Confronting the Antimicrobial Resistance Crisis in China: Emerging Superbugs, Genomic Surveillance, and Innovative Countermeasures

Qian Tong^1,2, Liping Zeng³, Yixin Ge⁴, Jia Jia^1,#

1. Deparment of Immunology and Pathogen Biology, Research Centre for Infection and Immunity, School of Medicine, Tongji University, Shanghai, China.

2. Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou City, Zhejiang Province, China.

3. Department of Pathogen Biology, Jiangsu Key Laboratory of Pathogen Biology, Nanjing Medical University, Nanjing City, Jiangsu Province, China.

4. Huadong Research Institute for Medicine and Biotechniques, Nanjing City, Jiangsu Province, China.

^# Corresponding author: Jia Jia, jiajia25@tongji.edu.cn.

The antimicrobial resistance (AMR) crisis in China has escalated into a critical public health threat. Extensive antibiotic use in both clinical and agricultural settings has created strong selective pressures, promoting the emergence of resistant strains and accelerating their dissemination. This increasing threat is exemplified by the rapid spread of multidrug-resistant bacteria. Consequently, genomic surveillance of these pathogens and the development of effective countermeasures are urgently needed. In this paper, we highlight three critical dimensions of the AMR challenge in China, which include the recent emergence of resistant bacteria, genomic surveillance efforts, and progress in the development of novel antimicrobial agents. By synthesizing recent research on the evolutionary dynamics of drug-resistant pathogens in China and outlining innovative antimicrobial strategies, this study provides insights to guide evidence-based antimicrobial stewardship programs.

遏制中国抗菌耐药性危机：新发超级细菌的发现、基因组监测与创新对策

童倩^1,2；曾利平³；葛艺欣⁴；贾佳^1,#

1. 免疫与病原生物学系，感染与免疫研究中心，医学院，同济大学，上海，中国；

2. 实验室医学中心，浙江省人民医院检验医学中心输血科，杭州医学院附属人民医院，杭州市，浙江省，中国；

3. 病原与生物学系，江苏省病原生物学重点实验室，南京医科大学，南京市，江苏省，中国；

4. 华东医学生物技术研究所，南京市，江苏省，中国。

^# 通讯作者：贾佳, jiajia25@tongji.edu.cn。

中国的抗菌药物耐药性（AMR）问题已逐渐升级为一项严峻的公共卫生威胁。在临床医疗和农业领域中，抗生素的广泛使用产生了强大的选择压力，这不仅促使耐药菌株的出现，也加速了其传播。多重耐药菌的迅速蔓延正是这一威胁不断加剧的明证。因此，亟需加强对这些病原体的基因组监测，并开发有效的应对策略。本文聚焦于中国AMR挑战的三个关键方面：耐药菌的近期出现情况、基因组监测的进展以及新型抗菌药物的研发动态。通过整合国内关于耐药病原体进化演变机制的最新研究，并概述创新性的抗菌策略，本研究为推进循证抗菌药物管理计划提供了理论依据与实践见解。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.197

Genomic Surveillance and Phylogenetic Analysis of Monkeypox Virus Sampled from Clinical Monkeypox Cases and Sewage — Sichuan Province, China, 2023

Ranran Cao¹; Chengxia Liu¹; Ying Shi²; Can Luo¹; Xin Chen³_; Li Liu¹; Chaohua Xu¹; Ming Pan¹; Changcheng Wu^4,#; Li Zhang^1,#; Wenjie Tan^4,#

1. Sichuan Center for Disease Control and Prevention, Chendu City, Sichuan Province, China;

2. Sichuan International Travel Healthcare Center (Chengdu Customs Port Clinic), Chendu City, Sichuan Province, China;

3. Jinjiang Center for Disease Control and Prevention, Chendu City, Sichuan Province, China;

4. National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

^# Corresponding author: Changcheng Wu, wucc@ivdc.chinacdc.cn; Li Zhang, Zhanglilyscdc@163.com; Wenjie Tan, tanwj@ivdc.chinacdc.cn.

