Skip to content

Advertisement

  • Research article
  • Open Access

LBJMR medium: a new polyvalent culture medium for isolating and selecting vancomycin and colistin-resistant bacteria

†Contributed equally
BMC MicrobiologyBMC series – open, inclusive and trusted201717:220

https://doi.org/10.1186/s12866-017-1128-x

©  The Author(s). 2017

  • Received: 25 August 2017
  • Accepted: 15 November 2017
  • Published:

Abstract

Background

Multi-drug resistant bacteria are a phenomenon which is on the increase around the world, particularly with the emergence of colistin-resistant Enterobacteriaceae and vancomycin-resistant enterococci strains. The recent discovery of a plasmid-mediated colistin resistance with the description of the transferable mcr-1 gene raised concerns about the need for an efficient detection method for these pathogens, to isolate infected patients as early as possible. The LBJMR medium was developed to screen for all polymyxin-resistant Gram-negative bacteria, including mcr-1 positive isolates, and vancomycin-resistant Gram-positive bacteria.

Results

The LBJMR medium was developed by adding colistin sulfate salt at a low concentration (4 μg/mL) and vancomycin (50 μg/mL), with glucose (7.5 g/L) as a fermentative substrate, to a Purple Agar Base (31 g/L). A total of 143 bacterial strains were used to evaluate this universal culture medium, and the sensitivity and specificity of detection were 100% for the growth of resistant strains. 68 stool samples were cultured on LBJMR, and both colistin-resistant Gram-negative and vancomycin-resistant Gram-positive strains were specifically detected.

Conclusions

The LBJMR medium is a multipurpose selective medium which makes it possible to identify bacteria of interest from clinical samples and to isolate contaminated patients in hospital settings. This is a simple medium that could be easily used for screening in clinical microbiology laboratories.

Keywords

  • Colistin resistance
  • Culture media
  • Mcr-1
  • mcr genes
  • Vancomycin-resistant enterococci
  • Enterobacteriaceae
  • Multi-drug resistant
  • Detection method
  • Screening method

Background

The worldwide emergence of multidrug-resistant (MDR) bacteria represents a major public health issue. Controlling the spread of these bacteria relies upon both reducing the prescription of antibiotics and preventing transmission from carrier patients to others [1]. More specifically, this prevention targets the emerging carbapenemase-producing Enterobacteriaceae and vancomycin-resistant enterococci (VRE) strains, with the development of specific detection methods, mostly based on chromogenic and selective culture media [2].

The increase in infections due to carbapenemase-producing Enterobacteriaceae has led to the revival of colistin as a last-resort treatment [3]. Its widespread use, particularly in the livestock food in many countries [4], has inevitably led to the emergence of colistin-resistant strains over the past ten years [5, 6]. Until recently, all colistin resistance mechanisms which had been described were attributed to chromosomic mutations [7]. In China in 2015, Liu and colleagues were the first to report the plasmid-mediated colistin-resistance gene in animals and humans, which they named mcr-1 [8]. This was followed by descriptions of the variants mcr-1.2 and mcr-1.3 [9, 10], mcr-2, mcr-3, mcr-4 and mcr-5 genes [11–14]. A significant number of human cases (in the majority of cases asymptomatic carriers) was described [15, 16]. Particularly, the worldwide analysis of colistin-resistant strains with an unknown mechanism allowed the detection of a consequent number of mcr-1-positive bacteria [17–19]. This mobile colistin resistance gene presents low resistance levels, with minimal inhibitory concentrations (MIC) of colistin around 4 μg/ml, which is close to the clinical breakpoint of colistin resistance (> 2 μg/mL), according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) [20]. Those data raised concerns about the detection and isolation of these pathogens, and the screening of the mcr-1 gene into carbapenemase-producing bacteria has been added to recommendations for clinical microbiology laboratories in France [21]. While carbapenemase screening is well-defined with phenotypic and molecular techniques [22], there is a need for colistin-resistance screening tools [2]. Given the diversity of mechanisms of colistin resistance [23], phenotypic methods, such as chromogenic culture media [2, 24] are preferred for a rapid detection.

In addition to colistin-resistant Enterobacteriaceae, the detection of vancomycin-resistant enterococci isolates is of clinical concern. The prevalence of VRE strains is increasing in Europe, especially Enterococcus faecium [25] and has led to nosocomial infections in the United States [26], and their dissemination is associated with high mortality rates [27]. The development of an effective screening tool for the early detection of those multi-drug resistant pathogens has become a priority, in order to adapt treatment and isolate patients who are either infected or carriers.

For such purposes, we developed a polyvalent selective culture medium which can isolate both colistin-resistant Gram-negative bacteria, including Enterobacteriaceae strains harboring the mcr-1 gene, and vancomycin-resistant Gram-positive bacteria. In this study, we evaluated the performances of this medium on a representative set of bacterial strains and fecal samples. This universal culture medium was named LBJMR, standing for Lucie Bardet-Jean-Marc Rolain, and has recently been patented [28].

Methods

Bacterial strains and samples cultured on LBJMR

A total of 143 bacterial strains were used in this study, of which 101 were Enterobacteriaceae: 75 with an acquired mechanism of resistance to colistin (including 32 strains harboring the mcr-1 gene [6, 19, 29–37] and 43 to another resistance mechanism), six with an intrinsic colistin resistance mechanism [38], and 20 colistin-susceptible strains (Additional file 1: Table S1). This set also comprised 17 non-fermentative Gram-negative bacteria: ten were colistin-resistant strains [39] including one Pseudomonas aeruginosa, one Acinetobacter baumannii [39] and other pathogens that are frequently diagnosed in samples from patients with cystic fibrosis, and seven colistin-susceptible strains [40, 41]. Finally, 25 Gram-positive strains, including eight vancomycin-resistant enterococci [42], three intrinsically vancomycin-resistant genera and 14 vancomycin-susceptible strains [43] were also included in this study (Additional file 1: Table S1).

