Skip to main content
Download PDF

Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring blaNDM-5 in E. Coli ST167: implications for antibiotic resistance management

BMC Microbiology volume 24, Article number: 178 (2024) Cite this article

Abstract

Background

The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5-carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China.

Results

Phenotypic and genotypic evaluations confirmed that the E. coli ST167 strain GZ04-0083 is a multidrug-resistant organism, showing resistance to diverse classes of antibiotics including ß-lactams, carbapenems, fluoroquinolones, aminoglycosides, and sulfonamides, while maintaining susceptibility to monobactams. Investigations involving S1 pulsed-field gel electrophoresis, Southern blot analysis, and conjugation experiments, alongside genomic sequencing, confirmed the presence of the blaNDM-5 gene within a 146-kb IncFIB plasmid pNDM-5-0083. This evidence underscores a significant risk for the horizontal transfer of resistance genes among bacterial populations. Detailed annotations of genetic elements—such as resistance genes, transposons, and insertion sequences—and comparative BLAST analyses with other blaNDM-5-carrying plasmids, revealed a unique architectural configuration in the pNDM-5-0083. The MDR region of this plasmid shares a conserved gene arrangement (repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-aadA2-dfrA12) with three previously reported plasmids, indicating a potential for dynamic genetic recombination and evolution within the MDR region. Additionally, the integration of virulence factors, including the iro and sit gene clusters and enolase, into its genetic architecture poses further therapeutic challenges by enhancing the strain’s pathogenicity through improved host tissue colonization, immune evasion, and increased infection severity.

Conclusions

The detailed identification and characterization of pNDM-5-0083 enhance our understanding of the mechanisms facilitating the spread of carbapenem resistance. This study illuminates the intricate interplay among various genetic elements within the novel blaNDM-5-carrying plasmid, which are crucial for the stability and mobility of resistance genes across bacterial populations. These insights highlight the urgent need for ongoing surveillance and the development of effective strategies to curb the proliferation of antibiotic resistance.

Peer Review reports

Background

Multi-drug-resistance (MDR) bacterial pathogens have been increasing worldwide and is now considered a significant public health threat. Several recent studies have documented the emergence of MDR Enterobacteriaceae from various sources [1,2,3,4,5,6,7], underscoring the need for proper antibiotic use. Besides, routine antimicrobial susceptibility testing is crucial to determine the most effective antibiotic treatments and to monitor the spread of emerging MDR strains. According to recent surveillance, the World Health Organization (WHO) has ranked carbapenemase-producing Enterobacteriaceae (CPE) as the third MDR bacteria in priority level one [8, 9], due to their ability to resist carbapenems which considered the last line of defense against MDR infections [4, 10]. These pathogens, including prominent species like Klebsiella pneumoniae and Escherichia coli (E. coli), have shown a disturbing increase in prevalence across various regions worldwide [11, 12]. This surge is largely driven by the acquisition and dissemination of carbapenemase genes such as blaKPC, blaNDM, and blaOXA [13, 14], which confer high-level resistance to nearly all ß-lactams, including carbapenems.

To date, 24 variants of the New Delhi metallo-ß-lactamase (NDM) gene have been identified in bacteria harboring blaNDM across the globe [13, 15,16,17], in which the NDM-5 is one of the most common variants encountered among Enterobacteriaceae with highly restricted availability of sensitive antibiotics [18]. Although reports of CPE carrying blaNDM-5 from various regions have attracted widespread attention [18,19,20], its genetic backgrounds are highly conserved and often located on mobile genetic elements as well as virulence factors that facilitate their spread [21].

Mobile elements such as insertion sequences and transposons are pivotal in the homologous recombination processes that boost the adaptability and survival of CPE. These genetic elements facilitate the acquisition and dissemination of antimicrobial resistance genes and contribute to the structural rearrangement of plasmids, impacting the fitness and virulence of bacterial pathogens [22, 23]. For example, insertion sequences like IS26 can initiate the formation of composite transposons that harbor multiple resistance genes, complicating the treatment of infections caused by these bacteria [24, 25]. Additionally, the incorporation of toxin-antitoxin systems and virulence factors, such as the pemK/pemI, iro, and sit gene clusters, into these plasmids enhances the pathogenic potential of bacteria. These elements help bacteria more effectively colonize host tissues, evade immune responses, and increase the severity of infections [26,27,28,29]. Otherwise, both resistance and virulence genes play crucial roles in the formation of biofilms, which significantly contribute to bacterial resistance to antibiotics through multiple mechanisms, including limited antibiotic penetration, nutrient limitation, slow growth, and adaptive stress responses [30, 31]. Therefore, studying the mobile genetic elements and virulence factors within plasmids provides crucial insights that can help prevent and treat infections associated with clinical multidrug-resistant strains harboring the blaNDM-5.

This study aims to thoroughly characterize a MDR plasmid harboring the blaNDM-5 gene in an E. coli isolate, emphasizing the elucidation of its genetic architecture and the mechanisms underlying the spread of this resistance factor. Specifically, the research focuses on analyzing the origins and consequences of homologous recombination within the MDR region of the plasmid, as well as the roles played by mobile genetic elements and virulence factors in the dissemination of resistance. By gaining a deeper understanding of these mechanisms, this study seeks to contribute substantially to the development of more effective strategies for managing and controlling the spread of CPE infections, thereby addressing an urgent need in the field of antibiotic resistance management.

Materials and methods

Isolation and identification of strain GZ04-0083

Strain GZ04-0083 was found in a stool specimen collected from a 37-year-old male patient with renal insufficiency who had been undergoing peritoneal dialysis for over five years. The patient was admitted to the intensive care unit (ICU) of Zhongshan City People’s Hospital in Zhongshan, Guangdong Province of China due to dialysis-related peritonitis, fever, and severe diarrhea. Fecal swabs were inoculated onto blood agar plates (KMJ, Shanghai, China) and incubated at 37? overnight to promote growth. Using sterile loop, single colony was streaked onto MacConkey agar (CRmicrobio, Jiangmen, China) and incubated at 37? for 18–24 h to isolate gram-negative bacteria as described by Kelly. M. T et al. [32]. Suspected E. coli colonies were adjusted to a 0.5 McFarland standard for consistency and subsequently confirmed through biochemical assays using the Vitek-2 compact system (bioMérieux, Marcy-l’Étoile, France). This system evaluates various enzymatic activities characteristic of E. coli, following both the manufacturer’s guidelines and the established clinical procedures detailed by Perez-Vazquez, M [33]. Ethical approval for this study was obtained from the Clinical Research and Laboratory Animal Ethics Committee of Zhongshan People’s Hospital (approval #K2022-008).

