Journal of global antimicrobial resistance最新文献_第2页

Coexistence of seven different carbapenemase producers in a single hospital admission screening confirmed by whole-genome sequencing 通过全基因组测序，证实在一次入院筛查中同时存在七种不同的碳青霉烯酶生产者。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-10-16 DOI: 10.1016/j.jgar.2024.09.005

Objective

To molecularly characterize several extensively drug-resistant isolates from a single hospital admission screening of a war-injured patient from Ukraine.

Methods

Admission screening included swabs from skin, wounds, catheters, nasopharyngeum and rectum. Bacterial identification, antimicrobial susceptibility testing and rapid multiplex PCR assays targeting resistance genes were performed during routine diagnostics. Isolates positive by PCR had their genomes sequenced using short- and long read-platforms (MiSeq and MinION) to confirm species, identify resistance genes and plasmids and investigate clonality with core-genome MLST.

Results

Seven Gram-negative pathogens (Acinetobacter baumannii (n = 2; ST78, ST2), Klebsiella pneumoniae (n = 2; ST395), Pseudomonas aeruginosa (n = 1; ST1047), Escherichia coli (n = 1; ST46), Enterobacter cloacae complex (n = 1; ST231)) were molecularly confirmed non-identical. Antimicrobial susceptibility testing showed resistance to carbapenems (7/7 isolates) and last-resort treatment options such as ceftazidime-avibactam (6/7 isolates) and cefiderocol (4/7 isolates). All isolates were colistin susceptible. Sequencing identified the E. cloacae complex as Enterobacter hormaechei subsp. xiangfangensis. Six acquired carbapenemase genes (bla_IMP-1, bla_NDM-1, bla_OXA-48, bla_NDM-5, bla_OXA-23 and bla_OXA-72) were detected. Both A. baumannii isolates differed in sequence type, carbapenemases and cefiderocol susceptibility. Both K. pneumoniae isolates shared sequence type and some resistance genes on an IncR plasmid but were different in core-genome MLST and carbapenemases (OXA-48 or NDM-1). One vancomycin-resistant Enterococcus faecium was also detected (VanA).

Conclusions

War-injured patients from Ukraine may carry different clones of multidrug-resistant pathogens with limited treatment options and diverse resistance genes at risk for dissemination. Infection control measures should include early molecular characterization of isolates for detection of routes of transmission.

目的对来自乌克兰的一名战争伤员的一次入院筛查中分离出的几种广泛耐药菌株进行分子鉴定：入院筛查包括从皮肤、伤口、导管、鼻咽和直肠采集拭子。在常规诊断过程中进行了细菌鉴定、抗菌药物药敏试验（AST）和针对耐药基因的快速多重 PCR 检测。利用长短读取平台（MiSeq 和 MinION）对 PCR 检测结果呈阳性的分离菌进行基因组测序，以确认菌种、鉴定耐药基因和质粒，并利用核心基因组 MLST（cgMLST）研究克隆性：结果：7 种革兰氏阴性病原体（鲍曼不动杆菌（n=2；ST78、ST2）、肺炎克雷伯氏菌（n=2；ST395）、铜绿假单胞菌（n=1；ST1047）、大肠埃希菌（n=1；ST46）、复合泄殖腔肠杆菌（n=1；ST231））经分子鉴定为非同种。AST 显示出对碳青霉烯类（7/7 个分离株）和头孢唑肟-阿维巴坦（6/7 个分离株）和头孢克洛（4/7 个分离株）等最后治疗方案的耐药性。所有分离物均对秋水仙碱敏感。通过测序，确定泄殖腔大肠杆菌复合体为 E. hormaechei 亚种 xiangfangensis。检测到六个获得性碳青霉烯酶基因（blaIMP-1、blaNDM-1、blaOXA-48、blaNDM-5、blaOXA-23 和 blaOXA-72）。这两种鲍曼尼氏菌分离物在序列类型、碳青霉烯酶和头孢羟氨苄敏感性方面存在差异。两个肺炎克氏菌分离株共享序列类型和 IncR 质粒上的一些耐药基因，但在 cgMLST 和碳青霉烯酶（OXA-48 或 NDM-1）方面存在差异。此外，还检测到一种耐万古霉素的粪肠球菌（VanA）：结论：乌克兰的战争伤员可能携带不同克隆的耐多药病原体，治疗方案有限，耐药基因多样，存在传播风险。感染控制措施应包括及早对分离物进行分子鉴定，以检测传播途径。

