Characterisation of a cointegrate plasmid harbouring blaNDM-1 in a clinical Salmonella Lomita strain

Clonal spread of blaNDM-1-carrying Salmonella enterica serovar Typhimurium clone ST34 and wide spread of IncHI2/ST3-blaNDM-5 plasmid in China

OBJECTIVES

To characterize blaNDM-carrying Salmonella recovered from a pig slaughterhouse.

METHODS

In this study, 46 environment samples were collected from a slaughterhouse in China, and screened for carbapenem-resistant Enterobacterales. WGS, antimicrobial susceptibility testing and conjugation experiments were carried out to identify the isolates' resistance phenotypes and genetic characteristics. The phylogenetic relatedness of the Salmonella isolates obtained in this study and Salmonella (ST34 and ST29) in GenBank was determined.

RESULTS

Two ST34 Salmonella Typhimurium and one ST29 Salmonella Stanley, recovered from three environmental samples (6.52%), were positive for blaNDM-1 and blaNDM-5, respectively. The two ST34 S. Typhimurium strains exhibited a close relationship (10-36 SNPs) with two human-derived blaNDM-1-bearing isolates from China (Hong Kong and Guangxi Province) and two blaNDM-negative ST34 Salmonella strains from the UK. The blaNDM-1 genes were located on IncHI2/ST3 plasmids. The capture of blaNDM-1 by the IncHI2/ST3 plasmid seems to be due to homologous recombination mediated by circular structures, as the genetic arrangements of the blaNDM-1 gene contain two IS26 elements of the same orientation. The blaNDM-5 gene was also carried by the IncHI2/ST3 plasmid, which shares highly similar structures with other blaNDM-5-bearing IncHI2/ST3 plasmids from other sources (fish, chicken, duck, human).

CONCLUSIONS

This is the first report of a blaNDM-5-carrying IncHI2/ST3 plasmid in Salmonella. The clonal spread of NDM-1-producing ST34 S. Typhimurium across human and animal-associated environments, and the widespread dissemination of epidemic blaNDM-5-carrying IncHI2/ST3 plasmids among Enterobacteriaceae in China indicate the potential of further dissemination of blaNDM among Salmonella, which poses a threat to public health.

Design, synthesis and antibacterial activity evaluation of ebselen derivatives in NDM-1 producing bacteria

New Delhi-β-lactamase-1 (NDM-1) is a type of metal-β-lactamase. NDM-1-expressing bacteria can spread rapidly across the globe via plasmid transfer, which greatly undermines the clinical efficacy of the carbapenem. Research on NDM-1 inhibitors has attracted extensive attention. However, there are currently no clinically available NDM-1 inhibitors. Our research group has reported that 1,2-benzisoselenazol-3(2H)-one derivatives as covalent NDM-1 inhibitors can restore the efficacy of meropenem (Mem) against NDM-1 producing strains. In this study, 22 compounds were designed and synthesized, which restored the Mem susceptibility of NDM-1-expressing Escherichia coli. and its minimum inhibitory concentration (MIC) was reduced by 2-16 times. Representative compound A4 showed significant synergistic antibacterial activity against NDM-1-producing carbapenem-resistant Enterobacteriaceae (CRE) isolates. The in vitro NDM-1 enzyme inhibitory activity test showed that the IC50 was 1.26 ± 0.37 μM, which had low cytotoxicity. When combined with meropenem, it showed good combined antibacterial activity. Electrospray ionization mass spectrometry (ESI-MS) analysis demonstrates that compound A4 covalently binds to NDM-1 enzyme. In summary, compound A4 is a potent NDM-1 covalent inhibitor and provides a potential lead compound for drug development in resistant bacteria.

Genomic insights into the evolution and mechanisms of carbapenem-resistant hypervirulent Klebsiella pneumoniae co-harboring blaKPC and blaNDM: implications for public health threat mitigation

BACKGROUND

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) co-producing blaKPC and blaNDM poses a serious threat to public health. This study aimed to investigate the mechanisms underlying the resistance and virulence of CR-hvKP isolates collected from a Chinese hospital, with a focus on blaKPC and blaNDM dual-positive hvKP strains.

