Study on the epidemiology and genetic background of <italic style="font-style: italic">Enterobacteriaceae</italic> co-harboring <italic style="font-style: italic">bla</italic><sub>KPC</sub> and <italic style="font-style: italic">mcr</italic> genes based on NCBI database

FU Jing-jing; HU Xiao-feng; WANG Bo-qian; HU Gui-fang; HE Ya-qing

doi:10.12211/2096-8280.2025-079

您当前的位置：

首页 >

文章列表页 >

Study on the epidemiology and genetic background of Enterobacteriaceae co-harboring bla_KPC and mcr genes based on NCBI database

更新时间：2025-11-10

- Study on the epidemiology and genetic background of Enterobacteriaceae co-harboring bla_KPC and mcr genes based on NCBI database
- Synthetic Biology Journal Pages: 1-11(2025)
- 作者机构：
  
  1.南方医科大学公共卫生学院，广东广州 510515
  2.深圳市疾病预防控制中心，病原微生物检测所，广东深圳 518055
  3.中国人民解放军疾病预防控制中心，北京 100071
  4.军事科学院军事医学研究院，病原微生物生物安全国家重点实验室，北京 100071
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2025-079
  CLC： R378
- Received：30 July 2025，
  
  Revised：2025-11-06，
  
  Online First：10 December 2025，
- 稿件说明：
移动端阅览
付晶晶，胡晓丰，王博千，胡贵方，何雅青. 基于NCBI数据库的共同携带bla_KPC和mcr基因肠杆菌科细菌流行现状和耐药基因遗传背景研究［J］. 合成生物学， 2025， 6. DOI： 10.12211/2096-8280.2025-079

FU Jing-jing， HU Xiao-feng， WANG Bo-qian， HU Gui-fang， HE Ya-qing. Study on the epidemiology and genetic background of Enterobacteriaceae co-harboring bla_KPC and mcr genes based on NCBI database［J］. Synthetic Biology Journal， 2025， 6. DOI： 10.12211/2096-8280.2025-079
付晶晶，胡晓丰，王博千，胡贵方，何雅青. 基于NCBI数据库的共同携带bla_KPC和mcr基因肠杆菌科细菌流行现状和耐药基因遗传背景研究［J］. 合成生物学， 2025， 6. DOI： 10.12211/2096-8280.2025-079 DOI：

FU Jing-jing， HU Xiao-feng， WANG Bo-qian， HU Gui-fang， HE Ya-qing. Study on the epidemiology and genetic background of Enterobacteriaceae co-harboring bla_KPC and mcr genes based on NCBI database［J］. Synthetic Biology Journal， 2025， 6. DOI： 10.12211/2096-8280.2025-079 DOI：

