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Characterization of an NDM-5 carbapenemase-producing Escherichia coli ST156 isolate from a poultry farm in Zhejiang, China
- Biao Tang†1, 4,
- Jiang Chang†1, 2, 4,
- Liujie Cao1, 4,
- Qixia Luo3,
- Hao Xu3,
- Wentao Lyu1,
- Mingrong Qian1, 4,
- Xiaofeng Ji1, 4,
- Qiaoyan Zhang1, 4,
- Xiaodong Xia2Email author and
- Hua Yang1, 4Email author
© The Author(s). 2019
- Received: 2 September 2018
- Accepted: 9 April 2019
- Published: 25 April 2019
The emergence of carbapenem-resistant Enterobacteriaceae strains has posed a severe threat to public health in recent years. The mobile elements carrying the New Delhi metallo-β-lactqtamase (NDM) gene have been regarded as the major mechanism leading to the rapid increase of carbapenem-resistant Enterobacteriaceae strains isolated from clinics and animals.
We describe an NDM-5-producing Escherichia coli strain, ECCRA-119 (sequence type 156 [ST156]), isolated from a poultry farm in Zhejiang, China. ECCRA-119 is a multidrug-resistant (MDR) isolate that exhibited resistance to 27 antimicrobial compounds, including imipenem and meropenem, as detected by antimicrobial susceptibility testing (AST). The complete genome sequence of the ECCRA-119 isolate was also obtained using the PacBio RS II platform. Eleven acquired resistance genes were identified in the chromosome; four were detected in plasmid pTB201, while six were detected in plasmid pTB202. Importantly, the carbapenem-resistant gene blaNDM-5 was detected in the IncX3 plasmid pTB203. In addition, seven virulence genes and one metal-resistance gene were also detected. The results of conjugation experiments and the transfer regions identification indicated that the blaNDM-5-harboring plasmid pTB203 could be transferred between E. coli strains.
The results reflected the severe bacterial resistance in a poultry farm in Zhejiang province and increased our understanding of the presence and transmission of the blaNDM-5 gene.
- bla NDM-5
- Escherichia coli
- Multidrug resistance
- Poultry farm
The overuse of antibiotics has led to the emergence of a large number of multidrug-resistant pathogens, which constitutes a serious threat to public health . Imipenem and meropenem are carbapenem antibiotics that have been used as last resorts in the treatment of infections caused by gram-negative bacteria, especially multidrug-resistant gram-negative pathogens . In 2008, a novel carbapenem resistance gene, New Delhi metallo-β-lactamase (NDM), was detected in Klebsiella pneumoniae isolated from a Swedish patient of Indian origin. This gene attracted international attention for the high level of resistance it confers to bacteria against most β-lactams, except aztreonam, and its spread to over 50 countries . The NDM variant NDM-5 was first reported in 2011 in Escherichia coli isolated from a patient in the United Kingdom who had received treatment in India . Subsequently, NDM-5 was reported in many other countries, including India , Algeria , Japan , South Korea , Australia , China , Denmark , Italy , America , Spain , Egypt , France , and New Zealand . In China, many pathogens carrying blaNDM-5 have been isolated from patients [18–21]. In addition, blaNDM-5 can also be isolated from pigs [22, 23], dairy cows  and vegetables . The complete sequences of blaNDM-5-harboring plasmids have been helpful for the study of the transmission of the blaNDM-5 gene, although not all of these plasmids have been reported.
In this study, we first describe the NDM-5-producing carbapenem-resistant E. coli strain, ECCRA-119, isolated from a layer hen farm in Zhejiang, China. We obtained the complete genome sequence, predicted the possible mechanism of multidrug resistance and assessed the transmission ability of the plasmid harboring blaNDM-5 from the ECCRA-119 isolate. These results increased our understanding of the diversity and complexity of the strains harboring blaNDM-5.
Two hundred nineteen of the samples studied tested positive for E. coli, and E. coli isolates from all of these samples were obtained and characterized by antimicrobial susceptibility testing (AST) using the VITEK® 2 COMPACT system (BioMérieux, France). The highest overall levels of resistance were observed toward ampicillin, with 74.43% of all isolates resistant to this antimicrobial. High rates of resistance were also observed toward trimethoprim (54.34%), with lower levels of resistance observed toward piperacillin (1.83%), amikacin (2.29%), and amoxicillin (0.91%). No strain was determined to be resistant to tigecycline. One hundred eighty isolates (82.2%) were resistant to at least one antimicrobial agent, and 92 isolates (42.01%) were resistant to three or more antimicrobial agents. Of the 219 E. coli isolates, a carbapenem-resistant strain was identified that showed resistance toward ertapenem and imipenem, which is rare in poultry.
