Is Kawasaki Disease Caused by a Respiratory Virus?

BACKGROUND: Kawasaki disease is characterized by high fever, rash, cervical lymphadenopathy, conjunctival injection, oral mucous membrane changes and swelling of the extremities followed by skin sloughing. Despite >50 years of study, no bacterial, viral or other infectious agent has been consistently associated with the illness. The lockdown and social distancing for COVID-19 in March 2020 led to a marked decrease in respiratory virus circulation. This provided an "experiment of nature" to determine whether Kawasaki disease would decline in parallel. METHODS: Discharge ICD-10 diagnosis codes were obtained from the Vizient Clinical Data Base for Kawasaki disease and respiratory viruses, and analyzed for the age group < 5 years. Weekly respiratory virus positivity data were also obtained from BioFire Diagnostics. RESULTS: Common enveloped respiratory viruses declined precipitously from April 2020 through March 2021 to levels at or below historical seasonal minimum levels. Kawasaki Disease declined about 40% compared with 2018-2019, which is distinctly different from the pattern seen for the enveloped respiratory viruses. Strong seasonality was seen for Kawasaki disease as far back as 2010, and correlated most closely with respiratory syncytial virus, human metapneumovirus and less so with influenza virus suggesting there is a baseline level of Kawasaki disease activity that is heightened during yearly respiratory virus activity but that remains at a certain level even in the near total absence of respiratory viruses. CONCLUSIONS: The striking decrease in enveloped respiratory viruses after lockdown and social distancing was not paralleled by a comparable decrease in Kawasaki disease incidence, suggesting a different epidemiology.

Target capture sequencing of SARS-CoV-2 genomes using the ONETest Coronaviruses Plus.

We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence the SARS-CoV-2 genome and select loci of other respiratory viruses. We applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a PCR assay. For 48 of the samples, we also applied the ARTIC protocol. Of the 70 ONETest libraries, 45 (64%) had a (near-)complete sequence (>29,000 bases and >90% covered by >9 reads). Of the 48 ARTIC libraries, 25 (52%) had a (near-)complete sequence. In 19 out of 25 (76%) samples in which both the ONETest and ARTIC yielded (near-)complete sequences, the lineages assigned were identical. As a target capture approach, the ONETest is less prone to loss of sequence coverage than amplicon approaches, and thus can provide complete genomic information more often to track and monitor SARS-CoV-2 variants.

Dissemination mechanisms of NDM genes in hospitalized patients.

BACKGROUND: NDM-producing Enterobacteriaceae are a major clinical concern worldwide. We characterized NDM-positive pathogens isolated from patients and assessed the dissemination patterns of the bla NDM genes in a hospital setting. METHODS: Eleven NDM-positive Enterobacteriaceae (three Enterobacter hormaechei, six Klebsiella pneumoniae and two Escherichia coli) were isolated from nine patients over a 1 year period. Antimicrobial susceptibility was assessed by MICs. A combination of short- and long-read WGS was used for genome analysis. Clinical treatment history of patients was linked with genetic features of individual isolates to investigate the dissemination patterns of the bla NDM genes and NDM-positive strains. RESULTS: bla NDM in clonal K. pneumoniae were transmitted between two patients. In other instances, an identical IncC plasmid encoding NDM-1 was transmitted between E. coli and K. pneumoniae isolated from the same patient, and an IncX3 plasmid, carrying bla NDM-1 or bla NDM-5, was harboured in non-clonal E. hormaechei. Varying patterns of IS elements were identified as a critical transmission mechanism in association with bla NDM genes. CONCLUSIONS: Multiple transmission patterns were identified in hospitalized patients, including dissemination of clonal bacterial strains carrying resistance genes and horizontal transfer of resistance genes among divergent bacterial strains. Controlling spread of NDM is complex: while attention to standard infection control practices is critically important, this needs to be matched by aggressive efforts to limit unnecessary antimicrobial use, to minimize the selection for and risk of transfer of 'high mobility' resistance genes among Enterobacteriaceae.

Performance of a Semiquantitative Multiplex Bacterial and Viral PCR Panel Compared With Standard Microbiological Laboratory Results: 396 Patients Studied With the BioFire Pneumonia Panel.

