Annals of Clinical Microbiology and Antimicrobials最新文献_第10页

Integrated approach for detection of SARS-CoV-2 and its variant by utilizing LAMP and ARMS-PCR 利用 LAMP 和 ARMS-PCR 检测 SARS-CoV-2 及其变种的综合方法

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-02-01 DOI: 10.1186/s12941-023-00665-0

Maryam Nawab, Syeda Kiran Riaz, Eiman Ismail, Alfar Ahamed, Aaysha Tariq, Muhammad Faraz Arshad Malik, Naeem F. Qusty, Farkad Bantun, Petr Slama, Massab Umair, Shafiul Haque, D. Katterine Bonilla-Aldana, Alfonso J. Rodriguez-Morales

Global impact of COVID-19 pandemic has heightened the urgency for efficient virus detection and identification of variants such as the Q57H mutation. Early and efficient detection of SARS-CoV-2 among densely populated developing countries is paramount objective. Although RT-PCR assays offer accuracy, however, dependence on expansive kits and availability of allied health resources pose an immense challenge for developing countries. In the current study, RT-LAMP based detection of SARS-Cov-2 with subsequent confirmation of Q57H variant through ARMS-PCR was performed. Among the 212 collected samples, 134 yielded positive results, while 78 tested negative using RT-LAMP. Oropharyngeal swabs of suspected individuals were collected and processed for viral RNA isolation. Isolated viral RNA was processed further by using either commercially available WarmStart Master Mix or our in house developed LAMP master mix separately. Subsequently, the end results of each specimen were evaluated by colorimetry. For LAMP assays, primers targeting three genes (ORF1ab, N and S) were designed using PrimerExplorer software. Interestingly, pooling of these three genes in single reaction tube increased sensitivity (95.5%) and specificity (93.5%) of LAMP assay. SARS-CoV-2 positive specimens were screened further for Q57H mutation using ARMS-PCR. Based on amplicon size variation, later confirmed by sequencing, our data showed 18.5% samples positive for Q57H mutation. Hence, these findings strongly advocate use of RT-LAMP-based assay for SARS-CoV-2 screening within suspected general population. Furthermore, ARMS-PCR also provides an efficient mean to detect prevalent mutations against SARS-Cov-2.

COVID-19 大流行对全球的影响加剧了高效病毒检测和变异（如 Q57H 突变）鉴定的紧迫性。在人口稠密的发展中国家及早有效地检测出 SARS-CoV-2 是最重要的目标。尽管 RT-PCR 检测法具有准确性，但对大型试剂盒的依赖性和相关卫生资源的可用性给发展中国家带来了巨大挑战。本研究基于 RT-LAMP 检测 SARS-Cov-2 并随后通过 ARMS-PCR 确认 Q57H 变体。在采集的 212 份样本中，134 份样本检测结果呈阳性，78 份样本检测结果呈阴性。收集疑似患者的口咽拭子并进行病毒 RNA 分离处理。分离出的病毒 RNA 分别使用市售的 WarmStart 混合母液或我们自行开发的 LAMP 混合母液进行进一步处理。随后，用比色法评估每个样本的最终结果。在 LAMP 检测中，使用 PrimerExplorer 软件设计了针对三个基因（ORF1ab、N 和 S）的引物。有趣的是，将这三个基因集中到一个反应管中可提高 LAMP 检测的灵敏度（95.5%）和特异性（93.5%）。使用 ARMS-PCR 进一步筛查 SARS-CoV-2 阳性标本中的 Q57H 突变。根据扩增子大小的变化（后经测序证实），我们的数据显示 18.5% 的样本对 Q57H 突变呈阳性。因此，这些研究结果强烈建议在可疑的普通人群中使用基于 RT-LAMP 的检测方法筛查 SARS-CoV-2。此外，ARMS-PCR 也是检测 SARS-Cov-2 流行突变的有效方法。

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引用次数: 0

Dissemination of mcr-1 and β-lactamase genes among Pseudomonas aeruginosa: molecular characterization of MDR strains in broiler chicks and dead-in-shell chicks infections. 铜绿假单胞菌中 mcr-1 和 β-内酰胺酶基因的传播：肉用仔鸡和死雏鸡感染的 MDR 菌株的分子特征。

IF 4.6 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-28 DOI: 10.1186/s12941-024-00669-4

Mona Salem, Gamal Younis, Asmaa Sadat, Nehal Ahmed Talaat Nouh, Dalal Nasser Binjawhar, Mohamed M Abdel-Daim, Mohamed Elbadawy, Amal Awad

