The COVID-19 pandemic affected the epidemiology of infectious diseases and changed the operation of health care systems and health care seeking behavior. Our study aimed to analyze the utilization of systemic antibiotics in ambulatory care in Hungary after the COVID-19 pandemic and compare it to the period before COVID. We defined three periods (24 months each): Before COVID, COVID, and After COVID. Monthly trends in systemic antibiotic (J01) use were calculated using the WHO ATC-DDD index and expressed as DDD/1000 inhabitants/day (DID) and number of exposed patients per active agent. The data were further categorized by the WHO AWaRe classification. In the After COVID period, we detected almost the same (11.61 vs. 11.11 DID) mean monthly use of systemic antibiotics in ambulatory care compared to the Before COVID period. We observed a decrease in the seasonality index in the After COVID period (46.86% vs. 39.86%). In the After COVID period, the use of cephalosporins and quinolones decreased significantly, while in the case of macrolides, a significant increase was observed compared to the Before COVID period, with excessive azithromycin use (66,869 vs. 97,367 exposed patients). This study demonstrated significant changes in the pattern of ambulatory care antibiotic use in Hungary.
{"title":"Returned Rate and Changed Patterns of Systemic Antibiotic Use in Ambulatory Care in Hungary after the Pandemic—A Longitudinal Ecological Study","authors":"Helga Hambalek, Mária Matuz, Roxána Ruzsa, Erika Papfalvi, Róbert Nacsa, Zsófia Engi, Márta Csatordai, Gyöngyvér Soós, Edit Hajdú, Dezső Csupor, Ria Benkő","doi":"10.3390/antibiotics13090848","DOIUrl":"https://doi.org/10.3390/antibiotics13090848","url":null,"abstract":"The COVID-19 pandemic affected the epidemiology of infectious diseases and changed the operation of health care systems and health care seeking behavior. Our study aimed to analyze the utilization of systemic antibiotics in ambulatory care in Hungary after the COVID-19 pandemic and compare it to the period before COVID. We defined three periods (24 months each): Before COVID, COVID, and After COVID. Monthly trends in systemic antibiotic (J01) use were calculated using the WHO ATC-DDD index and expressed as DDD/1000 inhabitants/day (DID) and number of exposed patients per active agent. The data were further categorized by the WHO AWaRe classification. In the After COVID period, we detected almost the same (11.61 vs. 11.11 DID) mean monthly use of systemic antibiotics in ambulatory care compared to the Before COVID period. We observed a decrease in the seasonality index in the After COVID period (46.86% vs. 39.86%). In the After COVID period, the use of cephalosporins and quinolones decreased significantly, while in the case of macrolides, a significant increase was observed compared to the Before COVID period, with excessive azithromycin use (66,869 vs. 97,367 exposed patients). This study demonstrated significant changes in the pattern of ambulatory care antibiotic use in Hungary.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of 260 E. coli isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 E. coli isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with IncF plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the E. coli isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs.
{"title":"Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia","authors":"Deneke Wolde, Tadesse Eguale, Girmay Medhin, Aklilu Feleke Haile, Haile Alemayehu, Adane Mihret, Mateja Pirs, Katja Strašek Smrdel, Jana Avberšek, Darja Kušar, Tjaša Cerar Kišek, Tea Janko, Andrej Steyer, Marjanca Starčič Erjavec","doi":"10.3390/antibiotics13090851","DOIUrl":"https://doi.org/10.3390/antibiotics13090851","url":null,"abstract":"The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of 260 E. coli isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 E. coli isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with IncF plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the E. coli isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/antibiotics13090839
Houda Bennani, Louise Whatford, Jessica Myers, Nicholas Mays, Rebecca Glover, Barbara Häsler
The five-year UK antimicrobial resistance (AMR) National Action Plan (NAP) was published in 2019 focusing on reducing the need for, and unintentional exposure to antimicrobials (AMs); optimising the use of AMs; and investing in innovation, supply and access of AMs. This study aimed to evaluate the progress made in the beef cattle sub-sector in addressing specific NAP commitments related to improving animal health and welfare and responsible antimicrobial use (AMU). A thematic analysis was conducted of 21 semi-structured interviews with stakeholders from government organisations, farms, veterinary practices, levy boards and livestock associations. The findings indicate substantial progress, with various initiatives implemented targeting data collection, farmer and veterinarian engagement, and herd health planning. However, there remain a number of challenges and barriers that need to be addressed in order to assess the impacts of these initiatives, such as the availability of AMU and AMR data. Ensuring the adequacy of resources was found to be critical for the sustainability of effective initiatives, considering competing demands on people’s time. Additionally, the importance of other outcomes from these initiatives such as developing and strengthening the farmer–veterinarian relationship should not be underestimated since it is fundamental to successfully addressing issues such as AMR.