Monkeypox (Mpox) has reemerged globally, with thousands of confirmed cases reported in China. However, limited data exists on the genomic variations and transmission patterns of monkeypox virus (MPXV) in southwestern China. Clinical samples from Mpox cases and sewage samples from wastewater treatment plants were collected from Sichuan Province for whole-genome sequencing and MPXV analysis. In the second half of 2023, 96 clinical samples from MPOX patients were collected, yielding 58 full-length viral genomes. All sequenced viruses belonged to the Western African clade (IIb), comprising three C.1 and fifty-five C.1.1 sequences. This study determined that MPOX cases in Sichuan originated from both importation and subsequent local transmission, with evidence of at least six distinct transmission clusters. Additionally, 26 sewage samples were collected and 3 complete MPXV genomes were constructed. Analysis of viral genomes from sewage samples demonstrated a 95% concordance in high-frequency mutation sites with those observed in clinical cases, suggesting that sewage surveillance effectively captures diagnosed cases and serves as a robust complement to conventional monitoring. The integration of newly sequenced genomes with published data revealed an increased mutation rate in MPXV, along with fluctuating patterns of expansion and contraction of the effective viral population size. This study provides preliminary insights into MPXV transmission dynamics and genomic evolution in Sichuan and demonstrates the utility of sewage monitoring in tracking viral diversity.

猴痘临床病例及污水中猴痘病毒基因组监测及系统发育分析 — 四川省，中国，2023年

曹冉冉¹；刘晨霞¹；石莹²；罗灿¹；陈欣³；刘李¹；徐朝花¹；潘明¹；吴长城^{4, #}；张丽^1,#；谭文杰^4,#

1 四川省疾病预防控制中心，成都市，四川省，中国

2 四川国际旅行卫生保健中心（成都海关口岸门诊部），成都市，四川省，中国

3 锦江区疾病预防控制中心，成都市，四川省，中国

4 传染病溯源预警与智能决策国家重点实验室, 中国疾病预防控制中心病毒所，北京，中国。

^# 通信作者：吴长城，wucc@ivdc.chinacdc.cn；张丽， Zhanglilyscdc@163.com；谭文杰，tanwj@ivdc.chinacdc.cn。

猴痘再次在全球范围内流行，中国也报告了数千例确诊病例。然而，有关中国西南地区猴痘病毒基因组变异和传播模式的报道仍然较少。采集四川省猴痘病例临床样本和污水处理厂污水样本，用于进行猴痘病毒全基因组测序和分析。2023年下半年，共采集96份猴痘病例临床样本，获得58个猴痘病毒全长基因组序列。所有序列均属于IIb分支，包含3个C.1和55个C.1.1。四川省猴痘流行株既有输入来源，也有后续本地传播，并存在至少六个不同的传播簇。此外，研究采集了26份污水样本并成功构建3个完整的猴痘病毒基因组。污水中猴痘病毒全基因组分析显示，污水与临床病例来源的猴痘病毒高频突变位点一致性为95%，这表明污水监测能有效捕获确诊病例感染病毒的基因组信息，是传统监测手段的有力补充。通过整合分析本研究新测得基因组数据与已发表数据，发现猴痘病毒突变率上升，以及病毒有效种群规模呈现扩张与收缩的波动模式。本研究初步揭示了四川省猴痘病毒的传播动态和基因组进化特征，并印证了污水监测在追踪病毒多样性方面的应用价值。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.198

Cost-effectiveness Assessment of A Smart Health Education Pillbox for Canine Echinococcosis Control During A Cluster-Randomized Trial — Western China, 2023–2024

Shijie Yang¹; Chenqing Sun¹; Ning Xiao¹; Shuai Han¹; Liying Wang¹; Ying Wang¹; Jiangshan Zhao²; Shanglin Wu³; Xiao Ma⁴; Yu Feng⁵; Benfu Li⁶; Tongmin Wang⁷; Yuhua Li⁸; Yuancheng Yang⁸; Kaisaier Tuerxunjiang²; Zonglin Shen⁸; Xiao-nong Zhou^1#

1. National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Health Commission Key Laboratory on Parasite and Vector Biology, WHO Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China; 