BACKGROUND: Microbiologic results are critical to optimal management of patients with lower respiratory tract infection, but standard methods may take several days. The multiplex polymerase chain reaction BioFire Pneumonia (PN) panel detects 15 common bacterial species semiquantitatively as copy number/mL, 8 viral species, and 7 resistance genes in about an hour within the clinical laboratory. METHODS: We tested 396 unique endotracheal or bronchoalveolar lavage specimens with the BioFire Pneumonia panel and compared the bacterial detections to conventional gram stain and culture results. RESULTS: Of the 396 patients, 138 grew at least 1 bacterium that had a target on the PN panel, and 136/138 (98.6%) were detected by the panel. A total of 177 isolates were recovered in culture and the PN panel detected 174/177 (98.3%). A further 20% of patients had additional targets detected that were not found on standard culture (specificity 69%, positive predictive value 63%, and negative predictive value 98.9%). Copy number was strongly related to standard semiquantitative growth on plates reported by the laboratory (eg, 1+, 2+, 3+ growths) and was significantly higher in those specimens that grew a potential pathogen. Both higher copy number and bacterial detections found by the PN panel, but not found in culture, were strongly positively related to the level of white blood cells reported in the initial gram stain. CONCLUSIONS: Higher copy number and bacterial detections by the PN panel are related to the host respiratory tract inflammatory response. If laboratories can achieve a rapid turnaround time, the PN panel should have a significant impact both on patient management and on antibiotic stewardship.

Impact of a Point-of-care Respiratory PCR Panel in a Pediatric Clinic on Postvisit Communication and Follow-up Visits.

While the FilmArray Respiratory Panel EZ has been proven to reduce inappropriate antibiotic use in the outpatient pediatric setting, it is unclear whether its implementation will also reduce downstream health costs such as provider visits and telephone calls. This analysis will help pediatricians make more informed decisions on the implementation and judicious use of the Respiratory Panel EZ in their clinical practice.

Hourly Effect of Pretreatment With IV Antibiotics on Blood Culture Positivity Rate in Emergency Department Patients.

Although it is intuitive that antibiotics administered before obtaining a blood culture would reduce the likelihood of obtaining a positive culture, it is not clear exactly how rapidly and to what extent blood becomes sterile after administration of intravenous (IV) antibiotics. Using a large data set of patients admitted from the UFHealth Shands Adult Emergency Department (ED) between 2012 and 2016 (n = 25 686), we had the opportunity to more closely examine the effect of starting IV antibiotics before vs after obtaining blood cultures. We present data on the effect of pretreatment with IV antibiotics for both septic and nonseptic ED patients on the blood culture positivity rate on an hour-by-hour basis, as well as the effects on distribution of species recovered and the impact of antibiotic resistance in empiric treatment with antibiotics.

Dose optimization of moxifloxacin and linezolid against tuberculosis using mathematical modeling and simulation.

INTRODUCTION: There is an urgent need for new anti-tuberculosis (TB) drugs and optimization of current TB treatment. Moxifloxacin and linezolid are valuable options for the treatment of drug-resistant TB; however, it is crucial to find a dose at which these drugs not only show high efficacy but also suppress the development of further drug resistance. METHODS: Activity of moxifloxacin and linezolid against Mycobacterium tuberculosis was studied in the hollow-fiber infection model system in log-phase growth under neutral pH and slow growth in an acidic environment. Doses that achieved maximum bacterial kill while suppressing the emergence of drug resistance were determined. Through Monte Carlo simulations the quantitative output of this in vitro study was bridged to the human patient population to inform optimal dosage regimens while accounting for clinical minimum inhibitory concentration (MIC) distributions. RESULTS AND DISCUSSION: Moxifloxacin activity was significantly decreased in an acidified environment. The loss of activity was compensated by accumulation of the drug in TB lung lesions; therefore, moderate efficacy can be expected. Moxifloxacin 800 mg/day is the dose that most likely leads to resistance suppression while exerting maximum bacterial kill. Linezolid demonstrated very good activity even at a reduced pH. Linezolid 900 mg once-daily (QD) is likely to achieve a maximum killing effect and prevent the emergence of drug resistance; 600 mg QD in a robust drug regimen may have similar potential.

