Comparative Analysis of Antibiotic Resistance and Genomic Characteristics of Enterococcus faecium and Enterococcus lactis Along the Food Chain — 5 PLADs, China, 2015–2024

Wenbin Chen^1,2,3; Xiaoyi Zheng³; Hao Wu³; Yiwen Jing⁴; Zehong Ye²; Zixin Peng^1,2,#; Shaofu Qiu^3,#

1. School of Public Health, Southern Medical University, Guangzhou City, Guangdong Province, China;

2. NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China;

3. Center for Disease Control and Prevention of Chinese PLA, Beijing, China;

4. Fengjie County Center for Disease Control and Prevention, Chongqing, China.

^# Corresponding author: Zixin Peng, pengzixin@cfsa.net.cn; Shaofu Qiu, qiushf0613@hotmail.com.

Foodborne antibiotic-resistant enterococci pose significant risks to One Health and clinical antimicrobial efficacy through food chain transmission. Following the taxonomic reclassification of Enterococcus faecium (E. faecium), comprehensive long-term surveillance data on antibiotic resistance (ABR) patterns and genomic characteristics of E. faecium and Enterococcus lactis (E. lactis) across food animals, environmental sources, and human populations remain limited. A total of 2,233 samples were collected from multiple nodes along the food chain across 5 Chinese provincial-level administrative divisions (PLADs) during 2015–2019 and 2023–2024. E. faecium (87 isolates) and E. lactis (153 isolates) were identified through whole-genome sequencing and average nucleotide identity analysis. Antimicrobial susceptibility testing, comprehensive genomic content analysis, and pan-genome-wide association studies were performed. E. faecium demonstrated significantly higher resistance rates to 12 antimicrobials compared with E. lactis (P<0.05). Conversely, E. lactis exhibited a higher resistance rate to erythromycin than E. faecium (P<0.01). The multidrug-resistant (MDR) rate of E. faecium (43/87, 49.4%) substantially exceeded that of E. lactis (16/153, 10.5%) (P<0.001). Genomic analysis revealed that E. faecium harbors significantly more antibiotic resistance genes, mobile genetic elements, and plasmid replicons than E. lactis. No significant interspecies differences were observed in virulence gene profiles associated with adhesion, immune modulation, biofilm formation, and exotoxin production. E. faecium presents substantially greater ABR risks than E. lactis within the Chinese food chain, necessitating enhanced species-specific surveillance programs. Future interventions should prioritize targeted control strategies tailored to each species to effectively mitigate One Health threats.

食物链中屎肠球菌与乳酸肠球菌的抗生素耐药性及基因组内容比较分析 — 5省份，中国，2015–2024年

陈文彬^1,2,3；郑枭弋³；吴昊³；敬怡雯⁴；叶泽弘²；彭子欣^1,2,#；邱少富^3,#

1. 公共卫生学院，南方医科大学，广州市，广东省，中国；

2. 国家卫生健康委员会食品安全风险评估重点实验室，中国医学科学院研究单元（2019RU014），国家食品安全风险评估中心，北京，中国；

3. 中国人民解放军疾病预防控制中心，北京，中国；

4. 奉节县疾病预防控制中心，重庆，中国。

^# 通信作者: 彭子欣，pengzixin@cfsa.net.cn；邱少富，qiushf0613@hotmail.com。

食源性耐菌肠球菌可通过食物链对 “同一健康”（One Health）及临床抗菌效果构成风险。在屎肠球菌重新分类后，针对食用动物、环境及人体内屎肠球菌与乳酸肠球菌的耐菌性及基因组内容，目前仍缺乏长期监测数据。2015–2019 年及 2023–2024 年期间，在我国 5 个省级行政区的食物链中采集样本共计 2,233 份。通过全基因组测序及平均核苷酸一致性分析，鉴定出 87 株屎肠球菌与 153 株乳酸肠球菌，并开展了抗菌药物敏感性试验、基因组内容分析及泛基因组关联研究。屎肠球菌对 12 种抗菌药物的耐药率均高于乳酸肠球菌（P<0.05）；但乳酸肠球菌对红霉素的耐药率高于屎肠球菌（P<0.01）。屎肠球菌的多重耐药率（43 株 / 87 株，49.4%）显著高于乳酸肠球菌（16 株 / 153 株，10.5%）（P<0.001）。基因组层面上，屎肠球菌携带的耐菌基因、可移动遗传元件及质粒复制子数量均多于乳酸肠球菌。而在与黏附、免疫调节、生物膜形成及外毒素产生相关的毒力基因方面，两种肠球菌未表现出显著差异。在我国食物链中，屎肠球菌带来的耐菌风险显著高于乳酸肠球菌，需开展针对性监测。未来应重点制定特定菌种的防控策略，以降低 “同一健康” 面临的威胁。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.240

Antibiotic Susceptibility of Nocardia Clinical Isolates Collected from Chinese Patients –– China, 2014–2024

Pan Zhao^1,2, Shuai Xu¹, Min Yuan¹, Zhiguo Liu¹, Xiaotong Qiu¹, Zhenjun Li^1,#

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

2. Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou City, Zhejiang Province, China.

