Journal of global antimicrobial resistance最新文献_第7页

No genetic link between E. coli isolates carrying mcr-1 in bovines and humans in France 在法国的牛和人身上携带mcr-1的大肠杆菌分离株之间没有遗传联系。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-03 DOI: 10.1016/j.jgar.2024.12.021

Marisa Haenni , Pierre Châtre , Racha Beyrouthy , Antoine Drapeau , Pauline François , Jean-Yves Madec , Richard Bonnet

Background

Colistin is a last-line antibiotic used to treat severe human infections caused by carbapenemase-producing Gram-negative bacteria. In parallel, colistin has massively been used in the veterinary field so that mcr-1-positive E. coli have spread worldwide in livestock, potentially constituting a reservoir of colistin-resistant isolates that can be further transmitted to humans.

Objectives

In France, the mcr-1 gene was frequently identified in E. coli of bovine origin. This genomic study assessed whether French human mcr-1-positive E. coli might originate or derive from the bovine reservoir.

Material and methods

Human (n = 24) and bovine (n = 127) isolates collected between 2011 and 2019 were included and colistin-resistance was confirmed by MICs. The detection of mcr-1 was performed by PCR. Isolates were short-read whole-genome sequenced and a cgMLST-based phylogeny was constructed. The genetic support of mcr-1 was identified using short-read sequences or Southern blots.

Results

The mcr-1 gene was carried by a high diversity of genetic backgrounds, among which ST167 and ST10 were the most widespread. No clonally-related isolates between bovines and humans were observed. In bovines, mcr-1 was identified on IncHI2 and IncX4 plasmids and increasingly on the chromosome, while it was also found on IncI2 and p0111 plasmids in humans.

Conclusion

Although similar STs (ST744 and ST88) and plasmid types (IncHI2, IncX4) carried mcr-1, no hypothesis of a transfer from bovines to humans could be supported by the data. Furthermore, the increasing chromosomal location of mcr-1 over time may reflect an animal-specific evolutionary pathway deserving further investigation.

背景：粘菌素是用于治疗由产碳青霉烯酶革兰氏阴性菌引起的严重人类感染的最后一线抗生素。与此同时，粘菌素已大量用于兽医领域，因此mcr-1阳性大肠杆菌已在全世界的牲畜中传播，可能构成可进一步传播给人类的耐粘菌素分离株的储存库。目的：在法国，mcr-1基因经常在牛源性大肠杆菌中被鉴定出来。这项基因组研究评估了法国人mcr-1阳性大肠杆菌是否可能起源于或来源于牛宿主。材料和方法：纳入2011-2019年间收集的人（n=24）和牛（n=127）分离株，并通过mic确认粘菌素耐药性。PCR检测mcr-1。对分离株进行短读全基因组测序，构建了基于cgmlst的系统发育。mcr-1的遗传支持是通过短读序列或Southern blots鉴定的。结果：mcr-1基因具有高度多样性的遗传背景，其中以ST167和ST10最为广泛。未观察到牛与人之间的克隆相关分离株。在牛中，mcr-1在IncHI2和IncX4质粒上被发现，并且越来越多地在染色体上被发现，而在人的inc2和p0111质粒上也发现了mcr-1。结论：虽然相似的STs （ST744和ST88）和质粒类型（IncHI2, IncX4）携带mcr-1，但数据不能支持从牛向人转移的假设。此外，随着时间的推移，mcr-1染色体位置的增加可能反映了一种值得进一步研究的动物特异性进化途径。

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引用次数: 0

Co-existence of two blaNDM-5 and blaOXA-181 on distinct plasmids in a carbapenem-resistant Klebsiella pneumoniae from a tertiary hospital, Tanzania 坦桑尼亚某三级医院碳青霉烯耐药肺炎克雷伯菌的两种blaNDM-5和blaOXA-181在不同质粒上共存

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-02 DOI: 10.1016/j.jgar.2024.12.011

Lawrence Mapunda , Anthon Mwingwa , Doreen Kamori , Happiness Kumburu , Marco van Zwetselaar , Bjorn Blomberg , Joel Manyahi

Purpose

To understand the mechanisms of carbapenem-resistant Klebsiella pneumoniae (CRKP) from Tanzania and characterize the genomes carrying the carbapenemase genes.

