Among 63 patients enrolled in a prospective cohort study of gut colonization with fluoroquinolone-resistant Escherichia coli, the sensitivity of perirectal swab compared to stool sample was 90% (95% confidence interval [CI], 70 to 99%) and the specificity was 100% (95% CI, 91 to 100%). For rectal swab, the sensitivity was 90% (95% CI, 68 to 99%) and the specificity was 100% (95% CI, 91 to 100%).Resistance to many antimicrobial drugs has increased significantly among gram-negative bacilli (GNB) in recent years (5,6,9,10). GNB colonizing the gastrointestinal (GI) tract serve as both the reservoir for the person-to-person spread of resistant bacteria and the likely source for subsequent clinical infection in colonized individuals (4). Timely and accurate identification of patients with GI tract colonization with resistant GNB is thus critical.Currently, the culture of a stool sample is considered the "gold standard" for identification of GI tract colonization with resistant GNB. However, for both infection control programs and research studies, this approach is often infeasible or impractical. Thus, hospital epidemiologists and researchers often rely on perirectal or rectal swabs to identify patients colonized with resistant organisms (1,2,8). Despite the widespread use of these approaches, no data exist describing their sensitivity and specificity for detection of resistant GNB compared to the gold standard of stool sample.We conducted this study to determine the test characteristics (i.e., sensitivities and specificities) of perirectal and rectal swabs, and we used stool sample as the gold standard. This is the first study to investigate this issue for GNB. We specifically focused on detection of GI tract colonization with fluoroquinolone (FQ)-resistant Escherichia coli (FQREC).The study was performed at two hospitals within the University of Pennsylvania Health System: (i) The Hospital of the University of Pennsylvania, an academic tertiary care medical center with 625 patient beds; and (ii) Presbyterian Medical Center, a 344-bed urban community hospital. This study was reviewed and approved by the Committee on Studies Involving Human Beings of the University of Pennsylvania. We conducted a cross-sectional study of subjects enrolled in an ongoing prospective cohort study. This larger cohort study, in which all hospitalized patients were eligible to participate, investigated the incidence of new GI tract colonization with nosocomial FQREC. Over a 12-month period, all study subjects enrolled in the ongoing cohort study, for which a perirectal swab, rectal swab, and stool sample were collected within the same 24-hour period, were included in our study. A rectal swab was not required for neutropenic subjects; hence, neutropenic subjects were included if a perirectal swab and stool sample were collected within the same 24-hour period. Study subjects known to be FQREC colonized were oversampled to ensure that they accounted for at least 25% of the study cohort. The same research nurse collected perirectal and rectal s...