The colistin-resistance genes which were potentially involved were previously screened by RT-PCR for Enterobacteriaceae [6, 44], as were the vancomycin resistance genes vanA and vanB for the VRE strains [45]. MICs of colistin and vancomycin were determined using E-test® strips (BioMérieux, Marcy l’Étoile, France) for Gram-negative and Gram-positive strains, respectively, and MICs of daptomycin were determined for the four reference strains of Enterococcus faecium (DSM 17050, 25,698, 25,697 and 13,590), and were evaluated according to the EUCAST guidelines [20].

In addition, 68 samples were cultivated on LBJMR medium, including 66 stool samples (56 from humans and ten from chickens) that were previously screened for mcr-1 by RT-PCR (56 positive and ten negative) and two clinical rectal swabs obtained from patients in the La Timone hospital, from which a vancomycin-resistant E. faecium VRE strain was isolated. Colonies with different morphologies isolated by culture of samples on LBJMR were isolated by subculture on Trypticase Soy Agar (TSA, Becton-Dickinson, Heidelberg, Germany), and the species were identified using Matrix-Assisted Laser Desorption-Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS), as described previously [46].

LBJMR development

In order to choose the most suitable medium for selecting colistin-resistant Enterobacteriaceae, including strains harboring the mcr-1 gene, five commercial differential media usually used for the detection of Enterobacteriaceae were supplemented with a range of concentration of colistin sulfate salt (MP Biomedicals, Illkirch, France) from 0 to 32 μg/mL: Drigalski Lactose Agar (Biokar diagnostics, France), BBL™ Eosin Methylene Blue Agar (EMB; Becton-Dickinson, Heidelberg, Germany), Difco™ Violet Red Bile Agar (Becton-Dickinson, Heidelberg, Germany), BBL™ MacConkey Agar II (Becton-Dickinson, Heidelberg, Germany), and Difco™ Purple Agar Base (Becton-Dickinson, Heidelberg, Germany) supplemented with 7.5 g /L of glucose (MP Biomedicals, Illkirch, France). Four Klebsiella pneumoniae, including two colistin-resistant, and four Escherichia coli, including two which were colistin-resistant with the mcr-1 gene, were inoculated at 106 CFU on each prepared agar [19].

The Purple Agar Base supplemented with glucose (7.5 g/L), colistin sulfate (0, 4 and 8 μg/mL) and vancomycin (0 and 50 μg/mL) (Sandoz, Levallois-Perret, France) was evaluated with 24 representative strains, including 20 Enterobacteriaceae (five intrinsic genera, eight with acquired resistance and seven colistin-susceptible strains as control) and four Gram-positive strains susceptible to vancomycin, which were inoculated at 106 CFU. This experiment was also conducted by replacing glucose with lactose (Laboratoires Humeau, La Chapelle-sur-Erdre, France). The optimum concentration of vancomycin for the medium composition was then determined using 20 Gram-positive strains representative of vancomycin resistance (three intrinsically-resistant genera and 17 enterococci, including seven VRE) and ten chicken stool samples from Algeria, five of which were positive for mcr-1 by RT-PCR, and five of which were negative [19, 44].

LBJMR evaluation

The sensitivity and specificity of the LBJMR medium to detect all colistin-resistant Gram-negative bacteria and all vancomycin-resistant Gram-positive bacteria were evaluated with all the strains listed in Additional file 1: Table S1 and samples listed in Additional file 1: Table S2, which were incubated on LBJMR in an aerobic atmosphere at 37 °C for between 24 and 48 h.

Inocula of the strains were prepared at 0.5 McFarland (corresponding to 1.5 × 108 CFU/mL according to the EUCAST expert system) and serial 10-fold dilutions were then performed in Phosphate Buffer Saline. 10 μL of these suspensions were deposited on agars and simultaneously on TSA medium to determine the detection limits for each bacterium by assessing the viable concentration by colony count. Growth or inhibition of these microorganisms was observed after overnight incubation at 37 °C in an aerobic atmosphere. Those experiments were performed in duplicate.

Finally, as the LBJMR medium was developed so as to avoid Proteus swarming, Proteus mirabilis and Proteus vulgaris strains were inoculated alone or mixed with E. coli P10 (mcr-1) at the same concentration to evaluate the isolation ability of the LBJMR medium. Cultures were incubated at 37 °C for 72 h.

Mcr-1 screening on stool samples

A total of 1052 stool samples were used in this study, 899 from humans from different regions of the world: Marseille (n = 212) and Angers (n = 128) in France, Thailand (n = 212), Laos (n = 189), Nigeria (n = 143), and Senegal (n = 15). 153 samples were from animals, including chickens from Algeria (n = 10), rodents from Cambodia (n = 21), and rodents (n = 60), pigs (n = 16) and goats (n = 46) from Laos.

The presence of the mcr-1 gene in those stools was first screened using RT-PCR as previously described [44]. Briefly, the DNA of the stools was extracted, after pre-treatment by proteinase K and incubation at 95 °C, using Biorobot EZ1 Advanced XL (Qiagen, Hilden, Germany). Positive DNA was confirmed using standard PCR. Samples with positive DNA were then cultured on LBJMR, after a prior enrichment step performed by inoculating approximately 1 g of the sample in tryptic soy broth (TSB) medium (BioMérieux, Marcy l’Étoile, France) and incubating for 24 h at 37 °C. 100 μL of these liquid media were then plated on agars that were also incubated at 37 °C for 24 h.

For each Gram-negative isolate identified by MALDI-TOF MS, colistin MIC was determined with a colistin E-test® strip. For each colistin-resistant isolate, the presence of mcr-1 was investigated by RT-PCR as previously described [44]. Susceptibility testing to 26 antibiotics was performed on mcr-1-positive strains using the disk diffusion method, and interpreted according to the EUCAST guidelines [20].

