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Purpose With over 50 SARS-CoV-2 gene amplification assays that have been EUA cleared with minimal experimental validation performed, it is likely that not all of these assays are comparable in their ability to detect SARS-CoV-2 in clinical specimens. Thermo Fisher Scientific is a relatively new company in the molecular diagnostics field and the purpose of this study was to compare the performance of the Thermo Fisher TaqPath™ Combo Kit with an established test, the Cepheid Xpert® Xpress SARS-CoV-2 assay, for its ability to detect SARS-CoV-2 in nasopharyngeal specimens.Methods A total of 300 randomly selected nasopharyngeal specimens were evaluated and tested by the TaqPath and GeneXpert assays. Discordant test specimens were arbitrated by performing an alternative PCR assay and Sanger sequencing.Results The TaqPath assay had a 96.7% and 99.6% positive and negative agreement respectively when compared to the Xpert Xpress test. However, after test arbitration, the three discordant specimens were arbitrated in favor of the TaqPath assay producing a positive and negative percent agreement of 100% for the TaqPath Combo Kit while the Xpress SARS-CoV-2 assay had a positive and negative percent agreement of 98.3% and 99.2% respectively.Conclusions The TaqPath Combo Kit is a high complexity assay that compares favorably with the Xpert Xpress test and can be reliably used for the detection of SARS-CoV-2 in nasopharyngeal specimens.

The QIAstat-Dx Respiratory Panel (QIAstat-Dx RP) is a multiplex in vitro diagnostic test for the qualitative detection of 20 pathogens directly from nasopharyngeal swab (NPS) specimens. The assay is performed using a simple sample-to-answer platform with results available in approximately 69 min. The pathogens identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus A and B, influenza A, influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus/enterovirus, respiratory syncytial virus A and B, Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae., The QIAstat-Dx Respiratory Panel (QIAstat-Dx RP) is a multiplex in vitro diagnostic test for the qualitative detection of 20 pathogens directly from nasopharyngeal swab (NPS) specimens. The assay is performed using a simple sample-to-answer platform with results available in approximately 69 min. The pathogens identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus A and B, influenza A, influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus/enterovirus, respiratory syncytial virus A and B, Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae. This multicenter evaluation provides data obtained from 1,994 prospectively collected and 310 retrospectively collected (archived) NPS specimens with performance compared to that of the BioFire FilmArray Respiratory Panel, version 1.7. The overall percent agreement between QIAstat-Dx RP and the comparator testing was 99.5%. In the prospective cohort, the QIAstat-Dx RP demonstrated a positive percent agreement of 94.0% or greater for the detection of all but four analytes: coronaviruses 229E, NL63, and OC43 and rhinovirus/enterovirus. The test also demonstrated a negative percent agreement of ≥97.9% for all analytes. The QIAstat-Dx RP is a robust and accurate assay for rapid, comprehensive testing for respiratory pathogens.

Herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), and varicella-zoster virus (VZV) are taxonomically closely related viruses that produce clinically distinct diseases but share common features of infection. HSV-1 and HSV-2 both produce cutaneous and mucocutaneous primary infections followed by reactivation disease occurring at the same or a nearby anatomic site. Primary VZV infection, also known as chickenpox, is usually a childhood disease that produces pox-like cutaneous lesions distributed over the entire body. Reactivation VZV infection, often called herpes zoster, generally occurs later in life but, unlike HSV disease, produces pox-like lesions at a different anatomic location, typically along dermatomes. As such, the clinical differential diagnosis of reactivation HSV infection and zoster is generally based upon the anatomic location and the appearance of the lesion(s). The recent availability of molecular assays has resulted in the unexpected diagnosis of zoster infections in male and female patients who presented with genital lesions. The purpose of this article is to present a brief overview of HSV and VZV infections and to relate a laboratory experience that resulted in the diagnosis of zoster infections using a molecular assay in which almost 10% of the 282 positive VZV specimens were from genital sites.

Objectives A report on the multicenter evaluation of the Bruker MALDI Biotyper CA System (MBT-CA; Bruker Daltonics, Billerica, MA) for the identification of clinically important bacteria and yeasts. Methods In total, 4,399 isolates of medically important bacteria and yeasts were assessed in the MBT-CA. These included 2,262 aerobic gram-positive (AGP) bacteria, 792 aerobic gram-negative (AGN) bacteria 530 anaerobic (AnA) bacteria, and 815 yeasts (YSTs). Three processing methods were assesed. Results Overall, 98.4% (4,329/4,399) of all bacterial and yeast isolates were correctly identified to the genus and species/species complex level, and 95.7% of isolates were identified with a high degree of confidence. The percentage correctly identified and the percentage identified correctly with a high level of confidence, respectively, were as follows: AGP bacteria (98.6%/96.5%), AGN bacteria (98.5%/96.8%), AnA bacteria (98.5%/97.4%), and YSTs (97.8%/87.6%). The extended direct transfer method was only minimally superior to the direct transfer method for bacteria (89.9% vs 86.8%, respectively) but significantly superior for yeast isolates (74.0% vs 48.9%, respectively). Conclusions The Bruker MALDI Biotyper CA System accurately identifies most clinically important bacteria and yeasts and has optional processing methods to improve isolate characterization.

