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Background The cornerstone of treatment for acute cholangitis is source control with biliary drainage and early antibiotics. The primary aim of this study was to describe the microbiology of bile aspirate pathogens obtained at the time of endoscopic retrograde cholangiopancreatography (ERCP) in patients suspected of having acute cholangitis. Methods In this single-center retrospective study, patients were included if a bile aspirate was collected at ERCP for suspicion of acute cholangitis, from 1 January 2010 to 31 December 2016. Results There were 721 ERCP procedures for suspected acute cholangitis with bile culture results, with 662 positive bile cultures (91.8 %). Pathogens included: Enterococcus species (spp.) 448 (67.7 %); Klebsiella spp. 295 (44.6 %); Escherichia coli 269 (40.6 %); Pseudomonas spp. 52 (7.9 %); and anaerobes 64 (9.7 %). Susceptibility of Klebsiella pneumoniae and E.coli isolates to ciprofloxacin was 88 % and 64 %, respectively. Extended-spectrum beta-lactamases and carbapenem resistance were found in 7.9 % and 3.6 % of Enterobacteriaceae, respectively. There were 437 concurrent blood cultures, of which 174 were positive (39.8 % of cultures drawn). Prior biliary endoscopic sphincterotomy (ES) was evident in 459 ERCP cases (63.7 %), and was associated with increased frequency of Klebsiella spp., Pseudomonas aeruginosa, Enterobacter spp., and Enterococcus spp. Prior biliary ES significantly increased the probability of vancomycin-resistant Enterococcus (VRE). Conclusions The vast majority of bile cultures (91.8 %) were positive. The susceptibilities of E.coli and K.pneumoniae to ciprofloxacin are lower than historically noted. A notable portion of cultures contained pathogenic drug-resistant organisms. Prior biliary ES is associated with a higher frequency of certain organisms and higher frequency of VRE.

The classification of viruses remains relevant to several disciplines, including clinical virology. Since the original publication of this review in 2019, many known viruses have undergone taxonomic revisions, and several novel human and animal viruses have been described. Here, we provide an update to our previous reviews of taxonomic changes for disease-causing viruses of humans, covering changes that occurred between 2020 and 2022. As with previous editions, this update was informed by recent advances in virus taxonomy made by the International Committee on Taxonomy of Viruses; the changes and additions noted herein are not all-inclusive.

Diseases caused by many highly pathogenic viruses, including Ebola virus (EBOV) and Lassa virus (LASV), present with nonspecific signs and symptoms that overlap with common tropical diseases such as malaria. Initial diagnostic tests performed on patients under investigation for viral hemorrhagic fevers routinely include analysis of peripheral blood smears to detect and quantify Plasmodium species. In light of recent and ongoing Ebola virus disease and Lassa fever epidemics, clinical laboratories around the world require protocols for dealing with highly infectious specimens from patients with suspected or confirmed high-consequence diseases. Few validated protocols for safe analysis of peripheral blood smears are available, revealing a need for further research. In this study, we evaluated the performance of two plastic microscope slide types that offer safe alternatives to glass slides, determined the temporal parameters required to inactivate EBOV and LASV in thin blood smears by methanol fixation, and assessed the virucidal activity of Giemsa stain. Both types of plastic microscope slides performed optimally; there were no significant differences in blood cell morphology or tinctorial properties nor were differences noted in Plasmodium ovale morphology or staining, when compared with glass slides. For both EBOV and LASV, viable viruses were not detected in thin blood smears following fixation in absolute methanol for at least 2 minutes. By contrast, viable EBOV and LASV were recovered from all Giemsa-stained thick blood smears.

The global incidence of tick-borne infectious diseases has increased since the beginning of the 21st century. The expansion of tick populations into new geographic locations and a variety of anthropogenic and natural factors are all drivers of the increase. In addition to the establishment of known tick-borne pathogens in new areas, several novel agents, including many viruses, have also emerged. At present in North America, there are five tick-borne viruses that are known to cause human disease: deer tick virus, Powassan virus, Colorado tick fever virus, Heartland virus, and Bourbon virus. Although uncommon causes of disease, these viruses pose formidable threats to the health of individuals residing in regions of endemicity, especially since there are currently no medical countermeasures available to combat them. This review focuses on the basic biology, ecology, epidemiology, transmission, clinical presentation, diagnosis, treatment, and prevention of these North American tick-borne arboviruses.

