Genetic analysis of multiple vancomycin-resistant Enterococcus isolates obtained serially from two long-term-care patients

Genomic Analysis of Vancomycin-Resistant Staphylococcus aureus Isolates from the 3rd Case Identified in the United States Reveals Chromosomal Integration of the vanA Locus

Vancomycin-resistant Staphylococcus aureus (VRSA) is a human pathogen of significant public health concern. Although the genome sequences of individual VRSA isolates have been published over the years, very little is known about the genetic changes of VRSA within a patient over time. A total of 11 VRSA, 3 vancomycin-resistant enterococci (VRE), and 4 methicillin-resistant S. aureus (MRSA) isolates, collected over a period of 4.5 months in 2004 from a patient in a long-term-care facility in New York State, were sequenced. A combination of long- and short-read sequencing technologies was used to obtain closed assemblies for chromosomes and plasmids. Our results indicate that a VRSA isolate emerged as the result of the transfer of a multidrug resistance plasmid from a coinfecting VRE to an MRSA isolate. The plasmid then integrated into the chromosome via homologous recombination mediated between two regions derived from remnants of transposon Tn5405. Once integrated, the plasmid underwent further reorganization in one isolate, while two others lost the staphylococcal cassette chromosome mec element (SCCmec) determinant that confers methicillin-resistance. The results presented here explain how a few recombination events can lead to multiple pulsed-field gel electrophoresis (PFGE) patterns that could be mistaken for vastly different strains. A vanA gene cluster that is located on a multidrug resistance plasmid that is integrated into the chromosome could result in the continuous propagation of resistance, even in the absence of selective pressure from antibiotics. The genome comparison presented here sheds light on the emergence and evolution of VRSA within a single patient that will enhance our understanding VRSA genetics. IMPORTANCE High-level vancomycin-resistant Staphylococcus aureus (VRSA) began to emerge in the United States in 2002 and has since then been reported worldwide. Our study reports the closed genome sequences of multiple VRSA isolates obtained in 2004 from a single patient in New York State. Our results show that the vanA resistance locus is located on a mosaic plasmid that confers resistance to multiple antibiotics. In some isolates, this plasmid integrated into the chromosome via homologous recombination between two ant(6)-sat4-aph(3') antibiotic resistance loci. This is, to our knowledge, the first report of a chromosomal vanA locus in VRSA; the effect of this integration event on MIC values and plasmid stability in the absence of antibiotic selection remains poorly understood. These findings highlight the need for a better understanding of the genetics of the vanA locus and plasmid maintenance in S. aureus to address the increase of vancomycin resistance in the health care setting.

Debate—Guidelines for GRE control—the case for optimism

Although at first sight the spread of glycopeptide-resistant enterococci (GREs) appears to be following the same unrelenting path as that of methicillin-resistant Staphylococcus aureus, closer inspection of the Literature indicates success of certain interventions, particularly the control of antibiotic usage. There are grounds for optimism that assiduous application of antibiotic control and other infection control measures may further reduce the prevalence of GREs.

Molecular characterization of vancomycin-resistant Enterococci repopulating the gastrointestinal tract following treatment with a novel glycolipodepsipeptide, ramoplanin

We characterized baseline and repopulating stool isolates recovered during a phase II trial of ramoplanin for the treatment of patients with stool carriage of vancomycin-resistant enterococci (VRE). Repopulation with a strain with a related genotype was found in 74, 60, and 53% of individuals in groups treated with placebo, 100 mg of ramoplanin, and 400 mg of ramoplanin, respectively. All ramoplanin-treated patients with a culture positive for VRE at day 7 had a relapse caused by a genotypically related isolate. In ramoplanin-treated patients, antibiotics with activities against anaerobic organisms were associated with positive cultures on day 7 (relative risk [RR] = 8.8; P = 0.004), and the avoidance of such antibiotics was significantly associated with culture negativity through day 21 (RR = 0.16; P = 0.02).

Clinical and molecular characterization of vancomycin-resistant Enterococcus faecium strains during establishment of endemicity

To characterize the molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREF) in Tennessee, VREF isolates that were recovered from patients during a 3-year period at a tertiary care center and throughout the state were typed by means of pulsed-field gel electrophoresis. Clinical characteristics and outcomes of patients colonized or infected with different strain types were also examined. A total of 34 different strain types were identified. A single VREF strain (type O) predominated (63 [61%] of 103 single-patient isolates (i.e., 1 isolate per patient) obtained from 7 different health care institutions). There were no significant differences between patients harboring type O strains and those harboring non-type O strains (P> or =.05). The rate of recovery of type O subtypes and strains other than type O increased over the 3-year study period. Establishment of VREF endemicity was initially characterized by clonal spread of type O strains. Subsequently, polyclonal dissemination may have been due to microevolutionary changes among type O strains.

