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detection of MCR-1 plasmid-mediated colistin resistance. 2. Category: New Technologies for Infectious and Tropical Diseases. 3. Short title (for the running ...
Accepted Manuscript Real- time quantitative PCR assay with Taqman* probe for rapid detection of MCR-1 plasmid-mediated colistin resistance Selma Chabou, Thongpan Leangapichart, Liliane Okdah, Stephanie Le Page, Linda Hadjadj, Jean-Marc Rolain PII:

S2052-2975(16)30071-3

DOI:

10.1016/j.nmni.2016.06.017

Reference:

NMNI 202

To appear in:

New Microbes and New Infections

Received Date: 4 May 2016 Revised Date:

29 June 2016

Accepted Date: 30 June 2016

Please cite this article as: Chabou S, Leangapichart T, Okdah L, Le Page S, Hadjadj L, Rolain J-M, Real- time quantitative PCR assay with Taqman* probe for rapid detection of MCR-1 plasmid-mediated colistin resistance, New Microbes and New Infections (2016), doi: 10.1016/j.nmni.2016.06.017. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

ACCEPTED MANUSCRIPT

Full-length title: Real- Time quantitative PCR assay with Taqman* probe for rapid

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detection of MCR-1 plasmid-mediated colistin resistance.

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Category: New Technologies for Infectious and Tropical Diseases

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Short title (for the running head): mcr-1 colistin resistance qPCR assay

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Author list: Selma Chabou1, Thongpan Leangapichart1, Liliane Okdah1, Stephanie Le Page1,

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Linda Hadjadj 1, and Jean-Marc Rolain1*

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Affiliations: 1 URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée

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Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, 27 boulevard Jean

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Moulin, 13385 Marseille CEDEX 05, France

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* Corresponding author: [email protected]

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Key words: colistin resistance; mcr-1 gene; antibiotic resistance surveillance;

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Number of text words: 1006

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Number of figures: 1

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Number of tables: 2

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Number of references: 18

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Abstract word count: 100

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ABSTRACT

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Here we report the development of two rapid real-time quantitative PCR assays with TaqMan®

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probes to detect MCR-1 plasmid-mediated colistin resistance gene from bacterial isolates and

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fecal samples from chickens. Specificity and sensitivity of the assay were at 100% on bacterial

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isolates including 18 colistin-resistant isolates carrying the mcr-1 gene (6 K. pneumoniae and 12

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E. coli) with a calibration curve linear from 101 to 108 DNA copies. Five out of 833 fecal samples

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from chickens from Algeria were positive from which 3 E. coli strains were isolated and

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confirmed to harbor the mcr-1 gene by standard PCR and sequencing.

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INTRODUCTION

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The increasing prevalence of infections caused by multidrug-resistant (MDR) Gram-negative

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bacteria combined with few antimicrobial agents being in development has led to a resurgence in

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interest in colistin as a last-line therapy with the inevitable risk of emerging resistance (1-3).

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MCR-1 plasmid-mediated colistin resistance is a member of the phosphoethanolamine transferase

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enzyme family, with expression in Escherichia coli resulting in the addition of

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phosphoethanolamine to lipid A and resistance to colistin (4). This plasmid-mediated colistin

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resistance is an emerging concern that has already spread worldwide (5) in E. coli and K.

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pneumoniae from pigs, chicken, retail meat, pork and humans (4). In animal health, colistin is

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used to prevent infections from E. coli isolates that are known to cause serious side effects such

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as diarrhea, sepsis and colibacillosis, which result in huge economic losses (6) . The extensive

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use of antibiotics in food-animal production has been shown to increase the risk of transferring

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resistant bacteria to humans (7).

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There is a need to screen for colistin resistance in patients even without prior history of colistin

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usage for the timely detection and isolation of patients harboring such resistant strains to prevent

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clonal transmission (8). For this reason the aim of this study was to develop rapid real-time

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quantitative PCR to detect the MCR-1 plasmid-mediated colistin resistance and to evaluate its

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sensitivity and specificity both from strains and stool samples.

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MATERIALS AND METHODS

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Specific primers and probes designer

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We design specific primers and probes to develop two real-time quantitative PCR assays (PE1

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and PE2) for detection of MCR-1 encoding gene (Table 1). Specificity of the primers and probes

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were verified in silico by blastN analysis on the National Center for Biotechnology Information

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(NCBI) database.

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Sample collection

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Bacterial strains

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A total of 100 strains from humans and animals were used in this study including 18 colistin-

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resistant isolates carrying the mcr-1 gene (6 K. pneumoniae and 12 E. coli). Phenotypic and

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genotypic features of these strains are summarized in Table 2.

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Chicken stool collection

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A total of 833 feces of broilers were collected between August and February 2015 from 8

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regions in Algeria (El Tarf, Souk Ahras, Skikda, Setif, Jijel, Algiers, Biskra, and Ourgla; n = 503)

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and in three slaughterhouses in Marseille (n = 330). All extracted DNA from the 833 feces of

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broilers were tested using our qPCR assay and positive samples were inoculated on agar for

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isolation of positive mcr-1 isolates.