Objectives: Pseudomonas aeruginosa (P. aeruginosa) is one of the most serious pathogens implicated in antimicrobial resistance, and it has been identified as an ESKAPE along with other extremely significant multidrug resistance pathogens. The present study was carried out to explore prevalence, antibiotic susceptibility phenotypes, virulence-associated genes, integron (int1), colistin (mcr-1), and β-lactamase resistance' genes (ESBls), as well as biofilm profiling of P. aeruginosa isolated from broiler chicks and dead in-shell chicks.Design: A total of 300 samples from broiler chicks (n = 200) and dead in-shell chicks (n = 100) collected from different farms and hatcheries located at Mansoura, Dakahlia Governorate, Egypt were included in this study. Bacteriological examination was performed by cultivation of the samples on the surface of both Cetrimide and MacConkey's agar. Presumptive colonies were then subjected to biochemical tests and Polymerase Chain Reaction (PCR) targeting 16S rRNA. The recovered isolates were tested for the presence of three selected virulence-associated genes (lasB, toxA, and exoS). Furthermore, the retrieved isolates were subjected to phenotypic antimicrobial susceptibility testing by Kirby-Bauer disc diffusion method as well as phenotypic detection of ESBLs by both Double Disc Synergy Test (DDST) and the Phenotypic Confirmatory Disc Diffusion Test (PCDDT). P. aeruginosa isolates were then tested for the presence of antibiotic resistance genes (ARGs): int1, mcr-1, and ESBL genes (OXA-10, OXA-2, VEB-1, SHV, TEM, and CTX-M). Additionally, biofilm production was examined by the Tube Adherent method (TA) and Microtiter Plate assay (MTP).Results: Fifty -five isolates were confirmed to be P. aeruginosa, including 35 isolates from broiler chicks and 20 isolates from dead in-shell chicks. The three tested virulence genes (lasB, toxA, and exoS) were detected in all isolates. Antibiogram results showed complete resistance against penicillin, amoxicillin, ceftriaxone, ceftazidime, streptomycin, erythromycin, spectinomycin, and doxycycline, while a higher sensitivity was observed against meropenem, imipenem, colistin sulfate, ciprofloxacin, and gentamicin. ESBL production was confirmed in 12 (21.8%) and 15 (27.3%) isolates by DDST and PCDDT, respectively. Antibiotic resistance genes (ARGs): int1, mcr-1, and ESBL genes (OXA-10, SHV, TEM, and CTX-M), were detected in 87.3%, 18.2%, 16.4%, 69.1%, 72.7%, and 54.5% of the examined isolates respectively, whereas no isolate harbored the OXA-2 or VEB-1 genes. Based on the results of both methods used for detection of biofilm formation, Kappa statistics [kappa 0.324] revealed a poor agreement between both methods.Conclusions: the emergence of mcr-1 and its coexistence with other resistance genes such as β-lactamase genes, particularly blaOXA-10, for the first time in P. aeruginosa from youn

目的：铜绿假单胞菌（P. aeruginosa）是涉及抗菌药耐药性的最严重病原体之一，它与其他极其重要的多重耐药性病原体一起被确定为 ESKAPE。本研究旨在探讨从肉鸡和壳内死鸡中分离出的铜绿假单胞菌的流行率、抗生素敏感性表型、毒力相关基因、整合素（int1）、可乐定（mcr-1）和β-内酰胺酶耐药基因（ESBls）以及生物膜图谱：本研究从埃及达卡利亚省曼苏拉市的不同农场和孵化场收集了 300 份肉鸡样本（n = 200）和壳内死鸡样本（n = 100）。通过在西曲肽琼脂和麦康凯琼脂表面培养样本，进行细菌学检查。然后对推定菌落进行生化测试和针对 16S rRNA 的聚合酶链式反应（PCR）。对回收的分离物进行检测，以确定是否存在三种选定的毒力相关基因（lasB、toxA 和 exoS）。此外，还采用柯比-鲍尔盘扩散法对回收的分离株进行表型抗菌药敏感性检测，并采用双盘协同试验（DDST）和表型确证盘扩散试验（PCDDT）对 ESBLs 进行表型检测。然后检测铜绿假单胞菌分离物是否存在抗生素耐药基因（ARGs）：int1、mcr-1 和 ESBL 基因（OXA-10、OXA-2、VEB-1、SHV、TEM 和 CTX-M）。此外，还采用试管粘附法（TA）和微孔板检测法（MTP）检测了生物膜的产生：结果：55 个分离株被确认为铜绿假单胞菌，其中 35 个来自肉鸡，20 个来自壳内死鸡。在所有分离株中都检测到了三种经测试的毒力基因（lasB、toxA 和 exoS）。抗菌谱结果显示，分离物对青霉素、阿莫西林、头孢曲松、头孢他啶、链霉素、红霉素、广谱霉素和强力霉素完全耐药，而对美罗培南、亚胺培南、硫酸考来烯胺、环丙沙星和庆大霉素的敏感性较高。经 DDST 和 PCDDT 检测，分别有 12 个（21.8%）和 15 个（27.3%）分离菌株证实产生了 ESBL。抗生素耐药基因（ARGs）：int1、mcr-1 和 ESBL 基因（OXA-10、SHV、TEM 和 CTX-M）分别在 87.3%、18.2%、16.4%、69.1%、72.7% 和 54.5%的受检分离物中检测到，而没有分离物携带 OXA-2 或 VEB-1 基因。结论：mcr-1 的出现及其与其他耐药基因（如 β-内酰胺酶基因，尤其是 blaOXA-10）的共存，首次出现在埃及幼雏肉鸡和壳内死鸡中的铜绿假单胞菌中，这不仅对家禽业，而且对公众健康都构成了威胁。