为期五年的英国抗菌药耐药性(AMR)国家行动计划(NAP)于 2019 年发布,重点关注减少对抗菌药(AMs)的需求和无意接触;优化 AMs 的使用;以及投资于 AMs 的创新、供应和获取。本研究旨在评估肉牛分行业在履行与改善动物健康和福利以及负责任地使用抗菌药 (AMU) 相关的具体国家行动方案承诺方面所取得的进展。我们对 21 个半结构式访谈进行了专题分析,访谈对象包括政府组织、农场、兽医诊所、征收委员会和畜牧协会的利益相关者。研究结果表明,随着针对数据收集、农场主和兽医参与以及畜群健康规划的各种举措的实施,取得了实质性进展。然而,为了评估这些举措的影响,仍有一些挑战和障碍需要解决,例如 AMU 和 AMR 数据的可用性。考虑到对人们时间的竞争性需求,确保充足的资源对于有效举措的可持续性至关重要。此外,不应低估这些举措所产生的其他成果的重要性,如发展和加强农民与兽医之间的关系,因为这对于成功解决 AMR 等问题至关重要。
{"title":"Progress and Challenges: Implementation of the UK Antimicrobial Resistance National Action Plan 2019–2024 within the Beef Cattle Sub-Sector","authors":"Houda Bennani, Louise Whatford, Jessica Myers, Nicholas Mays, Rebecca Glover, Barbara Häsler","doi":"10.3390/antibiotics13090839","DOIUrl":"https://doi.org/10.3390/antibiotics13090839","url":null,"abstract":"The five-year UK antimicrobial resistance (AMR) National Action Plan (NAP) was published in 2019 focusing on reducing the need for, and unintentional exposure to antimicrobials (AMs); optimising the use of AMs; and investing in innovation, supply and access of AMs. This study aimed to evaluate the progress made in the beef cattle sub-sector in addressing specific NAP commitments related to improving animal health and welfare and responsible antimicrobial use (AMU). A thematic analysis was conducted of 21 semi-structured interviews with stakeholders from government organisations, farms, veterinary practices, levy boards and livestock associations. The findings indicate substantial progress, with various initiatives implemented targeting data collection, farmer and veterinarian engagement, and herd health planning. However, there remain a number of challenges and barriers that need to be addressed in order to assess the impacts of these initiatives, such as the availability of AMU and AMR data. Ensuring the adequacy of resources was found to be critical for the sustainability of effective initiatives, considering competing demands on people’s time. Additionally, the importance of other outcomes from these initiatives such as developing and strengthening the farmer–veterinarian relationship should not be underestimated since it is fundamental to successfully addressing issues such as AMR.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/antibiotics13090842
Antonio Sciurti, Valentina Baccolini, Mariateresa Ceparano, Claudia Isonne, Giuseppe Migliara, Jessica Iera, Francesco Alessandri, Giancarlo Ceccarelli, Carolina Marzuillo, Guglielmo Tellan, Maria De Giusti, Francesco Pugliese, Paolo Villari, the Collaborating Group
To manage the number of critical COVID-19 patients, Umberto I Teaching Hospital in Rome established a temporary ICU on March 1, 2021. This study investigated the incidence and risk factors of healthcare-associated infections (HAIs) among these patients during various COVID-19 waves. Patients were grouped by admission date according to the dominant SARS-CoV-2 variant prevalent at the time (Alpha, Delta, Omicron BA.1, Omicron BA.2, Omicron BA.5, and Omicron XBB). First-HAI and mortality rates were calculated per 1000 patient-days. Predictors of first-HAI occurrence were investigated using a multivariable Fine–Gray regression model considering death as a competing event. Among 355 admitted patients, 27.3% experienced at least one HAI, and 49.6% died. Patient characteristics varied over time, with older and more complex cases in the later phases, while HAI and mortality rates were higher in the first year. Pathogens responsible for HAIs varied over time, with first Acinetobacter baumannii and then Klebsiella pneumoniae being progressively predominant. Multivariable analysis confirmed that, compared to Alpha, admission during the Omicron BA.1, BA.2, BA.5, and XBB periods was associated with lower hazards of HAI. Despite worsening COVID-19 patient conditions, late-phase HAI rates decreased, likely due to evolving pathogen characteristics, improved immunity, but also better clinical management, and adherence to infection prevention practices. Enhanced HAI prevention in emergency situations is crucial.
