Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories.

Next-generation sequencing (NGS) has applications in research, epidemiology, oncology, and infectious disease diagnostics. Wide variability exists in NGS wet laboratory techniques and dry laboratory analytical considerations. Thus, many questions remain unanswered when NGS methods are implemented in laboratories for infectious disease testing.

Carbapenem-Resistant Klebsiella pneumoniae in Large Public Acute-Care Healthcare System, New York, New York, USA, 2016-2022.

Controlling the spread of carbapenem-resistant Enterobacterales is a global priority. Using National Healthcare Safety Network data, we characterized the changing epidemiology of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a large public health system in New York, New York, USA. During 2016-2020, CRKP cases declined; however, during 2021-June 2022, a notable increase occurred.

Direct detection of drug-resistant using targeted next generation sequencing.

complex (MTBC) infections are treated with combinations of antibiotics; however, these regimens are not as efficacious against multidrug and extensively drug resistant MTBC. Phenotypic (growth-based) drug susceptibility testing on slow growing bacteria like MTBC requires many weeks to months to complete, whereas sequencing-based approaches can predict drug resistance (DR) with reduced turnaround time. We sought to develop a multiplexed, targeted next generation sequencing (tNGS) assay that can predict DR and can be performed directly on clinical respiratory specimens.

Considerations from the College of American Pathologists for Implementation of an Assay for SARS-CoV-2 Testing after a Change in Regulatory Status.

The U.S. Food & Drug Administration (FDA) regulates the marketing of manufacturers' diagnostic tests (IVDs), including assays for the detection of SARS-CoV-2.

Novel 6-Month Treatment for Drug-Resistant Tuberculosis, United States.

The US Food and Drug Administration approved a 6-month regimen of pretomanid, bedaquiline, and linezolid for extensively drug-resistant or multidrug-intolerant tuberculosis after a trial in South Africa demonstrated 90% effectiveness 6 months posttreatment. We report on a patient who completed the regimen using a lower linezolid dose.

Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation.

Background: Whole genome sequencing (WGS) has enabled the development of new approaches to track Mycobacterium tuberculosis (Mtb) transmission between tuberculosis (TB) cases but its utility may be challenged by the discovery that Mtb diversifies within hosts. Nevertheless, there is limited data on the presence and degree of within-host evolution.

Methods: We profiled a well-documented Mtb transmission cluster with three pulmonary TB cases to investigate within-host evolution and describe its impact on recent transmission estimates.

Comparative Performance of the Reverse Algorithm Using Architect Syphilis TP Versus the Traditional Algorithm Using Rapid Plasma Reagin in Florida's Public Health Testing Population.

In Florida, where syphilis is a reportable disease, the number of primary and secondary (P&S) syphilis cases has increased from 3,266 in 2008-2010 to 5,340 in 2013-2015, a 63% increase. The objective of this study was to compare the performance and sensitivity of the syphilis reverse algorithm with the traditional algorithm for detecting P&S (infectious) syphilis cases. Clinical specimens from individuals who self-referred for syphilis testing at public health clinics were processed using the traditional algorithm (non-treponemal rapid plasma reagin (RPR) test followed by a confirmatory treponemal (EIA) test) and then further tested with the Architect Syphilis TP (ASTP) immunoassay (Abbott Diagnostics, Chicago, IL, USA) or by RPR confirmation, if needed (reverse algorithm).

Outbreak of Tattoo-associated Nontuberculous Mycobacterial Skin Infections.

Background: On 29 April 2015, the Florida Department of Health in Miami-Dade County (DOH Miami-Dade) was notified by a local dermatologist of 3 patients with suspected nontuberculous mycobacterial (NTM) infection after receiving tattoos at a local tattoo studio.

Methods: DOH Miami-Dade conducted interviews and offered testing, described below, to tattoo studio clients reporting rashes. Culture of clinical isolates and identification were performed at the Florida Bureau of Public Health Laboratories.

Initial Public Health Laboratory Response After Hurricane Maria - Puerto Rico, 2017.

Hurricane Maria made landfall in Puerto Rico on September 20, 2017, causing major damage to infrastructure and severely limiting access to potable water, electric power, transportation, and communications. Public services that were affected included operations of the Puerto Rico Department of Health (PRDOH), which provides critical laboratory testing and surveillance for diseases and other health hazards. PRDOH requested assistance from CDC for the restoration of laboratory infrastructure, surveillance capacity, and diagnostic testing for selected priority diseases, including influenza, rabies, leptospirosis, salmonellosis, and tuberculosis.

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.

