Skip to main content

Low prevalence of mcr-1 in Escherichia coli from food-producing animals and food products in China

Abstract

Background

mcr-1-positive Escherichia coli has emerged as a significant threat to human health, veterinary health, and food safety in recent years. After the prohibition of colistin as a feed additive in animal husbandry in China, a noticeable reduction in both colistin resistance and the prevalence of mcr-1 was observed in E. coli from animals and humans.

Objectives

To assess the prevalence of the colistin resistance gene mcr-1 and characterize its genetic context in E. coli strains derived from fecal and meat samples from food-producing animals in China.

Methods

A total of 1,353 fecal samples and 836 food samples were collected between 2019 and 2020 in China. E. coli isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and their susceptibility to colistin were determined using the broth microdilution method. The colistin-resistant E. coli isolates were screened for the presence of mcr by PCR analysis and sequencing. The minimal inhibitory concentrations (MICs) of 15 antimicrobial agents against the mcr-1-positive strains were further tested using the agar dilution method, conjugation assays were performed, and whole genome sequencing was performed using Illumina HiSeq.

Results

In total, 1,403 E. coli strains were isolated. Thirteen isolates from chicken meat (n = 7), chickens (n = 3), and pigs (n = 3) were resistant to colistin with MIC values of 4 to 16 mg/L, and carried mcr-1. All mcr-1-positive strains, except for isolate AH20PE105, contained multiple resistance genes and exhibited multidrug-resistant phenotypes. They belonged to 10 sequence types (STs), including a novel ST (ST14521). mcr-1 was located on IncI2 (n = 9), IncX4 (n = 2), and IncHI2 (n = 2) plasmids, which were highly similar to other mcr-1-carrying plasmids sharing the same incompatibility type. Seven mcr-1-carrying plasmids could be successfully conjugally transferred to E. coli C600.

Conclusions

While the low prevalence of mcr-1 (0.93%) identified in this study may not immediately seem alarming, the very emergence of this gene merits attention given its implications for colistin resistance and public health. Hence, ongoing surveillance of mcr-1 in E. coli remains crucial.

Peer Review reports

Introduction

The emergence and rapid growth of antibiotic-resistant bacteria pose major challenges to human health, veterinary health, and food safety on a global scale because of the improper use of antibiotics in clinical application and livestock farming [1]. A lack of novel antibacterial agents to combat multidrug-resistant (MDR) Gram-negative bacteria has led to the reuse of polymyxins, particularly colistin, in treatment programs [1]. However, resistance to colistin has been on the rise following the emergence and widespread distribution of the plasmid-borne colistin resistance gene mcr-1 [1,2,3,4]. To date, 10 mcr variants and many subvariants have been globally identified in diverse bacterial species, particularly Escherichia coli, Klebsiella pneumoniae, and Salmonella species, from various sources [1, 5]. Among the 10 mcr variants, mcr-1 stands out as the predominant type [1].

E. coli are Gram-negative bacteria. Commensal variants of E. coli are harmless, whereas pathogenic variants can trigger intestinal or parenteral infections in humans and many animal hosts [6]. Statistically, 48 per 100,000 individuals in high-income countries are diagnosed with E. coli bacteremia infections every year [6]. A major concern is that MDR E. coli may cause treatment failures because they are a potential reservoir of drug resistance genes, particularly mcr-1, which confers resistance to colistin [7]. E. coli isolates carrying mcr-1 prevail significantly among food-producing animals and exhibit widespread distribution across various sources, including humans, wildlife, companion animals, food products, and the environment [1,2,3,4, 8]. The rapid dissemination can be attributed to the use of colistin in veterinary medicine or as a growth promoter, along with the capability of mcr-1 for horizontal transfer [1, 3, 8]. The insertion sequence ISApl1, transposon Tn6330 (ISApl1mcr-1–ISApl1), and many plasmids (such as IncX4, IncI2, and IncHI2) have been reported to be involved in mcr-1 transmission among various sources [1, 3, 4].

Following the prohibition of adding colistin to animal feed for growth promotion on April 30, 2017, significant effects have been observed in China, notably in reducing both colistin resistance and the prevalence of mcr-1-positive E. coli [9]. To further assess the prevalence of mcr-1, we examined the dissemination of mcr-1 in E. coli from food-producing animals and retail raw meats and analyzed the genetic environment of mcr-1 in this study.