摘要

（目的）利用生物信息学技术，系统研究NCBI数据库中共同携带碳青霉烯类耐药基因（

bla

KPC

）和多黏菌素耐药基因（

mcr

）肠杆菌科细菌流行分布特征，及耐药基因遗传背景，为共耐药菌株的感染防控提供参考依据。（方法）从NCBI数据库中下载了携带

bla

KPC

和

mcr

基因的细菌全基因组数据，分析并鉴定了菌株中

bla

KPC

和

mcr

的不同亚型。通过对细菌质粒的注释和复制子类型的鉴定，揭示这两种耐药基因在特定质粒中的存在情况，并分析了

bla

KPC

和

mcr

基因的上下游遗传结构。（结果）共同携带

bla

KPC

和

mcr

基因细菌主要为肠杆菌科细菌，且以美国、英国和中国为主要分布国家。共同携带

bla

KPC

和

mcr

基因菌株菌属分布多样性在2012年至2018年有所增加。

bla

KPC-2

mcr-9.1

以及

bla

KPC-3

mcr-9.1

为优势基因型组合，且本研究中

bla

KPC-2

mcr-9.1

mcr-9.2

基因型分布于多种STs的大肠埃希氏菌（58，46.03%）。遗传环境分析表明：

bla

KPC

主要位于pKPC-CAV1193质粒，并大量鉴定到

tnpR-tnpA

-IS

kpn7

bla

KPC

-IS

kpn6

（Tn

4401b

）这一转座子结构；

mcr-9.1

主要位于IncHI2（2A）质粒中，且上下游遗传结构保守，核心结构为

rcnR-rcnA-pcoE-pcoS

-IS

903B

mcr-9.1

wbuC

-IS

。（结论）共同携带

bla

KPC

和

mcr

基因菌株有显著的地域分布差异；应特别关注特定ST型大肠埃希氏菌（如ST167和ST10）在传播中的潜力，及在临床环境中的变化。耐药基因

bla

KPC

和

mcr

分别主要通过pKPC-CAV1193及IncHI2（2A）质粒介导传播，并通过转座子等可移动遗传元件进行扩散，极大增加了耐药性传播的风险，应引起高度重视。

Abstract

(Objective)

To systematically study the global distribution characteristics of

Enterobacteriaceae

harboring carbapenem resistance gene (

bla

KPC

) and polymyxin resistance gene (

mcr

) based on NCBI database

as well as the genetic background of these resistance genes

providing a reference for disease prevention and control.

(Methods)

Whole-genome data of bacteria harboring

bla

KPC

and

mcr

genes were downloaded from the NCBI database. Different subtypes of

bla

KPC

and

mcr

genes in the strains were analyzed and identified. By annotating bacterial plasmids and identifying replicon types

the presence of these resistance genes in specific plasmids was revealed. The upstream and downstream genetic structures of the

bla

KPC

and

mcr

genes were also analyzed.

(Results)

The bacteria co-harboring

bla

KPC

and

mcr

genes were primarily from the

Enterobacteriaceae

family

with the main distribution in the United States

the United Kingdom

and China. The diversity of bacterial genera harboring both

bla

KPC

and

mcr

genes increased from 2012 to 2018. The dominant genotype combinations were

bla

KPC-2

mcr-9.1

and

bla

KPC-3

mcr-9.1

. In this study

the genotype

bla

KPC-2

mcr-9.1

mcr-9.2

was found in various STs of

Escherichia coli

(58

46.03%). Genetic environment analysis showed that

bla

KPC

is mainly located on the pKPC-CAV1193 plasmid

with a significant identification of the

tnpR

tnpA

-IS

kpn7

bla

KPC

-IS

kpn6

(Tn

4401b

) transposon structure.

mcr-9.1

is mainly located on the IncHI2 (2A) plasmid

with conserved upstream and downstream genetic structures

the core structure being

rcnR

rcnA

pcoE

pcoS

-IS

903B

mcr-9.1

wbuC

-IS

(Conclusion)

Strains co-harboring the

bla

KPC

and

mcr

genes show significant geographic distribution differences. Special attention should be given to the potential for transmission of specific ST types of

Escherichia coli

(such as ST167 and ST10) and their changes in clinical environments. The resistance genes

bla

KPC

and

mcr

are transmitted through specific plasmids

pKPC-CAV1193 and IncHI2 (2A)

respectively

and spread via transposons and other mobile genetic elements

greatly increasing the risk of resistance transmission

which warrants urgent attention.

关键词

Keywords

references

ZHU L , LI P , ZHANG G , et al . Role of the IS Kpn element in mediating mgrB gene mutations in ST11 hypervirulent colistin-resistant Klebsiella pneumoniae [J ] . Frontiers in Microbiology , 2023 , 14 : 1277320 .

HUSSEIN NH , AL-KADMY IMS , TAHA BM , et al . Mobilized colistin resistance ( mcr ) genes from 1 to 10: a comprehensive review [J ] . Molecular Biology Reports , 2021 , 48 ( 3 ): 2897 - 2907 .

YU H , QU F , SHAN B , et al . Detection of the mcr-1 Colistin Resistance Gene in Carbapenem-Resistant Enterobacteriaceae from Different Hospitals in China [J ] . Antimicrobial Agents and Chemotherapy , 2016 , 60 ( 8 ): 5033 - 5 .

FALGENHAUER L , WAEZSADA SE , YAO Y , et al . Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany [J ] . The Lancet Infectious Diseases , 2016 , 16 ( 3 ): 282 - 3 .

POIREL L , KIEFFER N , LIASSINE N , et al . Plasmid-mediated carbapenem and colistin resistance in a clinical isolate of Escherichia coli [J ] . The Lancet Infectious Diseases , 2016 , 16 ( 3 ): 281 .