为了管理 COVID-19 危重病人的数量,罗马翁贝托一世教学医院于 2021 年 3 月 1 日成立了临时重症监护室。本研究调查了这些患者在 COVID-19 各次波及期间的医护相关感染 (HAI) 发生率和风险因素。根据当时流行的 SARS-CoV-2 主要变异体(Alpha、Delta、Omicron BA.1、Omicron BA.2、Omicron BA.5 和 Omicron XBB),按入院日期对患者进行分组。首次 HAI 发生率和死亡率按每 1000 个患者日计算。使用多变量 Fine-Gray 回归模型对首次发生急性呼吸道感染的预测因素进行了研究,并将死亡作为一个竞争事件。在355名入院患者中,27.3%至少发生过一次HAI,49.6%死亡。患者特征随时间而变化,后期病例年龄更大、更复杂,而第一年的 HAI 和死亡率更高。造成 HAI 的病原体也随时间变化,首先是鲍曼不动杆菌,然后是肺炎克雷伯菌,并逐渐成为主要病原体。多变量分析证实,与 Alpha 相比,在 Omicron BA.1、BA.2、BA.5 和 XBB 期间入院的患者发生 HAI 的风险较低。尽管 COVID-19 患者的病情恶化,但后期阶段的 HAI 发生率却有所下降,这可能是由于病原体特征不断变化、免疫力提高、临床管理改善以及坚持感染预防实践所致。在紧急情况下加强 HAI 预防至关重要。
{"title":"Incidence and Predictors of Healthcare-Associated Infections in Patients Admitted to a Temporary Intensive Care Unit during the COVID-19 Pandemic Waves: A Two-Year (2021–2023) Retrospective Cohort Study in Rome, Italy","authors":"Antonio Sciurti, Valentina Baccolini, Mariateresa Ceparano, Claudia Isonne, Giuseppe Migliara, Jessica Iera, Francesco Alessandri, Giancarlo Ceccarelli, Carolina Marzuillo, Guglielmo Tellan, Maria De Giusti, Francesco Pugliese, Paolo Villari, the Collaborating Group","doi":"10.3390/antibiotics13090842","DOIUrl":"https://doi.org/10.3390/antibiotics13090842","url":null,"abstract":"To manage the number of critical COVID-19 patients, Umberto I Teaching Hospital in Rome established a temporary ICU on March 1, 2021. This study investigated the incidence and risk factors of healthcare-associated infections (HAIs) among these patients during various COVID-19 waves. Patients were grouped by admission date according to the dominant SARS-CoV-2 variant prevalent at the time (Alpha, Delta, Omicron BA.1, Omicron BA.2, Omicron BA.5, and Omicron XBB). First-HAI and mortality rates were calculated per 1000 patient-days. Predictors of first-HAI occurrence were investigated using a multivariable Fine–Gray regression model considering death as a competing event. Among 355 admitted patients, 27.3% experienced at least one HAI, and 49.6% died. Patient characteristics varied over time, with older and more complex cases in the later phases, while HAI and mortality rates were higher in the first year. Pathogens responsible for HAIs varied over time, with first Acinetobacter baumannii and then Klebsiella pneumoniae being progressively predominant. Multivariable analysis confirmed that, compared to Alpha, admission during the Omicron BA.1, BA.2, BA.5, and XBB periods was associated with lower hazards of HAI. Despite worsening COVID-19 patient conditions, late-phase HAI rates decreased, likely due to evolving pathogen characteristics, improved immunity, but also better clinical management, and adherence to infection prevention practices. Enhanced HAI prevention in emergency situations is crucial.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/antibiotics13090841
Shubham Yashwant Dakhode, Woo Sub Kim, Hyun Jin Kim, Seung Yeol Lee
Taurolidine, known for its broad-spectrum antimicrobial properties and low toxicity, has shown promise in reducing infections in various surgical settings. However, it has not been extensively evaluated in orthopedic surgery. This study assessed the efficacy of taurolidine irrigation in reducing surgical site infections in patients undergoing ankle fracture surgery. A retrospective review was conducted for patients >20 years old who underwent ankle fracture surgery between March 2016 and March 2023, with follow-ups exceeding 6 months. Patients were classified into the following two groups: those who underwent normal saline (NS) irrigation and those who underwent taurolidine irrigation. Minor infections were defined as requiring additional oral antibiotics postoperatively, while major infections were characterized by hospitalization or reoperation due to infection within 3 months. Of 844 patients, 688 were included. The taurolidine group (n = 328) had a significant reduction in minor infections (7.3% vs. 22.5%, odds ratio = 0.410, p = 0.028) compared to the NS group (n = 360). Major infections were fewer in the NS group (1.2% vs. 0%, p = 0.051), but the number of cases was too small for reliable analysis. Taurolidine irrigation significantly reduces the occurrence of minor infections in ankle fracture surgeries when compared to normal saline irrigation.