METHODS

Five CR-hvKP strains were isolated from a teaching hospital in China. Antimicrobial susceptibility and plasmid stability testing, plasmid conjugation, pulsed-field gel electrophoresis, and whole-genome sequencing (WGS) were performed to examine the mechanisms of resistance and virulence. The virulence of CR-hvKP was evaluated through serum-killing assay and Galleria mellonella lethality experiments. Phylogenetic analysis based on 16 highly homologous carbapenem-resistant K. pneumoniae (CRKP) producing KPC-2 isolates from the same hospital was conducted to elucidate the potential evolutionary pathway of CRKP co-producing NDM and KPC.

RESULTS

WGS revealed that five isolates individually carried three unique plasmids: an IncFIB/IncHI1B-type virulence plasmid, IncFII/IncR-type plasmid harboring KPC-2 and IncC-type plasmid harboring NDM-1. The conjugation test results indicated that the transference of KPC-2 harboring IncFII/IncR-type plasmid was unsuccessful on their own, but could be transferred by forming a hybrid plasmid with the IncC plasmid harboring NDM. Further genetic analysis confirmed that the pJNKPN26-KPC plasmid was entirely integrated into the IncC-type plasmid via the copy-in route, which was mediated by TnAs1 and IS26.

CONCLUSION

KPC-NDM-CR-hvKP likely evolved from a KPC-2-CRKP ancestor and later acquired a highly transferable blaNDM-1 plasmid. ST11-KL64 CRKP exhibited enhanced plasticity. The identification of KPC-2-NDM-1-CR-hvKP highlights the urgent need for effective preventive strategies against aggravated accumulation of resistance genes.

Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli

Large cointegrate plasmids recruit genetic features of their parental plasmids and serve as important vectors in the spread of antibiotic resistance. They are now frequently found in clinical settings, raising the issue of how to limit their further transmission. Here, we conducted evolutionary research of a large blaNDM-positive cointegrate within Escherichia coli C600, and discovered that adaptive evolution of chromosome and plasmid jointly improved bacterial fitness, which was manifested as enhanced survival ability for in vivo and in vitro pairwise competition, biofilm formation, and gut colonization ability. From the plasmid aspect, large-scale DNA fragment loss is observed in an evolved clone. Although the evolved plasmid imposes a negligible fitness cost on host bacteria, its conjugation frequency is greatly reduced, and the deficiency of anti-SOS gene psiB is found responsible for the impaired horizontal transferability rather than the reduced fitness cost. These findings unveil an evolutionary strategy in which the plasmid horizontal transferability and fitness cost are balanced. From the chromosome perspective, all evolved clones exhibit parallel mutations in the transcriptional regulatory stringent starvation Protein A gene sspA. Through a sspA knockout mutant, transcriptome analysis, in vitro transcriptional activity assay, RT-qPCR, motility test, and scanning electron microscopy techniques, we demonstrated that the mutation in sspA reduces its transcriptional inhibitory capacity, thereby improving bacterial fitness, biofilm formation ability, and gut colonization ability by promoting bacterial flagella synthesis. These findings expand our knowledge of how cointegrate plasmids adapt to new bacterial hosts.

Dynamic evolution and transmission of a blaNDM-1-bearing fusion plasmid in a clinical Escherichia coli

Plasmids are the main driving forces for the rapid dissemination of blaNDM-1. In recent years, blaNDM-1-carrying fusion plasmids have been frequently reported. However, the evolutionary patterns of blaNDM-1-carrying fusion plasmids remain largely unknown. Herein, we reported a blaNDM-1-bearing fusion plasmid pZX35-269k possessing IncFII and IncA/C2 replicons from clinical ST349 E. coli 13ZX35. The backbone of pZX35-269k was structurally unstable, which was manifested in different types of structural dissociation during conjugation and passage, thereby forming various daughter plasmids. Moreover, the same events were observed in the clinical setting as well. We found that pZX35-269k exhibited highly identical to two plasmids (pZX30-70k and pZX30-192k) in 13ZX30, both of which were isolated from the same hospital. Sequence analysis highlighted that two plasmids in 13ZX30 evolved from pZX35-269k through homologous recombination of a 4856-bp fragment. Collectively, this study confirmed the transmission and structural evolution of a blaNDM-1-bearing fusion plasmid in both laboratory and clinical settings, and provided clear evidence of plasmid spread and evolution in clinical settings. Such versatile plasmids may represent a potential risk for the public health.

IS26-Mediated Formation of a Hybrid Plasmid Carrying mcr-1.1

PURPOSE

The objective of this study was to elucidate the characteristics and mechanism of formation of the fusion plasmid pHNSHP24 carrying mcr-1.1.

