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Background  The most prevalent strains of  Mycobacterium tuberculosis  ( M.tb ) in Beijing belong to the Beijing genotype family. The influence of Beijing genotype prevalence on the development of drug resistance, and the association of infection with Beijing genotype  M.tb  with population characteristics, in Beijing, however, are still unclear.    Methods  In this retrospective study, 1189 isolates were subjected to drug susceptibility testing (DST) and molecular epidemiological analysis, and differences in the percentage of drug resistance between Beijing and non-Beijing genotype strains were compared. The association between the occurrence of drug resistance and the prevalence of Beijing genotype  M.tb  was analyzed using statistical methods.    Results  The Beijing genotype family was the dominant genotype (83.3%) among the 1189  M.tb  isolates. Beijing genotype  M.tb  strains were more likely to spread among males [ p  = 0.018, OR (95% CI):1.127(1.004–1.264)] and people in the 45–64 age group [ p  = 0.016, OR (95% CI): 1.438 (1.027–2.015)]. On the contrary, non-Beijing genotype  M.tb  strains were more probably disseminated among the over 65 [ p  = 0.005, OR (95% CI):0.653 (0.474–0.9)] and non-resident population [ p  = 0.035, OR (95% CI):1.185(0.985–1.427)]. DST results showed that 849 (71.4%) strains were fully sensitive to first-line drugs, while 340 (28.6%) strains were resistant to at least one drug, and 9% (107/1189) were MDR-TB. The frequency of INH-resistance among Beijing genotype strains was significantly lower than that among non-Beijing genotype strains ( p  = 0.032). In addition, the Beijing genotype family readily formed clusters.    Conclusions  Our findings indicate that male and middle-aged people were more probably be infected by Beijing genotype  M.tb , older people and non-residents were more probably be infected by non-Beijing genotype  M.tb . The high percentage of resistance to INH occurring in non-Beijing genotype strains suggested that non-Beijing genotype strains should be given much more interest in Beijing.    Electronic supplementary material  The online version of this article (10.1186/s12879-018-3578-7) contains supplementary material, which is available to authorized users.

Characterization of Mycobacterium tuberculosis strains in Beijing, China: drug susceptibility phenotypes and Beijing genotype family transmission