Materials and methods

Detection of mcr and antimicrobial susceptibility testing

From June 2019 to November 2020, a total of 1,353 fecal samples were collected from food-producing animals including pigs (n = 212), chickens (n = 358), cattle (n = 752), and pigeons (n = 31) from farms located in Anhui, Henan, Liaoning, Jiangsu, Guangdong, Shandong, and Xinjiang in China and 836 food samples including pork (n = 377), chicken meat (n = 341), and beef (n = 118), were collected from a slaughterhouse, farmers’ markets, and supermarkets in the aforementioned provinces and Shanghai (Supplementary Table S1). The isolation of E. coli using previously described methods with minor modifications [10, 11]. The samples were cultured for 18–24 h in buffered peptone water (BPW) broth at 37 °C. The positive growth was further streaked on a MacConkey agar plate and incubated at 37 °C for 24 h. One pink colony from each plate was inoculated onto an eosin methylene blue (EMB) agar plate for 24 h at 37 °C. A colony with metallic sheen color (presumptive E. coli) was inoculated onto another EMB agar plate for purification. One E. coli isolate was randomly chosen from each plate and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (Bruker Daltonik GmbH, Bremen, Germany).

The susceptibility of all E. coli isolates to colistin was assessed using the broth microdilution method according to the International Standards ISO 20776-1 (https://www.iso.org/standard/70464.html). The colistin-resistant E. coli isolates were screened for the presence of mcr by PCR analysis and sequencing using the primers listed in Supplementary Table S2. The susceptibility of the mcr-positive isolates to 15 antimicrobial agents was further assessed using the agar dilution method following the guidelines of the Clinical and Laboratory Standards Institute (CLSI) M07 [12]. The results were interpreted according to the 30th edition of the CLSI M100 [13]. E. coli ATCC 25,922 served as the quality control in antimicrobial susceptibility testing.

Whole genome sequencing and analysis

Genomic DNA was extracted from all mcr-1-positive E. coli isolates using the TIANamp Bacteria DNA Kit (Tiangen, Beijing, China), according to the manufacturer’s instructions. The Illumina HiSeq platform was used to sequence all mcr-1-positive isolates, and SPAdes v.3.8.2 was used to assemble the sequence reads into contigs. Multilocus sequence typing (MLST), acquired resistance genes, chromosomal mutations, and plasmid incompatibility groups were detected using the CGE database (http://www.genomicepidemiology.org/). PCR analysis and Sanger sequencing were performed to assemble plasmid contigs into a complete plasmid sequence (Supplementary Table S3). Initial analysis and annotation of contigs or plasmids containing mcr-1 were using the RAST (https://rast.nmpdr.org/rast.cgi), ISfinder (https://www-is.biotoul.fr/), BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and Gene Construction kit 4.5 (Textco BioSoftware, Inc., Raleigh, NC). The genetic structures of mcr-1 in plasmids were drawn using Vector NTI 11 (Thermo Fisher Scientific, Inc., Waltham, MA) and manually adjusted. All whole genome sequences and mcr-1-carrying plasmids have been deposited in GenBank under the accession numbers PRJNA967092 and PRJNA974499, respectively.

Conjugation experiments

As mentioned previously, conjugation experiments were performed using all mcr-1-positive E. coli isolates [14]. The mcr-1-positive E. coli isolates were used as the donors and high-level streptomycin-resistant E. coli C600 was used as the recipient; they were mixed in a ratio of 1:4. Transconjugants were selected on EMB agar containing colistin (2 µg/mL) and streptomycin (3000 µg/mL) and were further confirmed by detecting mcr-1 using PCR. The experiments were performed in triplicate, and the conjugal frequency of mcr-1 was estimated as the number of transconjugants per recipient.

Results

Characterization of mcr-1 -positive E. coli isolates

In total, 1,403 E. coli strains were isolated from food-producing animals and retail meat products (Supplementary Table S1). Of these, 13 isolates (0.93%) from chicken meat (n = 7), chickens (n = 3), and pigs (n = 3) exhibited resistance to colistin with minimum inhibitory concentration (MIC) values of 4 to 16 mg/L. No other mcr variants were detected, except for mcr-1 (Table 1). A low detection rate of mcr-1 among E. coli isolates originating from food-producing animals (0.62%, 6/974) and animal-derived food (1.63%, 7/429) was observed in this study.

