Introduction: 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. Methods: 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. Results: 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 gene, 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. Conclusion: 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.

BackgroundEnteric fever primarily affects the southwestern and central regions of China. Although the overall incidence rate has declined, certain areas have seen an increase in cases, necessitating further investigation into their geographic distribution, clustering areas, and potential influencing factors.MethodsCity-level data from 2001 to 2020 were analyzed. Spatial clustering was identified, and wavelet transform analysis explored periodic and seasonal characteristics. Determinants were identified using generalized estimating equation and distributed lag non-linear model.ResultsIncidence declined from 2001 to 2008 but leveled off since 2009, shifting eastward. Two clustering areas were identified: Guangxi-Guizhou-Yunnan and Zhejiang. In the Zhejiang, incidence was negatively correlated with GDP per capita and popularization rate of safe drinking water in rural areas. Temperature and relative humidity had delayed effects on incidence in Zhejiang, showing linear or parabolic patterns. In the Guangxi-Guizhou-Yunnan, incidence was positively correlated with the proportion of water bodies. Temperature and relative humidity had delayed effects on incidence in Guangxi-Guizhou-Yunnan, and these effects exhibited fluctuating patterns.ConclusionsOver the past 20 years, enteric fever incidence in China has shown a rapid early decline but has stabilized more recently. The factors influencing enteric fever prevalence vary between clustering areas, indicating the need for region-specific measures.

The lytic bacteriophage VP1 specifically targets Vibrio cholerae (V. cholerae), showing excellent therapeutic potential. It features a 55-min latency period, large burst size (255 virions/cell), and remarkable stability (pH 5-12). Genomic sequencing revealed a double-stranded DNA genome of 42,845 bp with a G + C content of 45.49 %. Among the 61 predicted open reading frames (ORFs), 55 were validated by proteomic analysis, while only 16 exhibited functional homology to known proteins in public databases. The genome lacks tRNA genes, CRISPR-associated elements, virulence factors, or antibiotic resistance genes, underscoring its safety profile. It effectively lyses O1 and O139 V. cholerae strains while showing no activity against other Vibrio species. Comparative genomic analysis showed VP1 shares limited similarity (<71.39 % identity) with five Vibrio phages. Phylogenetic analysis of terminase large subunit (TerL) and major capsid protein (MCP) genes further confirmed VP1's distinct evolutionary position, clustering with V. splendidus phage but forming a separate clade from established Caudovirales families. Given its potent lytic activity, genomic stability, unique phylogenetic position, and absence of harmful genetic elements, VP1 represents a putative novel phage lineage within Podovirales.

OBJECTIVES:Outbreak of enteric fever and the spread of antimicrobial-resistant Salmonella Typhi and S. Paratyphi pose significant public health challenges in low- and middle-income countries. Understanding the transmission dynamics of these pathogens is essential for developing effective control strategies. METHODS:We conducted phylogenomic analyses and integrated epidemiological data from 135 S. Typhi and 271 S. Paratyphi A isolates collected in Shenzhen from 2001 to 2017. Phylogenetic and temporal analyses were performed to identify prevalent genotypes and assess transmission patterns. RESULTS:Analyses of S. Typhi isolates in Shenzhen revealed high genetic diversity, with genotypes 3.2.1 (37.8%) and 2.1.7 (20%) being most prevalent. Genotype 3.2.1 formed an independent lineage due to mutations in the quinolone resistance-determining region (QRDR). The multidrug-resistant haplotype 58 (genotype 4.3.1) has been present since 2006. S. Paratyphi A isolates were predominantly genotype 2.3.3 (98.5%). Pathogen exchange occurred with at least four other provinces. A cutoff of ≤3 single nucleotide polymorphisms (SNPs) was effective for outbreak investigation, and 22 genomic clusters were found, suggesting undetected outbreaks or transmission events. While 80% of isolates were susceptible to first-line antibiotics, 16.9% of S. Paratyphi A isolates were multidrug-resistant. CONCLUSIONS:This study provides insights into the transmission dynamics of enteric fever in Shenzhen, underscoring the need for ongoing genomic surveillance to manage and control outbreaks effectively.