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引用次数: 0

Emergence of OXA-48 carbapenemase-producing Salmonella enterica in the Netherlands, 2023. 2023 年荷兰出现产 OXA-48 碳青霉烯酶的肠炎沙门氏菌。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-10-15 DOI: 10.1016/j.jgar.2024.09.008

Gijs Teunis, Maren Lanzl, Kees T Veldman, Roan Pijnacker, Fabian Landman, Jeroen Bos, Michael S M Brouwer, Jenny Schuch, Karola Waar, Eelco Franz, Antoni P A Hendrickx

引用次数: 0

Two novel plasmids harbouring the multiresistance gene cfr in porcine Staphylococcus equorum 猪马葡萄球菌中携带多重抗性基因 cfr 的两种新型质粒。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-10-01 DOI: 10.1016/j.jgar.2024.09.004

Background

The emergence and transmission of the multidrug resistance gene cfr have raised public health concerns worldwide.

Objectives

Multidrug-resistant Staphylococcus equorum isolates can pose a threat to public health. In this study, we have characterised the whole-genome of one Staphylococcus equorum isolate harbouring two distinct cfr-carrying plasmids.

Methods

Antimicrobial susceptibility testing was performed by broth microdilution. Genomic DNA was sequenced using both the Illumina HiSeq X Ten and Nanopore MinION platforms. De novo hybrid assembly was performed by Unicycler. Genomic data were assessed by in silico prediction and bioinformatic tools.

Results

Staphylococcus equorum isolate SN42 exhibited resistance or high MICs to linezolid, erythromycin, tetracycline, oxacillin, clindamycin, virginiamycin, tiamulin, chloramphenicol and florfenicol. It carried two cfr-harbouring plasmids: the RepA N-family plasmid pSN42–51 K and the Inc18-family plasmid pSN42–50 K. These two plasmids exhibited low structural similarities to the so far reported cfr-carrying plasmids. Both plasmids harboured an arsenic resistance operon, copper and cadmium resistance genes as well as the lincosamide-pleuromutilin-streptogramin A resistance gene lsa(B). In addition, plasmid pSN42–51 K carried two erm(B) genes for macrolide-lincosamide-streptogramin B resistance, the streptomycin resistance gene ant(6)-Ia as well as mercury resistance genes while pSN42–50 K was associated with the heavy metal translocating P-type ATPase gene hmtp. The co-carriage and co-existence of these antimicrobial resistance and heavy metal resistance genes increases the likelihood of co-selection of the cfr-carrying plasmids.

Conclusion

This is the first report of S. equorum carrying two distinct cfr-carrying plasmids, underscoring the need for ongoing surveillance to address the potential dissemination of multi-drug resistance in bacteria from food-producing animals to ensure food safety and public health.

背景耐多药基因 cfr 的出现和传播引起了全球公共卫生的关注：耐多药的马葡萄球菌可对公共卫生构成威胁。在这项研究中，我们对一个携带两种不同的 cfr 质粒的马葡萄球菌分离株的全基因组进行了鉴定：方法：采用肉汤微稀释法进行抗菌药敏感性测试。使用 Illumina HiSeq X Ten 和 Nanopore MinION 平台对基因组 DNA 进行测序。由 Unicycler 进行从头杂交组装。基因组数据通过硅预测和生物信息学工具进行评估：马葡萄球菌分离株 SN42 对利奈唑胺、红霉素、四环素、氧西林、克林霉素、维吉尼霉素、替米考林、氯霉素和氟苯尼考具有耐药性或高 MICs。它携带了两个携带 cfr 的质粒：RepA N-家族质粒 pSN42-51K 和 Inc18-家族质粒 pSN42-50K。这两个质粒在结构上与迄今报道的携带 cfr 的质粒相似度较低。这两个质粒都含有抗砷操作子、抗铜和镉基因以及抗林可霉素-缬氨嘧啶-链霉毒素 A 基因 lsa(B)。此外，质粒 pSN42-51K 还携带了两个抗大环内酯-林可酰胺-链霉素 B 的 erm(B) 基因、链霉素抗性基因 ant(6)-Ia 以及汞抗性基因，而 pSN42-50K 则与重金属转运 P 型 ATP 酶基因 hmtp 有关。这些抗菌素抗性基因和重金属抗性基因的共同携带和共存增加了携带 cfr 的质粒共同选择的可能性：这是首次报告马铃薯沙门氏菌（S. equorum）携带两种不同的cfr-携带质粒，这突出表明有必要进行持续监测，以应对产自食用动物的细菌可能传播的多重耐药性，从而确保食品安全和公众健康。