Enhanced in vitro activity of tigecycline in the presence of chelating agents.

The lack of availability of novel antibiotic agents and the rise of resistance to existing therapies has led clinicians to utilise combination therapy to adequately treat bacterial infections. Here we examined how chelators may impact the in vitro activity of tigecycline (TIG) against Pseudomonas aeruginosa, Escherichia coli and Klebsiella pneumoniae. Minimum inhibitory concentrations (MICs) were determined by broth dilution with and without various combinations of chelators (EDTA and other tetracyclines) and metal ions (i.e. calcium, magnesium). Trimethoprim (TMP) was used as a non-chelating control. Addition of metal ions led to increases in MICs, whilst addition of EDTA led to decreases in MICs. The chelating effects of EDTA were reversed by addition of magnesium and most profoundly calcium. Similar effects of EDTA and calcium were observed for tetracycline (TET) and TMP. When other tetracyclines (TET, oxytetracycline (OXY) and chlortetracycline (CHL)) were used as chelators at concentrations below their MICs, TIG MICs decreased for P. aeruginosa but not for E. coli. Some decreases in TIG MICs were observed for K. pneumoniae when TET and CHL were added. A dose-dependent decrease in TIG MIC was observed for TET and was reversed by the addition of calcium. The presence of effects of EDTA and calcium on TMP MICs indicates that mechanisms outside of TIG chelation likely play a role in enhanced activity. Full characterisation of an unexpected interaction such as TIG-TET with different microorganisms could provide valuable insights into the underlying mechanisms and design of physiologically viable chelators as candidates for future combinations regimens.

A Gastrointestinal PCR Panel Improves Clinical Management and Lowers Health Care Costs.

Conventional methods for the identification of gastrointestinal pathogens are time-consuming and expensive and have limited sensitivity. The aim of this study was to determine the clinical impact of a comprehensive molecular test, the BioFire FilmArray gastrointestinal (GI) panel, which tests for many of the most common agents of infectious diarrhea in approximately 1 h. Patients with stool cultures submitted were tested on the GI panel (n = 241) and were compared with control patients (n = 594) from the year prior. The most common organisms detected by the GI panel were enteropathogenic Escherichia coli (EPEC, n = 21), norovirus (n = 21), rotavirus (n = 15), sapovirus (n = 9), and Salmonella (n = 8). Patients tested on the GI panel had an average of 0.58 other infectious stool tests compared with 3.02 in the control group (P = 0.0001). The numbers of days on antibiotic(s) per patient were 1.73 in the cases and 2.12 in the controls (P = 0.06). Patients with the GI panel had 0.18 abdomen and/or pelvic imaging studies per patient compared with 0.39 (P = 0.0002) in the controls. The average length of time from stool culture collection to discharge was 3.4 days in the GI panel group versus 3.9 days in the controls (P = 0.04). The overall health care cost could have decreased by $293.61 per patient tested. The GI panel improved patient care by rapidly identifying a broad range of pathogens which may not have otherwise been detected, reducing the need for other diagnostic tests, reducing unnecessary use of antibiotics, and leading to a reduction in hospital length of stay.

Relationship between bacteriology report time in the morning and length of stay in hospital after the report.

We studied the relationship between the time of day bacteriology reports were available in the electronic medical record (Epic, Verona, WI) and subsequent length of stay (LOS) following the last report before discharge. All patients ≥18years admitted to the UF Health Shands Hospital between 1/1/2014-2/29/2016 were included. We calculated the mean LOS following the report for each half-hour time period between 6AM and 1PM (N=14, 95.6% of all results) and tested the relationship to subsequent LOS. For patients whose total LOS was ≤168hours (N=13,830) there was a highly significant positive linear relationship between the report time and LOS following the last report (r=0.8813, P=0.00001556). For those patients with total LOS>168h, there was no clear relationship between report time in the morning and LOS after the last bacteriology report. The relationship between bacteriology report time in the morning and use of this information by physicians in discharge decision-making is likely to be complex and multi-factorial, but for those patients with a total hospital LOS ≤168h, there is a strong relationship between an earlier report and earlier patient discharge.

Semi-quantitative Influenza A population averages from a multiplex respiratory viral panel (RVP): potential for reflecting target sequence changes affecting the assay.

