Practical Guidance for Clinical Microbiology Laboratories: Mycobacteria.

Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.

Mycobacterial Taxonomy.

This article summarizes the most recent (since 2012) taxonomic changes in the genus Mycobacterium Only those mycobacteria that have been isolated from human specimens are included in this summary.

Defining the Clinical Significance of Alloscardovia omnincolens in the Urinary Tract.

The clinical significance of Alloscardovia omnincolens in the urinary tract has not been thoroughly evaluated. In this study, 15 patients with A. omnincolens present in their urine cultures were identified. A. omnincolens is only rarely associated with urinary tract symptoms and in some patients may play a commensal role.

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.

Executive summary: 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.

Achromobacter species endocarditis: A case report and literature review.

Endocarditis due to Achromobacter species is a rare, yet serious, endovascular infection. Achromobacter species infective endocarditis is associated with underlying immunodeficiencies or prosthetic heart valves and devices. A case of prosthetic pulmonary valve endocarditis secondary to Achromobacter xylosoxidans subspecies denitrificans is described in the present report. This life-threatening infection was successfully treated with combined valve replacement and prolonged antibiotic therapy. A Medline/PubMed literature review of Achromobacter endocarditis was also performed. Achromobacter species are an uncommon, yet important, cause of nosocomial endocarditis. Given the significant associated morbidity and mortality, along with a high degree of intrinsic antibiotic resistance, Achromobacter species infective endocarditis remains a clinical treatment challenge.

Clinical significance of Staphylococcus lugdunensis isolated from routine cultures.

Over 1 year, 42 Staphylococcus lugdunensis isolates, identified by phenotypic and genotypic testing, were recovered from clinical specimens. Thirty-six (86%) were clinically significant pathogens, mostly from healthy outpatients; 16 (44%) of 36 were isolated in pure culture; and 30 (83%) of 36 were from skin and soft-tissue infections.

Unusual form of oxacillin resistance in methicillin-resistant Staphylococcus aureus clinical strains.

The mechanisms by which there is differential expression of resistance to oxacillin within the populations of a single strain remains to be fully understood. The purpose of this study was to evaluate and characterize 25 GOA48 methicillin-resistant Staphylococcus aureus (MRSA) oxacillin-susceptible mecA-positive strains, which were obtained by screening consecutively 832 S. aureus isolates. These 25 isolates (3% of the total strains investigated) were uniformly detected by extending the 24-h oxacillin agar screen plate to 48 h (namely, GOA48-MRSA). Twenty-two isolates tested positive for penicillin-binding protein 2a, whereas the remaining 3 isolates were inconsistently mecA positive. Inconsistent detection of mecA by polymerase chain reaction (PCR) in the mentioned 3 isolates was investigated by colony hybridization using a mecA probe (> or = 80% of colonies hybridized poorly to the probe). A PCR product that amplified the empty SCCmec insertion site (attB), present only if the element was excised, resulted positive in all 3 isolates before oxacillin exposure, whereas integrated elements were positive only for oxacillin-grown isolates. The remaining 22 strains did not reveal excision demonstrating stable mecA. We concluded that resistance to beta-lactams in MRSA-positive mecA strains susceptible to oxacillin is associated to an extreme heterogeneous expression of resistance combined in some cases to oxacillin SCCmec excision.

A university hospital's 10-year experience with tuberculin testing: value of the 2-step tuberculin skin test.

BACKGROUND: The usefulness of the 2-step tuberculin skin test as a tool for monitoring tuberculosis exposure among health care workers is controversial. OBJECTIVES: We aimed to determine the cost-effectiveness and influence of initiation of a preemployment, 2-step tuberculin skin-testing program on the annual tuberculin skin conversion rate among a university hospital's health care workers. METHODS: The tuberculin skin test conversion rates among the recipients of 31,729 tuberculin skin tests over 10 years were retrospectively analyzed. Data from the first 6 years of this study were generated when a single preemployment tuberculin skin test was utilized. Data from the last 4 years were gathered after the advent of a preemployment 2-step program. A cost analysis of the 2-step tuberculin skin test process was performed to determine the annual cost of this program. RESULTS: Relative risk of a conversion was 8.43 times less during the 2-step period when compared with the years when a single tuberculin skin test was given at the start of employment (P < .001). A cost analysis showed that the annual added cost of the 2-step program was approximately 9,565 US dollars. CONCLUSION: A greater than 8-fold reduction in the number of annual tuberculin skin test conversion coincided with, but could not be attributed solely to, the initiation of a 2-step program in our hospital. The Infection Control Committee concluded that the 2-step testing program is essential to achieve the hospital's goal of a 0% annual tuberculin skin test conversion rate and that the annual cost is justified.

