Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics.

The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions.

Chagas Disease Diagnostic Practices at Four Major Hospital Systems in California and Texas.

Background: Chagas disease (CD) is a parasitic disease that affects ∼300 000 people living in the United States. CD leads to cardiac and/or gastrointestinal disease in up to 30% of untreated people. However, end-organ damage can be prevented with early diagnosis and antiparasitic therapy.

New records of Nitidulidae (Nitidulidae, Coleoptera) species in Canada, Ontario, and Manitoba.

Nitidulidae trapping performed from 2018 to 2021 to characterize flight behaviors of potential vectors of the oak wilt pathogen yielded three new species records for Canada, six new species records for Ontario, and three new species records for Manitoba. The new records for Canada include Carpophilus (Ecnomorphus) corticinus reported from Ontario, C. (Myothorax) nepos reported from Ontario and Manitoba, and Glischrochilus (Librodor) obtusus reported from Ontario.

Development of Primers Specific for Detection of , the Causal Agent of Beech Leaf Disease, in Plant Tissue.

Beech leaf disease (BLD), an emerging threat to American beech () in the northern United States and Canada, was recently confirmed to be caused by the nematode subsp (hereafter ). Consequently, there is a need for a rapid, sensitive, and accurate method for detecting for both diagnostic as well as control purposes. This research developed a new set of DNA primers that specifically amplify and allow for accurate detection of the nematode in plant tissue.

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing.

Mass Spectrometry-Based Detection of Beta Lactam Hydrolysis Enables Rapid Detection of Beta Lactamase Mediated Antibiotic Resistance.

Objective: Antibiotic resistance by beta lactamase expression is a serious and growing threat. We aimed to determine whether beta-lactamase activity is detectable in urine specimens to enable faster identification of resistance.

Methods: Urine specimens from patients with extended spectrum beta lactamase (ESBL)-expressing urinary infections were incubated with beta lactam antibiotics.

Assessing the climate suitability and potential economic impacts of Oak wilt in Canada.

We assess risks posed by oak wilt-a disease caused by the fungal pathogen Bretziella fagacearum. Though not currently found in Canada, our distribution models indicate that suitable climate conditions currently occur in southern Ontario for B. fagacearum and two of its main insect dispersal vectors, Colopterus truncatus and Carpophilus sayi.

Commercial Serology Assays Predict Neutralization Activity against SARS-CoV-2.

Background: It is unknown whether a positive serology result correlates with protective immunity against SARS-CoV-2. There are also concerns regarding the low positive predictive value of SARS-CoV-2 serology tests, especially when testing populations with low disease prevalence.

Methods: A neutralization assay was validated in a set of PCR-confirmed positive specimens and in a negative cohort.

Multi-Platform Comparison of SARS-CoV-2 Serology Assays for the Detection of COVID-19.

Background: COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel beta-coronavirus that is responsible for the 2019 coronavirus pandemic. Acute infections should be diagnosed by polymerase chain reaction (PCR) based tests, but serology tests can demonstrate previous exposure to the virus.

Methods: We compared the performance of the Diazyme, Roche, and Abbott SARS-CoV-2 serology assays using 179 negative participants to determine negative percentage agreement (NPA) and in 60 SARS-CoV-2 PCR-confirmed positive patients to determine positive percentage agreement (PPA) at 3 different time frames following a positive SARS-CoV-2 PCR result.

The Effect of Clostridioides difficile Diagnostic Stewardship Interventions on the Diagnosis of Hospital-Onset Clostridioides difficile Infections.

Background: Public reporting of Clostridioides difficile infection (CDI) using laboratory-identified events has led some institutions to revert from molecular-based tests to less sensitive testing modalities. At one academic medical center, researchers chose to use nucleic acid amplification test alone in CDI diagnosis with institutional protocols aimed at diagnostic stewardship.

Methods: A single-center, quasi-experimental study was conducted to introduce and analyze the effects of various diagnostic stewardship interventions.

Longitudinal Monitoring of SARS-CoV-2 IgM and IgG Seropositivity to Detect COVID-19.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a novel beta-coronavirus that has recently emerged as the cause of the 2019 coronavirus pandemic (COVID-19). Polymerase chain reaction (PCR) based tests are optimal and recommended for the diagnosis of an acute SARS-CoV-2 infection. Serology tests for viral antibodies provide an important tool to diagnose previous exposure to the virus.

Risk factors and outcomes of culture-proven acute Coccidioides spp. infection in San Diego, California, United States.

Background: Coccidioides spp. are dimorphic fungi endemic to parts of the United States, Mexico, Central and South America. Infection can cause a range of disease from self-limited acute pneumonia to severe disseminated disease.