Comparison of the LBJMR medium with other polymyxin-containing media

The sensitivity and specificity of the LBJMR medium was first compared to the BD™ Cepacia Medium (Cepacia, Becton-Dickinson, Heidelberg, Germany) medium with all the colistin-resistant Enterobacteriaceae strains listed in Additional file 1: Table S1. The LBJMR medium was then compared to the SuperPolymyxin medium with 103 bacterial strains, including 61 of the Enterobacteriaceae, 17 non-fermentative Gram-negative, and 25 Gram-positive strains (Additional file 1: Table S1). Other polymyxin-containing media were also compared concomitantly to the LBJMR medium, using EMB Agar (Sigma-Aldrich, Illkirch, Germany) as a control, with some of these strains as described below. Inocula were prepared following the same protocol as for the LBJMR evaluation.

Columbia Colistin Nalidixic Acid Agar +5% sheep blood (CNA) (BioMérieux, Marcy l’Étoile, France) and three mixed culture media: EMB with colistin sulfate (4 μg/mL) and vancomycin (50 μg/mL), LBJMR with Daptomycin (10 μg/ml, Novartis, Horsham, United Kingdom) in place of vancomycin and LBJMR with Amphotericin B (5 μg/ml, Bristol-Myers Squibb, Rueil-Malmaison, France) were concomitantly tested with 45 Enterobacteriaceae strains representative of colistin resistance (30 mcr-1, ten susceptible and five intrinsically resistant genera). LBJMR with Amphotericin B was also evaluated with the eight VRE strains. Finally, the LBJMR medium was compared to the SuperPolymyxin medium with 12 samples, including the two clinical rectal swabs from the La Timone hospital and ten human stools from Thailand, five of which had been identified as positive by culture for the detection of an isolate harboring the mcr-1 gene, and five controls that were negative for mcr-1 using RT-PCR.

Statistical analysis

The data were analyzed using a Chi-test to compare the Cepacia and LBJMR media and a Student-t test for a pairwise comparison of SuperPolymyxin and LBJMR selective media for the detection of non-fermentative Gram-negative colistin-resistant strains. Significance was assessed at p < 0.05.

Results

LBJMR development

Because colistin is a cationic molecule, we looked for a medium which was deprived of any ions in its original composition and which was also deprived of any electrolytes to avoid Proteus spp. swarming. The optimal conditions for LBJMR medium (growth of colistin- and vancomycin-resistant strains and inhibition of colistin- or vancomycin susceptible strains) were obtained on Purple Agar Base with glucose (Additional file 1: Table S3), 4 μg/mL of colistin sulfate and 50 μg/ml of vancomycin (Additional file 1: Table S4). The culture of ten chicken stools from Algeria enabled the detection of E. coli strains harboring the mcr-1 gene from three of the five samples which were positive for mcr-1 by RT-PCR, including strain 235 which had previously been isolated on Cepacia medium [19] and no Gram-negative strains were detected from the five negative samples (Additional file 1: Table S2). A correlation was observed between the Ct-values that reflect the DNA concentration and the results of culture (Additional file 1: Table S2).

The final preparation of the LBJMR medium was as follows: 31 g/L of Purple Agar Base, 7.5 g/L of glucose, 4 μg/mL of colistin sulfate and 50 μg/mL of vancomycin. 7.5 g/L of lactose was used in place of glucose for the 24 strains initially tested and the same results were obtained. Glucose was selected because, combined with bromocresol purple, a pH indicator, it revealed the polyvalent capacity of the LBJMR medium with an easy and fast visualization of the species of interest in the clinical routine: both Enterobacteriaceae and enterococci gave yellow colonies, contrasting on the purple agar and exhibiting different sizes (2–3 mm and 0.1–1 mm, respectively).

LBJMR evaluation

All the polymyxin-resistant Enterobacteriaceae strains (n = 81) tested were able to grow on the LBJMR medium, with the lowest detection limit (101 CFU), including those with the mcr-1 gene, as well as all the colistin-resistant non-fermentative Gram-negative (n = 10) and vancomycin-resistant Gram-positive strains (n = 11), with detection limits dependent on their MIC, as shown in Table 1. Meanwhile, all the bacteria susceptible to colistin or vancomycin were inhibited (not detected at 105 CFU), giving rise to 100% sensitivity and specificity for the growth of Gram-negative colistin-resistant and Gram-positive vancomycin-resistant strains (Table 1). The swarming of Proteus sp. strains was fully inhibited on LBJMR, even after 48 h of incubation.
Table 1

Detection limits of targeted bacteria on LBJMR and SuperPolymyxin culture media

Bacterial strains

Detection limits on culture media (CFU):

Gram-negatives

 

