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Age- and sex-stratified trends in carbapenem-resistant Acinetobacter baumannii and Enterobacterales: insights from MuGSI (2012–2022) 耐碳青霉烯鲍曼不动杆菌和肠杆菌的年龄和性别分层趋势:来自MuGSI的见解(2012-2022)。
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-13 DOI: 10.1016/j.jhin.2025.11.002
Y. Takefuji
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引用次数: 0
Uncovering a hidden threat from OXA-48-carbapenemase-producing Enterobacterales in a Scottish health board 在苏格兰健康委员会发现OXA-48碳青霉烯酶产生肠杆菌的隐藏威胁。
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-24 DOI: 10.1016/j.jhin.2025.11.017
O. Osgerby-Lacey , D. Inverarity , J. Welsh , L. Guthrie , N.J. Gadsby , N. Henderson
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引用次数: 0
Transmission pathways and genogroup contribution in Stenotrophomonas maltophilia dissemination: experience from a French university hospital 嗜麦芽窄养单胞菌传播的传播途径和基因组贡献:来自法国大学医院的经验。
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-20 DOI: 10.1016/j.jhin.2025.11.010
C. Sakr , M. Danjean , M. Darty-Mercier , F. Cizeau , D. Ducellier , F. Fourreau , S. Romano-Bertrand , G. Royer , P-L. Woerther , J-W. Decousser

Background

Stenotrophomonas maltophilia is an environmental opportunistic pathogen that affects immunocompromised patients. Its genomic heterogeneity led to definition of the S. maltophilia complex, including different subpopulations (genogroups) with unknown respective dissemination potential. This study aimed to clarify the epidemiology and genogroup contribution of S. maltophilia in a hospital setting using a comprehensive whole genome sequencing (WGS) approach.

Methods

A prospective 16-month study was conducted in a 900-bed university hospital. In total, 204 strains from clinical and environmental samples underwent WGS. Core genome multi-locus sequence typing was performed to determine relatedness between strains, according to epidemiological data; allelic variation among clustered strains was analysed. Genogroups were identified from WGS, and their relative contribution among clustered and non-clustered strains was identified.

Results

Among the 189 non-duplicated genomes of human (N=156) and environmental (N=33) origin, 24 clusters (55 strains, two to six per cluster) were identified: four environmental, 16 human and four mixed. Temporal and/or geographical overlap was identified in 22 of 24 clusters. Although predominant among human strains, the main genogroups considered as human-adapted, such as genogroup 6, were not over-represented among clustered strains. Among clustered strains, up to six allelic variants were identified; six genes were involved in more than one allelic variant.

Conclusion

Although S. maltophilia is considered to have low cross-transmission potential, this longitudinal study highlighted some putative patient-to-patient cross-transmission events, without over-representation of some particular genogroups. Pending further larger studies, these results advocate for reinforcement of infection control around S. maltophilia carriers in high-risk settings.
背景:嗜麦芽窄养单胞菌(Sm)是一种影响免疫功能低下患者的环境条件致病菌。其基因组异质性导致Sm复杂的定义,包括不同的亚群(基因群),各自的传播潜力未知。本研究旨在利用全面的全基因组测序(WGS)方法澄清Sm流行病学和基因组在医院环境中的贡献。材料与方法:在一所拥有900张床位的大学医院进行了一项为期16个月的前瞻性研究。临床和环境样本共204株进行了WGS检测。根据流行病学资料,采用核心基因组MLST (cgMLST)来确定菌株之间的亲缘关系;分析了聚类菌株间的等位基因变异。从WGS中鉴定了基因群,并确定了它们在聚集型和非聚集型菌株中的相对贡献。结果:189个非重复的人源基因组(156个)和环境源基因组(33个)共鉴定出24个聚集型(55株,每个聚集型2 ~ 6株),其中环境源聚集型4个,人源聚集型16个,混合聚集型4个。在24个集群中,有22个集群确定了时间和/或地理重叠。虽然在人类菌株中占主导地位,但被认为是人类适应的主要基因群,如基因组6,在聚集型菌株中没有过度代表。在聚集型菌株中,鉴定出多达6个等位变异;6个基因参与了一个以上的等位基因变异。结论:尽管它被归类为低交叉传播的病原体,但这项纵向研究突出了一些假定的患者间交叉传播事件,没有过度代表某些特定的基因群体。在进一步的大型研究中,这些结果提倡在高风险环境中加强对Sm携带者的感染控制。
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引用次数: 0
Outbreak of Enterobacter kobei infections linked to a collagen-based adhesion barrier following lumbar disc surgery: an epidemiological and molecular study 腰椎间盘手术后与胶原黏附屏障相关的kobei肠杆菌感染爆发:流行病学和分子研究
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-11 DOI: 10.1016/j.jhin.2025.10.030
M.T. Işik , Y. Cezaroğlu , F. Tomakin , M. Büyüktepe