Antimicrobial susceptibility test

The antimicrobial susceptibility was assessed using the Vitek-2 compact system and minimum inhibitory concentration (MIC) test strips. E. coli ATCC 25,922 served as the control strain, with result analysis adhering to Clinical and Laboratory Standards Institute (CLSI) guidelines [34]. Briefly, colonies confirmed as E. coli, along with the control strain, were standardized to a 0.5 McFarland turbidity. This suspension was further diluted with 3 ml of 0.45% NaCl and 145 µL of bacterial suspension. The diluted sample was then processed using the AST-N334 card in the Vitek-2 system, according to the manufacturer’s instructions.

MIC values for various antibiotic classes, including ß-lactams, carbapenems, fluoroquinolones, and aminoglycosides as listed in Table 1, were determined using MTS. Briefly, the bacterial suspension was evenly spread on a Mueller-Hinton agar plate (Detgerm, Guangzhou, China), and MIC test strips (MTS, Liofilchem, Italy) were carefully placed on the agar surface. After incubating at 37 °C for 16–20 h, MIC values were read where the edge of the inhibition zone met the scale on the test strips. Results were categorized as susceptible (S), intermediate (I), or resistant (R). The isolates were classified as MDR, characterized by resistance to at least one agent in three or more antibiotic classes as defined by Magiorakos et al. [35]. The Multiple Antibiotic Resistance (MAR) Index was calculated by dividing the number of antibiotics to which the organism shows resistance by the total number of antibiotics tested, in accordance with Pauls et al. description [36] and CLSI guidelines.

Table 1 Antibiotic susceptibility results of E. coli GZ04-0083 isolate
Full size table

S1 pulsed-field gel electrophoresis, southern blot, and conjugation experiment

S1 endonuclease (Takara, Dalian, China) was used to analyze the bacterial genomic DNA of strain GZ04-0083. Pulsed-field gel electrophoresis (PFGE) was performed in a CHEF-DRIII system (Bio-Rad, Hercules, USA) to isolate DNA fragments and analyze the band patterns to obtain PFGE profiles at 6 V/cm with an initial pulse time of 0.22 s and a final pulse time of 26.29 s for 15 h. The separated plasmid DNA was transferred to a 0.45 µm positively charged nylon membrane (Solabio, Beijing, China) and hybridized with a digoxigenin-labeled DNA probe specific to the blaNDM-5 gene. The southern blot experiment was performed according to the manufacturer’s manual of the DIG High Prime DNA Labeling and Detection Start Kit I (Roche, Indianapolis, USA).

A conjugation experiment was conducted to assess the transferability of the resistance plasmids. The experiment was conducted with GZ04-0083 as donors and the sodium-azide-resistant E. Coli J53 as recipient. Firstly, GZ04-0083 was mixed with J53 at a ratio of 4:1 using a filter (0.22-µm pore size) mating assay, and the filter was incubated on a BHI agar (KMJ, Shanghai, China) at 37 °C overnight. Secondly, the transconjugants were selected on BHI agar plates supplemented with 4 mg/ml meropenem and 200 mg/ml sodium azide after 72 h of incubation, and the conjugation frequency was calculated as the ratio of transconjugants to recipient cells. Lastly, the plasmids in transconjugants were also confirmed by S1-PFGE.

Plasmid sequencing and bioinformatics analysis

The whole genomic DNA of GZ04-0083 was extracted from cultured bacteria using the High Pure PCR Template Preparation Kit (Roche, Basel, Switzerland), following the manufacturer’s instructions. Second-generation and nanopore sequencing was performed through the Illumina MiSeq sequencing platform and the Oxford Nanopore MinION sequencer, respectively.

The chromosome and plasmids were assembled using Unicycler (v0.4.8) to yield the complete gene sequences [37]. Seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA) of E. Coli GZ04-0083 were matched by the MLST website server (https://mlst.warwick.ac.uk/mlst/dbs/Ecoli) to obtain the sequence number of each allele and identify the multi-locus sequence typing of the strain [38].

The genomic sequences of the plasmids were annotated using the RAST Server and Protein BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) [39, 40], and the plasmids were indexed with the ISFinder database (https://www-is.biotoul.fr/) [41] for transposons, insertion sequences, and other structures in the genetic environment were identified. Plasmid Finder was used to identify the plasmids for the replication type (https://cge.cbs.dtu.dk/services/PlasmidFinder) [42]. The virulence-related genes in bacterial and plasmid genomes were identified by VFDB Blast (http://www.mgc.ac.cn/VFs) [43]. Inkscape 1.0 was used to map the overall structure of the plasmids, the fine structure comparison of the multi-resistant regions, and the near-source linear structural comparison of the multi-resistant regions of the plasmids. Sequence comparison and map generation were performed using BLAST (http://blast.ncbi.nlm.nih.gov) and Easyfig (version 2.1), respectively [44].

Results

Phenotypic multidrug resistance of E. coli Strain GZ04-0083

To present the phenotypic characteristics and antimicrobial resistance profile of the E. coli strain GZ04-0083 recovered from a clinical sample, antimicrobial susceptibility test was performed using both AST-N334 susceptibility card read by Vitek-2 and MIC test strips. In the analysis of 19 antibiotics, the E. coli strain GZ04-0083 exhibited resistance to a variety of commonly used antibiotics across different classes. It was resistant to ß-lactams, including ampicillin and ceftriaxone; carbapenems, such as ertapenem and imipenem; fluoroquinolones, including ciprofloxacin and levofloxacin; and aminoglycosides like amikacin and gentamicin. In contrast, the strain remained susceptible to the monobactam antibiotic aztreonam and exhibited intermediate resistance to nitrofurantoin. The detailed resistance profile is presented in Table 1. According to the criteria established by Magiorakos et al., strain GZ04-0083 is classified as a MDR strain, with the MAR index of 0.89.

