"Long before it's in the papers"
February 06, 2015


Student scientists find partially drug-resistant germs, scraps of anthrax DNA—all in the subway

Feb. 6, 2015
Courtesy of Rockefeller University
and World Science staff

For­get the five-million plus com­muters and un­told num­ber of rat­s—many of the liv­ing things crowd­ed in­to the New York ­city sub­way sys­tem are too small to see.

An in­ter­est in the more men­ac­ing among these mi­crobes led high school stu­dent Anya Dunaif, a par­ti­ci­pant in Sum­mer Sci­ence Re­search Pro­gram at Rock­e­fel­ler Uni­vers­ity in New York, to spend a vaca­t­ion swab­bing benches and turn­stiles be­neath the ­city. Among her find­ings: bac­te­ria im­per­vi­ous to two ma­jor an­ti­bi­otics.

As part of Path­omap, a proj­ect sam­pling en­vi­ron­men­tal DNA in New York City, stu­dents in Rock­e­fel­ler Uni­ver­si­ty's Sci­ence Out­reach Pro­gram swabbed sur­faces in the city's sub­way sys­tem.
(Cred­it: Rock­e­fel­ler U. Sci­ence Out­reach Pro­gram)

The in­i­tial re­sults are de­scribed in a pa­per pub­lished this week in the re­search jour­nal Cell Sys­tems.

“There’s no ques­tion, high school stu­dents can do le­git­i­mate pri­ma­ry re­search,” said Jeanne Gar­barino, di­rec­tor of Rock­e­fel­ler’s Sci­ence Out­reach Pro­gram. She stressed that Dunaif and fel­low stu­dent-researchers didn’t know what they would find when the project began.

The sam­ples Dunaif col­lect­ed and cul­tured in five sta­t­ions are a com­po­nent of a citywide en­vi­ron­men­tal DNA sam­pling ef­fort led by Chris Ma­son, an as­sis­tant pro­fes­sor at Weill Cor­nell Med­i­cal Col­lege in New York. The proj­ect, called Path­omap, seeks to pro­file the ­city’s mi­cro­bi­al com­mun­ity, or mi­cro­biome, while al­so cap­tur­ing DNA from oth­er or­gan­isms, all of which could be used to as­sess health threats. 

With help from fel­low high school stu­dent re­searcher Nell Kirch­berger, Dunaif col­lect­ed the bac­te­ria on swabs and tested to see if they would grow in Petri dishes con­tain­ing three com­monly used an­ti­bi­otics. Bac­te­ria from five of the 18 swabs she tested grew in spite of the pres­ence of ei­ther ampi­cillin or kan­a­my­cin, and in one case, both, the paper reported. None seemed re­sist­ant to a third an­ti­bi­ot­ic, chlo­ram­phen­icol.

An­ti­bi­ot­ic re­sis­tance—the abil­ity of dis­ease-caus­ing bac­te­ria to with­stand chem­i­cals used to kill them of­f—can make a once treat­able in­fec­tion more se­ri­ous, even life threat­en­ing. A nat­u­ral con­se­quence of ev­o­lu­tion, and the wide­spread use and mis­use of an­ti­bi­otics, re­sist­ance is in­creas­ing world­wide.

Join­ing her on the con­tin­u­ing search for drug-re­sist­ant bugs are Anya Au­er­bach, a sen­ior at the Eth­i­cal Cul­ture Field­ston School, and Will Lounsbery-Scaife, now a fresh­man at New York Uni­vers­ity. (Kirch­berger has since re­turned to Cal­i­for­nia.) Both took on their own proj­ects over the sum­mer, al­though their work was not in­clud­ed in the cur­rent Path­omap pub­lica­t­ion.

Lounsbery-Scaife spent his sum­mer swab­bing wa­ter foun­tains in Cen­tral Park. The se­quenc­ing re­sults aren’t com­plete yet, but the ex­pe­ri­ence, he said, has giv­en him a bet­ter un­der­stand­ing of the sci­en­tif­ic pro­cess, not just the re­sults.

In ad­di­tion to an­ti­bi­ot­ic-re­sist­ance, Path­omap’s sur­veys al­so turned up frag­ments of DNA that cor­re­spond to well-known dis­ease caus­ing mi­crobes, in­clud­ing plague and an­thrax bac­te­ria. How­ev­er, the au­thors note, mi­crobes that left be­hind this DNA don’t ap­pear to be caus­ing wide­spread dis­ease; in­stead they may simply rep­re­sent nor­mal in­hab­i­tants of ur­ban in­fra­struc­ture.

* * *

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Forget the five-million plus commuters and untold number of rats—many of the living things crowded into the New York City subway system are too small to see. An interest in the more menacing among these microbes led high school student Anya Dunaif, a participant in Summer Science Research Program at Rockefeller University in New York, to spend a vacation swabbing benches and turnstiles beneath the city. Among her findings: bacteria impervious to two major antibiotics. The project’s initial results are described in a paper published this week in the research journal Cell Systems. The samples she collected and cultured in five stations are a component of a city-scale environmental DNA sampling effort led by Chris Mason, an assistant professor at Weill Cornell Medical College, as well as from local, national and international collaborators. The project, called Pathomap, seeks to profile the city’s microbial community, or microbiome, while also capturing DNA from other organisms, all of which could potentially be used to assess biological threats, including those to human health. With help from fellow high school student researcher Nell Kirchberger, Dunaif collected the bacteria on swabs and tested to see if they would grow in Petri dishes containing three commonly used antibiotics. Bacteria from five of the 18 swabs she tested grew in spite of the presence of either ampicillin or kanamycin, and in one case, both. None of the cultured bacteria appeared resistant to a third antibiotic, chloramphenicol. Antibiotic resistance—the ability of disease-causing bacteria to withstand chemicals used to kill them off—can make a once treatable infection more serious, even life threatening. A natural consequence of evolution, and the widespread use and misuse of antibiotics, resistance is increasing worldwide. Joining her on the continuing search for drug-resistant bugs are Anya Auerbach, a senior at the Ethical Culture Fieldston School, and Will Lounsbery-Scaife, now a freshman at New York University. (Kirchberger has since returned to California.) Both took on their own projects over the summer, although their work was not included in the current Pathomap publication. “There’s no question, high school students can do legitimate primary research. If we are going to encourage critical thinking, which is important regardless of what you do in life, I think it is important to have them ask and attempt to answer open-ended questions,” said Jeanne Garbarino, director of Rockefeller’s Science Outreach Program. Lounsbery-Scaife spent his summer swabbing water fountains in Central Park. The sequencing results aren’t complete yet, but the experience, he said, has given him a better understanding of the scientific process, not just the results. In addition to antibiotic-resistance, Pathomap’s surveys also turned up fragments of DNA that correspond to well-known disease causing microbes, including plague and anthrax bacteria. However, the authors note, microbes that left behind this DNA don’t appear to be causing widespread disease; instead they may simply represent normal inhabitants of urban infrastructure.