^# Corresponding author: Zhenjun Li, lizhenjun@icdc.cn.

Nocardia species are found worldwide in soil rich in organic matter and can cause nocardiosis in humans. Trimethoprim-sulfamethoxazole has long been the first-line treatment for Nocardia infections; however, resistance to this therapy has recently been reported. Sixty-three clinical Nocardia isolates collected in China were tested against 32 antimicrobial agents using the broth microdilution method. Phylogenetic analysis of the 16S rRNA gene was was performed to identify the species. Three sequences from samples collected in Hainan Province did not match any known Nocardia species, suggesting significant genetic diversity among Nocardia isolates. Nocardia strains generally exhibited high resistance to clarithromycin, clindamycin, and isoniazid. Clinical and reference strains of N. farcinica and N. otitidiscaviarum were susceptible to amikacin and linezolid. Amoxicillin-clavulanate and imipenem were effective against all clinical and reference strains of N. farcinica, whereas gentamicin was effective against all clinical and reference strains of N. otitidiscaviarum. Linezolid and amikacin were the most consistently active drugs among the analyzed species. Variability of antimicrobial susceptibility was observed among clinical isolates of the same species and between clinical and reference isolates of the same species. Overall, this study highlights the need for better assessment of the burden of nocardiosis in China and for continuous monitoring of antimicrobial resistance among Nocardia isolates.

诺卡菌临床分离株抗生素药物敏感性分析 — 中国, 2014–2024年

赵盼^1,2, 徐帅¹, 袁敏¹, 刘志国¹, 邱小彤¹, 李振军^1,#

1. 传染病溯源预警与智能决策全国重点实验室，传染病预防控制所，中国疾病预防控制中心，北京，中国;

2. 卫生检验中心，杭州市疾病预防控制中心（杭州市卫生监督所），杭州市，浙江省，中国。

^# 通信作者：李振军，lizhenjun@icdc.cn。

诺卡菌广泛存在于富含有机物的土壤中，可感染人类并引起诺卡菌病。甲氧苄啶-磺胺甲噁唑是治疗诺卡菌感染的一线药物，但近期有对该治疗方案耐药的报道。本研究使用肉汤微量稀释法对63株中国诺卡菌临床分离株进行了32种抗生素的药敏试验。采用16S rRNA系统发育分析确定诺卡菌菌种。三株菌株（均分离自海南省）的序列无法归类到已知的诺卡菌物种，提示诺卡菌分离株间存在显著的遗传多样性。诺卡菌普遍对克拉霉素、克林霉素和异烟肼表现出高耐药率。脓肿诺卡菌和豚鼠耳炎诺卡菌临床株和标准株均对阿米卡星和利奈唑胺敏感。阿莫西林-克拉维酸和亚胺培南对脓肿诺卡菌临床株和标准株均有效，而庆大霉素则对豚鼠耳炎诺卡菌临床株和标准株均有效。在本研究分析的菌种中，利奈唑胺和阿米卡星是效果最一致的抗生素。在同一菌种的临床分离株之间，以及同一菌种的临床分离株与标准菌株之间，均发现了抗生素敏感性的差异。总体而言，本研究强调未来需更好地评估中国诺卡菌病的疾病负担，并对诺卡菌分离株的抗生素耐药性进行持续监测。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.241

Characteristics and Influencing Factors of Antimicrobial Resistance in Salmonella Isolated from Asymptomatic Workers — Yulin City, Guangxi Zhuang Autonomous Region, China, 2013–2024

Yao Peng^1,2,&, Ming Luo^3,&, Ziyu Liu^2,4, Changyu Zhou³, Hongqun Zhao², Zhenpeng Li^2,4, Biao Kan^1,2,#, Ning Jiang^3,#, Xin Lu^4,#

1. School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, China;

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

3. Yulin Center for Disease Control and Prevention, Yulin City, Guangxi Zhuang Autonomous Region, China;

4. Department of Microbiomics, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

^& Joint first authors.

^# Corresponding author: Ning Jiang, ylcdcjn@163.com; Biao Kan, kanbiao@icdc.cn; Xin Lu, luxin@icdc.cn.