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引用次数: 0

Corrigendum to “Occurrence and characteristics of blaOXA-181 - carrying Klebsiella aerogenes from swine in China” [Journal of Global Antimicrobial Resistance 38(2024) 35–41/JGAR_2323] 对 "中国猪群中携带 blaOXA-181 的产气克雷伯氏菌的出现和特征 "的更正[《全球抗菌药物耐药性杂志》38(2024) 35-41/JGAR_2323]

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-09-21 DOI: 10.1016/j.jgar.2024.08.009

引用次数: 0

Age and gender in drug resistance tuberculosis: A cross-sectional case study at a national tuberculosis reference hospital in Nigeria 耐药性结核病中的年龄与性别：尼日利亚一家国家结核病参考医院的横断面个案研究。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-09-19 DOI: 10.1016/j.jgar.2024.09.002

Objectives

Drug resistance in tuberculosis (TB) is a very important public health threat that should not be ignored. Understanding the gender, age, and characteristics of individuals affected by TB (without HIV, diabetes, or hepatitis B complications), particularly in terms of drug resistance or susceptibility, is crucial for effective prevention and management strategies, as most studies focus on TB/HIV co-infection.

Methods

A cross-sectional case study of age and gender was carried out in 140 individuals grouped into drug-resistant tuberculosis (DR-TB), drug-susceptible tuberculosis (DS-TB), and apparently healthy controls (AHCs). Data collection was through medical records and a structured questionnaire. Statistical analyses compared age, gender, and selected risk factors across the groups.

Results

The mean age of the DR-TB group was 32 years (SD ≈ 2). A total of 80.0% were ≤40 years of age and four times more likely to have DR-TB; 55% were male, with 1.22 times more likelihood of DR-TB in males. The mean age of the DS-TB group was 34 years (SD ≈ 12); 66.7% were ≤40 years old. The odds ratio of DS-TB in males was 2.16. Only 10% of DR-TB enrolees had BCG scars compared with 65% AHCs. A high percentage of the DR-TB group reported handling raw meat (75%) and drinking unpasteurised milk (70%) compared with the DS-TB group.

Conclusions

The observed gender disparities and age-related factors, particularly among the DR-TB group, highlight the importance of considering age and gender factors in DR-TB prevention, diagnosis, and treatment. Our findings also highlight the need to bridge gaps in awareness as well as for the prevention of zoonotic TB and issues around effective BCG vaccination and coverage.

目的：结核病（TB）的耐药性是一个非常重要的公共卫生威胁，不容忽视。了解结核病患者（无 HIV、糖尿病或乙肝并发症）的性别、年龄和特征，尤其是耐药性或敏感性，对于有效的预防和管理策略至关重要，因为大多数研究都侧重于结核病/HIV 合并感染：方法：对 140 名患者的年龄和性别进行横断面病例研究，分为耐药（DR-TB）、易药（DS-TB）和表面健康对照组（AHC）。数据收集通过医疗记录和结构化问卷进行。统计分析比较了各组的年龄、性别和选定的风险因素：DR-TB 组的平均年龄为 32 岁（SD≈ 2）。80.0%的人年龄小于 40 岁，患 DR-TB 的可能性是正常人的四倍。55%的患者为男性，男性患 DR-TB 的几率是其他男性的 1.22 倍。DS-TB 组的平均年龄为 34 岁（SD ≈ 12）。66.7%的患者年龄小于 40 岁。男性 DS-TB 患病率为 2.16。与 65% 的 AHCs 相比，只有 10% 的 DR-TB 患者有卡介苗疤痕。与 DS-TB 相比，DR-TB 报告处理生肉（75%）和饮用未消毒牛奶（70%）的比例较高：观察到的性别差异和年龄相关因素（尤其是在 DR-TB 中）凸显了在 DR-TB 的预防、诊断和治疗工作中考虑年龄和性别因素的重要性。研究结果还凸显了弥合人畜共患病结核病认识和预防方面的差距以及有效卡介苗接种和覆盖率问题的必要性。