2. Xinjiang Uygur Autonomous Region Center for Disease Control and Prevention, Urumqi City, Xinjiang Uygur Autonomous Region, China;

3. Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan City, Ningxia Hui Autonomous Region, China;

4. Qinghai Institute for Endemic Disease Prevention and Control, Xining City, Qinghai Province, China;

5. Department of Parasitic Diseases, Gansu Center for Disease Control and Prevention, Lanzhou City, Gansu Province, China;

6. Yunnan Institute of Parasitic Diseases, Kunming City, Yunnan Province, China;

7. Center for Disease Control and Prevention of Xinjiang Production and Construction Corps, Urumqi City, Xinjiang Uygur Autonomous Region, China;

8. Tianzhu Tibetan Autonomous County Center for Disease Control and Prevention, Wuwei City, Gansu Province, China.

^# Corresponding author: Xiao-nong Zhou, zhouxn1@chinacdc.cn.

Echinococcosis is a zoonotic parasitic disease that necessitates regular deworming of canines. The efficacy of CMD is impeded by geography, the workforce, and severe weather conditions. This study evaluated the effectiveness and cost-effectiveness of SHEP compared to CMD in canine echinococcosis control. A 12-month cluster randomized trial was conducted across nine endemic Chinese counties, where townships were randomly assigned to either the SHEP or CMD group. The primary outcomes included Echinococcus antigen positivity rates in dog feces, deworming frequency, and cost components. Data analysis was conducted using SPSS 27.0, employing Generalized Estimating Equations (GEE), odds ratios (OR), relative risk (RR), relative risk reduction (RRR), and protective efficacy (1/RR). SHEP implementation significantly reduced Echinococcus infection risk by 35.45% and demonstrated 1.55-fold higher protective efficacy than CMD. The total deworming costs decreased by 22.62%, with substantial savings in personnel (53.15%), transportation (79.48%), and operational time requirements (30.13%). The proportion of dogs that achieved the target annual deworming frequency (9–12 times) increased from 51.89% to 91.38%, representing a relative improvement of 52.59%. SHEP, which integrates automated reminders of praziquantel (PZQ) tablet delivery, is a promising tool for diminishing resource utilization and mitigating Echinococcus transmission in endemic areas.

犬棘球蚴病感染控制的成本效益评估：智能健康教育药盒的整群随机试验 — 中国西部，2023–2024年

杨诗杰¹；孙晨清¹；肖宁¹；韩帅¹；王立英¹；王莹¹；赵江山²；吴尚林³；马霄⁴；冯宇⁵；李奔福⁶；王童敏⁷；李玉花⁸；杨元成⁸；开赛尔·吐尔逊江²；沈棕林；周晓农^1,#

1.传染病溯源预警与智能决策全国重点实验室，国家卫生健康委员会寄生虫与媒介生物学重点实验室，世界卫生组织热带病合作中心，科技部国家热带病国际研究中心，寄生虫病预防控制所（国家热带病研究中心），中国疾病预防控制中心，上海，中国；