MATERIALS AND METHODS

mcr-1.1-bearing Escherichia coli SHP24 and the corresponding transconjugant were subjected to whole-genome sequencing (WGS) combining the Illumina and MinION platforms to obtain the complete sequences of the fusion plasmid and its original plasmids.

RESULTS

Complete sequence analysis and S1 nuclease-pulsed field gel electrophoresis (S1-PFGE) results indicated that E. coli SHP24 carried four plasmids: mcr-1.1-harboring phage-like plasmid pHNSHP24-3, F53:A-:B- plasmid pHNSHP24-4, pHNSHP24-1, and pHNSHP24-2. However, the plasmid pHNSHP24 carrying mcr-1.1 presents in the transconjugant differed from the four plasmids in the donor strain SHP24. Further analysis showed that pHNSHP24 may be the fusion product of pHNSHP24-3 and pHNSHP24-4 and is formed through a replicative transposition mechanism mediated by IS26 in E. coli SHP24.

CONCLUSION

This study is the first to report the fusion of an mcr-1.1-harboring phage-like pO111 plasmid and an F53:A-:B- plasmid mediated by IS26. Our findings revealed the role of phage-like and fusion plasmids in the dissemination of mcr-1.1.

Characterization of a genomic Island carrying the tet(X4) gene in porcine Acinetobacter towneri co-harboring plasmid-borne blaNDM−1 and blaOXA−58 genes

Tigecycline and carbapenems are last-resort antimicrobial agents to treat serious infections caused by multi-drug resistant bacterial pathogens. However, the co-occurrence of tigecycline and carbapenem resistance determinants challenges the clinical efficacy of these antimicrobial agents. In this study, we report the co-existence of tet(X4), bla_NDM−1 and bla_OXA−58 genes in the porcine Acinetobacter towneri isolate 19110F47. Sequence analysis revealed that tet(X4) gene, along with the florfenicol resistance gene floR, was flanked by three copies of IS91-like elements, which can form three different translocatable units (TUs), and were located in a 41,098-bp multidrug resistance region (MDRR) within a novel 100,354-bp genomic island (GI) region. TUs comprising floR-virD2-ISVsa3, hp-abh-tet(X4)-ISVsa3 and virD2-floR-ISVsa3-hp-abh-tet(X4)-ISVsa3 can be looped out from the chromosomal DNA and facilitate the transfer of the TU-based resistance genes into other plasmidic or chromosomal sites. In addition, the carbapenemase genes bla_NDM−1 and bla_OXA−58 were found on different non-conjugative multiresistance plasmids in this isolate, with the genetic contexts ISAba125-bla_NDM−1-ble_MBL-tnpR and ΔISAba3-bla_OXA−58-ISAba3, respectively. The simultaneous occurrence of tet(X4), bla_NDM−1 and bla_OXA−58 in the same porcine A. towneri isolate emphasizes the importance of antimicrobial resistance surveillance in food-producing animals.

Global prevalence, characteristics, and future prospects of IncX3 plasmids: A review

IncX3 plasmids are narrow host range plasmids mostly found in Enterobacteriaceae with great conjugation ability, high stability, no fitness cost, and the ability to improve biofilm formation in their bacterial hosts. IncX3 plasmids have spread swiftly, primarily in several nations and among different species over the last 10 years. blaNDM, blaKPC, and blaOXA-181 are the carbapenemase genes carried by IncX3 plasmids. Among them, blaNDM is often located on the IncX3 plasmid, which is deemed as the primary vehicle of blaNDM transmission. Isolates harboring IncX3 plasmids are found in nations all over the world from human, animal, and environmental sources. Cointegrate plasmids related to IncX3 have recently been discovered to increase the antibiotic resistance spectrum and potentially broaden the host range of plasmids, restricting the use of antibiotics in the clinic. There are, however, few reviews based on the physiological and epidemiological properties of IncX3 plasmid, as well as studies on the plasmid itself. Hence, we conducted a retrospective literature review to summarize the characteristics of IncX3 plasmids aiming to provide a theoretical basis for controlling the global prevalence of IncX3 plasmids and directions for further research on the functions of the related genes on the IncX3 plasmid.