Immune checkpoints (ICPs) consist of paired receptor-ligand molecules that exert inhibitory or stimulatory effects on immune defense, surveillance, regulation, and self-tolerance. ICPs exist in both membrane and soluble forms in vivo and in vitro. Imbalances between inhibitory and stimulatory membrane-bound ICPs (mICPs) in malignant cells and immune cells in the tumor immune microenvironment (TIME) have been well documented. Blockades of inhibitory mICPs have emerged as an immense breakthrough in cancer therapeutics. However, the origin, structure, production regulation, and biological significance of soluble ICPs (sICPs) in health and disease largely remains elusive. Soluble ICPs can be generated through either alternative mRNA splicing and secretion or protease-mediated shedding from mICPs. Since sICPs are found in the bloodstream, they likely form a circulating immune regulatory system. In fact, there is increasing evidence that sICPs exhibit biological functions including (1) regulation of antibacterial immunity, (2) interaction with their mICP compartments to positively or negatively regulate immune responses, and (3) competition with their mICP compartments for binding to the ICP blocking antibodies, thereby reducing the efficacy of ICP blockade therapies. Here, we summarize current data of sICPs in cancer and infectious diseases. We particularly focus on sICPs in COVID-19 and HIV infection as they are the two ongoing global pandemics and have created the world’s most serious public health challenges. A “storm” of sICPs occurs in the peripheral circulation of COVID-19 patients and is associated with the severity of COVID-19. Similarly, sICPs are highly dysregulated in people living with HIV (PLHIV) and some sICPs remain dysregulated in PLHIV on antiretroviral therapy (ART), indicating these sICPs may serve as biomarkers of incomplete immune reconstitution in PLHIV on ART. We reveal that HIV infection in the setting of alcohol abuse exacerbates sICP dysregulation as PLHIV with heavy alcohol consumption have significantly elevated plasma levels of many sICPs. Thus, both stimulatory and inhibitory sICPs are present in the bloodstream of healthy people and their balance can be disrupted under pathophysiological conditions such as cancer, COVID-19, HIV infection, and alcohol abuse. There is an urgent need to study the role of sICPs in immune regulation in health and disease.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in a variety of clinical symptoms ranging from no or mild to severe disease. Currently, there are multiple postulated mechanisms that may push a moderate to severe disease into a critical state. Human serum contains abundant evidence of the immune status following infection. Cytokines, chemokines, and antibodies can be assayed to determine the extent to which a patient responded to a pathogen. We examined serum and plasma from a cohort of patients infected with SARS-CoV-2 early in the pandemic and compared them to negative-control sera. Cytokine and chemokine concentrations varied depending on the severity of infection, and antibody responses were significantly increased in severe cases compared to mild to moderate infections. Neutralization data revealed that patients with high titers against an early 2020 SARS-CoV-2 isolate had detectable but limited neutralizing antibodies against the emerging SARS-CoV-2 Alpha, Beta and Delta variants. This study highlights the potential of re-infection for recovered COVID-19 patients.

The COVID-19 pandemic highlighted the significance of readily available and easily performed viral testing for surveillance during future infectious pandemics. The objectives of this study were: to assess the performance of the Xpert Xpress Flu and/or RSV test, a multiplex PCR assay for detecting influenza A and B virus and respiratory syncytial virus nucleic acids in respiratory tract specimens, relative to the Quidel Lyra Influenza A+B assay and the Prodesse ProFlu+ assay, and the system's ease of use by minimally trained operators. Overall, the Xpert Xpress Flu/RSV test demonstrated a high positive and negative percent agreement with the comparator assays, and was easy to use and interpret results, based on the operators' feedback. We concluded that the Xpert Xpress Flu/RSV test is sensitive, specific, and easy to use for the diagnosis of influenza and RSV by minimally trained operators and can be a valuable tool in future infectious clusters or pandemics.

Background Demographic and clinical risk factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children presenting with respiratory viral symptoms are not well defined. An understanding of risk factors for SARS-CoV-2 infection can help prioritize testing. Methodology We evaluated potential demographic and clinical factors in children who had respiratory viral symptoms and were tested by polymerase chain reaction (PCR) for SARS-CoV-2 and other respiratory viral infections. Results Among the 263 symptomatic children tested for routine seasonal respiratory viruses by PCR, 18 (6.8%) tested positive for SARS-CoV-2. Overall, 22.2% of SARS-CoV-2-infected children and 37.1% of SARS-CoV-2-uninfected children had infection with one or more non-SARS-CoV-2 pathogens (p = 0.31). Higher proportions of children with compared to without SARS-CoV-2 infection were male (77.8 vs. 51.8%, p = 0.05), Hispanic (44.4% vs. 9.8%, p < 0.001), or had the symptoms of fatigue (22.2% vs. 2.5%, p = 0.003) or anosmia/ageusia (11.1% vs. 0%, p = 0.004). History of hypoxic-ischemic encephalopathy (HIE) and obesity were more common in children with versus without SARS-CoV-2 infection (11.1% vs. 1.2%, p = 0.04, and 11.1% vs. 0%, p = 0.004, respectively). In a multivariate analysis, Hispanic ethnicity, symptoms of fatigue or anosmia/ageusia, and presence of obesity (as noted on physical examination) or HIE were independently associated with SARS-CoV-2 infection. Numbers in each category were small, and these preliminary associations require confirmation in future studies. Conclusions In this area of the United States, infection with other viruses did not rule out infection with SARS-CoV-2. Additionally, children with respiratory viral symptoms who were of Hispanic ethnicity, had symptoms of weakness/fatigue, or had obesity or HIE were at an increased risk for SARS-CoV-2 infection. Future studies should assess if these factors are associated with risk in populations in other areas of the United States.