Comparison of Multiplex Gastrointestinal Pathogen Panel and Conventional Stool Testing for Evaluation of Patients With HIV Infection.

Background: Gastrointestinal pathogen panels (GPPs) are increasingly used to identify stool pathogens, but their impact in people with HIV (PWH) is unknown. We performed a retrospective cohort study comparing GPP and conventional stool evaluation in PWH.

Methods: We included all PWH who underwent GPP (Biofire Diagnostics; implemented September 15, 2015) or conventional testing, including stool culture, polymerase chain reaction testing, fluorescent smears for or and ova and parasite exams (O&P) from 2013 to 2017.

Endocarditis in a Homeless Man with Cat Exposure in San Diego, California.

We report a case of endocarditis in a homeless man with congenital bicuspid aortic valve and significant cat exposure living in downtown San Diego, California.

Universal HIV and Birth Cohort HCV Screening in San Diego Emergency Departments.

Universal HIV and HCV screening in emergency departments (ED) can reach populations who are less likely to get tested otherwise. The objective of this analysis was to evaluate universal opt-out HIV and HCV screening in two EDs in San Diego. HIV screening for persons aged 13-64 years (excluding persons known to be HIV+ or reporting HIV testing within last 12 months) was implemented using a 4 generation HIV antigen/antibody assay; HCV screening was offered to persons born between 1945 and 1965.

Predictors of Failure from Primary Therapy for Giardiasis in San Diego: A Single Institution Retrospective Review.

This study aimed to determine the presence of giardiasis among HIV patients in San Diego, the rate of failure of metronidazole treatment, and factors associated with treatment failure. We used a 7 year retrospective single-center case series of HIV-infected individuals with giardiasis at University of California San Diego Medical Center. Data were analyzed for the changes in the hematological, biochemical, and immunologic results at pre- and at-diagnosis levels.

Point-of-care diagnosis of invasive aspergillosis in non-neutropenic patients: Aspergillus Galactomannan Lateral Flow Assay versus Aspergillus-specific Lateral Flow Device test in bronchoalveolar lavage.

Background: We compared new Aspergillus Galactomannan Lateral Flow Assay with the newly formatted Aspergillus-specific Lateral Flow device tests for the diagnosis of invasive pulmonary aspergillosis (IPA) in non-neutropenic patients.

Methods: We performed both tests in 82 bronchoalveolar lavage fluid samples from 82 patients at risk for IPA but without underlying haematologic malignancy. Samples were collected between September 2016 and September 2018 at the University of California San Diego, United States.

Phytophthora Species Detected in Two Ozark Forests with Unusual Patterns of White Oak Mortality.

Widespread decline and mortality of white oaks (Quercus alba) occurred in Missouri Ozark forests between 2011 and 2017. Symptoms included rapid crown death with bronzing of leaves, retention of dead leaves, crown dieback and thinning, and loss of large limbs within one year of death. Decline and mortality were associated with hillside drainages and fit descriptions of European oak forests predisposed to decline by pathogenic Phytophthora species.

Cysteine proteases in protozoan parasites.

Cysteine proteases (CPs) play key roles in the pathogenesis of protozoan parasites, including cell/tissue penetration, hydrolysis of host or parasite proteins, autophagy, and evasion or modulation of the host immune response, making them attractive chemotherapeutic and vaccine targets. This review highlights current knowledge on clan CA cysteine proteases, the best-characterized group of cysteine proteases, from 7 protozoan organisms causing human diseases with significant impact: Entamoeba histolytica, Leishmania species (sp.), Trypanosoma brucei, T.

Rare mould infections caused by Mucorales, Lomentospora prolificans and Fusarium, in San Diego, CA: the role of antifungal combination therapy.

Non-Aspergillus invasive mould infections (IMIs) are associated with devastating morbidity and mortality rates and are increasingly diagnosed in immunocompromised hosts. The aim of this study was to describe the epidemiology and outcomes of non-Aspergillus IMIs at a university hospital in San Diego, California, USA. A retrospective chart review of the medical records of all patients with cultures growing non-Aspergillus moulds at the microbiology laboratory in the Center for Academic Laboratory Medicine, Department of Pathology, University of California, San Diego (UCSD) Health between mid-2014 and mid-2017 (3-year period) was performed.

Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology.

Background: Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy.

Why Funding for Neglected Tropical Diseases Should Be a Global Priority.

Neglected tropical diseases affect >1 billion of the world's poorest persons. Control programs range from near-elimination (dracunculiasis) to increasing prevalence (dengue and cutaneous leishmaniasis). These are some of the most cost-effective public health interventions and should be a global priority.