CT MIC

LBJMR

SuperPolymyxin

Colistin-resistant Enterobacteriaceae

E. coli SE65

4

101

101

E. coli 117R

4

101

101

E. coli 1R

4

101

101

E. coli 1R 2104

4

101

101

E. coli 44A

4

101

101

E. coli 6R

4

101

101

E. coli 85R

4

101

101

E. coli 95R

4

101

101

E. coli 96R

4

101

101

E. coli 134R

3

101

101

E. coli 143R

3

101

101

E. coli LH121

16

101

101

E. coli LH140 1

12

101

101

E. coli LH257

12

101

101

E. coli LH57 1

8

101

101

E. coli LH1

6

101

101

E. coli LH30

6

101

101

E. coli TH214

6

101

101

E. coli TH99

4

101

101

E. coli 235

4

101

101

E. coli P6

6

101

101

E. coli P10

4

101

101

E. coli P17

4

101

101

E. coli FHA1022

12

101

101

E. coli FHM193

12

101

101

E. coli FHA1134

12

101

101

E. coli NH945

12

101

101

E. coli TH176

6

101

101

K. pneumoniae FHA60

8

101

101

K. pneumoniae FHM128

4

101

101

K. pneumoniae 119R

3

101

101

K. pneumoniae LH131 6

32

101

101

K. pneumoniae LH61 7

24

101

101

K. pneumoniae LH17

12

101

101

K. pneumoniae LH92

12

101

101

K. pneumoniae LB16

32

101

101

P. mirabilis FH112

>256

101

101

P. vulgaris PV148

>256

101

101

P. alcalifaciens TH44

>256

101

101

M. morganii FM102

>256

101

101

S. marcescens E13

128

101

101

Others colistin-resistant

B. cepacia FHM-BC1

64

103

105

B. cepacia FHM-BC2

>256

101

101

A. xylosoxidans FHM-AX

3

101

>105

S. maltophilia FHM-SM

12

103

>105

I. limosus FHM-IL

>256

104

104

P. pulmonicola FHM-PP

>256

101

103

S. putrefaciens FHM-SP

NC

103

>105

O. anthropi FHM-OA

NC

102

>105

P. aeruginosa FHM-PACOLR1

>256

101

101

A. baumannii ABIsac_ColiR

8

102

101

Colistin-susceptible

E. asburiae P113

0,19

>105

>105

E. cloacae NH151

0,50

>105

>105

E. cloacae NH74

0,38

>105

>105

K. pneumoniae CIP 82.91

0,125

>105

>105

K. pneumoniae LB2

0,128

>105

>105

K. pneumoniae TH20S

0,125

>105

>105

K. pneumoniae TH28S

0,125

>105

>105

Proteus vulgaris P100

0,94

>105

>105

S. enterica 108R

1

>105

>105

S. enterica 122R

0,5

>105

>105

E. coli ATCC 25922 CIP 76.24

0,094

>105

>105

E. coli 161

0,094

>105

>105

E. coli 169

0,094

>105

>105

E. coli FHM88S

0,125

>105

>105

E. coli TH134S

0,094

>105

>105

E. coli LH53S

0,094

>105

>105

E. coli LH165S

0,074

>105

>105

E. coli TH77S

0,064

>105

>105

E. coli 282S

0,074

>105

>105

E. coli FHM19S

0,125

>105

>105

P. aeruginosa FHM-PA4

2

>105

>105

P. aeruginosa FHM-PA5

0,50

>105

>105

P. aeruginosa FHM-PA6

0,38

>105

>105

S. xianemensis 111P

0,125

>105

>105

S. xianemensis 111A

0,094

>105

>105

A. nosocomialis ABG13S

0,064

>105

>105

A. pitti MK

0,125

>105

>105

Gram-positives

 

VCN MIC

  

Vancomycin-resistant

E. faecium DSM17050a

>256

101

>105

E. faecium DSM13590a

>256

101

>105

E. faecium DSM25698a

>256

102

>105

E. faecium DSM25697a

>256

101

>105

E. faecium FHMVRE1a

>256

101

>105

E. faecium FHMVRE2a

>256

101

>105

E. faecium VRE

24

103

>105

E. faecalis JH2–2: Tn 1549b

64

102

>105

W. cibaria P18A

>256

101

>105

W. cibaria P18B

>256

101

>105

L. lactis P18C

>256

101

>105

Vancomycin-susceptible

S. aureus CF_Marseille

1

>105

>105

E. faecium TH26

0,75

>105

>105

E. faecium 349

0,75

>105

>105

E. faecium TH12

2

>105

>105

E. faecium LH165

0,75

>105

>105

E. faecium Al7

0,75

>105

>105

E. faecium TH43

0,75

>105

>105

E. faecium TH95

0,75

>105

>105

E. faecium 282

0,75

>105

>105

E. faecalis JH2–2: C2

1,5

>105

>105

E. faecalis JH2–2S

1,5

>105

>105

E. gallinarum SE3

1,5

>105

>105

E. casseliflavus SE3

1,5

>105

>105

E. hirae LH111

1

>105

>105

MIC of colistin (CT) and vancomycin (VCN) are given in μg/mL. Enterobacteriaceae with mcr-1 gene are in bold font

Colistin-resistant strains with a mutation on another gene are indicated as follow: 1 phoP E375K, 2 pmrB A159V, 3 pmrB P7-Q12(del 6aa), 4 pmrB T156 K, 5 pmrB I92 insertion, 6 mgrB Stop, 7 mgrB Sub, 8 pmrB T157P. Enterococci strains with vancomycin-resistant genes are indicated as follows: a vanA and b vanB

Of the 1052 stools screened for mcr-1 by RT-PCR, 66 were cultured on LBJMR, including 56 that were positive after 32 cycles of RT-PCR, as well as ten negative stool samples as controls. 16 cultures were positive on LBJMR medium, enabling the detection of 17 colistin-resistant Enterobacteriaceae strains harboring the mcr-1 gene (colistin MICs ranging from 2 to 8 μg/mL): 15 were identified as E. coli and two as K. pneumoniae by MALDI-TOF MS (Additional file 1: Table S2). Indeed, two bacterial species, E. coli and K. pneumoniae, were detected from the culture of the same sample (FHM128) (Additional file 1: Table S2). Five isolates were already known from a previous study on Cepacia medium [6, 19]. All the E. coli isolates from France were Extended-Spectrum Beta-Lactamase-producing strains (data not shown). In conclusion, the LBJMR medium enabled the isolation of new colistin-resistant strains harboring the mcr-1 gene. The weak culture results compared to PCR could be explained by the length of storage of the tested samples (up to four years) at −80 °C, possibly inducing the death of bacteria while their DNA was still detectable [47]. However, it should be noted that, for some samples, we isolated another kind of strain, mostly Gram-positive bacteria which have an intrinsic resistance to vancomycin, largely Pediococcus pentosaceus and Weissela cibaria, as shown in Additional file 1: Table S2.

Finally, the culture of two clinical samples from the hospital enabled the isolation of two vancomycin-resistant E. faecium isolates (VRE1 and VRE2). In addition, two colistin-resistant Enterobacteriaceae isolates were also detected in the VRE2 sample, identified as K. pneumoniae LB3 (MIC = 64 μg/mL) and E. coli LB4 (MIC = 16 μg/mL), both negative for the mcr-1 gene (Fig. 1).
Fig. 1
Fig. 1

Aspect of the different types of colonies on LBJMR after culture of a clinical sample. Enterobacteriaceae exhibited yellow colonies that are larger (2–3 mm) than enterococci (0.1–1 mm)

Comparison between LBJMR and other selective polymyxin-containing media

The LBJMR medium was more sensitive than the Cepacia and CNA media for detecting the strains exhibiting the mcr-1 gene (Additional file 1: Table S5). Indeed, only four of those strains could grow on the CNA medium, because it also contains nalidixic acid and fewer than half of them grew on the Cepacia medium. Comparison of the sensitivities of the LBJMR (100%) and Cepacia (47%) media using a Chi-square statistical test gave a significant p-value (<10−4).