COVID-19 starts as a respiratory disease that can progress to pneumonia, severe acute respiratory syndrome (SARS), and multi-organ failure. Growing evidence suggests that COVID-19 is a systemic illness that primarily injures the vascular endothelium, yet the underlying mechanisms remain unknown. SARS-CoV-2 infection is believed to trigger a cytokine storm that plays a critical role in the pathogenesis of endothelialitis and vascular injury, eventually leading to respiratory and multi-organ failure in COVID-19 patients. We used a multiplex immunoassay to systematically profile and compare 65 inflammatory cytokines/chemokines/growth factors in plasma samples from 24 hospitalized (severe/critical) COVID-19 patients, 14 mild/moderate cases, and 13 healthy controls (HCs). Patients with severe/critical and mild/moderate COVID-19 had significantly higher plasma levels of 20 analytes than HCs. Surprisingly, only one cytokine (MIF) was among these altered analytes, while the rest were chemokines and growth factors. In addition, only MMP-1 and VEGF-A were significantly elevated in hospitalized COVID-19 patients when compared to mild/moderate cases. Given that excessive MMP-1 plays a central role in tissue destruction in a wide variety of vascular diseases and that elevated VEGF-A, an EC activation marker, increases vascular permeability, we further studied MMP-1 enzymatic activity and other EC activation markers such as soluble forms of CD146, ICAM-1, and VCAM-1. We found that plasma MMP-1 enzymatic activity and plasma levels of MMP-1 and EC activation markers were highly dysregulated in COVID-19 patients. Some dysregulations were associated with patients’ age or gender, but not with race. Our results demonstrate that COVID-19 patients have distinct inflammatory profiles that are distinguished from the cytokine storms in other human diseases. Excessive MMP-1 and hyperactivation of ECs occur in COVID-19 patients and are associated with the severity of COVID-19.

Acinetobacter baumannii has been recognized as a critical pathogen that causes severe infections worldwide not only because of the emergence of extensively drug-resistant (XDR) derivatives, but also because of its ability to persist in medical environments and colonize compromised patients. While there are numerous reports describing the mechanisms by which this pathogen acquires resistance genes, little is known regarding A. baumannii’s virulence functions associated with rare manifestations of infection such as necrotizing fasciitis, making the determination and implementation of alternative therapeutic targets problematic. To address this knowledge gap, this report describes the analysis of the NFAb-1 and NFAb-2 XDR isolates, which were obtained at two time points during a fatal case of necrotizing fasciitis, at the genomic and functional levels. The comparative genomic analysis of these isolates with the ATCC 19606T and ATCC 17978 strains showed that the NFAb-1 and NFAb-2 isolates are genetically different from each other as well as different from the ATCC 19606T and ATCC 17978 clinical isolates. These genomic differences could be reflected in phenotypic differences observed in these NFAb isolates. Biofilm, cell viability and flow cytometry assays indicate that all tested strains caused significant decreases in A549 human alveolar epithelial cell viability with ATCC 17978, NFAb-1 and NFAb-2 producing significantly less biofilm and significantly more hemolysis and capacity for intracellular invasion than ATCC 19606T. NFAb-1 and NFAb-2 also demonstrated negligible surface motility but significant twitching motility compared to ATCC 19606T and ATCC 17978, likely due to the presence of pili exceeding 2 µm in length, which are significantly longer and different from those previously described in the ATCC 19606T and ATCC 17978 strains. Interestingly, infection with cells of the NFAb-1 isolate, which were obtained from a premortem blood sample, lead to significantly higher mortality rates than NFAb-2 bacteria, which were obtained from postmortem tissue samples, when tested using the Galleria mellonella in vivo infection model. These observations suggest potential changes in the virulence phenotype of the A. baumannii necrotizing fasciitis isolates over the course of infection by mechanisms and cell processes that remain to be identified.

