Optical #DNA #Mapping Combined with #Cas9-Targeted #Resistance #Gene #Identification for Rapid #Tracking of Resistance #Plasmids in a #NICU #Outbreak (mBio, abstract)

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

Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak

Santosh K. Bikkarolla, Viveka Nordberg, Fredrika Rajer, Vilhelm Müller, Muhammad Humaun Kabir, Sriram KK, Albertas Dvirnas, Tobias Ambjörnsson, Christian G. Giske, Lars Navér,Linus Sandegren, Fredrik Westerlund

Spyros Pournaras, Invited Editor, Karen Bush, Editor

DOI: 10.1128/mBio.00347-19



The global spread of antibiotic resistance among Enterobacteriaceae is largely due to multidrug resistance plasmids that can transfer between different bacterial strains and species. Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. We have developed a method, based on optical DNA mapping combined with Cas9-assisted identification of resistance genes, which is used here to characterize plasmids during an extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBL-producing Klebsiella pneumoniae (ESBL-KP), some of which were found to carry additional ESBL-producing Escherichia coli (ESBL-EC) in follow-up samples. We demonstrate that all ESBL-KP isolates contained two plasmids with the blaCTX-M-15 gene located on the smaller one (~80 kbp). The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the blaCTX-M-15 gene was stable throughout this time period. However, extensive genetic rearrangements within the second plasmid were observed in the optical DNA maps for several of the ESBL-KP isolates. Optical mapping also demonstrated that even though other bacterial clones and species carrying blaCTX-M group 1 genes were found in some neonates, no transfer of resistance plasmids had occurred. The data instead pointed toward unrelated acquisition of ESBL-producing Enterobacteriaceae (EPE). In addition to revealing important information about the specific outbreak, the method presented is a promising tool for surveillance and infection control in clinical settings.


This study presents how a novel method, based on visualizing single plasmids using sequence-specific fluorescent labeling, could be used to analyze the genetic dynamics of an outbreak of resistant bacteria in a neonatal intensive care unit at a Swedish hospital. Plasmids are a central reason for the rapid global spread of bacterial resistance to antibiotics. In a single experimental procedure, this method replaces many traditional plasmid analysis techniques that together provide limited details and are slow to perform. The method is much faster than long-read whole-genome sequencing and offers direct genetic comparison of patient samples. We could conclude that no transfer of resistance plasmids had occurred between different bacteria during the outbreak and that secondary cases of ESBL-producing Enterobacteriaceae carriage were instead likely due to influx of new strains. We believe that the method offers potential in improving surveillance and infection control of resistant bacteria in hospitals.

Keywords: Antibiotics; Drugs Resistance; Enterobacteriaceae; Beta-lactams; Nosocomial Outbreaks; Diagnostic tests.



#Hospital-Associated Multicenter #Outbreak of Emerging Fungus #Candida auris, #Colombia, 2016 (Emerg Infect Dis., abstract)

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

Volume 25, Number 7—July 2019 / CME ACTIVITY – Research

Hospital-Associated Multicenter Outbreak of Emerging Fungus Candida auris, Colombia, 2016

Paige A. Armstrong1  , Sandra M. Rivera1  , Patricia Escandon, Diego H. Caceres, Nancy Chow, Matthew J. Stuckey, Jorge Díaz, Adriana Gomez, Norida Vélez, Andres Espinosa-Bode, Soraya Salcedo, Adriana Marin, Indira Berrio, Carmen Varón, Angel Guzman, Jairo E. Pérez-Franco, Julian D. Escobar, Nohora Villalobos, Juan M. Correa, Anastasia P. Litvintseva, Shawn R. Lockhart, Ryan Fagan, Tom M. Chiller, Brendan Jackson2, and Oscar Pacheco2

Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (P.A. Armstrong, D.H. Caceres, N. Chow, M.J. Stuckey, A. Espinosa-Bode, A.P. Litvintseva, S.R. Lockhart, R. Fagan, T.M. Chiller, B. Jackson); Instituto Nacional de Salud, Bogotá, Colombia (S.M. Rivera, P. Escandon, J. Díaz, A. Gomez, N. Vélez, O. Pacheco); Clínica General del Norte, Barranquilla, Colombia (S. Salcedo, A. Marin); Clínica El Rosario, Medellín, Colombia (I. Berrio); Corporación para Investigaciones Biológicas (CIB), Medellín (I. Berrio); Hospital General de Medellín, Medellín (I. Berrio); Hospital Doña Pilar, Cartagena, Colombia (C. Varón, A. Guzman); Hospital Militar Central, Bogotá (J.E. Pérez-Franco, J.D. Escobar); Clínica los Nogales, Bogotá (N. Villalobos, J.M. Correa)



