Aquatic Bacteria Reveal a Common Genetic Link to a Deadly Human Pathogen

Researchers use genetic clues to track the spread of antibiotic resistant bacteria from the environment to patients.

Iris
Iris Kulbatski, PhD

Iris Kulbatski, a neuroscientist by training and word surgeon by trade, is a science editor with The Scientist's Creative Services Team. She holds a PhD in Medical Science and a Certificate in Creative Writing from the University of Toronto.

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Mar 7, 2022

In 1675, when Dutch self-taught scientist Antoni van Leeuwenhoek first used his homemade microscope to examine a drop of rainwater, he made a discovery that would have an immeasurable impact on human health centuries later. Replicating his observations with lake, pond, well, and sea water, Leeuwenhoek revealed “within every drop of water…an amazing world of life,” teeming with “living creatures…wee animalcules.”1,2 Among the living creatures were the first bacteria ever visualized, earning Leeuwenhoek the title of Father of Microbiology and launching a microbiological tale spanning centuries and the globe. 

Steven Djordjevic and his team characterized Elizabethkingia from Australian aquatic samples.
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Almost three hundred years later and an ocean away, American microbiologist Elizabeth O. King was tasked by the US Centers for Disease Control and Prevention with characterizing a novel pathogen responsible for a lethal outbreak of meningitis—inflammation of the membranes surrounding the brain. She classified the bacterium from clinical samples and named it Flavobacterium meningosepticum,3 which was later renamed Elizabethkingia meningoseptica in her honor.4 In the following decades, fatal Elizabethkingia infections appeared in healthcare settings worldwide5,6 due to contaminated water systems, equipment, and medical devices.7,8,9 Elizabethkingia are now recognized as emerging, lethally opportunistic pathogens that cause antimicrobial resistant infections, with waterbodies—such as those Leeuwenhoek studied—acting as reservoirs.10  

Almost 350 years after Leeuwenhoek first made eye contact with bacteria in a drop of water, Steven Djordjevic, a microbiologist at the University of Technology in Australia, and his team collected dam, river, and wetland water samples, characterized whole-genome sequences of 94 Elizabethkingia isolates from these aquatic environments, and compared them to clinical strains from Australia and abroad to understand the implications for clinical transmission.11 In a recently published study in Current Research in Microbial Sciences,11 the researchers analyzed these isolates’ genomes, demonstrated the genetic relationships between Elizabethkingia species from aquatic and clinical samples, and identified genetic elements that contribute to the spread of antimicrobial resistance.  

Connecting the Branches of the Phylogenetic Tree

The researchers developed a phylogenetic tree—a branched diagram illustrating evolutionary relationships—that contained 148 Elizabethkingia isolates: 94 local aquatic samples, 27 local clinical and hospital samples, and 27 international strains from GenBank, a publicly-available database. Overall, they classified the 148 isolates into seven phylogenetically-distinct species, the most abundant of which were the known human pathogens Elizabethkingia miricola and Elizabethkingia anophelis. Amongst these, Djordjevic’s team identified a possible yet-undiscovered and pathogenic species of Elizabethkingia, which they named Elizabethkingia umeracha, that had over 60 disease-enabling genes in common with E. miricola and E. anophelis isolates. The genetic patterns of three E. anophelis isolates from the wetland and dam samples were closely related to several E. anophelis isolates from Australian hospital sinks12 and antibiotic resistant sepsis patients, indicating a potential pathway from the environment to the clinic.

Tracking the Genetic Flow of Antibiotic Resistance 

Researchers use bacterial whole genome sequencing to compare the phylogenetic relationship between environmental and clinical samples.
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“Waterborne infections that are already resistant to our most powerful antibiotics are a real threat to human health. Perhaps not on a wide scale, but often scale doesn’t matter to the person who has the Elizabethkingia infection,” explained Djordjevic. Metallo-β-lactamases (MBLs)—bacterial enzymes that deactivate the most widely-used β-lactam antibiotics—are among the mechanisms that bacteria exploit to confer antibiotic resistance. As the only organisms with three genes responsible for activating MBLs, Elizabethkingia are naturally resistant to three major antibiotic classes: carbapenems, β-lactams, and cephalosporins. Djordjevic and his colleagues found that all 94 aquatic Elizabethkingia samples carried these three genes, variants of which were present in several Elizabethkingia species that were highly resistant to β-lactams and other clinically-important last line antibiotics. Additional isolates were further resistant to other antibiotic classes, suggesting that the bacteria employ novel antimicrobial resistance processes.