The iC-GPC Assay (iCubate, Huntsville, AL) is a qualitative multiplex test for the detection of five of the most common Gram-positive bacteria (Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Enterococcus faecalis, and Enterococcus faecium) responsible for bacterial bloodstream infections, performed directly from positive blood cultures. The assay also detects the presence of the mecA, vanA, and vanB resistance determinants., The iC-GPC Assay (iCubate, Huntsville, AL) is a qualitative multiplex test for the detection of five of the most common Gram-positive bacteria (Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Enterococcus faecalis, and Enterococcus faecium) responsible for bacterial bloodstream infections, performed directly from positive blood cultures. The assay also detects the presence of the mecA, vanA, and vanB resistance determinants. This study comparatively evaluated the performance of the iC-GPC Assay against the Verigene Gram-positive blood culture (BC-GP) assay (Luminex Corp., Austin, TX) for 1,134 patient blood culture specimens positive for Gram-positive cocci. The iC-GPC Assay had an overall percent agreement with the BC-GP assay of 95.5%. Discordant specimens were further analyzed by PCR and a bidirectional sequencing method. The results indicate that the iC-GPC Assay together with the iCubate system is an accurate and reliable tool for the detection of the five most common Gram-positive bacteria and their resistance markers responsible for bloodstream infections.

We describe results from a multicenter study evaluating the Accelerate Pheno system, a first of its kind diagnostic system that rapidly identifies common bloodstream pathogens from positive blood cultures within 90 min and determines bacterial phenotypic antimicrobial susceptibility testing (AST) results within ∼7 h. A combination of fresh clinical and seeded blood cultures were tested, and results from the Accelerate Pheno system were compared to Vitek 2 results for identification (ID) and broth microdilution or disk diffusion for AST. The Accelerate Pheno system accurately identified 14 common bacterial pathogens and two Candida spp. with sensitivities ranging from 94.6 to 100%. Of fresh positive blood cultures, 89% received a monomicrobial call with a positive predictive value of 97.3%. Six common Gram-positive cocci were evaluated for ID. Five were tested against eight antibiotics, two resistance phenotypes (methicillin-resistant Staphylococcus aureus and Staphylococcus spp. [MRSA/MRS]), and inducible clindamycin resistance (MLSb). From the 4,142 AST results, the overall essential agreement (EA) and categorical agreement (CA) were 97.6% and 97.9%, respectively. Overall very major error (VME), major error (ME), and minor error (mE) rates were 1.0%, 0.7%, and 1.3%, respectively. Eight species of Gram-negative rods were evaluated against 15 antibiotics. From the 6,331 AST results, overall EA and CA were 95.4% and 94.3%, respectively. Overall VME, ME, and mE rates were 0.5%, 0.9%, and 4.8%, respectively. The Accelerate Pheno system has the unique ability to identify and provide phenotypic MIC and categorical AST results in a few hours directly from positive blood culture bottles and support accurate antimicrobial adjustment.

We compared group A Streptococcus (GAS) culture with a rapid helicase-dependent amplification (HDA) method using 1,082 throat swab specimens. The HDA method demonstrated 98.2% sensitivity and 97.2% specificity. GAS prevalence by culture was 20.7%, and it was 22.6% using the HDA method. In 35 min, the HDA method provided rapid, sensitive GAS detection, making culture confirmation unnecessary.

Clostridium difficile infection (CDI) is a high burden and significant cause of healthcare-acquired infectious diarrhea in the United States (US). Timely and accurate diagnosis of CDI enables the rapid initiation of antibiotic therapy and infection control policies to minimize disease transmission. Polymerase chain reaction (PCR) assays have become a preferred modality for diagnosing CDI in the US. The cobas Liat Cdiff PCR test is a novel assay that can be performed on-demand for hospital-based testing with a rapid 20-minute turnaround time from specimen collection to result reporting. We compared the clinical performance of the cobas Liat Cdiff test to the previously introduced Xpert C. difficile/Epi test; both tests are FDA-cleared PCR assays that detect the toxin B (tcdB) gene of C. difficile. Prospectively collected and remnant stool specimens from 310 patients with suspected CDI were obtained for analysis. The cobas Liat Cdiff and Xpert PCR tests showed an overall percent agreement of 97.4% (302/310; 95% CI: 95.0-98.9). Low bacterial burdens of toxigenic C. difficile, indicated by significantly delayed PCR cycle threshold (Ct) values, explained most of the discordance. Positive and negative percent agreement of the cobas Liat Cdiff test compared to the Xpert PCR test were 94.5% (52/55) and 98.0% (250/255), respectively. The clinical performance of the cobas Liat Cdiff test, combined with its simplicity of use and rapid result reporting, provides a reliable option for clinical laboratory use.

