A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)a

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

Distinguishing Characteristics between Pandemic 2009–2010 Influenza A (H1N1) and Other Viruses in Patients Hospitalized with Respiratory Illness

BACKGROUND: Differences in clinical presentation and outcomes among patients infected with pandemic 2009 influenza A H1N1 (pH1N1) compared to other respiratory viruses have not been fully elucidated. METHODOLOGY/PRINCIPAL FINDINGS: A retrospective study was performed of all hospitalized patients at the peak of the pH1N1 season in whom a single respiratory virus was detected by a molecular assay targeting 18 viruses/subtypes (RVP, Luminex xTAG). Fifty-two percent (615/1192) of patients from October, 2009 to December, 2009 had a single respiratory virus (291 pH1N1; 207 rhinovirus; 45 RSV A/B; 37 parainfluenza; 27 adenovirus; 6 coronavirus; and 2 metapneumovirus). No seasonal influenza A or B was detected. Individuals with pH1N1, compared to other viruses, were more likely to present with fever (92% & 70%), cough (92% & 86%), sore throat (32% & 16%), nausea (31% & 8%), vomiting (39% & 30%), abdominal pain (14% & 7%), and a lower white blood count (8,500/L & 13,600/L, all p-values<0.05). In patients with cough and gastrointestinal complaints, the presence of subjective fever/chills independently raised the likelihood of pH1N1 (OR 10). Fifty-five percent (336/615) of our cohort received antibacterial agents, 63% (385/615) received oseltamivir, and 41% (252/615) received steroids. The mortality rate of our cohort was 1% (7/615) and was higher in individuals with pH1N1 compared to other viruses (2.1% & 0.3%, respectively; p = 0.04). CONCLUSIONS/SIGNIFICANCE: During the peak pandemic 2009-2010 influenza season in Rhode Island, nearly half of patients admitted with influenza-like symptoms had respiratory viruses other than influenza A. A high proportion of patients were treated with antibiotics and pH1N1 infection had higher mortality compared to other respiratory viruses

Validation of the Automated Reading and Incubation System with Sensititre Plates for Antimicrobial Susceptibility Testing

The present study compared the antimicrobial susceptibility testing (AST) results generated by the Automated Incubation and Reading System (ARIS) with custom Sensititre plates (TREK Diagnostic Systems, Cleveland, Ohio) and MicroScan PC10 GP and NUMIC10 GN plates interpreted with the WalkAway-96 system (Dade Behring, West Sacramento, Calif.) for gram-positive (GP) and gram-negative (GN) organisms as part of an in-house validation. A total of 326 isolates (3,689 antimicrobial agent-organism combinations) were evaluated. Sensititre plates were inoculated according to the instructions of the manufacturer with a suspension adjusted to a 0.5 McFarland standard, while the Prompt Inoculation System was used for the MicroScan plates. ARIS and the WalkAway system were used for automated reading of the Sensititre and MicroScan plates, respectively, at 18 to 24 h. The results were analyzed for essential (±1 twofold dilution) and categorical (sensitive, intermediate, or resistant) agreements. Plates that resulted in ARIS interpretations with major (falsely resistant) or very major (falsely susceptible) errors compared to the results obtained with the WalkAway system were read manually to corroborate instrument readings. Isolates for which very major or major errors were obtained and for which the results were not resolved by manual reading were retested in parallel. Isolates for which very major or major errors were obtained and for which the results were not resolved upon repeat testing were tested by the National Committee for Clinical Laboratory Standards M7-A5 frozen reference microdilution method. Essential agreement was 95.8% for 246 GN isolates. The following categorical error rates were obtained for the GN isolates: 1.3% minor errors, 0% major errors, and 0.4% very major errors. For 95 GP isolates, there was 93.5% essential agreement. Categorical error rates for GP isolates were 0.9% minor errors, 0.6% major errors, and 0.4% very major errors. ARIS-Sensititre is a diagnostic system feasible for use for automated AST in a clinical laboratory