Identification of a bla NDM-5 Carrying Plasmid in GZ04-0083 isolate

The antimicrobial susceptibility testing indicated that the GZ04-0083 isolate might resist carbapenems by producing ß-lactamase. To determine the genetic basis of carbapenem resistance in the GZ04-0083 isolate and assess its potential for horizontal gene transfer among Enterobacteriaceae, the S1-PGFE analysis revealed the presence of three plasmids (about 140, 80, and 30 kb, respectively) in GZ04-0083, and the blaNDM-5 gene was found in the 140-kb plasmid by southern blot (Fig. 1and Supplementary Figs. 1 and 2). Further conjugation experiment suggested that the blaNDM-5-carrying plasmid was able to transfer from the donor strain GZ04-0083 to the recipient E. coli J53 strain with meropenem and sodium azide as co-selection markers, and the conjugation frequency was 3.38 ± 0.82 × 10-5 per recipient. Accordingly, the GZ04-0083 isolate demonstrated multidrug resistance characteristics, evidenced by its resistance to a broad spectrum of antibiotics, including carbapenems, and the presence of the blaNDM-5 gene on a 140-kb plasmid capable of conjugative transfer to other Enterobacteriaceae.

Fig. 1
figure 1

S1-PFGE and Southern blot of strain GZ04-0083. The left lane is the marker of the S1-PFGE profile of the reference strain; the middle lane of the S1-PFGE is a result of strain GZ04-0083 S1 enzymatically cleaved plasmid DNA; the right lane is southern blot hybridization of the blaNDM-5-specific probe

Full size image

Genome sequencing results confirming the presence of the NDM resistance gene

Whole-genome sequencing was conducted to validate the plasmid data and ascertain the molecular type of the E. coli GZ04-0083 strain. By assembling both short Illumina reads and long PromethION reads with Unicycler (v0.4.8), we established that the GZ04-0083 strain’s genome consists of a single chromosome (4.91 Mb) and three plasmids (146, 89, and 27 kb). MLST analysis classified the GZ04-0083 isolate as ST167, the predominant clone among NDM-producing E. coli strains in China. A BLAST alignment of blaNDM-1 and blaNDM-5 with the GZ04-0083 nucleotide sequence confirmed the presence of the blaNDM-5 gene within the 146-kb plasmid, aligning with the Southern blot findings presented in Fig. 1. A further plasmid MLST analysis identified the 14-kb blaNDM-5-carrying plasmid as an IncFIB-type plasmid with a linear topology, which was designated as pNDM-5-0083.

Genotypic multidrug resistance of E. coli Strain GZ04-0083

To explore the relationship between phenotypic resistance and genotypic features in the GZ04-0083 isolate, our analysis extended beyond the identification of the blaNDM-5-carrying plasmid. Table 1 demonstrates that the E. coli GZ04-0083 isolate exhibits a robust multidrug-resistant profile, supported by both phenotypic and genotypic evidence. Chromosomally encoded genes such as gyrA and parC are associated with fluoroquinolone resistance [45], while nfsA and nfsB contribute to decreased susceptibility to nitrofurantoin [46], underlying the strain’s inherent resistance mechanisms. Moreover, the pNDM-5-0083 plasmid harbors additional resistance genes, enhancing the isolate’s capability to withstand various antibiotics. These genes include blaNDM-5, which confers resistance to carbapenems, and blaTEM-1B, dfrA12, sul1, aadA2, and rmtB, which collectively provide resistance against ß-lactams, sulfonamides, trimethoprim, and aminoglycosides.

Genetic characterization of pNDM-5-0083 as a novel bla NDM-5-carrying plasmid

Studying the plasmid’s backbone and its array of mobile genetic elements and virulence factors will help elucidate the mechanisms underlying the propagation of resistance traits. Consequently, using ISFinder, PlasmidFinder and VFDB Blast for annotation, several key elements were identified in the plasmid, especially in the MDR region (Fig. 2). The backbone region of pNDM-5-0083 included a replication protein (repA), stabilization proteins (parA and parB), a conjugative splice transfer system of plasmids (traABCDEFGHIJKLMNPQRSTUVWY and trbABCDEFGIJ) and iron transporters as virulence factors (iroBCDEN, lucABC, and sitABCD). Within and surrounding the MDR region, the plasmid harbored another replication protein (repA2), resistance genes (blaNDM-5, blaTEM-1B, suI1, dfrA12, tetA, aadA2, and rmtB), transposon elements (intI1, Tn21, and Tn3), insertion sequences (IS15DIV, IS26, IS30, IS91, and insBCDOL) and a chaperone protein (GroEL) which are associated with resistance genes transmission. In addition, the pNDM-5-0083 plasmid also harbors a toxin-antitoxin system (pemK/pemI) and other virulence genes, including colicin-M and enolase.

Fig. 2
figure 2

Gene structure of E. Coli GZ04-0083 carrying plasmid pNDM-5-0083. The outer ring represents the annotation of the plasmid, and the genes are annotated with different colors according to their functions. Yellow represents transfer RNA (TransferRNA, tRNA); red represents ribosomal RNA (rRNA); blue-purple CDS (CondingSequence) is in mRNA, protein-coding region; black GC Content represents the content of the plasmid; GC Shew represents plasmid bias and measures the G versus C content of single-stranded DNA in the plasmid: Green GC Shew + represents plasmid single-stranded DNA with greater G content than C. Purple GC Shew- represents plasmid single-stranded DNA with less G content than C. Red frame represents pNDM-5-0083 plasmid carrying resistance genes

Full size image

To clarify whether the pNDM-5-0083 had fragments of different evolutionary origins, the pNDM-5-0083 plasmid was BLAST-matched in the NCBI database to screen for plasmids with homology to the pNDM-5-0083 plasmid (Fig. 3). The results revealed that pNDM-5-0083 shared a 99.89% identity with 79% query coverage to pCTXM-2271 plasmid (GenBank accession number MF589339.1) which is known MDR plasmid isolated from E. coli strain 2271 [47], and a 99.96% identity with 83% query coverage to plasmid A (CP010149.1) which was identified in E. coli strain D6 from dog. The high sequence identities but partial query coverages, particularly in the MDR region, indicate that pNDM-5-0083, while closely related to these known plasmids, likely contains unique genetic elements do not present in the aligned plasmids. This partial alignment suggests that pNDM-5-0083 may harbor unique sequences that contribute to its unique resistance profile, meriting further investigation to fully understand its role in antimicrobial resistance.