“The 1990s have been marked by a renewed recognition that our human species is still locked in a Darwinian struggle with our microbial and viral predators.” Although this unreferenced quotation was made by Nobel Laureate Joshua Lederberg, as he was discussing the acquired immunodeficiency syndrome (AIDS) and multidrug-resistant Mycobacterium tuberculosis epidemics that emerged in the early 1990s, his comment could also apply to almost any infectious disease process that has occurred since the recognition of the germ theory of disease in the late 1880s. For as we journey through the 21st century, and despite the advances of modern medicine and the continual development of new vaccines and anti-infective therapeutic agents, the human species continues to battle microbial predators in this Darwinian struggle for survival.

The Shiga Toxin Direct molecular assay (ST Direct) relies on nucleic acid amplification and solid array-based amplicon detection to identify Shiga toxin-producing Escherichia coli (STEC) in preserved stool specimens. Genes encoding Shiga toxin ( stx 1 and stx 2 ), as well as the E. coli serotype O:157-specific marker rfbE , are simultaneously detected within 2 h. ST Direct was evaluated using 1,084 prospectively collected preserved stool specimens across five clinical centers. An additional 55 retrospectively collected, frozen specimens were included to increase the number of positive specimens evaluated. Results were compared to results from routine culture and an enzyme immunoassay (EIA) specific for the recovery and identification of STEC. ST Direct was found to be 93.2% sensitive and 99.3% specific for detection of stx 1 and stx 2 and 95.7% sensitive and 99.3% specific for detection of E. coli serotype O:157. All specimens with false-positive results were found to contain stx 1 or stx 2 or were found to be positive for serotype O:157 when analyzed using alternative molecular methods. All 4 false-negative stx 1 or stx 2 results were reported for frozen, retrospectively tested specimens. In all cases, the specimens tested positive for stx by an alternative FDA-cleared nucleic acid amplification test (NAAT) but were negative for stx 1 and stx 2 following nucleic acid sequence analysis. Based on these data, culture and EIA-based methods for detection of STEC are only 33% sensitive compared to molecular tests. A retrospective cost analysis demonstrated 59% of the cost of routine stool culture to be attributable to the identification of STEC. Taken together, these data suggest that ST Direct may provide a cost-effective, rapid molecular alternative to routine culture for the identification of STEC in preserved stool specimens.

Background The Lyra™ Direct HSV 1+2/VZV Assay is a moderately complex, multiplex PCR assay that qualitatively detects the presence of HSV 1, HSV 2, and VZV DNA in cutaneous and mucocutaneous specimens with a time-to-result of less than 60 min. Objectives To report a one-year laboratory experience using Lyra assay for testing cutaneous and mucocutaneous specimens for HSV and VZV that resulted in the unexpected detection of VZV in 14 male and female genital specimens. Study design Over a one-year period, 2113 cutaneous and mucocutaneous specimens from male and female patients were submitted for testing using the Lyra assay. An unexpected 14 genital specimens were positive for the presence VZV DNA. Eleven of the 14 specimens were available for confirmatory testing using two alternative molecular methods and Sanger sequencing. Results Fourteen male and female genital specimens were positive for the presence of VZV DNA. All of the 11 specimens (9 female and 2 male) that were available for confirmatory testing by the alternative molecular method and Sanger sequencing were confirmed as containing VZV DNA. Conclusions Using of the Lyra assay over a one-year time period, VZV DNA was detected in 126 specimens of which 14 (11.1%) were from male and female genital sites. This rare and unexpected finding suggests that the appearance of zoster lesions in the genital area may not be as uncommon as previously thought and that this finding would have considerable impact on patient counseling and public health considerations.

Vaginitis is one of the most common diseases that affect women's health, with over 50% of women experiencing at least one episode of vaginal infection in their lifetime. Vaginal disease can be infectious, non-infectious, or chronic in nature. However, most cases of vaginitis are the result of infection that accounts for over 10 million physician office visits in the United States each year. Infectious vaginitis is most commonly grouped into three major categories of disease based upon microbial etiology: bacterial vaginosis, vaginal candidiasis, and vaginal trichomoniasis. Occasionally, the vulva is infected by these microorganisms, as well, and the disease is then called vulvovaginitis. Because these three infectious syndromes are caused by different groups of microorganisms, accurate and reliable diagnosis is necessary to institute appropriate treatment. The purpose of this article is to review the various types of vaginitis, discuss the pathogenesis and clinical presentation of each type of disease, and provide a brief summary of some of the various methods available for the laboratory diagnosis of infectious vaginitis.