Djordjevic and his team also found that 71 percent of the 94 Elizabethkingia environmental samples contained specific mobile genetic elements (MGEs)—genetic material that moves within or between genomes—that enable the spread of antibiotic resistance. MGEs that carry resistance genes can incorporate into the chromosomes of new bacterial hosts and create antibiotic resistant phenotypes,13 which contribute to emerging and ongoing pathogenesis in infected humans. This finding represents an important direction for future research into mitigating emerging pathogenesis. Erica Donner, an environmental scientist at the University of South Australia who coauthored this study, said “environmental sites can act as potential sources of future outbreak clones and [clinically challenging] genes can be lurking quietly all around us just waiting for the opportunity and encouragement through selective pressure to jump onto a mobile element and go rogue.”

Breeding Success Strategies

The microbial communities of the 1600’s have evolved significantly since Leeuwenhoek first observed his water samples. Daniel Jaén-Luchoro, a research fellow in infectious diseases at the University of Gothenburg in Sweden who was not involved in this work, highlights its importance for predicting “how resistance can be transmitted not only to strains of the same species, but also to other species. This knowledge is essential to designing strategies to prevent or fight infections caused by these emerging pathogens.” He explained that the pervasive use of antimicrobials in clinical, aquaculture, and agricultural settings leads to their environmental accumulation through wastewater contamination and agricultural runoff. As a result, environmental bacteria that have natural antibiotic resistance are exposed to strong selective pressure. This hastens the evolution and spread of highly resistant strains, which thrive, transfer resistance genes to other strains, and eventually colonize humans. 

According to Donner, “when we interrogate the environmental aspect of antimicrobial resistance, we start to appreciate why we should do everything we can to limit selective pressure so that we slow the evolution and spread of life-threatening superbugs.” Understanding the genetic signatures of these species may inform prevention and treatment strategies. For example, positive clinical outcomes in patients with Elizabethkingia infections depend on early diagnosis and antibiotic treatment that targets the unique resistance profile of the pathogen. Improved infection prevention strategies, such as sanitization, sink splash guards, and water purification are also critical to minimizing the spread of waterborne pathogens. 

This study highlights the interconnectedness between us and the vast world of microbes that we inhabit, providing evidence of the possible shared origins between aquatic bacteria and those that cause fatal hospital acquired infections. Leeuwenhoek blazed the trail when he first used his microscope to examine water and discover what others had missed. The genomic technology used by Djordjevic and his team—including whole genome sequencing—allows scientists to peer ever deeper into the microbiological wonders of a single drop of water, reminding us that what we see depends on the instruments of perception that we use.

References

  1.  A.V. Leeuwenhoek, “Observations, communicated to the publisher by Mr. Antony van Leewenhoeck, in a dutch letter of the 9th Octob. 1676. here English'd: concerning little animals by him observed in rain-well-sea- and snow water; as also in water wherein pepper had lain infused,” Phil Trans R Soc, 12821–31, 1677.
  2. N. Lane, “The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’,” Phil Trans R Soc B, 370:20140344, 2015.
  3. E.O. King et al., “Studies on a Group of Previously Unclassified Bacteria Associated with Meningitis in Infants,” Am J Clin Pathol, 31(3):1, 241–47, 1959.
  4. K.K. Kim et al., “Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov.,” Int J Syst Evol Microbiol, 55(Pt 3):1287-93, 2005. 
  5. E.J. Dziuban et al., “Elizabethkingia in Children: A Comprehensive Review of Symptomatic Cases Reported From 1944 to 2017,” Clin Infect Dis, 67(1):144–9, 2018.
  6. J.T. Kirby et al., “Antimicrobial susceptibility and epidemiology of a worldwide collection of Chryseobacterium spp: report from the SENTRY Antimicrobial Surveillance Program (1997-2001),” J Clin Microbiol, 42(1):445-8, 2004. 
  7. M.N Balm et al., “Bad design, bad practices, bad bugs: frustrations in controlling an outbreak of Elizabethkingia meningoseptica in intensive care units,” J Hosp Infect, 85(2):134-40, 2013.
  8. S.N. Hoque et al., “Chryseobacterium (Flavobacterium) meningosepticum outbreak associated with colonization of water taps in a neonatal intensive care unit,” J Hosp Infect, 47(3):188-92, 2001.
  9. Y.L. Lee et al., “A dominant strain of Elizabethkingia anophelis emerged from a hospital water system to cause a three-year outbreak in a respiratory care center,” J Hosp Infect, 108:43-51, 2021.
  10. J.F. Bernardet et al., “The genera Chryseobacterium and Elizabethkingia," The Prokaryotes, M. Dworkin et al., eds., New York: Springer, 7:638-76, 2006.
  11. S. Hem et al, “Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission,” Curr Res Microb Sci, 26;3:100083, 2021.
  12. D. Burnard et al., “Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveal nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines, and trimethoprim-sulfamethoxazole,” J Clin Microbiol, 24;58(9):e00730-20, 2020.
  13. J. Davies et al., “Origins and evolution of antibiotic resistance,” Microbiol Mol Biol Rev, 74(3):417-33, 2010.