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SHORT REPORT Open Access
Screening for fecal carriage of MCR-
producing Enterobacteriaceae in healthy
humans and primary care patients
Katrin Zurfluh1, Roger Stephan1, Andreas Widmer2, Laurent Poirel3, Patrice Nordmann3, Hans-Jakob Nüesch4,
Herbert Hächler1 and Magdalena Nüesch-Inderbinen1*
Abstract
Background: The extent of the occurrence of the plasmid-encoded colistin resistance genes mcr-1 and mcr-2
among humans is currently sparsely studied in Western Europe.
Objectives: To determine the occurrence of MCR-producing Enterobacteriaceae in fecal samples of healthy humans
with high occupational exposure to food and primary care patients in Switzerland.
Methods: Stool samples from 1091 healthy individuals and fecal swabs from 53 primary care patients were screened
for polymyxin-resistant Enterobacteriaceae using LB agar containing 4 mg/L colistin. Minimal inhibitory concentrations
(MICs) of colistin were determined for non-intrinsic colistin-resistant isolates. Isolates were screened by PCR for the
presence of mcr-1 and mcr-2 genes.
Results: The fecal carriage rate of colistin resistant (MIC value >2 mg/l) Enterobacteriaceae was 1.5% for healthy people and
3.8% for primary care patients. Isolates included Hafnia alvei (n= 9), Escherichia coli (n= 3), Enterobacter cloacae (n= 4),
Klebsiella pneumoniae (n= 1) and Raoultella ornithinolytica (n= 1). None of the isolates harbored the mcr-1 or mcr-2 genes.
Conclusions: There is no evidence for the presence of MCR-producers in the fecal flora of healthy people or primary
care patients. Therefore, the risk of transfer of mcr genes from animals, food or the environment to humans is likely to
be low in Switzerland.
Keywords: Colistin, MCR, Fecal carriage, Population
Introduction
Polymyxins are cationic polypeptide antibiotics that
interact with the lipopolysaccharides (LPS) and phos-
pholipids in the outer membrane of Gram-negative
bacteria [1]. Due to the lack of novel antimicrobials,
polymyxin E (colistin), once avoided because of its
nephro- and neurotoxicity, has become a last-resort
antimicrobial to treat life-threatening infections due to
multidrug resistant (MDR) Gram-negative bacteria [2].
However, in the agricultural sector, polymyxins are ap-
plied regularly for the treatment of gastrointestinal infec-
tions in livestock and their increased use may have
promoted the emergence of colistin-resistant bacteria
[3]. Acquired resistance to polymyxins in Enterobacteria-
ceae is mainly related to mutations or truncations in the
genes encoding the PmrA/PmrB and PhoP/PhoQ two
component systems (TCS), or to the expression of ac-
quired mcr-1 or mcr-2 genes, which are plasmid-located
[4, 5]. In both cases, resistance arises through the
modification of lipid A component of the outer
membrane by 4-amino-4-deoxy-L-arabinose (L-Ara4N)
or phosphoethanolamine (PEtN) [1]. Plasmid-mediated
colistin resistance has recently been acknowledged as a
major threat to public health [4]. There is evidence that
mcr-1 harboring Enterobacteriaceae have been occurring
globally in food-producing animals, in food and in
humans for several years, often associated with other
resistance genes including extended-spectrum ß-lacta-
mases (ESBL) and carbapenemases [6]. Further, the
recently identified mcr-2 gene, which shares 76.7%
* Correspondence: magdalena.nueesch-inderbinen@uzh.ch
1Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich,
Winterthurerstrasse 272, 8057 Zurich, Switzerland
Full list of author information is available at the end of the article
© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Zurfluh et al. Antimicrobial Resistance and Infection Control  (2017) 6:28 
DOI 10.1186/s13756-017-0186-z
nucleotide sequence homology with mcr-1, has been
found to be more prevalent than mcr-1 in porcine colis-
tin resistant Escherichia (E.) coli isolates in Belgium [5].
