A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus

Abstract

An oligonucleotide probe microarray for investigation of the evolution of epidemic Staphylococcus aureus strains has been constructed. The array comprises 383 probes based on virulence-associated genes present in four key strains. Twelve strains including seven for which the complete chromosomal nucleotide sequence was available were tested on the array. Twenty-six per cent of the probes were able to differentiate between strains to give a minimum of two gene differences between pairs. A gene difference distance tree based on the array data had approximately the same topology as one prepared using concatenated MLST sequences. Differences in the topologies of these trees were found to indicate that large-scale recombination events had occurred during the evolution of the species. One such occurrence appears to have been a key event in the genesis of the EMRSA-15 clone (ST22) that currently represents the most prevalent methicillin-resistant S. aureus (MRSA) in the UK. INTRODUCTIONStaphylococcus aureus is an important human pathogen responsible for bacterial infections seen both in the community and in hospitals. Over the last decades the emergence of multi-drug resistant strains has greatly increased the economic and health importance of staphylococcal infection (Chambers, 2001;Stefani & Varaldo, 2003;Wenzel, 1982). S. aureus is a highly adapted and extremely successful colonizer of the human nasopharynx, other mucosal surfaces and skin (Kluytmans et al., 1997;Williams, 1963). Colonization is generally asymptomatic but occasionally results in disease with a wide variety of signs and symptoms. These range from mild self-limiting infections of the skin to fulminating septicaemia (Lowy, 1998;Projan & Novick, 1997). Staphylococcal disease appears to result from an imbalance between the bacterium and the immune system and is associated with tissue invasion or unchecked growth. S. aureus is able to maintain its colonist status by producing a variety of proteins that interact with host-cell components (Baba et al., 2002;Kuroda et al., 2001). These proteins are described as virulence-associated and have functions such as extracellular matrix binding and host cell lysis. Expression of the S. aureus virulence-associated proteins is very carefully controlled by means of a network of regulatory genes including the agr and sar operons (Chien & Cheung, 1998;Sabersheikh & Saunders, 2004). Strain variation in these regulatory mechanisms may be an important factor influencing the switch from colonization to disease. Such variations may also contribute towards the success of the species by helping to minimize the emergence of immunity to essential S. aureus-specific antigens.Genome sequencing has shown that the species maintains a large number of virulence-associated genes but that not all are carried by each individual strain (Baba et al., 2002;Holden et al., 2004;Kuroda et al., 2001). Pairwise comparisons show as much as 20 % variation in the gene inventory of different S. aureus with most of the difference contributed by virule...

The agr Radiation: an Early Event in the Evolution of Staphylococci

“…Several studies have examined the presence of both mobile and stable genetic determinants of the staphylococcal virulon (2,33,34,41,50). From this analysis, along with the seven publicly available genomes and recent DNA microarray comparisons (3,8,45,52), it is apparent that most elements are not exclusively associated with one agr type-though there may be considerable variations in the frequency of carriage of these elements. This is clearly evident in a set of 198 isolates previously characterized by Jarraud et al using amplified fragment length polymorphism, where it was shown that these elements are found in multiple agr groups at different frequencies-and that some combinations of these elements are frequently found together or apart (20).…”

DNA Microarray Profiling of a Diverse Collection of Nosocomial Methicillin-Resistant Staphylococcus aureus Isolates Assigns the Majority to the Correct Sequence Type and Staphylococcal Cassette Chromosome mec (SCC mec ) Type and Results in the Subsequent Identification and Characterization of Novel SCC mec -SCC M1 Composite Islands

“…While these DNA microarray systems provide a large amount of information about the isolate's genome, their use is restricted mainly to specialized research laboratories, as data analysis is complicated (29,50,52,56). In contrast, several groups have recently developed more focused DNA microarrays (12,35,36,43), with one system in particular offering simultaneous highthroughput genotyping of S. aureus isolates by assigning isolates to an MLST clonal complex (CC) or ST and to an SCCmec type and detection of species-specific markers, accessory gene regulator (agr) alleles, capsule types, MSCRAMMs, and a range of clinically relevant antimicrobial resistance and virulence-associated genes (34)(35)(36).…”

Design, Validation, and Application of a Seven-Strain Staphylococcus aureus PCR Product Microarray for Comparative Genomics

“…Indeed, Fitzgerald et al used a microarray composed of approximately 92% of the S. aureus strain COL genome (2,817 open reading frames [ORFs]) to screen 36 clinical S. aureus isolates and found that 22% of the COL genome was missing in at least 1 of the test isolates (13). S. aureus microarrays with a subset of known virulence genes have also been described (27,37) and highlight substantial variation between isolates. For other bacteria, including Bordetella spp.…”