Bloodstream infection is a serious condition associated with significant morbidity and mortality. The outcome of these infections can be positively affected by the early implementation of effective antibiotic therapy based on the identification of the infecting organism and genetic markers associated with antibiotic resistance. In this study, we evaluated the microarray-based Verigene Gram-negative blood culture (BC-GN) assay in the identification of 8 genus or species targets and 6 genetic resistance determinants in positive blood culture broths. A total of 1,847 blood cultures containing Gram-negative organisms were tested using the BC-GN assay. This comprised 729 prospective fresh, 781 prospective or retrospective frozen, and 337 simulated cultures representing 7 types of aerobic culture media. The results were compared to those with standard bacterial culture and biochemical identification with nucleic acid sequence confirmation of the resistance determinants. Among monomicrobial cultures, the positive percent agreement (PPA) of the BC-GN assay with the reference method was as follows; Escherichia coli , 100%; Klebsiella pneumoniae , 92.9%; Klebsiella oxytoca , 95.5%; Enterobacter spp., 99.3%; Pseudomonas aeruginosa , 98.9%; Proteus spp., 100%; Acinetobacter spp., 98.4%; and Citrobacter spp., 100%. All organism identification targets demonstrated >99.5% negative percent agreement (NPA) with the reference method. Of note, 25/26 cultures containing K. pneumoniae that were reported as not detected by the BC-GN assay were subsequently identified as Klebsiella variicola . The PPA for identification of resistance determinants was as follows; bla CTX-M , 98.9%; bla KPC , 100%; bla NDM , 96.2%; bla OXA , 94.3%; bla VIM , 100%; and bla IMP , 100%. All resistance determinant targets demonstrated >99.9% NPA. Among polymicrobial specimens, the BC-GN assay correctly identified at least one organism in 95.4% of the broths and correctly identified all organisms present in 54.5% of the broths. The sample-to-result processing and automated reading of the detection microarray results enables results within 2 h of culture positivity.

The iC-GPC assay (iCubate, Huntsville, AL) provides a molecular option for the rapid, on-demand analysis of positive blood cultures. A preliminary evaluation of the iC-GPC assay using 203 clinical or seeded specimens demonstrated a sensitivity of 93.8% to 100% and a specificity of 98.0% to 100% for the identification of five Gram-positive bacterial species ( Staphylococcus aureus , Staphylococcus epidermidis , Streptococcus pneumoniae , Enterococcus faecalis , and Enterococcus faecium ) and three associated genetic resistance determinants ( mecA , vanA , and vanB ) in positive blood culture broths.

The AmpliVue HSV 1+2 assay was compared to the ELVIS HSV ID and D 3 Typing Culture System for the qualitative detection and differentiation of herpes simplex virus 1 (HSV-1) and HSV-2 DNA in 1,351 cutaneous and mucocutaneous specimens. Compared to ELVIS, AmpliVue had sensitivities of 95.7 and 97.6% for detecting HSV-1 and HSV-2, respectively. Following arbitration of discordant results by an independent molecular method, the AmpliVue assay had a resolved sensitivity and specificity of 99.2 and 99.7%, respectively, for both HSV-1 and HSV-2, whereas ELVIS had a resolved sensitivity of 87.1% for HSV-1 and 84.5% for HSV-2.

We evaluated the clinical performance (sensitivity and specificity) of the AmpliVue group A Streptococcus (GAS) isothermal helicase-dependent amplification assay using 1,192 pharyngeal swab specimens. AmpliVue GAS assay results were compared to the results of routine throat cultures on selective streptococcal blood agar plates. The sensitivity and specificity of the AmpliVue GAS assay were 98.3% (95% confidence interval [CI], 95 to 100%) and 93.2% (95% CI, 91 to 95%), respectively.