LBJMR and SuperPolymyxin media presented the same sensitivity for Enterobacteriaceae, with the growth of all colistin-resistant strains (detection limit of 101 CFU), including the 30 mcr-1 strains tested, and the inhibition of all susceptible strains (Table 1). In addition, the culture of ten human stools gave the same results: five were positive, with the detection of an E. coli positive for mcr-1, and the five controls remained negative (Additional file 1: Table S2). In contrast, the LBJMR medium showed a significantly higher sensitivity than the SuperPolymyxin medium for the detection of colistin-resistant non-fermentative Gram-negative strains, with a significant p-value of 0.019 (<0.01) with a pairwise comparison using a Student-t test (Table 1). More specifically, the LBJMR medium was able to detect those screened in the cystic fibrosis samples, such as Burkholderia cepacia, even at low concentrations, and could replace specific media such as the Cepacia medium for their isolation. The addition of amphotericin B or the replacement of vancomycin by daptomycin in the LBJMR medium did not affect the growth of Enterobacteriaceae strains (Additional file 1: Table S5). Finally, all the VRE strains were inhibited on the SuperPolymyxin medium because of the presence of daptomycin, while they were detected on the LBJMR medium (Table 1).

These results were confirmed by the culture of the two clinical samples from the hospital: vancomycin-resistant E. faecium could only grow on the LBJMR medium and not on the SuperPolymyxin medium for both samples, and the two Enterobacteriaceae from the VRE2 sample found on the LBJMR medium were also detected on the SuperPolymyxin medium.

Finally, the concomitant addition of colistin and vancomycin to EMB agar showed the systematic inhibition of E. coli strains harboring the mcr-1 gene, corresponding to the tested strains with the lowest MIC.

Discussion

In accordance with recommendations aiming to isolate patients carrying multi-drug resistant bacteria, it is becoming essential to detect colistin-resistant Gram-negative pathogens, particularly with the recent description of plasmid-mediated colistin-resistant genes among Enterobacteriaceae strains [8–12]. We do not currently know the potential consequences of patient colonization by those resistant bacteria, as it has already been demonstrated that acquisition of resistance is associated with a decrease in virulence [48–50], but it is necessary to implement efficient tools to prevent and monitor as closely as possible any epidemic outbreak and develop a rapid therapeutic strategy.

Currently, the only available method for detecting colistin resistance, according to joint EUCAST and Clinical Laboratory Standard Institute (CLSI) expert systems, is antibiotic susceptibility testing using broth microdilution, which is not suitable for daily screening in clinical microbiology laboratories. Current polymyxin-containing culture media are also not appropriate because of their high concentration of polymyxin. Indeed, they were not developed to isolate Enterobacteriaceae but to specifically detect bacteria that are intrinsically resistant to polymyxins, avoiding contaminants such as Enterobacteriaceae species. Thus, the establishment of an effective protocol to detect colistin resistance with the development of a reliable culture medium was necessary in clinical microbiology laboratory.

The significant number of strains tested on our selective medium showed that the LBJMR medium allows all colistin-resistant Enterobacteriaceae strains to grow, even those with a very low MIC for colistin and harboring the mcr-1 gene, when all the susceptible strains were inhibited. Furthermore, the screening conducted on stool samples that were positive for mcr-1 by PCR allowed the isolation of new mcr-1 strains (Additional file 1: Table S2). The LBJMR medium could also detect colistin-resistant non-fermentative Gram-negative bacteria, including pathogens which are often found in patients suffering from cystic fibrosis (Table 1). We thereby created a universal culture medium, able to replace specific polymyxin-containing culture media usually used in routine diagnosis. All the vancomycin-resistant bacteria tested were detected at low concentrations on the LBJMR medium, including the VRE strains, when susceptible were inhibited. To attest this capacity, the LBJMR medium should be tested on more VRE strains and comparatively to VRE selective culture media.

The performances of the LBJMR medium are summarized in Table 2: samples can be cultured directly on the LBJMR selective medium, without a previous decontamination step, and colonies can be directly analyzed from the primary culture, without subcultures. Bacteria of interest are easily recognizable, as shown in Fig. 1: both colistin-resistant Enterobacteriaceae and vancomycin-resistant enterococci exhibit yellow colonies (2–3 mm and 0.1–1 mm respectively), on a purple agar base. Because LBJMR also permits the growth of intrinsic resistant bacteria, screening should be completed with a rapid identification using MALDI-TOF MS [51], directly from the LBJMR medium. Antibiotic susceptibility testing and PCR screening can be performed in the same time.
Table 2

Performance of LBJMR medium

Criteria

LBJMR medium

Isolates screened

Colistin-resistant Gram-negatives:

- Enterobacteriaceae, including those harboring the mcr-1 gene

- Non-fermentative Gram-negative colistin-resistant strains, including those involves in cystic fibrosis samples

Vancomycin-resistant Gram positives, including Enterococci

Aspect of colonies

Yellow on purple agar: 2–3 mm for Enterobacteriaceae, 0.1–1 mm for Enterococci

Incubation

Aerobic atmosphere, 37 °C, 24H (sterile at 48H)

Culture of samples

Direct on LBJMR, no previous decontamination

Isolates analysis

Colonies can be picked directly from primary cultures on LBJMR for analysis:

- MALDI-TOF identification

- Antibiotic Susceptibility testing

- PCR screening for resistance genes.

