Lab Matters Summer 2016 | Page 11

feature New York City is known for its hot, dog days of summer, when air conditioners buzz across the city. When Kimberlee Musser, PhD, answered a call from the New York City (NYC) Public Health Laboratory in July 2015, it turned out to be directly related to these crucial cooling systems. miles from the Opera House Hotel. Although there was some heterogeneity, the isolates from the East Bronx and South Bronx were quite similar. Musser, who oversees bacterial disease testing at the Wadsworth Center—New York’s state PHL—had worked with the NYC laboratory just months earlier to screen building cooling tower water for Legionella pneumophila, the causative agent for the sometimes fatal pneumonia known as Legionnaires disease—spread through aerosolized water. City health officials suspected a Legionnaires disease outbreak was unfolding in the South Bronx. And they wanted to stop it. “Then we stepped back and realized something,” said Musser. “Sometimes you have to think about which reference genome you’re using to align your sequence data to.” The Wadsworth scientists had been using a genome from a 1976 Legionnaire’s disease outbreak in Philadelphia, and had been able to match 88% of the genome with confidence. Then they switched to one of the environmental strains from the Opera House Hotel “to understand if we were missing anything by not using the whole genome.” (In this case, CDC did the testing using a PacBio WGS platform, which is able to perform long reads and generate a completed, closed genome.) Musser and her staff agreed to support the public health investigation by once again screening cooling tower water and potable water via PCR (327 water samples in all) and conducting WGS on clinical and environmental samples (80 samples over a two-week period). At the same time, NYC and Wadsworth scientists performed pulsed field gel electrophoresis on all Legionella isolates and CDC scientists performed a second typing method, sequence-based typing, on a subset of isolates. Results were stark: The 41 clinical isolates from the South Bronx outbreak and five environmental isolates from the Opera House Hotel were identical. Moreover, the East Bronx clinical and environmental isolates differed from the South Bronx isolates by just eight base pairs—out of a 3.4 million-base-pair genome. Several historic Legionella isolates recovered from NYC and Wadsworth archives were also one to eight base pairs different from the South Bronx strain. “When we looked at all of that data,” said Musser, “we could determine that there was one hotel, the Opera House Hotel, that had several environmental isolates that matched well to all of the epi-linked cases in the South Bronx. It looked like a solid investigation.” Said Musser, “WGS provided extra discrimination in a situation where it was really needed.” She said, “We think this strain has been in NYC at least since 2007 and slowly evolving in different niches. We’re calling it a persistent endemic strain.” Then a second, smaller Legionella outbreak was detected in the East Bronx. Subsequent testing led authorities to a cooling tower on a college campus about seven Needless to say, the state governor and NYC health commissioner promulgated new regulations requiring registration, regular testing and, where necessary, disinfection of all water cooling towers to help prevent future problems. One of the biggest advantages of the technology, said Robert Myers, PhD, is its “pretty exquisite discrimination” among microbes, enabling epidemiologists to identify novel microbes and to tightly define outbreak definitions CDC’s AMD program currently funds about two dozen program areas. Armstrong said those likely to experience “the earliest impact” are food safety, TB, influenza and antimicrobial resistance. The technology is most useful in situations where investigators need a lot of information from one isolate, such as virulence markers, drug resistance markers, drug resistance mechanisms (such as p