Background

Postoperative infections following spinal surgery are typically caused by skin flora or hospital-acquired pathogens. This article reports a novel outbreak of Enterobacter kobei infections linked to a collagen-based adhesion barrier.

Aim

To identify the source of increased surgical site infections in lumbar disc herniation (LDH) procedures, and to describe the outbreak investigation and containment measures implemented.

Methods

A multi-disciplinary outbreak team conducted epidemiological, environmental and microbiological investigations at a secondary care hospital in Turkey. Molecular typing using pulsed-field gel electrophoresis (PFGE) was employed to assess the clonal relationships of the isolates.

Findings

Between 19th May and 9th June 2023, 10 of 12 patients who underwent LDH surgery developed surgical site infections. Environmental cultures tested negative. Enterobacter cloacae was isolated from wound, blood and collagen-based adhesion barrier samples. Isolates sent to the National Public Health Laboratory were identified as E. kobei. PFGE analysis revealed two distinct but clonally related groups. The outbreak was contained following a nationwide recall of the adhesion barrier.

Conclusion

This incident marks the first reported outbreak of E. kobei associated with a surgical adhesion barrier. This highlights the need for vigilant infection control and careful monitoring of non-sterilized surgical materials to prevent similar events in the future.
背景:脊柱手术后感染通常是由皮肤菌群或医院获得性病原体引起的。本文报道了一种与胶原蛋白黏附屏障有关的新爆发的神北肠杆菌感染。目的:确定腰椎间盘突出症(LDH)手术部位感染增加的来源,并描述爆发调查和实施的控制措施。方法:一个多学科暴发小组在土耳其的一家二级护理医院进行了流行病学、环境和微生物学调查。采用脉冲场凝胶电泳(PFGE)进行分子分型,鉴定分离株的克隆关系。结果:在2023年5月19日至6月9日期间,12例接受LDH手术的患者中有10例发生手术部位感染。环境文化测试呈阴性。从伤口、血液和胶原基黏附屏障样本中分离出阴沟肠杆菌。送交国家公共卫生实验室的分离株经鉴定为北肠杆菌。PFGE分析显示了两个不同但克隆相关的群体。在全国范围内召回粘连屏障后,疫情得到了控制。结论:该事件标志着首次报道的与手术粘连屏障相关的北肠杆菌暴发。这强调了警惕感染控制和仔细监测未消毒手术材料的必要性,以防止今后发生类似事件。
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引用次数: 0
Risk factors and colistin resistance in multi-drug-resistant Pseudomonas aeruginosa: insights from a urology and kidney transplant ward 多药耐药铜绿假单胞菌的危险因素和粘菌素耐药性:来自泌尿科和肾移植病房的见解。
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-10-10 DOI: 10.1016/j.jhin.2025.09.017
M.D. Almeida , B. Parada , S.M. Johansson , P. Valada , J. Pereira , R. Leal , C. Chaves , J. Frade , A.R. Rebelo , T. Gonçalves , G.J. Da Silva , R.S. Hendriksen , C. Nogueira
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引用次数: 0
Molecular epidemiology of a nationwide Pseudomonas aeruginosa outbreak in Norway reveals multiple distinct clusters, including high-risk clone ST244 挪威全国铜绿假单胞菌暴发的分子流行病学揭示了多个不同的聚集性,包括高风险克隆ST244。
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-19 DOI: 10.1016/j.jhin.2025.11.004
T. Pedersen , A. Hesselberg Løvestad , A. Ingebretsen , D.H. Skutlaberg , C.G. Ås , A. Blomfeldt

Background

A nationwide collection of Pseudomonas aeruginosa bacteraemia isolates was assembled during a wild-type P. aeruginosa ST3875 outbreak affecting approximately 400 patients across 40 hospitals in Norway in 2021–2022.

