Rectal Swabs Are Suitable for Quantifying the Carriage Load of KPC-Producing Carbapenem-Resistant Enterobacteriaceae

Abstract

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...

Relative Fecal Abundance of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains and Their Occurrence in Urinary Tract Infections in Women

“…This may be relevant for clinical research because swabs are easier to obtain, on demand, than fecal samples. Recently, rectal swabs were similarly used to assess the RA of KPC-producing K. pneumoniae rather than DC (28).…”

Evaluation of the Xpert Carba-R (Cepheid) Assay Using Contrived Bronchial Specimens from Patients with Suspicion of Ventilator-Associated Pneumonia for the Detection of Prevalent Carbapenemases

“…In addition, the possible presence in patient samples of DNA in dead cells could interfere with test results if performed before DNA degradation takes place. Nevertheless, in one study that evaluated whether rectal swabs are suitable for quantifying the carriage load of KPC-producing carbapenem-resistant Enterobacteriaceae , the authors found that the results of a quantitative PCR assay performed directly on rectal swabs showed a higher correlation than the quantitative culture-based method with the reference method (concentration of 16S rRNA genes), and that this quantitative PCR was suitable for quantifying these microorganisms [30]. In summary, our results need to be considered with caution and the strong correlation detected between Ct values and bacterial counts would need to be confirmed in clinical samples.…”

Phenotypic Screening for Asymptomatic Rectal Colonization by Resistant Enterobacteriaceae and Nasal MRSA Colonization in Critical Care Patients

“…After incubating overnight at 37°C, the presence of an expanded growth inhibition zone between the two discs or increase of zone size of more than 7 mm in the disc potentiated with the EDTA (chelating agents) was interpreted as positive for MBL production All the tests and their interpretations were according to the CLSIGuidelines (M100 27 th edition 2017) and well-accepted methods by various authorities. (Lerner A et al, 2013, Rodrigues C et al, 2004, Neena V et al, 2012& Shamsadh Begum et al, 2015] the identity of the isolates and resistance pattern was further confirmed by using Vitek 2 GN ID (BioMerieux, France) with appropriate quality control. (Table 2).…”

“…Rectal samples were collected in the sterile swab by inserting the swab 1cm into the rectum while rotating the swab. Rectal swabs are an appropriate alternative to stool specimens (Lerner et al, 2013). Total transit time to the laboratory was within 30 minutes.…”

“…Total transit time to the laboratory was within 30 minutes. Samples were processed as per the standard protocols (Deepa et al, 2014& Lerner et al, 2013 All isolates of staphylococcus aureus from nasal swabs were processed routinely and tested with 30 mg cefoxitin discs (Hi-Media) on Mueller-Hinton agar plates by disk diffusion methodfor MRSA detection ((M100 27 th edition 2017),16,17).…”