An #international #outbreak of #Salmonella enterica serotype Enteritidis linked to #eggs from #Poland: a microbiological and epidemiological study (Lancet Infect Dis., abstract)

[Source: The Lancet Infectious Diseases, full page: (LINK). Abstract, edited.]

An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study

Roan Pijnacker, MSc  *, Timothy J Dallman, PhD *, Aloys S L Tijsma, PhD, Gillian Hawkins, MBChB, Lesley Larkin, BVSc, Saara M Kotila, MSc, Giusi Amore, PhD, Ettore Amato, PhD, Pamina M Suzuki, MSc, Sarah Denayer, PhD, Sofieke Klamer, MSc, Judit Pászti, Jacquelyn McCormick, MPH, Hassan Hartman, PhD, Gareth J Hughes, PhD, Lin C T Brandal, PhD, Derek Brown, MSc, Joël Mossong, PhD, Cecilia Jernberg, PhD, Luise Müller, MSc, Daniel Palm, PhD, Ettore Severi, MSc, Joannna Gołębiowska, DVM, Blaženka Hunjak, PhD, Slawomir Owczarek, MSc, Simon Le Hello, PhD, Patricia Garvey, PhD, Kirsten Mooijman, MSc, Ingrid H M Friesema, PhD, Coen van der Weijden, BSc, Menno van der Voort, PhD, Valentina Rizzi, PhD, Eelco Franz, PhD on behalf of theInternational Outbreak Investigation Team †

Published: May 24, 2019 / DOI:




Salmonella spp are a major cause of food-borne outbreaks in Europe. We investigated a large multi-country outbreak ofSalmonella enterica serotype Enteritidis in the EU and European Economic Area (EEA).


A confirmed case was defined as a laboratory-confirmed infection with the outbreak strains of S Enteritidis based on whole-genome sequencing (WGS), occurring between May 1, 2015, and Oct 31, 2018. A probable case was defined as laboratory-confirmed infection withS Enteritidis with the multiple-locus variable-number tandem repeat analysis outbreak profile. Multi-country epidemiological, trace-back, trace-forward, and environmental investigations were done. We did a case-control study including confirmed and probable cases and controls randomly sampled from the population registry (frequency matched by age, sex, and postal code). Odds ratios (ORs) for exposure rates between cases and controls were calculated with unmatched univariable and multivariable logistic regression.


18 EU and EEA countries reported 838 confirmed and 371 probable cases. 509 (42%) cases were reported in 2016, after which the number of cases steadily increased. The case-control study results showed that cases more often ate in food establishments than did controls (OR 3·4 [95% CI 1·6–7·3]), but no specific food item was identified. Recipe-based food trace-back investigations among cases who ate in food establishments identified eggs from Poland as the vehicle of infection in October, 2016. Phylogenetic analysis identified two strains of S Enteritidis in human cases that were subsequently identified in salmonella-positive eggs and primary production premises in Poland, confirming the source of the outbreak. After control measures were implemented, the number of cases decreased, but increased again in March, 2017, and the increase continued into 2018.


This outbreak highlights the public health value of multi-country sharing of epidemiological, trace-back, and microbiological data. The re-emergence of cases suggests that outbreak strains have continued to enter the food chain, although changes in strain population dynamics and fewer cases indicate that control measures had some effect. Routine use of WGS in salmonella surveillance and outbreak response promises to identify and stop outbreaks in the future.


European Centre for Disease Prevention and Control; Directorate General for Health and Food Safety, European Commission; and National Public Health and Food Safety Institutes of the authors’ countries (see Acknowledgments for full list).

Keywords: Food Safety; EU; European Region; Samonella spp.


#Salmonella harbouring the #mcr1 gene isolated from #food in #China between 2012 and 2016 (J Antimicrob Chemother., abstract)

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

Salmonella harbouring the mcr-1 gene isolated from food in China between 2012 and 2016

Yujie Hu, Séamus Fanning, Xin Gan, Chang Liu, Scott Nguyen, Meimei Wang, Wei Wang, Tao Jiang, Jin Xu, Fengqin Li

Journal of Antimicrobial Chemotherapy, dky496,

Published: 02 January 2019



In November 2015, plasmid-mediated transferable colistin resistance encoded by the mcr-1 gene in Escherichia coli and Klebsiella pneumonia isolates was reported in China with a high rate of in vitro horizontal transfer (10−1–10−3 cells per recipient cell by conjugation).1 At that time, the mcr-1 gene had already been identified in >30 countries across five continents, with novel mcr-2mcr-3mcr-4 and mcr-5 genes being reported subsequently.2–5 Recently, a surveillance study was performed on mainland China to investigate the prevalence of the mcr-1 gene in foodborne Salmonella isolates isolated from various food matrices and others collected…

Issue Section:  Research letter

© 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:

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (

Keywords: Food Safety; Antibiotics; Drugs Resistance; MCR1; Colistin; Salmonella spp.