Methods

Clinical CRKP isolates were selected from ongoing antimicrobial resistance surveillance at Muhimbili National Hospital, Dar es Salaam, Tanzania. Whole-genome sequencing was performed utilizing Illumina and Nanopore platforms.

Results

A total of twelve CRKP were analyzed in this study. Six different multilocus sequence types were detected, six isolates were sequence type ST437 and one belonged to a novel sequence type, ST6258. Resistance to carbapenems was multifactorial with co-existence of bla_NDM-5 and bla_OXA-181 in six CRKP, and bla_NDM-5 and bla_OXA-232 in one isolate, and chromosomal mutation of ompK36 and ompK37 in all twelve isolates. All the CRKP carried genes conferring resistance to 3rd generation cephalosporins, penicillin, aminoglycosides, fosfomycin, trimethoprim-sulfamethoxazole, and quinolones. The hybrid assemblies of 001BS and 002PS2 revealed that they harbored seven and six different plasmids, respectively. The 001BS carried two bla_NDM-5 on distinct plasmids. The first bla_NDM-5 gene was carried on an IncFIB(K) plasmid; and the second bla_NDM-5 co-existed with bla_OXA-181 on the ColPK3-IncX3 plasmid. In contrast, in 002PS2 the bla_NDM-5 and bla_OXA-181 were carried on the IncFIB(K)-IncFII(K) and ColPK3-IncX3 plasmids, respectively. The genetic environment of the bla_NDM-5 gene on both plasmids was flanked by the same genetic core IS26–IS30–bla_NDM-5 –ble–trpF–DsbD–ISCR1–sul1– QacE–IS3000.

Conclusion

Clonally related CRKP ST437 with multiple co-existing carbapenemase genes were detected for the first time at the tertiary hospital in Tanzania. The existence of this high-risk clone poses a great risk for further spread at our facility.

目的：了解坦桑尼亚碳青霉烯耐药肺炎克雷伯菌（CRKP）的发病机制，并对携带碳青霉烯酶基因的基因组进行鉴定。方法：从坦桑尼亚达累斯萨拉姆Muhimbili国立医院正在进行的抗微生物药物耐药性监测中选择临床CRKP分离株。利用Illumina和Nanopore平台进行全基因组测序。结果：本研究共分析了12个CRKP。检测到6种不同的多位点序列类型，其中6株为ST437序列类型，1株为ST6258序列类型。6株CRKP中blaNDM-5和blaOXA-181共存，1株CRKP中blaNDM-5和blaOXA-232共存，12株CRKP中均存在ompK36和ompK37染色体突变。所有的CRKP都携带了对第三代头孢菌素、青霉素、氨基糖苷类、磷霉素、甲氧苄啶-磺胺甲恶唑和喹诺酮类药物耐药的基因。001BS和002PS2的杂交组合显示它们分别含有7个和6个不同的质粒。001BS在不同的质粒上携带两个blaNDM-5。第一个blaNDM-5基因携带在IncFIB(K)质粒上；第二个blaNDM-5与blaOXA-181共存于ColPK3-IncX3质粒上。相比之下，在002PS2中，blaNDM-5和blaOXA-181分别携带在IncFIB(K)-IncFII(K)和ColPK3-IncX3质粒上。blaNDM-5基因在两个质粒上的遗传环境由相同的遗传核心IS26-IS30-blaNDM-5 -ble- trpf - dsbd - iscr1 -sul1- QacE-IS3000组成。结论：在坦桑尼亚三级医院首次检测到与碳青霉烯酶多基因共存的克隆相关的CRKP ST437。这个高风险克隆体的存在给我们的设施带来了进一步传播的巨大风险。

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引用次数: 0

Genomic and phylogenetic analysis of a NDM-1 producing ST152 Klebsiella pneumoniae isolated from a bloodstream infection in China 一株产NDM-1的ST152肺炎克雷伯菌的基因组和系统发育分析

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.005

Renchi Fang , Lingfang Di , Xuebin Tian , Yongfeng Bai

Purpose

The aim of this study was to characterize the genomic structure of the first isolated ST152 Klebsiella pneumoniae strain carrying bla_NDM-1 in China.

Methods

Antimicrobial susceptibility was determined by broth microdilution method. Whole-genome sequencing was conducted using the Illumina HiSeq and Oxford Nanopore GridION X5 platforms, and the genomic features were analyzed using a range of bioinformatics tools.

