The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp

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1. 

   Version published to 10.7554/elife.83107 on eLife

   Jul 6, 2023
2. 

   eLife

   Mar 27, 2023

   Author Response

   Reviewer #1 (Public Review):

   Rosas et al studied the mechanism/s that enabled carbapenems resistance of a Klebsiella isolate, FK688, which was isolated from an infected patient. To identify and characterize this mechanism, they used a combination of multiple methods. They started by sequencing the genome of this strain by a combination of short and long read sequencing. They show that Klebsiella FK688 does not encode a carbapenemase, and thus looked for other mechanisms that can explain this resistance. They discover that both DHA-1 (located on the mega-plasmid) and an inactivation of the porin OmpK36, are required for carbapenem resistance in this strain. By using experimental evolution, it was shown that resistance is lost rapidly in the absence of antibiotics selection, by a deletion in pNAR1 that removed blaDHA-1. …

   Author Response

   Reviewer #1 (Public Review):

   Rosas et al studied the mechanism/s that enabled carbapenems resistance of a Klebsiella isolate, FK688, which was isolated from an infected patient. To identify and characterize this mechanism, they used a combination of multiple methods. They started by sequencing the genome of this strain by a combination of short and long read sequencing. They show that Klebsiella FK688 does not encode a carbapenemase, and thus looked for other mechanisms that can explain this resistance. They discover that both DHA-1 (located on the mega-plasmid) and an inactivation of the porin OmpK36, are required for carbapenem resistance in this strain. By using experimental evolution, it was shown that resistance is lost rapidly in the absence of antibiotics selection, by a deletion in pNAR1 that removed blaDHA-1. Moreover, their results suggested that it is likely that exposure to other antibiotics selected for the acquisition of the mega-plasmid that carries DHA-1, which then enabled this strain to gain resistance to carbapenemase by a single deletion.

   The major strength of this study is the use of various approaches, to tackle an important and interesting problem.

   The conclusions of this paper are mostly well supported by data, but one aspect is not clear enough. The description of the evolutionary experiment is not clear. I could not find a clear description of the names of the evolved populations. However, the authors describe strains B3 and A2, but their source is not clear. The legends of the relevant figure (Figure 5) are confusing. For example, the text describing panel B is not related to the image shown in this panel. Moreover, it is shown in panel C (and written in the main text) that the OmpK36+ evolved populations had only translucent colonies, so what is the source of B3(o)?

   We appreciate the point and in response have added a panel to Figure 5 (in the revised paper this is now Fig. 5A) to illustrate the evolutionary experiment and specify that there are two lineages (A and B) with 20 replicates each that, after 200 generations of evolution, give rise to populations of which A2 and B3 are the exemplars characterized.

   We have corrected the legends in Figure 5.

   We now explain (sentence starting on Line 197) that the B3 (o) is the single isolate of an opaque colony from lineage B3, it is the only colony that we identified from out of 595 colonies observed in the B3 population. B3(o) was sequenced and analysed as a comparator and has some value in that regard, despite being an anomaly.

   Reviewer #2 (Public Review):

   The authors sequenced a clinical pathogen, Klebsiella FK688, and definitively establish the genetic basis of the carbapenem-resistance phenotype of this strain. They also show that the causal mutations confer reduced fitness under laboratory conditions, and that carbapenem sensitivity readily re-evolves in the lab due to the fitness costs associated with the resistance mutations in the clinical isolate. They also establish that subinhibitory concentrations of ceftazidime select for the otherwise deleterious blaDHA-1 gene. Based on this finding the authors speculate that prior beta-lactam selection faced by the ancestors of Klebsiella FK688 potentiated the evolution of the carbapenem-resistance phenotype of this strain. If this hypothesis is true, then prior history of beta-lactam exposure may generally potentiate the evolution of carbapenem resistance.

   Strengths:

   From a technical perspective, the findings in this paper are solid. In addition, the authors establish a simple genetic basis for carbapenem resistance in a clinical strain, which is a valuable and non-trivial finding (i.e. they show that the CRE phenotype in this strain is not an omnigenic trait distributed over hundreds of loci).

   Weaknesses:

   The main weakness of this paper is that the authors draw overly broad conclusions of a conceptual nature from narrow experimental findings. This could be addressed by drawing more modest and narrow implications from the findings.