#Epidemiology and #antimicrobial #resistance of invasive non-typhoidal #Salmonellosis in rural #Thailand from 2006-2014 (PLoS Negl Trop Dis., abstract)

[Source: PLoS Neglected Tropical Diseases, full page: (LINK). Abstract, edited.]


Epidemiology and antimicrobial resistance of invasive non-typhoidal Salmonellosis in rural Thailand from 2006-2014

Toni Whistler , Patranuch Sapchookul, David W. McCormick, Ornuma Sangwichian, Possawat Jorakate, Sirirat Makprasert, Anchalee Jatapai, Sathapana Naorat, Uraiwan Surin, Surathinee Koosakunwat, Surachai Supcharassaeng, Barameht Piralam, Mathew Mikoleit,  [ … ], Christopher J. Gregory

Published: August 6, 2018 / DOI: / This is an uncorrected proof.




Invasive salmonellosis is a common cause of bloodstream infection in Southeast Asia. Limited epidemiologic and antimicrobial resistance data are available from the region.


Blood cultures performed in all 20 hospitals in the northeastern province of Nakhon Phanom (NP) and eastern province of Sa Kaeo (SK), Thailand were captured in a bloodstream infection surveillance system. Cultures were performed as clinically indicated in hospitalized patients; patients with multiple positive cultures had only the first included. Bottles were incubated using the BacT/Alert system (bioMérieux, Thailand) and isolates were identified using standard microbiological techniques; all Salmonella isolates were classified to at least the serogroup level. Antimicrobial resistance was assessed using disk diffusion.


Salmonella was the fifth most common pathogen identified in 147,535 cultures with 525 cases (211 in Nakhon Phanom (NP) and 314 in Sa Kaeo (SK)). The overall adjusted iNTS incidence rate in NP was 4.0 cases/100,000 person-years (95% CI 3.5–4.5) and in SK 6.4 cases/100,000 person-years (95% CI 5.7–7.1; p = 0.001). The most common serogroups were C (39.4%), D (35.0%) and B (9.9%). Serogroup D predominated in NP (103/211) with 59.2% of this serogroup being Salmonella serovar Enteritidis. Serogroup C predominated in SK (166/314) with 84.3% of this serogroup being Salmonella serovar Choleraesuis. Antibiotic resistance was 68.2% (343/503) for ampicillin, 1.2% (6/482) for ciprofloxacin (or 58.1% (280/482) if both intermediate and resistant phenotypes are considered), 17.0% (87/512) for trimethoprim-sulfamethoxazole, and 12.2% (59/484) for third-generation cephalosporins (cefotaxime or ceftazidime). Multidrug resistance was seen in 99/516 isolates (19.2%).


The NTS isolates causing bloodstream infections in rural Thailand are commonly resistant to ampicillin, cefotaxime, and TMP-SMX. Observed differences between NP and SK indicate that serogroup distribution and antibiotic resistance may substantially differ throughout Thailand and the region.


Author summary

Invasive strains of non-typhoidal salmonella (iNTS) are a common cause of bloodstream infection in Southeast Asia, however limited epidemiologic and antimicrobial resistance data are available and no population-based studies have been published from the region. We use nine years of bloodstream infections data from surveillance conducted in two Thai border provinces to report on the incidence, serotype distribution and antimicrobial resistance patterns. Incidence of iNTS was 5.1 cases/100,000 population (95% CI 4.7–5.6), likely an under estimate of the true burden of disease as we only used hospitalized cases and less sensitive blood culture for bacterial isolation. Levels of drug non-susceptibility were high among isolates, especially for fluoroquinolones such as ciprofloxacin (~60%) and third-generation cephalosporins such as cefotaxime or ceftazidime (~15%) that are commonly prescribed to provide empirical coverage against these pathogens. Multidrug resistance was widespread at 20% of isolates. Our data emphasizes the need for increased microbiological surveillance, and support the need for rational antibiotic therapy and the development of treatment guidelines.


Citation: Whistler T, Sapchookul P, McCormick DW, Sangwichian O, Jorakate P, Makprasert S, et al. (2018) Epidemiology and antimicrobial resistance of invasive non-typhoidal Salmonellosis in rural Thailand from 2006-2014. PLoS Negl Trop Dis 12(8): e0006718.

Editor: Thomas C. Darton, Oxford University Clinical Research Unit Vietnam, VIET NAM

Received: May 18, 2018; Accepted: July 25, 2018; Published: August 6, 2018

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Data Availability: Data sets belong to the Thai Ministry of Health and access is restricted but available on request with an accompanying explanation as to what the data will be used for. Please contact Dr. John MacArthur ( to request the relevant data used for this manuscript. He can direct your query to appropriate contacts within the Thai MOPH.