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引用次数: 0

Complete genome of Escherichia coli sequence type 73 with acquired blaTEM-1 and high genotypic virulence load identified in human saliva 在人类唾液中鉴定出具有获得性 blaTEM-1 和高基因型毒力负荷的 73 型大肠埃希菌序列的完整基因组。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-09-19 DOI: 10.1016/j.jgar.2024.08.011

Objectives

Escherichia coli sequence type (ST) 73 is a pandemic lineage of the ExPEC (Extraintestinal Pathogenic E. coli) family associated with conserved virulence. We report the complete genome of a genomically hypervirulent E. coli ST73 strain isolated from the oral cavity of a patient with a diagnosis of treatment resistant schizophrenia and receiving clozapine treatment.

Methods

E. coli strain GABEEC132 underwent second and third generation sequencing with Illumina and Oxford-Nanopore-Technologies (ONT) platforms. Antibiotic resistance genes (ARGs) and virulence factors (VFs) were bioinformatically identified using the NCBI-AMR-Finder-Plus database and Virulence-Factors-database (VFDB), respectively. To contextualize the genome within a broader epidemiological framework, phylogenetic analysis was conducted using representative genomes of E. coli ST73 O6:H1 (n = 55).

Results

E. coli strain GABEEC132 was identified as possessing the O6:H1 serotype and classified within the B2 phylogroup. The strain exhibited a high genomic virulence load, encoding for 194 VFs. Additionally, it encoded three ARGs, including an acquired blaTEM-1 located on a rep_cluster_2350 8 237 Kb mobilisable plasmid, presenting phenotypic resistance to ampicillin and piperacillin.

Conclusion

This report provides novel insights into the oral prevalence of genotypically hypervirulent and drug-resistant E. coli ST73, a pandemic lineage.

目的：大肠埃希氏菌序列类型（ST）73是ExPEC（肠道外致病性大肠杆菌）家族中的一个大流行菌系，具有保守的毒力。我们报告了从一名被诊断为耐药精神分裂症并接受氯氮平治疗的患者口腔中分离出的一株基因组高病毒性大肠杆菌 ST73 的完整基因组：大肠杆菌 GABEEC132 株通过 Illumina 和 Oxford-Nanopore-Technologies (ONT) 平台进行了第二代和第三代测序。利用 NCBI-AMR-Finder-Plus 数据库和病毒活性因子数据库（VFDB）分别对抗生素耐药基因（ARGs）和病毒活性因子（VFs）进行了生物信息学鉴定。为了将基因组置于更广泛的流行病学框架内，利用大肠杆菌 ST73 O6:H1 的代表性基因组（n=55）进行了系统进化分析：结果：大肠杆菌菌株 GABEEC132 被鉴定为具有 O6:H1 血清型，并被归入 B2 系统群。该菌株表现出较高的基因组毒力负荷，编码 194 个 VFs。此外，它还编码了三个 ARGs，包括位于 rep_cluster_2350 8 237 Kb 可移动质粒上的获得性 blaTEM-1，表现出对氨苄西林和哌拉西林的表型耐药性：本报告为了解大肠杆菌 ST73 这一流行菌系的高病毒性和耐药性基因型的口腔流行情况提供了新的视角。

{"title":"Complete genome of Escherichia coli sequence type 73 with acquired blaTEM-1 and high genotypic virulence load identified in human saliva","authors":"","doi":"10.1016/j.jgar.2024.08.011","DOIUrl":"10.1016/j.jgar.2024.08.011","url":null,"abstract":"<div><h3>Objectives</h3><div><em>Escherichia coli</em> sequence type (ST) 73 is a pandemic lineage of the ExPEC (Extraintestinal Pathogenic <em>E. coli</em>) family associated with conserved virulence. We report the complete genome of a genomically hypervirulent <em>E. coli</em> ST73 strain isolated from the oral cavity of a patient with a diagnosis of treatment resistant schizophrenia and receiving clozapine treatment.</div></div><div><h3>Methods</h3><div><em>E. coli</em> strain GABEEC132 underwent second and third generation sequencing with Illumina and Oxford-Nanopore-Technologies (ONT) platforms. Antibiotic resistance genes (ARGs) and virulence factors (VFs) were bioinformatically identified using the NCBI-AMR-Finder-Plus database and Virulence-Factors-database (VFDB), respectively. To contextualize the genome within a broader epidemiological framework, phylogenetic analysis was conducted using representative genomes of <em>E. coli</em> ST73 O6:H1 (<em>n</em> = 55).</div></div><div><h3>Results</h3><div><em>E. coli</em> strain GABEEC132 was identified as possessing the O6:H1 serotype and classified within the B2 phylogroup. The strain exhibited a high genomic virulence load, encoding for 194 VFs. Additionally, it encoded three ARGs, including an acquired <em>blaTEM-1</em> located on a rep_cluster_2350 8 237 Kb mobilisable plasmid, presenting phenotypic resistance to ampicillin and piperacillin.</div></div><div><h3>Conclusion</h3><div>This report provides novel insights into the oral prevalence of genotypically hypervirulent and drug-resistant <em>E. coli</em> ST73, a pandemic lineage.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142289190","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

