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DNA points to likely septic contamination of potable water system in residential apartment building

A resident of an apartment building in New York City contacted Microbe Detectives to see if the potable water supplied to his apartment could be analyzed for microbiological contamination. He said people are getting sick in the building and he thinks the problem could be with their water.

One water sample was analyzed using Microbe Detectives’ 16S and 18S rRNA sequencing methodology. This analysis identified nearly all Bacteria, Archaea, and Eukarya (e.g., fungi, algae, amoeba, etc.) known in environmental science that were present in the water sample and the % relative abundance of each. The data was then checked for the presence of genus identities that contain pathogens and microbes known to be associated with fecal contamination.

Potential pathogens observed

Fifteen (15) genus identities that contain pathogens were observed to be present as shown below. Since the pathogens are identified at the species level, and this DNA analysis identifies at the genus level, this analysis could not confirm the presence of pathogens. However, a healthy potable water system should be free from all of these organisms. Therefore, the presence of these organisms was rated as a warning that pathogens species may be present.

Yersinia – The 4th most abundant microbe observed @7.2% relative abundance

Yersinia are bacteria that can cause illnesses in humans. Y. enterolitica are the most common species causing human enteric (intestinal) yersiniosis.(1) The organism is transmitted to humans as a foodborne or waterborne pathogen, and infection results in an acute gastrointestinal condition known as yersiniosis.(2)

DNA points to likely septic contamination

The gut is the most colonized human organ with up to 100 trillion microbes, about 10 times the number of the human cells. The predominance of these microbe groups consists of only 4 major phyla: Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria (3).

A phylum analysis of the clients potable water sample observed the presence of all four human gut associated phyla, as shown below. This is the first major clue that the potable water system may be contaminated with human feces.

Enterobacterales are a large order of different types of bacteria that commonly cause infections in healthcare settings, and are generally associated with microbes found in the human gut.(4) Nine bacteria grouped under the Enterbacterales Order were observed to be present, as shown below.
A few descriptions of Enterobacterales genera observed present include the following.

Citrobacter – @1.3% relative abundance

Citrobacter spp. primarily are inhabitants of the intestinal tract of mammals and other vertebrates. Their isolation from environmental sources such as water and soil likely is the result of fecal excretion.(5)

Clostridium – @0.7% relative abundance

Clostridium bacteria are found in soil, water, and the intestinal tracts of humans and other animals. Most species grow only in the complete absence of oxygen.(6)

Klebsiella – @0.2% relative abundance

Klebsiella is a type of gram-negative bacteria that can cause different types of healthcare-associated infections. Increasingly, Klebsiella bacteria have developed antimicrobial resistance, most recently to the class of antibiotics known as carbapenems. Klebsiella bacteria are normally found in the human intestines and in the human stool (feces).(7)

Other clues of fecal

Bacteroidia – @0.5% relative abundance

Bacteroidia is the Class that contains Bacteriodes which is a standard fecal contamination indicator. While Bacteriodes was not observed to be present, detection of the Class Bacteroidia strengthens the case suggesting that the potable water system may have been contaminated with fecal matter.

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References

  1. Centers for Disease Control and Prevention, website (https://www.cdc.gov/yersinia/about/index.html)
  2. Rogers, Kara. “Yersinia”. Encyclopedia Britannica, 28 Apr. 2016, (https://www.britannica.com/science/Yersinia)
  3. Rizzatti G, Lopetuso LR, Gibiino G, Binda C, Gasbarrini A. Proteobacteria: A Common Factor in Human Diseases. Biomed Res Int. 2017;2017:9351507. doi: 10.1155/2017/9351507. Epub 2017 Nov 2. PMID: 29230419; PMCID: PMC5688358.
  4. Centers for Disease Control and Prevention website. (https://www.cdc.gov/cre/about/?CDC_AAref_Val=https://www.cdc.gov/hai/organisms/cre/index.html#
  5. Stella Antonara, Monica I. Ardura, 141 – Citrobacter Species,
    Editor(s): Sarah S. Long, Charles G. Prober, Marc Fischer, Principles and Practice of Pediatric Infectious Diseases (Fifth Edition), Elsevier, 2018, ISBN 9780323401814, https://doi.org/10.1016/B978-0-323-40181-4.00141-9. (https://www.sciencedirect.com/science/article/pii/B9780323401814001419)
  6. Britannica, The Editors of Encyclopaedia. “clostridium”. Encyclopedia Britannica, 5 Jan. 2022, https://www.britannica.com/science/Clostridium. Accessed 12 May 2024.
  7. Centers for Disease Control and Prevention, website (https://www.cdc.gov/klebsiella/about/?CDC_AAref_Val=https://www.cdc.gov/hai/organisms/klebsiella/klebsiella.html)

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