A #hospital #cluster combined with a #family cluster of #avian #influenza #H7N9 #infection in #Anhui Province, #China (J Infect., abstract)

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

J Infect. 2019 May 14. pii: S0163-4453(19)30152-5. doi: 10.1016/j.jinf.2019.05.008. [Epub ahead of print]

A hospital cluster combined with a family cluster of avian influenza H7N9 infection in Anhui Province, China.

Zhang W1, Zhao K1, Jin J1, He J2, Zhou W1, Wu J1, Tang R1, Ma W3, Ding C4, Liu W1, Zhang L1, Gao R5.

Author information: 1 Hefei Center for Disease Control and Prevention, Heifei, Anhui Province, China, 230061. 2 Anhui Provincial Center for Disease Control and Prevention, Heifei, Anhui Province, China, 230601. 3 Lujiang County People’s Hospital, Heifei, Anhui Province, China, 231501. 4 The Second Hospital of Anhui Medical University, Heifei, Anhui Province, China, 230601. 5 National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory of Medical Virology and Viral Diseases, National Health Commission of People’s Republic of China, Beijing, China, 102206. Electronic address: gaorongbao@cnic.org.cn.




To identify human-to-human transmission of H7N9 avian influenza virus, we investigated a hospital cluster combined with family cluster in this study.


We obtained and analyzed clinical, epidemiological and virological data from the three patients. RT-PCR, viral culture and sequencing were conducted for determination of causative pathogen.


The index case presented developed pneumonia with fever after exposure to chicken in a poultry farm. Case A presented pneumonia with high fever on day 3 after she shared a hospital room with the index case. Case B, the father of the index case, presented pneumonia with high fever on day 15 after he took care of the index case. H7N9 virus circulated in the local farm to which the index case was exposed. Full genomic sequence of virus showed 99.8 to 100% identity shared between the index case and case A or case B. Compared to the earliest virus of Anhui, a total of 29 amino acid variation sites were observed in the 8 segments.


A hospital cluster combined with family cluster of H7N9 avian influenza infection was identified. Air transmission resulted in the hospital cluster possibly. A poultry farm was the initially infectious source of the cluster.

Copyright © 2019. Published by Elsevier Ltd.

KEYWORDS: Air transmission; Avian influenza virus; Family cluster; H7N9; Hospital cluster; Human-to-human transmission

PMID: 31100362 DOI: 10.1016/j.jinf.2019.05.008

Keywords: Avian Influenza; H7N9; Human; Poultry; Nosocomial Outbreaks; Anhui; China.



Comparative Analysis of Eleven #Healthcare-Associated #Outbreaks of Middle East Respiratory Syndrome #Coronavirus (#MERS-CoV) from 2015 to 2017 (Sci Rep., abstract)

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

Sci Rep. 2019 May 14;9(1):7385. doi: 10.1038/s41598-019-43586-9.

Comparative Analysis of Eleven Healthcare-Associated Outbreaks of Middle East Respiratory Syndrome Coronavirus (Mers-Cov) from 2015 to 2017.

Bernard-Stoecklin S1,2, Nikolay B3, Assiri A4, Bin Saeed AA5,6, Ben Embarek PK7, El Bushra H5, Ki M8, Malik MR9, Fontanet A10,11,12, Cauchemez S3, Van Kerkhove MD13,14.

Author information: 1 Formerly Outbreak Investigation Task Force, Centre for Global Health, Institut Pasteur, 75015, Paris, France. 2 Direction of infectious diseases, Santé publique France, Saint-Maurice, 94410, France. 3 Mathematical Modelling of Infectious Diseases, Institut Pasteur, UMR2000, CNRS, 75015, Paris, France. 4 Ministry of Health, Riyadh, Saudi Arabia. 5 Formerly Ministry of Health, Riyadh, Saudi Arabia. 6 Department of Family and Community Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia. 7 International Food Safety Authorities Network (INFOSAN) Management, Department of Food Safety and Zoonoses, World Health Organization, Geneva, Switzerland. 8 Department of Cancer Control and Policy, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea. 9 Infectious Hazard Management Unit, Department of Health Emergencies, World Health Organization Regional Office for the Eastern Mediterranean, Cairo, Egypt. 10 Emerging Diseases Epidemiology Unit, Institut Pasteur, 75015, Paris, France. 11 Centre for Global Health, Institut Pasteur, 75015, Paris, France. 12 Conservatoire National des Arts et Métiers, Paris, France. 13 Formerly Outbreak Investigation Task Force, Centre for Global Health, Institut Pasteur, 75015, Paris, France. vankerkhovem@who.int. 14 Infectious Hazards Management, Health Emergencies Programme, World Health Organization, Geneva, Switzerland. vankerkhovem@who.int.