The prompt and accurate identification of bacterial pathogens is fundamental to patient health and outcome. Recent advances in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) have revolutionized bacterial identification in the clinical laboratory, but uniform incorporation of this technology in the U.S. market has been delayed by a lack of FDA-cleared systems. In this study, we conducted a multicenter evaluation of the MALDI Biotyper CA (MBT-CA) System (Bruker Daltonics Inc, Billerica, MA) for the identification of aerobic gram-negative bacteria as part of a 510(k) submission to the FDA. A total of 2,263 aerobic gram negative bacterial isolates were tested representing 23 genera and 61 species. Isolates were collected from various clinical sources and results obtained from the MBT-CA System were compared to DNA sequencing and/or biochemical testing. Isolates that failed to report as a "high confidence species ID" [log(score) ≥2.00] were re-tested using an extraction method. The MBT-CA System identified 96.8% and 3.1% of isolates with either a "high confidence" or a "low confidence" [log(score) value between 1.70 and

Leishmaniasis is a zoonotic disease caused by an intracellular protozoan that is transmitted to humans following the bite of an infected female sand fly (1). An estimated 112 million people worldwide have leishmaniasis, with more than 400,000 new cases reported annually (2). Infection is endemic to certain geographic areas of the world, with the highest incidence in the Middle East, India, Nepal, Sudan, and certain countries in Central and South America (3,4). We report a case of cutaneous leishmaniasis in a 49year-old male who presented to our emergency room for evaluation of an ulcerative lesion on his finger. Microscopic examination of a Giemsa-stained touch preparation from the finger lesion showed intracellular protozoa suggestive of Leishmania species. The protozoan was recovered by culture from a biopsy specimen, and its identity was subsequently confirmed as Viannia (Leishmania) panamensis by using molecular methods. Case Report A 49-year-old non-English-speaking male presented to our emergency room for evaluation of an ulcerative lesion on the fifth finger of his left hand. Through a translator, it was determined that the patient was born in Cuba but spent most of his adult life traveling with others through the jungles of Panama and Colombia. He eventually arrived in the United States from Ecuador and resided for 3 months with relatives in the Syracuse, New York, area before his finger lesion was evaluated in our emergency room. The patient reported that initially, a very tiny black particle came out of the wound, followed by the development of the skin ulcer that progressively worsened (Fig. 1). The patient’s past medical history was unremarkable, except for an appendectomy several years previously. Physical examination was completely within normal limits, except for the presence of the painful, ulcerative lesion on his finger. An infectious disease physician was consulted for evaluation of the patient. Given his history of extensive and prolonged travel through the jungles of Central America, the initial diagnostic impression was that the patient might have cutaneous leishmaniasis. A touch preparation of the ulcerative skin lesion was prepared and stained by the Giemsa method. On microscopic examination, the smear showed the presence of intracellular protozoa (Fig. 2) that were highly suggestive of Leishmania species. A biopsy specimen from the lesion was submitted for testing to the Centers for Disease Control and Prevention, where a Leishmania species was recovered by culture. The protozoan was identified to the species level as Viannia (Leishmania) panamensis by using PCR and isoenzyme analyses. The patient was treated for 2 months with sodium stibogluconate (Pentostam), a pentavalent antimonial compound, with gradual resolution and healing of his finger lesion. Discussion

The terms normal microbial flora, normal commensal flora, and indigenous flora are synonymous and are used to describe microorganisms that are frequently found in particular anatomic sites in healthy individuals. Microbial flora is associated with the skin and mucous membranes of every human from shortly after birth until death and represents an extremely large and diverse population of microorganisms. The normal microbial flora for various anatomic sites is reviewed in this chapter. The microbial factors that contribute to the virulence of a microorganism can be divided into three major categories: (i) those that promote colonization of host surfaces, (ii) those that evade the host’s immune system and promote tissue invasion, and (iii) those that produce toxins that result in tissue damage in the human host. Most infections are initiated by the attachment or adherence of the microbe to host tissue, followed by microbial replication in order to establish colonization. Organisms within biofilms are more resistant to antibiotics than individual bacteria and are partially protected from phagocytes as well. Some mucosal surfaces, such as the mouth, stomach, and small intestine, are protected from microbial colonization because they are constantly being washed with fluids. Toxins produced by certain microorganisms during growth may alter the normal metabolism of human cells with damaging and sometimes deleterious effects on the host. Many pathogenic organisms produce extracellular enzymes such as hyaluronidase, proteases, DNases, collagenase, elastinase, and phospholipases which are capable of hydrolyzing host tissues and disrupting cellular structure.

Clostridium difficile is a Gram-positive bacterium commonly found in health care and long-term-care facilities and is the most common cause of antibiotic-associated diarrhea. Rapid detection of this bacterium can assist physicians in implementing contact precautions and appropriate antibiotic therapy in a timely manner. The purpose of this study was to compare the clinical performance of the Quidel Lyra Direct C. difficile assay (Lyra assay) (Quidel, San Diego, CA) to that of a direct cell culture cytotoxicity neutralization assay (CCNA) and enhanced toxigenic culture. This study was performed at three geographically diverse laboratories within the United States using residual stool specimens submitted for routine C. difficile testing. Residual samples were tested using the Lyra assay on three real-time PCR platforms, and results were compared to those for direct CCNA and enhanced toxigenic culture. The test results for all platforms were consistent across all three test sites. The sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500 Fast DX, and ABI QuantStudio DX instruments compared to CCNA were 90.0% and 93.3%, 95.0% and 94.2%, and 93.8% and 95.0%, respectively. Compared to enhanced toxigenic culture, the sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500, and QuantStudio instruments were 82.1% and 96.9%, 89.3% and 98.8%, and 85.7% and 99.0%, respectively. Overall, the Lyra assay is easy to use and versatile and compares well to C. difficile culture methods.