AST of the ECCRA-119 isolate using a panel of 46 antimicrobial agents
Characterization of the genome sequence of strain ECCRA-119
Characteristic features of the genome of the ECCRA-119 isolate
Genome size (bp)
G + C content (%)
No. of predicted coding sequences (CDS)
No. of CRISPR regions
Acquired antibiotic resistance genes of strain ECCRA-119
Position in contig
Seven virulence factors were detected in the whole genome sequence (Additional file 1: Table S2), four in the chromosome and three in the pTB201 plasmid, indicating the potential virulence of the ECCRA-119 isolate. These virulence factors are grouped into five classes (iss, gad, lpfA, iroN, and cma), which are related to serum survival, glutamate decarboxylase, long polar fimbriae, enterobactin siderophore receptor protein, and colicin M, respectively. In addition, one mercury resistance-related gene, merA, was identified on plasmid pTB201 (Additional file 1: Table S3).
Transferability of plasmids
Conjugation assays confirmed that blaNDM-5 could be transferred between E. coli strains, with an observed transfer frequency of (1.39 ± 0.12) × 10− 5. The antibiotic susceptibility testing results showed that the transconjugants, confirmed by PCR and sequencing, were resistant to meropenem (4 mg/L). The transfer regions of the three plasmids of strain ECCRA-119 were successfully identified (Figs. 1 and 2b) by oriTfinder, including the origin of transfer region (oriT), relaxase gene, bacterial type IV secretion system (T4SS) apparatus gene clusters and the type IV coupling protein (T4CP) gene. Plasmid pTB201 was observed to possess an oriT (52,884–52,969 bp in the plasmid), relaxase gene, T4CP and T4SSs, indicating a high potential for self-transferability . Plasmid pTB202 was observed to harbor a relaxase but lacked an oriT, T4CP and/or T4SS, indicating that it is not a mobilizable plasmid . Plasmid pTB203 possess a relaxase gene, T4CP and T4SSs, but lacked a typical oriT sequence, demonstrating its potential to be transferred to other bacteria , with its transfer ability having been confirmed experimentally.
Phylogenetic analysis of strain ECCRA-119 with other E. coli ST156 isolates
MLST analysis classified E. coli strain ECCRA-119 as ST156. Thus, we built a phylogenetic tree to determine its relationship among ST156 E. coli strains based on a SNP analysis (Additional file 1: Figure S1). We identified 52,076 SNPs from the 37 genome sequences available in GenBank. Of these, 17,953 and 34,123 were identified as core and noncore SNPs, respectively. We excluded the noncore SNPs for the further analysis and constructed a phylogenetic tree based on the genome-wide core SNPs. The core genome analysis identified 5 groups (Additional file 1: Figure S1). E. coli strain ECCRA-119 is grouped with the strains 174,900, SCEC020022 and VREC0575, which were isolated from Bangladesh, China and the United Kingdom, respectively. There were 7 group-specific core SNPs in this group. The number of strain-specific SNPs identified in strains ECCRA-119, 174,900, SCEC020022 and VREC0575 was 59, 71, 134 and 160, respectively. Interestingly, most isolates identified from the same region or source are not in the same lineage. Isolates from different countries were observed to be clustered together (strains 157–1949 and SE11). Similarly, strains isolated from different hosts (wild animals, livestock and poultry, and dog) clustered into the same branch (strains MOD1-EC5693, CVM N33633PS and MOD1-EC6498).