Real-time reverse transcription polymerase chain reaction (rRT-PCR) is the primary method used for the detection and diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since SARS-CoV-2’s entrance into the United States, numerous clinical laboratories and in vitro diagnostic companies have developed rRT-PCR assays, some requiring specialized materials and reagents. One such assay includes the cobas® SARS-CoV-2 Qualitative Assay for use on the cobas® 6800/8800 (Roche Molecular Systems, Inc.). Since initiation of this assay at our facility, our ability to run testing at full capacity has been limited due to restricted supply of the omni cobas® Processing Plate (Product Number 05534917001), a 96 deep well plate used for all sample processing and total nucleic acid extraction via MagNA Pure magnetic beads. To work around this limiting factor, we have successfully designed and tested a cleaning protocol utilizing the widely available laboratory resources of bleach, ethyl-alcohol and autoclaving, for omni cobas® Processing Plate re-use.

Infection with Histoplasma capsulatum typically manifests as a self-limiting pulmonary disease in immunocompetent patients. Systemic symptoms such as cutaneous lesions are associated with immunodeficient states. Our patient was an immunocompetent 68-year-old male who presented with a plaque on his left infraorbital area that was concerning for malignancy. Histological examination of the lesion revealed granulomatous inflammation and small yeast forms suggestive of H. capsulatum. The lesion resolved spontaneously and recurred 1 year later. On recurrence, histological examination again revealed yeast forms consistent with H. capsulatum. Serum and urine testing for H. capsulatum antigen were negative. Next-generation sequencing detected H. capsulatum, which supported the diagnosis of a cutaneous infection. The patient was prescribed and started treatment with itraconazole for 1 year after recurrence of the lesion, and he has not reported further disease recurrence to date. This case is unique because of the presentation of a primary cutaneous recurrent H. capsulatum lesion, and it demonstrated the utility of laboratory testing in its diagnosis.

Lower respiratory tract infections, including hospital-acquired and ventilator-associated pneumonia, are common in hospitalized patient populations. Standard methods frequently fail to identify the infectious etiology due to the polymicrobial nature of respiratory specimens and the necessity of ordering specific tests to identify viral agents. The potential severity of these infections combined with a failure to clearly identify the causative pathogen results in administration of empirical antibiotic agents based on clinical presentation and other risk factors., Lower respiratory tract infections, including hospital-acquired and ventilator-associated pneumonia, are common in hospitalized patient populations. Standard methods frequently fail to identify the infectious etiology due to the polymicrobial nature of respiratory specimens and the necessity of ordering specific tests to identify viral agents. The potential severity of these infections combined with a failure to clearly identify the causative pathogen results in administration of empirical antibiotic agents based on clinical presentation and other risk factors. We examined the impact of the multiplexed, semiquantitative BioFire FilmArray Pneumonia panel (PN panel) test on laboratory reporting for 259 adult inpatients submitting bronchoalveolar lavage (BAL) specimens for laboratory analysis. The PN panel demonstrated a combined 96.2% positive percent agreement (PPA) and 98.1% negative percent agreement (NPA) for the qualitative identification of 15 bacterial targets compared to routine bacterial culture. Semiquantitative values reported by the PN panel were frequently higher than values reported by culture, resulting in semiquantitative agreement (within the same log10 value) of 43.6% between the PN panel and culture; however, all bacterial targets reported as >105 CFU/ml in culture were reported as ≥105 genomic copies/ml by the PN panel. Viral targets were identified by the PN panel in 17.7% of specimens tested, of which 39.1% were detected in conjunction with a bacterial target. A review of patient medical records, including clinically prescribed antibiotics, revealed the potential for antibiotic adjustment in 70.7% of patients based on the PN panel result, including discontinuation or de-escalation in 48.2% of patients, resulting in an average savings of 6.2 antibiotic days/patient.

SARS-CoV-2, the causative agent of COVID-19, is widespread in several countries around the world following its late-2019 emergence in the human population. Rapid development of molecular diagnostic tests and subunit vaccines have been prioritized, and as such evaluating the SARS-CoV-2 genomic plasticity and evolutionary dynamics is an urgent need. We determined the SARS-CoV-2 selectome by calculating rates of pervasive and episodic diversifying selection for every amino acid coding position in the SARS-CoV-2 genome. To provide context for evolutionary dynamics of a highly pathogenic betacoronavirus following a zoonotic spillover into human hosts, we also determined the selectomes of SARS-CoV and MERS-CoV, and performed evolvability calculations for SARS-CoV-2 based on SARS-CoV. These analyses identify the amino acid sites within each coding sequence that have been subjected to pervasive diversifying selection or episodic diversifying selection, and report significantly evolvable sites in the ORF1a polyprotein, the spike protein, and the membrane protein of SARS-CoV-2. These findings provide a comprehensive view of zoonotic, highly pathogenic betacoronavirus evolutionary dynamics that can be directly applied to diagnostic assay and vaccine design for SARS-CoV-2.