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引用次数: 0

Combination antimicrobial therapy: in vitro synergistic effect of anti-staphylococcal drug oxacillin with antimicrobial peptide nisin against Staphylococcus epidermidis clinical isolates and Staphylococcus aureus biofilms 联合抗菌疗法：抗葡萄球菌药物氧青霉素与抗菌肽尼生素对表皮葡萄球菌临床分离株和金黄色葡萄球菌生物膜的体外协同作用

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-20 DOI: 10.1186/s12941-024-00667-6

Toktam Sharafi, Ezzat Allah Ghaemi, Maryam Rafiee, Abdollah Ardebili

The ability of Staphylococcus epidermidis and S. aureus to form strong biofilm on plastic devices makes them the major pathogens associated with device-related infections (DRIs). Biofilm-embedded bacteria are more resistant to antibiotics, making biofilm infections very difficult to effectively treat. Here, we evaluate the in vitro activities of anti-staphylococcal drug oxacillin and antimicrobial peptide nisin, alone and in combination, against methicillin-resistant S. epidermidis (MRSE) clinical isolates and the methicillin-resistant S. aureus ATCC 43,300. The minimum inhibitory concentrations (MIC) and minimum biofilm eradication concentrations (MBEC) of oxacillin and nisin were determined using the microbroth dilution method. The anti-biofilm activities of oxacillin and nisin, alone or in combination, were evaluated. In addition, the effects of antimicrobial agents on the expression of icaA gene were examined by quantitative real-time PCR. MIC values for oxacillin and nisin ranged 4–8 µg/mL and 64–128 µg/mL, respectively. Oxacillin and nisin reduced biofilm biomass in all bacteria in a dose-dependent manner and this inhibitory effect was enhanced with combinatorial treatment. MBEC ranges for oxacillin and nisin were 2048–8192 µg/mL and 2048–4096 µg/mL, respectively. The addition of nisin significantly decreased the oxacillin MBECs from 8- to 32-fold in all bacteria. At the 1× MIC and 1/2× MIC, both oxacillin and nisin decreased significantly the expression of icaA gene in comparison with untreated control. When two antimicrobial agents were combined at 1/2× MIC concentration, the expression of icaA were significantly lower than when were used alone. Nisin/conventional oxacillin combination showed considerable anti-biofilm effects, including inhibition of biofilm formation, eradication of mature biofilm, and down-regulation of biofilm-related genes, proposing its applications for treating or preventing staphylococcal biofilm-associated infections, including device-related infections.

表皮葡萄球菌和金黄色葡萄球菌能够在塑料设备上形成强大的生物膜，因此它们是与设备相关感染（DRIs）有关的主要病原体。生物膜嵌入的细菌对抗生素的耐药性更强，因此生物膜感染很难得到有效治疗。在此，我们评估了抗葡萄球菌药物奥沙西林和抗菌肽尼生素单独或联合使用对耐甲氧西林表皮葡萄球菌（MRSE）临床分离株和耐甲氧西林金黄色葡萄球菌 ATCC 43,300 株的体外活性。采用微流稀释法测定了奥沙西林和尼生素的最低抑菌浓度（MIC）和最低生物膜根除浓度（MBEC）。评估了奥沙西林和尼生素单独或联合使用的抗生物膜活性。此外，还通过实时定量 PCR 检测了抗菌剂对 icaA 基因表达的影响。奥沙西林和尼辛的 MIC 值分别为 4-8 µg/mL 和 64-128 µg/mL。奥沙西林和尼生素以剂量依赖的方式减少了所有细菌的生物膜生物量，并且这种抑制作用在组合处理中得到了增强。氧青霉素和尼生素的 MBEC 范围分别为 2048-8192 µg/mL 和 2048-4096 µg/mL。加入尼生素后，所有细菌的氧青霉素 MBECs 都明显降低了 8 到 32 倍。与未处理的对照组相比，在 1 倍 MIC 和 1/2 倍 MIC 浓度下，氧青霉素和尼生素都能明显降低 icaA 基因的表达。当两种抗菌剂以 1/2 倍 MIC 浓度混合使用时，icaA 基因的表达量明显低于单独使用时的表达量。Nisin/conventional oxacillin 复方制剂显示出相当大的抗生物膜作用，包括抑制生物膜的形成、消除成熟的生物膜以及下调生物膜相关基因，因此可用于治疗或预防葡萄球菌生物膜相关感染，包括器械相关感染。

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引用次数: 0

Pulmonary co-infections by Pneumocystis jirovecii and Herpesviridae: a seven-year retrospective study 肺孢子虫和疱疹病毒共同感染：一项为期七年的回顾性研究

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-20 DOI: 10.1186/s12941-023-00663-2