Hence, there is need for continuous surveillance of co-
listin resistance in Enterobacteriaceae in order to reduce
the risk to human health. The intestinal microbiota
forms a major reservoir of antibiotic resistant bacteria in
humans [7], therefore asymptomatic carriage of MCR
producers must be taken into account in prevention and
control efforts. A recent study showed that 10% of trav-
elers returning from India were fecal carriers of colistin
resistant Enterobacteriaceae, and had probably acquired
such strains via the food chain [8]. This study was con-
ducted in order to (i) assess the occurrence of colistin-
resistant Enterobacteriaceae in the fecal flora of healthy
people with high occupational exposure to food and of
primary care patients in Switzerland during the period
of June to October 2016, and (ii) determine whether any
of the resistant isolates harbored mcr-1 or mcr-2.
Because Switzerland is situated at the geographical cen-
ter of Europe and represents a socioeconomic and
demographic intersection of the surrounding countries,
this country is ideal for observing temporal-spatial
trends in the occurrence of antibiotic resistance in the
population of central Europe.
Materials and methods
In total, 1144 non-duplicate samples were analysed.
Stool samples (n = 1091) were obtained by the National
Centre for Enteropathogenic Bacteria and Listeria
(NENT) from employees of food-processing companies
located throughout Switzerland between July and Octo-
ber 2016, during a yearly routine fecal screening for
Salmonellae. Fecal swabs (n = 53) were obtained from
adult primary care patients consulting their general
practitioner in a suburban community in the greater
area of Zurich, Switzerland, during a period of 2 weeks
in September 2016. Informed consent was obtained from
each participating patient and the study was approved
by the local ethics committee of Zürich (BASEC-Nr.
Req-2016-00374).
Stool samples (one loopful each) and swabs were
enriched in 5 ml Enterobacteriaceae enrichment (EE)
broth (BD, Franklin Lakes, NJ, USA) for 24 h at 37 °C.
Thereafter, one loopful was streaked onto LB agar plates
containing 4 mg/L colistin, 10 mg/L vancomycin and
5 mg/L amphotericin B for selection of colistin-resistant
Gram-negative bacteria. Colonies were identified using
API ID 32 E (bioMérieux, Marcy l’Etoile, France) or by
16S rRNA or rpoB custom sequencing (Microsynth,
Balgach, Switzerland). Species with intrinsic resistance
to polymyxins (Serratia marcescens, Proteus spp.,
Providencia spp. and Morganella spp.) were discarded.
All other isolates were selected for further analysis.
Determination of the minimum inhibitory concentration
(MIC) of colistin was performed by broth microdilution ac-
cording to the European Committee on Antimicrobial
Susceptibility Testing EUCAST (eucast.org). Screening by
PCR for mcr-1 and mcr-2 was performed as described pre-
viously [4, 9] using DNA from mcr-1 harboring strain
OW3E1 [10] and plasmid “Plasmid-MCR2-Positivkon-
trolle” (P. Keller, personal communication) as positive
controls.
Results and discussion
A total of 62 isolates were obtained from the selective
plates. Thereof, 18 were resistant to colistin (MIC >2
mg/L), including Hafnia (H.) alvei (n = 9), E. coli (n = 3),
Enterobacter (E.) cloacae (n = 4), Klebsiella (K.) pneumo-
niae (n = 1) and Raoultella (R.) ornithinolytica (n = 1).
H. alvei and E. coli were identified using API 32 E, R.
ornithinolytica by 16S rRNA sequencing, K. pneumoniae
and E. cloacae by rpoB sequencing. Resistant isolates
originated from 16 (1.5%) of the healthy people and 2
(3.8%) of the primary care patients (Table 1). Of the pri-
mary care patients, both were male and the median age
was 54.5 years. Underlying conditions were diabetes (2/
2, 100%) and cardiovascular diseases (2/2, 100%). Both
(100%) had had contact with a hospital as outpatients
for diagnostic radiography or colonoscopy. Neither of
the patients had a recent history of travel or treatment
with antimicrobials within 6 months prior to sampling.
Neither of the patients’ professional occupations were
associated with close contact to agriculture.
Results of the PCR screening for mcr-1 and mcr-2
remained negative for all 62 isolates.