Avoid contamination

- Inhibition of Proteus swarming

- Inhibition of yeast possible by adding amphotericin B

Nordmann et al. developed a different selective medium called SuperPolymyxin, based on EMB agar and containing 3.5 μg/mL of colistin sulfate, 10 μg/mL of daptomycin and 5 μg/mL of amphotericin B [52], associated with a complementary phenotypic test, the rapid polymyxin NP [53], to screen for colistin-resistant Gram-negative bacteria [54]. These two media are differential and are able to recognize bacterial species based on color. Sensitivities for colistin-resistant Enterobacteriaceae were the same for the SuperPolymyxin and LBJMR media, but only the LBJMR medium could detect VRE strains (Table 1). Indeed, the SuperPolymyxin medium is composed of daptomycin and amphotericin B, which prevents the growth of contaminants including bacteria of interest such as VRE strains, because they are mostly susceptible to daptomycin. In our study, we tested stool samples and obtained some contaminants, including Gram-positive bacteria which were intrinsically resistant to vancomycin (Additional file 1: Table S2) or some yeasts.

More recently, the culture medium ChromAgar COL-APSE was developed and compared to the SuperPolymyxin medium [55]. The comparison of the LBJMR and the CHROMAgar COL-APSE performances have to be assessed. All those media should be also evaluated on heteroresistant strains, as they are difficult to detect and their frequence is widely underestimated [56].

The advantage of the LBJMR medium in terms of isolating vancomycin resistant enterococci can be also a disadvantage in a few cases, because Gram-positive bacteria which are intrinsically resistant to vancomycin bacteria, including Pediococcus, can also be isolated. In the LBJMR medium, Gram-positive bacteria appear with small colonies and a simple identification by MALDI-TOF can identify them. For the elimination of yeast in samples, amphotericin B can be added in our medium.

Conclusion

The LBJMR medium is an adequate screening tool for all colistin-resistant isolates from clinical samples, independently of their resistance level or mechanism. LBJMR could be used in routine laboratory work to detect colistin-resistant and vancomycin-resistant bacteria, allowing for the direct analysis of colonies and, thus, the early isolation of contaminated patients in hospital settings. This medium is currently being investigated as a routine medium in our institute to determine its usefulness in detecting such bacteria.

Abbreviations

CLSI: 

Clinical Laboratory Standard Institute

CNA: 

Colistin Nalidixic Acid

EMB: 

Eosin-Methylene Blue

EUCAST: 

European Committee on Antimicrobial Susceptibility Testing

MALDI-TOF MS: 

Matrix-Assisted Laser Desorption-Ionization-Time Of Flight Mass Spectrometry

MIC: 

Minimum Inhibitory Concentration

TSA: 

Trypticase Soya Agar

VRE: 

Vancomycin-Resistant Enterococci

Declarations

Acknowledgements

We thank to Marielle Bedotto-Buffet for technical assistance and TradOnline for English corrections.

Funding

IHU Méditerranée Infection.

Availability of data and materials

Ok

Authors’ contributions

LB designed the study, performed the experiments and analyzed and interpreted the data. SLP was analyzed, interpreted the data and involved in revising the manuscript. TL contributed to the development and analysis of data. JMR was responsible for the conception and design of the study, and the analysis of data. All authors read and approved the final manuscript.

Ethics approval and consent to participate

Not applicable

Consent for publication

Not applicable

Competing interests

The authors declare that they have no competing interests

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Open AccessThis 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.

Authors’ Affiliations

(1)
URMITE, Aix Marseille Université UM63, CNRS 7278, IRD 198, INSERM 1095 IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France