Fig. 3
figure 3

Genomic comparison of pNDM-5-0083 with pCTXM-2271 (GenBank accession number MF589339.1) as well as the plasmid A plasmid (GenBank accession number CP010149.1). The blue color indicates resistance genes, and each arrow represents one gene. The depth of grey shading indicates the similarity of each part of the genome with the sequence of the pNDM-5-0083 genome. The darker the shade of grey, the higher the degree of similarity. The graph shows fragments with at least 65% similarity, so fragments below this threshold are not shown

Full size image

Comparative analysis of the MDR Region in pNDM-5-0083

To elucidate the evolutionary dynamics of the MDR region in the pNDM-5-0083 plasmid, we profiled gene clusters analogous to the MDR region of pNDM-5-0083 and constructed a linear analysis of these gene clusters. As shown in Fig. 4, the analysis revealed that the MDR region of pNDM-5-0083 encompasses seven drug resistance genes: blaNDM-5, blaTEM-1B, bleMBL, sul2, aadA2, and drfA12. BLAST comparison showed high similarity between the MDR region of pNDM-5-0083 and those of pNDM-d2e9 (CP026201.1), pLZ135-NDM (MF353156.1), and Plasmid unnamed2 (CP104348.1), which are associated with CPE isolates. These plasmids share a conserved gene arrangement: repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-addA2-dfrA12, featuring identical resistance genes and insertion sequences. This consistent arrangement highlights a common evolutionary origin and suggests a mechanism for the persistence and propagation of resistance traits among these plasmids.

Fig. 4
figure 4

Comparison of the MDR region gene clusters of pNDM-5-0083, pNDM-d2e9, pLZ135-NDM, and Plasmid unnamed2. Arrows indicate open reading frames (ORFs) and transcriptional direction. Green arrows indicate the replicons (repA encodes the replication initiation protein). Black arrows indicate the insertion sequence (IS) of mobile elements. Red arrows indicate drug resistance genes (blaNDM-5, blaTEM-1B, and bleMBL). Blue arrows indicate stability-related genes and hypothetical protein-coding genes. Grey shading indicates regions of high homology between the four plasmids. Plasmid pNDM-d2e9 is derived from the Escherichia coli ECONIH6 strain. Plasmid pLZ135-NDM is derived from E. coli. Plasmid unnamed2 is derived from E. coli strain FDAARGOS_433

Full size image

Discussion

In recent years, blaNDM-5-producing E. coli ST167 has been reported across various countries and regions globally [48,49,50,51,52]. Researchers indicates that the blaNDM-5 resistance gene in E. coli tends to spread through a plasmid-mediated horizontal transmission [53], significantly contributing to the rapid proliferation of this resistance gene among E. coli population. Whole-genome sequencing analysis can enhance our understanding of the mechanisms behind the spread of blaNDM-5, providing detailed insights into the mobile genetic elements that facilitate this transmission and the evolutionary pressures that drive the dissemination of resistance across different environments [54].

The pNDM-5-0083 plasmid harbored seven resistance genes, including blaNDM-5, blaTEM-1B, dfrA12, suI1, tet(A), aadA2, and rmtB, which has similarities to a strain of E. coli isolated from urine sample carrying blaNDM-5 [55], indicating a rise in the prevalence of MDR E. coli strains. Although pNDM-5-0083 closely resembles pCTXM-2271, another multidrug-resistant plasmid found in E. coli, it shares common elements such as the mobile insertion sequence IS91, the replication initiator repA, plasmid replication-associated gene parA, parB and IncF plasmid conjugative transfer protein trbABCDEGIJ, along with virulence factors like sitABCD and iroBCDEN involved in iron acquisition. However, pNDM-5-0083 lacks the floR resistance gene found in pCTXM-2271 and features a distinct MDR region that sets it apart from pCTXM-2271 [47].

Researchers discovered that the insertion sequences [56, 57], transposons [58] and integrons [59] play key roles in facilitating recombination events and extensive transfer of resistance genes. In pNDM-5-0083, the complex transposon structure repA-IsI5DIV-InsB-blaTEM1-RmtB-GroEL-IS26-IS30-blaNDM-5-bleMBL-IS91 includes the repA element which initiates replication of the MDR region. It is paired with the pemK/pemI toxin-antitoxin system, utilizing postsegregational killing to ensure plasmid stability during bacterial transfer [60]. Following this, IS15DIV, a member of the IS6 family similar to IS26 [61], is inserted, promoting duplications of target site sequences of MDR region alongside an integron InsB. This upstream arrangement in the MDR region—repA-pemK/I-IsI5DIV-InsB-blaTEM1-RmtB—is analogous to that in the unnamed plasmid A (CP104348.1). while the sequence IS26-IS30-blaNDM-5-bleMBL-IS91 is consistent with those in pNDM-d2e9 and pLZ135-NDM, highlighting a common strategy for the horizontal transfer and homologous recombination of the resistance genes blaTEM,blaNDM-5, and bleMBL under antibiotic pressure. This complex genetic architecture underscores the dynamic capability of IS15DIV, IS26, IS30 and IS91 elements to facilitate the spread and evolution of resistance genes across bacterial populations.

In addition, unlike these three homologous plasmids, pNDM-5-0083 contains the transposon Tn21 and integron intI1 at the 3’-end of its MDR region. Previous studies have confirmed that Tn21, known for harboring integrons like intI1 that incorporate aminoglycoside and beta-lactam resistance genes, is widespread among both clinical and environmental gram-negative isolates [62,63,64]. This highlights the crucial roles of intI1 and Tn21 as primary vectors in the dissemination of antibiotic resistance genes. The presence of these mobile genetic elements at the terminal end of the MDR region in pNDM-5-0083 suggests they may contribute to frequent homologous recombination events, resulting in a novel variable region compared to its related plasmids. Moreover, another integron insB and the molecular chaperone GroEL are integrated within the MDR region, enhancing the expression, and ensuring the proper folding of antibiotic resistance proteins, respectively. Together, the strategic incorporation of these elements within the MDR region not only augments the functionality of resistance genes but also plays a pivotal role in enhancing plasmid stability. It promotes the horizontal transfer of the multidrug resistance attributes between different plasmids and the widespread dissemination across various bacterial strains, while ensuring the effective and stable expression of resistance determinants.