BACKGROUND: Yearly influenza virus mutations potentially affect the performance of molecular assays, if nucleic acid changes involve the sequences in the assay. Because individual patient viral loads depend on variables such as duration of illness, specimen type, age, and immunosuppression, we examined seasonal population averages of positive tests to smooth inherent variability. METHODS: We studied the population seasonal averages of the semi-quantitative nAMPs for the influenza matrix and hemagglutinin genes in the GenMark (Carlsbad, CA) Respiratory Viral Panel assay between 3 institutions over 3 Influenza seasons. RESULTS: Population average nAMPs were strikingly consistent between separate institutions, but differed substantially between H3N2 and H1N1 seasons. In the 2012-2013 and 2014-2015 influenza seasons, matrix gene H3N2 nAMP averages were 50-70% less than those of the same assay in the 2013-2014 H1N1 season. Influenza strains representative of these seasons were grown in tissue culture and when the supernatant virus was adjusted to the same copy number using a TaqMan assay, the same relative differences were reproduced in the RVP assay. Because the sequences for the PCR and PCR product detection in the GenMark assay are proprietary, the manufacturer provided single stranded DNA matching the capture probe for the representative H3N2 (3 mismatches) and H1N1 strains (2 different mismatches). Equimolar concentrations of these synthetic DNA sequences gave average nAMP values that closely correlated with the average nAMPS of the representative strains and their respective seasonal averages. CONCLUSIONS: Seasonal averages of semi-quantitative data may provide a means to follow assay performance as a reflection of the effects of molecular drift.

Incidence of central venous catheter hub contamination.

PURPOSE: To investigate microorganisms causing central venous catheter contamination and how this contamination differs across different catheter metrics. MATERIALS AND METHODS: After obtaining IRB approval and informed consent, 830 cultures were prospectively obtained from 45 ICU patients with central venous catheter or peripherally inserted central catheter. Bacterial colonies were identified by mass spectrometry. RESULTS: Bacterial contamination of central catheter hubs occurred 44% of the time in this study in the ICU setting. Coagulase-positive staphylococci cultures had higher median (±interquartile range) CFUs (12±232) versus coagulase-negative (3±10) and other bacteria (1±3; P<0.001). Bacterial contamination was associated with various metrics. Higher incidence (P<0.05) of coagulase-positive staphylococci cultures was associated with hub-only connections (a "hub" being a female connection; 10.9% vs. 7.9% male connections), connections without a manifold (1lumen device that mixes multiple infusions together; 9.7% vs. 0% with manifold); and central venous pressure monitoring connections (25.8% vs. 7.1% without). Internal jugular sites (10.0% vs. 2.7% femoral, 6.2% PICC, P=0.031) and medial lumens of triple lumen catheters (11.9% vs. 5.6% distal, 7.0% proximal, P=0.049) had increased incidence of higher bacteria loads (>15 CFUs). CONCLUSIONS: This study found a high incidence of central access catheter hub bacterial contamination, which correlated with positive blood cultures in 2 of 3 total bacteremia cases identified in the 45 patients.

Hemagglutinin Gene Clade 3C.2a Influenza A(H3N2) Viruses, Alachua County, Florida, USA, 2014-15.

Influenza A(H3N2) strains isolated during 2014-15 in Alachua County, Florida, USA, belonged to hemagglutinin gene clade 3C.2a. High rates of influenza-like illness and confirmed influenza cases in children were associated with a decrease in estimated vaccine effectiveness. Illnesses were milder than in 2013-14; severe cases were concentrated in elderly patients with underlying diseases.

Sample-to-result molecular infectious disease assays: clinical implications, limitations and potential.

Molecular infectious disease diagnostic tests have undergone major advances in the past decade and will continue to rapidly evolve. Assays have become extraordinarily simple to perform, eliminating the need for pre-analytic sample preparation and post-amplification analysis. This allows these tests to be performed in settings without sophisticated expertise in molecular biology, including locations with limited resources. Additionally, the sensitivity and specificity of these assays is superb and many offer extremely fast turn-around times. These tests have major impacts on patient care, but also have some limitations.

Clinical and economic impact of antimicrobial stewardship interventions with the FilmArray blood culture identification panel.

