#EVD68 #outbreak #detection through a syndromic disease #epidemiology #network (J Clin Virol., abstract)

[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]

Journal of Clinical Virology / Available online 16 January 2020, 104262 / In Press, Journal Pre-proof

Enterovirus D68 outbreak detection through a syndromic disease epidemiology network

Authors: Lindsay Meyers a, Jennifer Dien Bard bc, Ben Galvin a, Jeff Nawrocki a, Hubert G.M. Niesters d, Kathleen A. Stellrecht e, Kirsten St. George f, Judy A. Daly gh, Anne J. Blaschke i, Christine Robinson j, Huanyu Wang k, Camille V. Cook a, Ferdaus Hassan l, Sam R. Dominguez j, Kristin Pretty j, Samia Naccache b, Katherine E. Olin a, Benjamin M. Althousem n, Jay D. Jones a, Christine C. Ginocchioao p, Mark A. Poritz q2, Amy Leber k1, Rangaraj Selvarangan l1

{a} BioFire Diagnostics, Salt Lake City, UT, 84103, United States; {b} Department of Pathology and Laboratory Medicine, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, United States; {c} Keck School of Medicine, University of Southern California, Los Angeles, CA 90039, United States; {d} The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands; {e} Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY 12208, United States; {f} New York State Department of Health, Albany, NY, 12202, United States; {g} Department of Pathology, University of Utah, Salt Lake City, UT 84132, United States; {h} Division of Inpatient Medicine, Primary Children’s Hospital, Salt Lake City, UT 84132, United States; {i} Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, United States; {j} Department of Pathology and Laboratory Medicine, Children’s Colorado, Aurora, CO 80045, United States; {k} Department of Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, United States; {l} Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO 64108, United States; {m} Information School, University of Washington, Seattle, WA, 98105, United States; {n} Department of Biology, New Mexico State University, Las Cruces, NM, 88003, United States; {o} Global Medical Affairs, bioMérieux, Durham, NC 27712, United States; {p}
Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, United States; {q} BioFire Defense, Salt Lake City, UT 84107, United States

Received 3 June 2019, Revised 8 January 2020, Accepted 14 January 2020, Available online 16 January 2020. DOI: https://doi.org/10.1016/j.jcv.2020.104262



  • An algorithm to predict the presence enterovirus D68 among hinovirus/Enterovirus results obtained from a commercial respiratory disease diagnostic test was developed
  • The algorithm was used in conjunction with test results exported to a cloud-based epidemiology network for use in real-time monitoring and historical outbreak prediction
  • Historical outbreak predictions coincide with known periods of high EV-D68 circulation in 2014 and 2016
  • The algorithm alerted participating clinical laboratories of the potential circulation of EV-D68 in 2018, prompting clinical testing for EV-D68 at one site

Keywords: EV-D68; USA.


Characteristics of #Patients with Acute Flaccid #Myelitis [#AFM], #USA, 2015–2018 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 2—February 2020 / CME ACTIVITY – Research

Characteristics of Patients with Acute Flaccid Myelitis, United States, 2015–2018

Nilay McLaren, Adriana Lopez, Sarah Kidd, John X. Zhang, W. Allan Nix, Ruth Link-Gelles, Adria Lee, and Janell A. Routh

Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA



Observed peaks of acute flaccid myelitis (AFM) cases have occurred biennially since 2014 in the United States. We aimed to determine if AFM etiology differed between peak and nonpeak years, considering that clinical features of AFM differ by virus etiology. We compared clinical and laboratory characteristics of AFM cases that occurred during peak (2016 and 2018, n = 366) and nonpeak (2015 and 2017, n = 50) years. AFM patients in peak years were younger (5.2 years) than those in nonpeak years (8.3 years). A higher percentage of patients in peak years than nonpeak years had pleocytosis (86% vs. 60%), upper extremity involvement (33% vs. 16%), and an illness preceding limb weakness (90% vs. 62%) and were positive for enterovirus or rhinovirus RNA (38% vs. 16%). Enterovirus D68 infection was associated with AFM only in peak years. Our findings suggest AFM etiology differs between peak and nonpeak years.

Keywords: EV-D68; Enterovirus; Rhinovirus; AFM; USA.


In vitro Evaluation of #Antifungal Drug #Combinations against #MDR #Candida auris isolates from #NY #Outbreak (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

In vitro Evaluation of Antifungal Drug Combinations against Multidrug-resistant Candida auris isolates from New York Outbreak