Asymptomatic carriers of antibiotic-resistant Salmonella constitute a significant yet frequently overlooked public health threat. This study aimed to characterize AMR patterns in Salmonella isolated from asymptomatic workers in Yulin, China, over a 12-year period (2013–2024) and to identify the potential influence of natural and socioeconomic factors. Antimicrobial susceptibility testing was performed against 11 antimicrobial agents. We analyzed temporal trends in AMR rates using the Mann-Kendall test and assessed associations between AMR rates and natural or socioeconomic variables using Spearman's rank correlation, Principal Component Regression (PCR), and Least Absolute Shrinkage and Selection Operator (LASSO) regression. An Autoregressive Integrated Moving Average (ARIMA) model was employed to forecast future resistance trends. Resistance to tetracycline (TET) was most prevalent (mean rate: 66.2%). The overall multidrug resistance (MDR) rate was 41.9%, exhibiting a significant increasing trend (P<0.05). Most alarmingly, the tigecycline (TGC) resistance rate surged from 0% to 24.4% by 2024. PCR model analysis revealed that a composite "Socioeconomic and Healthcare Development Index" served as the primary predictor of this increase, explaining 54.9% of the variance in TGC resistance rates. The ARIMA model forecasted a continued upward trajectory for TGC resistance through 2025–2026. Our findings demonstrate a significant rise in MDR Salmonella among asymptomatic workers in Yulin, establishing them as important reservoirs of antibiotic-resistant Salmonella. The emergence and rapid escalation of TGC resistance is strongly associated with regional socioeconomic and healthcare development. These results underscore the urgent need for integrated surveillance within the One Health framework to effectively address AMR transmission.

健康从业人员携带沙门菌耐药流行特征及影响因素分析 — 玉林市，广西壮族自治区，中国，2013–2024年

彭遥^1,2.&，罗铭^3,&，刘子瑜^2,4，周昶宇³，赵宏群²，李臻鹏^2,4，阚飙^1,2,#，蒋宁^3,#，卢昕^4,#

1. 南京医科大学公共卫生学院，南京市，江苏省，中国；

2. 传染病溯源预警和智能决策全国重点实验室，中国疾病预防控制中心传染病预防控制所，  北京，中国；

3. 玉林市疾病预防控制中心，玉林市，广西壮族自治区，中国；

4. 中国疾病预防控制中心传染病预防控制所微生物组学研究室，北京，中国。

^& 共同第一作者。

^# 通讯作者: 蒋宁，ylcdcjn@163.com；阚飙，kanbiao@icdc.cn；卢昕，luxin@icdc.cn。

携带耐药沙门菌的无症状人群作为一个隐蔽的传染源，构成了较大但常被忽视的公共卫生风险。本研究旨在分析2013至2024年间从玉林市无症状从业人员粪便样本中分离的沙门菌的耐药特征，并探究抗生素耐药率与自然及社会经济因素之间的关联性。采用微量肉汤稀释法检测其对11种抗生素的敏感性。采用Mann-Kendall检验分析耐药率时间趋势；通过斯皮尔曼秩相关、主成分回归（PCR）和LASSO回归分析耐药率与自然及社会经济变量之间的相关性。构建ARIMA模型预测替加环素的耐药率趋势变化。四环素（TET）耐药率最高（平均66.2%），多重耐药（MDR）率高达41.9%。替加环素（TGC）耐药率从2013年的0%急剧上升至2024年的24.4%。PCR分析显示，“社会经济与医疗卫生发展指数”是TGC耐药率上升的关键驱动因素。ARIMA模型预测TGC耐药率在2025-2026年将持续上升。玉林市无症状从业人员已成为多重耐药沙门菌的重要储存库与传播源，其流行形势日趋严峻。替加环素耐药率的快速上升与区域社会经济及医疗发展水平密切相关。当前迫切需要基于“同一健康”理念，构建针对此类高风险人群的综合监测与防控体系，以阻断耐药菌株的潜在传播链条。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.242

High Prevalence and Genomic Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Yellow River and Source Water from A One Health Perspective — Henan Province, China, 2023–2024

Tiantian Tian^1,2,3, Yan Sun¹, Yunfeng Shi¹, Shimin Zhang¹, Shuxia Xu¹, Jiran Zhang¹, Xitian Yang³, Yu Zhang^2,4,#

1. College of Life Sciences, Henan Agricultural University, Zhengzhou City, Henan Province, China

2. Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China

3. College of Forestry, Henan Agricultural University, Zhengzhou City, Henan Province, China

4. University of Chinese Academy of Sciences, Beijing, China.

^# Corresponding authors: Yu Zhang, zhangyu@rcees.ac.cn.

