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Pathogen-based factors associated with tuberculosis (TB) in eastern Sudan are not well defined. We investigated genetic diversity, drug resistance, and possible transmission clusters of Mycobacterium tuberculosis complex (MTBC) strains by using a genomic epidemiology approach. We collected 383 sputum specimens at 3 hospitals in 2014 and 2016 from patients with symptoms suggestive of TB; of these, 171 grew MTBC strains. Whole-genome sequencing could be performed on 166 MTBC strains; phylogenetic classification revealed that most (73.4%; n = 122) belonged to lineage 3 (L3). Genome-based cluster analysis showed that 76 strains (45.9%) were grouped into 29 molecular clusters, comprising 2-8 strains/patients. Of the strains investigated, 9.0% (15/166) were multidrug resistant (MDR); 10 MDR MTBC strains were linked to 1 large MDR transmission network. Our findings indicate that L3 strains are the main causative agent of TB in eastern Sudan; MDR TB is caused mainly by transmission of MDR L3 strains.

The sixth author’s name is spelled incorrectly. The correct name is: Abdhalah Ziraba. The correct citation is: Kerubo G, Khamadi S, Okoth V, Madise N, Ezeh A, Ziraba A, et al. (2015) Hepatitis B, Hepatitis C and HIV-1 Coinfection in Two Informal Urban Settlements in Nairobi, Kenya. PLoS ONE 10(6): e0129247. doi:10.1371/journal.pone.0129247.

Background Anti-tuberculosis drug resistance is an emerging health problem in Kenya and especially in slums. Slum environments create a conducive environment for the spread of tuberculosis (TB) due to high population density and lack of basic amenities such as decent housing, access to clean water, lack of drainage and basic sanitation. Furthermore, ineffective health services in crowded and poorer populations, poor patient compliance, a large pool of untreated cases, delayed diagnosis and inappropriate treatment regimens are likely to favour selection and spread of drug resistant Mycobacterium tuberculosis (Mtb) strains in such settings, however, precise data on this problem are only sparsely available. To address this question, this study aimed at determining drug resistance patterns of Mtb strains obtained from pulmonary TB patients who sought health care in randomly selected informal settings. Methods This is a cross-sectional study conducted between September 2014 and March 2015, sputum samples were collected from 223 consenting adult patients and subjected to primary isolation and drug susceptibility testing. Socio-demographic data was collected and all data analysed using SPSS v20. Results Drug susceptibility testing against first line drugs was successfully carried out on 184 isolates. Resistance to at-least one drug was observed in 33 % of the isolates. The highest prevalence of resistance to any drug was identified against isoniazid,(INH) (23.9 %) followed by Ethambutol (EMB) (13.6 %). The highest proportion of mono resistance was observed against INH, 25 (13.6 %). Multidrug resistance (MDR) was observed in 4.4 % of the new cases. There was no significant difference in the proportion of any resistance by sex, age or previous treatment. Conclusion Levels of drug resistance have reached an alarming level in this population. Capacity of laboratories to conduct TB culture and DST should be strengthened in order to adequately manage TB patients and stop further creation and spread of MDR TB. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1920-5) contains supplementary material, which is available to authorized users.