{"title":"Is Taurolidine Irrigation Effective in Preventing Surgical Site Infection during Fracture Surgery?","authors":"Shubham Yashwant Dakhode, Woo Sub Kim, Hyun Jin Kim, Seung Yeol Lee","doi":"10.3390/antibiotics13090841","DOIUrl":"https://doi.org/10.3390/antibiotics13090841","url":null,"abstract":"Taurolidine, known for its broad-spectrum antimicrobial properties and low toxicity, has shown promise in reducing infections in various surgical settings. However, it has not been extensively evaluated in orthopedic surgery. This study assessed the efficacy of taurolidine irrigation in reducing surgical site infections in patients undergoing ankle fracture surgery. A retrospective review was conducted for patients >20 years old who underwent ankle fracture surgery between March 2016 and March 2023, with follow-ups exceeding 6 months. Patients were classified into the following two groups: those who underwent normal saline (NS) irrigation and those who underwent taurolidine irrigation. Minor infections were defined as requiring additional oral antibiotics postoperatively, while major infections were characterized by hospitalization or reoperation due to infection within 3 months. Of 844 patients, 688 were included. The taurolidine group (n = 328) had a significant reduction in minor infections (7.3% vs. 22.5%, odds ratio = 0.410, p = 0.028) compared to the NS group (n = 360). Major infections were fewer in the NS group (1.2% vs. 0%, p = 0.051), but the number of cases was too small for reliable analysis. Taurolidine irrigation significantly reduces the occurrence of minor infections in ankle fracture surgeries when compared to normal saline irrigation.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/antibiotics13090840
Mohammad Asadzadeh, Suhail Ahmad, Wadha Alfouzan, Inaam Al-Obaid, Bram Spruijtenburg, Eelco F. J. Meijer, Jacques F. Meis, Eiman Mokaddas
Multidrug-resistant Candida auris has recently caused major outbreaks in healthcare facilities. Rapid and accurate antifungal susceptibility testing (AST) of C. auris is crucial for proper management of invasive infections. The Commercial Sensititre Yeast One and Vitek 2 methods underestimate or overestimate the resistance of C. auris to fluconazole and amphotericin B (AMB). This study evaluated the AST results of C. auris against fluconazole and AMB by gradient-MIC-strip (Etest) and broth microdilution-based MICRONAUT-AM-EUCAST (MCN-AM) assays. Clinical C. auris isolates (n = 121) identified by phenotypic and molecular methods were tested. Essential agreement (EA, ±1 two-fold dilution) between the two methods and categorical agreement (CA) based on the Centers for Disease Control and Prevention’s (CDC’s) tentative resistance breakpoints were determined. Fluconazole resistance-associated mutations were detected by PCR-sequencing of ERG11. All isolates identified as C. auris belonged to South Asian clade I and contained the ERG11 Y132F or K143R mutation. The Etest–MCN-AM EA was poor (33%) for fluconazole and moderate (76%) for AMB. The CA for fluconazole was higher (94.2%, 7 discrepancies) than for AMB (91.7%, 10 discrepancies). Discrepancies were reduced when an MCN-AM upper-limit value of 4 µg/mL for fluconazole-susceptible C. auris and an Etest upper-limit value of 8 µg/mL for the wild type for AMB were used. Our data show that resistance to fluconazole was underestimated by MCN-AM, while resistance to AMB was overestimated by Etest when using the CDC’s tentative resistance breakpoints of ≥32 µg/mL for fluconazole and ≥2 µg/mL for AMB. Method-specific resistance breakpoints should be devised for accurate AST of clinical C. auris isolates for proper patient management.
