Risk factors and clinical outcomes associated with multiple as opposed to single pathogens detected on the gastrointestinal disease polymerase chain reaction assay.

Background: The use of gastrointestinal disease multiplex polymerase chain reaction (GI PCR) testing has become common for suspected gastrointestinal infection. Patients often test positive for multiple pathogens simultaneously through GI PCR, although the clinical significance of this is uncertain.

Methods: This retrospective cohort study investigated risk factors and clinical outcomes associated with detection of multiple (as opposed to single) pathogens on GI PCR.

Timing and clinical risk factors for early acquisition of gut pathogen colonization with multidrug resistant organisms in the intensive care unit.

Background: Microbiome restitution therapies are being developed to prevent gut pathogen colonization among patients in the intensive care unit (ICU) and in other select populations. If preventive therapies are to be effective, they must be administered prior to pathogen acquisition. The timing and risk factors for early acquisition of gut pathogen colonization (within 72 h) are currently unknown and could be helpful to guide ICU trial design.

Impact of active surveillance and decolonization strategies for methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit.

Objective: To assess the impact of active surveillance and decolonization strategies on methicillin-resistant Staphylococcus aureus (MRSA) infection rates in a NICU.

Study Design: MRSA infection rates were compared before (2014-2016) and during (2017-2022) an active surveillance program. Eligible infants were decolonized with chlorohexidine gluconate (CHG) bathing and/or topical mupirocin.

Assessing respiratory viral exclusion and affinity interactions through co-infection incidence in a pediatric population during the 2022 resurgence of influenza and RSV.

Introduction: In the Northeast US, respiratory viruses such as influenza and respiratory syncytial virus (RSV), which were largely suppressed by COVID-19-related social distancing, made an unprecedented resurgence during 2022, leading to a substantial rise in viral co-infections. However, the relative rates of co-infection with seasonal respiratory viruses over this period have not been assessed.

Methods: Here we reviewed multiplex respiratory viral PCR data (BioFire FilmArray™ Respiratory Panel v2.

A case of novel, rapidly-growing Mycolicibacter kumamotonensis infection in a patient with severe pulmonary disease treated in New York City.

Introduction: Mycolicibacter kumamotonensis is a slowly growing, non-chromogenic non-tuberculous mycobacteria (NTM) that was initially distinguished from the M. terrae complex in 2006. Since then it has been rarely reported as the cause of pulmonary and soft-tissue infections in both immunocompromised and immunocompetent patients.

Genomic and Epidemiological Features of Two Dominant Methicillin-Susceptible Staphylococcus aureus Clones from a Neonatal Intensive Care Unit Surveillance Effort.

Methicillin-susceptible Staphylococcus aureus (MSSA) is a more prevalent neonatal intensive care unit (NICU) pathogen than methicillin-resistant S. aureus (MRSA). However, the introduction and spread of MSSA, the role of systematic decolonization, and optimal infection prevention and control strategies remain incompletely understood.

Impact of Implementing the Cerebrospinal Fluid FilmArray Meningitis/Encephalitis Panel on Duration of Intravenous Acyclovir Treatment.

Background: Herpes simplex virus-1 is the most common cause of sporadic encephalitis worldwide and requires prompt antiviral treatment. Traditionally, herpes simplex virus-1 (HSV-1) cerebrospinal fluid (CSF) testing is conducted using standalone polymerase chain reaction (PCR). The BioFire CSF FilmArray Meningitis/Encephalitis Panel (BioFire ME Panel) was introduced in 2015 at our institution, providing an alternative method of HSV-1 CSF testing.

Successful diagnostic stewardship for testing in pediatrics.

Objective: To reduce both inappropriate testing for and diagnosis of healthcare-onset (HO) infections (CDIs).

Design: We performed a retrospective analysis of testing from hospitalized children before (October 2017-October 2018) and after (November 2018-October 2020) implementing restrictive computerized provider order entry (CPOE).

Setting: Study sites included hospital A (a ∼250-bed freestanding children's hospital) and hospital B (a ∼100-bed children's hospital within a larger hospital) that are part of the same multicampus institution.

Bacterial Pneumonia and Respiratory Culture Utilization among Hospitalized Patients with and without COVID-19 in a New York City Hospital.

COVID-19 is associated with prolonged hospitalization and a high risk of intubation, which raises concern for bacterial coinfection and antimicrobial resistance. Previous research has shown a wide range of bacterial pneumonia rates for COVID-19 patients in a variety of clinical and demographic settings, but none have compared hospitalized COVID-19 patients to patients testing negative for severe acute respiratory syndrome coronavirus (SARS-CoV-2) in similar care settings. We performed a retrospective cohort study on hospitalized patients with COVID-19 testing from March 10th, 2020 to December 31st, 2020.