Since its emergence in 2012, 2,260 cases and 803 deaths due to Middle East respiratory syndrome coronavirus (MERS-CoV) have been reported to the World Health Organization. Most cases were due to transmission in healthcare settings, sometimes causing large outbreaks. We analyzed epidemiologic and clinical data of laboratory-confirmed MERS-CoV cases from eleven healthcare-associated outbreaks in the Kingdom of Saudi Arabia and the Republic of Korea between 2015-2017. We quantified key epidemiological differences between outbreaks. Twenty-five percent (n = 105/422) of MERS cases who acquired infection in a hospital setting were healthcare personnel. In multivariate analyses, age ≥65 (OR 4.8, 95%CI: 2.6-8.7) and the presence of underlying comorbidities (OR: 2.7, 95% CI: 1.3-5.7) were associated with increased mortality whereas working as healthcare personnel was protective (OR 0.07, 95% CI: 0.01-0.34). At the start of these outbreaks, the reproduction number ranged from 1.0 to 5.7; it dropped below 1 within 2 to 6 weeks. This study provides a comprehensive characterization of MERS HCA-outbreaks. Our results highlight heterogeneities in the epidemiological profile of healthcare-associated outbreaks. The limitations of our study stress the urgent need for standardized data collection for high-threat respiratory pathogens, such as MERS-CoV.

PMID: 31089148 DOI: 10.1038/s41598-019-43586-9

Keywords: MERS-CoV; Nosocomial Outbreaks.


#Patient-to-Patient #Transmission of #Acinetobacter baumannii #Gastrointestinal Colonization in the #ICU (Antimicrob Agents Chemother., abstract)

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

Patient-to-Patient Transmission of Acinetobacter baumannii Gastrointestinal Colonization in the Intensive Care Unit

Anthony D Harris [MD, MPH], J. Kristie Johnson [PhD], Lisa Pineles [MA], Lyndsay M O’Hara [MPH, PhD], Robert A. Bonomo [MD], Kerri A Thom [MD, MS]

DOI: 10.1128/AAC.00392-19




Acinetobacter baumannii is an important nosocomial pathogen. The objective of this study was to determine the proportion of A. baumannii due to patient-to-patient transmission by analyzing the molecular epidemiology of patients who acquired A. baumannii using peri-anal surveillance cultures in a large 2-year intensive care unit population.


Prospective cohort study


Patients who were admitted to the medical and surgical intensive care units (ICUs) at the University of Maryland Medical Center from 2011 to 2013 underwent admission, weekly and discharge peri-anal cultures collected. Using multilocus sequence typing (MLST) with subsequent pulsed-field gel electrophoresis (PFGE) for increased discrimination, and hospital overlap, the number of patients that acquired A. baumannii due to patient-to-patient transmission was determined.


Our cohort consisted of 3452 patients. In total, 196 cohort patients were colonized with A. baumannii; 130 patients were positive at ICU admission and 66 patients acquired A. baumannii during their stay. Among the 196 A. baumannii patient isolates, there were 91 unique MLST types. Among the 66 patients who acquired A. baumannii, 31 (50%) were considered genetically related by MLST and/or PFGE type and 11 (17%) were considered patient-to-patient transmission by genetic-relatedness and overlapping hospital stay.


Our data shows that, of those cases of A. baumannii acquisition, at least 17% were cases of patient-to-patient transmission.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Acinetobacter baumannii; ICU; Nosocomial outbreaks.


Challenge of drug #resistance in #Pseudomonas aeruginosa: clonal spread of #NDM1-positive ST-308 within a tertiary #hospital (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

Challenge of drug resistance in Pseudomonas aeruginosa: clonal spread of NDM-1-positive ST-308 within a tertiary hospital

Ka Lip Chew, Sophie Octavia, Oon Tek Ng, Kalisvar Marimuthu, Indumathi Venkatachalam, Bernadette Cheng, Raymond T P Lin, Jeanette W P Teo

Journal of Antimicrobial Chemotherapy, dkz169, https://doi.org/10.1093/jac/dkz169

Published: 12 May 2019




MDR Pseudomonas aeruginosa is a serious global threat to healthcare institutions. The mechanism by which drug resistance can be acquired is variable, but acquired carbapenemase production has been reported in P. aeruginosa. An investigation was performed to determine the rate and genomic epidemiology of New Delhi MBL (NDM) in β-lactam-non-susceptible isolates.


P. aeruginosa isolates from a tertiary hospital in Singapore between January 2015 and February 2018 were investigated for the presence of NDM genes.