耐多药念珠菌最近在医疗机构中引起了大规模爆发。对念珠菌进行快速、准确的抗真菌药敏试验(AST)对于正确处理侵袭性感染至关重要。商用 Sensititre Yeast One 和 Vitek 2 方法会低估或高估真菌对氟康唑和两性霉素 B (AMB) 的耐药性。本研究通过梯度-MIC-条带(Etest)和基于肉汤微量稀释的 MICRONAUT-AM-EUCAST (MCN-AM)检测法,评估了球孢子菌对氟康唑和两性霉素 B(AMB)的 AST 检测结果。对通过表型和分子方法鉴定的临床阴道杆菌分离株(n = 121)进行了检测。确定了两种方法之间的基本一致(EA,±1 倍稀释)和基于美国疾病控制和预防中心(CDC)暂定耐药性断点的分类一致(CA)。通过对 ERG11 进行 PCR 测序,检测出与氟康唑耐药性相关的突变。所有被鉴定为阿氏杆菌的分离物都属于南亚支系 I,并含有 ERG11 Y132F 或 K143R 突变。对于氟康唑,Etest-MCN-AM 的 EA 较差(33%),对于 AMB,EA 中等(76%)。氟康唑的 CA 值(94.2%,7 个差异)高于 AMB(91.7%,10 个差异)。当使用对氟康唑敏感的阿米巴痢疾杆菌的 MCN-AM 上限为 4 µg/mL 和对 AMB 的野生型的 Etest 上限为 8 µg/mL 时,差异有所减少。我们的数据显示,当使用疾控中心暂定的耐药性断点(氟康唑≥32 µg/mL,AMB≥2 µg/mL)时,MCN-AM 低估了对氟康唑的耐药性,而 Etest 则高估了对 AMB 的耐药性。应设计出针对特定方法的耐药性断点,以便对临床分离出的球孢子菌进行准确的 AST 检测,从而对患者进行适当的管理。
{"title":"Evaluation of Etest and MICRONAUT-AM Assay for Antifungal Susceptibility Testing of Candida auris: Underestimation of Fluconazole Resistance by MICRONAUT-AM and Overestimation of Amphotericin B Resistance by Etest","authors":"Mohammad Asadzadeh, Suhail Ahmad, Wadha Alfouzan, Inaam Al-Obaid, Bram Spruijtenburg, Eelco F. J. Meijer, Jacques F. Meis, Eiman Mokaddas","doi":"10.3390/antibiotics13090840","DOIUrl":"https://doi.org/10.3390/antibiotics13090840","url":null,"abstract":"Multidrug-resistant Candida auris has recently caused major outbreaks in healthcare facilities. Rapid and accurate antifungal susceptibility testing (AST) of C. auris is crucial for proper management of invasive infections. The Commercial Sensititre Yeast One and Vitek 2 methods underestimate or overestimate the resistance of C. auris to fluconazole and amphotericin B (AMB). This study evaluated the AST results of C. auris against fluconazole and AMB by gradient-MIC-strip (Etest) and broth microdilution-based MICRONAUT-AM-EUCAST (MCN-AM) assays. Clinical C. auris isolates (n = 121) identified by phenotypic and molecular methods were tested. Essential agreement (EA, ±1 two-fold dilution) between the two methods and categorical agreement (CA) based on the Centers for Disease Control and Prevention’s (CDC’s) tentative resistance breakpoints were determined. Fluconazole resistance-associated mutations were detected by PCR-sequencing of ERG11. All isolates identified as C. auris belonged to South Asian clade I and contained the ERG11 Y132F or K143R mutation. The Etest–MCN-AM EA was poor (33%) for fluconazole and moderate (76%) for AMB. The CA for fluconazole was higher (94.2%, 7 discrepancies) than for AMB (91.7%, 10 discrepancies). Discrepancies were reduced when an MCN-AM upper-limit value of 4 µg/mL for fluconazole-susceptible C. auris and an Etest upper-limit value of 8 µg/mL for the wild type for AMB were used. Our data show that resistance to fluconazole was underestimated by MCN-AM, while resistance to AMB was overestimated by Etest when using the CDC’s tentative resistance breakpoints of ≥32 µg/mL for fluconazole and ≥2 µg/mL for AMB. Method-specific resistance breakpoints should be devised for accurate AST of clinical C. auris isolates for proper patient management.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/antibiotics13090843
Max Chung, Ethan Dudley, Hatem Kittana, Alexis C. Thompson, Matthew Scott, Keri Norman, Robert Valeris-Chacin
Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements.
