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Isolation of Carbapenem-Resistant Pseudomonas Spp. From Food
Isolation of Carbapenem-Resistant Pseudomonas Spp. From Food
Isolation of Carbapenem-Resistant Pseudomonas Spp. From Food
A R T I C L E I N F O A B S T R A C T
Article history: Pseudomonas spp. are ubiquitous in nature. Carbapenem resistance in environmental isolates of
Received 8 January 2015 members of this genus is thought to be rare but the exact resistance rate is unknown. In this study,
Received in revised form 10 March 2015 carbapenem-resistant Pseudomonas spp. were isolated from chicken and pork samples and the
Accepted 13 March 2015
mechanisms underlying the carbapenem resistance in these strains were investigated. A total of 16
carbapenem-resistant Pseudomonas aeruginosa, Pseudomonas putida and Pseudomonas otitidis isolates
Keywords: were recovered from eight samples of chicken and pork. The isolates exhibited meropenem minimum
Carbapenem
inhibitory concentrations (MICs) of 8 to 32 mg/L and imipenem MICs of <0.5–16 mg/L yet did not
Pseudomonas aeruginosa
Pseudomonas putida
harbour any acquired carbapenemase genes. Meropenem resistance in various strains was found to be
Pseudomonas otitidis mediated by efflux systems only, whereas overexpression of MexAB–OprM efflux pump and lack of OprD
Food porin were responsible for carbapenem resistance in P. aeruginosa. The intrinsic metallo-b-lactamase
gene blaPOM in P. otitidis and overexpression of the TtgABC efflux system in P. putida were also responsible
for carbapenem resistance in these organisms. In conclusion, this study reports for the first time the
isolation of carbapenem-resistant P. aeruginosa, P. otitidis and P. putida strains from food. The resistance
mechanisms of these strains are rarely due to production of carbapenemases. Further selection of such
carbapenem-resistant Pseudomonas spp. in the environment and the risk by which they are transmitted
to clinical settings are of great public health concern.
ß 2015 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All
rights reserved.
http://dx.doi.org/10.1016/j.jgar.2015.03.006
2213-7165/ß 2015 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.
Please cite this article in press as: Wong M-, et al. Isolation of carbapenem-resistant Pseudomonas spp. from food. J Global Antimicrob
Resist (2015), http://dx.doi.org/10.1016/j.jgar.2015.03.006
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JGAR-146; No. of Pages 6
2 M..-. Wong et al. / Journal of Global Antimicrobial Resistance xxx (2015) xxx–xxx
The incidence of carbapenem resistance in foodborne isolates is 18 h using a CHEF-DR1 II Electrophoresis System (Bio-Rad,
estimated to be low as carbapenems are not used in animal Hercules, CA) with pulse times of 0.5–30 s. The gels were stained
farming. However, carbapenem-resistant micro-organisms in food with GelRedTM (Biotium, Hayward, CA) and DNA bands were
production animals have become detectable recently [8,9]. visualised with ultraviolet transillumination (Bio-Rad). Fragment
Dissemination of this category of potential pathogens between patterns were interpreted as described previously [11].
environmental and nosocomial settings is of particular concern.
