Dataset Information

Plasmid-Encoded bla_NDM-5 Gene That Confers High-Level Carbapenem Resistance in Salmonella Typhimurium of Pork Origin.

ABSTRACT:

Purpose

Carbapenem resistance is rarely reported in Salmonella Typhimurium, especially from a food origin. Here, we report a plasmid-mediated mobile carbapenem-resistant bla_NDM-5 gene in Salmonella Typhimurium isolated from pork in Shanghai, China in 2016.

Patients and methods

In July 2016, the S. Typhimurium SH160 strain was recovered from minced pork meat purchased from a supermarket in Yangpu District, Shanghai, China. Antimicrobial susceptibility testing, multi-locus sequence typing, conjugation, S1-PFGE, southern hybridization, whole-genome sequencing and data analysis were performed.

Results

This isolate was found to be a ST34 strain and resistant to carbapenems, cephalosporins, and most other commonly used antibiotics. The bla_NDM-5 gene was harbored by a 46161-bp IncX3 plasmid which was found to be transferable. The IncX3 plasmid contains a composite cassette, consisting of ISSwil-IS3000-ΔISAba125-IS5-bla_NDM-5-bleMBL-trpF-dsbC-IS26-ctuA1-ΔumuD. In addition, this strain was found to harbor an additional 161706-bp IncHI2 plasmid which carries nine resistant genes, such as aadA1, aadA3, aph(3')-la, sul1, sul2, sul3, floR, cmlA and dfrA12.

Conclusion

We reported the S. Typhimurium with transferable IncX3 plasmid harboring bla_NDM-5 gene from minced pork. We characterized the complete genetic features of the plasmid, which demonstrated the potential for spreading in different bacterial pathogens. Therefore, extensive surveillance and monitoring for carbapenem-resistant bacterium in the food chain and public health are urgently required.

SUBMITTER: Gao Y

PROVIDER: S-EPMC7250698 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Plasmid-Encoded <i>bla<sub>NDM-5</sub></i> Gene That Confers High-Level Carbapenem Resistance in <i>Salmonella</i> Typhimurium of Pork Origin.

Gao Yuan Y Wen Junping J Wang Shaojun S Xu Xuebin X Zhan Zeqiang Z Chen Zhengquan Z Bai Jie J Qu Xiaoyun X Zhang Hongxia H Zhang Jianmin J Liao Ming M

Infection and drug resistance 20200519

<h4>Purpose</h4>Carbapenem resistance is rarely reported in <i>Salmonella</i> Typhimurium, especially from a food origin. Here, we report a plasmid-mediated mobile carbapenem-resistant <i>bla<sub>NDM-5</sub></i> gene in <i>Salmonella</i> Typhimurium isolated from pork in Shanghai, China in 2016.<h4>Patients and methods</h4>In July 2016, the <i>S</i>. Typhimurium SH160 strain was recovered from minced pork meat purchased from a supermarket in Yangpu District, Shanghai, China. Antimicrobial suscep ...[more]

PMID: 32547117

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Project description:ObjectivesWe identified a novel hybrid plasmid simultaneously carrying bla NDM-1 and bla IMP-4 in an ST20-K28 carbapenem-resistant Klebsiella pneumoniae (CRKP) strain AZS099 and reported its detailed genetic and phenotypic characterization.MethodsAntimicrobial susceptibility was characterized using broth microdilution method. Complete genome characteristics and plasmid detailed analysis were carried out by PacBio Sequel and Illumina sequencing and further bioinformatics analysis. Conjugation assay, S1-PFGE, Southern blot, plasmid stability, and fitness cost were conducted to the phenotypic characterization of this novel hybrid plasmid.ResultsAZS099 was isolated from a blood specimen obtained from a 3-month baby who presented with biliary tract infection. Susceptibility testing showed that AZS099 was resistant to almost all β-lactams examined, including cephalosporins, combinations of β-lactams and β-lactamase inhibitors, carbapenems, and aztreonam. PacBio and Illumina sequencing together with S1-PFGE and Southern blot showed that bla NDM-1 and bla IMP-4 were simultaneously located on a 296 kb IncFIB(K)/IncHI1B/IncX3 plasmid (pAZS099-NDM-IMP), which consists of four main parts that came from four different types of plasmids. The region harboring bla IMP-4 is located in a class 1 integron designated as In0, which is located in an IS6100-IS26 transposon-like structure with a total length of ~5 kb. The region harboring bla NDM-1 is located in the Tn125 transposon remnant. Conjugation and transformation assay confirmed that the plasmid pAZS099-NDM-IMP has the potential for horizontal transfer and displayed high stability (retention rate > 95%). Furthermore, growth curve assessment confirmed that the presence of pAZS099-NDM-IMP exhibits no growth pressure on bacteria.ConclusionOur research reported a hybrid plasmid coharboring bla NDM-1 and bla IMP-4 in an ST20-K28 CRKP strain. The emergence of novel hybrid plasmid could threaten the control of antimicrobial resistance and should be closely supervised.