0196-4399/00 (see frontmatter) © 2010 Elsevier Clinical Microbiology Newsletter 32:19,2010 In 2008, the World Health Organization (1) reported that one-third of the world’s population, or over 2 billion people, are infected withMycobacterium tuberculosis. Most individuals infected with M. tuberculosis have asymptomatic disease, but an estimated 9 million people develop active tuberculosis infections each year resulting in over 2 million deaths. Most cases of tuberculosis are pulmonary in nature, but extrapulmonary infections are not uncommon. Extrapulmonary infections may involve the central nervous and skeletal systems, the kidney, and/or the gastrointestinal tract (2). This case report describes a patient with tuberculous cervical lymphadenitis who presented with no evidence of primary pulmonary infection and a negative tuberculin skin test. This case should serve to remind the reader of the importance of extrapulmonary tuberculous disease in the absence of primary pulmonary infection. Case Report A previously healthy 28-year-old male presented to his primary care physician for evaluation of a mass on the left side of his neck. The neck mass was of sudden onset, and the patient gave no history of febrile episodes, chills, sweats, or sore throat. The patient was employed as a research assistant at a local medical school and, as part of his routine and periodic health assessment, had a tuberculin skin test 5 months previously, which was read as negative. The patient was born in the Philippines, but when he was 6 years old, he moved to the United States with his Mailing Address: Paul A. Granato, Ph.D., Department of Microbiology and Immunology, WH 2204, SUNY Upstate Medical University, 750 East Adams St., Syracuse, NY 13210. Tel.: 315-464-7653. Fax: 315-464-4417. E-mail: granatop@ upstate.edu Case Report

0196-4399/00 (see frontmatter) © 2009 Elsevier Clinical Microbiology Newsletter 31:12,2009 Streptococcus pneumoniae is a wellrecognized human pathogen, particularly in patients in the pediatric age group. Most pediatric pneumococcal infections are localized in the respiratory tract; however, more serious, but less common, disseminated infections are well documented (1,2). Septic arthritis is one of the more serious systemic infections caused by S. pneumoniae. In one study (3), S. pneumoniae was reported to cause up to 20% of bacterial joint infections in children, while in another study (4), a much lower incidence of 4% was reported. Regardless, the incidence of pneumococcal septic arthritis, as well as other pneumococcal infections, has been steadily decreasing because of the widespread use of Prevnar, the heptavalent pneumococcal conjugate vaccine (PCV7) that was licensed for use in 2000 (1,5,6). This report describes a case of pneumococcal septic arthritis in a 15-month-old female who had been vaccinated with four doses of PCV7.

Lyme disease, human babesiosis, and human granulocytic ehrlichiosis are vector-borne diseases that are increasingly recognized as important pathogens in the northeast and upper midwestern regions of the United States (1-6). The etiologic agents of these human infections, Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum, respectively, are maintained in the same tick vector (Ixodes scapularis also known as Ixodes dammini or the deer tick) and the rodent reservoir (Peromyscus leucopus, the white-footed mouse). The definitive host of the tick vector is the white-tailed deer (Odocoileus virginianus). The proliferation of the deer populations in certain geographical areas of the U.S. during the mid-20th century has been the basis for the emergence of these infections (7). Because I. scapularis serves as the tick-borne reservoir for B. burgdorferi, B. microti, and A. phagocytophilum, mixed infections with any two, or perhaps all three, of these agents are possible. In fact, in one study (8) of 93 patients with culture-proven Lyme disease, 2% of the patients were coinfected with B. microti and another 2% were coinfected with A. phagocytophilum. Other studies (9,10) have shown that up to 10% of patients may have Borrelia and Babesia coinfections. These coinfections may cause a confusing clinical picture, and some investigators have reported that coinfected patients may have more severe or persistent illness (10,11). This case report describes a 79-yearold patient who acquired a coinfection with B. burgdorferi and B. microti while on a 2-week family camping trip in Massachusetts.