Understanding the prevalence and dissemination pathways of the clinically relevant extended-spectrum β-lactamase (ESBL) genes and ESBL-producing Escherichia coli (E. coli) within the Yellow River is essential from a One Health perspective to control antibiotic resistance dissemination from environmental reservoirs to human populations. Water samples were collected from the Yellow River and two of its major tributaries in Henan Province during 2023 and 2024. TaqMan quantitative polymerase chain reaction (qPCR) was used to quantify the abundance of the ESBL gene bla_CTX-M-G9. Twenty-three E. coli isolates underwent whole-genome sequencing (WGS), and 167 publicly available E. coli genomes from diverse sources were incorporated into the comparative phylogenetic analysis. The bla_CTX-M-G9 gene was ubiquitous across all sampling sites, exhibiting significantly higher relative abundance during the dry season compared to the flat season. The multidrug-resistant E. coli sequence type (ST) 6802 carrying bla_CTX-M-14 emerged as the predominant clone. Strong positive correlations were observed between bla_CTX-M-G9 abundance and plasmids carried by E. coli ST6802 in the Yellow River, providing evidence for clonal expansion during the dry season. Furthermore, comparative phylogenetic analysis integrating human, animal, and environmental isolates demonstrated that ST6802 strains from this study were closely related to those previously identified in anaerobic digestion systems treating pig manure in China, suggesting an animal-to-environment transmission pathway. These findings emphasize the urgent need to implement targeted interventions that prevent the transmission of antibiotic resistance from animal sources into aquatic environments, thereby protecting public health and preserving the integrity of critical water resources.

从同一健康视角看黄河及水源水中产ESBL大肠杆菌的高流行率与基因组特征 — 河南省，中国，2023–2024年

田甜甜^1,2,3，孙燕¹，史韵风¹，张世敏¹，徐淑霞¹，张继冉¹，杨喜田³，张昱^2,4,#

1. 生命科学学院，河南农业大学，郑州市，河南省，中国；

2. 环境水质学重点实验室，区域环境安全全国重点实验室，中国科学院生态环境研究中心，北京，中国；

3. 林学院，河南农业大学，郑州市，河南省，中国；

4. 中国科学院大学，北京，中国。

^# 通信作者：张昱，zhangyu@rcees.ac.cn。

黄河是中国北方地区重要的饮用水源，同时也是抗生素耐药细菌及耐药基因从环境向人群传播的重要媒介。本研究旨在揭示黄河河南段及水源水中临床相关的超广谱β-内酰胺酶（Extended-Spectrum β-Lactamase, ESBL）基因bla_CTX-M-G9的时空分布特征，从同一健康视角解析产ESBL大肠杆菌的基因组遗传特征与传播路径。2023-2024年，分别在丰水期、枯水期和平水期采集黄河河南段干流及两条支流的水样。采用qPCR检测ESBL基因bla_CTX-M-G9及相关可移动元件的丰度。选取23株头孢噻肟耐药大肠杆菌进行全基因组测序与分析，并结合公共数据库中167个不同来源的大肠杆菌基因组数据，基于单核苷酸多态性差异和全基因组多位点序列分型进行基因组系统进化分析。ESBL基因bla_CTX-M-G9普遍存在于黄河河南段及支流中，且枯水期其相对丰度显著高于平水期。携带bla_CTX-M-14基因型的多重耐药大肠杆菌序列分型（Sequence type, ST）6802为枯水期的优势克隆。在枯水期，黄河中bla_CTX-M-G9的丰度与大肠杆菌ST6802携带的质粒（IncHI2、IncHI2A、IncX1和IncFIB）的丰度显著正相关，进一步证明了枯水期ST6802菌株的克隆传播。此外，基于"同一健康"视角的系统进化分析表明，本研究中的大肠杆菌ST6802分离株与猪粪厌氧消化系统中发现的ST6802菌株在遗传进化上高度一致，提示该菌株存在环境传播风险及潜在动物来源。该研究为从“同一健康”视角监测和管控动物源抗生素耐药性的环境传播风险提供了科学依据，同时为制定抗生素耐药性的源头阻控策略、推动抗生素耐药性综合公众教育及广泛的社会参与提供了重要参考。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.243

Genomic Surveillance of Salmonella London and Rissen Reveals International Transmission Patterns and Expanding Antimicrobial Resistance — Shanghai Municipality, China, 2020–2024

Xueer Li^1,2, Ling Zhong^1,3, Yanru Liang², Shuqi You², Yahui Zhan⁴, Qing Cao⁵, Zhemin Zhou⁶, Lifeng Pan^2,#, Heng Li^1,3,#

1. Key Laboratory of Alkene-carbon Fibres-based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou City, Jiangsu Province, China;

2. Department of Microbiology, Pudong District Center for Disease Control and Prevention, Shanghai, China;

3. Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou City, Jiangsu Province, China;

4. Suzhou Center for Disease Control and Prevention, Suzhou City, Jiangsu Province, China;

5. Department of Infectious Disease, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China;

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

^# Corresponding authors: Lifeng Pan, lfpan@pdcdc.sh.cn; Heng Li, hli@suda.edu.cn.