Phylogenetic and comparative analysis of pTB203 and other bla NDM-5-harboring IncX3 plasmids
An SNP-based phylogenetic analysis was conducted using the 52 complete sequences of blaNDM-5-harboring IncX3 plasmids available in GenBank (Fig. 2a). Among these sequences, 41 originated from bacterial strains from humans, 1 from a pig, 5 from geese, 1 from a vegetable, 1 from a layer hen, 1 from sewage, and 2 from unknown sources. Our results showed that the IncX3 plasmids have an extensive host range. Among these 52 plasmids, 43 were isolated in China and 33 were from E. coli. Five plasmids from geese became available in January 2019 but were not published. Among these plasmids, 9 published plasmids were selected and constructed by BRIG (Fig. 2b), including pVH1 (vegetable, China, 46,161 bp) , pNDM_MGR194 (human, India, 46,253 bp) , pECNDM101 (swine, China, 46,165 bp) , pEC463-NDM5 (human, China, 46,145 bp) , pBJ114–46 (human, China, 46,161 bp) , pEsco-5256cz (human, Czech, 46,161 bp) , pEc1929 (human, China, 46,164 bp) , pTB203 (layer hen, China, 46,161 bp, in this study), and pZSH6-blaNDM-5 (human, China, 46,161 bp) . The results of BLAST homology analyses showed that these plasmids had more than 99.9% identity and 99.8% query coverage with each other. The comparative analysis of 9 blaNDM-5-harboring IncX3 plasmids (~ 46 kb) revealed that these plasmids are highly similar to each other, possessing the same backbone that includes the IncX3 replication, blaNDM-5 gene and conjugation/type IV secretion components. This result was further confirmed by the comparative analysis of 52 blaNDM-5-harboring IncX3 plasmids, with the exception of pD2-NDM_1_1 (human, South Korea, 79,613 bp) (Additional file 1: Figure S2). The results of our analysis showed that blaNDM-5-harboring IncX3 plasmids with an ~ 46 kb backbone have extensive host adaptability in Enterobacteriaceae.
Complete sequences of plasmids harboring bla NDM variants from China
Comparative analysis of plasmids pTB201 and pTB202
The extensive use of antibacterials has led to the emergence of drug resistance as an increasingly serious issue, which poses a great threat to public health. There have been widespread reports of the isolation of multidrug resistant E. coli from hospitals, poultry, livestock, food, and the environment . In this study, we identified a blaNDM-5-harboring E. coli isolate from a layer hen farm in Zhejiang, China, and we obtained detailed data through bioinformatics and experimental analyses. The AST results showed that the ECCRA-119 isolate is resistant to 27 different compounds used as therapeutics and food animal feeding, indicating its strong environmental adaptability under antibiotic selection pressure. There is no doubt that the multidrug resistance of this strain may present a serious risk to clinical and veterinary medicine. Apart from a few cases, acquired antimicrobial resistance genes and genomic mutations can largely explain drug resistance phenotypes. The identification of the antimicrobial resistance genes acquired by this strain show that this isolate may have a broad spectrum of drug resistance. For example, the presence of the fosA3 gene in the chromosome could result in fosfomycin resistance , but further experiments are needed to confirm this possibility.
The iss gene was detected on both the chromosome and on plasmid pTB201, indicating the potential virulence of the ECCRA-119 isolate. The protein encoded by the iss gene is part of an outer membrane protein and is involved in the anti-complement effect of bacteria, possibly enhancing the serum resistance of E. coli and enabling the strain to rapidly proliferate in the host. It is widely believed that the iss gene is closely associated with the virulence of avian E. coli .
The merA gene was detected in plasmid pTB201, which can confer resistance to mercury and increase the viability of the ECCRA-119 isolate. Furthermore, the results suggested that plasmid pTB201 had a high potential for self-transferability. Therefore, it is likely that the mercury resistance of the ECCRA-119 isolate may be transferred to other bacteria . Thus, the ECCRA-119 isolate has strong environmental resilience and a high potential to survival in a complicated breeding environment for a long time.
To the best of our knowledge, this is the first time a blaNDM-5-harboring plasmid has been reported in layer chickens. E. coli ST156 has not been a predominant multidrug-resistant clone observed worldwide in the past, but it is associated with the distribution of blaNDM-1 and blaCTX-M-15 in humans and poultry [37, 38]. The genes mcr-1 and blaNDM-5 have been reported to be detected in E. coli ST156 from Muscovy duck in China . E. coli ST156 has spread to many countries and can be isolated from many types of hosts, suggesting that E. coli ST156 has the potential to play an important role in the transmission of the blaNDM-5 gene. In this study, the blaNDM-5-harboring plasmid was first detected from E. coli ST156 in the feces of a layer hen in China, which may increase our understanding of the transmission of blaNDM-5.