This study presents the first report on the occurrence
of colistin-resistant Enterobacteriaceae in the fecal flora
Table 1 Colistin resistant Enterobacteriaceae isolated from the fecal flora of 1091 healthy humans and 53 primary care patients
Species No. of isolates from No. of isolates with MIC of colistin [mg/L] with values of
Healthy people Primary care patients 4 8 64
H. alvei 8 1 5 4 0
E. coli 3 0 1 2
E. cloacae 3 1 4
R. ornithinolytica 1 0 1
K. pneumoniae 1 0 1
Zurfluh et al. Antimicrobial Resistance and Infection Control  (2017) 6:28 Page 2 of 4
of healthy humans and primary care patients in
Switzerland and Europe. The absence of MCR producers
in the fecal flora of healthy people as well as primary
care patients is of major epidemiological interest. It
indicates that the risk of transfer of mcr genes from ani-
mals, food or the environment is currently very low in
the community, despite the fact that colistin is used for
treating infections in livestock. Indeed, there is recent
evidence that food-producing animals in Switzerland do
not represent an mcr-1 or mcr-2 reservoir, thus a risk of
transfer from livestock to humans may be excluded [11].
By contrast, 25.8% of (partly imported) poultry meat
samples in Swiss retail stores contain mcr-1 harboring E.
coli [12]. Despite this potential threat to public health,
the risk of transfer of mcr-1 genes from food to humans
appears to be very low, even for individuals working in
the food-processing industry, as demonstrated by the
data presented here. This finding correlates with previ-
ous reports on the low prevalence (<1%) of infections of
humans with MCR-producing Enterobacteriaceae in
Switzerland [9]. MCR producers have so far been de-
tected rarely in stool samples of healthy individuals and
reports are currently restricted to Asian countries [13,
14]. Additional studies should be carried out in order to
continuously evaluate the dissemination of mcr genes
among enteric bacteria in animals, food and humans. Fi-
nally, fecal carriage of clinically significant bacteria such
as E. coli, E. cloacae and K. pneumoniae with likely non-
transmissible colistin resistance may be of concern,
should such bacteria acquire multidrug resistance
plasmids.
Conclusions
Currently, plasmid-mediated colistin resistance poses no
threat to public health in Switzerland. Regular and up-
dated information on the occurrence of mcr genes in
bacterial isolates from animals, the food chain and
humans at global, national and regional levels is essential
to anticipate future trends in the prevalence and dissem-
ination of plasmid-mediated colistin resistance.
Abbreviations
EE: Enterobacteriaceae enrichment; ESBL: Extended-spectrum ß-lactamases;
EUCAST: European Committee on Antimicrobial Susceptibility Testing; L-Ara4N: 4-
amino-4-deoxy-L-arabinose; LPS: Lipopolysaccharides; MDR: Multidrug resistant;
MICs: Minimal inhibitory concentrations; NENT: National Centre for Enteropathogenic
Bacteria and Listeria; PEtN: Phosphoethanolamine; TCS: Two component system
Acknowledgements
The authors thank P. Keller from the Institute of Medical Microbiology,
University of Zürich for plasmid “Plasmid-MCR2-Positivkontrolle”.
Funding
This work was supported by the Swiss Federal Office of Public Health,
Division Communicable Diseases, the University of Fribourg, and by a grant
of the ANIWHA ERA-NET project (Switzerland).
Availability of data and materials
The raw data of this research can be made available upon request.
Authors’ contributions
RS, HH and HJN designed the study. KZ carried out the microbiological and
molecular biological tests. KZ, MNI, LP, PN and AW analyzed and interpreted
the data. MNI drafted the manuscript. All authors read and approved the
final manuscript.
Competing interests
The authors declare that they have no competing interest.
Consent for publication
Not applicable.
Ethics approval and consent to participate
All procedures performed in studies involving human participants were in
accordance with the ethical standards of the institutional and/or national
research committee and with the 1964 Helsinki declaration and its later
amendments or comparable ethical standards. This type of study is approved
by the local ethics committee of Zürich (BASEC-Nr. Req-2016-00374).
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.
Author details
1Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich,
Winterthurerstrasse 272, 8057 Zurich, Switzerland. 2Division of Infectious
Diseases and Hospital Epidemiology, University of Basel, 4031 Basel,
Switzerland. 3Emerging Antibiotic Resistance, Medical and Molecular
Microbiology Unit, Department of Medicine, University of Fribourg, 1700
Fribourg, Switzerland. 4Practice for General Medicine, Birchstrasse 2, 8472
Seuzach, Switzerland.
Received: 9 December 2016 Accepted: 9 March 2017
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