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.

Automation of the clinical microbiology laboratory has become more prominent as laboratories face higher specimen volumes and understaffing and are becoming more consolidated. One recent advancement is the use of digital image analysis to rapidly distinguish between chromogenic growth for screening bacterial cultures. In this study, colony segregation software developed by Copan (Brescia, Italy) was evaluated to distinguish between significant growth and no growth of urine cultures plated onto standard blood and MacConkey agars. Specimens from 3 sites were processed on a WASP instrument (Copan) and incubated on the WASPLab platform (Copan), and plates were imaged at 0 and 24 hours postinoculation. Images were read by technologists following validated laboratory protocols (VLPs), and results were recorded in the laboratory information systems (LIS). Image analysis performed colony counts on the 24-hour images, and results were compared with the VLP. A total of 12,931 urine cultures were tested and analyzed with an overall sensitivity and specificity of 99.8% and 72.0%, respectively. After secondary review, 91.1% of manual-positive/automation-negative specimens were due to expert rules that reported the plate as contaminated or growing only normal flora and not due to threshold counts. Nine specimens were found to be manual-positive/automation-negative; a secondary review demonstrated that the results of 8 of these specimens were due to growth of microcolonies that were programmed to be ignored by the software and 1 were due to a colony count near the limit of significance. Overall, the image analysis software proved to be highly sensitive and can be utilized by laboratories to batch-review negative cultures to improve laboratory workflow.

The incidence of neonatal Group B streptococcal (GBS) disease has significantly declined since the widespread implementation of prenatal screening of expectant mothers for urogenital and gastrointestinal tract GBS colonization. Screening methods have evolved from exclusively culture-based approaches to more rapid and highly sensitive molecular methods. We chose to evaluate the performance of 4 commercially available GBS molecular tests for detection of GBS colonization using 299 antepartum rectal–vaginal specimens submitted to our laboratory for routine GBS screening. In 97% of instances, there was agreement between all 3 systems. When testing 1, 6, and 12 samples simultaneously, all methods performed comparably, but the ARIES® GBS assay required the least total hands-on time and the illumigene® Group B Streptococcus assay required the most hands-on time.

The genus Pontibacter is a recent addition to the family Cytophagaceae, phylum Bacteroidetes. Previous reports of its cultivation and molecular detection are from a variety of environmental sources, including marine and desert habitats. We report the first description of a Pontibacter sp., which was initially identified as Elizabethkingia meningoseptica, isolated from a human clinical specimen. On the basis of 16S rRNA gene sequence, unique mass spectral profile and phenotypic characterization, this isolate represents a novel species within the genus Pontibacter that has been named Pontibacter altruii, sp. nov., strain Grand Forks.

The ongoing epidemic of Zika fever in the Western Hemisphere has drawn considerable attention from the medical and scientific communities as well as the general public, largely because of its association with birth defects and postinfectious sequelae. Since its appearance in Brazil in 2015, Zika virus has spread to more than 45 countries in the Western Hemisphere and has caused countless infections. To date, no treatment or vaccine exists, but a considerable multinational effort to halt Zika virus transmission is underway. This article reviews the basic biology, epidemiology, pathophysiology, diagnosis, and treatment of Zika virus and Zika fever.

Histoplasmosis is a global disease endemic to regions of all six inhabited continents. The areas of highest endemicity lie within the Mississippi and Ohio River Valleys of North America and parts of Central and South America. As a result of climate change and anthropogenic land utilization, the conditions suitable for Histoplasma capsulatum are changing, leading to a corresponding change in epidemiology. The clinical manifestations of histoplasmosis are protean, variably resembling other common conditions such as community-acquired pneumonia, tuberculosis, sarcoidosis, Crohn's disease, or malignancy. Making a successful diagnosis is contingent on a thorough understanding of epidemiology, common clinical presentations, and best testing practices for histoplasmosis. While most subclinical or self-limited diseases do not require treatment in immunocompetent patients, all immunocompromised patients and those with progressive disseminated disease or chronic pulmonary disease should be treated. Liposomal amphotericin B is the preferred agent for severe or disseminated disease, while itraconazole is adequate for milder cases and “step-down” therapy following response to amphotericin B. In this review, we discuss the current evidence-based approaches to the epidemiology, diagnosis, and management of histoplasmosis.