IncX3 plasmids are narrow host range plasmids of Enterobacteriaceae and are believed to have a low prevalence . Since the first discovery of blaNDM-5 in China, this gene has been identified in a variety of Enterobacteriaceae [21, 31], with IncX3 being the primary type of Inc. to harbor blaNDM-5 . From our results, the IncX3 plasmids harboring blaNDM-5 were highly similar to each other in different countries and host sources, suggesting its ability to be an efficient vehicle for blaNDM-5 dissemination among humans, animals, food and the environment, potentially indicating its role in the rapid spread of blaNDM-5-harboring isolates [21, 28]. The BRIG analysis results showed that blaNDM-5-harboring IncX3 plasmids have a conserved backbone of ~ 46 kb, indicating that these plasmids had a common ancestor, and the conjugation/type IV secretion components in the backbone may be a factor promoting its transmission.
The blaNDM-5-harboring plasmids were initially detected from isolates from human [4, 27, 28]. However, they have also been detected in food, the environment and livestock and poultry sources in recent years. For example, plasmid pNDM5_025943 (unpublished) was detected in sewage, and plasmid pVH1 was detected from a cucumber . Carbapenem resistance is well known to be a universal phenomenon because of its frequent usage in clinics. Thus, it is interesting that the blaNDM-5-harboring plasmid has an increasing host range, which reflects the development of serious carbapenem resistance. In particular, the blaNDM-5 gene has been detected from livestock animals in recent years, such as swine  and dairy cows . In this study, the complete sequence of a blaNDM-5-harboring plasmid isolated from layer hen feces was first published, which is important evidence of blaNDM-5 transmission in poultry in China.
Sample collection and antimicrobial susceptibility testing
The E. coli isolate recovered was designated ECCRA-119 and showed resistance to meropenem (8 mg/L) and imipenem (4 mg/L). This isolate was selected for AST using the broth dilution method with the Biofosun® Gram-negative panel (Fosun Diagnostics, Shanghai, China). The criteria from the Clinical and Laboratory Standards Institute (CLSI) were used to interpret the results, and the US National Antimicrobial Resistance Monitoring System (NARMS) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) protocol was used when CLSI standards were not appropriate. The panel of antimicrobial compounds tested included ampicillin, amoxicillin/clavulanic acid, tetracycline, doxycycline, gentamicin, spectinomycin, sulfisoxazole, trimethoprim/sulfamethoxazole, ceftiofur, ceftazidime, florfenicol, enrofloxacin, ofloxacin, colistin, meropenem, and mequindox from among livestock antibiotics, and ampicillin, ampicillin/sulbactam, tetracycline, chloramphenicol, trimethoprim/sulfamethoxazole, cefazolin, cefotaxime, ceftazidime, cefoxitin, gentamicin, imipenem, nalidixic acid, azithromycin, sulfisoxazole, ciprofloxacin, amoxicillin/clavulanate, Cefotaxime/clavulanate, ceftazidime/clavulanate, colistin, polymyxin B, minocycline, amikacin, aztreonam, cefepime, meropenem, levofloxacin, doxycycline, kanamycin, streptomycin, and gemifloxacin from among medical antibiotics.
Whole genome sequencing, assembly and annotation
After genomic DNA extraction and quality checks, a 20-kb fragment library was constructed for the sample when the concentration and purity met the sequencing requirements. Whole-genome sequencing was performed using a PacBio RS II instrument . The assembly of the reads was performed following the Hierarchical Genome Assembly Process (HGAP) workflow . In this process, the Celera Assembler, following the OLC algorithm, was used to assemble the sequences , and Quiver was used to optimize the assembly results . The gene prediction and annotation of the genomes was performed using the NCBI Prokaryotic Genome Annotation Pipeline . The complete genome of the ECCRA-119 isolate was deposited in GenBank under the accession numbers CP029242 (chromosome), CP029243 (plasmid pTB201), CP029244 (plasmid pTB202) and CP029245 (plasmid pTB203).