   1. The title of this paper is "Treatment history shapes the evolution of complex carbapenem-resistant phenotypes in Klebsiella spp." But they provide no data on the treatment history of the patient from whom this strain was isolated from. Therefore, the authors have no evidence to support their central claim. Indeed, it is completely possible that this strain never faced beta-lactam selection in the past, or that the patient's hypothetical history of betalactamase was irrelevant for the evolution of FK688. First, it is completely possible that this is a hospital-acquired infection, such that the history of this strain is due to selection in other contexts in the hospital that have little to do with the patient's treatment history. Second, it is completely possible that this strain (the chromosome anyway) has no prior history of beta-lactamase selection, and that it acquired the megaplasmid containing blaDHA-1 via conjugation from some other strain. In this second hypothetical scenario, it is possible that the fitness cost of the blaDHA-1 gene is not particularly high in a different source strain, but that it has some cost in the FK688 strain that it was isolated from. And of course, fitness costs in the human host could be very different than fitness costs in the laboratory, where strains are evolving under strong selection for fast growth. And given the benefit of resistance, it's clear that this strain clearly has a strong fitness advantage over faster-growing sensitive strains in the context of the source patient under antibiotic treatment.

   My general point here is that the broad claims made about patient history or prior history shaping the evolution of this strain are largely indefensible because there is no data here to make solid inferences about how prior history shaped the evolution of this strain.

   We appreciate the point and have changed our title and scaled back the strength of our conclusions regarding patient treatment history.

   1. Historical contingency. The authors claim that their work shows how historical contingency shapes the evolution of resistance. One problem with this claim is that it is trivial- this is only a significant claim if the reader believes that prior history is not important in the evolution of antibiotic resistance, which is a straw-man null hypothesis, to mix a couple metaphors. To be more concrete, clearly strain background (prior history) matters-eliminating the plasmid with the resistance gene eliminates resistance. But that is not particularly surprising, given the past 50 years of evolutionary microbiology literature on plasmids and resistance. By contrast to this work, the major contribution of papers that examine the role of historical contingency in evolution (i.e. various Lenski papers) is that those works quantitatively measure the role of history in comparison to other factors (chance, adaptation). Since this work is a deep dive into a single clinical isolate, the data presented here do not and cannot shed light on the role of historical contingency in the emergence of this strain. The authors' claims about the prior history that led to the CRE phenotype are reasonable- but are fundamentally speculative. I have nothing against speculation, as long as it is clear what claims are speculative, and what are concrete implications. But the authors frame these speculative claims as concrete implications of their findings.

   This is a fair point. We have reframed the study to not focus on historical contingency.

   As the reviewer points out, any discussion about historical contingency in the context of evolution is trivial in one sense. One of the reasons that the studies of Lenski and Blount provide new insights into the role of historical evolution because they knew the history of their populations (at, least for the number of generations since the LTEE began), and had a high degree of control and understanding of the growth conditions where the trait evolved. As such, they could go back to time points before the trait evolved, and then repeat the evolution experiment many times, in the exact same environment where the trait originally evolved, and then count how often they observed the evolution of that trait.

   Here we study a clinical isolate, and have less understanding of the evolutionary history of our strain. While we cannot re-evolve carbapenem resistant in the exact same environment experienced by the FK688 strain, we did test the capacity for the wild type, and two possible intermediate genotypes genotypes, to evolve carbapenem resistance in growth media with carbapenem.

   Altogether- we have comprehensive evidence for the genetic cause of carbapenem resistance: the BLA1 plasmid + OmpK36. We showed, by experiment, that it is much more likely for carbapenem resistance to evolve in a FK688 strain that carries the BLA1 plasmid, than in an FK688 strain that did not carry the plasmid even if it had acquired the OmpK36 mutation. We think this not trivial because a significant proportion of all of the carbapenem resistant Klebsiella that have been isolated are non-carbapenemase CRE. Our reconstruction provides a plausible explanation for why non-carbapenemase CRE evolve – because they are evolving from strains that have already been treated with a non-carbapenem beta-lactam drug and have thereby selected for the presence of a beta-lactamase (that is not a carbapenemase).

   So, while we have scaled back the strength of our claims, we do think that our results can provide some insight into how the evolutionary history of a pathogen can shape the molecular path to antibiotic resistance.

   1. The authors claim that "[This work] suggests that the strategic combinations of antibiotics could direct the evolution of low-fitness, drug-resistant genotypes". I suppose this is true, but I also think this is a stretch of an implication given these findings. To be blunt, while I suppose it's better to have costly resistance variants that re-evolve sensitivity than to have low-cost high-resistance strains circulating, I think the patient's family would probably disagree that the evolution of a low-fitness drug-resistant genotype was good or strategic in the clinical context, even if better from a public health perspective. Low-fitness drug-resistant strains are just as lethal under clinical antibiotic concentrations!