Brittany O’Brien, Sudha Chaturvedi, Vishnu Chaturvedi

DOI: 10.1128/AAC.02195-19



Since 2016, New York hospitals and healthcare facilities have faced an unprecedented outbreak of the pathogenic yeast Candida auris. We tested over one thousand C. auris isolates from affected facilities and found high-resistance to fluconazole (MIC > 256 mg/L), and variable resistance to other antifungal drugs. Therefore, we tested if two-drug combinations are effective in vitro against multidrug-resistant C. auris. Broth micro-dilution antifungal combination plates were custom-manufactured by TREK Diagnostic System. We used 100% inhibition endpoints for the drug combination as reported earlier for the intra- and inter-laboratory agreements against Candida species. The results were derived from 12,960 readings, for fifteen C. auris isolates tested against 864 two-drug antifungal combinations for nine antifungal drugs. Flucytosine (5FC) at 1.0 mg/L potentiated the most combinations. For nine C. auris isolates resistant to amphotericin B (AMB, MIC ≥ 2.0 mg/L]), AMB/5FC (0.25/1.0 mg/L) yielded 100% inhibition. Six C. auris isolates resistant to three echinocandins (anidulafungin [AFG, MIC ≥ 4.0 mg/L], caspofungin [CAS, MIC ≥ 2.0 mg/L], and micafungin [MFG, MIC ≥ 4.0 mg/L]), were 100% inhibited by AFG/5FC and CAS/5FC (0.0078/1 mg/L), and MFG/5FC (0.12/1 mg/L). None of the combinations were effective for C. auris 18-1 and 18-13 (FLC > 256 mg/L, 5FC > 32 mg/L) except MFG/5FC (0.1/0.006 mg/L). Thirteen isolates with high voriconazole MIC (VRC, > 2 mg/L) were 100% inhibited by the VRC/5FC (0.015/1 mg/L). The simplified two-drug combination susceptibility test format would permit laboratories to provide clinicians and public health experts with additional data to manage multidrug-resistant C. auris.

Copyright © 2020 American Society for Microbiology. All Rights Reserved.

Keywords: Drugs Resistance; Candida auris; USA.


#Incidence, #trends, and #outcomes of #infection sites among #hospitalizations of #sepsis: A nationwide study (PLOS One, abstract)

[Source: PLOS One, full page: (LINK). Abstract, edited.]


Incidence, trends, and outcomes of infection sites among hospitalizations of sepsis: A nationwide study

Eric H. Chou, Shaynna Mann, Tzu-Chun Hsu, Wan-Ting Hsu, Carolyn Chia-Yu Liu, Toral Bhakta, Dahlia M. Hassani, Chien-Chang Lee


Published: January 13, 2020 / DOI: https://doi.org/10.1371/journal.pone.0227752




To determine the trends of infection sites and outcome of sepsis using a national population-based database.

Materials and methods

Using the Nationwide Inpatient Sample database of the US, adult sepsis hospitalizations and infection sites were identified using a validated approach that selects admissions with explicit ICD-9-CM codes for sepsis and diagnosis/procedure codes for acute organ dysfunctions. The primary outcome was the trend of incidence and in-hospital mortality of specific infection sites in sepsis patients. The secondary outcome was the impact of specific infection sites on in-hospital mortality.


During the 9-year period, we identified 7,860,687 admissions of adult sepsis. Genitourinary tract infection (36.7%), lower respiratory tract infection (36.6%), and systemic fungal infection (9.2%) were the leading three sites of infection in patients with sepsis. Intra-abdominal infection (30.7%), lower respiratory tract infection (27.7%), and biliary tract infection (25.5%) were associated with highest mortality rate. The incidences of all sites of infections were trending upward. Musculoskeletal infection (annual increase: 34.2%) and skin and skin structure infection (annual increase: 23.0%) had the steepest increase. Mortality from all sites of infection has decreased significantly (trend p<0.001). Skin and skin structure infection had the fastest declining rate (annual decrease: 5.5%) followed by primary bacteremia (annual decrease: 5.3%) and catheter related bloodstream infection (annual decrease: 4.8%).


The anatomic site of infection does have a differential impact on the mortality of septic patients. Intra-abdominal infection, lower respiratory tract infection, and biliary tract infection are associated with higher mortality in septic patients.


Citation: Chou EH, Mann S, Hsu T-C, Hsu W-T, Liu CC-Y, Bhakta T, et al. (2020) Incidence, trends, and outcomes of infection sites among hospitalizations of sepsis: A nationwide study. PLoS ONE 15(1): e0227752. https://doi.org/10.1371/journal.pone.0227752

Editor: Florian B. Mayr, University of Pittsburgh, UNITED STATES

Received: June 5, 2019; Accepted: December 27, 2019; Published: January 13, 2020

Copyright: © 2020 Chou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: The author(s) received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Sepsis; USA.