Table 1 Characteristics of mcr-1-carrying E. coli isolates in this study

As shown in Table 1, all colistin-resistant E. coli isolates, except for isolate AH20PE105, were also resistant to multiple antibiotics. Eleven isolates were resistant to ampicillin, tetracycline, and chloramphenicol. Additionally, among the 13 mcr-1-positive isolates, resistance to streptomycin, sulfamethoxazole/trimethoprim, and gentamicin was observed in 10, 10, and nine cases, respectively. Nine isolates contained blaCTX−M, including blaCTX−M−55 (n = 6), blaCTX−M−14 (n = 3), blaCTX−M−65 (n = 1), and blaCTX−M−123 (n = 1), and were resistant to cefazolin and cefotaxime. Two isolates, SD20MCE26 and LN19MCE7, carried both blaCTX−M−55 and blaCTX−M−14. Furthermore, nine MCR-1-producing E. coli strains exhibited resistance to florfenicol, a common veterinary antimicrobial agent, and carried the florfenicol resistance gene floR. The fosfomycin resistance gene fosA3 and 16S rRNA methylase gene rmtB were identified in six fosfomycin-resistant strains and one amikacin-resistant strain, respectively. In addition, gyrA (S83L and D87N/Y) and parC (S80I) mutations were observed in 10 E. coli strains, thereby explaining their nalidixic acid- and ciprofloxacin-resistant phenotypes. The presence of the multidrug efflux pump genes oqxAB and quinolone resistance gene qnrS2 and the existence of a single mutation in parC (A56T) in isolate SD20MCE26 were responsible for its resistance to nalidixic acid.

MLST analysis based on whole genome sequencing revealed that 13 mcr-1-positive E. coli isolates belonged to 10 sequence types (STs), including ST10 (n = 2), ST101 (n = 2), ST156 (n = 2), ST155, ST48, ST6388, ST1011, ST3871, ST1589, and a new ST (ST14521) (Table 1). Three to seven plasmid replicons were identified in mcr-1-positive E. coli strains (Table 1). By analyzing mcr-1-carrying contigs or plasmids, we found that mcr-1 was located on plasmids in all isolates and that IncI2 was predominant (n = 9), followed by IncX4 (n = 2) and IncHI2 (n = 2) (Table 1).

Characterization of mcr-1 -carrying IncI2 plasmids in nine E. coli isolates

The mcr-1-carrying IncI2 plasmids in this study were similar to the first reported mcr-1-carrying plasmid pHNSHP45 (E. coli, pig, China, KP347127) (Fig. 1). The transposable element ISApl1 observed upstream of mcr-1 in pHNSHP45 was not present in eight mcr-1-carrying plasmids. Moreover, only one plasmid (pYUYZMC13-MCR) from the isolate YZ19MCE13 contained an incomplete ISApl1 upstream of mcr-1 (Fig. 1). In addition to mcr-1, the plasmids pYUAHC37-MCR, pYUAHC39-MCR, and pYUSDMC15-MCR from the isolates AH20CE37, AH20CE39, and SD20MCE15, respectively, carried blaCTX−M−55. It was located in a typical transposition unit (ISEcp1blaCTX−M−55orf477) with 5-bp direct repeats (DRs, 5′-GAAAA-3′), while ISEcp1 was interrupted by IS1294 in pYUAHC37-MCR and pYUAHC39-MCR (Fig. 1).

Fig. 1
figure 1

Genetic structure of mcr-1 in nine plasmids and structural comparison with related mcr-1-carrying IncI2 plasmids. Regions with > 99% identity are shaded in gray. Thick arrow indicates ORF. Red thin red arrow indicates resistance genes. Box indicates insertion sequences. The delta symbol (Δ) indicates a truncated gene or mobile element. Direct repeats are indicated by arrows and sequences