References

  1. Haut Conseil de la Santé Publique. Prévention de la transmission croisée des Bactéries Hautement Résistantes aux antibiotiques émergentes ( BHRe ). 2013.Google Scholar
  2. Perry JDA. Decade of development of chromogenic culture media for clinical microbiology in an era of molecular diagnostics. Clin Microbiol Rev. 2017;30:449–79.View ArticlePubMedGoogle Scholar
  3. Biswas S, Brunel J-M, Dubus J-C, Reynaud-Gaubert M, Rolain J-M. Colistin: an update on the antibiotic of the 21st century. Expert Rev Anti-Infect Ther. 2012;10:917–34.View ArticlePubMedGoogle Scholar
  4. Olaitan AO, Morand S. Rolain J-MM. Emergence of colistin-resistant bacteria in humans without colistin usage: a new worry and cause for vigilance. Int J Antimicrob Agents. 2016;47:1–3.View ArticlePubMedGoogle Scholar
  5. Kempf I, Fleury MA, Drider D, et al. What do we know about resistance to colistin in Enterobacteriaceae in avian and pig production in Europe? Int J Antimicrob Agents. 2013;42:379–83.View ArticlePubMedGoogle Scholar
  6. Olaitan AO, Diene SM, Kempf M, et al. Worldwide emergence of colistin resistance in Klebsiella pneumoniae from healthy humans and patients in Lao PDR, Thailand, Israel, Nigeria and France owing to inactivation of the PhoP/PhoQ regulator mgrB: an epidemiological and molecular stu. Int J Antimicrob Agents. 2014;44:500–7.View ArticlePubMedGoogle Scholar
  7. Olaitan AO, Morand S, Rolain J-M. Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria. Front Microbiol. 2014;5:643.View ArticlePubMedPubMed CentralGoogle Scholar
  8. Liu Y-Y, Wang Y, Walsh TR, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis. 2016;16:161–8.View ArticlePubMedGoogle Scholar
  9. Di Pilato V, Arena F, Tascini C, et al. mcr-1.2, a new mcr variant carried on a transferable plasmid from a colistin-resistant KPC carbapenemase-producing Klebsiella pneumoniae strain of sequence type 512. Antimicrob Agents Chemother. 2016;60:5612–5.View ArticlePubMedPubMed CentralGoogle Scholar
  10. Yang Y-Q, Li Y-X, Song T, et al. Colistin resistance gene mcr-1 and its variant in Escherichia coli isolates from chickens in China. Antimicrob Agents Chemother. 2017;AAC:01204–16.Google Scholar
  11. Xavier BB, Lammens C, Ruhal R, et al. Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016. Euro Surveill. 2016;21:6–11.View ArticleGoogle Scholar
  12. Yin W, Li H, Shen Y, et al. Novel plasmid-mediated Colistin resistance gene mcr-3 in Escherichia coli. MBio. 2017;8:4–9.Google Scholar
  13. Carattoli A, Villa L, Feudi C, et al. Novel plasmid-mediated colistin resistance mcr-4 gene in Salmonella and Escherichia coli, Italy 2013, Spain and Belgium, 2015 to 2016. Eur Secur. 2017;22:30589.Google Scholar
  14. Borowiak M, Fischer J, Hammerl JA, Hendriksen RS, Szabo I, Malorny B. Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B. J Antimicrob Chemother 2017; published online Sept 18. DOI:10.1093/jac/dkx327.
  15. Baron S, Hadjadj L, Rolain J-M, Olaitan AO. Molecular mechanisms of polymyxin resistance: knowns and unknowns. Int J Antimicrob Agents. 2016;48:583–91.View ArticlePubMedGoogle Scholar
  16. Poirel L, Jayol A, Nordmann P. Polymyxins: antibacterial activity, susceptibility testing, and resistance mechanisms encoded by plasmids or chromosomes. Clin Microbiol Rev. 2017;30:557–96.View ArticlePubMedGoogle Scholar
  17. Rolain J-M, Olaitan AO. Plasmid-mediated colistin resistance: the final blow to colistin? Int J Antimicrob Agents. 2016;47:4–5.View ArticlePubMedGoogle Scholar
  18. Skov RL, Monnet DL. Plasmid-mediated colistin resistance (mcr-1 gene): three months later, the story unfolds. Euro Surveill. 2016;21:30155.View ArticlePubMedGoogle Scholar
  19. Olaitan AO, Chabou S, Okdah L, Morand S, Rolain J-M. Dissemination of the mcr-1 colistin resistance gene. Lancet Infect Dis. 2016;16:147.View ArticlePubMedGoogle Scholar
  20. European Committee on Antimicrobial Susceptibility Testing (EUCAST). Breakpoint tables for interpretation of MICs and zone diameters. Version 71 2017; Version 7.: 0–94.Google Scholar
  21. Haut Conseil de la santé publique. Avis relatif aux mesures à prendre en lien avec l’émergence d’une résistance plasmidique à la colistin (mcr-1) chez les entérobactéries. 2016.Google Scholar
  22. Bialvaei AZ, Kafil HS, Asgharzadeh M, Yousef Memar M, Yousefi M. Current methods for the identification of carbapenemases. J Chemother. 2016;28:1–19.View ArticlePubMedGoogle Scholar
  23. Jeannot K, Bolard A, Plésiat P. Resistance to polymyxins in gram-negative organisms. Int J Antimicrob Agents. 2017;49:526–35.View ArticlePubMedGoogle Scholar
  24. Caniaux I, van Belkum A, Zambardi G, Poirel L, Gros MFMCR. Modern colistin resistance. Eur J Clin Microbiol Infect Dis. 2017;36:415–20.View ArticlePubMedGoogle Scholar
  25. Mendes RE, Castanheira M, Farrell DJ, Flamm RK, Sader HS, Jones RN. Longitudinal (2001-14) analysis of enterococci and VRE causing invasive infections in European and US hospitals, including a contemporary (2010-13) analysis of oritavancin in vitro potency. J Antimicrob Chemother. 2016;71:3453–8.View ArticlePubMedGoogle Scholar
  26. Reyes K, Bardossy AC, Zervos M. Vancomycin-resistant enterococci: epidemiology, infection prevention, and control. Infect Dis Clin N Am. 2016;30:953–65.View ArticleGoogle Scholar
  27. Chiang H-Y, Perencevich EN, Nair R, et al. Incidence and outcomes associated with infections caused by vancomycin-resistant enterococci in the united states: systematic literature review and meta-analysis. Infect Control Hosp Epidemiol. 2017;38:203–15.View ArticlePubMedGoogle Scholar
  28. Bardet L, Le Page S, Rolain J-M. Milieu de culture sélectif polyvalent pour l’isolement et la sélection de bactéries résistantes à la colistine et à la vancomycine. 2016.Google Scholar
  29. Berrazeg M, Hadjadj L, Ayad A, Drissi M, Rolain J-M. First detected human case in algeria of mcr-1 plasmid-mediated colistin resistance in a 2011 Escherichia coli isolate. Antimicrob Agents Chemother. 2016;60:6996–7.View ArticlePubMedPubMed CentralGoogle Scholar
  30. Rolain J-M, Kempf M, Leangapichart T, et al. Plasmid-mediated mcr-1 gene in colistin-resistant clinical isolates of Klebsiella pneumoniae in France and Laos. Antimicrob Agents Chemother. 2016;60:6994–5.View ArticlePubMedPubMed CentralGoogle Scholar
