Tracy Kevin C, McKaig Jordan, Kinnear Clare, Millar Jess, King Aaron A, Read Andrew F, Woods Robert J
Department of Computational Medicine and Bioinformatics, University of Michigan.
Program in Biology, University of Michigan.
bioRxiv. 2024 Jun 3:2024.06.03.597162. doi: 10.1101/2024.06.03.597162.
Bacterial pathogens that are successful in hospital environments must survive times of intense antibiotic exposure and times of no antibiotic exposure. When these organisms are closely associated with human hosts, they must also transmit from one patient to another for the resistance to spread. The resulting evolutionary dynamics have, in some settings, led to rising levels of resistance in hospitals. Here, we focus on an important but understudied aspect of this dynamic: the loss of resistance when the resistant organisms evolve in environments where the antibiotic pressure is removed. Based on prior data, we hypothesize that resistance arising in the context of strong selection may carry a high cost and revert to sensitivity quickly once the selective pressure is removed. Conversely, resistant isolates that persist through times of no antibiotic pressure should carry a lower cost and revert less quickly. To test this hypothesis, we utilize a genetically diverse set of patient-derived, daptomycin-resistant isolates that include cases of both emergence of resistance within patients and putatively transmitted resistance. Both of these sets of strains have survived periods of antibiotic exposure, but only putatively transmitted resistant strains have survived extended periods without antibiotic exposure. These strains were then allowed to evolve in antibiotic free laboratory conditions. We find that putatively transmitted resistant strains tended to have lower level resistance but that evolution in antibiotic-free conditions resulted in minimal loss of resistance. In contrast, resistance that arose within patients was higher level but exhibited greater declines in resistance . Sequencing of the experimentally evolved isolates revealed that reversal of high level resistance resulted from evolutionary pathways that were frequently genetically associated with the unique resistance mutations of that strain. Thus, the rapid reversal of high-level resistance was associated with accessible evolutionary pathways where an increase in fitness is associated with decreased resistance. We describe how this rapid loss of resistance may limit the spread of resistance within the hospital and shape the diversity of resistance phenotypes across patients.
在医院环境中成功生存的细菌病原体，必须在抗生素大量使用期和无抗生素使用期都能存活下来。当这些微生物与人类宿主密切相关时，它们还必须从一个患者传播到另一个患者，以便耐药性得以传播。在某些情况下，由此产生的进化动态导致了医院中耐药水平的上升。在此，我们关注这一动态中一个重要但未被充分研究的方面：当耐药微生物在抗生素压力消除的环境中进化时，耐药性的丧失。基于先前的数据，我们假设在强选择背景下产生的耐药性可能代价高昂，一旦选择压力消除，就会迅速恢复为敏感性。相反，在无抗生素压力时期持续存在的耐药菌株应该代价较低，恢复敏感性的速度也较慢。为了验证这一假设，我们使用了一组遗传多样性的患者来源的达托霉素耐药菌株，其中包括患者体内出现耐药性的病例和推定的传播性耐药病例。这两组菌株都在抗生素暴露期存活了下来，但只有推定的传播性耐药菌株在无抗生素暴露的延长时期存活了下来。然后让这些菌株在无抗生素的实验室条件下进化。我们发现，推定的传播性耐药菌株往往耐药水平较低，但在无抗生素条件下的进化导致耐药性的损失最小。相比之下，患者体内产生的耐药性水平较高，但耐药性下降幅度更大。对实验进化菌株的测序表明，高水平耐药性的逆转是由与该菌株独特耐药突变经常发生遗传关联的进化途径导致的。因此，高水平耐药性的快速逆转与可及的进化途径相关，在这些途径中，适应性的增加与耐药性的降低相关。我们描述了这种耐药性的快速丧失如何可能限制医院内耐药性的传播，并塑造患者间耐药表型的多样性。