The frequency of AmpC overproduction, OprD downregulation and OprM efflux pump expression in Pseudomonas aeruginosa: A comprehensive meta-analysis 铜绿假单胞菌中 AmpC 过量产生、OprD 下调和 OprM 出流泵表达的频率：一项全面的 Meta 分析。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-09-18 DOI: 10.1016/j.jgar.2024.08.014

Objectives

Pseudomonas aeruginosa is a major opportunistic pathogen responsible for a wide range of infections. The emergence of antibiotic resistance in this pathogen poses a significant public health challenge. This study aims to conduct a comprehensive meta-analysis of studies conducted in Iran to determine the frequency of key antibiotic resistance mechanisms in Pseudomonas aeruginosa and their association with multidrug-resistant and extensively drug-resistant strains or pandrug-resistant strains.

Methods

Systematic database searches encompassing literature up to June 2023 were undertaken. The selected studies centered on OprD downregulation, efflux pump (mexAB-OprM, mexXY-OprM) expression, and AmpC overproduction. Extracted data were synthesised in a meta-analysis for pooled frequency determination of each resistance mechanism.

Results

In total, 24 studies were included. OprD downregulation exhibited a pooled frequency of 61%. Efflux pump component frequency ranged from 48% to 77.5%. AmpC overproduction was identified in 29.1% of isolates. Polymyxin B and colistin demonstrated lower antibiotic resistance rates, with pooled frequency of 1% and 1.6%, respectively. Conversely, resistance to other antibiotics ranged widely, with pooled frequency spanning 38.4% to 98.2%.

Conclusions

This study underscores the concerning frequency of diverse antibiotic resistance mechanisms in Pseudomonas aeruginosa strains from Iran. Concurrent OprD downregulation, mexAB, mexXY, OprM expression, and AmpC overproduction highlight the urgent need for stringent infection control and prudent antibiotic usage to curb the dissemination of these resistant strains.

PROSPERO

CRD42022379311

背景：铜绿假单胞菌是一种主要的机会性病原体，可导致多种感染。这种病原体出现的抗生素耐药性对公共卫生构成了重大挑战。本研究旨在对在伊朗进行的研究进行全面的荟萃分析，以确定铜绿假单胞菌主要抗生素耐药机制的频率及其与多重耐药菌株、广泛耐药菌株或泛耐药菌株的关联：对截至 2023 年 6 月的文献进行了系统的数据库检索。所选研究以 OprD 下调、外排泵（mexAB-OprM、mexXY-OprM）表达和 AmpC 过量产生为中心。对提取的数据进行荟萃分析，以确定每种抗药性机制的集合频率：结果：共纳入 24 项研究。OprD下调的集合频率为61%。外排泵成分的频率从 48% 到 77.5% 不等。29.1%的分离菌株发现了AmpC过量产生。多粘菌素 B 和秋水仙素的耐药率较低，分别为 1%和 1.6%。相反，对其他抗生素的耐药性范围很广，集合频率从 38.4% 到 98.2%：本研究强调了伊朗铜绿假单胞菌菌株中多种抗生素耐药机制的频率。同时出现的 OprD 下调、mexAB、mexXY、OprM 表达和 AmpC 过量产生突出表明，迫切需要进行严格的感染控制和谨慎使用抗生素，以遏制这些耐药菌株的传播：CRD42022379311。

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引用次数: 0

Synthetic lincosamides iboxamycin and cresomycin are active against ocular multidrug-resistant methicillin-resistant Staphylococcus aureus carrying erm genes 合成林可酰胺类药物伊博霉素和链霉素对携带erm基因的眼部耐多药甲氧西林金黄色葡萄球菌有活性。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-09-16 DOI: 10.1016/j.jgar.2024.09.001

Objective

Antimicrobial resistance is a global pandemic that poses a major threat to vision health as ocular bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA), are becoming increasingly resistant to first-line therapies. Here we evaluated the antimicrobial activity of new synthetic lincosamides in comparison to currently used antibiotics against clinical ocular MRSA isolates.