In addition to the resistance genes located on both chromosomal and plasmid DNA, mechanisms of antibacterial resistance in E. coli often involve virulence factors that promote drug efflux and enhance biofilm formation [30, 31]. Biofilms contribute to antibiotic resistance by creating a protective environment that limits antibiotic penetration and supports the persistence of resistance genes within bacterial communities. In our study, chromosomally encoded virulence genes such as fdeC, yagX/ecpC, and vgrG/tssI were found to enhance bacterial adhesion to host cells, potentially facilitating biofilm formation [65,66,67]. Moreover, virulence determinants carried by the pNDM-5-0083 plasmid, such as the iron acquisition systems (e.g., the iro and sit gene families), may indirectly bolster biofilm maintenance by impacting the nutritional status and survival capabilities of the bacteria [68, 69]. While virulence factors like colicin M and enolase do not directly induce biofilm formation, they augment bacterial resilience to environmental stresses, thereby aiding the transmission and endurance of resistance genes [70, 71].

However, our study recognizes certain limitations, particularly the absence of gene editing experiments to confirm the functionality of mobile genetic elements and virulence factors within the plasmid post-annotation. Future research should prioritize experimental studies on biofilm formation to thoroughly investigate the intricate relationships between biofilm development, virulence factors, and antibiotic resistance. This approach will deepen our understanding of the mechanisms that facilitate the persistence and transmission of antibiotic-resistant E. coli strains. Additionally, infection control statistics from our institution from 2017 to 2023 have demonstrated a relatively stable CPE isolation rate, fluctuating between 2.5% and 5.4%. Within this dataset, the highest resistance rates for Klebsiella pneumoniae against imipenem and meropenem reached 5.8% and 6.8%, respectively, while for E. coli, they peaked at 1.2% and 1.4%. Compared to the data from the China Antimicrobial Resistance Surveillance System (CHINET), our institution’s rates of carbapenem-resistant Klebsiella pneumoniae are lower, whereas those of carbapenem-resistant E. coli align with national averages. Although the newly discovered balNDM-5-carrying plasmid has not increased the CPE isolation rate at our institution, this study still holds significant value for understanding and managing antibiotic resistance in a broader context.

Conclusion

This study presents a detailed analysis of pNDM-5-0083, a novel blaNDM-5-carrying plasmid discovered in an E. coli isolate. Our comprehensive genomic annotation and analysis shed light on the evolutionary dynamics of MDR region in pNDM-5-0083 and illuminated the genetic elements which might facilitate the genetic recombination to form a unique plasmid architecture. These insights highlight potential targets for combatting the spread of antibiotic resistance, emphasizing the importance of understanding plasmid dynamics in microbial resistance mechanisms.

Availability of data and materials

Sequence data generated for this study have been uploaded in the NCBI GenBank, CP140466 to CP140469. The public data used in this study were CP026201.1, MF353156.1, CP104348.1, MF589339.1, and CP010149.1, respectively.

Abbreviations

AmpC:

AmpC ß-lactamase

BLAST:

the basic local alignment search tool

CLSI:

Clinical and Laboratory Standards Institute

CPE:

carbapenemase-producing Enterobacteriaceae

E. coli :

Escherichia coli

ESBL:

extended-spectrum ß-lactamase

ICU:

intensive care unit

MIC:

minimum inhibitory concentration

MLST:

multi-locus sequence typing

MTS:

minimum inhibitory concentration test strips

NDM :

New Delhi metallo-ß-lactamase

PFGE:

pulsed-field gel electrophoresis

References

  1. Algammal AM, Wahdan A, Elhaig MM. Potential efficiency of conventional and advanced approaches used to detect Mycobacterium bovis in cattle. Microb Pathog. 2019;134:103574.

    Article  PubMed  Google Scholar 

  2. Shafiq M, Zeng M, Permana B, Bilal H, Huang J, Yao F, et al. Coexistence of bla (NDM-5) and tet(X4) in international high-risk Escherichia coli clone ST648 of human origin in China. Front Microbiol. 2022;13:1031688. https://doi.org/10.3389/fmicb.2022.1031688.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Elbehiry A, Marzouk E, Aldubaib M, Moussa I, Abalkhail A, Ibrahem M, et al. Pseudomonas species prevalence, protein analysis, and antibiotic resistance: an evolving public health challenge. AMB Express. 2022;12(1):53. https://doi.org/10.1186/s13568-022-01390-1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Algammal AM, Ibrahim RA, Alfifi KJ, Ghabban H, Alghamdi S, Kabrah A, et al. A first report of molecular typing, virulence traits, and phenotypic and genotypic resistance patterns of newly emerging XDR and MDR Aeromonas veronii in Mugil Seheli. Pathogens. 2022;11(11):1262.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Algammal AM, El-Tarabili RM, Alfifi KJ, Al-Otaibi AS, Hashem MEA, El-Maghraby MM, et al. Virulence determinant and antimicrobial resistance traits of emerging MDR Shiga toxigenic E. coli in diarrheic dogs. AMB Express. 2022;12(1):34. https://doi.org/10.1186/s13568-022-01371-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Algammal AM, El-Tarabili RM, Abd El-Ghany WA, Almanzalawi EA, Alqahtani TM, Ghabban H, et al. Resistance profiles, virulence and antimicrobial resistance genes of XDR S. Enteritidis and S. Typhimurium. AMB Express. 2023;13(1):110. https://doi.org/10.1186/s13568-023-01615-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Algammal AM, Abo Hashem ME, Alfifi KJ, Al-Otaibi AS, Alatawy M, ElTarabili RM, et al. Sequence analysis, Antibiogram Profile, Virulence and Antibiotic Resistance genes of XDR and MDR Gallibacterium anatis isolated from layer chickens in Egypt. Infect Drug Resist. 2022;15:4321–34. https://doi.org/10.2147/IDR.S377797.

    Article  PubMed  PubMed Central  Google Scholar 

  8. WHO priority pathogens list for R&D of new antibiotics. 2017. http://www.who.int/mediacentre/news/releases/2017/bacteria-antibiotics-needed/en/. Accessed 27 Feb 2017.

  9. van Duin D, Arias CA, Komarow L, Chen L, Hanson BM, Weston G, et al. Molecular and clinical epidemiology of carbapenem-resistant enterobacterales in the USA (CRACKLE-2): a prospective cohort study. Lancet Infect Dis. 2020;20(6):731–41. https://doi.org/10.1016/S1473-3099(19)30755-8.

    Article  PubMed  PubMed Central  Google Scholar 

  10. Suay-Garcia B, Perez-Gracia MT. Present and Future of Carbapenem-resistant Enterobacteriaceae (CRE) Infections. Antibiotics (Basel). 2019;8(3). https://doi.org/10.3390/antibiotics8030122.