Time to blood culture positivity as a predictor of clinical outcome of Staphylococcus aureus bloodstream infection.

Few studies have assessed the time to blood culture positivity as a predictor of clinical outcome in bloodstream infections (BSIs). The purpose of this study was to evaluate the time to positivity (TTP) of blood cultures in patients with Staphylococcus aureus BSIs and to assess its impact on clinical outcome. We performed a historical cohort study with 91 adult patients with S. aureus BSIs. TTP was defined as the time between the start of incubation and the time that the automated alert signal indicating growth in the culture bottle sounded. Patients with BSIs and TTPs of culture of 12 h (n = 47) were compared. Septic shock occurred in 13.6% of patients with TTPs of 12 h (P = 0.51). A central venous catheter source was more common with a BSI TTP of /=3, the failure of at least one organ (respiratory, cardiovascular, renal, hematologic, or hepatic), infection with methicillin-resistant S. aureus, and TTPs of /=20 at BSI onset, inadequate empirical antibiotic therapy, hospital-acquired bacteremia, and endocarditis were not associated with mortality. Multivariate analysis revealed that independent predictors of hospital mortality were a Charlson score of >/=3 (odds ratio [OR], 14.4; 95% confidence interval [CI], 2.24 to 92.55), infection with methicillin-resistant S. aureus (OR, 9.3; 95% CI, 1.45 to 59.23), and TTPs of

Comparison of a new lateral-flow chromatographic membrane immunoassay to viral culture for rapid detection and differentiation of influenza A and B viruses in respiratory specimens.

The performance of a new rapid lateral-flow chromatographic membrane immunoassay test kit for detection of influenza virus was evaluated and compared to that of viral culture in respiratory secretions collected from 400 adults and children seen at three large university hospitals during the recent 2003 influenza season. The rapid test provided results in 15 min, with excellent overall performance statistics (sensitivity, 94.4%; specificity, 100%; positive predictive value, 100%; negative predictive value, 97.5%). Both influenza A and B type viruses were reliably detected, with no significant difference in performance statistics noted by influenza virus type or by the center performing the test.

Introducing a molecular test into the clinical microbiology laboratory: development, evaluation, and validation.

CONTEXT: In the mid-1980s, the polymerase chain reaction methodology for the amplification of minute amounts of target DNA was successfully developed and then introduced into clinical use; such technology has led to a revolution in diagnostic testing. Despite enormous advances in the detection of infectious agents by amplification methods, there are also limitations that must be addressed. OBJECTIVE: To highlight the pertinent steps and issues associated with the introduction of an amplification assay into a clinical microbiology laboratory as well as the subsequent ongoing activities following its introduction into routine laboratory use. DATA SOURCES: Data were obtained from literature searches from 1990 through September 2002 using the subject headings "polymerase chain reaction," "molecular assays," and "amplification" as well as publications of the National Committee for Clinical Laboratory Standards. DATA EXTRACTION AND SYNTHESIS: Using the findings obtained from these studies and publications, the process of introducing a molecular assay into the clinical microbiology laboratory was broken down into 4 major components: (1) initial phase of assay development, (2) polymerase chain reaction assay verification in which analytic sensitivity and specificity is determined, (3) assay validation to determine clinical sensitivity and specificity, and (4) interpretation of results and ongoing, required activities. The approach, as well as the advantages and limitations involved in each step of the process, was highlighted and discussed within the context of the published literature. CONCLUSIONS: The application of molecular testing methods in the clinical laboratory has dramatically improved our ability to diagnose infectious diseases. However, the clinical usefulness of molecular testing will only be maximized to its fullest benefit by appropriate and careful studies correlating clinical findings with assay results.