Genomic Epidemiology of Salmonella enterica Serovar Give Reveals Clonal Expansion and Increasing Prevalence of qnrB19 — China, 2017–2024

Bowei Sun¹; Fenxia Fan¹; Zhigang Cui¹; Xiaoli Du¹; Jieren Wang¹; Haijian Zhou¹; Biao Kan¹; Meiying Yan^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.

^# Corresponding author: Meiying Yan, yanmeiying@icdc.cn.

Most current research on Salmonella has targeted prevalent serotypes, such as S. Typhimurium and S. Enteritidis, but the epidemiology and molecular characteristics of less prevalent serotypes remain insufficiently characterized. This study focused on S. Give, a less common serotype, to elucidate its genomic characteristics and antimicrobial resistance gene (ARG) profiles in China. The whole-genome sequences of 185 isolates of S. Give were extracted from the Chinese Pathogen Identification Network database from 2017 to 2024 and subjected to ARG detection and phylogenetic analysis. Two major sequence types (STs) were identified among the S. Give isolates, with ST516 being the predominant ST (92.43%) in China - consistent with the global ST distribution, except in the U.S., where ST654 prevailed (82.70%). The multidrug resistance (concurrent carriage of ≥3 ARGs) rate was 3.51%. All 185 isolates harbored the T57S point mutation in the parC gene on the chromosome, and an increasing trend was observed in the quinolone resistance gene qnrB19 prevalence in China from 2020 to 2024. In the major sublineage, 80% of the isolates contained the qnrB19 genes, and 86.41% of the isolates carried the small mobilizable plasmid Col (pHAD28) harboring the qnrB19 gene. Six clusters were detected, indicating several potential outbreaks within China.Moreover a close phylogenetic relationship with European strains was exhibited. This study shows that S. Give predominates in China and is characterized by clonal expansion and the widespread presence of qnrB19-harboring plasmids. S. Give’s sporadic outbreaks and multidrug resistance represent emerging public health threats. Moreover, the ongoing genomic surveillance of uncommon serotypes is essential to identify and mitigate concealed risks to public health.

吉韦沙门菌基因组流行病学研究：克隆群扩张与 qnrB19 基因流行率上升 — 中国，2017-2024年

孙博威¹；樊粉霞¹；崔志刚¹；杜小莉¹；王偈人¹；周海健¹；阚飙¹；闫梅英^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（中国预防医学科学院），北京，中国。

^# 通信作者: 闫梅英，yanmeiying@icdc.cn。

当前关于沙门氏菌的研究多聚焦于鼠伤寒沙门氏菌和肠炎沙门氏菌等常见血清型，而少见血清型的流行病学特征与分子特性尚缺乏充分阐释。本研究以少见沙门氏菌血清型吉韦（S. Give）为对象，阐明其在中国的基因组特征及耐药基因谱。从2017至2024年中国致病菌识别网数据库中提取185株吉韦沙门菌的全基因组序列，进行抗菌药物耐药基因（ARG）检测及系统发育分析。185株吉韦沙门菌分为两种主要序列型（ST），其中ST516在中国占主导地位（92.43%），这与全球ST分布一致，但美国例外，其以ST654为主（82.70%）。多重耐药率（同时携带≥3种耐药基因）为3.51%，185株分离株染色体上均携带parC基因的T57S点突变，且2020-2024年间喹诺酮耐药基因qnrB19在中国的流行率呈上升趋势。主要亚谱系中80%分离株携带qnrB19基因，86.41% 菌株携带含qnrB19的小型可移动质粒 Col（pHADR28）。共检测到 6 个聚类簇，提示我国境内存在多起潜在暴发事件。此外，这些菌株与欧洲菌株呈现出较近的系统发育亲缘关系。本研究表明，吉韦沙门菌在我国以克隆扩张为主要流行特征，并广泛携带含qnrB19的质粒。该血清型的散发性暴发与多重耐药表型已构成潜在的公共卫生新威胁。加强对少见沙门菌血清型的持续基因组监测，对识别和防控潜在公共卫生风险具有重要意义。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2026.037