  11. Tran DM, Larsson M, Olson L, Hoang NTB, Le NK, Khu DTK, et al. High prevalence of colonisation with carbapenem-resistant Enterobacteriaceae among patients admitted to Vietnamese hospitals: risk factors and burden of disease. J Infect. 2019;79(2):115–22. https://doi.org/10.1016/j.jinf.2019.05.013.

    Article  PubMed  Google Scholar 

  12. Oldenkamp R, Schultsz C, Mancini E, Cappuccio A. Filling the gaps in the global prevalence map of clinical antimicrobial resistance. Proc Natl Acad Sci U S A. 2021;118(1):e2013515118.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Tekeli A, Dolapci I, Evren E, Oguzman E, Karahan ZC. Characterization of Klebsiella pneumoniae coproducing KPC and NDM-1 carbapenemases from Turkey. Microb Drug Resist. 2020;26(2):118–25. https://doi.org/10.1089/mdr.2019.0086.

    Article  CAS  PubMed  Google Scholar 

  14. Lee H, Shin J, Chung YJ, Park M, Kang KJ, Baek JY, et al. Co-introduction of plasmids harbouring the carbapenemase genes, bla(NDM-1) and bla(OXA-232), increases fitness and virulence of bacterial host. J Biomed Sci. 2020;27(1):8. https://doi.org/10.1186/s12929-019-0603-0.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Hu F, Guo Y, Yang Y, Zheng Y, Wu S, Jiang X, et al. Resistance reported from China antimicrobial surveillance network (CHINET) in 2018. Eur J Clin Microbiol Infect Dis. 2019;38(12):2275–81. https://doi.org/10.1007/s10096-019-03673-1.

    Article  CAS  PubMed  Google Scholar 

  16. Tamma PD, Goodman KE, Harris AD, Tekle T, Roberts A, Taiwo A, et al. Comparing the outcomes of patients with carbapenemase-producing and non-carbapenemase-producing Carbapenem-Resistant Enterobacteriaceae Bacteremia. Clin Infect Dis. 2017;64(3):257–64. https://doi.org/10.1093/cid/ciw741.

    Article  CAS  PubMed  Google Scholar 

  17. Liu Z, Li J, Wang X, Liu D, Ke Y, Wang Y, et al. Novel variant of New Delhi metallo-ß-lactamase, NDM-20, in Escherichia coli. Front Microbiol. 2018;9:248.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Zhu YQ, Zhao JY, Xu C, Zhao H, Jia N, Li YN. Identification of an NDM-5-producing Escherichia coli sequence type 167 in a neonatal patient in China. Sci Rep. 2016;6(1):29934.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Bleichenbacher S, Stevens MJA, Zurfluh K, Perreten V, Endimiani A, Stephan R, et al. Environmental dissemination of carbapenemase-producing Enterobacteriaceae in rivers in Switzerland. Environ Pollut. 2020;265(Pt B):115081.

    Article  CAS  PubMed  Google Scholar 

  20. Alba P, Taddei R, Cordaro G, Fontana MC, Toschi E, Gaibani P, et al. Carbapenemase IncF-borne bla(NDM-5) gene in the E. coli ST167 high-risk clone from canine clinical infection, Italy. Vet Microbiol. 2021;256:109045. https://doi.org/10.1016/j.vetmic.2021.109045.

    Article  CAS  PubMed  Google Scholar 

  21. Kock R, Daniels-Haardt I, Becker K, Mellmann A, Friedrich AW, Mevius D, et al. Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals: a systematic review. Clin Microbiol Infect. 2018;24(12):1241–50. https://doi.org/10.1016/j.cmi.2018.04.004.

    Article  CAS  PubMed  Google Scholar 

  22. Wang J, Zeng ZL, Huang XY, Ma ZB, Guo ZW, Lv LC, et al. Evolution and Comparative Genomics of F33:A-:B- Plasmids Carrying bla(CTX-M-55) or bla(CTX-M-65) in Escherichia coli and Klebsiella pneumoniae Isolated from Animals, Food Products, and Humans in China. mSphere. 2018;3(4). https://doi.org/10.1128/mSphere.00137-18.

  23. Sharma VK, Akavaram S, Schaut RG, Bayles DO. Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7. BMC Genomics. 2019;20(1):196. https://doi.org/10.1186/s12864-019-5568-6.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Sun YW, Liu YY, Wu H, Wang LF, Liu JH, Yuan L, et al. IS26-flanked composite transposon Tn6539 carrying the tet(M) gene in IncHI2-Type conjugative plasmids from Escherichia coli isolated from ducks in China. Front Microbiol. 2018;9:3168. https://doi.org/10.3389/fmicb.2018.03168.

    Article  PubMed  Google Scholar 

  25. Singh NS, Singhal N, Virdi JS. Genetic environment of bla(TEM-1), bla(CTX-M-15), bla(CMY-42) and characterization of integrons of Escherichia coli isolated from an Indian urban aquatic environment. Front Microbiol. 2018;9:382. https://doi.org/10.3389/fmicb.2018.00382.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Agarwal S, Agarwal S, Bhatnagar R. Identification and characterization of a novel toxin-antitoxin module from Bacillus anthracis. FEBS Lett. 2007;581(9):1727–34. https://doi.org/10.1016/j.febslet.2007.03.051.

    Article  CAS  PubMed  Google Scholar 

  27. Sabri M, Leveille S, Dozois CM. A SitABCD homologue from an avian pathogenic Escherichia coli strain mediates transport of iron and manganese and resistance to hydrogen peroxide. Microbiol (Reading). 2006;152(Pt 3):745–58. https://doi.org/10.1099/mic.0.28682-0.