Project description:Tigecycline is a last-resort antimicrobial against carbapenemase-producing Enterobacterales (CPE). However, mobile tigecycline resistance genes, tet(X) and tmexCD-toprJ, have emerged in China and have spread possibly worldwide. Tet(X) family proteins function as tigecycline-inactivating enzymes, and TMexCD-TOprJ complexes function as efflux pumps for tigecycline. Here, to the best of our knowledge we report a CPE isolate harboring both emerging tigecycline resistance factors for the first time. A carbapenem- and tigecycline-resistant Klebsiella aerogenes strain, NUITM-VK5, was isolated from an urban drainage in Vietnam in 2021, and a plasmid, pNUITM-VK5_mdr, cocarrying tet(X) and tmexCD3-toprJ3 along with the carbapenemase gene blaNDM-4 was identified in NUITM-VK5. pNUITM-VK5_mdr was transferred to Escherichia coli by conjugation and simultaneously conferred high-level resistance against multiple antimicrobials, including carbapenems and tigecycline. An efflux pump inhibitor reduced TMexCD3-TOprJ3-mediated tigecycline resistance, suggesting that both tigecycline resistance factors independently and additively contribute to the high-level resistance. The plasmid had the IncX3 and IncC replicons and was estimated to be a hybrid of plasmids with different backbones. Unlike IncX3 plasmids, IncC plasmids are stably maintained in an extremely broad range of bacterial hosts in humans, animals, and the environment. Thus, the future global spread of multidrug resistance plasmids such as pNUITM-VK5_mdr poses a public health crisis. IMPORTANCE Tigecycline is important as a last-resort antimicrobial and effective against antimicrobial-resistant bacteria, such as carbapenem-producing Enterobacterales (CPE), whose infections are difficult to treat with antimicrobials. Since 2019, mobile tigecycline resistance genes, tet(X) and tmexCD-toprJ, and their variants have been reported mainly from China, and it has become important to understand their epidemiological situation and detailed genetic mechanisms. In this study, we identified a bacterial isolate coharboring tet(X) and tmexCD-toprJ on the same plasmid. A Klebsiella aerogenes isolate in Vietnam carried both these tigecycline resistance genes on a transferable plasmid leading to high-level resistance to multiple clinically important antimicrobials, including carbapenem and tigecycline, and could actually transfer the plasmid to other bacteria. The spread of such a multidrug resistance plasmid among bacterial pathogens should be of great concern because there are few antimicrobials to combat bacteria that have acquired the plasmid.

Project description:Dissemination of blaNDM, which is carried on the IncX3 plasmid, among Enterobacterales has been reported worldwide. In particular, blaNDM-5-carrying IncX3 plasmids can spread among several hosts, facilitating their dissemination. Other variants, such as blaNDM-17-, blaNDM-19-, blaNDM-20-, blaNDM-21-, and blaNDM-33-carrying IncX3 plasmids, have also been reported. Here, we characterized, using whole-genome sequencing (WGS), a blaNDM-16b-carrying IncX3 plasmid harbored by Escherichia coli strain TA8571, which was isolated from a urine specimen of a hospital inpatient in Tokyo, Japan. The blaNDM-16b differed in sequence from blaNDM-5 (C > T at site 698, resulting in an Ala233Val substitution). This blaNDM-16b-carrying IncX3 plasmid (pTMTA8571-1) is 46,161 bp in length and transferred via conjugation. Transconjugants showed high resistance to β-lactam antimicrobials (except for aztreonam). Because pTMTA8571-1, which carries the Tn125-related region containing blaNDM and conjugative transfer genes, was similar to the previously reported IncX3 plasmids, we performed phylogenetic analysis based on the sequence of 34 shared genes in 142 blaNDM-carrying IncX3 plasmids (22,846/46,923 bp). Comparative analysis of the shared genes revealed short branches on the phylogenetic tree (average of 1.08 nucleotide substitutions per shared genes), but each blaNDM variant was divided into separate groups, and the structure of the tree correlated with the flowchart of blaNDM nucleotide substitutions. The blaNDM-carrying IncX3 plasmids may thereby have evolved from the same ancestral plasmid with subsequent mutation of the blaNDM. Therefore, pTMTA8571-1 likely emerged from a blaNDM-5-carrying IncX3 plasmid. This study suggested that the spread of blaNDM-carrying IncX3 plasmids may be a hotbed for the emergence of novel variants of blaNDM. IMPORTANCE blaNDM-carrying IncX3 plasmids have been reported worldwide. Harbored blaNDM variants were mainly blaNDM-5, but there were also rare variants like blaNDM-17, blaNDM-19, blaNDM-20, blaNDM-21, and blaNDM-33, including blaNDM-16b detected in this study. For these plasmids, previous reports analyzed whole genomes or parts of sequences among a small number of samples, whereas, in this study, we performed an analysis of 142 blaNDM-carrying IncX3 plasmids detected around the world. The results showed that regardless of the blaNDM variants, blaNDM-carrying IncX3 plasmids harbored highly similar shared genes. Because these plasmids already spread worldwide may be a hotbed for the emergence of rare or novel variants of blaNDM, increased attention should be paid to blaNDM-carrying IncX3 plasmids in the future.

