It is more convenient and practical to collect rectal swabs than stool specimens to study carriage of colon pathogens. In this study, we examined the ability to use rectal swabs rather than stool specimens to quantify Klebsiella pneumoniae carbapenemase (KPC)-producing carbapenem-resistant Enterobacteriaceae (CRE). We used a quantitative real-time PCR (qPCR) assay to determine the concentration of the bla KPC gene relative to the concentration of 16S rRNA genes and a quantitative culture-based method to quantify CRE relative to total aerobic bacteria. Our results demonstrated that rectal swabs are suitable for quantifying the concentration of KPC-producing CRE and that qPCR showed higher correlation between rectal swabs and stool specimens than the culture-based method.
Klebsiella pneumoniae carbapenemase (KPC)-type enzymes are -lactamases, capable of hydrolyzing all known -lactam antibiotics (1). The spread of the bla KPC genes has led to the emergence of carbapenem-resistant Enterobacteriaceae (CRE), mostly K. pneumoniae, as important nosocomial pathogens causing outbreaks in various parts of the world (2). Infections by these pathogens are severe, with an estimated case fatality rate of 35%, and thus considered a clinical and public health threat (3).Active surveillance of high-risk patients has been advocated in areas where CRE are endemic or where there are ongoing outbreaks (4). Although stool samples are considered the "gold standard" specimen for studying gut bacteria in general (5, 6) and for detecting CRE in particular (7), hospital epidemiologists, clinical microbiologists, and researchers frequently use rectal swabs due to practical considerations, such as ease of collection, handling, and processing (8-11). Several studies compared the qualitative sensitivity of rectal swabs versus stool specimens for the recovery and detection of various pathogens, such as Campylobacter fetus subsp. jejuni, vancomycin-resistant Enterococcus faecium (VRE), and Lawsonia intracellularis, by culturing and/or molecular quantification methods (12)(13)(14). These studies had mixed results, with some studies reporting comparable test sensitivity with either sample type (12-14) and others reporting significantly lower sensitivity with rectal swabs (15, 16). For quantitative testing, rectal swabs are believed to be inadequate due to the high variation in the quantity of fecal material on each swab and the difficulties in determining this quantity (17)(18)(19)(20).As the human colon flora is a diverse ecosystem, which is populated by both anaerobic and aerobic microorganisms (21), development of quantitative methods, such as culture-and quantitative real-time PCR (qPCR)-based techniques is important for studying the bacterial composition of this complex ecosystem. The use of these methods can lead to a thorough knowledge about gastrointestinal community composition, the effects of antibiotics, and their roles in health and disease.Here, we suggest an alternate methodology for quantifying pathogens that would overcome the pr...