   Thank you for the comment, we see how this sentence could be seen as too strong a conclusion and have rewritten the last sentence of the DISCUSSION (line 351):

   “These results show how an individual’s treatment history might shape the evolution of AMR, and should be taken into consideration in order to explain the evolution of non-carbapenemase CRE”

   The authors do show the plausibility of their hypothesis/model that prior beta-lactam selection is sufficient to potentiate the evolution of carbapenem-resistance (by the additional ompK loss-of-function mutation). I think those findings are very nice. But the authors undermine their results by extrapolating too far from their data. Hence, I think narrowing the scope of the implications would improve this paper.

   In addition to narrowing the scope of the implications as written, I also would like to add that there may be other ways of framing this paper (other than historical contingency) that may make the significance of this work more apparent to a broader audience. This may be worth considering during the revision process.

   We have taken these suggestions on board and have re-framed the final sentences of the ABSTRACT, INTRODUCTION and DISCUSSION accordingly. Specifically, we have removed reference to historical contingency and instead have reframed our experiments as providing a genetic and evolutionary explanation for an interesting and concerning cause of antibiotic resistance – non-carbapenemase CRE.

   Read the original source
3. 

   eLife

   Mar 24, 2023

   eLife assessment

   The study integrates experiments and data of various kinds to address the important biomedical problem of carbapenems resistance in Klebsiella. The authors present compelling evidence for loci that are sufficient for carbapenem resistance in this strain, with further evidence of their fitness cost. This study will be of interest to those across multiple audiences, including the microbial evolution community, and those interested in the biomedical problem of antibiotic resistance.

   Read the original source
4. 

   eLife

   Mar 24, 2023

   Reviewer #1 (Public Review):

   Rosas et al studied the mechanism/s that enabled carbapenems resistance of a Klebsiella isolate, FK688, which was isolated from an infected patient. To identify and characterize this mechanism, they used a combination of multiple methods. They started by sequencing the genome of this strain by a combination of short and long read sequencing. They show that Klebsiella FK688 does not encode a carbapenemase, and thus looked for other mechanisms that can explain this resistance. They discover that both DHA-1 (located on the mega-plasmid) and an inactivation of the porin OmpK36, are required for carbapenem resistance in this strain. By using experimental evolution, it was shown that resistance is lost rapidly in the absence of antibiotics selection, by a deletion in pNAR1 that removed blaDHA-1. Moreover, their …

   Reviewer #1 (Public Review):

   Rosas et al studied the mechanism/s that enabled carbapenems resistance of a Klebsiella isolate, FK688, which was isolated from an infected patient. To identify and characterize this mechanism, they used a combination of multiple methods. They started by sequencing the genome of this strain by a combination of short and long read sequencing. They show that Klebsiella FK688 does not encode a carbapenemase, and thus looked for other mechanisms that can explain this resistance. They discover that both DHA-1 (located on the mega-plasmid) and an inactivation of the porin OmpK36, are required for carbapenem resistance in this strain. By using experimental evolution, it was shown that resistance is lost rapidly in the absence of antibiotics selection, by a deletion in pNAR1 that removed blaDHA-1. Moreover, their results suggested that it is likely that exposure to other antibiotics selected for the acquisition of the mega-plasmid that carries DHA-1, which then enabled this strain to gain resistance to carbapenemase by a single deletion.

   The major strength of this study is the use of various approaches, to tackle an important and interesting problem.

   The conclusions of this paper are mostly well supported by data, but one aspect is not clear enough. The description of the evolutionary experiment is not clear. I could not find a clear description of the names of the evolved populations. However, the authors describe strains B3 and A2, but their source is not clear. The legends of the relevant figure (Figure 5) are confusing. For example, the text describing panel B is not related to the image shown in this panel. Moreover, it is shown in panel C (and written in the main text) that the OmpK36+ evolved populations had only translucent colonies, so what is the source of B3(o)?

   Read the original source
5. 

   eLife

   Mar 24, 2023

   Reviewer #2 (Public Review):

   The authors sequenced a clinical pathogen, Klebsiella FK688, and definitively establish the genetic basis of the carbapenem-resistance phenotype of this strain. They also show that the causal mutations confer reduced fitness under laboratory conditions, and that carbapenem sensitivity readily re-evolves in the lab due to the fitness costs associated with the resistance mutations in the clinical isolate. They also establish that subinhibitory concentrations of ceftazidime select for the otherwise deleterious blaDHA-1 gene. Based on this finding the authors speculate that prior beta-lactam selection faced by the ancestors of Klebsiella FK688 potentiated the evolution of the carbapenem-resistance phenotype of this strain. If this hypothesis is true, then prior history of beta-lactam exposure may generally …

   Reviewer #2 (Public Review):

   The authors sequenced a clinical pathogen, Klebsiella FK688, and definitively establish the genetic basis of the carbapenem-resistance phenotype of this strain. They also show that the causal mutations confer reduced fitness under laboratory conditions, and that carbapenem sensitivity readily re-evolves in the lab due to the fitness costs associated with the resistance mutations in the clinical isolate. They also establish that subinhibitory concentrations of ceftazidime select for the otherwise deleterious blaDHA-1 gene. Based on this finding the authors speculate that prior beta-lactam selection faced by the ancestors of Klebsiella FK688 potentiated the evolution of the carbapenem-resistance phenotype of this strain. If this hypothesis is true, then prior history of beta-lactam exposure may generally potentiate the evolution of carbapenem resistance.