Introduction:Salmonella 4,[5],12:i:-, a globally emerging pathogen with multidrug resistance (MDR), is spreading in China. Nationwide data on the antimicrobial resistance (AMR) and genomic characteristics of Salmonella 4,[5],12:i:- from human sources in China are scarce. This study aimed to characterize the prevalence, genetic diversity, and AMR profiles of Salmonella 4,[5],12:i:- in China. Methods:All information, including geographical data, antimicrobial susceptibility test results, and whole-genome sequences, was extracted from the Chinese Pathogen Identification Network database from 2017 to 2023. Antimicrobial resistance phenotypes of 2,736 human-derived isolates were determined, and genomic analysis was applied to assess their genetic heterogeneity. Additionally, resistance genes were detected. Results:Salmonella 4,[5],12:i:- strains exhibited varying levels of resistance to the tested antibiotics, with an overall resistance rate of 98.83%, MDR rate of 87.98%, and cefotaxime resistance of 25.91%. An increasing trend was observed for resistance to key antibiotics and AMR determinants from 2020-2023. Whole-genome analysis revealed five clades with high genetic diversity (A-E), with 97.33% belonging to ST34. Clade D carried a significant proportion of ESBL genes. Moreover, we identified 15 meropenem-resistant isolates primarily harboring widely distributed plasmids containing multiple resistance genes, including bla NDM-5 and bla OXA-10. Conclusion:Salmonella 4,[5],12:i:- is highly sporadic in China but remains phylogenetically linked to the prevalent MDR clone with a distinct resistance profile worldwide. The emergence of elevated resistance to third-generation cephalosporins and sharp rise in carbapenem resistance, coupled with the detection of plasmid-mediated resistance determinants, suggests the evolution of endemic MDR clones circulating within China. These findings emphasize the need for enhanced surveillance, stricter regulations on antibiotic use in agriculture, comprehensive risk factor surveys, and targeted interventions to prevent outbreaks.

Food workers have frequent contact with unprocessed foods, but their carriage of Salmonella and potential influence on public health have not been comprehensively assessed. We investigated Salmonella carriage among food workers compared with non-food workers based on occupational health screening of 260,315 asymptomatic workers over an 8-year surveillance period in Yulin, China. We confirmed that healthy carriers serve as natural reservoirs for Salmonella, with higher carriage rates in food workers than non-food workers. The isolates from food workers also exhibited greater serovar diversity and likely higher levels of antimicrobial resistance than those from non-food workers. Factors such as meteorological, social, and hygiene factors potentially influenced the carriage rate. Genomic analysis revealed a consistent increase in antimicrobial resistance genes among Salmonella isolates over the study period, with the majority of these antimicrobial resistance genes located on plasmids. Additionally, we identified numerous closely related bacterial clusters, which might reflect clusters of hidden local foodborne infections. This study underscores the elevated risk posed by food workers in the persistence and dissemination of Salmonella as vectors/fomites. Enhanced monitoring and targeted interventions in this group may reduce the dissemination of pathogens and antimicrobial resistance genes. Salmonella is a significant cause of gastrointestinal infection and asymptomatic carriage can contribute to transmission. Here, the authors investigate the prevalence of asymptomatic carriage of Salmonella in Yulin, China through occupational health screening and find that carriage was higher in food workers.

Introduction: Over the last 12 years, there has been a consistent decline in the cases of typhoid/ paratyphoid fever in China. Studying the epidemiological patterns of these diseases in various provincial-level administrative divisions (PLADs) and examining potential influencing factors can provide crucial information for implementing successful control strategies. Methods: In this study, we analyzed the cases and incidence rates of typhoid/paratyphoid fever reported in various PLADs of China from 2011 to 2022, along with exploring potential influencing factors. We initially studied spatial shifts in the incidence rates through centroid shift analysis. Seasonal variations in typhoid/paratyphoid fever onset were examined using heatmaps. Spatial autocorrelation analysis was utilized to understand the spatial correlations among different PLADs. To assess potential factors, we utilized a generalized estimating equations model that integrated spatial lag effects and sequence comparison analysis. Results: The study identified significant geographical clustering of typhoid/paratyphoid fever cases in southwestern China. A decrease in incidence rates in the west resulted in a movement of the disease center towards the east. Higher incidence occurred during warmer seasons, highlighting the seasonal pattern of the diseases. Factors such as meteorological conditions and socioeconomic status were probable influencers of typhoid/paratyphoid fever. Conclusions: The geographical and temporal spread of typhoid/paratyphoid fever can be impacted by meteorological and socioeconomic factors. Enhancing economic conditions, particularly in regions with high disease prevalence, could aid in the prevention and management of these fevers.