Funding: Support for this project was provided by the Global Disease Detection program of the U.S. Centers for Disease Control and Prevention, and the Pneumococcal Vaccines Accelerated Development and Introduction Plan (PneumoADIP) ( funded by the GAVI Alliance ( based at the Johns Hopkins Bloomberg School of Public Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

Keywords: Antibiotics; Drugs Resistance; Salmonella spp.; Thailand.


#NYC House #Mice (Mus musculus) as Potential #Reservoirs for Pathogenic #Bacteria and #Antimicrobial Resistance Determinants (mBio, abstract)

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

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants

Simon H. Williams a,  Xiaoyu Che a,  Ashley Paulick b, Cheng Guo a, Bohyun Lee a, Dorothy Muller a, Anne-Catrin Uhlemann c, Franklin D. Lowy c, Robert M. Corrigan d, W. Ian Lipkin a

a Center for Infection and Immunity, Columbia University, New York, New York, USA; b Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA; c Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, USA; d RMC Pest Management Consulting, Briarcliff Manor, New York, USA

Claire M. Fraser, Editor

Author Affiliations: University of Maryland, School of Medicine

Address correspondence to W. Ian Lipkin,



House mice (Mus musculus) thrive in large urban centers worldwide. Nonetheless, little is known about the role that they may play in contributing to environmental contamination with potentially pathogenic bacteria. Here, we describe the fecal microbiome of house mice with emphasis on detection of pathogenic bacteria and antimicrobial resistance genes by molecular methods. Four hundred sixteen mice were collected from predominantly residential buildings in seven sites across New York City over a period of 13 months. 16S rRNA sequencing identified Bacteroidetes as dominant and revealed high levels of Proteobacteria. A targeted PCR screen of 11 bacteria, as indicated by 16S rRNA analyses, found that mice are carriers of several gastrointestinal disease-causing agents, including Shigella, Salmonella, Clostridium difficile, and diarrheagenic Escherichia coli. Furthermore, genes mediating antimicrobial resistance to fluoroquinolones (qnrB) and β-lactam drugs (blaSHV and blaACT/MIR) were widely distributed. Culture and molecular strain typing of C. difficile revealed that mice harbor ribotypes associated with human disease, and screening of kidney samples demonstrated genetic evidence of pathogenic Leptospira species. In concert, these findings support the need for further research into the role of house mice as potential reservoirs for human pathogens and antimicrobial resistance in the built environment.



Mice are commensal pests often found in close proximity to humans, especially in urban centers. We surveyed mice from seven sites across New York City and found multiple pathogenic bacteria associated with febrile and gastrointestinal disease as well as an array of antimicrobial resistance genes.

KEYWORDS: antimicrobial resistance –  bacteriome –  mice –  New York City



Citation Williams SH, Che X, Paulick A, Guo C, Lee B, Muller D, Uhlemann A-C, Lowy FD, Corrigan RM, Lipkin WI. 2018. New York City house mice (Mus musculus) as potential reservoirs for pathogenic bacteria and antimicrobial resistance determinants. mBio 9:e00624-18.

For a companion article on this topic, see

Received 19 March 2018  – Accepted 22 March 2018  – Published 17 April 2018

Copyright © 2018 Williams et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Keywords: USA; New York City; House Mice; Antibiotics; Drugs Resistance; Clostridium difficile; Leptospira spp.; Shigella spp.; Salmonella spp.; E. Coli.


#Plasmid-borne #colistin #resistance gene #mcr3 in #Salmonella isolates from #human #infections, #Denmark, 2009–17 (@eurosurveillanc, abstract)

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

Eurosurveillance, Volume 22, Issue 31, 03 August 2017 / Rapid communication

Plasmid-borne colistin resistance gene mcr-3 in Salmonella isolates from human infections, Denmark, 2009–17

E Litrup 1 , K Kiil 1 , AM Hammerum 1 , L Roer 1 , EM Nielsen 1 , M Torpdahl 1

Author affiliations: 1. Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

Correspondence: Eva Litrup (

Citation style for this article: Litrup E, Kiil K, Hammerum AM, Roer L, Nielsen EM, Torpdahl M. Plasmid-borne colistin resistance gene mcr-3 in Salmonella isolates from human infections, Denmark, 2009–17. Euro Surveill. 2017;22(31):pii=30587. DOI:

Received:07 July 2017; Accepted:31 July 2017



This report describes one Salmonella isolate harbouring both mcr-1 and mcr-3. We also found nine other Salmonella isolates positive for the plasmid-borne colistin resistance gene, mcr-3. The strains were isolated from patients in Denmark between 2009 and 2017 and five of the patients had travelled to Asia. In addition to mcr-3, all strains were found positive for blaTEM-1, strA, strB, sul2 and tet(A) or tet(B), and most strains were positive for blaCTX-M-55 and qnrS.

Keywords: Antibiotics; Drugs Resistance; Colistin; Salmonella spp.; Denmark; MCR1; MCR3.