   Strengths:

   From a technical perspective, the findings in this paper are solid. In addition, the authors establish a simple genetic basis for carbapenem resistance in a clinical strain, which is a valuable and non-trivial finding (i.e. they show that the CRE phenotype in this strain is not an omnigenic trait distributed over hundreds of loci).

   Weaknesses:

   The main weakness of this paper is that the authors draw overly broad conclusions of a conceptual nature from narrow experimental findings. This could be addressed by drawing more modest and narrow implications from the findings.

   1. The title of this paper is "Treatment history shapes the evolution of complex carbapenem-resistant phenotypes in Klebsiella spp." But they provide no data on the treatment history of the patient from whom this strain was isolated from. Therefore, the authors have no evidence to support their central claim. Indeed, it is completely possible that this strain never faced beta-lactam selection in the past, or that the patient's hypothetical history of betalactamase was irrelevant for the evolution of FK688. First, it is completely possible that this is a hospital-acquired infection, such that the history of this strain is due to selection in other contexts in the hospital that have little to do with the patient's treatment history. Second, it is completely possible that this strain (the chromosome anyway) has no prior history of beta-lactamase selection, and that it acquired the megaplasmid containing blaDHA-1 via conjugation from some other strain. In this second hypothetical scenario, it is possible that the fitness cost of the blaDHA-1 gene is not particularly high in a different source strain, but that it has some cost in the FK688 strain that it was isolated from. And of course, fitness costs in the human host could be very different than fitness costs in the laboratory, where strains are evolving under strong selection for fast growth. And given the benefit of resistance, it's clear that this strain clearly has a strong fitness advantage over faster-growing sensitive strains in the context of the source patient under antibiotic treatment.

   My general point here is that the broad claims made about patient history or prior history shaping the evolution of this strain are largely indefensible because there is no data here to make solid inferences about *how* prior history shaped the evolution of this strain.

   1. Historical contingency. The authors claim that their work shows how historical contingency shapes the evolution of resistance. One problem with this claim is that it is trivial- this is only a significant claim if the reader believes that prior history is not important in the evolution of antibiotic resistance, which is a straw-man null hypothesis, to mix a couple metaphors. To be more concrete, clearly strain background (prior history) matters-eliminating the plasmid with the resistance gene eliminates resistance. But that is not particularly surprising, given the past 50 years of evolutionary microbiology literature on plasmids and resistance. By contrast to this work, the major contribution of papers that examine the role of historical contingency in evolution (i.e. various Lenski papers) is that those works *quantitatively* measure the role of history in comparison to other factors (chance, adaptation). Since this work is a deep dive into a single clinical isolate, the data presented here do not and cannot shed light on the role of historical contingency in the emergence of this strain. The authors' claims about the prior history that led to the CRE phenotype are reasonable- but are fundamentally speculative. I have nothing against speculation, as long as it is clear what claims are speculative, and what are concrete implications. But the authors frame these speculative claims as concrete implications of their findings.

   2. The authors claim that "[This work] suggests that the strategic combinations of antibiotics could direct the evolution of low-fitness, drug-resistant genotypes". I suppose this is true, but I also think this is a stretch of an implication given these findings. To be blunt, while I suppose it's better to have costly resistance variants that re-evolve sensitivity than to have low-cost high-resistance strains circulating, I think the patient's family would probably disagree that the evolution of a low-fitness drug-resistant genotype was good or strategic in the clinical context, even if better from a public health perspective. Low-fitness drug-resistant strains are just as lethal under clinical antibiotic concentrations!

   The authors do show the plausibility of their hypothesis/model that prior beta-lactam selection is sufficient to potentiate the evolution of carbapenem-resistance (by the additional ompK loss-of-function mutation). I think those findings are very nice. But the authors undermine their results by extrapolating too far from their data. Hence, I think narrowing the scope of the implications would improve this paper.

   In addition to narrowing the scope of the implications as written, I also would like to add that there may be other ways of framing this paper (other than historical contingency) that may make the significance of this work more apparent to a broader audience. This may be worth considering during the revision process.

   Read the original source
6. 

   Version published to 10.1101/2022.08.30.505938v1 on bioRxiv

   Aug 30, 2022