目的 回顾性分析2007-2017年我国人来源和动物来源印第安纳沙门菌的耐药表型及遗传特征,为耐药性产生来源提供线索.方法 对2007-2017年分离的100株印第安纳沙门菌,采用微量肉汤稀释法测定所有菌株对23种抗菌药物的耐药表型.对全部菌株进行基因组测序,利用ResFinder和PlasmidFinder数据库进行耐药基因和质粒型别鉴定,并构建基于核心基因组SNPs的系统发育树进行菌株间遗传进化关系分析.结果 100株印第安纳沙门菌对多种药物都呈现高水平耐药,且对阿米卡星、头孢他啶、头孢噻肟、头孢吡肟、左氧氟沙星、吉米沙星的耐药率均呈现逐年上升趋势.阿莫西林-克拉维酸钾和阿奇霉素动物分离株耐药率高于人源株.IncH家族为印第安纳沙门菌携带质粒主要型别,菌株耐药表型与耐药基因携带一致率在95％以上.基于核心基因组SNPs的系统进化树表明印第安纳沙门菌分布呈现一定的时空聚集性,动物分离株与人分离株交叉分布,部分动物株与人源株聚集在一起.结论 我国人源及动物源印第安纳沙门菌的多重耐药现象均较严重.随着时间的推移,菌株对多数药物耐药水平呈上升趋势,人与动物之间存在潜在的交互传播,提示我们应密切关注并加强沙门菌在人间及动物间耐药性变迁的监测,以便及时发现耐药克隆播散.

目的 了解广西壮族自治区玉林市健康人携带的单相鼠伤寒沙门菌的耐药情况及菌株间的同源性.方法 对2021-2022年分离自健康饮食从业人群的147株单相鼠伤寒沙门菌进行血清学鉴定,采用微量肉汤稀释法进行16种药物的敏感性试验,应用脉冲场凝胶电泳(PFGE)进行分子分型及聚类分析,同时进行全基因组测序及多位点序列分型分析.结果 单相鼠伤寒沙门菌普遍耐药,耐药菌株占98.64％,对链霉素的耐药率最高(96.60％),其次为氨苄西林和四环素(均为91.16％).多重耐药率高达85.71％,主要耐药谱为氨苄西林-链霉素-四环素三重耐药.147株菌分为132种PFGE带型,研究发现成簇菌株存在,但菌株基因组遗传差异较大.核心基因组进化树分析提示存在3起聚集.多位点序列分型显示,序列型ST34占绝对优势(96.60％).结论 玉林市健康人携带单相鼠伤寒沙门菌耐药严重,菌株具有明显的遗传多样性,存在潜在暴发风险,提示应加强重点人群健康监测及暴露危险因素的调查,降低该耐药新血清型沙门菌扩散风险.

Objective To establish a rapid detection method for Salmonella based on the combination of enzymatic re-combinase amplification(ERA)and lateral flow chromatography(LF),so as to provide technical support for the on-site detection of Salmonella.Methods Specific ERA primers and probes were designed based on the highly conserved fla-gella gene fimY in Salmonella.The primers were screened using capillary electrophoresis,and the probes were designed according to the amplification range of the screened primers.The amplification temperature and time were optimized to establish the amplification method,and the product was detected using LF strips.A standard strain of Salmonella was used to verify the sensitivity,10 other gut bacteria were used to to verify the specificity and sensitivity,and the nucle-ic acid of the actual Salmonella strains was amplified to verify the detectability.Results After screening for Salmonel-la-specific primers using capillary electrophoresis,the minimum detection concentration was 5 copies/μL under the am-plification temperature of 37 ℃ and reaction time of 20 minutes.This method had a positive amplification result for Salmonella nucleic acid,and the amplification results of 10 other gut bacteria were all negative,with good specificity.Conclusion This method provides a possibility for on-site point of care testing of Salmonella infection.

Yersinia pestis, the cause of plague, is a newly evolved Gram-negative bacterium. Through the acquisition of the plasminogen activator (Pla), Y. pestis gained the means to rapidly disseminate throughout its mammalian hosts. It was suggested that Y. pestis utilizes Pla to interact with the DEC-205 (CD205) receptor on antigen-presenting cells (APCs) to initiate host dissemination and infection. However, the evolutionary origin of Pla has not been fully elucidated. The PgtE enzyme of Salmonella enterica, involved in host dissemination, shows sequence similarity with the Y. pestis Pla. In this study, we demonstrated that both Escherichia coli K-12 and Y. pestis bacteria expressing the PgtE-protein were able to interact with primary alveolar macrophages and DEC-205-transfected CHO cells. The interaction between PgtE-expressing bacteria and DEC-205-expressing transfectants could be inhibited by the application of an anti-DEC-205 antibody. Moreover, PgtE-expressing Y. pestis partially re-gained the ability to promote host dissemination and infection. In conclusion, the DEC-205-PgtE interaction plays a role in promoting the dissemination and infection of Y. pestis, suggesting that Pla and the PgtE of S. enterica might share a common evolutionary origin.