    Article  CAS  Google Scholar 

  28. Roshani M, Taheri M, Goodarzi A, Yosefimashouf R, Shokoohizadeh L. Evaluation of antibiotic resistance, toxin-antitoxin systems, virulence factors, biofilm-forming strength and genetic linkage of Escherichia coli strains isolated from bloodstream infections of leukemia patients. BMC Microbiol. 2023;23(1):327. https://doi.org/10.1186/s12866-023-03081-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Shah C, Baral R, Bartaula B, Shrestha LB. Virulence factors of uropathogenic Escherichia coli (UPEC) and correlation with antimicrobial resistance. BMC Microbiol. 2019;19(1):204. https://doi.org/10.1186/s12866-019-1587-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Srinivasan R, Santhakumari S, Poonguzhali P, Geetha M, Dyavaiah M, Xiangmin L. Bacterial biofilm inhibition: a focused review on recent therapeutic strategies for combating the Biofilm mediated infections. Front Microbiol. 2021;12:676458.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Sharma D, Misba L, Khan AU. Antibiotics versus biofilm: an emerging battleground in microbial communities. Antimicrob Resist Infect Control. 2019;8:76. https://doi.org/10.1186/s13756-019-0533-3.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Kelly MT, Stroh EM, Jessop J. Comparison of blood agar, ampicillin blood agar, MacConkey-ampicillin-tween agar, and modified cefsulodin-irgasan-novobiocin agar for isolation of Aeromonas spp. from stool specimens. J Clin Microbiol. 1988;26(9):1738–40. https://doi.org/10.1128/jcm.26.9.1738-1740.1988.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Perez-Vazquez M, Oliver A, Sanchez del Saz B, Loza E, Baquero F, Canton R. Performance of the VITEK2 system for identification and susceptibility testing of routine Enterobacteriaceae clinical isolates. Int J Antimicrob Agents. 2001;17(5):371–6. https://doi.org/10.1016/s0924-8579(01)00318-1.

    Article  CAS  PubMed  Google Scholar 

  34. CLSI. Performance Standards for Antimicrobial Susceptibility Testing. 32nd ed. CLSI supplement M100. Clinical and Laboratory Standards Institute; 2022.

  35. Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18(3):268–81. https://doi.org/10.1111/j.1469-0691.2011.03570.x.

    Article  CAS  PubMed  Google Scholar 

  36. Paul S, Bezbaruah RL, Roy MK, Ghosh AC. Multiple antibiotic resistance (MAR) index and its reversion in Pseudomonas aeruginosa. Lett Appl Microbiol. 1997;24(3):169–71. https://doi.org/10.1046/j.1472-765x.1997.00364.x.

    Article  CAS  PubMed  Google Scholar 

  37. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. https://doi.org/10.1371/journal.pcbi.1005595.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355–61. https://doi.org/10.1128/JCM.06094-11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9(1):75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Yang M, Derbyshire MK, Yamashita RA, Marchler-Bauer A. NCBI’s conserved domain database and tools for protein domain analysis. Curr Protoc Bioinf. 2020;69(1):e90. https://doi.org/10.1002/cpbi.90.

    Article  CAS  Google Scholar 

  41. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34(Database issue):D32-36. https://doi.org/10.1093/nar/gkj014.

    Article  CAS  PubMed  Google Scholar 

  42. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–903. https://doi.org/10.1128/AAC.02412-14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402. https://doi.org/10.1093/nar/25.17.3389.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27(7):1009–10. https://doi.org/10.1093/bioinformatics/btr039.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Nguyen KV, Nguyen TV, Nguyen HTT, Le DV. Mutations in the gyrA, parC, and mexR genes provide functional insights into the fluoroquinolone-resistant Pseudomonas aeruginosa isolated in Vietnam. Infect Drug Resist. 2018;11:275–82. https://doi.org/10.2147/IDR.S147581.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Wan Y, Mills E, Leung RCY, Vieira A, Zhi X, Croucher NJ, et al. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom. 2021;7(12). https://doi.org/10.1099/mgen.0.000702.

  47. Liu X, Li R, Chan EW, Chen S. Complete genetic analysis of plasmids carrying multiple resistance, virulence, and phage-like genes in Foodborne Escherichia coli isolate. Microbiol Spectr. 2023;11(2):e0282022. https://doi.org/10.1128/spectrum.02820-22.

    Article  CAS  PubMed  Google Scholar 

  48. Xu L, Wang P, Cheng J, Qin S, Xie W. Characterization of a novel bla (NDM-5)-harboring IncFII plasmid and an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate. Infect Drug Resist. 2019;12:511–9. https://doi.org/10.2147/IDR.S192998.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Garcia-Fernandez A, Villa L, Bibbolino G, Bressan A, Trancassini M, Pietropaolo V, et al. Novel insights and features of the NDM-5-Producing Escherichia coli sequence type 167 high-risk clone. mSphere. 2020;5(2):e00269-00220. https://doi.org/10.1128/mSphere.00269-20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Manyahi J, Moyo SJ, Kibwana U, Goodman RN, Allman E, Hubbard ATM, et al. First identification of bla (NDM-5) producing Escherichia coli from neonates and a HIV infected adult in Tanzania. J Med Microbiol. 2022;71(2):001513. https://doi.org/10.1099/jmm.0.001513.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Devanga Ragupathi NK, Veeraraghavan B, Muthuirulandi Sethuvel DP, Anandan S, Vasudevan K, Neeravi AR, et al. First Indian report on genome-wide comparison of multidrug-resistant Escherichia coli from blood stream infections. PLoS One. 2020;15(2):e0220428.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Peterhans S, Stevens MJ, Nüesch-Inderbinen M, Schmitt S, Stephan R, Zurfluh K. First report of a blaNDM-5-harbouring Escherichia coli ST167 isolated from a wound infection in a dog in Switzerland. J Global Antimicrob Resist. 2018;15:226–7.

    Article  Google Scholar 

  53. Li P, Wan P, Zhao R, Chen J, Li X, Li J, et al. Targeted elimination of bla (NDM-5) gene in Escherichia coli by Conjugative CRISPR-Cas9 System. Infect Drug Resist. 2022;15:1707–16. https://doi.org/10.2147/IDR.S357470.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Waddington C, Carey ME, Boinett CJ, Higginson E, Veeraraghavan B, Baker S. Exploiting genomics to mitigate the public health impact of antimicrobial resistance. Genome Med. 2022;14(1):15. https://doi.org/10.1186/s13073-022-01020-2.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Sun L, Xu J, He F. Draft genome sequence of an NDM-5, CTX-M-15 and OXA-1 co-producing Escherichia coli ST167 clinical strain isolated from a urine sample. J Glob Antimicrob Resist. 2018;14:284–6. https://doi.org/10.1016/j.jgar.2018.08.005.

    Article  PubMed  Google Scholar 

  56. Li X, He J, Jiang Y, Peng M, Yu Y, Fu Y. Genetic characterization and passage instability of a hybrid plasmid co-harboring bla(IMP-4) and bla(NDM-1) reveal the contribution of insertion sequences during plasmid formation and evolution. Microbiol Spectr. 2021;9(3):e0157721. https://doi.org/10.1128/Spectrum.01577-21.