Aim

To investigate the molecular epidemiology of P. aeruginosa in Norway through a multi-centre retrospective study.

Methods

All available isolates collected over 18 months were retrieved from 20 microbiology laboratories, and underwent whole-genome sequencing at five university hospitals. Metadata, including demographics, sampling dates and locations, were collated. Phylogenetic and comparative genomic analyses were performed to identify sequence types (STs), clusters, resistance determinants, and virulence factors.

Findings

This study included 376 unique patients with P. aeruginosa bacteraemia from 33 hospitals (69% male; median age 76 years), representing >90% of the national catchment area. Incidence varied regionally (5.1–16.3 per 100,000). The ST was resolved for 362 isolates, revealing 164 distinct types. Global high-risk and epidemic clones (e.g. ST233, ST244, ST277, ST298, ST308) comprised 30% of the collection. None of the isolates carried carbapenemases or extended-spectrum β-lactamases. Aside from the ST3875 outbreak clone (N=56), nine unrecognized phylogenetic clusters (two to 20 cases each) spanning multiple hospitals and regions were identified, including a widespread ST244 cluster harbouring a novel genomic island with putative virulence determinants, indicating a selective advantage for dissemination.

Conclusions

This comprehensive genomic surveillance study uncovered multiple unexpected clusters of P. aeruginosa bacteraemia isolates in Norway, along with widespread presence of susceptible epidemic clones. Routine multi-level surveillance integrating sequencing with epidemiological data could enable earlier recognition of emerging high-risk clones and outbreaks, thereby strengthening infection prevention efforts.
背景:在2021- 2022年挪威40家医院的铜绿假单胞菌ST3875野生型爆发期间,收集了全国范围内的铜绿假单胞菌菌血症分离株。目的:通过多中心回顾性研究,探讨挪威铜绿假单胞菌的分子流行病学。方法:从5所大学附属医院的20个微生物实验室收集18个月以上的分离株,并进行全基因组测序。元数据,包括人口统计,采样日期和地点,被整理。进行了系统发育和比较基因组分析,以确定序列类型(STs)、簇、抗性决定因素和毒力因子。研究结果:我们纳入了来自33家医院的376例独特的铜绿假单胞菌菌血症患者(69%为男性,中位年龄76岁),占全国集水区的90%。发病率因地区而异(5.1-16.3 / 10万)。分离得到362株分离株,共分离出164种不同类型。全球高风险和流行克隆(如ST233、ST244、ST277、ST298、ST308)占收集量的30%。没有分离物携带碳青霉烯酶或广谱β-内酰胺酶。除了ST3875暴发克隆(N = 56)外,还发现了跨越多个医院和地区的9个未被识别的系统发育集群(每个集群2-20例),包括广泛存在的ST244集群,其中包含一个具有假定毒力决定因素的新基因组岛,表明传播具有选择优势。结论:这项全面的基因组监测研究在挪威发现了多个意想不到的铜绿假单胞菌菌血症分离群,以及广泛存在的易感流行克隆。将测序与流行病学数据相结合的常规多层次监测可使早期识别新出现的高风险克隆和疫情,从而加强感染预防工作。
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引用次数: 0
Colonization status and risk factors for infection by carbapenem-resistant Gram-negative bacteria in intensive care units in Colombia 哥伦比亚重症监护病房(ICU)耐碳青霉烯革兰氏阴性菌感染的定植状况和危险因素
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-13 DOI: 10.1016/j.jhin.2025.11.003
C. Espitia-Acero , J.C. García-Betancur , E. De La Cadena , C.J. Pallares , N. Restrepo-Arbeláez , E. Patiño-Guevara , M. Coy , M.V. Villegas

Background

Carbapenem-resistant Gram-negative bacteria (CRGNB) are increasing globally, leading to high mortality, extended hospital stays, and higher costs. Colombia is a hotspot for carbapenem resistance, but intensive care unit (ICU) surveillance for CRGNB is limited.

Aim

To assess the association between colonization by carbapenem-resistant organisms (CROs) on ICU admission and subsequent infection, along with other risk factors.