A multiple inversion system called shufflon was first identified in the IncI1 plasmid R64 and later discovered in other Inc types, including IncIγ, IncI2, IncK, and IncZ plasmids [15]. The rearrangement of shufflon regions results in the generation of different C-terminal ends of the PilV protein, which is involved in bacterial conjugation [15]. The shufflon region of nine IncI2 plasmids was distinct and included eight arrangements, and it was interrupted by ISEc8 in pYUYZMC28-MCR (Fig. 1). A similar ISEc8 insertion was observed in the recombinase gene rci in pYUYZMC34-MCR (Fig. 1). In pYUYZMC13-MCR, the mokparA fragment (2007 bp) was absent because of the insertion of IS1294 and the type IV pilus transmembrane gene pilR was interrupted by IS2, generating 5-bp DRs (5′-CCGCG-3′) (Fig. 1). The insertion of mobile elements into the conjugal region may explain the failure of conjugation of the three abovementioned mcr-1-carrying plasmids. Three plasmids in this study (pYUYZMC6-MCR, pYUSDMC15-MCR, and pYUAHP105-MCR) could be successfully transferred to E. coli C600 at a frequency of 5.79 × 10− 6, 8.99 × 10− 3, and 1.9 × 10− 4 transconjugants per recipient, respectively.

Characterization of mcr -1-carrying IncX4 plasmids in two E. coli isolates

Two mcr-1-carrying IncX4 plasmids, pYUAHP7-MCR and pYUYZP15-MCR, were obtained from isolates AH20PE7 and YZ19PE15, respectively, with a size of 34,541–36,021 bp. Both plasmids had typical IncX4 plasmid backbones, including genes encoding replication proteins and conjugal transfer proteins and those responsible for maintenance and stability (Fig. 2). Moreover, their organization was similar to that of other mcr-1-carrying IncX4 plasmids from animals or food products in China, such as pHNSHP10 (pig, MF774182) and pPY1 (pork, KX711708) from E. coli (Fig. 2). However, ISApl1 was inserted downstream of mcr-1pap2 in pY1, which was not present in our plasmids. Moreover, the mcr-1pap2 segment was inserted in pPY1 in reverse orientation. Instead, one copy of IS26 was inserted into the backbone of the two plasmids at the same site, generating 8-bp DRs (5′-CTGTGTGA-3′) (Fig. 2). In addition to IS26, one copy of IS679-like was inserted into hns with 8-bp DRs in pYUAHP7-MCR. Moreover, topB was interrupted by the insertion of ISKpn40 in pYUYZP15-MCR (Fig. 2). As described previously [4, 16, 17], the IncX4 plasmids pYUAHP7-MCR and pYUYZP15-MCR did not carry any drug resistance genes, except for mcr-1. They were transferable at a frequency of 3.75 × 10− 4 and 2.03 × 10− 3 transconjugants per recipient, respectively.

Fig. 2
figure 2

Genetic structure of mcr-1 in two plasmids and structural comparison with related mcr-1-carrying IncX4 plasmids. Regions with > 99% identity are shaded in gray. Red arrow indicates resistance genes. Purple arrow represents conjugal transfer genes. Green arrow represents plasmid replication genes. Blue arrow represents genes for maintenance and stability. Black arrow indicates other genes. The delta symbol (Δ) indicates a truncated gene or mobile element. Direct repeats are indicated by arrows and sequences

Characterization of mcr-1 -carrying contigs associated with IncHI2 plasmids in two E. coli isolates

In strains SD20MCE26 and AH20CE15, mcr-1-carrying contigs (101,306 bp and 106,757 bp, respectively) were highly similar to the IncHI2 plasmids pHN6DS2 (E. coli, MH459020), pSI-16E242 (Salmonella, ON960347), and pEC15-MCR-50 (E. coli, MG656414) (Fig. 3). The mcr-1-positive contigs in SD20MCE26 and AH20CE15 harbored tellurium resistance genes (terYXWZABCDEF) and genes responsible for conjugal transfer (trhINUWFOZCVBKELA and htdKFATVO). The insert sequence ISApl1 observed upstream of mcr-1 in pHN6DS2 was present in SD20MCE26 but absent in AH20CE15 (Fig. 3). As IncHI2 plasmid replicons were identified in SD20MCE26 and AH20CE15 (Table 1) and mcr-1 from SD20MCE26 and AH20CE15 could be transferred to E. coli C600 at a frequency of 3.24 × 10− 5 and 1.94 × 10− 5 transconjugants per recipient, respectively, mcr-1 in SD20MCE26 and AH20CE15 may be associated with IncHI2 plasmids.