The ability to provide timely identification of the causative agents of lower respiratory tract infections can promote better patient outcomes and support antimicrobial stewardship efforts. Current diagnostic testing options include culture, molecular testing, and antigen detection. These methods may require collection of various specimens, involve extensive sample treatment, and can suffer from low sensitivity and long turnaround times. This study assessed the performance of the BioFire FilmArray Pneumonia Panel (PN panel) and Pneumonia Plus Panel (PNplus panel), an FDA-cleared sample-to-answer assay that enables the detection of viruses, atypical bacteria, bacteria, and antimicrobial resistance marker genes from lower respiratory tract specimens (sputum and bronchoalveolar lavage [BAL] fluid)., The ability to provide timely identification of the causative agents of lower respiratory tract infections can promote better patient outcomes and support antimicrobial stewardship efforts. Current diagnostic testing options include culture, molecular testing, and antigen detection. These methods may require collection of various specimens, involve extensive sample treatment, and can suffer from low sensitivity and long turnaround times. This study assessed the performance of the BioFire FilmArray Pneumonia Panel (PN panel) and Pneumonia Plus Panel (PNplus panel), an FDA-cleared sample-to-answer assay that enables the detection of viruses, atypical bacteria, bacteria, and antimicrobial resistance marker genes from lower respiratory tract specimens (sputum and bronchoalveolar lavage [BAL] fluid). Semiquantitative results are also provided for the bacterial targets. This paper describes selected analytical and clinical studies that were conducted to evaluate performance of the panel for regulatory clearance. Prospectively collected respiratory specimens (846 BAL and 836 sputum specimens) evaluated with the PN panel were also tested by quantitative reference culture and molecular methods for comparison. The PN panel showed a sensitivity of 100% for 15/22 etiologic targets using BAL specimens and for 10/24 using sputum specimens. All other targets had sensitivities of ≥75% or were unable to be calculated due to low prevalence in the study population. Specificity for all targets was ≥87.2%, with many false-positive results compared to culture that were confirmed by alternative molecular methods. Appropriate adoption of this test could provide actionable diagnostic information that is anticipated to impact patient care and antimicrobial stewardship decisions.

Background: To date, at least 50 species of Legionella have been described. These organisms are ubiquitous in nature and have been isolated from diverse ecological environments, including man-made structures such as cooling towers and spas. Legionellae have also been isolated from human and veterinary clinical specimens, and their roles in disease are well-established. This report describes the isolation of a novel Legionella species from a respiratory specimen from a patient with influenza and suspected pulmonary embolus. Case: A 68-year-old male presented to an Indianapolis-area hospital with pulmonary disease; upon workup, he was found to have influenza A. Bronchoalveolar lavage fluid was also submitted for conventional bacterial culture and Legionella culture. The patient was prescribed a broad-spectrum antibiotic and recovered. Results: A Legionella-like bacterium was isolated on buffered charcoal yeast extract agar, and mass spectrometry and comparative 16S rRNA gene sequencing inconclusively identified the isolate as a Legionella sp. Further analysis of the 16S rRNA gene confirmed the strain to be a new species, related to Legionella hackeliae. Physiochemical and morphological testing were used to confirm the discovery of a novel species, Legionella indianapolisensis sp. nov., type strain SMNF-IS. Keywords: Legionella indianapolisensis, Legionella, Legionellae, Pulmonary abscess, Influenza, Co-infection, Lobar pneumonia

Common causes of chronic diarrhea among travelers worldwide include protozoan parasites. The majority of parasitic infections are caused by Giardia duodenalis , Entamoeba histolytica , Cryptosporidium parvum , and Cryptosporidium hominis . Similarly, these species cause the majority of parasitic diarrhea acquired in the United States. Detection of parasites by gold standard microscopic methods is time-consuming and requires considerable expertise; enzyme immunoassays and direct fluorescent-antibody (DFA) stains have lowered hands-on time for testing, but improvements in sensitivity and technical time may be possible with a PCR assay. We performed a clinical evaluation of a multiplex PCR panel, the enteric parasite panel (EPP), for the detection of these common parasites using the BD Max instrument, which performs automated extraction and amplification. A total of 2,495 compliant specimens were enrolled, including 2,104 (84%) specimens collected prospectively and 391 (16%) specimens collected retrospectively. Approximately equal numbers were received in 10% formalin (1,273 specimens) and unpreserved (1,222 specimens). The results from the EPP were compared to those from alternate PCR and bidirectional sequencing (APCR), as well as DFA ( G. duodenalis and C. parvum or C. hominis ) or trichrome stain ( E. histolytica ). The sensitivity and specificity for prospective and retrospective specimens combined were 98.2% and 99.5% for G. duodenalis , 95.5% and 99.6 for C. parvum or C. hominis , and 100% and 100% for E. histolytica , respectively. The performance of the FDA-approved BD Max EPP compared well to the reference methods and may be an appropriate substitute for microscopic examination or immunoassays.