Alan Rucar, Anne Totet, Yohann Le Govic, Baptiste Demey, Céline Damiani

Pneumocystis jirovecii (P. jirovecii) is an opportunistic fungus responsible for Pneumocystis pneumonia (PCP) in deeply immunocompromised patients and for pulmonary colonization in individuals with mild immunosuppression or impaired respiratory function. PCP and Cytomegalovirus (CMV) co-infections have been widely described whereas those involving other Herpesviruses (HVs) such as Epstein-Barr virus (EBV), Herpes simplex virus type 1 and type 2 (HSV-1 and -2), and Varicella zoster virus (VZV) remain scarce. To date, no data are available concerning HVs co-infections in P. jirovecii colonization. Our main objective was to evaluate the frequency of HVs in bronchoalveolar lavage fluid (BALF) samples from patients with PCP or with pulmonary colonization. The secondary objective was to assess the relationship between HVs and the mortality rate in PCP patients. A retrospective single-center study over a seven-year period was conducted. All patients with P. jirovecii detected using PCR in a BALF sample and for whom a PCR assay for HVs detection was performed were included in the study. One hundred and twenty-five patients were included, corresponding to 77 patients with PCP and 48 colonized patients. At least one HV was detected in 54/77 (70.1%) PCP patients and in 28/48 (58.3%) colonized patients. EBV was the most frequent in both groups. Furthermore, the 30-day survival rate in PCP patients was significantly lower with [EBV + CMV] co-infection than that with EBV co-infection, [EBV + HSV-1] co-infection and without HV co-infection. Our results show that the frequency of HV, alone or in combination is similar in PCP and colonization. They also suggest that [EBV + CMV] detection in BALF samples from PCP patients is associated with an increased mortality rate, underlying the significance to detect HVs in the course of PCP.

吉罗韦氏肺孢子菌（P. jirovecii）是一种机会性真菌，在免疫力极度低下的患者中可引起肺孢子菌肺炎（PCP），在轻度免疫抑制或呼吸功能受损的患者中可引起肺定植。五氯苯酚和巨细胞病毒（CMV）合并感染的病例已被广泛报道，而涉及其他疱疹病毒（HVs），如爱泼斯坦-巴尔病毒（EBV）、单纯疱疹病毒 1 型和 2 型（HSV-1 和 -2）以及水痘带状疱疹病毒（VZV）的病例仍然很少。迄今为止，还没有关于 P. jirovecii 定殖中 HVs 合并感染的数据。我们的主要目的是评估支气管肺泡灌洗液（BALF）样本中 HVs 在五氯苯酚患者或肺定植患者中的频率。次要目标是评估 HVs 与五氯苯酚患者死亡率之间的关系。这是一项为期七年的单中心回顾性研究。所有在 BALF 样本中使用 PCR 检测到 P. jirovecii 的患者，以及使用 PCR 检测 HVs 的患者均被纳入研究范围。研究共纳入了 125 名患者，其中 77 人为 PCP 患者，48 人为定植患者。在 54/77 例（70.1%）五氯苯酚患者和 28/48 例（58.3%）定植患者中至少检测到一种 HV。两组患者中最常见的都是 EBV。此外，与 EBV 合并感染、[EBV + HSV-1]合并感染和无 HV 合并感染相比，[EBV + CMV] 合并感染的 PCP 患者的 30 天存活率明显较低。我们的结果表明，HV 单独或合并感染在 PCP 和定植中的频率相似。这些结果还表明，在五氯苯酚患者的 BALF 样本中检测到[EBV + CMV]与死亡率升高有关，这也说明了在五氯苯酚病程中检测 HV 的重要性。

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引用次数: 0

Genomic diversity of β-lactamase producing Pseudomonas aeruginosa in Iran; the impact of global high-risk clones 伊朗产β-内酰胺酶铜绿假单胞菌的基因组多样性；全球高风险克隆的影响

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-13 DOI: 10.1186/s12941-024-00668-5

Nazila Ahmadi, Himen Salimizand, Abolfazl Rafati Zomorodi, Jalileh Ebn Abbas, Rashid Ramazanzadeh, Fakhri Haghi, Sepideh Hassanzadeh, Mojdeh Jahantigh, Mojtaba Shahin

Hospital-acquired infections caused by multidrug-resistant Pseudomonas aeruginosa incline hospital stay and costs of treatment that resulted in an increased mortality rate. The frequency of P. aeruginosa high-risk clones producing carbapenemases was investigated in our clinical samples. In this cross-sectional study, 155 non-repetitive P. aeruginosa isolates were included from different medical centers of Iran. Antibiotic susceptibility testing was determined, and the presence of β-lactamases were sought by phenotypic and genotypic methods. The clonal relationship of all isolates was investigated, and multi-locus sequence typing (MLST) was used for finding the sequence types of carbapenemase-producers. The agent with highest percent susceptibility rate was recorded for colistin (94.9%). MOX and FOX were found both as low as 1.95% (3/155). The most frequent narrow spectrum β-lactamase was SHV with 7.7% (12/155) followed by PER, OXA-1, and TEM with the frequency of 7.1% (11/155), 3.2% (5/155), and 1.3% (2/155), respectively. Carbapenemases were detected in 28 isolates (18%). The most frequent carbapenemase was IMP with 9% (14/155) followed by NDM, 8.4% (13/155). OXA-48 and VIM were also detected both per one isolate (0.65%). MLST of carbapenem resistant P. aeruginosa isolates revealed that ST244, ST664, ST235, and ST357 were spread in subjected clinical settings. REP-PCR uncovered high genomic diversity in our clinical setting. Clonal proliferation of ST235 strain plays a key role in the propagation of MDR pattern in P. aeruginosa. Our data showed that high-risk clones has distributed in Iran, and programs are required to limit spreading of these clones.