The purpose of this study was to evaluate the impact of the FilmArray Blood Culture Identification (BCID) Panel on the management of patients with blood cultures growing gram positive cocci and Candida. We retrospectively compared clinical and economic outcomes between patients during the BCID testing period and a matched historical control group before BCID testing was introduced. A total of 84 BCID patients were matched to 252 historical controls. BCID identification of coagulase negative staphylococci contaminants resulted in shorter post-culture length of stay (P < 0.008) and saved roughly $30,000 per 100 patients tested. The BCID led to shorter duration of empirical vancomycin for patients with contaminated blood cultures (P = 0.005) and methicillin-susceptible Staphylococcus aureus bacteremia (P < 0.001). Patients with vancomycin-resistant enterococcal bacteremia received active therapy earlier than historical controls (P = 0.047). The BCID, coupled with antimicrobial stewardship intervention, was a cost effective tool to improve patient care.

A rare case of classical Hodgkin's lymphoma in the setting of a newly diagnosed left atrial myxoma.

We report a rare case of left atrial myxoma with concomitant classical Hodgkin's lymphoma in a 36-year-old woman with a non-significant medical history and 4 months of progressively worsening palpitations, dyspnoea on exertion, chest discomfort and fatigue. Outpatient echocardiography revealed functional mitral valve stenosis as a result of a large left atrial cardiac mass. Preoperative thoracic imaging revealed an anterior mediastinal mass with associated lymphadenopathy. The patient underwent successful resection of the anterior mediastinal mass and left atrial mass. Surgical pathology revealed myxoma in the left atrium and classical Hodgkin's lymphoma in the anterior mediastinum. Thus the patient was diagnosed with early-stage classical Hodgkin's lymphoma. This clinical vignette emphasises the importance of a comprehensive diagnostic evaluation in the setting of a newly discovered atrial tumour.

Multiplex gastrointestinal pathogen panels: implications for infection control.

In the acute care hospital inpatient setting, there is a wide variety of causes for both infectious and noninfectious diarrhea. However, without molecular assays for the wide range of agents causing gastroenteritis, there is no reliable way to determine which individuals should be placed in contact precautions, as recommended by CDC. We tested 158 inpatient diarrheal stool specimens with the FilmArray GI Panel (BioFire Diagnostics, Salt Lake City, UT, USA) that had been stored at -70°C after testing negative by conventional methods for Clostridium difficile and/or rotavirus. We found that 22.2% had at least 1 other infectious agent detected, and 60% of these patients were never placed in appropriate isolation for a total of 109 patient-days. In addition, 20.3% of patients with negative GI panel results could have been removed from isolation. Use of multiplex gastrointestinal panels may improve decisions regarding patient isolation and reduce nosocomial transmission.

Detection of Neisseria meningitidis from negative blood cultures and cerebrospinal fluid with the FilmArray blood culture identification panel.

The FilmArray blood culture identification (BCID) panel is a rapid molecular diagnostic test approved for use with positive blood culture material. We describe a fatal case of meningococcemia with central nervous system (CNS) involvement detected using the BCID test with culture-negative blood and cerebrospinal fluid.

Direct identification of bacteria in positive blood cultures: comparison of two rapid methods, FilmArray and mass spectrometry.

We evaluated the accuracy and performance of the FilmArray Direct from Positive Blood Culture system (BCID) (BioFire Diagnostics, Salt Lake City, UT, USA) and the VITEK Mass Spectrometry System (Vitek MS; bioMerieux, Durham, NC, USA) to identify bacterial isolates from 161 positive blood culture bottles. The BCID uses multiplex PCR to identify 90-95% of common isolates to the genus or species/complex level as well as mecA, Van A/B, and bla(KPC) genes in approximately 1 hour. Of 151 monomicrobic isolates, the FilmArray correctly identified 48/49 (98%) to the genus and 84/84 (100%) to the species/complex level, while 18/151 (12%) gave no identification, as expected from the database. Mass spectrometry correctly identified 142/151 (94%) monomicrobic cultures to the genus level, 137/151 (91%) to the species level, with only 8/151(5%) giving no identification. Although mass spectrometry has a much larger database, the filtration system was cumbersome in contrast to the 3-5 minutes hands-on-time for the BCID.