Results

The strain HZKP1 demonstrated resistance to cefepime, ceftazidime, amoxicillin-clavulanic acid, amikacin, ciprofloxacin, meropenem, imipenem, and ertapenem, while showing sensitivity to tigecycline and colistin. It was classified as sequence type (ST) 152, K locus (KL) 105 and OC locus (OCL) O3b, respectively. The bla_NDM-1 gene was identified on the IncX3 plasmid pHZKP1-NDM (54,035 bp), located downstream of the ISKox3-IS3000-ISAba125-IS5 segment and upstream of the ble_MBL-IS26-bla_SHV-69-IS26 segment. Phylogenetic analysis indicated its closest relative to be a strain isolated from a wound swab sample in Tanzania in 2013, differing by 598 alleles.

Conclusion

We characterized genomic features of the first ST152 K. pneumoniae strain isolated in China. Our findings provide insights into the current status of resistance in new lineages within the region and enhance comprehension of K. pneumoniae carbapenem resistance transmission from a genetic structure perspective.

目的：研究中国首次分离到的携带blaNDM-1的ST152肺炎克雷伯菌的基因组结构。方法：采用微量肉汤稀释法测定药敏。使用Illumina HiSeq和Oxford Nanopore MinION平台进行全基因组测序，并使用一系列生物信息学工具分析基因组特征。结果：菌株HZKP1对头孢吡肟、头孢他啶、阿莫西林-克拉维酸、阿米卡星、环丙沙星、美罗培南、亚胺培南、厄他培南耐药，对替加环素、粘菌素敏感。序列型（ST） 152， K位点（KL） 105， OC位点（OCL） O3b。blaNDM-1基因位于IncX3质粒pHZKP1-NDM （54,035 bp）上，位于ISKox3-IS3000-ISAba125-IS5片段的下游和blemll - is26 - blashv -69- is26片段的上游。系统发育分析表明，其最近的近亲是2013年从坦桑尼亚伤口拭子样本中分离出来的菌株，存在598个等位基因差异。结论：初步鉴定了中国首例分离到的ST152肺炎克雷伯菌的基因组特征。我们的研究结果为该地区新谱系的耐药现状提供了见解，并从遗传结构的角度增强了对肺炎克雷伯菌碳青霉烯类耐药传播的理解。

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引用次数: 0

Amikacin, in combination with cations, prevents growth of a carbapenem-resistant/multidrug-resistant Klebsiella pneumoniae strain isolated from a patient with COVID-19 阿米卡星与阳离子联合使用可防止从COVID-19患者分离出的碳青霉烯耐药/多重耐药肺炎克雷伯菌菌株的生长。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.007

Angel J. Magaña , David Ngo , Diego Faccone , Sonia Gomez , Alejandra Corso , Fernando Pasteran , María Soledad Ramirez , Marcelo E. Tolmasky

引用次数: 0

Characterisation, management, and outcomes of New Delhi metallo-β-lactamase-producing Escherichia coli: A case series 新德里金属β-内酰胺酶（NDM）产生大肠杆菌的特征、管理和结果：一个病例系列。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.017

Anita Shallal , Michael P. Veve , Rachel M. Kenney , George Alangaden , Geehan Suleyman

Objective

New Delhi metallo-β-lactamase (NDM)-producing carbapenem-resistant Enterobacterales (CRE) is a globally growing threat. We sought to describe the microbiology, management and outcomes of patients with this infection at our facility.

Methods

This is a descriptive case series of patients with NDM-producing Escherichia coli isolated from culture in Detroit between July 2021 and February 2023. Demographics, risk factors, clinical characteristics, management and outcomes were described.

Results

Nine patients were included in the study. Most patients were female with a median age of 67 years. Hepatobiliary disease accounted for 90% of underlying conditions. Nearly all patients had prior antibiotic exposure and the most common specimen source was intra-abdominal fluid. Three patients were not treated due to colonisation; among those treated, the majority received trimethoprim-sulfamethoxazole. The median treatment duration and length of stay were 7 and 15.5 days, respectively. Six (67%) patients survived.