耐多药铜绿假单胞菌引起的医院感染会延长住院时间，增加治疗费用，导致死亡率上升。我们对临床样本中产生碳青霉烯酶的铜绿假单胞菌高危克隆的频率进行了调查。在这项横断面研究中，从伊朗不同的医疗中心分离出 155 株非重复性铜绿假单胞菌。通过表型和基因型方法确定了对抗生素的敏感性，并检测了β-内酰胺酶的存在。对所有分离菌株的克隆关系进行了调查，并使用多焦点序列分型（MLST）来确定碳青霉烯酶生产者的序列类型。结果显示，对可乐定的敏感率最高（94.9%）。MOX和FOX的敏感率均低至1.95%（3/155）。最常见的窄谱β-内酰胺酶是 SHV，频率为 7.7%（12/155），其次是 PER、OXA-1 和 TEM，频率分别为 7.1%（11/155）、3.2%（5/155）和 1.3%（2/155）。在 28 个分离株（18%）中检测到碳青霉烯酶。最常见的碳青霉烯酶是 IMP，占 9%（14/155），其次是 NDM，占 8.4%（13/155）。在一个分离物中还检测到了 OXA-48 和 VIM（0.65%）。对碳青霉烯类耐药铜绿假单胞菌分离物的 MLST 显示，ST244、ST664、ST235 和 ST357 在受试临床环境中广泛传播。REP-PCR 在我们的临床环境中发现了高度的基因组多样性。ST235 菌株的克隆增殖在铜绿假单胞菌 MDR 模式的传播中起到了关键作用。我们的数据表明，高风险克隆已在伊朗分布，因此需要制定计划来限制这些克隆的传播。

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引用次数: 0

Molecular characterization of extended-spectrum β-lactamase-producing Escherichia coli isolated from lower respiratory tract samples between 2002 and 2019 in the Central Slovenia region 2002 年至 2019 年期间从斯洛文尼亚中部地区下呼吸道样本中分离出的产扩展谱 β-内酰胺酶大肠埃希菌的分子特征描述

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-13 DOI: 10.1186/s12941-023-00664-1

Katja Hrovat, Katja Molan, Katja Seme, Jerneja Ambrožič Avguštin

Antibiotic resistance is one of the most serious global health problems and threatens the effective treatment of bacterial infections. Of greatest concern are infections caused by extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC). The aim of our study was to evaluate the prevalence and molecular characteristics of ESBL-EC isolated over an 18-year pre-COVID period from lower respiratory tract (LRT) samples collected from selected Slovenian hospitals. All isolates were identified by MALDI-TOF and phenotypically confirmed as ESBLs by a disk diffusion assay. Using a PCR approach, 487 non-repetitive isolates were assigned to phylogroups, sequence type groups, and clonal groups. Isolates were also screened for virulence-associated genes (VAGs) and antimicrobial resistance genes. The prevalence of ESBL-EC isolates from LRT in a large university hospital was low (1.4%) in 2005 and increased to 10.8% by 2019. The resistance profile of 487 non-repetitive isolates included in the study showed a high frequency of group 1 blaCTX-M (77.4%; n = 377), blaTEM (54.4%; n = 265) and aac(6')-Ib-cr (52%; n = 253) genes and a low proportion of blaSHV and qnr genes. Isolates were predominantly assigned to phylogroup B2 (73.1%; n = 356), which was significantly associated with clonal group ST131. The ST131 group accounted for 67.6% (n = 329) of all isolates and had a higher number of virulence factor genes than the non-ST131 group. The virulence gene profile of ST131 was consistent with that of other extraintestinal pathogenic E. coli (ExPEC) strains and was significantly associated with ten of sixteen virulence factor genes tested. Using ERIC-PCR fingerprinting, isolates with the same ERIC-profile in samples from different patients, and at different locations and sampling dates were confirmed, indicating the presence of “hospital-adapted” strains. Our results suggest that the ESBL-EC isolates from LRT do not represent a specific pathotype, but rather resemble other ExPEC isolates, and may be adapted to the hospital environment. To our knowledge, this is the first study of ESBL-EC isolated from LRT samples collected over a long period of time.

抗生素耐药性是最严重的全球健康问题之一，威胁着细菌感染的有效治疗。最令人担忧的是由产广谱β-内酰胺酶大肠埃希菌（ESBL-EC）引起的感染。我们的研究旨在评估 COVID 前 18 年间从斯洛文尼亚部分医院采集的下呼吸道（LRT）样本中分离出的 ESBL-EC 的流行率和分子特征。所有分离物均通过 MALDI-TOF 进行鉴定，并通过磁盘扩散试验进行表型确认为 ESBLs。采用 PCR 方法将 487 个非重复性分离株归入系统组、序列类型组和克隆组。此外，还对分离株进行了毒力相关基因（VAG）和抗菌药耐药性基因的筛查。2005 年，一家大型大学医院从 LRT 分离出的 ESBL-EC 感染率较低（1.4%），到 2019 年已增至 10.8%。研究中 487 个非重复分离株的耐药性特征显示，第 1 组 blaCTX-M（77.4%；n = 377）、blaTEM（54.4%；n = 265）和 aac(6')-Ib-cr （52%；n = 253）基因的频率较高，而 blaSHV 和 qnr 基因的比例较低。分离菌主要归入系统组 B2（73.1%；n = 356），该系统组与克隆组 ST131 显著相关。ST131组占所有分离株的67.6%（n = 329），其毒力因子基因数量高于非ST131组。ST131 的毒力基因谱与其他肠道外致病性大肠杆菌（ExPEC）菌株的毒力基因谱一致，并与所检测的 16 个毒力因子基因中的 10 个基因有显著关联。通过ERIC-PCR指纹图谱分析，从不同患者、不同地点和不同采样日期的样本中分离出的具有相同ERIC图谱的菌株得到了证实，这表明存在 "医院适应型 "菌株。我们的研究结果表明，从 LRT 分离出的 ESBL-EC 并不代表一种特定的病原型，而是与其他 ExPEC 分离物相似，并可能适应了医院环境。据我们所知，这是首次对从长期收集的 LRT 样本中分离出的 ESBL-EC 进行研究。