#Human #parainfluenza virus #circulation, #USA, 2011-2019 (J Clin Virol., abstract)

[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]

Journal of Clinical Virology / Available online 9 January 2020, 104261 / In Press, Journal Pre-proof

Human parainfluenza virus circulation, United States, 2011-2019

Authors: Nicholas P. DeGroote a, Amber K. Haynes a, Calli Taylor b, Marie E. Killerby a, Rebecca M.Dahl c, Desiree Mustaquim b, Susan I.Gerber a, John T. Watson a

{a} Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA; {b} Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA; {c} Maximus Federal, Contracting agency to the Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA

Received 31 October 2019, Revised 2 January 2020, Accepted 8 January 2020, Available online 9 January 2020. DOI: https://doi.org/10.1016/j.jcv.2020.104261



  • Human parainfluenza virus type 3 is the most commonly reported parainfluenza virus followed by types 1, 2, and 4, respectively.
  • Each parainfluenza virus type exhibited a unique circulation pattern.
  • Parainfluenza type 4 circulated annually and peaked during the winter months.
  • No remarkable distinction in regional versus national seasonal circulation patterns.
  • The majority of parainfluenza virus detections with available age data occurred among children aged ≤2 years.




Human parainfluenza viruses (HPIVs) cause upper and lower respiratory tract illnesses, most frequently among infants and young children, but also in the elderly. While seasonal patterns of HPIV types 1-3 have been described, less is known about national patterns of HPIV-4 circulation.


To describe patterns of HPIVs circulation in the United States (US).

Study design

We used data from the National Respiratory and Enteric Virus Surveillance System (NREVSS), a voluntary passive laboratory-based surveillance system, to characterize the epidemiology and circulation patterns of HPIVs in the US during 2011-2019. We summarized the number of weekly aggregated HPIV detections nationally and by US census region, and used a subset of data submitted to NREVSS from public health laboratories and several clinical laboratories during 2015-2019 to analyze differences in patient demographics.


During July 2011 – June 2019, 2,700,135 HPIV tests were reported; 122,852 (5%) were positive for any HPIV including 22,446 for HPIV-1 (18%), 17,474 for HPIV-2 (14%), 67,649 for HPIV-3 (55%), and 15,283 for HPIV-4 (13%). HPIV testing increased substantially each year. The majority of detections occurred in children aged ≤ 2 years (36%) with fluctuations in the distribution of age by type.


HPIVs were detected year-round during 2011-2019, with type-specific year-to-year variations in circulation patterns. Among HPIV detections where age was known, the majority were aged ≤ 2 years. HPIV-4 exhibited an annual fall-winter seasonality, both nationally and regionally. Continued surveillance is needed to better understand national patterns of HPIV circulation.

Keywords: parainfluenza virus – respiratory virus surveillance – PIV circulation

© 2020 Published by Elsevier B.V.

Keywords: Parainfluenza virus; Pediatrics; USA.


#NDM-β-Lactamase-5–Producing #Escherichia coli in Companion #Animals, #USA (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 2—February 2020 / Research Letter

New Delhi Metallo-β-Lactamase-5–Producing Escherichia coli in Companion Animals, United States

Stephen D. Cole, Laura Peak, Gregory H. Tyson, Renate Reimschuessel, Olgica Ceric, and Shelley C. Rankin

Author affiliations: University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA (S.D. Cole, S.C. Rankin); Louisiana State University, Baton Rouge, Louisiana USA (L. Peak); US Food and Drug Administration, Silver Spring, Maryland, USA (G.H. Tyson, R. Reimscheussel, O. Ceric)



We report isolation of a New Delhi metallo-β-lactamase-5–producing carbapenem-resistant Escherichia coli sequence type 167 from companion animals in the United States. Reports of carbapenem-resistant Enterobacteriaceae in companion animals are rare. We describe a unique cluster of blaNDM-5–producing E. coli in a veterinary hospital.

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Beta-lactams; NDM1; USA.


#Risk of #yellowfever virus #importation into the #USA from #Brazil, #outbreak years 2016–2017 and 2017–2018 (Sci Rep., abstract)

[Source: Scientific Reports, full page: (LINK). Abstract, edited.]

Risk of yellow fever virus importation into the United States from Brazil, outbreak years 2016–2017 and 2017–2018

Ilaria Dorigatti,  Stephanie Morrison,  Christl A. Donnelly,  Tini Garske,  Sarah Bowden &  Ardath Grills

Scientific Reports volume 9, Article number: 20420 (2019)



Southeast Brazil has experienced two large yellow fever (YF) outbreaks since 2016. While the 2016–2017 outbreak mainly affected the states of Espírito Santo and Minas Gerais, the 2017–2018 YF outbreak primarily involved the states of Minas Gerais, São Paulo, and Rio de Janeiro, the latter two of which are highly populated and popular destinations for international travelers. This analysis quantifies the risk of YF virus (YFV) infected travelers arriving in the United States via air travel from Brazil, including both incoming Brazilian travelers and returning US travelers. We assumed that US travelers were subject to the same daily risk of YF infection as Brazilian residents. During both YF outbreaks in Southeast Brazil, three international airports—Miami, New York-John F. Kennedy, and Orlando—had the highest risk of receiving a traveler infected with YFV. Most of the risk was observed among incoming Brazilian travelers. Overall, we found low risk of YFV introduction into the United States during the 2016–2017 and 2017–2018 outbreaks. Decision makers can use these results to employ the most efficient and least restrictive actions and interventions.

Keywords: Yellow fever; USA; Brazil.