Conclusions

This report describes a large case series of NDM-producing E. coli infection. Patients with significant comorbidities remain at high risk for CRE infection. Antibiotic options for the treatment of NDM organisms are very limited; new and effective therapies are urgently needed.

背景：产生新德里金属β-内酰胺酶（NDM）的耐碳青霉烯肠杆菌（CRE）是全球日益严重的威胁。我们试图描述在我们的设施中感染的患者的微生物学，管理和结果。方法：对2021年7月至2023年2月在底特律培养分离的产ndm大肠杆菌患者进行描述性病例系列研究。描述了人口统计学、危险因素、临床特征、管理和结果。结果：9例患者纳入研究。大多数患者为女性，中位年龄为67岁。肝胆疾病占基础疾病的90%。几乎所有患者之前都有抗生素接触。最常见的标本来源是腹腔内液体。3例患者因定植而未治疗；在接受治疗的患者中，大多数接受了甲氧苄啶-磺胺甲恶唑治疗。中位治疗时间和住院时间分别为7天和15.5天。6例（67%）患者存活。结论：本报告描述了一个产生ndm的大肠杆菌感染的大病例系列。有明显合并症的患者仍然是CRE感染的高危人群。用于治疗非传染性疾病生物的抗生素选择非常有限；迫切需要新的和有效的治疗方法。

{"title":"Characterisation, management, and outcomes of New Delhi metallo-β-lactamase-producing Escherichia coli: A case series","authors":"Anita Shallal , Michael P. Veve , Rachel M. Kenney , George Alangaden , Geehan Suleyman","doi":"10.1016/j.jgar.2024.11.017","DOIUrl":"10.1016/j.jgar.2024.11.017","url":null,"abstract":"<div><h3>Objective</h3><div>New Delhi metallo-β-lactamase (NDM)-producing carbapenem-resistant <em>Enterobacterales</em> (CRE) is a globally growing threat. We sought to describe the microbiology, management and outcomes of patients with this infection at our facility.</div></div><div><h3>Methods</h3><div>This is a descriptive case series of patients with NDM-producing <em>Escherichia coli</em> isolated from culture in Detroit between July 2021 and February 2023. Demographics, risk factors, clinical characteristics, management and outcomes were described.</div></div><div><h3>Results</h3><div>Nine patients were included in the study. Most patients were female with a median age of 67 years. Hepatobiliary disease accounted for 90% of underlying conditions. Nearly all patients had prior antibiotic exposure and the most common specimen source was intra-abdominal fluid. Three patients were not treated due to colonisation; among those treated, the majority received trimethoprim-sulfamethoxazole. The median treatment duration and length of stay were 7 and 15.5 days, respectively. Six (67%) patients survived.</div></div><div><h3>Conclusions</h3><div>This report describes a large case series of NDM-producing <em>E. coli</em> infection. Patients with significant comorbidities remain at high risk for CRE infection. Antibiotic options for the treatment of NDM organisms are very limited; new and effective therapies are urgently needed.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"40 ","pages":"Pages 42-46"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coexistence of blaMIR-1 and blaNDM-1 resistance genes with a novel ST type in Enterobacter roggenkampii from a stool sample: A genome sequencing study 来自粪便样本的罗格根坎皮肠杆菌中blaMIR-1和blaNDM-1耐药基因与新型ST型共存：一项基因组测序研究

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.006

Qin Wang , Sayyed Salman , Ye Luo , XiaoMei Tong

Objective

The Enterobacter cloacae complex, known for causing infections in hospitalised patients, displays resistance to β-lactam antibiotics due to AmpC β-lactamase expression. This study emphasises the genome sequence of Enterobacter roggenkampii, which coexists with MIR-1 and NDM-1 genes, isolated from the stool of a hospitalised patient in China.

Methods

A faecal sample was diluted in Luria-Bertani broth and incubated overnight. Cultures were then spread on MacConkey agar containing meropenem and incubated for 18–24 h to select carbapenem-resistant Enterobacteriaceae. Individual colonies were isolated, and bacterial species were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and 16S rRNA gene sequencing. Genomic DNA was extracted and sequenced via Illumina and Oxford Nanopore sequencing.

Results

Genomic analysis of E. roggenkampii L3897 revealed a 4 897 636 bp genome with 55.9% GC content and confirmed its classification as E. roggenkampii through average nucleotide identity-based analysis. A new sequence type distinct from ST2392, ST3014, with a unique rplB genotype was identified. Additionally, the genome harbours three antibiotic resistance genes and a newly discovered plasmid, pL3897_NDM, highlighting the need for surveillance of drug-resistant pathogens.