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引用次数: 0

Impact of Helicobacter pylori colonization density and depth on gastritis severity. 幽门螺旋杆菌定植密度和深度对胃炎严重程度的影响

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-12 DOI: 10.1186/s12941-024-00666-7

Jianxiang Peng, Jinliang Xie, Dingwei Liu, Kaijie Yang, Shuang Wu, Dongsheng Liu, Deqiang Huang, Yong Xie

Background and objectives: Helicobacter pylori (H. pylori) infection is the most common etiology of chronic gastric. H. pylori gastritis would gradually evolve into gastric atrophy, intestinal metaplasia, dysplasia and malignant lesions. Herein, this study aimed to investigate the potential impact of H. pylori colonization density and depth on the severity of histological parameters of gastritis.

Methods: A prospective monocentric study was conducted from December 2019 to July 2022, enrolling patients with confirmed chronic H. pylori infection via histopathological evaluation. H. pylori colonization status was detected by immunohistochemical staining, pathological changes of gastric specimens were detected by hematoxylin eosin staining. Epidemiological, endoscopic and histopathological data were collected.

Results: A total of 1120 patients with a mean age of 45.8 years were included. Regardless of the previous history of H. pylori eradication treatment, significant correlations were observed between the density and depth of H. pylori colonization and the intensity of gastritis activity (all P < 0.05). Patients with the lowest level of H. pylori colonization density and depth exhibited the highest level of mild activity. In whole participants and anti-H. pylori treatment-naive participants, H. pylori colonization density and depth were markedly correlated with the severity of chronic gastritis and gastric atrophy (all P < 0.05). H. pylori colonization density (P = 0.001) and depth (P = 0.047) were significantly associated with ulcer formation in patients naive to any anti-H. pylori treatment. No significant associations were observed between the density and depth of H. pylori colonization and other histopathological findings including lymphadenia, lymphoid follicle formation and dysplasia.

Conclusions: As the density and depth of H. pylori colonization increased, so did the activity and severity of gastritis, along with an elevated risk of ulcer formation.

背景和目的：幽门螺杆菌（H. pylori）感染是慢性胃病最常见的病因。幽门螺杆菌胃炎会逐渐演变为胃萎缩、肠化生、发育不良和恶性病变。本研究旨在探讨幽门螺杆菌定植密度和深度对胃炎组织学指标严重程度的潜在影响：2019年12月至2022年7月期间开展了一项前瞻性单中心研究，通过组织病理学评估入组了确诊为慢性幽门螺杆菌感染的患者。通过免疫组化染色检测幽门螺杆菌定植状态，通过苏木精伊红染色检测胃标本的病理变化。收集了流行病学、内镜和组织病理学数据：结果：共纳入 1120 名患者，平均年龄为 45.8 岁。无论之前是否接受过幽门螺杆菌根除治疗，幽门螺杆菌定植的密度和深度与胃炎活动的强度之间均存在显著相关性（均为 P 结论：幽门螺杆菌定植的密度和深度与胃炎活动的强度之间存在显著相关性：随着幽门螺杆菌定植密度和深度的增加，胃炎的活动性和严重程度也随之增加，溃疡形成的风险也随之升高。

{"title":"Impact of Helicobacter pylori colonization density and depth on gastritis severity.","authors":"Jianxiang Peng, Jinliang Xie, Dingwei Liu, Kaijie Yang, Shuang Wu, Dongsheng Liu, Deqiang Huang, Yong Xie","doi":"10.1186/s12941-024-00666-7","DOIUrl":"10.1186/s12941-024-00666-7","url":null,"abstract":"Background and objectives: Helicobacter pylori (H. pylori) infection is the most common etiology of chronic gastric. H. pylori gastritis would gradually evolve into gastric atrophy, intestinal metaplasia, dysplasia and malignant lesions. Herein, this study aimed to investigate the potential impact of H. pylori colonization density and depth on the severity of histological parameters of gastritis.Methods: A prospective monocentric study was conducted from December 2019 to July 2022, enrolling patients with confirmed chronic H. pylori infection via histopathological evaluation. H. pylori colonization status was detected by immunohistochemical staining, pathological changes of gastric specimens were detected by hematoxylin eosin staining. Epidemiological, endoscopic and histopathological data were collected.Results: A total of 1120 patients with a mean age of 45.8 years were included. Regardless of the previous history of H. pylori eradication treatment, significant correlations were observed between the density and depth of H. pylori colonization and the intensity of gastritis activity (all P < 0.05). Patients with the lowest level of H. pylori colonization density and depth exhibited the highest level of mild activity. In whole participants and anti-H. pylori treatment-naive participants, H. pylori colonization density and depth were markedly correlated with the severity of chronic gastritis and gastric atrophy (all P < 0.05). H. pylori colonization density (P = 0.001) and depth (P = 0.047) were significantly associated with ulcer formation in patients naive to any anti-H. pylori treatment. No significant associations were observed between the density and depth of H. pylori colonization and other histopathological findings including lymphadenia, lymphoid follicle formation and dysplasia.Conclusions: As the density and depth of H. pylori colonization increased, so did the activity and severity of gastritis, along with an elevated risk of ulcer formation.","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"4"},"PeriodicalIF":5.7,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10785438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139432097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 role of rapid syndromic diagnostic testing of gastrointestinal pathogens as a clinical decision support tool in a pediatric emergency department. 消化道病原体快速综合诊断检测作为儿科急诊室临床决策支持工具的作用。

