The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including Tickborne Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.

Background Travelers' diarrhea (TD) is a significant problem for travelers. TD is treatable once it occurs, but few options for prevention exist. Probiotics have been studied for prevention or treatment of TD; however, very few combination probiotics have been studied. Therefore, the purpose of this study was to determine if prophylactic use of an oral synbiotic could reduce the risk of acquiring TD and reduce antibiotic use if TD occurred. Methods Healthy subjects traveling to an area of the world with an increased risk of TD were eligible. All subjects received pre-travel counseling and were provided antibiotics and antidiarrheals (loperamide) for use only if TD developed. The subjects were blinded and randomized to take two capsules of placebo or oral synbiotic (a combination of two probiotics and a prebiotic) called Agri-King Synbiotic (AKSB) beginning 3days prior to departure, daily while traveling, and for 7days after return. All subjects kept symptom and medication diaries and submitted a stool sample for pathogen carriage within 7days of return. The study was powered to detect a 50% reduction in the incidence of TD. Results Of the 196 adults (over 18years of age) enrolled in the study, 54.3% were female and 80.9% were younger than 60years. The study randomized 94 people to the AKSB arm and 102 to placebo. The incidence of TD was 54.5% in the overall group with 55.3% in the AKSB arm and 53.9% in the placebo (p=0.8864). Among the subjects who experienced diarrhea (n=107) there was no significant difference in the proportion of subjects that took antibiotics versus those that did not take antibiotics (35% vs 29%, p=0.68). AKSB was safe with no difference in toxicity between the two arms. Conclusions The prophylactic oral synbiotic was safe but did not reduce the risk of developing TD among travelers, nor did it decrease the duration of TD or the use of antibiotics when TD occurred.

Objective. We compared laboratory developed real-time PCR assays for detection of Mycoplasma hominis and for detection and differentiation of Ureaplasma urealyticum and parvum to culture using genitourinary specimens submitted for M. hominis and Ureaplasma culture. Methods. 283 genitourinary specimens received in the clinical bacteriology laboratory for M. hominis and Ureaplasma species culture were evaluated. Nucleic acids were extracted using the Total Nucleic Acid Kit on the MagNA Pure 2.0. 5 μL of the extracts were combined with 15 μL of each of the two master mixes. Assays were performed on the LightCycler 480 II system. Culture was performed using routine methods. Results.  M. hominis PCR detected 38/42 M. hominis culture-positive specimens, as well as 2 that were culture negative (sensitivity, 90.5%; specificity, 99.2%). Ureaplasma PCR detected 139/144 Ureaplasma culture-positive specimens, as well as 9 that were culture negative (sensitivity, 96.5%; specificity, 93.6%). Of the specimens that tested positive for Ureaplasma species, U. urealyticum alone was detected in 33, U. parvum alone in 109, and both in 6. Conclusion. The described PCR assays are rapid alternatives to culture for detection of M. hominis and Ureaplasma species, and, unlike culture, the Ureaplasma assay easily distinguishes U. urealyticum from parvum.

This chapter covers protozoa, helminths, and arthropods. 1. Protozoa are single-celled, microscopic eukaryotic organisms like amebae and Giardia. Helminths are parasitic worms including nematodes (roundworms), cestodes (tapeworms), and trematodes (flukes). Arthropods, like ticks and mites, are generally considered parasites. Specific organisms reviewed include Giardia lamblia, Cyclospora cayetanensis, Blastocystis hominis, Entamoeba histolytica, Plasmodium falciparum, Babesia microti, and Toxoplasma gondii. Diagnosis and treatment of different types of infection are also reviewed.

Goals: To evaluate the yield of repeat stool polymerase chain reaction (PCR) testing in patients with suspected Clostridium difficile infection (CDI). Background: CDI is a major challenge in health care due to its frequent occurrence and high associated costs. Enzyme immunoassay and PCR are commonly performed diagnostic tests for CDI. Methods: Our microbiology laboratory database was queried from January 1, 2008 to June 30, 2010 for all patients who underwent PCR stool testing for suspected CDI. Data collected included age, sex, number of stool tests performed within a 14-day period after the first test, and location of patient (inpatient vs. outpatient). Analyses were performed using JMP version 9.0.1. Results: PCR testing was performed in 15,515 patients. The median age was 58.3 years (range, 10 d to 104.3 y) and 46.2% of patients were women. Repeat testing was infrequent; 87.3% of patients had testing performed only once in a 14-day period. Increased age, male sex, and inpatient location were predictors of repeat testing. The median time between an initial test and the first repeat test was 5 days. After an initial negative test, the percentage of patients having a subsequent positive test was low (2.7% in 7 d and 3.2% in 14 d). The percentage of repeat tests that was positive within 7 days (2.9%) was lower than the percentage that was positive from day 8 to day 14 (4.8%, P=0.05). Conclusions: Repeat testing for C. difficile has a low yield, and patients with an initial negative test should not routinely be retested.

