Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation

Simon Heilbronner,Jeremy R. Brozyna,Timothy J. Foster,Andreas Peschel,David E. Heinrichs,Ian R. Monk,Eric P. Skaar,Danielle A. Garsin

doi:10.1371/journal.pgen.1006246

Abstract

Staphylococcus lugdunensis is a coagulase negative bacterial pathogen that is particularly associated with severe cases of infectious endocarditis. Unique amongst the coagulase-negative staphylococci, S. lugdunensis harbors an iron regulated surface determinant locus (isd). This locus facilitates the acquisition of heme as a source of nutrient iron during infection and allows iron limitation caused by “nutritional immunity” to be overcome. The isd locus is duplicated in S. lugdunensis HKU09-01 and we show here that the duplication is intrinsically unstable and undergoes accordion-like amplification and segregation leading to extensive isd copy number variation. Amplification of the locus increased the level of expression of Isd proteins and improved binding of hemoglobin to the cell surface of S. lugdunensis. Furthermore, Isd overexpression provided an advantage when strains were competing for a limited amount of hemoglobin as the sole source of iron. Gene duplications and amplifications (GDA) are events of fundamental importance for bacterial evolution and are frequently associated with antibiotic resistance in many species. As such, GDAs are regarded as evolutionary adaptions to novel selective pressures in hostile environments pointing towards a special importance of isd for S. lugdunensis. For the first time we show an example of a GDA that involves a virulence factor of a Gram-positive pathogen and link the GDA directly to a competitive advantage when the bacteria were struggling with selective pressures mimicking “nutritional immunity”.

Highlights

Bacterial pathogens possess a tremendous ability to adapt to changing environmental conditions
We describe the gene duplications and amplifications (GDA) of the isd locus in a clinical isolate of Staphylococcus lugdunensis a bacterial species frequently associated with infectious endocarditis
This deepens our understanding about adaption processes of pathogens and demonstrates how selective pressures drive the evolution of pathogens to become more successful

Summary

Introduction

Bacterial pathogens possess a tremendous ability to adapt to changing environmental conditions This is especially noticeable within the hospital setting where strong artificial selective pressures such as antibiotics and disinfectants drive the evolution of pathogens to develop resistance to these agents. Encountered mechanisms of acquired resistance to antibacterial drugs or increased virulence involve horizontal gene transfer or spontaneous mutations Another mechanism is to acquire gene duplications and amplifications (GDA), a mechanism based on the RecA-dependent accordion-like expansion and contraction of repetitive DNA sequences leading to gene dosage effects. GDAs should hold the potential to enhance bacterial virulence or survival within the host, for example by increasing virulence gene expression, a possibility that has been neglected in the research community This disregard might be due to the fact that GDAs are in general difficult to detect using generation sequencing because of the sequence identity of the individual repeats (up to 100% on DNA level). Very little is known about the natural occurrence of GDAs in the chromosomes of pathogens and about how they can promote virulence, immune evasion or growth under in vivo-like conditions

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