Conclusions

The discovery of a new sequence type and the presence of an antibiotic resistance gene in E. roggenkampii L3897 underscores the need for ongoing genomic surveillance to effectively manage multidrug-resistant pathogens.

目的：以引起住院患者感染而闻名的阴沟肠杆菌复合体由于AmpC β-内酰胺酶的表达而对β-内酰胺类抗生素产生耐药性。本研究重点分析了从中国一位住院患者粪便中分离到的与MIR-1和NDM-1基因共存的罗根坎皮肠杆菌的基因组序列。方法：将粪便样品用Luria-Bertani肉汤稀释，孵育过夜。然后将培养物散布在含有美罗培南的麦康基琼脂上，孵育18-24小时，筛选耐碳青霉烯肠杆菌科（CRE）。分离单个菌落，利用基质辅助激光解吸电离飞行时间质谱法和16S rRNA基因测序对细菌种类进行鉴定。提取基因组DNA并通过Illumina和Oxford Nanopore测序进行测序。结果：罗根坎皮肠杆菌L3897基因组全长4897636 bp， GC含量55.9%，经ANIb分析确认为罗根坎皮肠杆菌。鉴定出与ST2392不同的具有独特rplB基因型的新序列型ST3014。此外，该基因组含有三个抗生素耐药基因和一个新发现的质粒pL3897_NDM，突出了耐药病原体监测的必要性。结论：在罗根kampii L3897中发现了一种新的序列类型和抗生素耐药基因的存在，强调了持续进行基因组监测以有效管理多重耐药病原体的必要性。

{"title":"Coexistence of blaMIR-1 and blaNDM-1 resistance genes with a novel ST type in Enterobacter roggenkampii from a stool sample: A genome sequencing study","authors":"Qin Wang , Sayyed Salman , Ye Luo , XiaoMei Tong","doi":"10.1016/j.jgar.2024.11.006","DOIUrl":"10.1016/j.jgar.2024.11.006","url":null,"abstract":"<div><h3>Objective</h3><div>The <em>Enterobacter cloacae</em> complex, known for causing infections in hospitalised patients, displays resistance to β-lactam antibiotics due to AmpC β-lactamase expression. This study emphasises the genome sequence of <em>Enterobacter roggenkampii</em>, which coexists with MIR-1 and NDM-1 genes, isolated from the stool of a hospitalised patient in China.</div></div><div><h3>Methods</h3><div>A faecal sample was diluted in Luria-Bertani broth and incubated overnight. Cultures were then spread on MacConkey agar containing meropenem and incubated for 18–24 h to select carbapenem-resistant Enterobacteriaceae. Individual colonies were isolated, and bacterial species were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and 16S rRNA gene sequencing. Genomic DNA was extracted and sequenced via Illumina and Oxford Nanopore sequencing.</div></div><div><h3>Results</h3><div>Genomic analysis of <em>E. roggenkampii</em> L3897 revealed a 4 897 636 bp genome with 55.9% GC content and confirmed its classification as <em>E. roggenkampii</em> through average nucleotide identity-based analysis. A new sequence type distinct from ST2392, ST3014, with a unique <em>rplB</em> genotype was identified. Additionally, the genome harbours three antibiotic resistance genes and a newly discovered plasmid, pL3897_NDM, highlighting the need for surveillance of drug-resistant pathogens.</div></div><div><h3>Conclusions</h3><div>The discovery of a new sequence type and the presence of an antibiotic resistance gene in <em>E. roggenkampii</em> L3897 underscores the need for ongoing genomic surveillance to effectively manage multidrug-resistant pathogens.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"40 ","pages":"Pages 37-41"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association between the rifampicin resistance mutations and rifabutin susceptibility in Mycobacterium tuberculosis: A meta-analysis 结核分枝杆菌利福平耐药突变与利福平易感性之间的关系：一项荟萃分析。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.014

Wenli Wang, Hongjuan Zhou, Long Cai, Tingting Yang

Objective

Certain rifampicin-resistant Mycobacterium tuberculosis (MTB) strains are susceptible to rifabutin (RFB) and may be amenable to RFB treatment. We performed a meta-analysis of available cross-sectional studies to determine the rifampicin (RIF) resistance mutations associated with RFB susceptibility.

