 107 (69%) were positive for M. tuberculosis complex (MTC). Six of the 10 HIV-positive patients were culture positive. M. tuberculosis specific sequences were identified in the DNA of each of 100 samples as assessed by RD10 targeted PCR, and each of the 95 isolates exhibited the M. tuberculosis specific TbD1 deletion by MLPA analysis. No M. bovis was identified. These results indicate that all the isolates were modern M. tuberculosis strains. Furthermore, MLPA studies confirmed that 42% of the isolates showed the Haarlem genotype and 12% displayed sequences compatible with INH resistance. No mutations conferring resistance to ethambutol or rifampicin were detected. CONCLUSIONS: Our data showed that M. tuberculosis strains had common characteristics with strains causing pulmonary TB, which appears to be the main etiological agent of TBLN.