Identification of resistance and virulence factors in an epidemic Enterobacter hormaechei outbreak strain

Abstract

Bacterial strains differ in their ability to cause hospital outbreaks. Using comparative genomic hybridization, Enterobacter cloacae complex isolates were studied to identify genetic markers specific for Enterobacter cloacae complex outbreak strains. No outbreak-specific genes were found that were common in all investigated outbreak strains. Therefore, the aim of our study was to identify specific genetic markers for an Enterobacter hormaechei outbreak strain (EHOS) that caused a nationwide outbreak in The Netherlands. Most EHOS isolates carried a large conjugative plasmid (pQC) containing genes encoding heavy-metal resistance, mobile elements, pili-associated proteins and exported proteins as well as multiple-resistance genes. Furthermore, the chromosomally encoded high-pathogenicity island (HPI) was highly associated with the EHOS strain. In addition, other DNA fragments were identified that were associated with virulence: three DNA fragments known to be located on a virulence plasmid (pLVPK), as well as phage-and plasmid-related sequences. Also, four DNA fragments encoding putative pili with the most homology to pili of Salmonella enterica were associated with the EHOS. Finally, four DNA fragments encoding putative outer-membrane proteins were negatively associated with the EHOS. In conclusion, resistance and putative virulence genes were identified in the EHOS that may have contributed to increased epidemicity. The high number of genes detected in the EHOS that were related to transferable elements reflects the genomic plasticity of the E. cloacae complex and may explain the emergence of the EHOS in the hospital environment. INTRODUCTIONIn the pre-antibiotic era, isolates of the Enterobacter cloacae complex were not detected in surveys of nosocomial bacteria; they were first described as nosocomial pathogens in the 1970s (Sanders & Sanders, 1997). In 2001, Enterobacter spp. caused 7 % of nosocomial infections in intensive care units in the USA (Jones, 2003;Streit et al., 2004). Therefore, the E. cloacae complex can be considered as an emerging pathogen, of which Enterobacter hormaechei is the most commonly isolated nosocomial pathogen (Delmas et al., 2006;Paauw et al., 2008). A nationwide outbreak occurred with an E. hormaechei outbreak strain (EHOS) in The Netherlands . This strain disseminated throughout hospitals despite adequate implementation of internationally accepted infection-prevention guidelines and caused invasive infections in more than 100 patients (Paauw et al., 2007). Previous studies showed that most EHOS isolates carried the conjugative plasmid pQC, with several complex integrons containing aadB, bla CTX-M-9 and qnrA1 genes that encoded resistance to aminoglycosides and thirdgeneration cephalosporins, and reduced susceptibility to fluoroquinolones, respectively . However, it was also shown that other Enterobacteriaceae including other E. cloacae complex isolates with the pQC did not become highly epidemic like the EHOS (Paauw et al., 2007). Furthermore, of aminoglycoside-susceptible E. cloa...

Subtractive Hybridization Yields a Silver Resistance Determinant Unique to Nosocomial Pathogens in the Enterobacter cloacae Complex

“…An extrachromosomal origin was also suggested by Davis et al (8), who isolated two highly silver-resistant E. cloacae strains from teeth. This is also in line with the recent findings by Paauw et al (36), who identified a large plasmid, pQC, in an E. hormaechei strain that caused a hos- pital-wide outbreak in the Netherlands. This plasmid also belonged to the IncHI-2 group and showed the highest similarity to plasmid R478.…”

“…Members of this complex have been isolated from plants (38), insects (11), and open bodies of water (19), reflecting the wide distribution of this intestinal commensal in the environment. However, the increasing number of epidemiological studies highlighting severe cases of bacteremia caused by the E. cloacae complex reflects the particular importance of these microorganisms as clinical pathogens (4,21,36). Especially at (neonatal) intensive care (2,10,12,24,25,29,34,44,45) and burn units (31, 32), (sub)species of the E. cloacae complex often emerge as the cause of severe outbreaks, with several patients being infected by the same clone.…”

Specific Distribution within the Enterobacter cloacae Complex of Strains Isolated from Infected Orthopedic Implants

“…In this regard, hsp60 gene sequencing-based identification appeared to be both discriminatory and easily implementable, whereas other sequence-based molecular methods for the identification of Enterobacter were not as accurate. The absence of a consensus for the analysis of an rpoB DNA fragment (1 kb or 500 bp) has led to contradictory results, particularly for the genetic discrimination of isolates within hsp60 gene sequencing-based clusters III, VI, and VIII (8,21), as well as to the confusing use of the species name E. hormaechei for strains that do not belong to hsp60 gene sequencing-based clusters VI to VIII (20). Similarly, sequence analysis of the gene encoding the DNA gyrase subunit B (gyrB) led to the hypothesis that most clinical isolates assigned to the E. cloacae complex by phenotypic semiautomated methods would belong to the E. hormaechei species (6).…”

“…dissolvens (cluster XII) (9). Although the name E. hormaechei was sometimes used as a generic name for strains belonging to different hsp60 gene sequencing-based clusters (20), clusters VI, VII, and VIII together formally constitute the E. hormaechei species, which has three subspecies: E. hormaechei subsp. oharae (cluster VI), E. hormaechei subsp.…”

Cultivation of Enterobacter Hormaechei from Human Atherosclerotic Tissue

“…isolates are associated with pneumonia and sepsis and carry multiple antibiotic resistance and virulence genes 22) . Enterobacteriaceae have been implicated in bloodstream infections, in addition to peritonitis, cholangitis, and other intraabdominal infections 23) .…”