Methods

Antimicrobial susceptibility testing was performed by broth microdilution for two novel synthetic lincosamides (iboxamycin and cresomycin) and eight comparator antibiotics against a collection of 50 genomically characterised ocular MRSA isolates, including isolates harbouring erm genes (n = 25).

Results

Both drugs were active against widespread MRSA clonal complexes CC8 and CC5. The MIC₅₀ and MIC₉₀ of iboxamycin were 0.06 and 2 mg/L, respectively. Cresomycin (MIC₅₀ = 0.06 mg/L) also displayed good activity with an in vitro potency four-fold higher (MIC₉₀ = 0.5 mg/L) than iboxamycin. In isolates harbouring erm genes, MIC₉₀ were >16, 2, and 0.5 mg/L for clindamycin, iboxamycin, and cresomycin, respectively. The in vitro potencies of iboxamycin and cresomycin were similar or higher than that of comparator agents and were not impacted by multidrug-resistance phenotypes or by the presence of erm genes when compared with clindamycin.

Conclusions

Our results demonstrate that iboxamycin and cresomycin display potent in vitro activity against ocular MRSA isolates, including multidrug-resistant isolates harbouring erm genes.

目的：抗菌药耐药性是一种全球性流行病，对视力健康构成重大威胁，因为眼部细菌，尤其是耐甲氧西林金黄色葡萄球菌（MRSA）对一线疗法的耐药性越来越强。在此，我们对新型合成林可酰胺类药物的抗菌活性进行了评估，并与目前使用的抗生素进行了比较，以了解其对临床眼部 MRSA 分离物的抗菌活性：方法：通过肉汤微量稀释法对两种新型合成林可酰胺类药物（伊博霉素和链霉素）和 8 种比较抗生素进行抗菌药敏感性测试，测试对象为 50 个具有基因组特征的眼部 MRSA 分离物，包括携带 erm 基因的分离物（n=25）：结果：两种药物对广泛存在的MRSA克隆复合体CC8和CC5都有活性。伊博霉素的 MIC50 和 MIC90 分别为 0.06 毫克/升和 2 毫克/升。克雷霉素（MIC50 = 0.06 mg/L）也显示出良好的活性，其体外效力（MIC90 = 0.5 mg/L）是伊博霉素的 4 倍。在携带erm基因的分离物中，克林霉素、伊博霉素和链霉素的MIC90分别大于16、2和0.5毫克/升。与克林霉素相比，伊博霉素和克雷霉素的体外药效与比较药相似或更高，且不受多重耐药表型或erm基因存在的影响：我们的研究结果表明，伊博霉素和克雷霉素对眼部MRSA分离株（包括携带erm基因的耐多药分离株）具有很强的体外活性。

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引用次数: 0

Activity of mecillinam against USA urinary tract clinical isolates from 2017 to 2020 including isolates resistant to comparator antibiotics 美西林对 2017-2020 年美国尿路临床分离株的活性，包括对比较抗生素耐药的分离株。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-09-13 DOI: 10.1016/j.jgar.2024.08.013

Objectives

To support the clinical development of mecillinam and pivmecillinam in the United States for the treatment of complicated and uncomplicated urinary tract infections (UTIs), this study investigated the activity of mecillinam compared with other antibiotics against Enterobacterales isolates from patients with UTIs in the United States during 2017 to 2020. Mecillinam is a first-in-class amidinopenicillin antibiotic, being the only β-lactam to exert its antibacterial activity through exclusive binding to penicillin-binding protein 2. Pivmecillinam is the oral prodrug of mecillinam and is recommended as a first-line therapy by the Infectious Disease Society of America guidelines for uncomplicated UTIs and is approved for the treatment of uncomplicated UTIs in Europe, Canada, and the United States.