This article covers the laboratory diagnosis of infections that occur predominantly in the tropics. The discussion includes diagnosis of blood and tissue parasites, intestinal parasites, and tropical infections caused by fungi, bacteria, and mycobacteria. The laboratory performance of techniques for the identification of intestinal parasites and special requirements for the collection of specimens for virology testing are also discussed. Images demonstrating the characteristic features of selected tropical parasites and fungi are included for reference.

ABSTRACT Actinobaculum species are anaerobic Gram-positive rods that have previously been associated with urinary tract infection (UTI) in the elderly. We report 12 patients with Actinobaculum bacteremia. Only 40% of blood cultures were clinically considered significant by the treating physicians, but most patients were treated for UTI, suggesting a possible urinary source of bacteremia. Clinicians should be aware of the pathogenic potential of Actinobaculum spp.

Robinsoniella peoriensis is a recently described anaerobic, spore-forming, Gram-positive bacillus originally recovered from swine manure. We report four human cases in which R. peoriensis was isolated from clinical samples.

Purpose:Clostridium difficile infection (CDI) is a major health-care challenge with an increasing incidence and severity, worsening outcomes, and high associated costs. There have been considerable recent advances in infection control and treatment of CDI, and newer stool tests are available with increased sensitivity and specificity. It has been a common practice to repeat a stool test for CDI if the initial test is negative. In the current study, we evaluated our practice regarding the yield of repeat polymerase chain reaction (PCR) testing in patients with suspected CDI. Methods: The microbiology laboratory database at Mayo Clinic, Rochester, MN was queried for all patients who underwent PCR stool testing for suspected CDI from June 1, 2007 to May 31, 2010. Data collected included age, gender, number and timing of stool tests and location of patient (inpatient versus outpatient). Descriptive and multivariate regression analyses were done with JMP version 9.0.1. Results: PCR testing was performed in 18,629 patients in the three-year period. The median age of patients was 58.3 years (range 10 days to 104.3 years) and 46.2% were females. Repetitive testing was infrequent; 86.3% of patients had testing done only once in a 14-day period. On multivariate analysis, increased age, male sex, and in-patient location were predictors of repetitive testing. Patients with an initial negative test did not have an increased likelihood of repeat testing than those with an initial positive test (11.4% versus 10.2%, p=0.06). The mean time between an index test and a first repeat test was 3.5 days in a 7-day time period and 5.3 days in a 14-day time period. After an initial negative test, the chance of having a subsequent positive test was unlikely (2.4% in 7 days and 3.2% in 14 days). Conclusion: The yield of repeat stool testing for CDI by PCR is low, and patients with an initial negative stool test should not be re-tested for that bout of diarrhea unless clinical suspicion for CDI remains high.

ABSTRACT We compared two commercial PCR assays, the Prodesse ProGastro CD assay and the BD GeneOhm Cdiff assay, with a laboratory-developed Clostridium difficile toxin PCR assay with previously established performance characteristics. Results of all methods were in agreement for 333 (96%) of 346 stool specimens. No significant difference in performance among the assays was found (P values, >0.05).

disease. The correlation of antibody titer changes (over time) with the final clinical outcome found for 11 echinococcosis-patients seen at Mayo from 1976 to 1990 confirms the value of the CF method in evalu-ating the success of surgery and the follow-up of treatment with antihelminthic drugs.