  31. Leangapichart T, Gautret P, Brouqui P, Mimish Z, Raoult D, Rolain J-M. Acquisition of mcr-1 plasmid-mediated colistin resistance in Escherichia coli and Klebsiella pneumoniae during hajj 2013 and 2014. Antimicrob Agents Chemother. 2016;60:6998–9.View ArticlePubMedPubMed CentralGoogle Scholar
  32. Olaitan AO, Dia NM, Gautret P, et al. Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during hajj. Int J Antimicrob Agents. 2015;45:600–4.View ArticlePubMedGoogle Scholar
  33. Diene SM, Merhej V, Henry M, et al. The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new “killer bugs” are created because of a sympatric lifestyle. Mol Biol Evol. 2013;30:369–83.View ArticlePubMedGoogle Scholar
  34. Olaitan AO, Rolain J-M. Interruption of mgrB in the mediation of colistin resistance in Klebsiella oxytoca. Int J Antimicrob Agents. 2015;46:354–5.View ArticlePubMedGoogle Scholar
  35. Bardet L, Baron S, Leangapichart T, Okdah L, Diene SM, Rolain J-M. Deciphering Heteroresistance to colistin in a Klebsiella pneumoniae isolate from Marseille, France. Antimicrob Agents Chemother. 2017;61:e00356–17.View ArticlePubMedGoogle Scholar
  36. Telke AA, Olaitan AO, Morand S, Rolain J-M. soxRS induces colistin hetero-resistance in Enterobacter asburiae and Enterobacter cloacae by regulating the acrAB-tolC efflux pump. J Antimicrob Chemother 2017; published online July 25. DOI:10.1093/jac/dkx215.
  37. Leangapichart T, Dia NM, Olaitan AO, Gautret P, Brouqui P, Rolain J-M. Acquisition of extended-spectrum b-lactamases by Escherichia coli and Klebsiella pneumoniae in gut microbiota of pilgrims during the hajj pilgrimage of 2013. Antimicrob Agents Chemother. 2016;60:3222–6.View ArticlePubMedPubMed CentralGoogle Scholar
  38. Olaitan AO, Diene SM, Assous MV, Rolain J-M. Genomic plasticity of multidrug-resistant NDM-1 positive clinical isolate of Providencia rettgeri. Genome Biol Evol. 2015;8:723–8.View ArticlePubMed CentralGoogle Scholar
  39. Rolain J-M, Diene SM, Kempf M, Gimenez G, Robert C, Raoult D. Real-time sequencing to decipher the molecular mechanism of resistance of a clinical pan-drug-resistant Acinetobacter baumannii isolate from Marseille, France. Antimicrob Agents Chemother. 2013;57:592–6.View ArticlePubMedPubMed CentralGoogle Scholar
  40. Vila-Farrès X, Ferrer-Navarro M, Callarisa AE, et al. Loss of LPS is involved in the virulence and resistance to colistin of colistin-resistant Acinetobacter nosocomialis mutants selected in vitro. J Antimicrob Chemother. 2015;70:2981–6.View ArticlePubMedGoogle Scholar
  41. Pailhoriès H, Hadjadj L, Mahieu R, Crochette N, Rolain J, Kempf M. Fortuitous diagnosis of NDM-1-producing Acinetobacter pittii carriage in a patient from France with no recent history of travel. J Antimicrob Chemother. 2017;72:942–4.PubMedGoogle Scholar
  42. Launay A, Ballard SA, Johnson PDR, et al. Transfer of vancomycin resistance transposon Tn 1549 from Clostridium symbiosum to Enterococcus spp. in the gut of gnotobiotic mice. Antimicrob Agents Chemother. 2006;50:1054–62.View ArticlePubMedPubMed CentralGoogle Scholar
  43. Rolain J-M, François P, Hernandez D, et al. Genomic analysis of an emerging multiresistant Staphylococcus aureus strain rapidly spreading in cystic fibrosis patients revealed the presence of an antibiotic inducible bacteriophage. Biol Direct. 2009;4:1.View ArticlePubMedPubMed CentralGoogle Scholar
  44. Chabou S, Leangapichart T, Okdah L, Le Page S, Hadjadj L. Rolain J-MM. Real-time quantitative PCR assay with Taqman* probe for rapid detection of MCR-1 plasmid-mediated colistin resistance. New Microbes New Infect. 2016;13:71–4.View ArticlePubMedPubMed CentralGoogle Scholar
  45. Domingo M-C, Huletsky A, Giroux R, et al. High prevalence of glycopeptide resistance genes vanB, vanD, and vanG not associated with enterococci in human fecal flora. Antimicrob Agents Chemother. 2005;49:4784–6.View ArticlePubMedPubMed CentralGoogle Scholar
  46. Seng P, Drancourt M, Gouriet F, et al. Ongoing revolution in bacteriology : routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis. 2009;49:543–51.View ArticlePubMedGoogle Scholar
  47. Postgate JR, Hunter JR. On the survival of frozen bacteria. J Gen Microbiol. 1961;26:367–78.View ArticlePubMedGoogle Scholar
  48. Hraiech S, Roch A, Lepidi H, et al. Impaired virulence and fitness of a colistin-resistant clinical isolate of Acinetobacter baumannii in a rat model of pneumonia. Antimicrob Agents Chemother. 2013;57:5120–1.View ArticlePubMedPubMed CentralGoogle Scholar
  49. Choi M-J, Ko KS. Loss of hypermucoviscosity and increased fitness cost in colistin-resistant Klebsiella pneumoniae sequence type 23 strains. Antimicrob Agents Chemother. 2015;59:6763–73.View ArticlePubMedPubMed CentralGoogle Scholar
  50. López-Rojas R, Domínguez-Herrera J, McConnell MJ, et al. Impaired virulence and in vivo fitness of colistin-resistant Acinetobacter baumannii. J Infect Dis. 2011;203:545–8.View ArticlePubMedPubMed CentralGoogle Scholar
  51. Seng P, Rolain J-M, Fournier PE, La Scola B, Drancourt M, Raoult D. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol. 2010;5:1733–54.View ArticlePubMedGoogle Scholar
  52. Nordmann P, Jayol A, Poirel LA. Universal culture medium for screening polymyxin-resistant gram-negative isolates. J Clin Microbiol. 2016;54:1395–9.View ArticlePubMedPubMed CentralGoogle Scholar
  53. Jayol A, Dubois V, Poirel L, Nordmann P. Rapid detection of polymyxin-resistant Enterobacteriaceae from blood cultures. J Clin Microbiol. 2016;54:2273–7.View ArticlePubMedPubMed CentralGoogle Scholar
  54. Saly M, Jayol A, Poirel L, Megraud F, Nordmann P, Dubois V. Prevalence of faecal carriage of colistin-resistant gram-negative rods in a university hospital in western France, 2016. J Med Microbiol. 2017;66:842–3.View ArticlePubMedGoogle Scholar
  55. Abdul Momin MHF, Bean DC, Hendriksen RS, Haenni M, Phee LM, Wareham DW. CHROMagar COL-APSE: a selective bacterial culture medium for the isolation and differentiation of colistin-resistant Gram-negative pathogens. J Med Microbiol 2017; published online Oct 6. DOI:10.1099/jmm.0.000602.
  56. Y-M A, Kim A-J, Lee J-Y. Colistin resistance in Klebsiella pneumoniae. Int J Antimicrob Agents. 2014;44:8–15.View ArticleGoogle Scholar

Copyright

© The Author(s). 2017

Advertisement

BMC Microbiology

ISSN: 1471-2180

Contact us