Utilization of commercially available rapid platforms for microbial identification from positive blood cultures is useful during periods of, or in laboratories with, limited expert staffing. We compared the results of the FilmArray® BCID Panel performed by non-expert technologists to those of conventional methods for organism identification performed by skilled microbiologists. Within 8 h of signalling positive by a continuous monitoring blood culture system, positive bottles were analysed by the FilmArray BCID Panel. Data from these analyses were compared to standard-of-care testing, which included conventional and automated methods. To gauge the ease of use of the BCID Panel by non-expert staff, technologists unfamiliar with diagnostic bacteriology performed the testing without prior knowledge of the Gram stain results, or even whether organisms were detected. Identifications of 172/200 (86 %) positive blood cultures using the BCID Panel were consistent with identifications provided by standard-of-care methods. Standard-of-care testing identified organisms in 20 positive blood cultures, which were not represented on the BCID Panel. Seven (3.5 %) blood cultures demonstrated a discrepancy between the methods, which could not be attributed to either a lack of representation on the panel or unclear separate detection of organisms in a mixed blood culture of a shared genus or grouping of organisms, e.g. Staphylococcus or Enterobacteriaceae . One (0.5 %) blood culture yielded invalid results on two separate panels, so it was eliminated from the study. The easy-to-use FilmArray® technology shows good correlation with blood culture identification and antibiotic resistance detection performed by conventional methods. This technology may be particularly useful in laboratories with limited staffing or limited technical expertise.

Although histoplasmosis is highly endemic in certain regions of the Americas, disease may be seen globally and should not be overlooked in patients with unexplained pulmonary or systemic illnesses. Most patients exhibit pulmonary signs and symptoms, accompanied by radiographic abnormalities, which often are mistaken for community-acquired pneumonia caused by bacterial or viral agents. Once a diagnosis is considered, a panel of mycologic and non-culture-based assays is adequate to establish a diagnosis in a few days to a week in most patients. Once diagnosed, the treatment is highly effective even in immunocompromised patients.

The coronavirus disease 19 (COVID-19) pandemic has infected tens of millions across the world, but there is a significant gap in our understanding about COVID-19 in the hematopoietic stem transplant (HSCT) recipient population. Prolonged viral shedding is frequently observed with severe acute respiratory syndrome coronavirus-2 (SARSCoV-2), but studies suggest viral loads decline 10 days after symptom onset. Current CDC guidance suggests that severely ill and immunocompromised hosts are no longer infectious after 20 days from symptom onset. Cycle threshold (Ct) values are inversely proportional to the viral load and are used to detect SARS-CoV-2 RNA concentration. Specimens with reverse transcriptase PCR (RT-PCR) Ct values > 33–34 have been associated with inability to culture virus, and have been used as a surrogate for diminished infectivity. We report two cases of allogeneic peripheral blood stem cell transplant (PBSCT) recipients who had prolonged durations of infectivity with SARSCov-2, based on culture positivity and persistently low Ct values for greater than 50 days.

Background The global COVID-19 pandemic has had a major impact on medical student education. As the pandemic spread nationwide, numerous universities shut down with only days’ notice, and medical students were removed from all patient care settings and restricted from campuses. Yet, the need and curiosity of these future physicians to understand this new disease was great, including how to interpret and integrate rapidly evolving information on the underlying viral and immune mechanisms, pathophysiology, and epidemiology. Time students spent away from patient care settings presented an opportunity to rapidly develop and deliver new curriculum covering SARS-CoV-2 and COVID-19. Methods A team of students and faculty at Indiana University developed a Fundamentals of COVID-19 course that included up-to-date information on the virology, immunology, and pathophysiology of COVID-19. The course was delivered online, with both synchronous and asynchronous activities. Virology and immunology of the coronavirus family, including current knowledge to-date of SARS-CoV-2, were delivered using a series of readings and brief videos, followed by a small group exercise that required students to choose and present to their peers a paper from the scientific literature on COVID-19. A similar approach was used to deliver content about the pathophysiology of COVID-19. To place the COVID-19 experience in context of other pandemics, students researched and educated their small group cohort on another historical pandemic. Results To measure course effectiveness, we administered a pre-course survey gauging students’ self-confidence in their knowledge of these topics; the same survey was administered after completion of the course. Surveys from 645 (89% of enrolled) 3rd and 4th year medical students who completed both surveys were analyzed. Results showed that the course elicited a 57% increase (p< 0.001) in students’ confidence in their knowledge of COVID-19 virology and immunology and a 64% increase (p< 0.001) in knowledge of the pathophysiology. Conclusion Data showed that the asynchronous content and group activities were successful in engaging and educating the students on foundational knowledge of COVID-19 and were an effective approach to rapidly evolving information when faced with a novel disease. Disclosures All Authors: No reported disclosures