HASMAN H , HAMMERUM AM , HANSEN F , et al . Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015 [J ] . Eurosurveillance , 2015 , 20 ( 49 ).

BRATU S , LANDMAN D , ALAM M , et al . Detection of KPC carbapenem-hydrolyzing enzymes in Enterobacter spp. from Brooklyn, New York [J ] . Antimicrobial Agents and Chemotherapy , 2005 , 49 ( 2 ): 776 - 8 .

MUNOZ-PRICE LS , POIREL L , BONOMO RA , et al . Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases [J ] . The Lancet Infectious Diseases , 2013 , 13 ( 9 ): 785 - 96 .

DING L , SHEN S , CHEN J , et al . Klebsiella pneumoniae carbapenemase variants: the new threat to global public health [J ] . Clinical Microbiology Reviews , 2023 , 36 ( 4 ): e0000823 .

CHEN L , MATHEMA B , CHAVDA KD , et al . Carbapenemase-producing Klebsiella pneumoniae : molecular and genetic decoding [J ] . Trends in Microbiology , 2014 , 22 ( 12 ): 686 - 96 .

CAI M , SONG K , WANG R , et al . Tracking intra-species and inter-genus transmission of KPC through global plasmids mining [J ] . Cell Reports , 2024 , 43 ( 6 ): 114351 .

WU R , YI LX , YU LF , et al . Fitness Advantage of mcr-1 -Bearing IncI2 and IncX4 Plasmids in Vitro [J ] . Frontiers in Microbiology , 2018 , 9 : 331 .

HADJADJ L , RIZIKI T , ZHU Y , et al . Study of mcr-1 Gene-Mediated Colistin Resistance in Enterobacteriaceae Isolated from Humans and Animals in Different Countries [J ] . Genes (Basel) , 2017 , 8 ( 12 ).

MATAMOROS S , VAN HATTEM JM , ARCILLA MS , et al . Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction [J ] . Scientific Reports , 2017 , 7 ( 1 ): 15364 .

MACESIC N , BLAKEWAY LV , STEWART JD , et al . Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 'superplasmids' in clinical carbapenem-resistant Enterobacterales [J ] . Clinical Microbiology and Infection , 2021 , 27 ( 12 ): 1856.e7 - 1856.e13 .

KUMAR S , STECHER G , LI M , et al . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms [J ] . Molecular Biology and Evolution , 2018 , 35 ( 6 ): 1547 - 1549 .

FELDGARDEN M , BROVER V , HAFT DH , et al . Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates [J ] . Antimicrobial Agents and Chemotherapy , 2019 , 63 ( 11 ).

KRAWCZYK PS , LIPINSKI L , DZIEMBOWSKI A . PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures [J ] . Nucleic Acids Research , 2018 , 46 ( 6 ): e35 .

CARATTOLI A , ZANKARI E , GARCÍA-FERNÁNDEZ A , et al . In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing [J ] . Antimicrobial Agents and Chemotherapy , 2014 , 58 ( 7 ): 3895 - 903 .

SCHWENGERS O , JELONEK L , DIECKMANN MA , et al . Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification [J ] . Microbial Genomics , 2021 , 7 ( 11 ).

SULLIVAN MJ , PETTY NK , BEATSON SA . Easyfig: a genome comparison visualizer [J ] . Bioinformatics , 2011 , 27 ( 7 ): 1009 - 10 .

ZHOU Z , ALIKHAN NF , SERGEANT MJ , et al . GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens [J ] . Genome Research , 2018 , 28 ( 9 ): 1395 - 1404 .

DORMAN CJ . H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria [J ] . Plasmid , 2014 , 75 : 1 - 11 .

NAVARRE WW , MCCLELLAND M , LIBBY SJ , et al . Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA [J ] . Genes & Development , 2007 , 21 ( 12 ): 1456 - 71 .

HAN X , ZHOU J , YU L , et al . Genome sequencing unveils bla KPC-2 -harboring plasmids as drivers of enhanced resistance and virulence in nosocomial Klebsiella pneumoniae [J ] . Msystems , 2024 , 9 ( 2 ): e0092423 .

ČUROVÁ K , SLEBODNÍKOVÁ R , KMEŤOVÁ M , et al . Virulence, phylogenetic background and antimicrobial resistance in Escherichia coli associated with extraintestinal infections [J ] . Journal of Infection and Public Health , 2020 , 13 ( 10 ): 1537 - 1543 .