2. 新疆维吾尔自治区疾病预防控制中心，乌鲁木齐市，新疆维吾尔自治区，中国；

3. 宁夏回族自治区疾病预防控制中心，银川市，宁夏回族自治区，中国；

4. 青海省地方病预防控制所，西宁市，青海省，中国；

5. 寄生虫病预防控制科，甘肃省疾病预防控制中心寄生虫病预防控制所，兰州市，甘肃省，中国；

6. 云南省寄生虫病防治所，昆明市，云南省，中国；

7. 新疆生产建设兵团疾病预防控制中心，乌鲁木齐市，新疆维吾尔自治区，中国；

8. 天祝藏族自治县疾病预防控制中心，武威市，甘肃省，中国。

^# 通信作者：周晓农，zhouxn1@chinacdc.cn。

棘球蚴病是人畜共患寄生虫病，需对犬科动物定期驱虫。传统驱虫模式（CMD）的实施效果受地理环境、人力资源及恶劣天气条件制约。本研究评估了智能健康教育药盒（SHEP）驱虫相较于CMD在犬棘球蚴病防控中的效果与成本效益。在中国9个流行县开展了为期12个月的整群随机试验，乡镇单位被随机分配至SHEP组或CMD组。主要结局指标包括犬粪棘球绦虫抗原阳性率、驱虫频率及成本构成。采用SPSS 27.0软件中广义估计方程（GEE）进行数据分析，并计算优势比（OR）、相对危险度（RR）、相对危险降低率（RRR）及保护效力（1/RR）等指标。SHEP实施使棘球绦虫感染风险显著降低35.45%，保护效力是CMD的1.55倍。驱虫总成本下降22.62%，其中人员成本（53.15%）、运输成本（79.48%）及时间成本（30.13%）显著下降。达到目标年驱虫频率（9-12次）的犬只比例从51.89%提升至91.38%，相对改善幅度达52.59%。集吡喹酮药片自动投送和提醒功能于一体的智能健康教育药盒，既能有效减少资源投入又能阻遏棘球绦虫传播，具有广阔应用前景。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.199

Analysis on Cross-Species Transmission of Human–Suidae Zoonotic Viruses — Global, 1882–2022

Mingchen Zhao^1,2; Xuechun Wang³; Erri Du⁴; Qiang Wang⁵; Tao Li⁶; Lifeng Zhang⁷; Zhongwei Jia^7,#

1. Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China;

2. Beijing Center for Disease Prevention and Control, Beijing, China;

3. Graduate School of Chinese PLA General Hospital, Beijing, China;

4. SILC Business School, Shanghai University, Shanghai, China;

5. Goodwill Hessian Health Technology Co., Ltd., Beijing, China;

6. National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China;

7. Department of Global Health, School of Public Health, Peking University, Beijing, China.

^# Corresponding author: Zhongwei Jia, jiazw@bjmu.edu.cn.

Suidae-associated zoonotic viruses represent a significant global public health threat through cross-species transmission events. Current research remains limited to localized outbreak investigations and lacks comprehensive, systematic global analysis. We collected human–Suidae virus data from the National Center for Biotechnology Information (NCBI) Virus Database, integrating viral characteristics, host information, and environmental and anthropogenic factors. Boosted Regression Trees (BRT) models were employed to evaluate cross-species transmission risk and identify key predictive factors. A total of 43 human–Suidae zoonotic viruses reported during 1882–2022 were evaluated. The Boosted Regression Trees (BRT) model achieved area under the curve (AUC) values of 0.924 (training) and 0.804 (testing). Host–human phylogenetic distance and viral genome size emerged as the primary predictors. Porcine circovirus 3 (PCV3) demonstrated the highest predicted risk (>0.9). This study establishes a data-driven framework for assessing cross-species transmission risk, supporting early warning systems and targeted prevention strategies. The findings underscore the critical importance of One Health approaches and recommend enhanced surveillance and biosecurity measures for high-risk viruses such as PCV3.

人猪共患病毒跨种传播研究 — 全球，1882–2022年

赵明辰^1,2；王雪纯³；杜尔日⁴；王强⁵；李涛⁶；张利锋⁷；贾忠伟^7,#

1. 北京大学公共卫生学院流行病与卫生统计学系，北京，中国；

2. 北京市疾病预防控制中心，北京，中国；

3. 中国人民解放军总医院研究生院，北京，中国；

4. 上海大学悉尼工商学院，上海，中国；

5. 北京嘉和海森健康科技有限公司，北京，中国；

6. 中国疾病预防控制中心结核病预防控制中心，北京，中国；

7. 北京大学公共卫生学院全球健康系，北京，中国。

^# 通讯作者: 贾忠伟, jiazw@bjmu.edu.cn。

猪科动物相关的人畜共患病毒可通过跨种传播威胁全球公共卫生，现有研究多集中于局部疫情，缺乏系统性、全球性分析。基于 NCBI Virus Database 收集人-猪病毒数据，整合病毒特征、宿主信息及环境和人为因素。利用梯度提升回归树（BRT）模型评估跨种传播风险，并识别关键预测因子。共评估1882–2022 年间报告的43种人-猪共患病毒。BRT 模型训练集与测试集 AUC 分别为 0.924和 0.804。宿主-人类系统发育距离和病毒基因组大小是主要预测因子。Porcine circovirus 3（PCV3）显示最高跨种传播风险（>0.9）。本研究提供了基于数据的跨种传播风险评估框架，支持早期预警和靶向防控。结果强调One Health策略在监测和预防人畜共患病毒中的重要性，并建议加强对高风险病毒如PCV3的监测和生物安全管理。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.200