Detection of Two Copies of a blaNDM-1-Encoding Plasmid in Escherichia coli Isolates from a Pediatric Patient with Diarrhea

Purpose

To elucidate the contribution of a transferable plasmid harboring the bla_NDM-1 gene in an Escherichia coli clinical isolate to the spread of resistance determinants.

Methods

Nine extended-spectrum β-lactamase-producing E. coli were collected from diarrhea samples from a pediatric patient and genetic linkage was investigated through enterobacteriaceae repetitive intragenic consensus polymerase chain reaction (PCR). Bacterial species were identified by 16s rRNA sequencing, susceptibility testing with the use of a BD Phoenix^TM-100 Automated Microbiology System, and assessment of virulence genes by PCR. The transferability of bla_NDM-1 in E. coli strain TCM3e1 was confirmed by conjugation experiments. Complete sequencing of E. coli strain TCM3e1 was determined with the PacBio and Illumina NovaSeq platforms and the characteristics were analyzed with bioinformatics software.

Results

The results showed that all nine E. coli strains were the same clone. E. coli strain TCM3e1 was resistant to 12 antimicrobial agents and carried the virulence gene EAST-1. Conjugation transfer analysis showed that bla_NDM-1 was carried on a self-transmissible plasmid. Two copies of the bla_NDM-1 gene were present on an IncC plasmid and some resistance genes with two or three copies were located downstream of the bla_NDM-1 gene and formed a tandem repeat fragment (bla_DNM-1-bleo-sul1- aadA17- dfrA12).

Conclusion

A transmissible plasmid harboring two copies of the bla_NDM-1 gene, including clonal dispersions of the bla_NDM-1 gene, was identified in clinical isolates. These findings emphasized the necessity of surveillance of the plasmid-borne bla_NDM-1 to prevent dissemination.

Structural Diversity, Fitness Cost, and Stability of a BlaNDM-1-Bearing Cointegrate Plasmid in Klebsiella pneumoniae and Escherichia coli

Cointegrate/hybrid plasmids combine the genetic elements of two or more plasmids and generally carry abundant antimicrobial resistance determinants. Hence, the spread of cointegrate plasmids will accelerate the transmission of AMR genes. To evaluate the transmission risk caused by cointegrate plasmids, we investigated the structural diversity, fitness cost, and stability of a cointegrate plasmid in Klebsiella pneumoniae YZ6 and Escherichia coli EC600. The cointegrate plasmid pSL131_IncA/C_IncX3 was from a clinical Salmonella Lomita strain. After transferring the plasmid into E. coli EC600 by conjugation, we observed plasmids with different structures, including a full-length original plasmid and two truncated versions. By contrast, DNA fragment deletion and bla_CTX-M-14 gene insertion in the plasmid were detected in a transconjugant derived from K. pneumoniae YZ6. These results suggest that the structure of the plasmid was unstable during conjugation. Furthermore, both the full-length plasmid in EC600 and the structurally reorganized plasmid in YZ6 imposed a fitness cost on the bacterial host and enhanced biofilm formation ability. Serial passaging in antibiotic-free medium resulted in a rapid decline of the plasmid in YZ6. However, the stability of the structurally reorganized plasmid in YZ6 was improved via serial passaging in antibiotic-containing medium. SNP calling revealed that mutations of the outer membrane porin may play an essential role in this process. These findings indicate that structural versatility could contribute to the dissemination of cointegrate plasmids. Although the plasmid incurred a fitness cost in other Enterobacteriaceae species, positive selection could alleviate the adverse effects.