Group B Streptococcus (GBS) is the leading cause of neonatal sepsis and meningitis in developed countries. Recommendations for antepartum GBS detection include enriched culture with several options for identifying GBS, some of which are time-consuming. To reduce the time for identification and determination of the maternal GBS colonization status, rapid nucleic acid amplification technologies have been developed and commercialized. For rapid detection of GBS, a three-site clinical study was conducted to evaluate the NeuMoDx GBS assay, a real-time PCR test performed for vaginal/rectal swab specimens in Lim broth enrichment culture on the NeuMoDx 288 molecular system (NeuMoDx system); these data were used to a support 510(k) submission. A total of 1,250 eligible remnant samples were prospectively enrolled and tested during the study. The results of the PCR assay were compared to the results of the Centers for Disease Control and Prevention (CDC)-recommended enriched-culture method, which served as the gold standard reference method for the study. The NeuMoDx GBS assay results yielded a sensitivity of 96.9% (95% confidence interval [CI] = 94.1 to 98.4), specificity of 96.0% (95% CI = 94.6 to 97.1), and a total agreement with the reference method of 96.2% (95% CI = 93.8 to 98.3). NeuMoDx GBS assay results were also compared to results obtained using the BD MAX GBS assay on the BD MAX system. The two systems demonstrated a total percent agreement of 98.0% (95% CI = 95.5 to 100.0). The performance of the NeuMoDx GBS assay implemented on the NeuMoDx system compared favorably to the CDC enriched-culture method and to the BD MAX GBS assay.

Molecular methods offer superior sensitivity and specificity and reduce testing turnaround time from days to hours for detection of Bordetella pertussis and Bordetella parapertussis. In this study, we evaluated the performance of the automated PCR-based Aries Bordetella Assay, which detects both B. pertussis and B. parapertussis directly from nasopharyngeal swab specimens. The limits of detection (LoDs) were 1,800 CFU·ml−1 for B. pertussis and 213 CFU·ml−1 for B. parapertussis. The assay detected 16/18 unique B. pertussis/B. parapertussis strains. Of 71 potentially cross-reacting organisms, 5 generated false positives in 1/6 replicates; none of 6 additional Bordetella spp. were erroneously detected. Specimens were stable at 20 to 25°C for at least 10 h, at 4 to 8°C for 10 days, and at temperatures not exceeding −70°C for 6 months. Of 1,052 nasopharyngeal specimens from patients with suspected pertussis, 3.0% (n = 32) were B. pertussis positive and 0.2% (n = 2) were B. parapertussis positive. Combining these data with Aries Bordetella Assay data from 57 nasopharyngeal samples with previously confirmed B. pertussis or B. parapertussis data and with data from 50 contrived B. parapertussis samples, the proportions of positive and negative agreement of the respective Aries assays with the reference assays were 97.1% and 99.0% for B. pertussis and 100% and 99.7% for B. parapertussis. The Aries Bordetella Assay provides accurate detection and distinction of B. pertussis and B. parapertussis infections within 2 h. (This study has been registered at ClinicalTrials.gov under registration no. NCT02862262.)

Molecular methods offer superior sensitivity and specificity and reduce testing turnaround time from days to hours for detection of Bordetella pertussis and Bordetella parapertussis. In this study, we evaluated the performance of the automated PCR-based Aries Bordetella Assay, which detects both B. pertussis and B. parapertussis directly from nasopharyngeal swab specimens. The limits of detection (LoDs) were 1,800 CFU·ml(−1) for B. pertussis and 213 CFU·ml(−1) for B. parapertussis. The assay detected 16/18 unique B. pertussis/B. parapertussis strains. Of 71 potentially cross-reacting organisms, 5 generated false positives in 1/6 replicates; none of 6 additional Bordetella spp. were erroneously detected. Specimens were stable at 20 to 25°C for at least 10 h, at 4 to 8°C for 10 days, and at temperatures not exceeding −70°C for 6 months. Of 1,052 nasopharyngeal specimens from patients with suspected pertussis, 3.0% (n = 32) were B. pertussis positive and 0.2% (n = 2) were B. parapertussis positive. Combining these data with Aries Bordetella Assay data from 57 nasopharyngeal samples with previously confirmed B. pertussis or B. parapertussis data and with data from 50 contrived B. parapertussis samples, the proportions of positive and negative agreement of the respective Aries assays with the reference assays were 97.1% and 99.0% for B. pertussis and 100% and 99.7% for B. parapertussis. The Aries Bordetella Assay provides accurate detection and distinction of B. pertussis and B. parapertussis infections within 2 h. (This study has been registered at ClinicalTrials.gov under registration no. NCT02862262.)