Earlier this year, the Wadsworth Center became the first and only state public health laboratory in the nation to perform whole genome sequencing (WGS) of tuberculosis (TB) specimens.
One case illustrates the enormous impact of WGS on TB testing and its central role in rapidly detecting and preventing the spread of drug-resistant TB strains among New York State’s general population.
| January | A 38-year-old male arrived in the United States from a country designated by the World Health Organization among the European Region’s 18 high-priority countries for TB control. The country is also among the world’s 27 high multi-drug resistant (MDR) TB burden countries, where 23 percent of the new TB cases and 62 percent of the re-treated TB cases are MDR. The Centers for Disease Control and Prevention defines MDR-TB as TB disease resistant to treatment with at least isoniazid and rifampin. |
| February | The patient was hospitalized with symptoms that suggested tuberculosis. Several sputa (matter coughed up through the mouth) were collected and cultured. |
| March | After one month of incubation, only one sputum generated a culture positive for TB. |
| March 23 | An isolate from the positive culture was referred to New York City Public Health Laboratory (NYC PHL) for drug susceptibility testing. |
| April 14 | The isolate was also referred to the Wadsworth Center Mycobacteriology Laboratory by the NYC PHL for whole genome sequencing. DNA sequencing is performed to detect mutations in certain genes, indicating drug resistance. |
| April 20 | Twenty-eight days after culture positivity, the NYC PHL reported resistance to all first-line TB drugs – rifampin, isoniazid, and pyrazinamide ethambutol – classifying this strain as MDR-TB. |
| April 25 | The Wadsworth Center Mycobacteriology Laboratory reported results indicating the presence of mutations in the following genes: rpoB (rifampin), katG (isoniazid), inhA (isoniazid), pncA (pyrazinamide), embB (ethambutol) and rpsL (streptomycin). The tests confirm the drug susceptibility findings of the NYC PHL. In addition, a mutation in gyrA was detected, predicting resistance to fluoroquinolone, a major class of second line drugs for treatment of MDR strains. This was crucial information that allowed the treating physician to modify the ongoing drug regimen prior to the availability of results from conventional second line drug susceptibility testing. |
| May 3 | Forty-one days after receiving the specimen, NYC PHL reported results for the susceptibility to second-line drugs. |
The conventional method took 28 days upon culture positivity to generate results for susceptibility to first-line drugs and 41 days to obtain results for susceptibility to second-line drugs.
In contrast, using WGS, Wadsworth Center reported a reliable susceptibility profile for first- and second-line drugs 11 days after receipt of the isolate.
Submitting the isolate for WGS immediately after the original culture became positive would have saved 17 days for first-line drugs and 30 days for second-line drugs.
TB infection can be spread for up to 2-3 weeks after beginning medication. Determining the correct drug and getting people started on it quickly reduces transmission of the disease.
Vincent E. Escuyer, Ph.D.
Director, Mycobacteriology Laboratory