BACKGROUND: In 2014, some New York City (NYC)-area laboratories began adopting multiplex polymerase chain reaction (PCR) tests to detect enteric bacteria and protozoa. We sought to characterize multiplex PCR usage trends in NYC.
METHODS: We determined number of NYC residents with diagnosis in 2014–2016 and positive laboratory test(s) reported for selected routinely investigated diseases (Cryptosporidium, Cyclospora, Salmonella, Shiga toxin-producing Escherichia coli [STEC], and non-cholera Vibrio) and non-routinely investigated diseases (Campylobacter, Entamoeba, Giardia, Shigella, and Yersinia). We calculated how many laboratories performed multiplex PCR testing, frequency of multiplex versus standard testing, frequency of reflexive testing following multiplex testing, percentage of multiplex tests confirmed at public health laboratories, and delay between specimen collection and first positive result notification. Multivariable logistic regression was performed to determine whether age, sex, race, ethnicity, area-based poverty, and other factors were associated with multiplex test receipt.
RESULTS: Of 14,304 patients, 9% received a multiplex test, ranging from <1% conducted by two laboratories in 2014 to 19% by 12 laboratories in 2016. The proportion of patients with a positive multiplex PCR result receiving additional testing ranged from 11% (17/151) for Giardia-infected patients to 91% (164/181) for Salmonella. The percentage of patients with a positive multiplex PCR result receiving confirmatory testing at a public health laboratory was >75% for cases infected with all pathogens except Giardia and Campylobacter. The proportion of these patients with a positive confirmatory test ranged from 27% (33/123) for STEC-infected patients to 100% for Entamoeba (1), Campylobacter (4), and Cyclospora (13). Among patients with routinely investigated diseases who had specimens tested at laboratories conducting multiplex PCR testing, multiplex test receipt was strongly associated with diagnosis in 2016, hospitalization, Hispanic ethnicity, and residing in the boroughs of Bronx and Manhattan. The median time between specimen collection and first positive result notification was two days for multiplex tests, five days for other tests.
CONCLUSIONS: Multiplex PCR use increased over time in NYC, contributing to higher case counts and timelier laboratory reporting, but necessitating additional testing for public health action. The proportions of cases with reflexively tested specimens and with positive confirmatory test results varied by pathogen. Limitations include the inability to distinguish whether negative confirmatory test results were attributable to false positive multiplex tests or poor specimen handling. Recognizing that multiplex and other non-culture-based tests pose challenges to public health practice, in 2016 the NYC Board of Health mandated reflexive testing following positive non-culture test results.