during march 2010october 2011 , we conducted a nationwide survey of persons from all 3 zones in the country who had pulmonary sputum smear  positive tb .
the survey was designed according to the guidelines of the world health organization ( who ) ( 5 ) by using cluster sampling of 39 diagnostic centers .
cases were classified as newly diagnosed or previously treated according to who definitions ( 6 ) .
we collected the following variables through a questionnaire administered during sputum collection : patient sex , age , country of birth , and treatment history ( new or previously treated ) .
a laboratory in south africa that is accredited for molecular testing by the national accreditation system tested sputum samples for resistance to rifampin and isoniazid by using genotype mtbdrplus assay ( hain lifescience gmbh , nehren , germany ) ( 7,8 ) .
the sensitivity of this assay to detect mutations known to confer resistance is higher for rifampin than for isoniazid ( 98.4% vs. 88.7% , respectively ) .
statistical analyses were performed in stata ( version 12 ; stata corp . , college station , tx , usa ) .
prevalence estimates were adjusted for fluxes in tb notifications from 2007 , the year on which sampling calculations were based , through 2010 , the year in which the survey started ( table footnote ; technical appendix figure ) . *
prevalence estimates were obtained by using logistic regression ( stata s svy : logit command , stata corp . , college station , tx , usa ) on the binary treatment history variable ; each new / retreatment case with a drug - susceptibility test result was weighted by the number of new / retreatment cases notified in its cluster in 2010 ( the year in which the survey started ) , divided by the total number of new / retreated cases with a drug - susceptibility test result in its cluster .
the estimation of odds ratios reported elsewhere in the text also included the expansion of categorical sex , age group , and zone variables ( xi : logit ) , with clustering and cis of variance .
the findings were robust to multiple imputation of missing data ( adding another 78 new and 18 retreatment cases to the sample ) , use of sampling weights based on 2007 notifications ( the year in which cluster samples were calculated ) , and no use of sampling weights at all ; prevalence estimates were equivalent to or slightly higher than those reported here .
ninety - six enrollees were subsequently excluded because of sample contamination ( 52 patients ) , insufficient material to perform the genotype mtbdrplus assay ( 41 patients ) , and isolation of mycobacteria spp .
the overall total drug susceptibility recovery rate was 89.9% , in line with the country expectations and who recommendations ( 5 ) .
of the patients retained in the study ( 754 persons with new cases and 96 persons with previously treated cases ) , the male - to - female ratio was 2.4:1.0 , and median age was 30 years ( range 486 years , interquartile range 2344 years ) .
mdr tb was detected in 5.2% ( 95% ci 2.87.5 ) of persons with newly diagnosed tb and 40.8% ( 95% ci 24.757.0 ) of persons with previously treated tb .
levels of resistance to isoniazid and rifampin and frequencies of any resistance and monoresistance are shown in the table .
history of previous anti - tb treatment was the strongest independent factor for mdr tb ( odds ratio [ or ] 23.0 , 95% ci 9.456.1 , p<0.001 ) , and living in the south - central region or in puntland was associated with a significantly higher risk for mdr tb than was living in somaliland ( or 3.6 , 95% ci 1.96.9 p<0.001 for living in puntland and or 4.3 , 95% ci 1.711.3 , p = 0.003 for living in the south - central region ) .
associations between mdr tb and sex , age , and country of birth were not significant .
compared with a study conducted in neighboring ethiopia in 2005 , where mdr tb was found in only 1.6% of new and 11.8% of previously treated tb cases ( 9,10 ) , and with surveys conducted in countries of the eastern mediterranean region , where the average proportion of mdr tb in new and previously treated tb cases was of 3.4% and 29.9% , respectively ( 4 ) , the proportions of mdr tb detected in somalia are high . at this level of resistance
, one would expect that among the 9,760 pulmonary tb cases notified in somalia in 2011 ( 4 ) , 750 were mdr tb and therefore required treatment with second - line drugs ; this number does not include other ( non - mdr ) cases of rifampin - resistant tb that would probably require an mdr tb regimen .
this finding presents a real emergency for the national tuberculosis control program considering the duration of second - line treatment ( > 2 years ) ( 11,12 ) , the current availability of such treatment in somalia for a only few patients , and the country s lack of laboratory capacity to diagnose drug resistance .
a systematic review of the cost effectiveness of mdr tb care ( 13 ) suggests that it would cost us$3,5005,900 to treat mdr tb on an outpatient basis in somalia . at < us$400 per disability - adjusted life - year
efforts are being made to treat mdr tb patients detected in the survey . because the cost of treating all 750 mdr tb patients is 32%54% of the us$8.2 million ( all of it from the global fund to fight aids , tuberculosis and malaria ) that was available to somalia in 2012 for its entire tb control program ( 4 ) , additional funding will be needed . in a drug quality survey conducted in somalia in 2010 , 60% of 10 products containing first - line anti - tb drugs that can be easily purchased from pharmacies and informal health care providers met international quality standards ( i. sindani , pers .
the extensive use of drugs of suboptimal quality , the widespread practice of using wrong medical prescriptions , and incomplete adherence of patients to treatment are the most likely reasons for the high levels of mdr tb in somalia .
these levels appear to be highest in the south - central region , where the security situation is most volatile and disruption of care more frequent .
this region also is most affected by recent food shortages ( 14 ) and has the most internally displaced persons ( 15 ) , factors that are expected to exacerbate disease progression and transmission of m. tuberculosis .
this study shows that nationwide surveys to monitor drug - resistant tb are possible even when social conditions are unstable .
two middle eastern countries , afghanistan and yemen , also were able to conclude nationwide drug resistance surveys in 2011 despite social unrest ( 4 ) .
sample collection , transportation , and monitoring of survey operations in our study have been challenging .
the analysis had to account for population movements and changes in the availability of and access to health services .
this study , conducted under difficult circumstances in a country with unstable social conditions , showed that mdr tb is a serious underdetected and widespread public health problem in somalia .
the documented levels of mdr tb are among the highest reported in africa and the middle east and suggest that 750 patients in the country had mdr tb in 2011 .
urgent measures should be introduced to improve access to diagnosis of drug resistance and availability of second - line medication for all patients who need them .
percentage change in total tuberculosis notifications by diagnostic center participating in the survey , somalia , 20072010 .
 in a nationwide survey in 2011 , multidrug - resistant tuberculosis ( mdr tb ) was found in 5.2% and 40.8% of patients with new and previously treated tb , respectively . 
 these levels of drug resistance are among the highest ever documented in africa and the middle east . 
 this finding presents a serious challenge for tb control in somalia . 