{"title":"Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA","authors":"Max Chung, Ethan Dudley, Hatem Kittana, Alexis C. Thompson, Matthew Scott, Keri Norman, Robert Valeris-Chacin","doi":"10.3390/antibiotics13090843","DOIUrl":"https://doi.org/10.3390/antibiotics13090843","url":null,"abstract":"Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-03DOI: 10.3390/antibiotics13090837
Winfried V. Kern, Michaela Steib-Bauert, Jürgen Baumann, Evelyn Kramme, Gesche Först, Katja de With
Background: Previous studies found that the coronavirus disease 2019 (COVID-19) pandemic had a variable impact on the consumption of antimicrobial drugs in human medicine, with trends in several European countries differing between community and inpatient prescribing. Aim: This study analysed changes in the volumes and use density of antibacterial and antifungal drugs dispensed in acute care hospitals in Germany between 2019 and 2022. Methods: Surveillance data for the four years available from 279 hospitals were expressed as the total volumes of daily doses or as use density (daily doses per 100 patient/occupied bed days) per year and analysed descriptively, using recommended hospital-adapted daily dose definitions (RDDs) and (as sensitivity analysis) WHO/ATC-defined daily dose definitions (DDD). Hospitals were stratified according to size (number of beds), university affiliation, and location (East, West, South). Results: There were significant decreases in both the total number of patient days and antibacterial drug volumes in 2020 through 2022 compared with 2019. The relative changes between 2019 and 2020, 2021, and 2022 were −12.8%, −13.5%, and −13.3% for patient days, and −9.7%, −11.0%, and −10.1% for antibacterial RDDs, respectively. Broad-spectrum betalactams, notably piperacillin–tazobactam and carbapenems, increased in volume, unlike most other drug classes. The resulting antibacterial drug use density was slightly but significantly increased, with pooled means (and medians) of 43.3 (40.0) RDD/100 in 2019 compared to 44.8 (41.7), 44.5 (40.80), and 44.9 (41.7) RDD/100 in the years 2020 through 2022, respectively. Antifungal drug volumes and use density increased after 2019 and peaked in 2021 (the difference between 2019 and 2021 for total volumes was +6.4%, and that for pooled mean use density values was +22.9%, respectively). These trends were similar in the different hospital strata and comparable when DDDs instead of RDDs were used. Conclusions: Similar to what has been observed in a majority of European countries, the total volume of antibacterial drug use in German acute care hospitals decreased with the pandemic, without a rebound phenomenon in 2022. In association with restricted hospital capacities and presumably more immunocompromised general medicine patients, however, inpatient prescribing of (primarily broad-spectrum) antibacterials and of antifungal drugs increased.
