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Study on the epidemiology and genetic background of
Enterobacteriaceae co-harboringbla KPC andmcr genes based on NCBI database- 合成生物学 2025年 页码：1-11
- 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：
付晶晶（2001—），女，硕士研究生。研究方向为碳青霉烯类和多黏菌素共耐药菌研究。
王博千（1990—），男，瑞典皇家理工计算机系统结构博士，助理研究员。研究方向为病原微生物基因组学相关领域的算法平台和硬件加速设计等。
胡贵方（1966—），男，南方医科大学公共卫生与热带医学学院流行病学系教授，硕士生导师，研究方向为主要从事传染病流行病学研究，研究方向涵盖病毒分子溯源、重组腺相关病毒构建及新冠病毒非结构蛋白变异分析。
何雅青（1965—），女，研究员，博士，博士生导师。研究方向为肠道病毒、腹泻病毒分子流行病学等。
- 基金信息：
DOI：10.12211/2096-8280.2025-079
中图分类号： R378收稿：2025-07-30，
修回：2025-11-06，
网络首发：2025-12-10，
- 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blaKPC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 blaKPC 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blaKPC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 blaKPC 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
26
。（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)
2
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)
2
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)
2
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
26
.
(Conclusion)
2
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.
2
关键词
Keywords
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