Methods

A multicentre prospective cohort study was conducted in two Colombian hospitals with high carbapenem resistance. CRO colonization status was determined upon ICU admission, and statistical analyses were performed to assess relations with infection development.

Findings

In general, 18.5% (82/442) of ICU patients were colonized by at least one CRO, with only six acquiring colonization during ICU stay. Pseudomonas spp. (70/106) and Klebsiella spp. (10/106) were the most common species; 28.3% of isolates harboured carbapenemase genes, mainly blaKPC and blaNDM. Bivariate analysis showed that readmission to the ICU (relative risk: 4.7; confidence interval 95%: 1.51–14.57) and the use of antibiotics in the last 30 days prior ICU admission (6.4; 1.76–23.13) were related to the development to bacterial infection, independently of the previous colonization status.

Conclusion

Identifying CRO colonization status, particularly in patients with risk factors and/or with frequent hospital transit, is crucial for effective infection control within the ICU.
碳青霉烯耐药革兰氏阴性菌(CRGNB)正在全球范围内增加,导致高死亡率、延长住院时间和更高的费用。哥伦比亚是碳青霉烯类耐药的热点地区,但ICU对CRGNB的监测有限。本研究旨在评估ICU入院时碳青霉烯耐药菌(CRO)定植与随后感染以及其他危险因素之间的关系。在哥伦比亚两家碳青霉烯类高耐药性医院进行了一项多中心前瞻性队列研究。在ICU入院时确定CRO定植状态,并进行统计分析以评估其与感染发展的关系。总体而言,18.5%(82/442)的ICU患者至少有一种CRO定植,只有6例患者在ICU住院期间获得定植。假单胞菌(70/106)和克雷伯氏菌(10/106)是最常见的菌种。28.3%的分离株含有碳青霉烯酶基因,主要为blaKPC和blaNDM。双因素分析显示,再次入住ICU (RR为4.7 [IC 95% 1.51 - 14.57])和入住前30天内使用抗生素(RR为6.4 [IC 95% 1.76 - 23.13])与细菌感染的发展有关,与之前的定殖状态无关。确定CRO定植状态,特别是在有危险因素和/或经常转院的患者中,对于在ICU内有效控制感染至关重要。
{"title":"Colonization status and risk factors for infection by carbapenem-resistant Gram-negative bacteria in intensive care units in Colombia","authors":"C. Espitia-Acero ,&nbsp;J.C. García-Betancur ,&nbsp;E. De La Cadena ,&nbsp;C.J. Pallares ,&nbsp;N. Restrepo-Arbeláez ,&nbsp;E. Patiño-Guevara ,&nbsp;M. Coy ,&nbsp;M.V. Villegas","doi":"10.1016/j.jhin.2025.11.003","DOIUrl":"10.1016/j.jhin.2025.11.003","url":null,"abstract":"<div><h3>Background</h3><div>Carbapenem-resistant Gram-negative bacteria (CRGNB) are increasing globally, leading to high mortality, extended hospital stays, and higher costs. Colombia is a hotspot for carbapenem resistance, but intensive care unit (ICU) surveillance for CRGNB is limited.</div></div><div><h3>Aim</h3><div>To assess the association between colonization by carbapenem-resistant organisms (CROs) on ICU admission and subsequent infection, along with other risk factors.</div></div><div><h3>Methods</h3><div>A multicentre prospective cohort study was conducted in two Colombian hospitals with high carbapenem resistance. CRO colonization status was determined upon ICU admission, and statistical analyses were performed to assess relations with infection development.</div></div><div><h3>Findings</h3><div>In general, 18.5% (82/442) of ICU patients were colonized by at least one CRO, with only six acquiring colonization during ICU stay. <em>Pseudomonas</em> spp. (70/106) and <em>Klebsiella</em> spp. (10/106) were the most common species; 28.3% of isolates harboured carbapenemase genes, mainly <em>bla</em><sub>KPC</sub> and <em>bla</em><sub>NDM</sub>. Bivariate analysis showed that readmission to the ICU (relative risk: 4.7; confidence interval 95%: 1.51–14.57) and the use of antibiotics in the last 30 days prior ICU admission (6.4; 1.76–23.13) were related to the development to bacterial infection, independently of the previous colonization status.</div></div><div><h3>Conclusion</h3><div>Identifying CRO colonization status, particularly in patients with risk factors and/or with frequent hospital transit, is crucial for effective infection control within the ICU.</div></div>","PeriodicalId":54806,"journal":{"name":"Journal of Hospital Infection","volume":"168 ","pages":"Pages 183-190"},"PeriodicalIF":3.1,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145530994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Across time and space: phylogenetic analysis of carbapenem-resistant Acinetobacter baumannii in a network of general and convalescent hospitals 跨越时间和空间:在普通和康复医院网络中耐碳青霉烯鲍曼不动杆菌的系统发育分析。
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-13 DOI: 10.1016/j.jhin.2025.11.001
E.T.L. Lui , C. Li , A.L.H. Lee , D.N. Sapugahawatte , W.S. Lee , G.C.S. Chiu , I.Y.Y. Cheung , V.C.Y. Chow , M. Ip