Methods

We identified studies through PubMed, Web of Science, Embase, and the Cochrane Library up to September 30, 2024. Studies that investigated RpoB mutations and reported phenotypic drug susceptibility to RIF and RFB met our criteria. The relationship between RIF-resistance mutations to RFB-susceptibility was evaluated using odds ratios (OR).

Results

Twenty-seven studies comprised 9222 clinical RIF-resistant MTB strains from 25 countries met the inclusion criteria. Of these strains, 14.93% (1377/9222) were susceptible to RFB. We found that 14 RIF-resistance mutations were associated with susceptibility to RFB. Among these, nine had high confidence (OR>10) in predicting RFB susceptibility: RpoB D435V, H445L, D435Y, D435F, S441L, L430P, H445G, S441Q, L430R. Among the strains carrying these mutations, 59.04% (702/1189) were susceptible to RFB. The ratio increased to 83.45% in studies following CLSI guidelines. The minimum inhibition concentrations (MICs) of these mutations revealed that they had low MIC to RFB and exhibited a lack of correlation between MICs for RIF and RFB. L452P, I491F, H445C, H445N, and D435G exhibited moderate confidence (5<OR≤10) in predicting susceptibility to RFB. S450L and S450W were associated with RFB-resistance (OR<1).

Conclusions

These results provide a theoretical basis for the molecular detection of RFB-susceptible tuberculosis and alternative treatment with RFB in patients with multidrug-resistant/rifampicin-resistant tuberculosis.

目的：某些耐利福平结核分枝杆菌（MTB）菌株对利福布汀（RFB）敏感，可能适合RFB治疗。我们对现有的横断面研究进行了荟萃分析，以确定与RFB易感性相关的利福平（RIF）耐药突变。方法：我们通过PubMed、Web of Science、Embase和Cochrane Library检索到2024年9月30日的研究。研究RpoB突变和报告对RIF和RFB的表型药物敏感性的研究符合我们的标准。使用比值比（OR）评估rif抗性突变与rfb敏感性之间的关系。结果：27项研究包括来自25个国家的9222株耐rif结核分枝杆菌符合纳入标准。其中，14.93%（1377/9222）菌株对RFB敏感。我们发现14个rif耐药突变与RFB易感性相关。其中，9个RpoB对RFB易感性具有高置信度（OR bbbb10），分别为：RpoB D435V、H445L、D435Y、D435F、S441L、L430P、H445G、S441Q、L430R。携带这些突变的菌株中，59.04%（702/1189）对RFB敏感。在遵循CLSI指南的研究中，这一比例增加到83.45%。这些突变的最低抑制浓度（MIC）表明，它们对RFB的MIC较低，且MIC对RIF和RFB缺乏相关性。L452P、I491F、H445C、H445N、D435G具有中度置信度(5)。结论：这些结果为RFB敏感结核病的分子检测和多药/利福平耐药结核病患者的RFB替代治疗提供了理论依据。

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引用次数: 0

Genomic insights into a clinical Salmonella Typhimurium isolate carrying plasmid-mediated blaNDM-5 携带质粒介导的blaNDM-5的鼠伤寒沙门氏菌临床分离株的基因组研究。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.009

Fan Huang , Genglin Guo , Lu Feng , Tongbo Cai , Xu Huang

Objective

Highly carbapenem-resistant Salmonella has emerged worldwide in recent years and is largely associated with the multiform transmission of resistance genes, which poses a huge challenge in clinical practice. Our study delves into the resistance mechanisms and epidemiology of bla_NDM-carrying plasmids.

Methods

Whole-genome sequencing was utilised to analyse the molecular characteristics and antimicrobial resistance mechanisms of Salmonella isolates recovered from the faeces of a paediatric patient at the Children's Hospital of Nanjing Medical University. Moreover, we conducted an epidemiologic analysis and focused on studying the mechanisms of plasmid-mediated bla_NDM transmission, incorporating genomes deposited in the NCBI Pathogen Detection database.

