Science1 publisher3 min readPublished
DTU researchers want susceptibility tests run at the pH and oxygen level of the infection site
A Trends in Microbiology opinion piece from DTU and Copenhagen argues that temperature, oxygen and pH decide whether a resistance gene makes a bacterium resistant, while the standard laboratory test holds all three fixed and returns one binary answer.
The Scientist · Science desk
What happened
- A new opinion piece in Trends in Microbiology, from researchers at the DTU National Food Institute and the University of Copenhagen, asks the field to set aside the idea that a bacterium is simply susceptible or resistant.
- Work at the DTU National Food Institute found that temperature, oxygen level and pH affect whether a bacterium carrying a resistance gene actually behaves in a resistant manner.
- Professor Frank Moller Aarestrup said the standard test measures at a fixed pH of 7.2, while the pH that decides whether a resistance gene functions could be 5 or 8.
- Standard susceptibility tests do not account for whether the bacterium sits in the oxygen-free gut or in the oxygenated bloodstream, or for whether the patient has a fever.
Compiled by The ScientistSomething wrong?How this is made
Why it matters
- constraint Comparable resistance figures across labs and countries exist because the measurement was standardized for decades, so every condition a lab starts varying adds biological realism and gives up that comparability.
- decision The figure for how many calls change under altered conditions is still unpublished, and the immediate work is method development and validation.
- capability Aarestrup puts a new option on the table: preferring antibiotics whose resistance only develops under conditions the human body never reaches, such as a particularly high temperature.
A resistance gene is a stretch of DNA. Whether it protects the cell depends on whether it is switched on, and on whether its protein works in the conditions around the cell. Temperature, oxygen level and pH all move that, according to the DTU National Food Institute work the opinion piece draws on [5][6]. "Resistance genes do not function in a vacuum," Professor Thomas Bjarnsholt of the University of Copenhagen said [10].
The fixed pH is the cleanest illustration. "Is it at a pH of 5 or 8, whereas we currently measure at a fixed pH of 7.2?" Professor Frank Moller Aarestrup said [8]. Because pH is a base-10 logarithm, 5 to 8 covers a thousandfold range in hydrogen ion concentration, and 7.2 is not near the middle of it; the midpoint of 5 and 8 is 6.5 [17]. A test run at 7.2 is about 158 times less acidic than pH 5 [18].
Trends in Microbiology published this as an opinion piece [4], and its target is a test that returns one of two answers [2]. The phys.org account does not name the species or the antibiotics, and it puts no number on the changes seen when conditions were varied [16]. The figure a standards committee would ask for first is still unpublished: the share of isolates whose susceptible or resistant call changes when the plate is made anoxic, acidic or warmer.
Both directions of error are in play. The authors say context-dependence may help explain why a course of antibiotics sometimes fails although the laboratory test says it should work, and sometimes works when the test says it should not [12].
The cost of testing more conditions falls on the laboratories. "This makes it more difficult to measure in the laboratory because we suddenly have to measure many different factors, whereas for many years we have gone to great lengths to standardize this type of measurement worldwide," Aarestrup said [11]. That standardized measurement is what the diagnosis of infections and the monitoring of resistance in humans, animals, food and the environment have been built on [3].
What the authors ask for is narrower than replacing the test. They want attention paid to which resistance genes an isolate carries and under what conditions that bacterium can cause disease [15]. Aarestrup also sketched a use for the finding: "the next step will be for us to choose to use antibiotics that only lead to the development of resistance if certain specific conditions are met. This could, for example, be at a particularly high temperature that does not occur in humans" [13]. Such a strategy needs the gating conditions mapped for each combination of gene, drug and organism, which is the same measurement problem Aarestrup called difficult.
What to watch
- The underlying DTU experiments in peer review: whether they name species, drugs, and measured shifts in minimum inhibitory concentration as pH, oxygen and temperature are varied.
- A published misclassification rate: the share of isolates whose susceptible or resistant call changes when standard conditions are altered.
- Whether the bodies that set standard test conditions respond to the opinion piece, and with what justification for the current fixed values.