Genomic Characterization of Clostridium Botulinum Isolates from Soil and Soybean Samples in High-Incidence Regions — Xinjiang, Inner Mongolia, and Qinghai PLADs, China, 2024

Yongsi Zhan^1,2, Xin Ma³, Xuebin Guo⁴, Meng Zhang⁵, Chunxia Cui⁶, Weiwei Li², Shaofei Yan², Shenghui Cui ⁷, Xingfen Yang^1,#, Yunchang Guo^1,2,#

1 Food Safety and Health Research Center, School of Public Health, Southern Medical University, Guangzhou City, Guangdong Province, China;

2 China National Center for Food Safety Risk Assessment, Beijing, China;

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

4 Qinghai Province Center for Disease Control and Prevention, Xining City, Qinghai Province, China;

5 Henan Province Center for Disease Control and Prevention, Zhengzhou City, Henan Province, China;

6 Inner Mongolia Center for Disease Control and Prevention, Hohhot City, Inner Mongolia Autonomous Region, China;

7 China National Institute for Food and Drug Control, Beijing, China.

^# Corresponding author: Yunchang Guo, gych@cfsa.net.cn; Xingfen Yang, yangalice79@smu.edu.cn.

Clostridium botulinum (C. botulinum) produces botulinum neurotoxins (BoNTs), the causative agents of botulism, a severe neuroparalytic disease prevalent in northwest China. Recent foodborne botulism outbreaks linked to commercially produced, vacuum-packaged, ready-to-eat foods were traced to raw meat contaminated with C. botulinum spores originating from soil, highlighting an emerging public health concern related to environmental reservoirs. However, genomic information on environmental isolates from high-incidence regions remains limited. A total of 23 C. botulinum strains isolated from soil and soybean samples in northwest China were sequenced in 2024. Genomes were analyzed for plasmids, prophages, antibiotic resistance genes, virulence factors, and bont. Evolutionary relationships and adaptive features were investigated via phylogenetic and functional analyses. The 23 isolates were classified into four BoNT subtypes [A5(B3), B2, B3, B4] and clustered according to subtype and geographic origin. Isolates from Qinghai formed distinct branches. Functional annotation revealed subtype-specific metabolic variations, particularly in carbohydrate metabolism. Although all isolates contained conserved bont clusters, some exhibited transposase insertions. One subtype A5(B3) isolate harbored bont within an incomplete prophage. These preliminary insights into environmental C. botulinum virulence, ecological adaptation, and evolutionary characteristics in northwest China provide a foundation for targeted surveillance and the development of preventive strategies against botulism in endemic regions.