Out of 298 pan-β-lactam-non-susceptible isolates, 31 were found to be NDM positive (10.4%). WGS demonstrated that all 31 NDM-positive isolates were clonal, belonging to ST-308. blaNDM was chromosomally inserted within an integrative and conjugative element (ICE), ICETn43716385. The NDM-P. aeruginosa isolates possessed an extensive repertoire of both cell-associated [flagella, pili, alginate/biofilm, LPS, type III secretion system (T3SS) and type VI secretion system (T6SS)] and secreted virulence factors. Antibiograms revealed higher rates of drug resistance in NDM-positive isolates compared with their non-NDM counterparts. The NDM isolates remained 100% susceptible only to colistin.


The combination of chromosomal mutations, acquired resistance genes and virulence factors likely facilitated the persistent and ongoing spread of the ST-308 clade of P. aeruginosa within the hospital. Our study illustrates the particular threat of NDM-positive P. aeruginosa in a tertiary hospital setting in the era of antimicrobial resistance.

Topic: pseudomonas aeruginosa – mutation – colistin – epidemiology – drug resistance – alginates – biofilms – bodily secretions – chromosomes – drug resistance, microbial – bacterial fimbria – flagella – genes – genome – lactams – singapore – persistence – virulence factors – antibiogram – resistance genes – type iii protein secretion system complex – whole genome sequencing


© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Beta-lactams; NDM1; Pseudomonas aeruginosa; Nosocomial outbreaks.


Emergence of #NDM1-producing #Klebsiella pneumoniae in #Greece: evidence of a #widespread clonal #outbreak (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

Emergence of NDM-1-producing Klebsiella pneumoniae in Greece: evidence of a widespread clonal outbreak

Lida Politi, Konstantina Gartzonika, Nicholas Spanakis, Olympia Zarkotou, Aggeliki Poulou, Lemonia Skoura, Georgia Vrioni, Athanasios Tsakris

Journal of Antimicrobial Chemotherapy, dkz176, https://doi.org/10.1093/jac/dkz176

Published: 07 May 2019




NDM-producing Enterobacteriaceae clinical isolates remain uncommon in the European region. We describe the emergence and broad dissemination of one successful NDM-1-producing Klebsiella pneumoniae clone in Greek hospitals.


During a 4 year survey (January 2013–December 2016), 480 single-patient carbapenem non-susceptible K. pneumoniae isolates, phenotypically MBL positive, were consecutively recovered in eight Greek hospitals from different locations and subjected to further investigation. Antimicrobial susceptibility testing, combined-disc test, identification of resistance genes by PCR and sequencing, molecular fingerprinting by PFGE, plasmid profiling, replicon typing, conjugation experiments and MLST were performed.


Molecular analysis confirmed the presence of the blaNDM-1 gene in 341 (71%) K. pneumoniae isolates. A substantially increasing trend of NDM-1-producing K. pneumoniae was noticed during the survey (R2 = 0.9724). Most blaNDM-1-carrying isolates contained blaCTX-M-15, blaOXA-1, blaOXA-2 and blaTEM-1genes. PFGE analysis clustered NDM-1 producers into five distinct clonal types, with five distinct STs related to each PFGE clone. The predominant ST11 PFGE clonal type was detected in all eight participating hospitals, despite adherence to the national infection control programme; it was identical to that observed in the original NDM-1 outbreak in Greece in 2011, as well as in a less-extensive NDM-1 outbreak in Bulgaria in 2015. The remaining four ST clonal types (ST15, ST70, ST258 and ST1883) were sporadically detected. blaNDM-1 was located in IncFII-type plasmids in all five clonal types.


This study gives evidence of possibly the largest NDM-1-producing K. pneumoniae outbreak in Europe; it may also reinforce the hypothesis of an NDM-1 clone circulating in the Balkans.

Topic: polymerase chain reaction – plasmids – carbapenem – bulgaria – clone cells – disease outbreaks – electrophoresis, gel, pulsed-field – enterobacteriaceae – genes – greece – ichthyosis, x-linked – infectious disease prevention / control – klebsiella pneumoniae  – replicon – sequence tagged sites – sodium thiosulfate – antimicrobial susceptibility test – beta-lactamase ndm-1 – resistance genes – molecular profiling


© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Carbapene; NDM1; Klebsiella pneumoniae; Greece; Nosocomial outbreaks.


#Influenza virus #RNA recovered from #droplets and droplet #nuclei emitted by #adults in an #acute #care setting (J Occup Environ Hyg., abstract)

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

J Occup Environ Hyg. 2019 May 3:1-8. doi: 10.1080/15459624.2019.1591626. [Epub ahead of print]

Influenza virus RNA recovered from droplets and droplet nuclei emitted by adults in an acute care setting.

Yip L1, Finn M1, Granados A2,3, Prost K1, McGeer A3,4, Gubbay JB2,3, Scott J5, Mubareka S1,3.

