Practical Applications of DNA Testing

  • Italy is Keeping Cities Beautiful by DNA Testing Dog-Droppings
  • Fines Issued to Owners who Don’t Pick Up
  • Smart Idea or Story-plot for an Italian Comic Opera?

As you know, I like to explore all things related to nucleic acids. In this post, I take a little respite from scientific analysis and instead explore an interesting real-life application for DNA testing. As summer comes to an end and we’ve all returned from our recent holidays, this post provides a tie-in to Naples, which is both a great vacation destination and a place where dog-droppings are a controversial topic. Sound intriguing? Read on.

Naples’ historic city center, which is listed by UNESCO as a World Heritage Site, is the largest in Europe, covering 4,200 acres and enclosing 27 centuries (!) of history. This historic city is leading the way in employing modern technology to keep its streets clean. Naples is the first metropolitan city to use “CSI-style” DNA forensics to rid its sidewalks of dog poop and impose stiff fines to those who let Fido leave his DNA behind. It’s a story that strangely juxtaposes quaint European old-city charm with an interesting mix of science and societal topics to evoke a wide spectrum of opinions.

By the way, in researching Naples, I learned that it has long been a major cultural center with a global sphere of influence, particularly during the Renaissance and Enlightenment eras. In the immediate vicinity of Naples are numerous culturally and historically significant sites, including the Palace of Caserta and the Roman ruins of Pompeii and Herculaneum. Naples is synonymous with pizza, which originated in the city as Neapolitan flatbread and migrated to America with the Italians. Neapolitan music has furthermore been highly influential, credited with the invention of the romantic guitar and the mandolin, as well as notable contributions to opera.

Good Idea or Waste of a City’s Resources?

Despite its glorious past, the city is not without it’s slew of current problems. Tommaso Sodano, the vice mayor of Naples, recently acknowledged in an interview that the city is facing many challenges related to huge debt, unfunded service agencies, wide-spread organized crime and general filth related to illegal dumps and dog droppings…yes, poop.

The city administration is positioning Naples ‘at the cutting edge of dog-waste eradication’. The initiative takes DNA samples of dogs to create a database used to identify and fine owners who leave their dog’s poop on city streets.

“I know some people find it funny,” Mr. Sodano is quoted as saying, smiling, “that with all the problems the city has, we would focus on dog poop. I know that.”

Via Toledo is Naples’s principal shopping street and a “must do” for tourists (taken from Wikipedia)

Via Toledo is Naples’s principal shopping street and a “must do” for tourists (taken from Wikipedia)

While it may sound a bit humerous at first, it’s an issue that is wide-spread and difficult to control as there are some 80,000 dogs in Naples. While other cities have tried everything from mailing dog poop back to its owner to publicly shaming offenders, Naples is pursuing a more modern approach. Blood samples will be taken from every dog in the city and used to create a database matched with contact information for the dog’s owner. ‘When an offending pile is discovered, it will be scraped up and subjected to DNA testing. If a match is made in the database, the owner will face a fine of up to 500 euros, or about $685.’ The program is in its infancy, but officials say it’s already making an impact on Via Toledo and surrounding areas where it’s being piloted.

Veterinary workers in Naples drew blood from Fiona, a pit bull, for the DNA database. Credit Gianni Cipriano for the NY Times.

Veterinary workers in Naples drew blood from Fiona, a pit bull, for the DNA database. Credit Gianni Cipriano for the NY Times.

Many residents and officials are skeptical that the program will work given the city’s existing challenges with basic services like garbage collection and sewage. Others disagree with the program’s expenditures in light of the city’s mounting debt. Sodano remains committed to the program saying “The main goal is respect for the rules.” He’s quick to add that other mounting issues shouldn’t prevent city administration from keeping Naples beautiful. “Governing Naples,” he said, “certainly requires a sparkle of madness.”

What’s the DNA-Based ID Used?