Results

The clinical isolate 23S9 belonged to serovar Typhimurium, antigenic profile 4:i:-, ST34, and carried pNDM_23S9 harbouring several antimicrobial resistance genes, including aac(6′)-Ib-cr6, OXA-1, catB3, arr-3, qacEdeltal and bla_NDM. Comparative analysis revealed that bla_NDM-5 can exist in different plasmids of different isolates, proving its transmission through plasmids. Furthermore, bla_NDM-carrying isolates are mostly resistant to beta-lactams, aminoglycosides, sulphonamide, macrolides, and trimethoprim.

Conclusions

These findings provided thorough and intuitive insights into the intercontinental spread of bla_NDM-carrying Salmonella. Ongoing surveillance is essential for effectively monitoring the worldwide dissemination of this high-risk carbapenem-resistant Salmonella.

目的：高碳青霉烯耐药沙门氏菌近年来在世界范围内出现，主要与耐药基因的多形式传播有关，给临床实践带来巨大挑战。本研究探讨了携带blandm的质粒的耐药机制和流行病学。方法：采用全基因组测序（WGS）对南京医科大学附属儿童医院1例患儿粪便中分离的沙门氏菌分子特征及耐药机制进行分析。此外，我们还结合NCBI病原体检测数据库中的基因组进行了流行病学分析，重点研究了质粒介导的blaNDM传播机制。结果：临床分离株23S9属于血清型鼠伤寒菌，抗原谱为4:i:-、ST34，携带pNDM_23S9，其中pNDM_23S9含有aac（6’）- ib -cr6、OXA-1、catB3、arr-3、qacEdeltal和blaNDM等耐药基因。对比分析显示blaNDM-5可存在于不同菌株的不同质粒中，证明其可通过质粒传播。此外，携带blandm的分离株主要对-内酰胺类、氨基糖苷类、磺胺类、大环内酯类和甲氧苄啶耐药。结论：这些发现为携带blandm的沙门氏菌的洲际传播提供了彻底和直观的见解。持续监测对于有效监测这种高风险耐碳青霉烯沙门氏菌的全球传播至关重要。

{"title":"Genomic insights into a clinical Salmonella Typhimurium isolate carrying plasmid-mediated blaNDM-5","authors":"Fan Huang , Genglin Guo , Lu Feng , Tongbo Cai , Xu Huang","doi":"10.1016/j.jgar.2024.11.009","DOIUrl":"10.1016/j.jgar.2024.11.009","url":null,"abstract":"<div><h3>Objective</h3><div>Highly carbapenem-resistant <em>Salmonella</em> has emerged worldwide in recent years and is largely associated with the multiform transmission of resistance genes, which poses a huge challenge in clinical practice. Our study delves into the resistance mechanisms and epidemiology of <em>bla</em><sub>NDM</sub>-carrying plasmids.</div></div><div><h3>Methods</h3><div>Whole-genome sequencing was utilised to analyse the molecular characteristics and antimicrobial resistance mechanisms of <em>Salmonella</em> isolates recovered from the faeces of a paediatric patient at the Children's Hospital of Nanjing Medical University. Moreover, we conducted an epidemiologic analysis and focused on studying the mechanisms of plasmid-mediated <em>bla</em><sub>NDM</sub> transmission, incorporating genomes deposited in the NCBI Pathogen Detection database.</div></div><div><h3>Results</h3><div>The clinical isolate 23S9 belonged to serovar Typhimurium, antigenic profile 4:i:-, ST34, and carried pNDM_23S9 harbouring several antimicrobial resistance genes, including aac(6′)-Ib-cr6, OXA-1, catB3, arr-3, qacEdeltal and <em>bla</em><sub>NDM</sub>. Comparative analysis revealed that <em>bla</em><sub>NDM-5</sub> can exist in different plasmids of different isolates, proving its transmission through plasmids. Furthermore, <em>bla</em><sub>NDM</sub>-carrying isolates are mostly resistant to beta-lactams, aminoglycosides, sulphonamide, macrolides, and trimethoprim.</div></div><div><h3>Conclusions</h3><div>These findings provided thorough and intuitive insights into the intercontinental spread of <em>bla</em><sub>NDM</sub>-carrying <em>Salmonella</em>. Ongoing surveillance is essential for effectively monitoring the worldwide dissemination of this high-risk carbapenem-resistant <em>Salmonella</em>.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"40 ","pages":"Pages 90-95"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

