Letter to the editor
Polymyxins, like colistin (polymyxin E), are a group of cationic antimicrobial cyclic
polypeptide, which have been extensively-used as prophylactic feed additives in animal
production since the 1960s [1]. A strong association has especially been drawn between
antimicrobial use and resistance in poultry and pig farms [2–5]. The advent and rise
of multi-drug resistant bacteria has now prompted the re-introduction of colistin
as a last-resort treatment option in human medicine [6,7]. However, the recent emergence
and diversity of plasmid-borne mobile colistin resistance determinants (mcr-1 to mcr-5)
in Enterobacteriaceae has severely challenged its use in a clinical setting [8–12].
In the past two years, mcr-1 has been detected in over 40 countries across 5 of 7
continents worldwide [13–15]. Except rare cases of chromosomally-integrated mcr-1
[16,17], its prevalent transmission relies on the transfer by diversified plasmids
of different replication incompatibilities [18,19].
Mechanistically, the mcr-1 gene that encodes phosphoethanolamine transferase mediates
the modification of the lipopolysaccharide layer (LPS) of the outer membrane of Gram-negative
bacteria through the addition of phosphoethanolamine (PEA) to the 1 (or 4′)-phosphate
position of lipid A moieties [20,21]. This reduces the affinity of polymyxin antibiotics
to their primary target, the LPS layer. Since its discovery during routine surveillance
in China [8], increasingly-accumulated evidence suggested the presence of mcr-1-bearing
bacteria in food producing animals and humans across the world. To the best of our
knowledge, the leading two types of mcr-1-harboring plasmids referred to IncI2 [8,18,22,23]
and IncX4 [24–26], have greatly facilitated global dissemination of mcr-1 colistin
resistance [14,27]. In Pakistan, the mcr-1 gene has been identified in Escherichia
coli (E. coli) isolates from human [28], wildlife [29] and a broiler suffering from
colibacillosis [30]. However, little is known about the prevalence of mcr-1 and its
genetic environment in commensal E. coli isolates from poultry in Pakistan.
From December 2016 to January 2017, cloacal swabs from a total of 100 healthy broiler
chicken were obtained from four commercial farms (n = 25 each) in the Faisalabad region
of Pakistan. To screen the colistin resistant E. coli, all the samples were seeded
directly onto MacConkey agar supplemented with 4 μg/ml of colistin and were incubated
at 37°C for 24 hours. Of 100 birds, colistin resistant E. coli were found in only
8 (8%) samples. A single colony of E. coli was selected per sample and identified
using API 20E biochemical strips (bioMérieux, Marcy l'Etoile, France). The presence
of mcr-1 gene was confirmed among all 8 E. coli isolates by conventional PCR as we
recently conducted [19,31]. Subsequently, the minimum inhibitory concentration (MIC)
of colistin among these strains was tested by micro-dilution according to the guidelines
of Clinical and Laboratory Standards Institute [32,33]. The mcr-1-positive E. coli
gave MIC of colistin between 2–8 μg/ml (Table 1). Plasmids were extracted from mcr-1-positive
E. coli using alkaline lysis method. To elucidate the genetic context of mcr-1 on
these plasmids, the conventional multiplex PCR with 7 primer sets was performed (Table S1)
as we recently described [3,19]. The plasmids isolated from the different strains
had unexpectedly similar PCR profiles with the exception of pPK112 which lacks the
tnpA loci (Fig. 1B). Genetic context of mcr-1 shows that all the plasmids lack the
insertion element ISApl1 (Fig. 1A), which has been responsible for insertion of mcr-1
in previous studies [34]. Also, these plasmids (Fig. 1A) are identical to the mcr-1-carrying
plasmid pE15017 isolated in China [19,22]. These bacteria were subjected to multi-locus
sequence typing analyses with the Warwick method (http://mlst.warwick.ac.uk/mlst/).
Diversified sequence types were detected, namely, ST10, ST2847, ST155, ST361 and ST6395.
Evidently, all strains belonged to different STs with the exception of two strains
of ST361 (Table 1). Despite that none of these STs have been reported from Pakistan
in the past, ST10 and ST155 have been reported in mcr-1-harboring E. coli isolated
from chicken in China [17,35].
Table 1.
Characteristics of mcr-1-positive E. coli isolates from healthy broilers in Faisalabad,
Pakistan.
Strains
Source
Date
MIC (μg/ml)
MLST
Farm no.