This study describes the isolation of carbapenem-resistant 2.2. Antimicrobial susceptibility and carbapenemase activity testing
Pseudomonas spp. from retail meat products in Hong Kong as
well as an analysis of the genetic and physiological basis of their Antimicrobial susceptibility testing was carried out by the agar
resistance phenotypes. dilution method with the antimicrobials listed in Table 1. Results
were interpreted following Clinical and Laboratory Standards
Institute (CLSI) guidelines [12]. Escherichia coli ATCC 25922 and
2. Materials and methods ATCC 35218 and P. aeruginosa ATCC 27853 were used as quality
control strains. The minimum inhibitory concentrations (MICs) of
2.1. Bacterial isolation and confirmation the efflux pump inhibitor phenylalanine–arginine b-naphthyla-
mide (PAbN) for the isolates was determined by the broth
A total of 16 chicken and pork meat samples (8 of each) were microdilution method. Involvement of efflux systems in reduced
purchased from two different supermarkets on four separate carbapenem susceptibility was tested by determining the mer-
sampling dates in Hong Kong during the summer of 2011. The openem MIC in the presence and absence of PAbN at a
samples were homogenised and enriched in Peptone Water (Oxoid concentration of 40 mg/mL [13]. The carbapenemase activity of
Ltd., Basingstoke, UK) for 24 h at 37 8C with shaking, followed by all isolates was tested by the Modified Hodge test (MHT) against
direct spreading on MacConkey agar (Oxoid Ltd.) containing 2 mg/ meropenem and imipenem using E. coli ATCC 25922 as the
L meropenem (Santa Cruz Biotech, Dallas, TX). Two colonies were indicator organism as described previously [12]. The Carba NP test
recovered from each plate and were purified and identified by was performed on the four P. otitidis isolates as described
API20E (bioMé rieux, Craponne, France) and 16S rRNA sequencing. previously [14]. A P. aeruginosa clinical strain carrying blaIMP
Isolates whose 16S rRNA sequencing results were ambiguous were was used in all tests as a positive control.
further subjected to confirmation by the VITEK1 2 system
(bioMérieux). Multilocus sequence typing (MLST) was performed 2.3. PCR screening and real-time PCR
and interpreted on P. aeruginosa isolates according to the PubMLST
scheme (http://pubmlst.org/paeruginosa/). 16S rRNA sequences of Carbapenemase genes that can be acquired by horizontal
P. putida isolates were aligned by the ClusterW2 algorithm and a transfer, including blaIMP, blaVIM, blaOXA, blaSIM, blaKPC, blaSPM,
phylogenetic tree was compiled by the maximum-likelihood blaDIM, blaGIM and blaNDM, were screened by PCR as described
algorithm approach using BioEdit software (http://www.mbio. previously [15]. The intrinsic MBL blaPOM in P. otitidis was detected
ncsu.edu/bioedit/bioedit.html). Pulsed-field gel electrophoresis by PCR and the corresponding nucleotide sequence was deter-
(PFGE) was performed as described previously [10]. Briefly, mined as described previously [4]. Total RNA was extracted using
agarose-embedded DNA was digested with XbaI (New England an RNeasy Protect Bacteria Mini Kit (QIAGEN, Hilden, Germany),
Bio-Labs, Ipswich, UK) at 37 8C for 1.5 h. The restriction fragments followed by DNase treatment. The quality and quantity of RNA was
were separated by electrophoresis in 0.5 TBE [Tris–borate– examined using a NanoDrop spectrophotometer (Thermo Fisher
ethylene diamine tetra-acetic acid (EDTA)] buffer at 14 8C for Scientific Inc., Hemel Hempstead, UK). Then, 1 mg of RNA was
Table 1
Isolation source and minimum inhibitory concentrations (MICs) of Pseudomonas spp. isolates in this study.
a b
Strain ID Species Source PFGE type MIC (mg/L)c
PIP FEP CTZ CIP [4] LEV [8] PMB [8] AMK CHL [32] IPM [8] IPM/ MEM [8] MEM/
[128] [32] [32] [64] PAbN PAbN
POTI, Pseudomonas otitidis; PPUT, Pseudomonas putida; PAER, Pseudomonas aeruginosa; PFGE, pulsed-field gel electrophoresis; PIP, piperacillin; FEP, cefepime; CTZ,
ceftazidime; CIP, ciprofloxacin; LEV, levofloxacin; PMB, polymyxin B; AMK, amikacin; CHL, chloramphenicol; IPM, imipenem; PAbN, phenylalanine–arginine
b-naphthylamide; MEM, meropenem.
a
C1–C5, chicken samples 1–5; P1–P3, pork samples 1–3.
b
Fragment patterns differing by six or more bands were regarded as different clones. Each clone is designated with a letter (e.g. A, B, C). Subtypes of each clone (difference
less than six bands) were shown as a letter with a number (e.g. B1, B2).
c
Numbers in brackets represent the Clinical and Laboratory Standards Institute (CLSI) breakpoint of the antimicrobials [12].