{"title":"Impact of the COVID-19 Pandemic on Inpatient Antibiotic and Antifungal Drug Prescribing Volumes in Germany","authors":"Winfried V. Kern, Michaela Steib-Bauert, Jürgen Baumann, Evelyn Kramme, Gesche Först, Katja de With","doi":"10.3390/antibiotics13090837","DOIUrl":"https://doi.org/10.3390/antibiotics13090837","url":null,"abstract":"Background: Previous studies found that the coronavirus disease 2019 (COVID-19) pandemic had a variable impact on the consumption of antimicrobial drugs in human medicine, with trends in several European countries differing between community and inpatient prescribing. Aim: This study analysed changes in the volumes and use density of antibacterial and antifungal drugs dispensed in acute care hospitals in Germany between 2019 and 2022. Methods: Surveillance data for the four years available from 279 hospitals were expressed as the total volumes of daily doses or as use density (daily doses per 100 patient/occupied bed days) per year and analysed descriptively, using recommended hospital-adapted daily dose definitions (RDDs) and (as sensitivity analysis) WHO/ATC-defined daily dose definitions (DDD). Hospitals were stratified according to size (number of beds), university affiliation, and location (East, West, South). Results: There were significant decreases in both the total number of patient days and antibacterial drug volumes in 2020 through 2022 compared with 2019. The relative changes between 2019 and 2020, 2021, and 2022 were −12.8%, −13.5%, and −13.3% for patient days, and −9.7%, −11.0%, and −10.1% for antibacterial RDDs, respectively. Broad-spectrum betalactams, notably piperacillin–tazobactam and carbapenems, increased in volume, unlike most other drug classes. The resulting antibacterial drug use density was slightly but significantly increased, with pooled means (and medians) of 43.3 (40.0) RDD/100 in 2019 compared to 44.8 (41.7), 44.5 (40.80), and 44.9 (41.7) RDD/100 in the years 2020 through 2022, respectively. Antifungal drug volumes and use density increased after 2019 and peaked in 2021 (the difference between 2019 and 2021 for total volumes was +6.4%, and that for pooled mean use density values was +22.9%, respectively). These trends were similar in the different hospital strata and comparable when DDDs instead of RDDs were used. Conclusions: Similar to what has been observed in a majority of European countries, the total volume of antibacterial drug use in German acute care hospitals decreased with the pandemic, without a rebound phenomenon in 2022. In association with restricted hospital capacities and presumably more immunocompromised general medicine patients, however, inpatient prescribing of (primarily broad-spectrum) antibacterials and of antifungal drugs increased.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-03DOI: 10.3390/antibiotics13090838
Cristian Piras, Rosario De Fazio, Antonella Di Francesco, Francesca Oppedisano, Anna Antonella Spina, Vincenzo Cunsolo, Paola Roncada, Rainer Cramer, Domenico Britti
Proteins involved in antibiotic resistance (resistome) and with antimicrobial activity are present in biological specimens. This study aims to explore the presence and abundance of antimicrobial peptides (AMPs) and resistome proteins in bovine milk from diverse breeds and from intensive (Pezzata rossa, Bruna alpina, and Frisona) and non-intensive farming (Podolica breeds). Liquid atmospheric pressure matrix-assisted laser desorption/ionization (LAP-MALDI) mass spectrometry (MS) profiling, bottom-up proteomics, and metaproteomics were used to comprehensively analyze milk samples from various bovine breeds in order to identify and characterize AMPs and to investigate resistome proteins. LAP-MALDI MS coupled with linear discriminant analysis (LDA) machine learning was employed as a rapid classification method for Podolica milk recognition against the milk of other bovine species. The results of the LAP-MALDI MS analysis of milk coupled with the linear discriminant analysis (LDA) demonstrate the potential of distinguishing between Podolica and control milk samples based on MS profiles. The classification accuracy achieved in the training set is 86% while it reaches 98.4% in the test set. Bottom-up proteomics revealed approximately 220 quantified bovine proteins (identified using the Bos taurus database), with cathelicidins and annexins exhibiting higher abundance levels in control cows (intensive farming breeds). On the other hand, the metaproteomics analysis highlighted the diversity within the milk’s microbial ecosystem with interesting results that may reflect the diverse environmental variables. The bottom-up proteomics data analysis using the Comprehensive Antibiotic Resistance Database (CARD) revealed beta-lactamases and tetracycline resistance proteins in both control and Podolica milk samples, with no relevant breed-specific differences observed.