TSENG C C , LIN W H , WU A B , et al . Escherichia coli FimH adhesins act synergistically with PapGII adhesins for enhancing establishment and maintenance of kid ney infection [J ] . Journal of Microbiology Immunology and Infection , 2022 , 55 ( 1 ): 44 - 50 .

GARNETT J A , MARTÍNEZ-SANTOS V I , SALDAÑA Z , et al . Structural insights into the biogenesis and biofilm formation by the Escherichia coli common pilus [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2012 , 109 ( 10 ): 3950 - 5 .

GOOTZ TD , LESCOE MK , DIB-HAJJ F , et al . Genetic organization of transposase regions surrounding bla KPC carbapenemase genes on plasmids from Klebsiella strains isolated in a New York City hospital [J ] . Antimicrobial Agents and Chemotherapy , 2009 , 53 ( 5 ): 1998 - 2004 .

LING Z , YIN W , SHEN Z , et al . Epidemiology of mobile colistin resistance genes mcr-1 to mcr-9 [J ] . Journal of Antimicrobial Chemotherapy , 2020 , 75 ( 11 ): 3087 - 3095 .

LUO Q , WU Y , BAO D , et al . Genomic epidemiology of mcr carrying multidrug-resistant ST34 Salmonella enterica serovar Typhimurium in a one health context: The evolution of a global menace [J ] . Science of The Total Environment , 2023 , 896 : 165203 .

WANG C , FENG Y , LIU L , et al . Identification of novel mobile colistin resistance gene mcr-10 [J ] . Emerging Microbes & Infections , 2020 , 9 ( 1 ): 508 - 516 .

CASTILLO F , BENMOHAMED A , SZATMARI G . Xer Site Specific Recombination: Double and Single Recombinase Systems [J ] . Frontiers in Microbiology , 2017 , 8 : 453 .

ZHU Y , GALANI I , KARAISKOS I , et al . Multifaceted mechanisms of colistin resistance revealed by genomic analysis of multidrug-resistant Klebsiella pneumoniae isolates from individual patients before and after colistin treatment [J ] . Journal of Infectious Diseases , 2019 , 79 ( 4 ): 312 - 321 .

LI W , HE Z , DI W , et al . Transposition mechanism of IS Apl1 -the determinant of colistin resistance disseminati on [J ] . Antimicrobial Agents and Chemotherapy , 2024 , 68 ( 3 ): e0123123 .

WANG Y , LIU H , WANG Q , et al . Fusion event mediated by IS 903B between chromosome and plasmid in two MCR-9- and KPC-2-co-producing Klebsiella pneumoniae isolates [J ] . Journal of Global Antimicrobial Resistance , 2024 , 77 : 101139 .

YUAN Q , XIA P , XIONG L , et al . First report of coexistence of bla KPC-2 -, bla NDM-1 - and mcr-9 -carrying plasmids in a clinical carbapenem-resistant Enterobacter hormaechei isolate [J ] . Frontiers in Microbiology , 2023 , 14 : 1153366 .

ZHU Z , WU S , ZHU J , et al . Emergence of Aeromonas veronii strain co-harboring bla KPC-2 , mcr-3.17 , and tmexC3.2-tmexD3.3-toprJ1b cluster from hospital sewage in China [J ] . Frontiers in Microbiology , 2023 , 14 : 1115740 .

WANG Y , LIU H , WANG Q , et al . Coexistence of bla KPC-2 -IncN and mcr-1 -IncX4 plasmids in a ST48 Escherichia coli strain in China [J ] . Journal of Global Antimicrobial Resistance , 2020 , 23 : 149 - 153 .

Views

下载量

CSCD

Alert me when the article has been cited

提交

Tools

Publicity Resources

No data

Related Author

No data

Related Institution

No data

⁰

Study on the epidemiology and genetic background of Enterobacteriaceae co-harboring blaKPC and mcr genes based on NCBI database

DOI：10.12211/2096-8280.2025-079

摘要

Abstract

关键词

Keywords

references

Study on the epidemiology and genetic background of Enterobacteriaceae co-harboring bla_KPC and mcr genes based on NCBI database