Please cite this article in press as: Wong M-, et al. Isolation of carbapenem-resistant Pseudomonas spp. from food. J Global Antimicrob
Resist (2015), http://dx.doi.org/10.1016/j.jgar.2015.03.006
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JGAR-146; No. of Pages 6
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subjected to reverse transcription using a Life Technologies High P. putida isolates were observable (Table 1). The identical PFGE
Capacity cDNA Kit (Life Technologies, Grand Island, NY). Quantita- patterns (type B1 and B3) may be due to duplicate isolates, except
tive reverse transcription PCR (qRT-PCR) was conducted on an iQ5 E1-13 and E1-14 which share the same PFGHE pattern (B2) that
iCycler (Bio-Rad) using SYBR Select Master Mix (Life Technologies). were isolated from independent samples.
Expression of mexB, mexD, mexE and ampC was normalised with Antimicrobial susceptibility testing showed that the isolates
the rpsL gene using primers described elsewhere and was were susceptible to all antimicrobials tested except imipenem and
compared with P. aeruginosa PAO1 type strain [16]. Expression meropenem; interestingly, all of the tested isolates were resistant
of ttgA was normalised with the 16S rRNA gene and was compared to meropenem (MIC 8 mg/L), yet only P. aeruginosa E1-17 was
with P. putida ATCC 12633 type strain. Data were analysed by the resistant to imipenem (MIC = 16 mg/L). The MIC of imipenem for
comparative CT method [17]. The full length of the oprD gene in P. other isolates ranged from 1 mg/L to 4 mg/L. An MIC 512 mg/L of
aeruginosa and P. putida isolates was amplified by PCR using the efflux pump inhibitor PAbN for all isolates was observed, and
primers oprD-F (50 -CGCCGACAAGAAGAATAGC) and oprD-R (50 - addition of PAbN abolished the meropenem resistance phenotype
GTCGATTACAGGATCGACAG) for P. aeruginosa, and oprD-PT-FL1 in all isolates with a 2–32-fold reduction in the MIC. Although it is
(50 -GTTAGCCGTGTCGATTGCCT) and oprD-PT-FL2 (50 -CGCAGCGG- believed that drug efflux was not the major mechanism of
TACTCTTCCTA) for P. putida. imipenem resistance, PAbN was found to attenuate imipenem
resistance in P. aeruginosa E1-17 by four-fold (16–4 mg/L). In
2.4. Nucleotide accession contrast, attenuation of imipenem resistance with the efflux pump
inhibitor was not obvious (0–2-fold reduction in MIC) in P. putida
The oprD sequences obtained from this study can be accessed and P. otitidis. These results suggested that efflux systems played a
on GenBank with the following accession nos.: P. aeruginosa E1-17, major role in carbapenem resistance in all Pseudomonas spp.
KP262046; P. aeruginosa LESB58, CAW29111.1; P. putida ATCC (Table 1). Production of carbapenemases against meropenem was
12633, KP025954; P. putida E1-8, KP025955; and P. putida E1-21, tested by the MHT using E. coli ATCC 25922 as the indicator strain,
KP025956. with the results being negative for all isolates. Consistently, all
isolates were negative in PCR screening of carbapenemase genes.