Introduction

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major threat to public health and is a common cause of nosocomial outbreaks.

Aim

To describe the genetic epidemiology of CRAB from both clinical and hospital environments in a network of hospitals in Hong Kong.

Methods

A collection of 185 CRAB strains from patients (N = 143) and nosocomial environments (N = 42) from the period 2012 to 2024 underwent whole-genome sequencing to investigate the phylogenetic relatedness, virulence genes, antibiotic resistance genes and possible lineages of the strains that caused nosocomial outbreaks. Clinical information and antibiotic susceptibility test reports were retrieved from electronic medical records. Time and spatial distribution of the strains was assessed.

Findings

The dominant sequence type of CRAB was ST2, accounting for 137 of 185 isolates (74.1%). It was followed by ST195 (N = 17, 9.2%) and ST49 (N = 16, 8.6%). All isolates carried the nreB gene that enhances environmental survival. Carriage of virulence factor genes was grossly similar between environmental and human isolates. Significantly more environmental isolates carried antimicrobial resistant genes conferring resistance to sulbactam-durlobactam, aminoglycosides and macrolides. Dissemination of CRAB across time and space in the regional network of hospitals was observed.

Conclusion

ST2 was the commonest sequence type in CRAB across clinical and nosocomial environment isolates of the entire hospital network, linking sporadic cases and clusters across different hospitals spanning over 10 years.
耐碳青霉烯鲍曼不动杆菌(CRAB)是对公共卫生的主要威胁,也是医院暴发的常见原因。目的:从香港医院网络的临床和医院环境描述螃蟹的遗传流行病学。方法:收集2012-2024年患者(N = 143)和医院环境(N = 42) 185株螃蟹菌株,进行全基因组测序,研究引起医院暴发的菌株的系统发育亲缘性、毒力基因、抗生素耐药基因和可能的谱系。通过电子病历检索临床资料和抗生素药敏试验报告。评估了菌株的时间和空间分布。结果:螃蟹的优势序列型为ST2型,占185株的137株(74.1%);其次是ST195 (N = 17, 9.2%)和ST49 (N = 16, 8.6%)。观察了区域性医院网络中CRAB跨时间和空间的传播。环境分离株比人类分离株具有更多的毒力因子编码基因(结论:在整个医院网络的临床和医院环境分离株中,ST2是螃蟹最常见的序列类型,将10多年来不同医院的散发病例和暴发联系起来。
{"title":"Across time and space: phylogenetic analysis of carbapenem-resistant Acinetobacter baumannii in a network of general and convalescent hospitals","authors":"E.T.L. Lui ,&nbsp;C. Li ,&nbsp;A.L.H. Lee ,&nbsp;D.N. Sapugahawatte ,&nbsp;W.S. Lee ,&nbsp;G.C.S. Chiu ,&nbsp;I.Y.Y. Cheung ,&nbsp;V.C.Y. Chow ,&nbsp;M. Ip","doi":"10.1016/j.jhin.2025.11.001","DOIUrl":"10.1016/j.jhin.2025.11.001","url":null,"abstract":"<div><h3>Introduction</h3><div>Carbapenem-resistant <em>Acinetobacter baumannii</em> (CRAB) is a major threat to public health and is a common cause of nosocomial outbreaks.</div></div><div><h3>Aim</h3><div>To describe the genetic epidemiology of CRAB from both clinical and hospital environments in a network of hospitals in Hong Kong.</div></div><div><h3>Methods</h3><div>A collection of 185 CRAB strains from patients (<em>N</em> = 143) and nosocomial environments (<em>N</em> = 42) from the period 2012 to 2024 underwent whole-genome sequencing to investigate the phylogenetic relatedness, virulence genes, antibiotic resistance genes and possible lineages of the strains that caused nosocomial outbreaks. Clinical information and antibiotic susceptibility test reports were retrieved from electronic medical records. Time and spatial distribution of the strains was assessed.</div></div><div><h3>Findings</h3><div>The dominant sequence type of CRAB was ST2, accounting for 137 of 185 isolates (74.1%). It was followed by ST195 (<em>N</em> = 17, 9.2%) and ST49 (<em>N</em> = 16, 8.6%). All isolates carried the nreB gene that enhances environmental survival. Carriage of virulence factor genes was grossly similar between environmental and human isolates. Significantly more environmental isolates carried antimicrobial resistant genes conferring resistance to sulbactam-durlobactam, aminoglycosides and macrolides. Dissemination of CRAB across time and space in the regional network of hospitals was observed.</div></div><div><h3>Conclusion</h3><div>ST2 was the commonest sequence type in CRAB across clinical and nosocomial environment isolates of the entire hospital network, linking sporadic cases and clusters across different hospitals spanning over 10 years.</div></div>","PeriodicalId":54806,"journal":{"name":"Journal of Hospital Infection","volume":"168 ","pages":"Pages 13-22"},"PeriodicalIF":3.1,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145530983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory 对速度的需求:在一线医院微生物实验室进行超高速高分辨率疫情分析。
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-29 DOI: 10.1016/j.jhin.2025.11.020
M. Bloomfield , S. Bakker , M. Burton , K. Dyet , A. Eustace , S. Hutton , J. Jeram , D. Macartney-Coxson , D.J. Winter , R.T. White