Fig. 3
figure 3

Genetic structure of mcr-1 in SD20MCE26 and AH20CE15 in this study and comparison with other IncHI2 plasmids. Regions with > 99% identity are shaded in gray. Thick arrow indicates ORF. Red thin red arrow indicates resistance genes. Box indicates insertion sequences

Discussion

Since its identification in 2015 in a porcine E. coli strain in China, the plasmid-mediated colistin resistance gene mcr-1 has rapidly disseminated worldwide, being identified in diverse bacterial species across various sources, predominantly hosted by E. coli [1,2,3,4, 8]. In our study, a low prevalence of mcr-1 was observed among E. coli isolates from food-producing animals and animal-derived food. It might be attributed to the random isolation of E. coli strains without employing a medium supplemented with colistin for selection. Furthermore, we identified colistin-resistant E. coli isolates from chickens (1.29%, 3/275) and pigs (1.09%, 3/232), while none were found in cattle (0/507) or pigeons (0/27). The absence in pigeons might be due to the limited numbers of E. coli isolates, and notably, colistin has never been approved for use in cattle in China. On the other hand, our findings align with the substantial decrease in colistin resistance and mcr prevalence following the ban of colistin-positive additives in China [9]. This underscores the critical significance and consequential effects of prohibiting colistin as an animal growth promoter in China. Although a low detection rate of E. coli isolates carrying mcr-1 gene was noted in this study, its presence in animals and food remains a considerable threat to public health, given the potential risk of zoonotic transmission to humans through the food chain and contact with backyard animals [1, 7]. In addition to mcr-1, 12 isolates investigated in this study contained multiple antimicrobial resistance genes, such as blaCTX−M, floR, oqxAB, qnrS, and mutations in gyrA and parC, consistent with their antibiotic-resistant phenotype. The emergence and spread of these MDR E. coli strains present a heightened risk, potentially resulting in difficult-to-treat infections and limiting therapeutic options against infections they cause [7]. More importantly, they serve as a significant reservoir of resistance determinants to most families of antimicrobial agents for animals and humans [7].

A high diversity of E. coli isolates with different STs carrying mcr-1 has been identified in animals, food products, and humans [4, 9, 16]. The STs identified in this study, such as ST10, ST48, ST101, ST155, ST156, ST1011 and ST1589, were also previously reported as common mcr-1 carriers in food-producing animals and humans in China [9, 16, 18]. These STs have also been recognized as mcr-1 carriers beyond China. For example, mcr-1-positive E. coli ST10, ST1011, and ST156 were identified in poultry samples from Poland [19]. In Egypt, two E. coli ST155 strains encoding Tet(X7) and MCR-1 were isolated from chicken meat, while three mcr-1-positive E. coli ST101 strains were recovered from pigs in Europe [20, 21]. The diversity observed in E. coli STs in our study and prior research suggests that horizontal transmission serves as the primary route for mcr-1 dissemination in animals and their food products. Nonetheless, it is noteworthy that the clonal spread of specific ST-type E. coli strains, such as E. coli ST93 among companion animals, and E. coli ST10 in swine farms, may also contribute to the spread of mcr-1 [22, 23].

Plasmids play an essential role in the global dissemination of resistance genes including mcr-1 in Enterobacteriaceae [1, 3, 4, 24]. While various plasmids, such as IncFII, IncY, IncP, and IncK2, have been described as vectors of mcr-1, the majority of identified plasmids were affiliated with three incompatibility groups: IncI2, IncX4, and IncHI2 [3, 4, 8, 17, 25]. These three prevalent plasmid types have served as the principal vehicles for disseminating mcr-1 globally, frequently detected in Enterobacteriaceae, particularly E. coli, across diverse origins [3, 4, 8]. Consistent with this trend, our study also detected the presence of mcr-1 on IncI2, IncX4, or IncHI2 plasmids, with high similarity to each other and previously reported mcr-1-carrying plasmids within the same incompatibility group. Furthermore, a diverse array of IS elements was found integrated into the plasmid backbone, leading to the loss or acquisition of genetic fragments and driving plasmid evolution among different lineages of E. coli strains. Seven mcr-1-carrying plasmids identified in our study possess conjugative capabilities, representing an increased risk of spreading mcr-1 between bacteria, even across different species. This conjugal transferability significantly contributes to the dissemination of both mcr-1 and colistin resistance among bacterial populations [8].