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-05 DOI: 10.1186/s12941-023-00662-3

Hyun Mi Kang, In Hyuk Yoo, Dae Chul Jeong

Purpose: This study aimed to investigate the role of rapid syndromic diagnostic testing of gastrointestinal pathogens as a clinical decision support tool in a pediatric emergency department (ED) by comparing clinical decision and patient outcome parameters pre- and post-implementation.

Methods: This was a big data analytical study of children < 18 years old without any underlying diseases, that visited the ED with acute moderate to severe diarrhea during a 34-month period from 2018 to 2022 using Seoul St. Mary's hospital's healthcare corporate data warehouse to retrieve demographic, clinical, and laboratory parameters. Outcome measures pre- and post-implementation of a rapid syndromic multiplex gastrointestinal panel (GI panel) were compared.

Results: A total of 4,184 patients' data were included in the analyses. Broad spectrum antibiotics were prescribed at a significantly lower rate to patients presenting with acute infectious diarrhea at discharge from the ED (9.9% vs 15.8%, P < 0.001) as well as upon admission (52.2% vs 66.0%, P < 0.001) during the post-implementation period compared to the pre-implementation period. Although the duration of ED stay was found to be significantly longer (6.5 vs 5.5 h, P < 0.0001), the rate of ED revisit due to persistent or aggravated symptoms was significantly lower (Δ in intercept, β = -0.027; SE = 0.013; P = 0.041), and the admission rate at follow up after being discharged from the ED shown to be significantly lower during the post-implementation period compared to the pre-implementation period (0.8% vs. 2.1%, P = 0.001, respectively). No significant difference in disease progression was observed (P = 1.000).

Conclusion: Using the GI panel in the ED was shown to decrease broad spectrum antibiotic prescribing practices and reduce revisits or admission at follow up by aiding clinical decisions and improving patient outcome.

目的：本研究旨在通过比较实施前后的临床决策和患者结果参数，研究胃肠道病原体快速综合诊断检测作为临床决策支持工具在儿科急诊室（ED）中的作用：方法：这是一项针对儿童的大数据分析研究：共有 4,184 名患者的数据被纳入分析。在急诊室出院时，急性感染性腹泻患者的广谱抗生素处方率明显降低（9.9% 对 15.8%，P 结论：在急诊室使用消化道分析仪可显著降低急性感染性腹泻患者的处方率：事实证明，在急诊室使用消化道检查面板可减少广谱抗生素处方的使用，并通过辅助临床决策和改善患者预后减少复诊或入院随访。

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引用次数: 0

Prevalence estimation of Tropheryma whipplei in duodenal biopsy tissues of Koreans. 对韩国人十二指肠活检组织中白痢疾杆菌流行率的估计。

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-03 DOI: 10.1186/s12941-023-00658-z

Sumi Yoon, Min Eui Hong, Soon Auck Hong, Tae-Hyoung Kim, Mi-Kyung Lee

Whipple's disease caused by Tropheryma whipplei is difficult to diagnose because of a broad spectrum of manifestations and non-specific clinical signs. In the current global era, the incidence of duodenal infection/inflammation caused by T. whipplei in Korea may has been underestimated. Here we estimated the prevalence of T. whipplei in duodenal biopsy tissues of Koreans using real-time PCRs (RT-PCRs). A total of 252 duodenal biopsy tissues were collected from Korean patients who underwent esophagogastroduodenoscopy and duodenal biopsy. DNA extracted from the duodenal biopsy tissues was analyzed using three RT-PCRs targeting T. whipplei-specific regions of the 16S-23S rRNA intergenic spacer, hsp65, and Dig15 in parallel. In the samples positive in RT-PCRs, direct sequencing was performed for each RT-PCR target. The prevalence of T. whipplei was estimated based on the RT-PCR and sequencing results. Among the analyzed samples, T. whipplei was not detected. The prevalence of T. whipplei in duodenal biopsy tissues of Koreans was estimated to be less than 0.4%. This is the first study to attempt to detect T. whipplei in duodenal biopsy tissues of Koreans and estimate its prevalence. Our findings infer that while T. whipplei carriers exist in Korea, the incidence of duodenal infection/inflammation caused by T. whipplei is extremely rare.