Identification of A Novel Human Adenovirus Type 114 Associated with An Acute Respiratory Disease Outbreak at An Elementary School — Beijing, China, September 2024

Xiuxia Wei¹; Min Li¹; Yi Wang¹; Yanna Yang¹; Ruoran Lyu¹; Guilan Lu^2#; Zhen Zhu^3,#

1. Beijing Economic-Technological Development Area Center for Disease Prevention and Control, Beijing, China;

2. Beijing Center for Disease Control and Prevention, Beijing, China;

3. World Health Organization Regional Office for the Western Pacific Regional Reference Poliovirus Laboratory, State Key Laboratory of Molecular Virology & Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

# Corresponding author: Guilan Lu, luguilan@bjcdc.org; Zhen Zhu, zhuzhen@ivdc.chinacdc.cn.

In September 2024, multiple cases of fever were reported at an elementary school in the Economic-Technological Development Area. Local disease control personnel identified the initial case through epidemiological investigations and simultaneously initiated active case searches and case sample collection. Laboratory personnel employed real-time quantitative RT-PCR for nucleic acid screening of various respiratory pathogens. Virus isolation and culture, along with conventional PCR, were used for amplification and sequencing of target gene sequences. Molecular tracing was conducted using gene homology and phylogenetic analysis. Based on the epidemiological investigations and laboratory test results, it was determined that the fever outbreak was caused by human adenovirus. Through sequence analysis of three target genes, Penton base, Hexon, and Fiber, the adenovirus genotype responsible for the outbreak was identified as HAdV-B114. This marks the first time in China that an outbreak caused by HAdV-B114 has been detected and reported. After undergoing genetic recombination, HAdV has become a novel HAdV strain with potential risks to human health, capable of causing new and sudden infectious disease outbreaks in the population. Therefore, surveillance efforts should be intensified.

一小学急性呼吸道感染暴发疫情相关的新型人腺病毒114型的鉴定 — 北京市，中国，2024年9月

尉秀霞¹；李敏¹；王祎¹；杨艳娜¹；吕若然¹；卢桂兰^2,#；朱贞^3,#

1. 北京经济技术开发区疾病预防控制中心，北京，中国；

2. 北京市疾病预防控制中心，北京，中国；

3. 世界卫生组织西太平洋区脊髓灰质炎参比实验室,国家卫生健康委员会医学病毒学和病毒病重点实验室，病毒病预防控制所，中国疾病预防控制中心，北京，中国。

^# 通讯作者: 卢桂兰，luguilan@bjcdc.org; 朱贞, zhuzhen@ivdc.chinacdc.cn。

2024年9月北京经济技术开发区一所学校出现了多个发热病例。当地疾控人员通过流行病学调查，确定首发病例，同时开展病例主动搜索和病例样本采集。实验室人员采用实时荧光定量RT-PCR方法进行呼吸道多种病原体的核酸筛查。采用病毒分离培养和普通PCR进行靶基因序列的扩增和测定。采用基因同源性和系统进化分析进行分子溯源。根据流行病学调查情况和实验室检测结果，判定此次发热疫情为一起由腺病毒感染引起的暴发疫情。通过Penton base、Hexon 和 Fiber的3个靶基因序列分析，确定此次暴发疫情的腺病毒基因型为HAdV-B114。这是我国首次发现并报告的由HAdV-B114引起暴发疫情。HAdV在发生基因重组后成为对人类健康具有潜在危险性的新型 HAdV，可在人群中引起新发突发传染病疫情，需加强监测。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.201