In this study, IncI2 plasmids emerged as the primary vehicle for mcr-1 transmission, sharing a similar backbone yet distinct shufflon regions. Intriguingly, a striking rise in the occurrence of IncI2-type plasmids was noticed among mcr-1-positive E. coli strains from animals and humans following the cessation of colistin as an animal growth promoter in China [9]. The precise reason behind this observation remains unclear. However, IncI2 plasmids often carry additional resistance genes such as blaCTX−M−55 in this study, besides mcr-1, potentially contributing to the preferential selection of these plasmids due to the extensive use of β-lactam antibiotics such as amoxicillin in animals and cephalosprins in human clinical settings [9]. Furthermore, the enhanced fitness conferred by mcr-1-carrying IncI2 and IncX4 plasmids supports their dissemination and persistence in bacterial populations even without antibiotic selection pressures [17]. Conversely, the acquisition of mcr-1-carrying IncHI2 plasmids imposes a competitive disadvantage [17, 26]. Nonetheless, these plasmids often carry diverse resistance genes (e.g., floR, blaCTX−M, and fosA3), co-selection by other antimicrobials might augment the further dissemination of IncHI2 plasmids carrying mcr-1 [8, 17, 22, 27].

The insertion sequence ISApl1 is involved in mobilizing mcr-1 among DNA molecules, such as plasmid or chromosomes [3, 4, 25, 28]. However, in this study, the presence of ISApl1, intact or incomplete, was observed upstream of mcr-1 in only two plasmids, while the mcr-1-pap2 structure (n = 11) was more prevalent. This observation aligns with a prior study indicating that ISApl1 upstream of the mcr-1 gene was present in 77.8% of IncHI2 plasmids, 37.9% of IncI2 plasmids, and absent in IncX4 plasmids [4]. The proposed hypothesis suggests that mcr-1 initially mobilizes through the mobile transposon unit Tn6330 (ISApl1-mcr-1-pap2-ISApl1), subsequently undergoing a gradual loss of ISApl1 at both ends, potentially ensuring the stability of mcr-1 before plasmid-mediated transmission [3, 29]. Consequently, this results in the formation of diverse genetic structures harboring mcr-1, with the mcr-1-pap2 structure being predominant, followed by the ISApl1-mcr-1-pap2 structure [3, 29].

However, our study has several limitations. We collected samples from only seven regions in China, however, certain sources (e.g., pigeons and beef) were limited in sample quantity and location. The uneven distribution of samples across different regions and types led to considerable variation in the number of strains isolated from different areas. For instance, there were notably fewer pig and pork samples and isolated strains from Guangdong province. Additionally, we exclusively detected mcr genes in colistin-resistant E. coli isolates. Notably, mcr-4.3 demonstrated a silent phenotype due to mutations (V179G and V236F), and silent transmission of inactivated mcr-1 and mcr-9 with inducible colistin resistance have been previously reported [30,31,32,33]. Hence, there remains a possibility that the colistin-susceptible E. coli strains yet to be identified in our study may carry mcr.

Conclusion

This study unveils a low detection rate (0.93%) of mcr-1 among E. coli isolates originating from food-producing animals and animal-derived food products, associated with the previously identified IncI2, IncX4 and IncHI2 epidemic plasmids. While the low prevalence of mcr-1 might not immediately appear threatening, its emergence merits attention given its implication for colistin resistance and public health. Considering the potential dissemination of mcr-1 facilitated by plasmids among bacteria, and the risk of co-selection with other commonly used antibiotics in animal husbandry, continuous surveillance of mcr-1 is imperative. This surveillance needs to monitor not only its prevalence and dissemination in E. coli but also in other Enterobacteriaceae species.

Data availability

The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request. All whole genome sequences and mcr-1-carrying plasmids are available in GenBank under the accession numbers PRJNA967092 and PRJNA974499, respectively.

References

  1. Bastidas-Caldes C, de Waard JH, Salgado MS, Villacís MJ, Coral-Almeida M, Yamamoto Y, et al. Worldwide prevalence of mcr-mediated colistin-resistance Escherichia coli in isolates of clinical samples, healthy humans, and livestock-A systematic review and meta-analysis. Pathogens. 2022;11(6):659.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, 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(2):161–8.

    Article  PubMed  Google Scholar 

  3. Wang R, van Dorp L, Shaw LP, Bradley P, Wang Q, Wang X, et al. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat Commun. 2018;9(1):1179.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Matamoros S, van Hattem JM, Arcilla MS, Willemse N, Melles DC, Penders J, et al. Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction. Sci Rep. 2017;7(1):15364.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Hussein NH, Al-Kadmy IMS, Taha BM, Hussein JD. Mobilized colistin resistance (mcr) genes from 1 to 10: a comprehensive review. Mol Biol Rep. 2021;48(3):2897–907.