Methods

A total of 3303 isolates were collected and antimicrobial susceptibility determined according to Clinical Laboratory and Standards Institute (CLSI) guidelines.

Results

Susceptibility was highest for fosfomycin (97.1% susceptible) and mecillinam (94.9% susceptible). Against extended-spectrum beta-lactamase (ESBL)-positive bacteria susceptibilities were highest for mecillinam (98.2% susceptible) and fosfomycin (97.3% susceptible) and against ESBL-positive K. pneumoniae only mecillinam and fosfomycin had > 80% susceptibility. Resistance to comparator antibiotics was highest for trimethoprim-sulfamethoxazole (27.1%), followed by ciprofloxacin (19.3%), ceftriaxone (19.2%), and nitrofurantoin (12.1%). Multi-drug-resistant isolates were most susceptible to mecillinam and fosfomycin.

Conclusion

研究目的为支持美西林和匹美西林在美国用于治疗复杂和非复杂性尿路感染的临床开发，本研究调查了 2017-2020 年期间美西林与其他抗生素相比对美国UTI 患者肠杆菌分离物的活性。美西林是第一类脒基青霉素类抗生素，是唯一通过与青霉素结合蛋白2独家结合而发挥抗菌活性的β-内酰胺类药物。Pivmecillinam是美西林的口服原药，被美国传染病学会指南推荐为治疗无并发症尿路感染的一线疗法，并在欧洲、加拿大和美国被批准用于治疗无并发症尿路感染：方法：共收集了 3303 个分离菌株，并根据 CLSI 指南测定其抗菌药敏感性：结果：对磷霉素（97.1% 易感）和美西林（94.9% 易感）的易感率最高。对广谱β-内酰胺酶（ESBL）阳性细菌的敏感性最高的是美西林（敏感性为98.2%）和磷霉素（敏感性为97.3%），而对ESBL阳性肺炎克氏菌的敏感性只有美西林和磷霉素大于80%。对比较抗生素耐药率最高的是三甲双胍-磺胺甲噁唑（27.1%），其次是环丙沙星（19.3%）、头孢曲松（19.2%）和硝基呋喃妥因（12.1%）。耐多药的分离株对美西林和磷霉素最敏感：这些数据进一步支持了美西林的临床开发和临床应用。

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引用次数: 0

Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy platform: Characterization of ESBL-producing Enterobacterales from bloodstream infections 利用开源银河平台为临床微生物学家轻松分析细菌全基因组测序数据：血流感染中产ESBL肠杆菌的特征描述。

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance

Pub Date : 2024-09-13 DOI: 10.1016/j.jgar.2024.08.012

Objectives

Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia.

Methods

We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed.

Results

The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were bla_CTX−M-15 (62.1%) and bla_CTX−M-27 (13.6%).

Conclusions

The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.

目的：临床微生物学家需要易于使用、具有图形界面的开放访问工具，以便在日常工作中进行细菌全基因组测序（WGS）。本研究旨在开源的 Galaxy 平台上建立一个生物信息学管道，以便在几个步骤内对细菌 WGS 数据进行全面、可重复的分析。然后，我们用它来描述从菌血症患者体内分离出的产 ESBL 肠杆菌在当地的流行病学特征：方法：我们建立了一个生物信息学管道，由以下连续工具组成：Fastp（输入数据修剪）；FastQC（读数质量控制）；SPAdes（基因组组装）；Quast（基因组组装质量控制）；Prokka（基因注释）；Staramr（ResFinder 数据库）和 ABRicate（CARD 数据库），用于抗菌药物耐药性（AMR）基因筛选和分子菌株分型。分析了一年来从菌血症患者体内分离的所有产ESBL的肠杆菌菌株的成对短读WGS数据：银河平台不需要命令行工具。结果：Galaxy 平台不需要命令行工具。只需上传 fastq 文件，就能一步完成从头组装基因组、MLST 分型和 AMR 基因筛选的系统化工作。在分析的66株产ESBL菌株中，最常见的两个ESBL基因是blaCTX-M-15（62.1%）和blaCTX-M-27（13.6%）：开放存取的银河平台提供了图形界面和易于使用的工具，适合没有生物信息学专家的临床微生物实验室常规使用。我们相信，该平台将有助于快速、低成本地分析细菌 WGS 数据，尤其是在资源有限的环境中。

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