First detection of the high‐risk Klebsiella pneumoniae ST147 clone producing NDM‐14 in a community setting in Morocco: A new public health concern 在摩洛哥社区环境中首次发现产生NDM-14的肺炎克雷伯菌高风险克隆ST147：一个新的公共卫生问题。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.010

Aboubakr Khazaz , Fatima El Otmani , Ihssane Benzaarate , Adil El Hamouchi , Fatna Bourjilat , Sylvain Brisse , Kaotar Nayme

引用次数: 0

Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker 无色杆菌基因组20的基因组特征及潜在物种特异性标记的鉴定。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2025-01-01 DOI: 10.1016/j.jgar.2024.11.012

Mariana Papalia , Rocio Stucchi , Valeria Alexander , Liliana Clara , Mariángeles Visus , Gabriel Gutkind , Marcela Radice

Objective

To describe the genome of Achromobacter genogroup 20 and explore the presence of resistance determinants.

Methods

Isolate 413638 was identified through nrdA and MLST analysis. Antimicrobial susceptibility testing was performed according CLSI 2024. NGS was conducted using Illumina MiSeq, on the NextSeq500 platform with 150 bp paired-end reads, and de novo assembly was assessed using Unicycler (Galaxy). Coding sequences were predicted and confirmed with RAST and BLAST, and resistance determinants were evaluated using Resfinder and manual curation. All Achromobacter spp. genomes were obtained from NCBI, and the presence of bla_OXA was investigated. Average nucleotide identity (ANI) and tetranucleotide analysis (TETRA) were calculated. Phylogenetic analysis of the new OXA variant was conducted against other species-specific markers in Achromobacter.

Results

Isolate 413638 was identified as Achromobacter genogroup 20 ST365, showing resistance to third- and fourth-generation cephalosporins, aminoglycosides, and fluoroquinolones. The genome included coding sequences for three putative β-lactamases (one new OXA type-class D β -lactamase and two new class C), 32 efflux pump proteins, two aminoglycoside-modifying enzymes and a dihydropteroate synthase; also, substitutions in parC and parE were detected. The OXA enzyme, designated OXA-1238 (PP446293), differs from OXA-114a by 85 amino acids, with 69% identity. In silico analysis found OXA-1238 variants in three additional Achromobacter spp. genomes, with 97% identity. Based on ANI and tetra analysis, the three genomes corresponded to Achromobacter genogroup 20.

Conclusion

Several resistance markers were found, probably contributing to the resistance profile observed in Achromobacter genogroup 20 ST365. The new OXA variant identified, OXA-1238, could constitute a useful molecular marker for species identification.

目的：描述无色杆菌20基因组基因组，探讨耐药决定因素的存在。方法：分离物413638经nrdA和MLST鉴定。按照CLSI 2024进行药敏试验。NGS使用Illumina MiSeq，在NextSeq500平台上进行，配对端reads为150 bp，使用Unicycler （Galaxy）评估从头组装。使用RAST和BLAST预测和确认编码序列，使用Resfinder和人工筛选评估抗性决定因素。从NCBI中获得了所有无色杆菌的基因组，并对blaOXA的存在进行了研究。计算平均核苷酸同一性（ANI）和四核苷酸分析（TETRA）。新的OXA变异体与无色杆菌中其他种特异性标记进行了系统发育分析。结果：分离物413638鉴定为无色杆菌基因组20 ST365，对第三代和第四代头孢菌素、氨基糖苷类药物和氟喹诺酮类药物耐药。基因组包含3个推测的β-内酰胺酶（1个新的OXA型- D类β-内酰胺酶和2个新的C类β-内酰胺酶）、32个外排泵蛋白、2个氨基糖苷修饰酶和1个二氢蝶呤合成酶的编码序列；此外，还检测到parC和parE的替换。OXA酶被命名为OXA-1238 (PP446293)，与OXA-114a有85个氨基酸的差异，同源性为69%。在计算机分析中发现OXA-1238变体在另外三个无色杆菌的基因组中，具有97%的一致性。基于ANI和四环素分析，这三个基因组对应于无色杆菌基因组20。结论：在20 ST365无色杆菌基因群中发现了多个耐药标记，可能与耐药谱有关。新发现的OXA变异OXA-1238可作为一种有用的物种鉴定分子标记。

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