Accuracy and reproducibility of the Etest to detect drug-resistant Neisseria gonorrhoeae to contemporary treatment.

Purpose: Neisseria gonorrhoeae is a sexually transmitted bacterial pathogen that continues to evolve to become resistant to known antibiotics. In preparing for potential emergence, the Centers for Disease Control and Prevention recommends that clinical laboratories maintain or develop protocols to assess antibiotic susceptibly for this organism. This study examines the intra-laboratory variability of using the Etest method to provide consistent MIC values for N.

Performance of the G4 Xpert MTB/RIF assay for the detection of Mycobacterium tuberculosis and rifampin resistance: a retrospective case-control study of analytical and clinical samples from high- and low-tuberculosis prevalence settings.

Background: The Xpert MTB/RIF (Xpert) assay is a rapid PCR-based assay for the detection of Mycobacterium tuberculosis complex DNA (MTBc) and mutations associated with rifampin resistance (RIF). An updated version introduced in 2011, the G4 Xpert, included modifications to probe B and updated analytic software.

Methods: An analytical study was performed to assess Xpert detection of mutations associated with rifampin resistance in rifampin-susceptible and -resistant isolates.

Bioterrorism: a laboratory who does it?

In October 2001, the first disseminated biological warfare attack was perpetrated on American soil. Initially, a few clinical microbiology laboratories were testing specimens from acutely ill patients and also being asked to test nasal swabs from the potentially exposed. Soon after, a significant number of clinical microbiology and public health laboratories received similar requests to test the worried well or evaluate potentially contaminated mail or environmental materials, sometimes from their own break rooms.

HIV single staging algorithm: integration and maximization of resources by reducing time between HIV diagnosis and treatment.

Background: Early HIV diagnosis, linkage and engagement into care are vital to improved personal health outcomes. The initiation of antiretroviral therapy, with retention in care and drug adherence leads to viral load suppression, a significant decrease in HIV transmission rates and ultimately a reduction in HIV incidence rates. In the U.

Phenotypic and molecular characterization of Solobacterium moorei isolates from patients with wound infection.

Though seldom reported, Solobacterium moorei, which was first described in 2000, has been identified in specimens from patients with root canals, periradicular lesions, periodontal disease, dentoalveolar abscesses, bacteremia, septic thrombophlebitis, and halitosis. In the present study, we describe 9 cases of mixed wound infection, from a pool of 400 surgical wound infections that we have studied, in which S. moorei was isolated or found in a clone library.

Gemella asaccharolytica sp. nov., isolated from human clinical specimens.

Three strains of an unidentified Gram-stain-variable, fastidious, catalase-negative, capnophilic, non-spore-forming, coccus-shaped bacterium from human wound specimens were characterized by phenotypic and molecular taxonomic methods. Initially, these strains were anaerobic; with repeated culture, they became aerotolerant. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically homogeneous and constituted a novel subline within the genus Gemella.

Penicillin G-resistant viridans group streptococcal endocarditis and interpretation of the American Heart Association's Guidelines for the Treatment of Infective Endocarditis.

We report a case of endocarditis due to a penicillin-"resistant" Streptococcus parasanguinis, discuss interpretations of the American Heart Association's guidelines for the treatment of viridans group streptococcal infection, and comment on therapy for infective endocarditis due to penicillin-resistant viridans group streptococci.

Determination of bft gene subtypes in Bacteroides fragilis clinical isolates.

A rapid multiplex PCR approach was developed to detect the bft gene subtypes in Bacteroides fragilis clinical isolates. This technique could be used to look at the epidemiology of enterotoxigenic strains of B. fragilis in clinical infections and whether there is a correlation between disease and the presence of B.

Clearance of Cellulosimicrobium cellulans bacteremia in a child without central venous catheter removal.

Cellulosimicrobium cellulans (formerly known as Oerskovia xanthineolytica) rarely causes human infection. Infections have been reported in immunocompromised hosts or in patients with foreign bodies, such as catheters, where treatment has generally involved removal of the foreign body. We report on a case in which the organism was isolated in multiple blood cultures from a 13-year-old male.

Isolation of a strictly anaerobic strain of Staphylococcus epidermidis.

Staphylococcus epidermidis is a well-characterized, nonfastidious, aerobic gram-positive coccus commonly isolated in the clinical microbiology laboratory. Although coagulase-negative staphylococci, including Staphylococcus epidermidis, are often considered a contaminant in the clinical laboratory, an increasing number of reports describe their pathogenesis, in particular in infections of prosthetic devices. This article describes the isolation of a strictly anaerobic strain of Staphylococcus epidermidis in pure culture from the site of an infected prosthetic hip.