Phenotypic and Molecular Characteristics of Carbapenem-Resistant Enterobacteriaceae in a Health Care System in Los Angeles, California, from 2011 to 2013

Abstract

c Carbapenem-resistant Enterobacteriaceae (CRE) are a concern for health care in the United States but remain relatively uncommon in California. We describe the phenotype, clonality, and carbapenemase-encoding genes present in CRE isolated from patients at a Californian tertiary health care system. CRE for this study were identified by evaluating the antibiograms of Enterobacteriaceae isolated in the UCLA Health System from 2011 to 2013 for isolates that were not susceptible to meropenem and/or imipenem. The identification of these isolates was subsequently confirmed by matrix-associated laser desorption ionizationtime of flight, and broth microdilution tests were repeated to confirm the CRE phenotype. Real-time PCR for bla KPC , bla SME , bla IMP , bla NDM-1 , bla VIM , and bla OXA-48 was performed. Clonality was assessed by repetitive sequence-based PCR (repPCR) and multilocus sequence typing (MLST). Of 15,839 nonduplicate clinical Enterobacteriaceae isolates, 115 (0.73%) met the study definition for CRE. This number increased from 0.5% (44/8165) in the first half of the study to 0.9% (71/7674) in the second (P ‫؍‬ 0.004). The most common CRE species were Klebsiella pneumoniae, Enterobacter aerogenes, and Escherichia coli. A carbapenemase-encoding gene was found in 81.7% (94/115) of CRE and included bla KPC (78.3%), bla NDM-1 (0.9%), and bla SME (2.6%). The majority of bla KPC genes were in K. pneumoniae isolates, which fell into 14 clonal groups on typing. bla KPC was identified in more than one species of CRE cultured from the same patient in four cases. Three bla SME -carrying Serratia marcescens isolates and one bla NDM-1 carrying Providencia rettgeri isolate were detected. CRE are increasing in California, and carbapenemases, particularly KPC, are a common mechanism for carbapenem resistance in this region.

Performance of Vitek 2 for Antimicrobial Susceptibility Testing of Enterobacteriaceae with Vitek 2 (2009 FDA) and 2014 CLSI Breakpoints

“…Three of these harbored the bla KPC gene, 1 harbored the bla SME gene, and 6 were PCR negative for the six carbapenemase genes tested (Table 1). These isolates were also negative for phenotypic carbapenemase production by the CarbaNP test, which was performed in another study (7). Using the Vitek 2 breakpoints, 3 MEs and 9 mEs were found ( Table 4).…”

“…The isolates were selected to represent a variety of resistance phenotypes that cover a wide range of MICs potentially encountered in the laboratory. Twenty-five carbapenem-resistant Enterobacteriaceae (CRE) that were previously assayed for the carbapenemase genes bla KPC , bla NDM-1 , bla VIM , bla SME , bla IMP , and bla OXA-48 were included (7). For the purpose of this study, CRE were defined as isolates with a meropenem MIC of Ͼ1 g/ml by BMD.…”

Use of Ancillary Carbapenemase Tests To Improve Specificity of Phenotypic Definitions for Carbapenemase-Producing Enterobacteriaceae

“…For instance, the Xpert Carba-R does not query for bla SME , a carbapenemase gene found sporadically on the chromosome of isolates of Serratia marcescens, including in our own patient isolates (19). While considered less of an epidemiological concern because the gene is not harbored on a plasmid, outbreaks of isolates that harbor this gene have been documented (24,25).…”

“…Some have concerns that this definition may overestimate CP-CRE because isolates resistant to ertapenem but not imipenem, meropenem, or doripenem often result from the presence of extended-spectrum beta-lactamases (ESBLs) or AmpC enzymes, which have some hydrolyzing activity against ertapenem, usually in combination with permeability defects. Similarly, some isolates without carbapenemases are resistant to imipenem, meropenem, and/or doripenem due to changes in porin proteins, often in conjunction with low-level AmpC or ESBL activities, albeit such isolates are less common (19). For instance, one study using the CDC definition found that 55% of isolates labeled as CP-CRE did not harbor carbapenemase genes (18).…”

Outbreak of carbapenem-resistant Providencia rettgeri in a tertiary hospital

“…[3] Immunocompromised or debilitated patients are highly susceptible to hospital-acquired infections -either after colonisation with environmental strains or following invasive procedures, such as catheterisation, bronchoscopy, colposcopy or surgical biopsies. [4] P. rettgeri is commonly found to cause traveller's diarrhoea and has also been isolated from more severe human infections such as meningitis. [3,5,6] Among the Providencia species, P. stuartii and P. rettgeri are the most common causes of infections, especially UTIs in hospitalised patients, although other infections can occur.…”