Author information: 1a Biological Sciences , Sunnybrook Research Institute , Toronto , Ontario , Canada. 2b Public Health Ontario , Toronto , Ontario , Canada. 3c Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada. 4d Sinai Health System , Toronto , Ontario , Canada. 5e Dalla Lana School of Public Health, University of Toronto , Toronto , Ontario , Canada.



Transmission in hospital settings of seasonal influenza viruses and novel agents such as the Middle East respiratory syndrome coronavirus (MERS-CoV) is well-described but poorly understood. The characterization of potentially infectious bio-aerosols in the healthcare setting remains an important yet ill-defined factor in the transmission of respiratory viruses. Empiric data describing the distribution of bio-aerosols enable discernment of potential exposure risk to respiratory viruses. We sought to determine the distribution of influenza virus RNA emitted into the air by participants with laboratory-confirmed influenza, and whether these emissions had the potential to reach healthcare workers’ breathing zones. Two-stage cyclone bio-aerosol samplers from the Centers for Disease Control and Prevention – National Institute for Occupational Safety and Health were placed 0.5-1.0 m (near field) and 2.1-2.5 m (far field) from infected patient participants, as well as in the corridor immediately outside their rooms. In addition, healthcare worker participants providing care to infected participants were recruited to wear a polytetrafluoroethylene (PTFE) filter cassette in their breathing zones. Viral RNA was detected from the air emitted by 37.5% of the 16 participants infected with influenza virus and distributed both in near and far fields and in all tested particle sizes (<1 µm, 1-4 µm, and >4 µm). Viral RNA was recovered in droplet nuclei and beyond 1 m from naturally-infected participants in the healthcare setting and from the breathing zone of one healthcare worker. There was no correlation between patient participant nasal viral load and recovery of viral RNA from the air, and we did not identify any significant association between RNA detection from the air and patient demographics or clinical presentation. A more substantial study is required to identify patient determinants of virus emission into the air and delineate implications for evidence-based policy for prevention and control.

KEYWORDS: Bio-aerosols; exposure; healthcare worker; respiratory virus

PMID: 31050610 DOI: 10.1080/15459624.2019.1591626

Keywords: Seasonal Influenza; Nosocomial outbreaks.


Phenotypic and #Genomic Analyses of #Burkholderia stabilis #Clinical #Contamination, #Switzerland (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 6—June 2019 / Research

Phenotypic and Genomic Analyses of Burkholderia stabilis Clinical Contamination, Switzerland

Helena M.B. Seth-Smith  , Carlo Casanova, Rami Sommerstein, Dominik M. Meinel1, Mohamed M.H. Abdelbary2, Dominique S. Blanc, Sara Droz, Urs Führer, Reto Lienhard, Claudia Lang, Olivier Dubuis, Matthias Schlegel, Andreas Widmer, Peter M. Keller, Jonas Marschall, and Adrian Egli

Author affiliations: University Hospital Basel, Basel, Switzerland (H.M.B. Seth-Smith, D.M. Meinel, A. Widmer, A. Egli); University of Basel, Basel (H.M.B. Seth-Smith, D.M. Meinel, A. Egli); University of Bern, Bern, Switzerland (C. Casanova, S. Droz); Bern University Hospital, Bern (R. Sommerstein, J. Marschall); Lausanne University Hospital, Lausanne, Switzerland (M.M.H. Abdelbary, D.S. Blanc); Biel Hospital, Biel, Switzerland (U. Führer); ADMED, La Chaux-de-Fonds, Switzerland (R. Lienhard); Viollier AG, Allschwil, Switzerland (C. Lang, O. Dubuis); Cantonal Hospital St. Gallen, St. Gallen, Switzerland (M. Schlegel); Swissnoso, National Center for Infection Prevention, Bern (M. Schlegel, A. Widmer, J. Marschall); University of Zurich, Zurich, Switzerland (P.M. Keller)



A recent hospital outbreak related to premoistened gloves used to wash patients exposed the difficulties of defining Burkholderia species in clinical settings. The outbreak strain displayed key B. stabilis phenotypes, including the inability to grow at 42°C; we used whole-genome sequencing to confirm the pathogen was B. stabilis. The outbreak strain genome comprises 3 chromosomes and a plasmid, sharing an average nucleotide identity of 98.4% with B. stabilis ATCC27515 BAA-67, but with 13% novel coding sequences. The genome lacks identifiable virulence factors and has no apparent increase in encoded antimicrobial drug resistance, few insertion sequences, and few pseudogenes, suggesting this outbreak was an opportunistic infection by an environmental strain not adapted to human pathogenicity. The diversity among outbreak isolates (22 from patients and 16 from washing gloves) is only 6 single-nucleotide polymorphisms, although the genome remains plastic, with large elements stochastically lost from outbreak isolates.

Keywords: Nosocomial outbreaks; Switzerland; Burkholderia stabilis.