CRISPRfinder (https://crispr.i2bc.paris-saclay.fr/Server/) was used to search for CRISPR loci in the genome of the ECCRA-119 isolate . MLST 2.0 (https://cge.cbs.dtu.dk/services/MLST/) was used to determine the ST . The plasmid replicon types were identified using PlasmidFinder-1.3 (https://cge.cbs.dtu.dk/services/PlasmidFinder/) . Acquired antimicrobial resistance genes were predicted using ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/) . VirulenceFinder (https://cge.cbs.dtu.dk/services/VirulenceFinder/) was used to identify the virulence factors , and oriTfinder (http://18.104.22.168/oriTfinder/oriTfinder.html) was used to identify the origin of transfer in the genome . The genome was investigated for metal resistance genes using the Antibacterial Biocide and Metal Resistance Genes Database (BacMet) (http://bacmet.biomedicine.gu.se/) . Easyfig  and BIRG  were used in the comparative analysis of the plasmids. Phylogenetic analysis of genome and plasmids was performed by KSNP based on the maximum-likelihood method . Clustal X was used to perform the alignment analysis of blaNDM based on nucleotide sequences . The phylogenetic tree was generated used in MEGA X  and iTOL .
Plasmid conjugation experiments were performed on the ECCRA-119 isolate as described previously by Lin et al. [23, 61]. A rifamycin-resistant E. coli EC600 strain was used as the recipient in the plasmid conjugation assay to test the transferability of the carbapenem resistance gene and other resistance genes harbored by the ECCRA-119 isolate. Briefly, transconjugants were selected on LB agar plates (Landbridge., Beijing, China) supplemented with rifamycin (400 mg/L) (Sangon Biotech., Shanghai, China) and meropenem (4 mg/L) (J&K Chemical Ltd., Shanghai, China). The transfer frequencies were calculated by dividing the number of colony-forming units (CFUs) of transconjugants by the number of CFUs of the recipients. Genome DNA was extracted from the E. coli transconjugant using a bacterial DNA extract kit (Generay, Shanghai, China). The blaNDM-5 primers (F: 5′-GTCTGGCAGCACACTTCCTA-3′; R: 5′- TAGTGCTCAGTGTCGGCATC-3′) were used to confirm that the transconjugant harbored the plasmid.
S1-PFGE was performed according to a standard protocol using the contour-clamped homogeneous electric field (CHEF) technique with 0.5 × TBE buffer . Salmonella enterica serotype Braenderup H9812 was used as a size marker . The gels were run at 6 V/cm and 14 °C with an angle of 120°, and initial and final pulses were set at 2.16 and 63.8 s, respectively. The running time was 16 h using the CHEF apparatus (CHEF MAPPER XA; Bio-Rad, USA).
In this study, we reported the isolation and characterization of a carbapenem-resistant E. coli strain ST156 harboring the blaNDM-5 gene from a layer hen farm in Zhejiang province, China. Three plasmids in ECCRA-119 were identified based on whole genome sequencing and S1-PFGE. Twenty-two acquired resistance genes were identified, and this finding is consistent with the MDR phenotype of strain ECCRA-119. In particular, the blaNDM-5 gene has a high risk of spreading widely due to the potential transfer ability of the IncX3 plasmid pTB203 in this strain. The results of our study may reflect the level of antimicrobial resistance in poultry breeding in Zhejiang province and increase our knowledge of the presence and transmission of the blaNDM-5 gene.
We would like to thank Shanghai Biofosun Biotech Co. Ltd. for providing antibiotic susceptibility test assistance.
This work was financially supported by the Public Welfare Technology Applied Research Projects in Zhejiang Province Project (2017C32021), the Natural Science Foundation for the Youth (31700007), the Youth Talent Training and International Cooperation program of Zhejiang Academy of Agricultural Sciences (2017R19R08E01), the Key research and development plan of Zhejiang Province (2015C02041) and the State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control (2011DS700124-ZZ1703). The funding bodies had no role in the design of the study, in the collection, analysis, interpretation of data, or in the writing of the manuscript.
Availability of data and materials
All of the data generated or analyzed during this study are included in this article and its supplementary information files. The genome sequence of Escherichia coli ECCRA-119 has been deposited in the GenBank database under accession numbers CP029242, CP029243, CP029244 and CP029245.
BT, JC, LJC, QXL, HX, MRQ, XFJ and QYZ conducted laboratory testing. JC, BT and WTL participated in the writing and revision of the manuscript. BT, XDX and HY supervised the laboratory testing and participated in the writing of the manuscript. All authors have read and approved the manuscript.
Ethics approval and consent to participate
For convenient sampling, fecal samples were collected for bacterial isolation after the farmer’s verbal consent. All of the activities in our study were approved by institutional review board of Zhejiang Academy of Agricultural Sciences.
Consent for publication
The authors declare that they have no competing interests.
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