Haemophilus influenzae is a wellrecognized human pathogen that can cause life-threatening systemic disease, as well as localized infections. In general, systemic infections, such as meningitis and bacteremia, are invariably caused by encapsulated strains, of which H. influenzae type b (HiB) is the most common. Localized infections may be caused by encapsulated or noncapsulated strains but are most frequently caused by the latter nontypeable strains (1). Systemic infection caused by a noncapsulated strain of H. influenzae in an immunocompetent patient with no underlying disease would be extremely unusual. This report describes a previously healthy 71-year-old woman with no known underlying disease who developed life-threatening meningitis and septicemia caused by a noncapsulated strain of H. influenzae.

© 2005 Elsevier 0196-4399/00 (see frontmatter) 23 Strongyloides stercoralis is a parasitic nematode that causes human disease worldwide but is most prevalent in tropical and subtropical regions of the world (1). Most Strongyloides infections produce asymptomatic disease that can remain dormant in the infected host throughout life. Predisposing factors, such as immunosuppression, can result in the development of symptomatic disease leading to a disseminated hyperinfection syndrome, and possibly death. This case report describes a previously healthy person who received short-term corticosteroid therapy that resulted in the development of pulmonary strongyloidiasis with a fatal outcome.

A chromogenic medium for identification of vancomycin-resistant Enterococcus faecalis and Enterococcus faecium , VRE Select , was compared to bile esculin azide agar with 6 μg/ml vancomycin (BEAV) for the isolation of vancomycin-resistant enterococci (VRE) from stool specimens. At 24 to 28 h, VRE Select demonstrated 98.7% (confidence interval [CI], 96.1 to 99.7%) sensitivity and 99.0% (CI, 98.0 to 99.6%) specificity versus 85.1% (CI, 79.8 to 89.5%) and 90.1% (CI, 79.8 to 89.5%) sensitivity and specificity, respectively, for BEAV.

The novel IsoAmp(®) HSV Assay employs isothermal helicase-dependent nucleic acid amplification and a user-friendly disposable test device to achieve rapid (1.5h), on-demand qualitative detection of herpes simplex virus (HSV) types 1 and 2 in oral and genital lesions.To compare performance of the IsoAmp(®) HSV Assay with the ELVIS(®) HSV ID/typing (shell-vial culture and DFA) test system for clinical specimens collected from oral and genital lesions in symptomatic patients.A total of 994 specimens from male and female genital and oral lesions were obtained and evaluated at five study sites in the United States. Results from the IsoAmp(®) HSV Assay were compared to those from the ELVIS(®) system. Separate reproducibility studies were performed at 3 sites using a blinded and randomized study panel. Discrepant specimens were resolved by bidirectional sequencing analysis.After discrepant analysis, overall agreement of IsoAmp(®) with ELVIS(®) was 98.8% with 37.0% overall prevalence (all study sites). Reproducibility rates were well within expectations.The IsoAmp(®) HSV Assay showed excellent performance for clinical use for detection of HSV in genital and oral specimens. In contrast to ELVIS(®), IsoAmp(®) HSV offers excellent sensitivity plus rapid on-demand testing and simpler specimen preparation.

Lactococcus garvieae is regarded as a veterinary pathogen, causing hemorrhagic septicemia in fish (1) and mastitis in cows (2). The organism has also been recovered from a variety of dairy products, such as unpasteurized milk (3) and cheese (4-6), as well as various meat products (5,6). L. garvieae is an uncommon cause of human infection, with only a limited number of cases reported worldwide (7-20). Most infections involve either native (7-11) or prosthetic (12-15) heart valves, but cases of osteomyelitis (16-17), hepatic abscess (18), and septicemia (19) have also been documented. In addition, a case of urinary tract infection with sepsis has also been reported (20). This report describes a patient with a history of congestive heart failure and pulmonary edema who developed native valve endocarditis caused by L. garvieae. Case Report A 62-year-old male with a history of congestive heart failure and pulmonary edema was evaluated in the emergency room for a lowgrade fever of several weeks duration. On physical examination, the patient had a loud diastolic murmur and was noted to be in severe congestive heart failure. He was admitted to the hospital for possible endocarditis, where a transesophageal echocardiogram (TEE) was performed. The TEE showed normal left ventricular function and moderately increased left ventricular cavity size. His overall ejection fraction was normal. The right aortic valve appeared to have a small leaflet abscess, and the leaflet appeared perforated. The patient was administered furosemide (Lasix), which resulted in symptomatic improvement of his congestive heart failure. The patient’s past medical history was also significant for hav ing Waldenstrom’s macroglobulinemia, for which he received periodic treatments with intravenous immune globulin (IVIG) administered through an indwelling catheter port. At the time of the patient’s admission, the indwelling port was removed but not cultured, because the port was not considered a likely source for the patient’s infection. Four sets of blood cultures were collected over a several-hour period on the patient’s first day of admission, and all the sets were reported by the microbiology laboratory as growing “gram-positive cocci” within 24 h of incubation. When grown on a 5% sheep blood agar plate, the colonial morphology of the blood culture isolate resembled that of Enterococcus spp. However, because the isolate could not be reliably identified by using conventional sys