IS1294 Reorganizes Plasmids in a Multidrug-Resistant Escherichia coli Strain

The aims of this study were to elucidate the role of IS1294 in plasmid reorganization and to analyze biological characteristics of cointegrates derived from different daughter plasmids. The genetic profiles of plasmids in Escherichia coli strain C21 and its transconjugants were characterized by conjugation, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern hybridization, whole-genome sequencing (WGS) analysis, and PCR. The traits of cointegrates were characterized by conjugation and stability assays. blaCTX-M-55-bearing IncI2 pC21-1 and nonresistant IncI1 pC21-3, as conjugative helper plasmids, were fused with nonconjugative rmtB-bearing IncN-X1 pC21-2, generating cointegrates pC21-F1 and pC21-F2. Similarly, pC21-1 and pC21-3 were fused with nonconjugative IncF33:A-:B- pHB37-2 from another E. coli strain to generate cointegrates pC21-F3 and pC21-F4 under experimental conditions. Four cointegrates were further conjugated into the E. coli strain J53 recipient at high conjugation frequencies, ranging from 2.8 × 10-3 to 3.2 × 10-2. The formation of pC21-F1 and pC21-F4 was the result of host- and IS1294-mediated reactions and occurred at high fusion frequencies of 9.9 × 10-4 and 2.1 × 10-4, respectively. Knockout of RecA resulted in a 100-fold decrease in the frequency of plasmid reorganization. The phenomenon of cointegrate pC21-F2 and its daughter plasmids coexisting in transconjugants was detected for the first time in plasmid stability experiments. IS26-orf-oqxAB was excised from cointegrate pC21-F2 through a circular intermediate at a very low frequency, which was experimentally observed. To the best of our knowledge, this is the first report of IS1294-mediated fusion between plasmids with different replicons. This study provides insight into the formation and evolution of cointegrate plasmids under different drug selection pressures, which can promote the dissemination of MDR plasmids. IMPORTANCE The increasing resistance to β-lactams and aminoglycoside antibiotics, mainly due to extended-spectrum β-lactamases (ESBLs) and 16S rRNA methylase genes, is becoming a serious problem in Gram-negative bacteria. Plasmids, as the vehicles for resistance gene capture and horizontal gene transfer, serve a key role in terms of antibiotic resistance emergence and transmission. IS26, present in many antibiotic-resistant plasmids from Gram-negative bacteria, plays a critical role in the spread, clustering, and reorganization of resistance determinant-encoding plasmids and in plasmid reorganization through replicative transposition mechanisms and homologous recombination. However, the role of IS1294, present in many MDR plasmids, in the formation of cointegrates remains unclear. Here, we investigated experimentally the intermolecular recombination of IS1294, which occurred with high frequencies and led to the formation of conjugative MDR cointegrates and facilitated the cotransfer of blaCTX-M-55 and rmtB, and we further uncovered the significance of IS1294 in the formation of cointegrates and the common features of IS1294-driven cointegration of plasmids.

Apramycin resistance in epidemic carbapenem-resistant Klebsiella pneumoniae ST258 strains

BACKGROUND

Recent studies indicated that the monosubstituted deoxystreptamine aminoglycoside apramycin is a potent antibiotic against a wide range of MDR Gram-negative pathogens.

OBJECTIVES

To evaluate the in vitro activity of apramycin against carbapenem-resistant Klebsiella pneumoniae (CRKp) isolates from New York and New Jersey, and to explore mechanisms of apramycin resistance.

METHODS

Apramycin MICs were determined by broth microdilution for 155 CRKp bloodstream isolates collected from 2013 to 2018. MLST STs, wzi capsular types and apramycin resistance gene aac(3')-IV were examined by PCR and Sanger sequencing. Selected isolates were further characterized by conjugation experiments and WGS.

RESULTS

Apramycin MIC50/90 values were 8 and >128 mg/L for CRKp isolates, which are much higher than previously reported. Twenty-four isolates (15.5%) were apramycin resistant (MIC ≥64 mg/L) and they were all from the K. pneumoniae ST258 background. The 24 apramycin-resistant K. pneumoniae ST258 strains belonged to six different capsular types and 91.7% of them harboured the apramycin resistance gene aac(3')-IV. Sequencing analysis showed that different ST258 capsular type strains shared a common non-conjugative IncR plasmid, co-harbouring aac(3')-IV and blaKPC. A novel IncR and IncX3 cointegrate plasmid, p59494-RX116.1, was also identified in an ST258 strain, demonstrating how apramycin resistance can be spread from a non-conjugative plasmid through cointegration.

CONCLUSIONS

We described a high apramycin resistance rate in clinical CRKp isolates in the New York/New Jersey region, mainly among the epidemic K. pneumoniae ST258 strains. The high resistance rate in an epidemic K. pneumoniae clone raises concern regarding the further optimization and development of apramycin and apramycin-like antibiotics.

Global clonal spread of mcr-3-carrying MDR ST34 Salmonella enterica serotype Typhimurium and monophasic 1,4,[5],12:i:- variants from clinical isolates

OBJECTIVES

To investigate the prevalence and transmission of mcr-3 among Salmonella enterica serotype Typhimurium and 1,4,[5],12:i:-.