Emergence of vancomycin-resistant enterococci at a university hospital in Taiwan: persistence of multiple species and multiple clones

OBJECTIVES

To describe the epidemiology of vancomycin-resistant enterococci (VRE) in a university hospital in Taipei, Taiwan.

DESIGN

Retrospective review over a 27-month period, from March 1996 to May 1998.

SETTING

A tertiary-care teaching hospital in Taiwan.

PARTICIPANTS

Patients with VRE isolated from any body site.

METHODS

Patients were identified through hospital microbiology and infection control records. Patient charts were reviewed for clinical and epidemiology data, including age, gender, previous hospital admissions, underlying diseases, types of infection, and recent antibiotic use. VRE isolates were characterized by their typical biochemical reactions, cellular fatty acid profiles, and the presence of van genes. Antibiotypes using the E-test and randomly amplified polymorphic DNA (RAPD) patterns of these isolates were used to determine the clonality.

RESULTS

Twenty-five isolates of VRE recovered from 12 patients were identified. One patient with a perianal abscess had 12 isolates of VRE (4 Enterococcus faecalis, 7 Enterococcus faecium, and 1 Enterococcus casseliflavus) recovered from perianal lesions. Among 3 patients who were hospitalized in the same room, 1 had a community-acquired cellulitis over the left leg caused by E. faecalis, and the other 2 patients both had anal colonization with 2 isolates of E. faecalis. The other 8 patients had 1 E. faecalis isolate each from various clinical specimens. All isolates possessed vanA resistance phenotype and vanA genes. Different antibiotypes and RAPD patterns of the isolates from different patients excluded the possibility of nosocomial spread at the hospital.

CONCLUSIONS

Multiple species of VRE (E. faecalis, E. faecium, and E. casseliflavus) and multiple clones of E. faecium could colonize or infect hospitalized patients. In addition, clones of VRE can persist long-term in patients' lower gastrointestinal tracts. These results extend our knowledge of the coexistence and the persistence of multiple species and multiple clones of VRE in hospitalized patients.

vanA and vanB incorporate into an endemic ampicillin-resistant vancomycin-sensitive Enterococcus faecium strain: effect on interpretation of clonality

Clonal spread and horizontal transfer in the spread of vancomycin resistance genes were investigated. Multiplex PCR, pulsed-field gel electrophoresis (PFGE), hybridization of enterococcal plasmids with the vanA and vanB probes, and sequencing of a fragment of vanB were used in the analysis. Before May 1996, 12 vancomycin-resistant Enterococcus faecium (VRE) isolates were found in Finland. Between May 1996 and October 1997, 156 VRE isolates were found in the Helsinki area. Between December 1997 and April 1998, fecal samples from 359 patients were cultured for VRE. One new case of colonization with VRE was found. During the outbreak period, 88% (137 of 155) of the VRE isolates belonged to two strains (VRE types I and II), as determined by PFGE. Each VRE type I isolate possessed vanB, and five isolates also had vanA. Of the 34 VRE type II isolates, 27 possessed vanA and 7 possessed vanB. Fifteen of 21 (71%) ampicillin-resistant, vancomycin-sensitive E. faecium (VSE) isolates found during and after the outbreak period in one ward were also of type II. Two VSE type II isolates were found in the hospital before the outbreak in 1995. By PFGE, the three groups (vanA, vanB, or no van gene) of type II shared the same band differences with the main type of VRE type II with vanA. None of the differences was specific to or determinative for any of the groups. Our material suggests that vanA and vanB incorporate into an endemic ampicillin-resistant VSE strain.

Vancomycin-resistant enterococci and use of avoparcin in animal feed: is there a link?

Australia is unique among Western countries in allowing animal use of this vancomycin-like antibiotic.

Issues in the management of resistant bacteria in long-term-care facilities

The prevalence of antibiotic-resistant bacteria in the long-term-care setting and the risk to nursing home residents is still unknown. Few studies have been done in community-based nursing homes, and most have focused on colonization rather than infection rates. Concerns about methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci have been expressed most often, while relatively scant attention has been paid to the problem of antibiotic resistance in gram-negative bacilli. Antibiotic resistance precautions need to be developed for nursing homes that are simple, effective, inexpensive, and recognize the unique rehabilitative and long-term custodial missions of chronic-care facilities.

Variation in structure and location of VanA glycopeptide resistance elements among enterococci from a single patient

Forty-six VanA glycopeptide-resistant enterococci (GRE) from a single patient were investigated for variation in structure and location of VanA resistance elements. Together with identification to species level and pulsed-field gel electrophoresis, these data divided the GRE into 10 groups and subgroups. Combining data in this manner appears helpful when investigating the epidemiology of GRE.