Campylobacter enteritis is a food-borne or waterborne illness caused almost exclusively by Campylobacter jejuni and, to a lesser extent, by Campylobacter coli . These organisms produce indistinguishable clinical diseases and together represent the second most common cause of bacterial diarrhea in the United States and the leading cause of enteric infection throughout the world. The conventional approach to the laboratory diagnosis of Campylobacter enteritis is based on the recovery of the organism from a stool specimen, which requires the use of a specialized medium incubated at 42°C for several days in an artificially created microaerophilic environment. Recently, several commercially available enzyme immunoassays (EIAs) have been developed for the direct detection of C. jejuni and C. coli in stool specimens. This study compared conventional culture with three EIA methods, the Premier CAMPY EIA (Meridian Bioscience, Cincinnati, OH), the ProSpecT Campylobacter EIA (Remel, Lenexa, KS), and the ImmunoCard STAT! CAMPY test (Meridian Bioscience, Cincinnati, OH), for the detection of C. jejuni and C. coli in 485 patient stool samples. Discordant results were arbitrated by using an in-house, real-time PCR assay that was developed and validated by a public health reference laboratory. Following analyses of the discrepant specimens by PCR, the sensitivity and specificity of both the Premier CAMPY and ProSpecT Campylobacter EIAs were 99.3% and 98%, respectively, while the ImmunoCard STAT! CAMPY test had a sensitivity of 98.5% and a specificity of 98.2%. By use of the PCR test as the reference standard, culture detected 127 of 135 Campylobacter -positive stool specimens, yielding a sensitivity of 94.1%. These results showed that the three EIAs evaluated in this study provide a rapid and reliable alternative for the laboratory diagnosis of enteric infections with C. jejuni and C. coli and that conventional culture may no longer be recognized as the “gold standard” for diagnosis.

Streptococcus salivarius, a member of the viridans group streptococci, is a prominent member of the microbiota of the human upper respiratory tract and other mucous membrane surfaces (1,2). Human infections caused by S. salivarius are uncommon and include bacteremia, endocarditis, and meningitis. They almost invariably result from an endogenous source (3), and documented cases of S. salivarius infections originating from an exogenous source are exceedingly rare. This case report describes a patient who developed iatrogenic S. salivarius meningitis following the administration of an epidural nerve block injection.

The QUIDEL Group B Strep Test is an enzyme immunoassay (EIA) that was compared with culture for the rapid detection of moderate to high levels of group B streptococci (GBS) colonization in pregnant women. A total of 331 pregnant women were included in the study protocol, and GBS were cultured from 19 of these patients in moderate or greater amounts (incidence of 5.7%). Compared with culture, the EIA had a sensitivity, specificity, and positive and negative predictive values of 89, 99, 89, and 99%, respectively. With a sensitivity of 89%, the 95% confidence interval for this assay is 88 to 90%. The QUIDEL EIA test can be performed in less than 10 min and appears to be a reliable method for detecting moderate or greater amounts of GBS in vaginal or cervical specimens.

0196-4399/00 (see frontmatter) © 2008 Elsevier Clinical Microbiology Newsletter 30:18,2008 Cardiobacterium hominis is a well-known but rare cause of bacterial endocarditis, with fewer than 70 cases reported in the English literature (1). The most common risk factor for the development of C. hominis endocarditis is the presence of preexisting cardiac disease involving anatomic defects of the aortic and mitral valves. Other important risk factors are the presence of a prosthetic valve implant or a history of rheumatic fever. This report describes a case of C. hominis endocarditis in a previously healthy 50-year-old male with a known history of mitral valve prolapse and serves to remind readers of the significance of this organism as a cause of serious infection in patients with predisposing risk factors.

Within the last decade, major technologic advances have been made in clinical microbiology that have resulted in the availability of a wide variety of different methods for the rapid reporting of test results. Included among these technologies are rapid methods for producing antimicrobial susceptibility reports that many regard as the most important information generated by the microbiology laboratory. Ideally, the early availability of this important information should favorably affect patient care by enabling the more judicious use of alternative drug therapies that are equally efficacious yet less toxic and less costly to the patient. Clinicians appear to have been reluctant to modify initial empiric therapies, however, despite the availability of the rapid antimicrobial susceptibility report. This article addresses some of the issues responsible for this long-standing problem and discusses and explores various strategies that can be implemented for improving the use and for controlling the cost of antimicrobial agents within the hospital.