    Article  CAS  PubMed  Google Scholar 

  6. Bonten M, Johnson JR, van den Biggelaar AHJ, Georgalis L, Geurtsen J, de Palacios PI, et al. Epidemiology of Escherichia coli bacteremia: a systematic literature review. Clin Infect Dis. 2021;72(7):1211–9.

    Article  PubMed  Google Scholar 

  7. Poirel L, Madec JY, Lupo A, Schink AK, Kieffer N, Nordmann P et al. Antimicrobial resistance in Escherichia coli. Microbiol Spectr 2018;6(4).

  8. Nang SC, Li J, Velkov T. The rise and spread of mcr plasmid-mediated polymyxin resistance. Crit Rev Microbiol. 2019;45(2):131–61.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Wang Y, Xu C, Zhang R, Chen Y, Shen Y, Hu F, et al. Changes in colistin resistance and mcr-1 abundance in Escherichia coli of animal and human origins following the ban of colistin-positive additives in China: an epidemiological comparative study. Lancet Infect Dis. 2020;20(10):1161–71.

    Article  CAS  PubMed  Google Scholar 

  10. Yang T, Zeng Z, Rao L, Chen X, He D, Lv L, et al. The association between occurrence of plasmid-mediated quinolone resistance and ciprofloxacin resistance in Escherichia coli isolates of different origins. Vet Microbiol. 2014;170(1–2):89–96.

    Article  CAS  PubMed  Google Scholar 

  11. Rahman MM, Lim SJ, Kim WH, Cho JY, Park YC. Prevalence data of diarrheagenic E. coli in the fecal pellets of wild rodents using culture methods and PCR assay. Data Brief. 2020;33:106439.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Clinical and Laboratory Standards Institute (CLSI). 2012. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. CLSI document M07-A9, 9th ed. Wayne, PA, USA.

  13. CLSI. 2020. Performance standards for antimicrobial susceptibility testing. CLSI supplement M100, 30th ed. Wayne, PA, USA.

  14. Chen L, Chen ZL, Liu JH, Zeng ZL, Ma JY, Jiang HX. Emergence of RmtB methylase-producing Escherichia coli and Enterobacter cloacae isolates from pigs in China. J Antimicrob Chemother. 2007;59(5):880–5.

    Article  CAS  PubMed  Google Scholar 

  15. Brouwer MS, Tagg KA, Mevius DJ, Iredell JR, Bossers A, Smith HE, et al. IncI shufflons: Assembly issues in the next-generation sequencing era. Plasmid. 2015;80:111–7.

    Article  CAS  PubMed  Google Scholar 

  16. Shen Y, Wu Z, Wang Y, Zhang R, Zhou HW, Wang S, et al. Heterogeneous and flexible transmission of mcr-1 in hospital-associated Escherichia coli. mBio. 2018;9(4):e00943–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Wu R, Yi LX, Yu LF, Wang J, Liu Y, Chen X, et al. Fitness advantage of mcr-1-bearing IncI2 and IncX4 plasmids in vitro. Front Microbiol. 2018;9:331.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Cheng P, Yang Y, Cao S, Liu H, Li X, Sun J, et al. Prevalence and characteristic of swine-origin mcr-1-positive Escherichia coli in northeastern China. Front Microbiol. 2021;12:712707.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Ćwiek K, Woźniak-Biel A, Karwańska M, Siedlecka M, Lammens C, Rebelo AR, et al. Phenotypic and genotypic characterization of mcr-1-positive multidrug-resistant Escherichia coli ST93, ST117, ST156, ST10, and ST744 isolated from poultry in Poland. Braz J Microbiol. 2021;52(3):1597–609.

    Article  PubMed  PubMed Central  Google Scholar 

  20. Soliman AM, Ramadan H, Zarad H, Sugawara Y, Yu L, Sugai M et al. Coproduction of tet(X7) conferring high-level tigecycline resistance, fosfomycin fosA4, and colistin mcr-1.1 in Escherichia coli strains from chickens in Egypt. Antimicrob Agents Chemother. 2021;65(6):e02084-20.

  21. El Garch F, Sauget M, Hocquet D, LeChaudee D, Woehrle F, Bertrand X. mcr-1 is borne by highly diverse Escherichia coli isolates since 2004 in food-producing animals in Europe. Clin Microbiol Infect. 2017;23(1):51e1–4.