高发区土壤及大豆样本中肉毒梭菌分离株的基因组特征分析 — 新疆、内蒙古和青海省级行政区，中国，2024年

詹咏斯^1,2马鑫³，郭学斌⁴，张濛⁵，崔春霞⁶，李薇薇²，闫韶飞²，崔生辉⁷，杨杏芬^1,#，郭云昌^1,2,#

1. 食物安全与健康研究中心，公共卫生学院，南方医科大学，广州市，广东省，中国；

2. 国家食品安全风险评估中心，北京市，中国；

3. 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；

4. 青海省疾病预防控制中心，西宁市，青海省，中国；

5. 河南省疾病预防控制中心，郑州市，河南省，中国；

6. 内蒙古自治区疾病预防控制中心，呼和浩特市，内蒙古自治区，中国；

7. 中国食品药品检定研究院，北京市，中国。

^# 通信作者：郭云昌，gych@cfsa.net.cn；杨杏芬，yangalice79@smu.edu.cn。

肉毒梭菌产生的肉毒毒素可引起严重的神经麻痹性疾病 — 肉毒中毒。食源性肉毒中毒在我国西北地区高发，近年来部分病例与真空包装即食肉制品相关，提示可能存在环境来源芽孢污染。本研究通过对我国西北地区环境及食品原料来源肉毒梭菌开展基因组学分析，以弥补相关数据空白。2024年，从我国西北地区土壤和黄豆样品中分离获得23株肉毒梭菌，使用Illumina平台进行全基因组测序，并对质粒、噬菌体、耐药基因、毒力因子及毒素基因簇进行生物信息学分析，探究其进化关系及适应特征。菌株23株分为A5(B3)、B2、B3和B4四种肉毒毒素亚型，并按亚型和地理来源聚类，青海来源菌株形成独立分支。功能注释显示不同亚型在碳水化合物代谢等方面存在差异。所有菌株均携带保守的bont基因簇，部分菌株存在转座酶插入，1株A5(B3)菌株的bont位于不完整前噬菌体中。本研究初步揭示了我国西北地区环境来源肉毒梭菌的基因组多样性及其生态适应特征，为高风险地区肉毒中毒的监测与防控提供基础数据支持。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2026.038

Comparative Transcriptome Analysis of Bartonella Species from Diverse Hosts Reveals Evolutionary Insights — Global, 2023-2025

Min Chen¹, Na Han¹, Wen Zhang¹, Yujun Qiang¹, Qiyong Liu¹, Dongmei 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 & Chinese Academy of Preventive Medicine, Beijing, China.

^# Corresponding author: Dongmei Li, lidongmei@icdc.cn.

To investigate transcriptional differences and their implications for evolutionary relationships among Bartonella species from diverse host origin. Illumina high-throughput sequencing technology was used to sequence the transcriptomes of eighty-seven Bartonella strains. The differences in gene expression among strains from different species and hosts were analyzed, and compared the similarities and differences with the results of the genome phylogenetic analysis were compared to explore the role and influencing factors of transcriptional leveltranscription levels in Bartonella species differentiation. The transcriptomes of Bartonella strains varied systematically by species and host origin, with numerous differentially expressed genes (DEGs) identified among strains from different sources. Experimental verification confirmed that the differentialdifferences in expression of bepC, secB, secDF, and ftsY played a key role in host-specific recognition. Furthermore, phylogenetic analysis based on transcriptomic data clearly reflected the taxonomic relationships among Bartonella species, indicating that their genetic evolution was primarily driven by host-related factors, a finding consistent with genome-based analysis. Transcriptome data provided a powerful approach for elucidatingclarifying species differentiation and evolutionary relationships within Bartonella spp., with potential applicability to other prokaryotic species. These findings provided critical insights for resolving taxonomic uncertainties and advancing systematic research.

不同宿主来源巴尔通体物种的比较转录组分析揭示其进化特征 — 全球，2023-2025年

陈敏¹，韩娜¹，张雯¹，强裕俊¹，刘起勇¹，栗冬梅^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（中国预防医学科学院），北京，中国。

^# 通信作者：栗冬梅，lidongmei@icdc.cn。

为探究不同宿主来源的巴尔通体物种之间的转录差异及其对进化关系的影响。采用Illumina高通量测序技术，对87株巴尔通体菌株进行转录组测序。分析不同种、不同宿主来源菌株间的基因表达差异，并比较与基因组系统发育分析结果的异同，以探究转录水平对巴尔通体物种分化的作用及影响因素。不同来源的巴尔通体间存在大量差异表达位点，其录组组成随物种与宿主来源变化而变化。实验证实，bepC、secB、secDF和ftsY的差异表达可能在宿主特异性识别中发挥关键作用。此外，转录组水平的系统发育关系分析可清晰反映巴尔通体物种分类关系，证实其遗传进化主要受到宿主因素的影响，与基因组分析结果一致。转录组数据为阐明巴尔通体属内的物种分化与进化关系提供了强有力的方法，并可能适用于其他原核生物物种。这些发现为解决分类学不确定性及推进系统学研究提供了关键见解。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2026.039

Field Investigation of Two Urban Cases of Severe Fever with Thrombocytopenia Syndrome — Nanjing City, Jiangsu Province, China, 2025Xueer Wu^1,&, Feiyan Liu^1,&, Hengxue Wang¹, Tao Ma¹, Shougang Zhang¹, Min He¹, Zheng He², Bingdong Song¹, Xuemin Chen¹, Songning Ding^1,3,#, Jie Ding^1,#

1. Nanjing Municipal Center for Disease Control and Prevention, Nanjing, Jiangsu, China;

2. Xuanwu District Center for Disease Control and Prevention, Nanjing, Jiangsu, China;

3. School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.

^& Joint first authors.

