The Next-Generation Sequencing (NGS) Quality Initiative addresses laboratory challenges faced when performing NGS by developing tools and resources to build a robust quality management system. Here, we illustrate how those products support laboratories in navigating complex regulatory environments and quality-related challenges while implementing NGS effectively in an evolving landscape.

Identification of the emerging multidrug-resistant yeast Candida auris is challenging. Here, we describe the role of the Mexico national reference laboratory Instituto de Diagnóstico y Referencia Epidemiológicos Dr. Manuel Martínez Báez (InDRE) and the Mexican national laboratory network in the identification of C. auris. Reference identification of six suspected isolates was done based on phenotypic and molecular laboratory methods, including growth in special media, evaluation of isolate micromorphology, and species-specific PCR and pan-fungal PCR and sequencing. The four C. auris isolates identified were able to grow on modified Sabouraud agar with 10% NaCl incubated at 42 °C. With one exception, isolates of C. auris were spherical to ovoid yeast-like cells and blastoconidia, with no hyphae or pseudohyphae on cornmeal agar. C. auris isolates were resistant to fluconazole. Species-specific and pan-fungal PCR confirmed isolates as C. auris. Sequence analysis revealed the presence of two different C. auris clades in Mexico, clade I (South Asia) and clade IV (South America).

Patient care and public health require timely, reliable laboratory testing. However, clinical laboratory professionals rarely know whether patient specimens contain infectious agents, making ensuring biosafety while performing testing procedures challenging. The importance of biosafety in clinical laboratories was highlighted during the 2014 Ebola outbreak, where concerns about biosafety resulted in delayed diagnoses and contributed to patient deaths. This review is a collaboration between subject matter experts from large and small laboratories and the federal government to evaluate the capability of clinical laboratories to manage biosafety risks and safely test patient specimens. We discuss the complexity of clinical laboratories, including anatomic pathology, and describe how applying current biosafety guidance may be difficult as these guidelines, largely based on practices in research laboratories, do not always correspond to the unique clinical laboratory environments and their specialized equipment and processes. We retrospectively describe the biosafety gaps and opportunities for improvement in the areas of risk assessment and management; automated and manual laboratory disciplines; specimen collection, processing, and storage; test utilization; equipment and instrumentation safety; disinfection practices; personal protective equipment; waste management; laboratory personnel training and competency assessment; accreditation processes; and ethical guidance. Also addressed are the unique biosafety challenges successfully handled by a Texas community hospital clinical laboratory that performed testing for patients with Ebola without a formal biocontainment unit. The gaps in knowledge and practices identified in previous and ongoing outbreaks demonstrate the need for collaborative, comprehensive solutions to improve clinical laboratory biosafety and to better combat future emerging infectious disease outbreaks.

To study teen birth rates, trends, and socio-demographic and pregnancy characteristics of AI/AN across geographic regions in the US. The birth rate for US teenagers 15-19 years reached a historic low in 2009 (39.1 per 1,000) and yet remains one of the highest teen birth rates among industrialized nations. In the US, teen birth rates among Hispanic, non-Hispanic black, and American Indian/Alaska Native (AI/AN) youth are consistently two to three times the rate among non-Hispanic white teens. Birth certificate data for females younger than age 20 were used to calculate birth rates (live births per 1,000 women) and joinpoint regression to describe trends in teen birth rates by age (<15, 15-17, 18-19) and region (Aberdeen, Alaska, Bemidji, Billings, California, Nashville, Oklahoma, Portland, Southwest). Birth rates for AI/AN teens varied across geographic regions. Among 15-19-year-old AI/AN, rates ranged from 24.35 (California) to 123.24 (Aberdeen). AI/AN teen birth rates declined from the early 1990s into the 2000s for all three age groups. Among 15-17-year-olds, trends were approximately level during the early 2000s-2007 in six regions and declined in the others. Among 18-19-year-olds, trends were significantly increasing during the early 2000s-2007 in three regions, significantly decreasing in one, and were level in the remaining regions. Among AI/AN, cesarean section rates were lower in Alaska (4.1%) than in other regions (16.4-26.6%). This is the first national study to describe regional variation in AI/AN teen birth rates. These data may be used to target limited resources for teen pregnancy intervention programs and guide research.

During May 2009-April 2010, we analyzed 692 samples of pandemic (H1N1) 2009 virus from patients in Mexico. We detected the H275Y substitution of the neuraminidase gene in a specimen from an infant with pandemic (H1N1) 2009 who was treated with oseltamivir. This virus was susceptible to zanamivir and resistant to adamantanes and oseltamivir.