    Article  Google Scholar 

  22. Wang J, Huang XY, Xia YB, Guo ZW, Ma ZB, Yi MY, et al. Clonal spread of Escherichia coli ST93 carrying mcr-1-harboring IncN1-IncHI2/ST3 plasmid among companion animals, China. Front Microbiol. 2018;9:2989.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Lee S, An JU, Woo J, Song H, Yi S, Kim WH, et al. Prevalence, characteristics, and clonal distribution of Escherichia coli carrying mobilized colistin resistance gene mcr-1.1 in swine farms and their differences according to swine production stages. Front Microbiol. 2022;13:873856.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, et al. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother. 2018;73(5):1121–37.

    Article  CAS  PubMed  Google Scholar 

  25. Mei CY, Jiang Y, Ma QC, Pan ZM, Jiao X, Wang J. Characterization of an IncP plasmid harbouring mcr-1 from Salmonella enterica Serovar Indiana from a sick chicken in China. J Glob Antimicrob Resist. 2022;31:185–6.

    Article  CAS  PubMed  Google Scholar 

  26. Ma K, Feng Y, Zong Z. Fitness cost of a mcr-1-carrying IncHI2 plasmid. PLoS ONE. 2018;13(12):e0209706.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Mei CY, Jiang Y, Ma QC, Lu MJ, Wu H, Wang ZY, et al. Chromosomally and plasmid-located mcr in Salmonella from animals and food products in China. Microbiol Spectr. 2022;10(6):e0277322.

    Article  PubMed  Google Scholar 

  28. Wang J, Jiang Y, Ji RY, Wang ZY, Lu MJ, Wu H, et al. Colistin- and tigecycline-resistant CTX-M-14-producing Salmonella enterica serovar Kentucky ST198 from retail chicken meat, China. Int J Antimicrob Agents. 2022;59(2):106504.

    Article  CAS  PubMed  Google Scholar 

  29. Snesrud E, McGann P, Chandler M. The birth and demise of the ISApl1-mcr-1-ISApl1 composite transposon: the vehicle for transferable colistin resistance. mBio. 2018;9(1):e02381–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang H, Hou M, Xu Y, Srinivas S, Huang M, Liu L, et al. Action and mechanism of the colistin resistance enzyme MCR-4. Commun Biol. 2019;2:36.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Zhou K, Luo Q, Wang Q, Huang C, Lu H, Rossen JWA, et al. Silent transmission of an IS1294b-deactivated mcr-1 gene with inducible colistin resistance. Int J Antimicrob Agents. 2018;51(6):822–8.

    Article  CAS  PubMed  Google Scholar 

  32. Pham Thanh D, Thanh Tuyen H, Nguyen Thi Nguyen T, Chung The H, Wick RR, Thwaites GE, et al. Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate. J Antimicrob Chemother. 2016;71(8):2314–7.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Kieffer N, Royer G, Decousser JW, Bourrel AS, Palmieri M, De La Ortiz JM, et al. mcr-9, an inducible gene encoding an acquired phosphoethanolamine transferase in Escherichia coli, and its origin. Antimicrob Agents Chemother. 2019;63(9):e00965–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This work was supported by grants from Key Research and Development Program (Modern Agriculture) project of Jiangsu Province (no.BE2021331), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Author information

Authors and Affiliations

Authors

Contributions

Mei CY wrote the main manuscript text and prepared Figs. 1, 2 and 3. Jiang Y analyzed the experimental data. Mei CY and Jiang Y contributed equally to this article. Ma QC, Lu MJ, Wu H, and Wang ZY provided experimental assistance. Jiao X and Wang J revised this manuscript. All authors reviewed the manuscript.

Corresponding authors

Correspondence to Xinan Jiao or Jing Wang.

Ethics declarations

Ethical approval and consent to participate

The collection of animal and slaughterhouse samples is approved by the owner, and food samples are purchased samples.

Consent for publication

Not applicable.

Ethical guidelines

Not applicable.

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s Note

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

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mei, CY., Jiang, Y., Ma, QC. et al. Low prevalence of mcr-1 in Escherichia coli from food-producing animals and food products in China. BMC Vet Res 20, 40 (2024). https://doi.org/10.1186/s12917-024-03891-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12917-024-03891-6

Keywords