Salmonellosis is one of the common food-borne diseases, local and cross-region outbreaks are not rare. The risk of cross-border transmission of Salmonella is increasing with the high frequency of global economic trades. The recently occurred multi-country outbreaks of Salmonella Typhimurium infection associated with chocolate products have highlighted the importance of improving capability of surveillance and warning of foodborne-disease, especially salmonellosis, in China. It is essential to strengthen the collaboration among clinical medicine, disease control and food safety institutions, improve the capability of whole-genome sequencing of Salmonella for the disease surveillance and tracing, and facilitate the information sharing and collaboration among the food safety related sectors for the timely detection, prevention and control of outbreaks of Salmonella infection in China.

Rapid and accurate identification of foodborne pathogenic bacteria is of great importance because they are often responsible for the majority of serious foodborne illnesses. The confocal Raman microspectroscopy (CRM) is a fast and easy-to-use method known for its effectiveness in detecting and identifying microorganisms. This study demonstrates that CRM combined with chemometrics can serve as a rapid, reliable, and efficient method for the detection and identification of foodborne pathogenic bacteria without any laborious pre-treatments. Six important foodborne pathogenic bacteria including S. flexneri, L. monocytogenes, V. cholerae, S. aureus, S. typhimurium, and C. botulinum were investigated with CRM. These pathogenic bacteria can be differentiated based on several characteristic peaks and peak intensity ratio. Principal component analysis (PCA) was used for investigating the difference of various samples and reducing the dimensionality of the dataset. Performances of some classical classifiers were compared for bacterial detection and identification including decision tree (DT), artificial neural network (ANN), and Fisher’s discriminant analysis (FDA). Correct recognition ratio (CRR), area under the receiver operating characteristic curve (ROC), cumulative gains, and lift charts were used to evaluate the performance of models. The impact of different pretreatment methods on the models was explored, and pretreatment methods include Savitzky–Golay algorithm smoothing (SG), standard normal variate (SNV), multivariate scatter correction (MSC), and Savitzky–Golay algorithm 1st Derivative (SG 1st Der). In the DT, ANN, and FDA model, FDA is more robust for overfitting problem and offers the highest accuracy. Most pretreatment methods raised the performance of the models except SNV. The results revealed that CRM coupled with chemometrics offers a powerful tool for the discrimination of foodborne pathogenic bacteria.

Some serovars of Salmonella are not or rare found to cause salmonellosis in human. In our clinic-based surveillance, three rare Salmonella 4,5,12:a:- strains were recovered from three patients with diarrhea. To explore their genetic and epidemiological characteristics and pathogenesis, we conducted whole-genome sequencing, in vitro invasion assays in mammalian cells, and in vivo virulence assays in an animal model. The three isolates had indistinguishable molecular patterns and similar genome sequences, and clustered together with an isolate from edible fish traded among countries. The isolates had biochemical reactions identical with those of Salmonella subspecies enterica but belonged to subspecies salamae according to genome phylogeny, revealing a new serovar, S. enterica subsp. II serovar 4,5,12:a:-. The strains contained multiple virulence genes, elicited temporary bacteremia and enteritidis and caused cell damage in the mouse liver and cecum. This study provides evidence that this new Salmonella salamae serovar can infect humans and cause clusters of cases, and whole-genome sequencing detection and surveillance of Salmonella can help to accurately define Salmonella classification and clonality, improve diagnosis, facilitate outbreak detection and aid in the source tracing of salmonellosis epidemics.

目的 基于猪霍乱沙门菌血清型特异性基因,建立TaqMan逆转录实时聚合酶链反应(TaqMamrRT-PCR)检测猪霍乱沙门菌的方法.方法 利用基因组序列比对筛选到猪霍乱沙门菌特有的基因SC0358,通过普通PCR及利用多种血清型沙门菌及非沙门菌菌株共计145株,评价该方法的菌株特异性,针对该基因设计TaqMan-rRT-PCR检测方法的引物,优化反应条件,建立针对该靶基因的TaqMan-rRT-PCR检测方法,以纯菌及血液模拟标本RNA为模板进行敏感性检测.结果 利用该方法检测26株猪霍乱沙门菌均为阳性,其余菌株扩增均阴性,对纯菌RNA检测中,TaqMan-rRT-PCR的最低检测限度为5 fg/反应,约为10个拷贝/反应.对全血液模拟样品分析中,敏感性达25 cfu/mL.结论 以猪霍乱沙门菌保守、特异基因SC0358建立的TaqMan-rRT-PCR方法,能够简便快捷区分猪霍乱沙门菌与其他血清型沙门菌,尤其能够区分与其有抗原式相同的丙型副伤寒沙门菌,此方法为猪霍乱沙门菌感染的快速诊断提供了简便的手段,可用于对猪霍乱沙门菌的早期诊断.