Candida auris is an emerging multidrug-resistant fungus that causes hospital-associated outbreaks of invasive infections with high death rates. During 2015–2016, health authorities in Colombia detected an outbreak of C. auris. We conducted an investigation to characterize the epidemiology, transmission mechanisms, and reservoirs of this organism. We investigated 4 hospitals with confirmed cases of C. auris candidemia in 3 cities in Colombia. We abstracted medical records and collected swabs from contemporaneously hospitalized patients to assess for skin colonization. We identified 40 cases; median patient age was 23 years (IQR 4 months–56 years). Twelve (30%) patients were <1 year of age, and 24 (60%) were male. The 30-day mortality was 43%. Cases clustered in time and location; axilla and groin were the most commonly colonized sites. Temporal and spatial clustering of cases and skin colonization suggest person-to-person transmission of C. auris. These cases highlight the importance of adherence to infection control recommendations.

Keywords: Candida auris; Nosocomial Outbreaks; IPC; Colombia.


#Candida auris in #Germany and Previous #Exposure to Foreign #Healthcare (Emerg Infect Dis., abstract)

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

Volume 25, Number 9—September 2019 / Research Letter

Candida auris in Germany and Previous Exposure to Foreign Healthcare

Axel Hamprecht, Amelia E. Barber, Sibylle C. Mellinghoff, Philipp Thelen, Grit Walther, Yanying Yu, Priya Neurgaonkar, Thomas Dandekar, Oliver A. Cornely, Ronny Martin, Oliver Kurzai  , and on behalf of the German Candida auris Study Group

Author affiliations: German Centre for Infection Research, Cologne, Germany (A. Hamprecht, S.C. Mellinghoff, O.A. Cornely); University of Cologne, Cologne (A. Hamprecht, O.A. Cornely); Leibniz Institute for Natural Product Research and Infection Biology–Hans-Knoell-Institute, Jena, Germany (A.E. Barber, G. Walther, O. Kurzai); University Hospital Cologne, Cologne (S.C. Mellinghoff, P. Thelen); University of Würzburg, Würzburg, Germany (Y. Yu, P. Neurgaonkar, T. Dandekar, R. Martin, O. Kurzai)



The emerging yeast Candida auris has disseminated worldwide. We report on 7 cases identified in Germany during 2015–2017. In 6 of these cases, C. auris was isolated from patients previously hospitalized abroad. Whole-genome sequencing and epidemiologic analyses revealed that all patients in Germany were infected with different strains.

Keywords: Candida auris; Germany; Nosocomial outbreaks.


#Epidemiology of Human #Parechovirus Type 3 #Upsurge in 2 #Hospitals, Freiburg, #Germany, 2018 (Emerg Infect Dis., abstract)

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

Volume 25, Number 7—July 2019 / Dispatch

Epidemiology of Human Parechovirus Type 3 Upsurge in 2 Hospitals, Freiburg, Germany, 2018

Roland Elling1, Sindy Böttcher1, Florian du Bois, Alexandra Müller, Christiane Prifert, Benedikt Weissbrich, Jörg Hofmann, Klaus Korn, Anna-Maria Eis-Hübinger, Markus Hufnagel, and Marcus Panning

Author affiliations: University of Freiburg Faculty of Medicine, Freiburg, Germany (R. Elling, F. du Bois, A. Müller, M. Hufnagel, M. Panning); Robert Koch-Institute, Berlin, Germany (S. Böttcher); University of Würzburg, Würzburg, Germany (C. Prifert, B. Weissbrich); Charité – Universitätsmedizin Berlin, Berlin (J. Hofmann); Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany (K. Korn); University of Bonn Medical Centre, Bonn, Germany (A.-M. Eis-Hübinger)



In 2018, a cluster of pediatric human parechovirus (HPeV) infections in 2 neighboring German hospitals was detected. Viral protein 1 sequence analysis demonstrated co-circulation of different HPeV-3 sublineages and of HPeV-1 and -5 strains, thereby excluding a nosocomial outbreak. Our findings underline the need for HPeV diagnostics and sequence analysis for outbreak investigations.

Keywords: Parechovirus; Nosocomial Outbreaks; Germany.


