Abstract
Small‐colony variants (SCVs) are commonly observed in evolution experiments and clinical isolates, being associated with antibiotic resistance and persistent infections. We recently observed the repeated emergence of Escherichia coli SCVs during adaptation to the interaction with macrophages. To identify the genetic targets underlying the emergence of this clinically relevant morphotype, we performed whole‐genome sequencing of independently evolved SCV clones. We uncovered novel mutational targets, not previously associated with SCVs (e.g. cydA, pepP) and observed widespread functional parallelism. All SCV clones had mutations in genes related to the electron‐transport chain. As SCVs emerged during adaptation to macrophages, and often show increased antibiotic resistance, we measured SCV fitness inside macrophages and measured their antibiotic resistance profiles. SCVs had a fitness advantage inside macrophages and showed increased aminoglycoside resistance in vitro, but had collateral sensitivity to other antibiotics (e.g. tetracycline). Importantly, we observed similar results in vivo. SCVs had a fitness advantage upon colonization of the mouse gut, which could be tuned by antibiotic treatment: kanamycin (aminoglycoside) increased SCV fitness, but tetracycline strongly reduced it. Our results highlight the power of using experimental evolution as the basis for identifying the causes and consequences of adaptation during host‐microbe interactions.
Highlights
Variation in colony morphology is often observed during in vitro bacterial adaptation (Miskinyte et al, 2013; Rainey & Travisano, 1998; Rozen & Lenski, 2000; Traverse, Mayo-Smith, Poltak, & Cooper, 2013)
Our results show that SCVs can have an intracellular advantage inside MΦs, and that this morphotype has a pattern of antagonistic pleiotropy for antibiotic resistance in vitro: SCVs were more resistant to aminoglycosides but more sensitive to tetracycline, nalidixic acid and ciprofloxacin, as well as cefotaxime
Small-colony variants are an important bacterial morphotype often associated with chronic infections and antibiotic resistance
Summary
Variation in colony morphology is often observed during in vitro bacterial adaptation (Miskinyte et al, 2013; Rainey & Travisano, 1998; Rozen & Lenski, 2000; Traverse, Mayo-Smith, Poltak, & Cooper, 2013). SCVs emerge in response to multiple selective pressures, including adaptation to: single (Rozen & Lenski, 2000) or multiple carbon sources (Friesen, Saxer, Travisano, & Doebeli, 2004), biofilm conditions (Penterman et al, 2014; Traverse et al, 2013), the mouse gut (Lee et al, 2010), antibiotics (Musher, Baughn, Templeton, & Minuth, 1977; Yegian, Gallo, & Toll, 1959), antimicrobial peptides (Pranting & Andersson, 2010) or the intracellular environment of nonprofessional phagocytes Our results show that E. coli SCVs that emerge in the presence of MΦs are caused by mutations in a common pathway and have important pleiotropic consequences for host-microbe interactions
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