Background. The rationale and lessons learned through the evolution of the National Survey for the Susceptibility of Bacteroides fragilis Group from its initiation in 1981 through 2007 are reviewed here. The survey was conceived in 1980 to track emerging antimicrobial resistance in Bacteroides species.Methods. Data from the last 11 years of the survey (1997-2007), including 6574 isolates from 13 medical centers, were analyzed for in vitro antimicrobial resistance to both frequently used and newly developed anti-anaerobic agents. The minimum inhibitory concentrations of the antibiotics were determined using agar dilution in accordance with Clinical and Laboratory Standards Institute recommendations.Results. The analyses revealed that the carbapenems (imipenem, meropenem, ertapenem, and doripenem) and piperacillin-tazobactam were the most active agents against these pathogens, with resistance rates of 0.9%-2.3%. In the most recent 3 years of the survey (2005-2007), resistance to some agents was shown to depend on the species, such as ampicillin-sulbactam against Bacteroides distasonis (20.6%) and tigecycline against Bacteroides uniformis and Bacteroides eggerthii (similar to 7%). Very high resistance rates (>50%) were noted for moxifloxacin and trovafloxacin, particularly against Bacteroides vulgatus. During that period of study, non-B. fragilis Bacteroides species had >40% resistance to clindamycin. Metronidazole-resistant Bacteroides strains were also first reported during that period.Conclusions. In summary, resistance to antibiotics was greater among non-B. fragilis Bacteroides species than among B. fragilis and was especially greater among species with a low frequency of isolation, such as Bacteroides caccae and B. uniformis. The emergence of resistance among the non-B. fragilis Bacteroides species underscores the need for speciation of B. fragilis group isolates and for clinicians to be aware of associations between species and drug resistance.

Background and Aim A recent study using lactulose hydrogen-breath testing suggests that small intestine bacterial overgrowth (SIBO) is a common cause of nonresponsive celiac disease (CD). The prevalence of SIBO in CD diagnosed by quantitative culture of intestinal aspirate is unknown. The aim of this study is to evaluate the prevalence and significance of SIBO in CD based on the results of quantitative culture of intestinal aspirate. Methods We studied patients with CD in whom culture of intestinal aspirate was evaluated for the presence of anaerobes and aerobes. Bacterial overgrowth was diagnosed if culture demonstrated >105 colony forming units/mL. The causes of nonresponsive CD were investigated. Results We included 149 biopsy-confirmed CD patients. The intestinal aspirate was collected in 79 (53%) patients with nonresponsive CD, 47 (32%) as initial work-up for malabsorption, and in 23 (15%) asymptomatic treated CD. SIBO was diagnosed in 14 (9.3%). Nine (11%) with nonresponsive CD, 5 (11%) at initial work-up for malabsorption, and 0 in asymptomatic treated CD. Patients with a positive culture had evidence of worse malabsorption. A coexistent disorder was found in 67% of patients with both nonresponsive CD and bacterial overgrowth. Conclusions The prevalence of SIBO diagnosed by quantitative culture of intestinal aspirate was 9.3% in patients with CD. Patients with symptomatic treated or untreated CD were affected. SIBO may coexist with other disorders associated with nonresponsive CD.

We previously developed a real-time polymerase chain reaction (PCR) assay for detection of the four Plasmodium species that infect humans. Recent studies have shown that natural transmission of the simian parasite Plasmodium knowlesi to humans occurs frequently in Southeast Asia. We have expanded our PCR assay to include detection of P. knowlesi.

Background. Approximately 4 million US travelers to developing countries are ill enough to seek health care, with 1500 malaria cases reported in the United States annually. The diagnosis of malaria is frequently delayed because of the time required to prepare malaria blood films and lack of technical expertise. An easy, reliable rapid diagnostic test (RDT) with high sensitivity and negative predictive value (NPV), particularly for Plasmodium falciparum, would be clinically useful. The objective of this study was to determine the diagnostic performance of a RDT approved by the US Food and Drug Administration compared with traditional thick and thin blood smears for malaria diagnosis.Methods. This prospective study tested 852 consecutive blood samples that underwent thick and thin smears and blinded malaria RDTs at 3 hospital laboratories during 2003-2006. Polymerase chain reaction verified positive test results and discordant results.Results. Malaria was noted in 95 (11%) of the 852 samples. The RDT had superior performance than the standard Giemsa thick blood smear (P = .003) The RDT's sensitivity for all malaria was 97% ( 92 of 95 samples), compared with 85% (81 of 95) for the blood smear, and the RDT had a superior NPV of 99.6%, compared with 98.2% for the blood smear (P = .001). The P. falciparum performance was excellent, with 100% rapid test sensitivity, compared with only 88% (65 of 74) by blood smear (P = .003).Conclusions. This operational study demonstrates that the US Food and Drug Administration-approved RDT for malaria is superior to a single set of blood smears performed under routine US clinical laboratory conditions. The most valuable clinical role of the RDT is in the rapid diagnosis or the exclusion of P. falciparum malaria, which is particularly useful in outpatient settings when evaluating febrile travelers.