Project description:ObjectiveA strain of Proteus penneri with carbapenem resistance was found in a patient with a diabetic foot infection. We studied drug resistance, genome, and homology of P. penneri to support clinical prevention and treatment of infection caused by carbapenem-resistant P. penneri (CR-PPE).MethodsThe strains were obtained through bacterial culture from purulence. VITEK 2 compact (GN13) and Kirby-Bauer (K-B) disk diffusion methods were used for antimicrobial susceptibility testing. Ceftriaxone, amikacin, gentamicin, ampicillin, aztreonam, ceftazidime, ciprofloxacin, levofloxacin, cefepime, trimethoprim-sulfamethoxazole, tobramycin, cefotetan, piperacillin-tazobactam, ampicillin-sulbactam, ertapenem, piperacillin, meropenem, cefuroxime, cefazolin, cefoperazone/sulbactam, cefoxitin, and imipenem were used for antimicrobial susceptibility testing. After bacterial genome extraction, sequencing, and sequence assembly, whole-genome sequencing (WGS) was performed to explore the CR-PPE genotype.ResultsCR-PPE was resistant to two carbapenems (imipenem and ertapenem), ceftriaxone, and cefazolin, and was sensitive to aztreonam, piperacillin-tazobactam, and cefotetan. WGS results depict that the resistant phenotype of CR-PPE is consistent with the genotype, without common virulence genes of Enterobacteriaceae bacteria detected (virulence factor database). The carbapenem resistance gene blaNMD-1 is contained in a new plasmid, pWF127-NDM. The transposon Tn125 in pWF127-NDM carrying blaNMD-1 has almost the same structure as Tn125 in the reference plasmid pHFK418-NDM (Accession: MH491967). In addition, through phylogenetic analysis, CR-PPE depicts the closest evolutionary relationship with GCF 024129515.1, which was found in Gallus gallus in the Czech Republic in 2019 (downloaded from National Center for Biotechnology Information database). According to the evolutionary tree, CR-PPE has high homology with the two P. penneri strains found in China.ConclusionCR-PPE exhibits strong drug resistance owing to the presence of multiple resistance genes. CR-PPE infection should receive more attention, especially in patients with underlying diseases, such as diabetes and weak immunity.

Dataset Information

Plasmid-Encoded bla_NDM-5 Gene That Confers High-Level Carbapenem Resistance in Salmonella Typhimurium of Pork Origin.

Purpose

Patients and methods

Results

Conclusion

Publications

Plasmid-Encoded <i>bla<sub>NDM-5</sub></i> Gene That Confers High-Level Carbapenem Resistance in <i>Salmonella</i> Typhimurium of Pork Origin.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

Plasmid-Encoded blaNDM-5 Gene That Confers High-Level Carbapenem Resistance in Salmonella Typhimurium of Pork Origin.

Purpose

Patients and methods

Results

Conclusion

Publications

Plasmid-Encoded <i>bla<sub>NDM-5</sub></i> Gene That Confers High-Level Carbapenem Resistance in <i>Salmonella</i> Typhimurium of Pork Origin.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Plasmid-Encoded bla_NDM-5 Gene That Confers High-Level Carbapenem Resistance in Salmonella Typhimurium of Pork Origin.