I tried, unsuccessfully, to find out what DNA-based identity testing is being used in Naples. In researching this, however, I did find the abstract of a relatively recent publication that suggests to me that Naples may be analyzing mitochondrial DNA (mtDNA), analogous to TriLink’s forensic products (mitoPrimers™) for human identity testing using PCR-sequencing.

According to this abstract, the researchers sequenced the entire ∼16 kb canine mtDNA genome of 100 unrelated domestic dogs (Canis lupus familiaris) and compared these to 246 published sequences to assess hypervariable region I (HVI) haplotype frequencies. They then used all available sequences to identify informative single nucleotide polymorphisms (SNPs) outside of the control region sequence—identical in all dogs—for use in further resolving mtDNA haplotypes corresponding to common HVI haplotypes. They identified a total of 71 informative SNPs that they concluded are “useful forensic tools to further resolve the identity of individual dogs from mitochondrial DNA (mtDNA).”

Even though we don’t know the exact details of the testing being used in Naples, I wrote this post because I find the practical applications of DNA-based testing to be fascinating. If you know of other real-life applications, please share them in the comments section below.

6 thoughts on “Practical Applications of DNA Testing

  1. comments from two of my friends:

    Matt: “When apartment shopping [in Austin], this was a selling point at one of the complexes. They would get the poop tested for identification and then go after the suspected culprits owner for a sample. They also said it was grounds for eviction lol.”

    Marie: “I think part of the complication of this, which the makers of the kits don’t realize, is how well the DNA evidence will hold up court. For example, purebred pets having a history of inbreeding can have results that cannot definitively prove if it came from a specific animal. With humans, the odds of the DNA matching any other person besides the one being compared is in the billions. With pets it goes exponentially down.”

    • Thank you Sasha, Matt and Marie for your comments. I’ll forward Marie’s comment to Eric Mayer at PooPrints and ask him to reply.

    • Thank you for the feedback!

      We certainly agree with Matt about the marketing advantage and indeed most communities do portray PooPrints in that way. If you think about it from a pet owner perspective (and from a non-owner perspective) would you rather live in a community where you KNOW pet waste will be picked up every time, or live in a community where you will see, smell, and potentially step in it? PooPrints promotes Cleaner and Greener living!

      To Marie’s point – we have done extensive R&D and can discern individual animals even when in-line breeding has occurred between relatives. BioPet’s PooPrints requires a minimum number of alleles to be present before calling a match to ensure the minimum degree of probability far exceeds the number of dogs at a community. Our statistics are based on samples in the DNA World Pet Registry, which contains tens of thousands of dogs. Based on our database and the frequency of the alleles present in a given DNA profile, the chances that a dog other than the listed match would have the same combination of alleles range from 1 in 20,000 to greater than 1 in 1 billion. In addition, we amplify a greater number of markers than the FBI’s CODIS in order to qualify a match. So I must respectfully disagree with Marie’s assertion that probability of a match in pets “goes exponentially down” compared to identifying humans.

      That said, waste has been used as a means of DNA collections for many years. It is one of the best methods to study animal populations in field studies as it allows for a low stress, non-invasive means of DNA collections.

  2. Thank you Jerry! i had no idea about this initiative in Naples. Great idea, very unique, but not easy to accomplish – in terms of time and $$ investment. I wonder if some of the big cities in the US will adopt it (hope not, as I am guilty- not always “scoop the poop” after our cocker spaniel 🙂

  3. Hello Dr. Zon!

    We have been closely watching the progress of this initiative in Naples. We are the inventors of the PooPrints DNA Pet Waste Management service here in the US, and as such this application of DNA technology is near and dear to us. I agree, it appears Naples have chosen to “reinvent the wheel” so to speak in creating their own DNA database and I would assume developing their own DNA extraction and analysis protocols, although it is difficult to find more details on the exact processes they are using (as you have noted in your blog).

    In any case, as a fellow molecular bio nut I wanted to introduce myself and our PooPrints service! If you are interested in learning any more about us or our canine DNA profiling/identification methods, I’d be happy to send more details.

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