3. Results and discussion Expression of multiple efflux systems (mexAB, mexCD and mexEF),
ampC and oprD was tested by qRT-PCR for the P. aeruginosa E1-17
For this analysis, pork and chicken samples (eight of each) were isolate in this study (Fig. 2). Expression of mexB, mexD, mexE and
purchased from supermarkets in Hong Kong. A total of 16 isolates mexX was found to be 3.08 0.6, 0.53 0.07, 0.83 0.1 and
were recovered from eight of the sixteen samples. The isolation 0.11 0.03-fold that of P. aeruginosa PAO1, respectively. Expression
rates for chicken and pork were 63% (5/8) and 38% (3/8), of ampC in E1-17 was comparable with that of PAO1 (1.21 0.2-fold).
respectively. 16S rRNA sequencing confirmed that these isolates Although it is believed that ampC is a major contributing factor in
were P. putida (n = 11), P. otitidis (n = 4) and P. aeruginosa (n = 1) carbapenem susceptibility, absence of ampC overexpression in
(Table 1). P. aeruginosa isolate E1-17 was found to be ST1756 by carbapenem-resistant P. aeruginosa has been reported previously
MLST. This type has not been reported in P. aeruginosa of clinical [18]. Expression of oprD was not detectable in E1-17. The full length
origin. Phylogenetic analysis was performed on 16S rRNA sequence of the oprD gene was obtained by PCR and no inactivation
sequences obtained from the 11 P. putida isolates in this study mutations or insertion sequences were found. BLASTn analysis
and was compared with the type strain P. putida ATCC 12633 and P. revealed that the OprD protein was almost identical (with one amino
putida KT2440 (Fig. 1). It was found that 8 of the 11 isolates showed acid substitution) to that of P. aeruginosa strain LESB58. Other than non-
99.7–99.9% identity with KT2440 and 99.1–99.2% identity with functional porin resulting from mutational events, absence of wild-
ATCC 12633. One isolate (E3-17) had 99.9% identity with ATCC type OprD expression in carbapenem-resistant P. aeruginosa isolates is
12633, whereas the two remaining isolates (E1-13 and E1-15) not uncommon. This may be due to a shift of regulatory pathways or
shared a slightly lower level of identity (97%) with the two P. putida disruption of promoter sequences [19]. Overall, this finding showed
type strains. These two isolates were confirmed to be P. putida by that the carbapenem resistance mechanisms in P. aeruginosa were
VITEK1 2. XbaI-PFGE typing revealed that the P. otitidis isolates mainly due to physiological changes and was consistent with what has
belonged to different clones, whereas seven clones among 11 been observed among carbapenem-resistant P. aeruginosa strains
Fig. 1. 16S rRNA phylogenetic tree depicting the relative genetic relatedness of 11 Pseudomonas putida isolates in this study as well as two P. putida type strains (ATCC 12633
and KT2440).
Please cite this article in press as: Wong M-, et al. Isolation of carbapenem-resistant Pseudomonas spp. from food. J Global Antimicrob
Resist (2015), http://dx.doi.org/10.1016/j.jgar.2015.03.006
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Fig. 3. Metallo-b-lactamase blaPOM sequences of Pseudomonas otitidis. E1-6, E1-7, E1-9 and E3-19 are P. otitidis isolates collected in this study and MCC10330 is a P. otitidis type
strain.
Please cite this article in press as: Wong M-, et al. Isolation of carbapenem-resistant Pseudomonas spp. from food. J Global Antimicrob
Resist (2015), http://dx.doi.org/10.1016/j.jgar.2015.03.006
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JGAR-146; No. of Pages 6
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Fig. 5. Alignment of OprD amino acid sequences of four Pseudomonas putida isolates. E1-8 and E1-21 are P. putida food isolates collected in this study and ATCC 12633 and
KT2440 are P. putida type strains.
Please cite this article in press as: Wong M-, et al. Isolation of carbapenem-resistant Pseudomonas spp. from food. J Global Antimicrob
Resist (2015), http://dx.doi.org/10.1016/j.jgar.2015.03.006
G Model
JGAR-146; No. of Pages 6
6 M..-. Wong et al. / Journal of Global Antimicrobial Resistance xxx (2015) xxx–xxx
Please cite this article in press as: Wong M-, et al. Isolation of carbapenem-resistant Pseudomonas spp. from food. J Global Antimicrob
Resist (2015), http://dx.doi.org/10.1016/j.jgar.2015.03.006