Non-typhoidal Salmonella (NTS) represents a major global cause of foodborne illness. The emergence and worldwide dissemination of specific serotypes, including Salmonella London and Rissen, constitute a significant public health threat due to their escalating association with antimicrobial resistance (AMR), which compromises the effectiveness of first-line antibiotic therapies. We performed a comprehensive genomic analysis integrating 200 local isolates collected between 2020 and 2024 from Shanghai, China, with a global dataset comprising 1,353 S. London and 882 S. Rissen genomes retrieved from EnteroBase. Through whole-genome sequencing, phylogenetic reconstruction, and AMR gene profiling, we systematically characterized the population structure, transmission dynamics, and resistance profiles of these serotypes. Phylogeographic analysis revealed contrasting dissemination patterns: S. London spread predominantly through historical, geographically segregated clades, whereas S. Rissen demonstrated recent intercontinental mixing, with Thailand identified as a primary global source. We detected high-risk plasmids harboring up to 15 resistance genes that drove elevated multidrug resistance rates in 64% of S. London and 59% of S. Rissen isolates. Notably, Chinese isolates exhibited the highest AMR burden, with clinical environments identified as critical hotspots for resistance amplification. The global dissemination of S. London and Rissen is directly linked to international food trade networks, and their evolving AMR landscape represents a critical public health concern. These findings underscore the urgent need for integrated One Health surveillance strategies to effectively control the spread of resistant foodborne pathogens.

沙门氏菌伦敦型和里森型基因组监测揭示国际传播模式及抗菌素耐药性扩展 — 上海，中国，2020–2024年

李雪儿^1,2，钟岭^1,3，梁艳茹²，尤舒琪²，詹亚惠⁴，曹清⁵，周哲敏⁶，潘丽峰^2,#，李恒^1,3,#

1. 纺织行业烯碳纤维基重大传染病检测技术与应用重点实验室，苏州大学苏州医学院，老年疾病与免疫学教育部重点实验室，苏州市，江苏省，中国；

2. 上海市浦东新区疾病预防控制中心，上海，中国；

3. 基础医学院，苏州大学苏州医学院，苏州市，江苏省，中国；

4. 苏州市疾病预防控制中心，苏州市，江苏省，中国；

5. 附属上海儿童医学中心，医学院，上海交通大学，上海，中国；

6. 传染病智能跟踪与预测国家重点实验室，传染病预防控制所，中国疾病预防控制中心，北京，中国。

^# 通信作者：潘丽峰, lfpan@pdcdc.sh.cn; 李恒, hli@suda.edu.cn。

非伤寒沙门氏菌（NTS）是引起全球食源性疾病的主要病原体之一。近年来，某些血清型（如沙门氏菌伦敦型和利森型）的出现及其全球传播，因其与抗菌素耐药性（AMR）的关联日益密切，对一线抗生素治疗构成挑战，已成为重大公共卫生威胁。本研究整合了2020–2024年间于上海地区采集的200株本地分离株，并从EnteroBase数据库中获取了1353株伦敦沙门氏菌与882株利森沙门氏菌基因组构成的全球数据集。通过全基因组测序、系统发育重建及AMR基因鉴定，我们系统解析了这两种血清型的种群结构、传播动态与耐药特征。系统地理学分析表明，伦敦沙门氏菌主要通过历史上形成的地理隔离进化枝传播，而利森沙门氏菌则呈现近期跨大陆混合传播模式，并溯源至泰国为其全球扩散的主要起源地。研究发现，携带多达15个耐药基因的高风险质粒广泛存在，导致高比例的多重耐药表型，分别见于64%的伦敦沙门氏菌和59%的利森沙门氏菌分离株。值得注意的是，中国分离株的AMR负荷最高，且临床环境被识别为耐药性扩增的关键热点。伦敦型与利森型沙门氏菌的全球传播与国际食品贸易密切相关，其不断演变的AMR态势亟需关注。本研究强调了实施整合“一个健康”监测策略在控制耐药性食源性病原体传播中的重要性。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.244