Mycobacterium tuberculosis complex whole-genome sequencing in New York State: Implementation of a reduced phenotypic drug susceptibility testing algorithm.

Whole-genome sequencing (WGS) can predict drug resistance and antimicrobial susceptibility in Mycobacterium tuberculosis complex (MTBC) and has shown promise in partially replacing culture-based phenotypic drug susceptibility testing (pDST). We performed a two-year side by side study comparing the prediction of drug resistance and antimicrobial susceptibility by WGS molecular DST (mDST) to pDST to determine resistance at the critical concentration by Mycobacterial Growth Indicator Tube (MGIT) and agar proportion testing. Negative predictive values of WGS results were consistently high for the first-line drugs: rifampin (99.9%), isoniazid (99.0%), pyrazinamide (98.5%), and ethambutol (99.8%); the rates of resistance to these drugs, among strains in our population, are 2.9%, 10.4%, 46.3%, and 2.3%, respectively. WGS results were available an average 8 days earlier than first-line MGIT pDST. Based on these findings, we implemented a new testing algorithm with an updated WGS workflow in which strains predicted pan-susceptible were no longer tested by pDST. This algorithm was applied to 1177 isolates between October 2018 and September 2020, eliminating pDST for 66.6% of samples and reducing pDST for an additional 22.0%. This algorithm change resulted in faster turnaround times and decreased cost while maintaining comprehensive antimicrobial susceptibility profiles of all culture-positive MTBC cases in New York.

Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York.

Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu. These strains, termed low-level RIF resistant, exhibit elevated RIF MICs compared to fully susceptible strains but remain phenotypically susceptible by mycobacterial growth indicator tube (MGIT) testing and have been associated with poor patient outcomes. Here, we assess RIF resistance prediction by whole-genome sequencing (WGS) among a set of 1,779 prospectively tested strains by both prevalence of rpoB gene mutation and phenotype as part of routine clinical testing during a 2.5-year period. During this time, 139 strains were found to have nonsynonymous rpoB mutations, 53 of which were associated with RIF resistance, including both low-level and high-level resistance. Resistance to RIF (1.0 µg/ml in MGIT) was identified in 43 (81.1%) isolates. The remaining 10 (18.9%) strains were susceptible by MGIT but were confirmed to be low-level RIF resistant by MIC testing. Full rpoB gene sequencing overcame the limitations of critical concentration phenotyping, probe-based genotyping, and partial gene sequencing methods. Universal clinical WGS with concurrent phenotypic testing provided a more complete understanding of the prevalence and type of rpoB mutations and their association with RIF resistance in New York.

Tuberculosis in health care workers during declining tuberculosis incidence in New York State.

BACKGROUND: Nosocomial tuberculosis (TB) transmission has decreased dramatically in New York State since 1992; however, health care workers (HCWs) still compose >3% of TB cases. METHODS: Aggregate surveillance data on incident TB cases from 1994 to 2002 were examined for trends among HCWs. Additional information was available for HCW cases from 1998 to 2002, including facility type, tuberculin skin test (TST) result at hire, and treatment of latent TB infection (TLTBI). RESULTS: In New York State, 2.5% of TB cases in 1994 and 4.0% in 2002 were in HCWs (P value for trend <.001). Fifty percent of HCWs TB cases in 1994 and 77.6% in 2002 were in non-US born (P = .002) HCWs. Multidrug-resistant TB in HCWs decreased from 15.6% in 1994 to 6.9% in 2002 (P = .001). Of 297 HCWs TB cases in 1998-2002, 54.9% were TST positive at hire, and 21.2% had unknown TST result; 50.2% of 221 HCWs who were TST positive at or after hire met guidelines for TLTBI, and 23.4% received treatment. The highest proportion with unknown TST at hire and the lowest proportion receiving TLTBI were in ambulatory facilities. CONCLUSION: Many HCWs who developed TB were either TST positive at hire and did not receive TLTBI or did not receive TST at hire. Facilities should encourage treatment for HCWs who meet criteria for TLTBI. Provider education should focus on ambulatory facilities.