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Molecular analysis

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Strategy for PCR amplification and sequencing

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Standard PCR amplification and sequencing of the MCR-1-encoding gene was used as the gold

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standard and performed as previously described (4). Quantification of the MCR-1 encoding gene

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using our two sets of primers and probes was performed using a quantitative CFX96Tm Real Time

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system C1000Tm Touch thermal cycler (Bio- Rad, Sangapour). The qPCR conditions were as

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follows: the reaction mixtures were kept at 95°C for 15 min and subsequently put through 35

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cycles of 95°C for 30s and 60°C for 1min.

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Specificity and reproducibility of the new system of Real time PCR

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The specificity of the primers and probes were verified in vitro using our local collection of 100

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strains (Table 2). The sensitivity of our assays were determined using tenfold serial dilutions

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(between 108 to 101 DNA copies) of E. coli strain P10 by triplicate amplification, the number of

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MCR-1 in each sample was calculated based on the DNA copy numbers. The obtained Ct values

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were used to generate the calibration curves as compared to the number of bacteria quantified by

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standard bacterial count on agar plates. The standard curve was constructed on the basis of the

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concordance between Ct values and number of log UFC/mL. The limit of detection was based on

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the final dilution detected by PCR. Efficacy of qPCR was calculated from a standard curve

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according to Rutledge and Cote (17).

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RESULTS

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Specificity and Technical sensitivity of the quantitative PCR

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BlastN analysis of the primers and probe designed for development of the real-time PCR assay

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showed in silico a 100% homology with the MCR-1-encoding gene only. The sensitivity of the

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real time PCR using the 18 mcr-1 positive strains using serial ten-fold dilutions of a calibrated

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inoculum was excellent with a calibration curve linear from 101–108 DNA copies corresponding

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to 35–21 Ct (Fig. 1). Regressions formula and PCR efficiency of the two real-time PCR assays

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are shown in Figure 1. The reproducibility of the two qPCR assays was excellent, with a positive

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PCR at 21.4 ± 0.4 Ct for PE1 and 20.8+/- 0.4 Ct for PE2 when testing one colony re-suspended in

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200µL of sterile water (Table 2). The specificity of the two qPCR assays in vitro against a panel

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of 82 clinically relevant bacteria negative for mcr-1 gene was at 100% (all real-time PCR were

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negative, Table 2).

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Screening of feces from broilers

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Five out of 503 fecal samples from chickens from Algeria were positive from which 3 E. coli

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strains were isolated and confirmed to harbor the mcr-1 gene by standard PCR and sequencing.

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None of the 330 samples from France were positive.

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DISCUSSION

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The recent description and emergence of mcr-1 plasmid-mediated resistance to colistin in humans

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and animals is a major concern worldwide (5). In this study, two new qPCR assays using

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Taqman* probes were developed that demonstrate high sensitivity and specificity for

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confirmation of the presence of this gene in colistin-resistant bacterial isolates as well as for

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screening directly from stool samples. Indeed both systems have the same performance to screen

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for the presence of mcr-1 containing isolates and in stools. We recommend to use PE1 as a first

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set of primers for the rapid screening of mcr-1 and PE2 system to confirm the positive results.

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Recently, Bontron et al have reported a real-time PCR assay using SYBR green as fluorescent

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marker with similar sensitivity (18). However it is well known that Taqman* probes enhance

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specificity that is a critical point when testing directly from biological samples. Our real time

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PCR assays had advantages including sensitivity, specificity and the possibility to detect MCR-1

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plasmid-mediated colistin resistance very quickly (256

None

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Algeria

unpublished data

S. marcescens (n=2)

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Algeria

unpublished data

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* ; Mutation, +; Positive, -; Negative.

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P. mirabilis (n=2)

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PE1

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10 10 7 6

10 5 10 4

21.39

7.50E+05

26.42 29.1

7.50E+04

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31.43

7.50E+03

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34.21

7.50E+02

PE1

log CFU/Reaction 8

R² = 0.9742

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y = -3.065x + 40.11

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slope = -3.065 20

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PCR efficiency = [(10-1/-3.065)-1] x 100% = 111.97%

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Limit of detection 75 CFU/ml

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7.50E+06

Con.

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Ct Avg.

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CFU/reaction

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Con.

PE2

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CFU/reaction

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7.50E+06

20.84

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7.50E+05

27.195

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7.50E+04

28.795

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7.50E+03

31.525

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35.825

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log CFU/Reaction

PE2

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Limit of detection 75 CFU/ml

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R² = 0.9588

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y = -3.43x + 42.11

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slope = -3.43

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PCR efficiency = [(10-1/-3.43)-1] x 100%= 95.68%

Fig 1. Real-time polymerase chain reaction (PCR) sensitivity test to detect -encoding plasmid-mediated colistin resistance (MCR-1) encoding gene from E.coli strain P10. PE1 and PE2 are two qPCR assays developed.