#Carbapenem and #Cephalosporin #Resistance among #Enterobacteriaceae in #Healthcare-Associated #Infections, #California, #USA (Emerg Infect Dis., abstract)

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

Volume 25, Number 7—July 2019 / Dispatch

Carbapenem and Cephalosporin Resistance among Enterobacteriaceae in Healthcare-Associated Infections, California, USA1

Kyle Rizzo  , Sam Horwich-Scholefield, and Erin Epson

Author affiliations: California Department of Public Health, Richmond, California, USA



We analyzed antimicrobial susceptibility test results reported in healthcare-associated infections by California hospitals during 2014–2017. Approximately 3.2% of Enterobacteriaceae reported in healthcare-associated infections were resistant to carbapenems and 26.9% were resistant to cephalosporins. The proportion of cephalosporin-resistant Escherichia coli increased 7% (risk ratio 1.07, 95% CI 1.04–1.11) per year during 2014–2017.

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Cephalosporins; Nosocomial Outbreraks; California; USA.


#Pathophysiological role of #respiratory #dysbiosis in #hospital-acquired #pneumonia (Lancet Resp Med., abstract)

[Source: The Lancet Respiratory Medicine, full page: (LINK). Abstract, edited.]

Pathophysiological role of respiratory dysbiosis in hospital-acquired pneumonia

Prof A Roquilly, MD, Prof A Torres, MD, Prof J A Villadangos, PhD, Prof M G Netea, MD, Prof R Dickson, MD, Prof B Becher, PhD, Prof K Asehnoune, MD

Published: June 07, 2019 / DOI: https://doi.org/10.1016/S2213-2600(19)30140-7



Hospital-acquired pneumonia is a major cause of morbidity and mortality. The incidence of hospital-acquired pneumonia remains high globally and treatment can often be ineffective. Here, we review the available data and unanswered questions surrounding hospital-acquired pneumonia, discuss alterations of the respiratory microbiome and of the mucosal immunity in patients admitted to hospital, and explore potential approaches to stratify patients for tailored treatments. The lungs have been considered a sterile organ for decades because microbiological culture techniques had shown negative results. Culture-independent techniques have shown that healthy lungs harbour a diverse and dynamic ecosystem of bacteria, changing our comprehension of respiratory physiopathology. Understanding dysbiosis of the respiratory microbiome and altered mucosal immunity in patients with critical illness holds great promise to develop targeted host-directed immunotherapy to reduce ineffective treatment, to improve patient outcomes, and to tackle the global threat of resistant bacteria that cause these infections.

Keywords: Antibiotics; Drugs Resistance; Microbiome; Pneumonia; Nosocomial Outbreaks.


#MERS #coronavirus in the last two years: #HCWs still at #risk (Am J Infect Control., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Am J Infect Control. 2019 May 22. pii: S0196-6553(19)30235-4. doi: 10.1016/j.ajic.2019.04.007. [Epub ahead of print]

Middle East respiratory syndrome coronavirus in the last two years: Health care workers still at risk.

Al-Tawfiq JA1, Memish ZA2.

Author information: 1 Specialty Internal Medicine Unit, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Quality and Patient Safety Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Electronic address: jaltawfi@yahoo.com. 2 College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Infectious Diseases Division, Department of Medicine, Prince Mohamed Bin Abdulaziz Hospital (“PMAH”), Ministry of Health, Riyadh, Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.




An important emerging respiratory virus is the Middle East respiratory syndrome coronavirus (MERS-CoV). MERS-CoV had been associated with a high case fatality rate especially among severe cases.


This is a retrospective analysis of reported MERS-CoV cases between December 2016 and January 2018, as retrieved from the World Health Organization. The aim of this study is to examine the epidemiology of reported cases and quantify the percentage of health care workers (HCWs) among reported cases.


There were 403 reported cases with a majority being men (n = 300; 74.4%). These cases were reported from Lebanon, Malaysia, Oman, Qatar, Saudi Arabia, and United Arab Emirates. HCWs represented 26% and comorbidities were reported among 71% of non-HCWs and 1.9% among HCWs (P < .0001). Camel exposure and camel milk ingestion were reported in 64% each, and the majority (97.8%) of those with camel exposures had camel milk ingestion. There were 58% primary cases and 42% were secondary cases. The case fatality rate was 16% among HCWs compared with 34% among other patients (P = .001). The mean age ± SD was 47.65 ± 16.28 for HCWs versus 54.23 ± 17.34 for non-HCWs (P = .001).


MERS-CoV infection continues to have a high case fatality rate and a large proportion of patients were HCWs. Further understanding of the disease transmission and prevention mainly in health care settings are needed.

Copyright © 2019 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

KEYWORDS: Healthcare workers; MERS; MERS-CoV; Middle East Respiratory Syndrome Coronavirus; emerging infectious disease; transmission

PMID: 31128983 DOI: 10.1016/j.ajic.2019.04.007

Keywords: MERS-CoV; Middle East Region; Nosocomial Outbreaks; HCWs.