Background

Many hospital laboratories have the technical capacity to perform microbial whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates delays that can be highly detrimental to outbreak responses. The Wellington Regional Hospital laboratory, which lacks on-site bioinformaticians, implemented real-time nanopore-based genome sequencing that has detected several hospital outbreaks at an early stage. This has required off-site analysis, often taking weeks. Solu Genomics, a cloud-based automated bioinformatic platform, requires no bioinformatic or command-line expertise and accepts basecalled sequence files or genome assemblies.

Aim

The aim of this study was to use Solu to replicate the analysis of two prior neonatal unit outbreaks detected by on-site genome sequencing, as if they had occurred now, and compare the output to ‘manual’ bioinformatic analysis.

Methods

Surveillance isolates that had been sequenced up until the beginning of each outbreak were loaded into Solu to replicate the background genomic data available when each outbreak occurred. The 13 methicillin-resistant Staphylococcus aureus (MRSA) and seven Klebsiella variicola outbreak isolates were then uploaded.

Findings

Including upload time, each Solu analysis was completed in under 40 min. The phylogenetic trees generated showed distinct clustering of outbreak isolates, with overall tree topologies similar to the manual analyses. Median pairwise single-nucleotide variant distances were 12 (range: 4–27) and 6 (range: 1–11) for the MRSA and K. variicola outbreaks, respectively, versus 6 (range: 0–14) and 18 (range: 0–54) for the manual analyses.