PK102
cloacal
27/12/2016
≥8
ST10
1
PK103
cloacal
27/12/2016
≥4
ST2847
1
PK105
cloacal
27/12/2016
≥8
ST155
1
PK107
cloacal
27/12/2016
≥8
New ST
1
PK109
cloacal
27/12/2016
≥4
ST361
1
PK110
cloacal
30/01/2017
≥4
ST6395
3
PK111
cloacal
30/01/2017
≥2
ST361
3
PK112
cloacal
30/01/2017
≥8
New ST
3
Figure 1.
Genetic analyses of mcr-1-harboring plasmids in this study A. Scheme of different
mcr-1-bearing plasmids B. PCR assays of mcr-1 and neighboring loci in plasmids 16S
rDNA is specific to the E. coli specie.
Subsequently, a representative mcr-1-carrying plasmid pPK105 (Table 1) was subjected
to whole genome sequencing using the method of Illumina HiSeq X-ten. The plasmid sequences
were annotated by RAST, and the genome maps were drawn with the Circos program. As
a result, the genome size of pPK105 was determined to be 60.499 kb (Acc. no.: MG808035,
Fig. 2A), encoding hundreds of open reading frames with a GC content of 42.3%. Unlike
the prevalent IncX4 type plasmid reported in Pakistan, Plasmid Finder at the web server
(https://cge.cbs.dtu.dk/services/PlasmidFinder/) indicated that pPK105 is a member
of IncI2-type plasmid family (Fig. 2B). Notably, mcr-1 is the only resistance gene
detected in pPK105 (Fig. 2B). It is quite different from the scenarios observed in
the other mcr-1-containing Pakistan isolate coharboring ESBL (extended-spectrum β-lactamase
gene) and heavy-metal resistance. Although that ISApl1 sequence is missing, pPK105
retains the two conjugative genes vir and pil (Fig. 2). Intriguingly, we noticed that
the mcr-1 gene in pPK105 is next to a sdrl gene, a serine-aspartate repeat surface
protein known to bind collagen (Fig. 2B). However, its relevance remains unclear.
Nevertheless, it has been shown earlier that ISApl1 transposon element is highly unstable
in IncI2 plasmid [36].
Figure 2.
The representative mcr-1-bearing plasmid in a colistin resistant E. coli isolate PK105
A. Diagram for the mcr-1-positive plasmid (pPK105) that exists in the E. coli isolate
PK105 B. Colinear comparison of the IncI2-type plasmid pPK105 with two closely-related
plasmids mcr-1-postive M18 and mcr-1-negative pColR644SK1.
For further investigation, the chemical modification of lipid A by the mcr-1 protein
product MCR-1, the bacterial LPS was extracted as we conducted earlier [20,37] and
then subjected to matrix-assisted laser desorption ionization–time of flight mass
spectrometry (MALDI-TOF MS) [38]. In comparison to E. coli MG1655 (m/z 1796.29, Fig. 3A),
a shift in the predominant lipid A species (m/z 1920.136, Fig. 3A) was observed in
the mcr-1-expressing PK105 strain (Δmass is close to 123) corresponding to the addition
of a PEA moiety (Fig. 3B). This new peak corresponds to a single modification that
may occur at either the 1 or the 4′ position (Fig. 3B). This highlighted that surface
remodeling by the mcr-1-encoding phosphoethanolamine transferase contributes to the
resultant colistin resistance [14].
Figure 3.
MALDI-TOF MS analyses of lipid A pools of E. coli strains with (or without) mcr-1
A. MS profile of the LPS-lipid A in the negative control strain E. coli MG1655 B.
MS spectrum of the LPS-lipid A in PK105, a representative strain of E. coli carrying
mcr-1. A single modification may occur at the 1 (or 4′) position. The position indicated
here is suggestive [20].
The discovery of the mcr-1 gene, prompted a shift in focus from chromosomal mutations
causing colistin-resistance to a transmissible plasmid-borne colistin resistance determinant.
In addition to clinical isolates in humans, antimicrobial surveillance programs in
Europe have identified mcr-1 in commensal bacterial populations from broilers, pigs
and turkeys [39]. This study shows a similar threatening scenario in the Faisalabad
region of Pakistan where high rates of mcr-1 positive E. coli were identified in healthy
broilers. Retrospectively, the discovery of diverse clonal backgrounds of E. coli
harboring the plasmid-borne mcr-1 is similar to scenarios observed earlier in Chinese
poultry.
Similarly, data on global population structure of mcr-1-positive E. coli showed large
diversity in STs but limited plasmid types, particularly with regional spread of IncHI2
plasmids in Europe and IncI2 in Asia [14]. This indicated the possible spread of a
single mcr-1 colistin resistance gene across large geographical distances. It seems
likely that farm animals act as a reservoir for the genetic diversity of mcr-1 [40].
Supplementary Material
1462060.zip