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

FU Jingjing; HU Xiaofeng; WANG Boqian; HU Guifang; HE Yaqing

doi:10.12211/2096-8280.2025-079

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

Research Article | 更新时间：2026-05-22

- Study with the NCBI database on the epidemiology and genetic background of Enterobacteriaceae co-harboring drug-resistance genes bla_KPC and mcr
- Synthetic Biology Journal Vol. 7, Issue 2, Pages: 441-452(2026)
- 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，病原微生物研究所，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，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，
  
  Published：30 April 2026
- 稿件说明：
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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， 2026， 7（2）： 441-452 DOI: 10.12211/2096-8280.2025-079.

FU Jingjing， HU Xiaofeng， WANG Boqian， HU Guifang， HE Yaqing. Study with the NCBI database on the epidemiology and genetic background of Enterobacteriaceae co-harboring drug-resistance genes bla_KPC and mcr［J］. Synthetic Biology Journal， 2026， 7（2）： 441-452 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， 2026， 7（2）： 441-452 DOI: 10.12211/2096-8280.2025-079. DOI：

FU Jingjing， HU Xiaofeng， WANG Boqian， HU Guifang， HE Yaqing. Study with the NCBI database on the epidemiology and genetic background of Enterobacteriaceae co-harboring drug-resistance genes bla_KPC and mcr［J］. Synthetic Biology Journal， 2026， 7（2）： 441-452 DOI: 10.12211/2096-8280.2025-079. DOI：

摘要

本研究目的是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。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。结果显示，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—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ST的大肠埃希氏菌（58株，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

。可得出结论：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

With the NCBI database

we systematically studied the global distribution characteristics of Enterobacteriaceae harboring carbapenem resistance gene (

bla

KPC

) and polymyxin resistance gene (

mcr

) as well as their genetic background to provide a reference for disease prevention and control. Whole-genome data of bacteria harboring

bla

KPC

and

mcr

genes were downloaded from the NCBI database

and 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

and the upstream and downstream genetic structures of the

bla

KPC

and

mcr

genes were also analyzed. The bacteria co-harboring

bla

KPC

and

mcr

genes were primarily fro

m 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

and 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

but

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

. Strains co-harboring the

bla

KPC

and

mcr

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

E. 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

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Related Author

FU Jing-jing

HU Xiao-feng

WANG Bo-qian

HU Gui-fang

HE Ya-qing

Related Institution

Institute of Pathogen Biology， Shenzhen Center for Disease Control and Prevention

Beijing Institute of Biotechnology， Laboratory of Advanced Biotechnology， State Key Laboratory of Pathogen and Biosecurity

⁰

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

DOI：10.12211/2096-8280.2025-079

摘要

Abstract

关键词

Keywords

references

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