Conclusion

Solu Genomics delivers high-resolution, actionable outbreak analysis for common hospital bacterial pathogens within minutes, transforming routine nanopore sequencing into infection prevention and control (IPC)-ready insights without on-site bioinformatics.
背景:许多医院实验室具有进行微生物全基因组测序的技术能力,但缺乏分析序列数据的生物信息学专业知识。将分离株送到参考实验室会造成延误,这对疫情应对非常不利。缺乏现场生物信息学家的惠灵顿地区医院实验室实施了基于纳米孔的实时基因组测序,在早期发现了几次医院暴发。这需要场外分析,通常需要数周时间。Solu Genomics是一个基于云的自动化生物信息学平台,不需要生物信息学或命令行专业知识,并接受基本的序列文件或基因组组装。目的:使用Solu对现场基因组测序检测到的两次新生儿单位暴发进行重复分析,就好像它们现在已经发生一样,并将输出与“人工”生物信息学分析进行比较。方法:将每次暴发开始前已测序的监测分离株加载到Solu中,以复制每次暴发发生时可用的背景基因组数据。随后上传了13株耐甲氧西林金黄色葡萄球菌(MRSA)和7株水痘克雷伯菌暴发分离株。结果:包括上传时间在内,每次Solu分析在40分钟内完成。生成的系统发育树显示了爆发分离物的明显聚类,总体树拓扑结构与手工分析相似。MRSA和variicola爆发的中位数单核苷酸变异距离分别为12(范围4-27)和6(范围1-11),而手工分析的中位数单核苷酸变异距离为6(范围0-14)和18(范围0-54)。结论:Solu Genomics可在几分钟内为常见的医院细菌性病原体提供高分辨率、可操作的爆发分析,将常规的纳米孔测序转化为无需现场生物信息学的感染预防和控制(IPC)准备好的见解。
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引用次数: 0
Comparison of two models of biofilm formation on reusable stainless steel medical device material 两种可重复使用不锈钢医疗器械材料生物膜形成模型的比较
IF 3.1 3区 医学 Q1 INFECTIOUS DISEASES Pub Date : 2026-02-01 Epub Date: 2025-11-19 DOI: 10.1016/j.jhin.2025.10.034
G.G. Anderson , S. James , S. Kovvali , F.W. Dang , A. Vishwakarma , M.-C. Gagnon , N. Goulet , F. Racine , P. Labrie , M. Eppihimer , J.W. Weeks , B. Haas , R. Pandey

Background

Reusable medical devices require reprocessing before subsequent patient use. Inadequate reprocessing can create suitable conditions for contaminating microbes to form biofilm. Despite this threat, there is a lack of guidance for medical device manufacturers to make biofilm assessment on their device labelling and instructions for use. Currently, there are no US Food and Drug Administration-recognized standardized models for biofilm formation on medical devices or device materials.

Aim

To assess established standard methods for their suitability to be used as validation tools for medical device manufacturers and regulatory agencies.

Methods

Pseudomonas aeruginosa biofilms were grown using a drip flow reactor and a CDC biofilm reactor (CDC-BR) biofilm reactor on stainless steel coupons as a medical device material surrogate surface. Growth duration, extraction procedure, and extraction medium were optimized within the parameters of the experiments. Suitability of the models was determined by the comparison of colony-forming units (cfu), protein concentration, and total organic carbon.

Findings

Data revealed that both the models developed similar levels of biofilm as quantified by cfu, despite different shear stress conditions. The results showed that protein and total organic carbon are potential analytes to quantify the biofilm biomass under the conditions tested. Additionally, results of each assay display low variability across multiple biofilm replicates.

Conclusion

Both models develop reproducible biofilm with a similar level of cfu but different levels of total organic carbon and protein. Our findings indicate that the CDC biofilm reactor and drip flow reactor provide reliable platforms for studying biofilm growth on medical device materials.
背景:可重复使用的医疗器械需要在患者后续使用前进行再处理。不充分的后处理可以为污染微生物形成生物膜创造适宜的条件。尽管存在这一威胁,但医疗器械制造商对其器械标签和使用说明进行生物膜评估缺乏指导。目前,没有fda认可的医疗器械或器械材料上生物膜形成的标准化模型。本研究旨在评估已建立的标准方法是否适合作为医疗器械制造商和监管机构的验证工具。方法:采用滴流反应器和CDC生物膜反应器在不锈钢片作为医疗器械材料的替代表面上培养铜绿假单胞菌生物膜。在实验参数范围内对生长时间、提取工艺、提取培养基进行优化。通过比较菌落形成单位、蛋白质浓度和总有机碳来确定模型的适用性。研究结果:数据显示,尽管剪切应力条件不同,但两种模型的菌落形成单位(CFU)量化的生物膜水平相似。结果表明,在试验条件下,蛋白质和总有机碳是量化生物膜生物量的潜在分析物。此外,每个分析的结果显示跨多个生物膜复制的低可变性。结论:两种模型均可形成可复制的生物膜,CFU水平相似,但TOC和蛋白质水平不同。我们的研究结果表明,CDC-BR和DFR为研究医疗器械材料的生物膜生长提供了可靠的平台。
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引用次数: 0
期刊
Journal of Hospital Infection
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