METHODS

A total of 4724 clinical Salmonella isolates were screened for the presence of mcr-3 in China during 2014-19. The clonal relationship of the mcr-3-positive isolates and their plasmid contents and complete sequence were also characterized based on WGS data from the Illumina and MinION platforms.

RESULTS

We identified 10 mcr-3-positive isolates, and all were MDR, mostly resistant to colistin, cefotaxime, ciprofloxacin, doxycycline and florfenicol. mcr-3 was co-present with blaCTX-M-55-qnrS1 on hybrid ST3-IncC-FII conjugatable plasmids (n = 6) and an ST3-IncC non-conjugatable plasmid (n = 1) and embedded into a pCHL5009T-like IncFII plasmid on the Salmonella chromosome (n = 3). Four distinctive genetic contexts surrounded mcr-3 and all but one were closely related to each other and to the corresponding region of IncFII plasmid pCHL5009T. IS15DI was most likely the vehicle for integration of mcr-3-carrying IncFII plasmids into ST3-IncC plasmids and the chromosome and for shaping the MDR regions. In addition, a phylogenetic tree based on the core genome revealed a unique Salmonella lineage (≤665 SNPs) that contained these 10 mcr-3-positive isolates and another 38 (33 from patients) mcr-3-positive Salmonella from five countries. In particular, most of the 51 mcr-3-positive isolates belonged to ST34 and harboured diverse antibiotic resistance genes (ARGs), including mcr-3-blaCTX-M-55-qnrS1, and possessed similar ARG profiles.

CONCLUSIONS

Our findings revealed global clonal spread of MDR ST34 Salmonella from clinical isolates co-harbouring mcr-3 with blaCTX-M-55 and qnrS1 and a flexibility of mcr-3 co-transmittance with other ARGs mediated by mobile genetic elements.

Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species

The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.

Molecular characterization of two novel NDM-1-producing atypical enteroaggregative Escherichia coli isolates from patients

To investigate NDM-1-producing atypical Enteroaggregative Escherichia coli (aEAEC) of sequence type 349 from hospitalized patients, the isolates 13ZX28 and 13ZX36 were subjected to antimicrobial susceptibility testing, conjugation and whole genome sequencing. Only one single nucleotide mutation was detected in chromosomes despite different plasmid profiles. Both isolates were positive for bla_NDM-1 mediating resistance to carbapenem. A novel plasmid p13ZX28-272 (~272-kb) from 13ZX28 encodes bla_NDM-1. Interestingly, its sequence was identical to the two plasmids p13ZX36-200 (~200-kb) and p13ZX36-70 (~70-kb) from 13ZX36. Formation of the former episome possibly involved homologous recombination through a 4948-bp large fragment located on each of the two latter plasmids. Furthermore, plasmid p13ZX28-272 could be resolved into a ~ 98-kb daughter plasmid by IS26 rearrangement following conjugation. The plasticity of the plasmids is recognized, which warrants further investigation to evaluate the underlying public health risk and understand how antibiotic selection pressure drives this process.

Characterization of IncC Plasmids in Enterobacterales of Food-Producing Animals Originating From China

Incompatibility group C (IncC) plasmids have received attention due to their broad host range and because they harbor key antibiotic resistance genes. Because these resistance genes can spread from food-producing animals to human, the proliferation of these plasmids represents a public health risk. In this study, a total of 20 IncC plasmids were collected from food-producing animals in China, and characterized by Oxford Nanopore Technologies long-read sequencing. Based on four key differences of the IncC backbone, 4 IncC plasmids were classified as type 1, 15 were classified as type 1/2 hybrid, and one was classified as type 2. The 15 type 1/2 hybrids were further divided into 13 type 1/2a and 2 type 1/2b, based on sequence differences arising from different homologous recombination events between type 1 and type 2 IncC backbones. Genome comparison of accessory resistance modules showed that different IncC plasmids exhibited various phenotypes via loss and gain of diverse modules, mainly within the bla_CMY-carrying region, and two antibiotic resistance islands designated ARI-A and ARI-B. Interestingly, in addition to insertion and deletion events, IS26 or IS1294-mediated large sequence inversions were found in the IncC genome of the 4 type1/2a plasmids, suggesting that insertion sequence-mediated rearrangements also promote the diversity of the IncC genome. This study provides insight into the structural diversification and multidrug resistance of IncC plasmids identified from food-producing animals in China.