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene.

Prevalence of Gastrointestinal Pathogens Detected by Multiplex Polymerase Chain Reaction in a Prospective Cohort of Men Who Have Sex With Men Taking Human Immunodeficiency Virus Preexposure Prophylaxis-New York City, 2019-2020.

Multiplex polymerase chain reaction testing for gastrointestinal pathogens was performed on a longitudinal cohort of 110 men who have sex with men taking human immunodeficiency virus preexposure prophylaxis. At least 1 pathogen was detected among 50 (45%) participants, with some participants testing positive for the same pathogen on multiple consecutive visits over a period of months.

Spa Typing of Staphylococcus aureus in a Neonatal Intensive Care Unit During Routine Surveillance.

Background: Staphylococcus aureus protein A (spa) typing can be used to expand characterization of the epidemiology of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) in neonatal intensive care units (NICU).

Clinical Significance of Positive Results of the BioFire Cerebrospinal Fluid FilmArray Meningitis/Encephalitis Panel at a Tertiary Medical Center in the United States.

Context.—: The FilmArray Meningitis/Encephalitis (ME) panel is the first US Food and Drug Administration-cleared multiplex polymerase chain reaction panel for the detection of central nervous system infections. While the assay's performance characteristics have been described, the real-world significance of positive results has not been fully characterized.

Cycle Thresholds Among Solid Organ Transplant Recipients Testing Positive for SARS-CoV-2.

Background: The optimal duration of transmission-based precautions among immunocompromised patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown.

Methods: Retrospective review of patients with solid organ transplant with positive SARS-CoV-2 polymerase chain reaction result from nasopharyngeal specimens admitted to the hospital between March 13, 2020 and May 15, 2020.

Results: Twenty-one percent of solid organ transplant recipients with positive SARS-CoV-2 polymerase chain reaction detected ≥20 d after symptom onset (or after first positive test among asymptomatic individuals) had a low cycle threshold (ie, high viral load).

Pretest Symptom Duration and Cycle Threshold Values for Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-Transcription Polymerase Chain Reaction Predict Coronavirus Disease 2019 Mortality.

Background: The relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and patient symptom duration in both in- and outpatients, and the impact of these factors on patient outcomes, are currently unknown. Understanding these associations is important to clinicians caring for patients with coronavirus disease 2019 (COVID-19).

Methods: We conducted an observational study between March 10 and May 30, 2020 at a large quaternary academic medical center in New York City.

Burden and risk factors for inappropriate Clostridioides Difficile infection testing among hospitalized patients.

Background: The purpose of this study was to identify the burden and risk factors for inappropriate Clostridioides difficile infection (CDI) testing.

Methods: This was a retrospective cohort study among adults hospitalized between 2010 and 2019. Inappropriate CDI testing was defined as a formed stool specimen, an order within 7 days of a previously negative test, or an order within 24 hours of laxative administration.

An ultra-high-density protein microarray for high throughput single-tier serological detection of Lyme disease.

Current serological immunoassays have inherent limitations for certain infectious diseases such as Lyme disease, a bacterial infection caused by Borrelia burgdorferi in North America. Here we report a novel method of manufacturing high-density multiplexed protein microarrays with the capacity to detect low levels of antibodies accurately from small blood volumes in a fully automated system. A panel of multiple serological markers for Lyme disease are measured using a protein microarray system, Lyme Immunochip, in a single step but interpreted adhering to the standard two-tiered testing algorithm (enzyme immunoassay followed by Western blot).

At-Home Testing for Sexually Transmitted Infections During the COVID-19 Pandemic.

During the COVID-19 pandemic in New York City, NewYork-Presbyterian Hospital provided HIV prevention patients with gonorrhea/chlamydia testing kits at home. This report describes the program implementation to provide other sexual health clinics with a roadmap in adapting to a "new normal" in providing comprehensive sexual health care virtually to patients.

Rapid Diagnosis of Meningococcal Meningitis in a Patient With Familial Mediterranean Fever by the FilmArray Meningitis/Encephalitis Panel: A Case Report.

Familial Mediterranean fever (FMF) is a rare autoinflammatory disorder of the innate immune system. Patients with innate immune system defects are at a high risk of meningococcal disease, although it is unclear if patients with FMF also have increased susceptibility to invasive infection. Herein, we present a diagnostically challenging case of a male adolescent with a past medical history of FMF stabilized on colchicine who presented with some of the early clinical features of community-acquired bacterial meningitis.

Clinical Performance of SARS-CoV-2 Molecular Tests.

Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the clinical performance of these tests is still poorly understood, particularly with regard to disease course, patient-specific factors, and viral shedding. From 10 March to 1 May 2020, NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed for 3,432 patients, of which 2,413 had initial negative and 802 had initial positive results.