由惠氏梭菌（Tropheryma whipplei）引起的惠普尔病很难诊断，因为该病的表现范围很广，而且临床症状不具特异性。在当今全球时代，韩国由惠氏梭菌引起的十二指肠感染/炎症的发病率可能被低估了。在此，我们使用实时 PCR（RT-PCR）技术估算了韩国人十二指肠活检组织中的白喉杆菌感染率。我们从接受食管胃十二指肠镜检查和十二指肠活检的韩国患者身上共收集了 252 份十二指肠活检组织。从十二指肠活检组织中提取的 DNA 采用三种 RT-PCR 方法进行分析，这些 RT-PCR 方法分别针对 16S-23S rRNA 基因间距、hsp65 和 Dig15 中的 T. whipplei 特异性区域。在 RT-PCR 检测结果呈阳性的样本中，对每个 RT-PCR 靶区都进行了直接测序。根据 RT-PCR 和测序结果估算了白喉杆菌的流行率。在分析的样本中，没有检测到白喉杆菌。据估计，韩国人十二指肠活检组织中的白喉杆菌感染率低于 0.4%。这是首次尝试检测韩国人十二指肠活检组织中的白喉杆菌并估计其流行率的研究。我们的研究结果推断，虽然韩国存在白喉杆菌携带者，但由白喉杆菌引起的十二指肠感染/炎症的发病率极为罕见。

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引用次数: 0

Changes in tuberculosis risk after transplantation in the setting of decreased community tuberculosis incidence: a national population-based study, 2008-2020. 社区结核病发病率下降背景下移植后结核病风险的变化：2008-2020 年全国人口研究。

IF 5.7 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials

Pub Date : 2024-01-03 DOI: 10.1186/s12941-023-00661-4

JongHoon Hyun, Myeongjee Lee, Inkyung Jung, Eunhwa Kim, Seung Min Hahn, Yu Ri Kim, Sungmin Lim, Kyong Ihn, Min Young Kim, Jong Gyun Ahn, Joon-Sup Yeom, Su Jin Jeong, Ji-Man Kang

Background: Transplant recipients are immunocompromised and vulnerable to developing tuberculosis. However, active tuberculosis incidence is rapidly declining in South Korea, but the trend of tuberculosis infection among transplant recipients has not been elucidated. This study aimed to evaluate the risk of active tuberculosis after transplantation, including risk factors for tuberculosis and standardized incidence ratios, compared with that in the general population.

Methods: This retrospective study was conducted based on the South Korean health insurance review and assessment database among those who underwent transplantation (62,484 recipients) between 2008 and 2020. Tuberculosis incidence was compared in recipients treated during higher- (2010-2012) and lower-disease burden (2016-2018) periods. Standardized incidence ratios were analyzed using the Korean Tuberculosis Surveillance System. The primary outcome was the number of new tuberculosis cases after transplantation.

Results: Of 57,103 recipients analyzed, the overall cumulative incidence rate 1 year after transplantation was 0.8% (95% confidence interval [CI]: 0.7-0.8), significantly higher in the higher-burden period than in the lower-burden period (1.7% vs. 1.0% 3 years after transplantation, P < 0.001). Individuals who underwent allogeneic hematopoietic stem cell transplantation had the highest tuberculosis incidence, followed by those who underwent solid organ transplantation and autologous hematopoietic stem cell transplantation (P < 0.001). The overall standardized incidence ratio was 3.9 (95% CI 3.7-4.2) and was the highest in children aged 0-19 years, at 9.0 (95% CI 5.7-13.5). Male sex, older age, tuberculosis history, liver transplantation, and allogeneic hematopoietic stem cell transplantation were risk factors for tuberculosis.

Conclusions: Transplant recipients are vulnerable to developing tuberculosis, possibly influenced by their immunocompromised status, solid organ transplant type, age, and community prevalence of tuberculosis. Tuberculosis prevalence by country, transplant type, and age should be considered to establish an appropriate tuberculosis prevention strategy for high-risk groups.

背景：移植受者免疫力低下，很容易患上结核病。然而，在韩国，活动性肺结核的发病率正在迅速下降，但移植受者感染肺结核的趋势尚未得到阐明。本研究旨在评估移植后患活动性肺结核的风险，包括肺结核的风险因素和标准化发病率比，并与普通人群进行比较：这项回顾性研究以韩国健康保险审查和评估数据库为基础，对 2008 年至 2020 年间接受移植手术的人（62484 名受者）进行了调查。比较了疾病负担较重时期（2010-2012 年）和疾病负担较轻时期（2016-2018 年）接受治疗的受者的结核病发病率。使用韩国结核病监测系统分析了标准化发病率比。主要结果是移植后新增结核病例数：结果：在分析的57103名受者中，移植后1年的总体累积发病率为0.8%（95%置信区间[CI]：0.7-0.8），高负担期显著高于低负担期（移植后3年为1.7% vs. 1.0%，P 结论：移植受者很容易罹患结核病：移植受者很容易患上结核病，这可能受到他们的免疫功能低下状况、实体器官移植类型、年龄和社区结核病流行率的影响。应考虑不同国家、移植类型和年龄的结核病流行情况，以便为高危人群制定适当的结核病预防策略。

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引用次数: 0