Whole-Genome Sequencing Identifies Multidrug-Resistant Tuberculosis Among Refugees

Whole genome sequencing proved useful in identifying patients with multidrug-resistant tuberculosis in an outbreak among African refugees in Europe.

Tuberculosis persists as a global health concern. It ranks number 9 in causes of death worldwide—above HIV—with 10.4 million new cases presenting in 2016; of those cases, 600,000 were resistant to rifampicin, a mainstay of tuberculosis treatment, and more than 80% were also resistant to other tuberculosis drugs. These multidrug-resistant cases are a serious obstacle to the eradication of tuberculosis, which the World Health Organization would like to achieve by 2030.

A group of European scientists took part in an investigation that began in early 2016 after 4 refugees from the Horn of Africa and Sudan who had arrived in Europe were found to have tuberculosis that was resistant to rifampicin, isoniazid, ethambutol, pyrazinamide, and capreomycin.

Further data was collected and analyzed, resulting in the discovery of 29 African refugees in Europe suffering from multidrug-resistant tuberculosis. Whole-genome sequencing helped reveal that the cases were of the same genotype. Another 29 refugees with multidrug-resistant tuberculosis were found who received diagnoses before this particular outbreak; although the genotypes in this group weren’t identical to those of the first, they shared the same drug-resistant mutation. This led the scientists to believe the cases all arose from a common source, most likely in Somalia or Djibouti.

Somalia and other countries in Africa have seen masses of citizens fleeing persecution and economic misery in hopes of finding a better life in Europe. Unfortunately, these African nations are often breeding grounds for tuberculosis, which the refugees bring with them to their new homelands. There are roughly 65 cases of tuberculosis per 100,000 people in Eritrea, 192 cases per 100,000 in Ethiopia, 274 cases per 100,000 in Somalia, and 378 cases per 100,000 in Djibouti. Somalia also has 29 cases of drug-resistant tuberculosis per 100,000 people, estimated to be the highest in Africa. The disease is easily transmitted during the journey to Europe, thanks to the unsanitary conditions under which refugees live and the dearth of medical care in holding areas. For example, many refugees are kept in crowded, unventilated bunkers in Libya, often for months at a time, before arriving at their final destinations.

The scientists, writing in The Lancet, described a united 6-month, 7-country effort to identify patients in the multidrug-resistant tuberculosis outbreak in Europe. Once gene sequencing revealed that a patient was a likely match for the outbreak, “epidemiological data were simultaneously collected at a country level and shared with national tuberculosis surveillance programmes, the European Centre for Disease Control and Prevention, and the international team of researchers aiding the analysis,” they wrote. “All patients remain on treatment under the supervision of local health-care teams, with the exception of one who was lost to follow-up.”

The authors cautioned that the retrospective nature of the data was a limitation of the study. Given the uncertain conditions the African refugees faced, it’s possible that some who were exposed to tuberculosis weren’t identified. Their recollections having to do with time and location could have been faulty, and the trauma experienced by some—along with fears of deportation—may have made it difficult for them to fully recount their experiences.

With more refugees expected to leave Africa for Europe in the near future, the need for ongoing screening and treatment is high, as is the need to step up efforts to prevent tuberculosis from spreading in the first place. Improved, more effective vaccines are crucial, as is the swift identification of tuberculosis cases that occur. This study provides an encouraging example of the role that whole-genome sequencing can play in helping to identify outbreaks of multidrug-resistant tuberculosis so they can be quickly addressed and contained.

Laurie Saloman, MS, is a health writer with more than 20 years of experience working for both consumer- and physician-focused publications. She is a graduate of Brandeis University and the Medill School of Journalism at Northwestern University. She lives in New Jersey with her family.