    Article  PubMed  Google Scholar 

  57. Pedro L, Banos RC, Aznar S, Madrid C, Balsalobre C, Juarez A. Antibiotics shaping bacterial genome: deletion of an IS 91 flanked virulence determinant upon exposure to Subinhibitory antibiotic concentrations. PLoS One. 2011;6(11):e27606.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Nicolas E, Lambin M, Dandoy D, Galloy C, Nguyen N, Oger CA, et al. The Tn3-family of replicative transposons. Microbiol Spectr. 2015;3(4):693–726. https://doi.org/10.1128/microbiolspec.MDNA3-0060-2014.

    Article  CAS  Google Scholar 

  59. Colello R, Etcheverria AI, Di Conza JA, Gutkind GO, Padola NL. Antibiotic resistance and integrons in Shiga toxin-producing Escherichia coli (STEC). Braz J Microbiol. 2015;46(1):1–5. https://doi.org/10.1590/S1517-838246120130698.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Yeo CC, Abu Bakar F, Chan WT, Espinosa M, Harikrishna JA. Heterologous expression of toxins from bacterial toxin-antitoxin systems in eukaryotic cells: strategies and applications. Toxins (Basel). 2016;8(2):49. https://doi.org/10.3390/toxins8020049.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Harmer CJ, Moran RA, Hall RM. Movement of IS26-associated antibiotic resistance genes occurs via a translocatable unit that includes a single IS26 and preferentially inserts adjacent to another IS26. MBio. 2014;5(5):e01801-01814. https://doi.org/10.1128/mBio.01801-14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Johansson C, Boukharta L, Eriksson J, Aqvist J, Sundstrom L. Mutagenesis and homology modeling of the Tn21 integron integrase IntI1. Biochemistry. 2009;48(8):1743–53. https://doi.org/10.1021/bi8020235.

    Article  CAS  PubMed  Google Scholar 

  63. Zheng W, Huyan J, Tian Z, Zhang Y, Wen X. Clinical class 1 integron-integrase gene - A promising indicator to monitor the abundance and elimination of antibiotic resistance genes in an urban wastewater treatment plant. Environ Int. 2020;135:105372.

    Article  CAS  PubMed  Google Scholar 

  64. Bass L, Liebert CA, Lee MD, Summers AO, White DG, Thayer SG, et al. Incidence and characterization of integrons, genetic elements mediating multiple-drug resistance, in avian Escherichia coli. Antimicrob Agents Chemother. 1999;43(12):2925–9. https://doi.org/10.1128/AAC.43.12.2925.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Yi X, Yamazaki A, Biddle E, Zeng Q, Yang CH. Genetic analysis of two phosphodiesterases reveals cyclic diguanylate regulation of virulence factors in Dickeya dadantii. Mol Microbiol. 2010;77(3):787–800. https://doi.org/10.1111/j.1365-2958.2010.07246.x.

    Article  CAS  PubMed  Google Scholar 

  66. Ma J, Sun M, Pan Z, Lu C, Yao H. Diverse toxic effectors are harbored by vgrG islands for interbacterial antagonism in type VI secretion system. Biochim Biophys Acta Gen Subj. 2018;1862(7):1635–43. https://doi.org/10.1016/j.bbagen.2018.04.010.

    Article  CAS  PubMed  Google Scholar 

  67. Segura A, Auffret P, Bibbal D, Bertoni M, Durand A, Jubelin G, et al. Factors involved in the persistence of a Shiga Toxin-Producing Escherichia coli O157:H7 strain in bovine feces and gastro-intestinal content. Front Microbiol. 2018;9:375.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Wang L, Yan J, Wise MJ, Liu Q, Asenso J, Huang Y, et al. Distribution patterns of polyphosphate metabolism pathway and its relationships with bacterial durability and virulence. Front Microbiol. 2018;9:782.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Gahamanyi N, Song DG, Yoon KY, Mboera LEG, Matee MI, Mutangana D, et al. Antimicrobial Resistance profiles, virulence genes, and genetic diversity of thermophilic campylobacter species isolated from a layer poultry farm in Korea. Front Microbiol. 2021;12:622275.

    Article  PubMed  PubMed Central  Google Scholar 

  70. Krucinska J, Falcone E, Erlandsen H, Hazeen A, Lombardo MN, Estrada A, et al. Structural and functional studies of bacterial enolase, a potential target against Gram-negative pathogens. Biochemistry. 2019;58(9):1188–97. https://doi.org/10.1021/acs.biochem.8b01298.

    Article  CAS  PubMed  Google Scholar 

  71. Kamensek S, Zgur-Bertok D. Global transcriptional responses to the bacteriocin colicin M in Escherichia coli. BMC Microbiol. 2013;13:42. https://doi.org/10.1186/1471-2180-13-42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This study is supported by the Health Projects of Zhongshan City (2022B1154, 2018B1081).

Author information

Authors and Affiliations

  1. Department of Laboratory Medicine, Zhongshan City People’s Hospital, Zhongshan, 528403, Guangdong, China

    Dengke Han, Suzhen Ma, Yuxing Yang & Lanfen Lu

  2. Department of Emergency, Zhongshan City People’s Hospital, Zhongshan, 528403, Guangdong, China

    Chenhong He

  3. Chinese PLA Center for Disease Control and Prevention, 20 DongDa Street, Fengtai District, Beijing, 100071, China

    Peng Li

Authors
  1. Dengke Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Suzhen Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chenhong He
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuxing Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Peng Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lanfen Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Lanfen Lu and Dengke Han conceived and designed the experiments. Dengke Han, Suzhen Ma, Chenhong He, and Yuxing Yang performed the experiments and analyzed the data. Peng Li performed library construction and genome sequencing. Dengke Han, Suzhen Ma and Chenhong He prepared the tables and figures and wrote the manuscript. Lanfen Lu and Peng Li finally revised the paper. All authors contributed to the article. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Lanfen Lu.

Ethics declarations

Ethics approval and consent to participate

This study involving clinical case and tests were conducted in accordance with the Declaration of Helsinki and clinical pathway. The Ethics approval and a waiver of informed consent was granted by the Ethics Committee of the Zhongshan City People’s Hospital, due to retrospective analysis of anonymized data.

Consent for publication

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.

Supplementary Information

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

Han, D., Ma, S., He, C. et al. Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring blaNDM-5 in E. Coli ST167: implications for antibiotic resistance management. BMC Microbiol 24, 178 (2024). https://doi.org/10.1186/s12866-024-03333-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12866-024-03333-1

Keywords

BMC Microbiology

ISSN: 1471-2180

Contact us