^# Corresponding authors: Songning Ding, njcdcdsn@stu.njmu.edu.cn; Jie Ding, E-yu2an2002@163.com.

Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne viral disease caused by the Dabie bandavirus (DBV), which is traditionally endemic in rural agricultural and tea plantation areas. The expansion of suitable tick habitats into urban green spaces raises concerns regarding urban transmission. In June 2025, two confirmed cases of SFTS were reported in an urban district of Nanjing, China. A Centers for Disease Control-led field investigation was conducted, including epidemiological investigations, environmental assessments, tick monitoring, and molecular analyses. Both cases involved elderly urban residents with no rural exposure or animal contact. Case 1 developed symptoms on June 11, recovered, and was discharged on June 19. Case 2 developed symptoms on June 17 and fully recovered by June 28. Neither patient experienced severe complications. At Case 2’s location, tick density was 4.0 ticks/100 m·h; 83.3% (10/12) tested positive for DBV, whereas at Case 1’s site, tick density was 1.25 ticks/100 m·h and all ticks tested negative. Sequencing of the L, M, and S segments showed 99.4–100% nucleotide similarity between patient- and tick-derived strains, indicating locally acquired infection and sporadic natural DBV foci in urban environments. The high DBV-positive rate in ticks from urban green spaces provides strong evidence of localized viral circulation, indicating the potential for SFTS transmission in urban environments. Our findings provide scientific support for targeted urban tick surveillance, vector control measures, and increased clinical awareness.

两例城市发热伴血小板减少综合征病例的现场调查 — 南京市，江苏省，中国，2025年

吴雪尔^1,&，刘飞燕^1,&，王恒学¹，马涛¹，张守刚¹，何敏¹，何整²，宋丙栋¹，陈学敏¹，丁松宁^1,3,#，丁洁^1,#

1. 南京市疾病预防控制中心（南京市卫生监督所），南京市，江苏省，中国；

2. 南京市玄武区疾病预防控制中心，南京市，江苏省，中国；

3. 南京医科大学公共卫生学院，南京市，江苏省，中国。

^& 共同第一作者。

^# 通信作者：丁松宁, njcdcdsn@stu.njmu.edu.cn; 丁洁, E-yu2an2002@163.com。

发热伴血小板减少综合征（SFTS）是由大别班达病毒（DBV）引起的蜱传病毒性疾病，既往主要流行于农村农业区和茶园地区。随着适宜蜱虫生境向城市绿地扩展，城区传播风险逐渐受到关注。2025年6月，南京市报告2例主城区SFTS确诊病例。市、区疾病预防控制中心联合开展流行病学调查、环境评估、蜱虫监测及分子生物学检测。两例病例均为城市老年居民，无农村暴露史及动物接触史。病例1于6月11日发病，6月19日康复；病例2于6月17日发病，6月28日康复。病例2监测点蜱密度为4.0只/100 m·h，DBV阳性率为83.3%（10/12）；病例1监测点蜱密度为1.25只/100 m·h，均为阴性。L、M、S基因片段测序结果显示患者与蜱来源病毒核苷酸相似性为99.4%–100%，提示为本地获得性感染及城市散在自然疫源地形成。主城区DBV阳性蜱虫的发现为局部病毒循环提供证据，提示城市传播潜在风险。本研究为城市蜱媒监测、媒介控制及临床识别提供科学依据。

For more information: https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2026.040