血清特异性抗体检测是诊断新型冠状病毒(SARS-CoV-2)感染的重要工具.然而在短时间内大量SARS-CoV-2血清学抗体检测试剂盒紧急上市,其准确性和有效性存在很大不确定性.本研究对国内外SARS-CoV-2血清学抗体检测试剂盒现状做简要综述,为医院和疾控人员的使用提供参考.

目的 比较3种沙门菌分子血清分型方法,获得一种准确度较高的方法用来替代传统的血清凝集技术用于沙门菌血清型判定.方法 对覆盖50个血清型的509株沙门菌提取核酸进行全基因组测序,根据全基因组序列分别利用多位点序列分型(MLST)、SalmonSeroPredicition 以及 SISTR(Salmonella in silico typing resource)3种方法在线预测获得每株菌的血清型,然后与传统血清凝集获得的血清型进行一致性比较分析,评估每种方法血清型预测的准确度.结果 SISTR、MLST以及SalmonSeroPredicition预测血清型的准确率分别为96.67％、93.52％、69.16％.常见沙门菌血清型印第安纳沙门菌和鼠伤寒沙门菌血清型预测正确率最高,为100％,德尔卑沙门菌、肠炎沙门菌血清型预测正确率分别为99.17％、95.74％.3种方法均预测错误的血清型有肠炎沙门菌、德尔卑沙门菌和沙门菌的萨拉姆亚种、亚利桑那亚种和双相亚利桑那亚种等;预测错误原因主要是基因序列丢失和鞭毛抗原基因未表达.结论 基于基因组序列的SISTR血清型预测方法具有较高的血清型预测准确度,在传统血清凝集难以开展或沙门菌鞭毛基因不表达的情况下,可以替代血清凝集试验进行沙门菌血清型判定.

目的 为了快速检测、鉴定沙门菌属细菌,提高食源性疾病暴发应对能力,本研究建立了针对沙门菌属的实时荧光定量聚合酶链式反应(qPCR)检测方法,并对其特异性、敏感性和检测下限进行评价.方法 筛选针对沙门菌的属特异基因,并建立该基因的qPCR检测体系,利用肠道不同种属细菌、不同亚种及血清型沙门菌属细菌、动物及人粪便样本评价该体系的特异度、灵敏度及检测下限.结果 获得沙门菌的属特异基因ttrA,建立基于该基因的qPCR检测方法.发现该方法对纯DNA的最低检测下限为2拷贝/反应.对沙门菌属以外的肠道致病菌无扩增,对1 100株不同亚种及血清型的沙门菌的扩增结果均为阳性,对150份沙门菌致腹泻患者的粪便增菌液和210份动物带菌粪便增菌液均检测阳性.结论 本研究建立的基于单一基因的沙门菌属快速分子检测方法具有特异度高、灵敏度高的特点,可用于快速筛查、鉴定沙门菌及由其引起的感染性腹泻.

SummaryVibrio cholerae can enter a viable but non‐culturable (VBNC) state when it encounters unfavourable environments; VBNC cells serve as important reservoirs and still pose threats to public health. The genetic regulation of V. cholerae entering its VBNC state is not well understood. Here, we show a confrontation strategy adapted by V. cholerae O1 in which it utilizes a quorum sensing (QS) system to prevent transition into a VBNC state under low nutrition and temperature conditions. The upregulation of hapR resulted in a prolonged culturable state of V. cholerae in artificial sea water at 4°C, whereas the mutation of hapR led to fast entry into the VBNC state. We also observed that different V. cholerae O1 natural isolates with distinct QS functions present a variety of abilities to maintain culturability during the transition to a VBNC state. The strain groups with higher or constitutive expression of QS genes exhibit a greater tendency to maintain the culturable state during VBNC induction than those lacking QS functional groups. In summary, HapR‐mediated QS regulation is associated with the transition to the VBNC state in V. cholerae. HapR expression causes V. cholerae to resist VBNC induction and become dominant over competitors in changing environments.