Evaluation of a Multiplex PCR Panel for the Microbiological Diagnosis of Pneumonia in Hospitalized Patients: Experience from an Academic Medical Center.

OBJECTIVES: We evaluated the value of BioFire® FilmArray® pneumonia panel in establishing a microbiological diagnosis of pneumonia. We evaluated opportunities for antimicrobial optimization from its use. METHODS: We included adult patients with pneumonia between May 2019 and January 2020. The pneumonia panel was used on high-quality sputum specimens, and the results were prospectively compared with sputum cultures and other tests performed according to standard of care. RESULTS: Seventy patients were included, sixty-nine of whom completed a 5-day antimicrobial course for pneumonia, and 14.3% died during hospitalization. There was a trend of higher rate of microbiological diagnosis among the patients with culture submitted before antimicrobial administration (9/15 vs. 20/55; p = 0.09). The panel increased the microbiological diagnosis from 29/70 to 59/70 (p < 0.001) patients. The per isolate analysis revealed an increase in the isolation of Haemophilus influenzae (p = 0.002) and Streptococcus pneumoniae (p = 0.05). On review of empiric antimicrobials, there was potential for antimicrobial optimization in 56/70 patients, including 9 bacteria among 9 patients, which were not covered by empiric treatment and another 70 antimicrobials in 49 patients that could have been stopped. CONCLUSIONS: Incorporation of the pneumonia panel in the diagnostic work-up of pneumonia substantially increased the rate of microbiological diagnosis and revealed abundant opportunities for antimicrobial optimization.

TOP1α, UPF1, and TTG2 regulate seed size in a parental dosage-dependent manner.

Cues of maternal and paternal origins interact to control seed development, and the underlying molecular mechanisms are still far from clear. Here, we show that TOPOISOMERASE Iα (TOP1α), UP-FRAMESHIFT SUPPRESSOR 1 (UPF1), and TRANSPARENT TESTA GLABRA2 (TTG2) gametophytically, biparentally regulate seed size in Arabidopsis. TOP1α and UPF1 are mainly expressed in antipodal cells, and loss of their function leads to ectopic TTG2 expression in these female gametophytic cells. We further demonstrate that TOP1α and UPF1 directly repress TTG2 expression through affecting its chromatin status and determine its relative expression in antipodal cells versus sperm cells, which controls seed size in a dosage-dependent and parent-of-origin-dependent manner. The molecular interplay among these three genes explains their biparental gametophytic effect during diploidy and interploidy reciprocal crosses. Taken together, our findings reveal a molecular framework of parental interaction for seed size control.

Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution.

The recent emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real-time reverse transcription-PCR (RT-PCR) platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. The two platforms demonstrate comparable performances; however, the run times for each assay are 3.5 h and 45 min, respectively. In search for a platform with a shorter turnaround time, we sought to evaluate the recently released Abbott ID Now COVID-19 assay, which is capable of producing positive results in as little as 5 min. We present here the results of comparisons between Abbott ID Now COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media and comparisons between Abbott ID Now COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media for Cepheid and dry nasal swabs for Abbott ID Now. Regardless of method of collection and sample type, Abbott ID Now COVID-19 had negative results in a third of the samples that tested positive by Cepheid Xpert Xpress when using nasopharyngeal swabs in viral transport media and 45% when using dry nasal swabs.

Epidemiology and diagnosis of hospital-acquired conjunctivitis among neonatal intensive care unit patients.

BACKGROUND: Few recent reports describe the epidemiology and risk factors for health care-associated conjunctivitis among neonatal intensive care unit (NICU) patients in developed countries. Reporting may be inaccurate in this population given that the National Nosocomial Infection Surveillance System (NNIS) definition is largely dependent on a positive culture, whereas clinical practice often consists of empiric treatment. OBJECTIVES: We describe the epidemiology of conjunctivitis among neonates in 2 level III-IV NICUs and compare the NNIS definition with our study definition: eye drainage and empiric treatment with or without a culture. METHODS: Patient demographics, clinical, device usage and conjunctivitis data collected prospectively from March 2001 through January 2003 were analyzed. RESULTS: Conjunctivitis occurred in 5% (n = 154/2935) of infants, of whom 51% (n =79) were in NICU 1 and 49% (n =75) in NICU 2. Predominant pathogens included coagulase-negative staphylococci (25%), Staphylococcus aureus (19%) and Klebsiella spp. (10%). Significant predictors of conjunctivitis included low birth weight, use of ventilator or nasal cannula continuous positive airway pressure and study year. Ophthalmologic examination was an additional predictor of infection in NICU 1. Eye examination data were unavailable for NICU 2. Only 62% of cases that met the study definition for conjunctivitis met the NNIS definition, because many infants received empiric treatment. CONCLUSIONS: Clinical conjunctivitis was associated with low birth weight and patient care factors that could lead to contamination of the eye with respiratory tract secretions. The NNIS definition failed to detect 38% of clinical infections. Consideration should be given to revising the definition of conjunctivitis for the NICU population.