生物样本中存在涉及抗生素耐药性(耐药性组)和具有抗菌活性的蛋白质。本研究旨在探讨不同品种、集约化养殖(Pezzata rossa、Bruna alpina 和 Frisona)和非集约化养殖(Podolica 品种)的牛乳中抗菌肽(AMPs)和抗生素组蛋白质的存在和丰度。研究人员利用液体常压基质辅助激光解吸/电离(LAP-MALDI)质谱(MS)分析、自下而上的蛋白质组学和元蛋白质组学对来自不同牛种的牛奶样本进行了全面分析,以确定AMPs的特征并研究抗性组蛋白质。将 LAP-MALDI MS 与线性判别分析 (LDA) 机器学习相结合,作为一种快速分类方法,用于识别 Podolica 牛奶与其他牛种牛奶的区别。对牛奶进行 LAP-MALDI MS 分析和线性判别分析(LDA)的结果表明,根据 MS 图谱区分 Podolica 牛奶样本和对照牛奶样本的潜力巨大。训练集的分类准确率为 86%,而测试集的准确率则达到 98.4%。自下而上的蛋白质组学发现了约 220 种量化的牛蛋白质(使用金牛数据库进行鉴定),对照组奶牛(集约化养殖品种)中的柔毛素和附件素含量较高。另一方面,元蛋白质组学分析强调了牛奶微生物生态系统的多样性,其有趣的结果可能反映了环境变量的多样性。使用抗生素耐药性综合数据库(CARD)进行的自下而上的蛋白质组学数据分析显示,对照组和 Podolica 牛奶样本中都有β-内酰胺酶和四环素耐药性蛋白质,没有观察到相关的品种特异性差异。
{"title":"Detection of Antimicrobial Proteins/Peptides and Bacterial Proteins Involved in Antimicrobial Resistance in Raw Cow’s Milk from Different Breeds","authors":"Cristian Piras, Rosario De Fazio, Antonella Di Francesco, Francesca Oppedisano, Anna Antonella Spina, Vincenzo Cunsolo, Paola Roncada, Rainer Cramer, Domenico Britti","doi":"10.3390/antibiotics13090838","DOIUrl":"https://doi.org/10.3390/antibiotics13090838","url":null,"abstract":"Proteins involved in antibiotic resistance (resistome) and with antimicrobial activity are present in biological specimens. This study aims to explore the presence and abundance of antimicrobial peptides (AMPs) and resistome proteins in bovine milk from diverse breeds and from intensive (Pezzata rossa, Bruna alpina, and Frisona) and non-intensive farming (Podolica breeds). Liquid atmospheric pressure matrix-assisted laser desorption/ionization (LAP-MALDI) mass spectrometry (MS) profiling, bottom-up proteomics, and metaproteomics were used to comprehensively analyze milk samples from various bovine breeds in order to identify and characterize AMPs and to investigate resistome proteins. LAP-MALDI MS coupled with linear discriminant analysis (LDA) machine learning was employed as a rapid classification method for Podolica milk recognition against the milk of other bovine species. The results of the LAP-MALDI MS analysis of milk coupled with the linear discriminant analysis (LDA) demonstrate the potential of distinguishing between Podolica and control milk samples based on MS profiles. The classification accuracy achieved in the training set is 86% while it reaches 98.4% in the test set. Bottom-up proteomics revealed approximately 220 quantified bovine proteins (identified using the Bos taurus database), with cathelicidins and annexins exhibiting higher abundance levels in control cows (intensive farming breeds). On the other hand, the metaproteomics analysis highlighted the diversity within the milk’s microbial ecosystem with interesting results that may reflect the diverse environmental variables. The bottom-up proteomics data analysis using the Comprehensive Antibiotic Resistance Database (CARD) revealed beta-lactamases and tetracycline resistance proteins in both control and Podolica milk samples, with no relevant breed-specific differences observed.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-02DOI: 10.3390/antibiotics13090833
Hanna Persha, Stephen A. Thacker, Krutika Mediwala Hornback, Gustavo R. Alvira-Arill, Richard Lueking, Taylor Morrisette
Introduction: Daptomycin (DAP) is a cyclic lipopeptide that exhibits potent in vitro activity against many drug-resistant gram-positive organisms, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Despite substantial reports evaluating the clinical outcomes of DAP within the adult population, real-world data are lacking in children. The primary goal of this evaluation was to describe the clinical characteristics and outcomes of DAP use in pediatric patients across a wide range of infections. Methods: This retrospective evaluation included patients < 18 years of age who were treated with DAP from January 2014 to May 2023. The primary objective was to evaluate the composite clinical success, which was defined as a 30-day survival, the lack of a 30-day microbiological recurrence, and the resolution of signs and symptoms of an acute infection without therapy modifications based on clinical failures. Secondary objectives included adverse effects potentially attributable to DAP and reasons for DAP utilization. Results: Forty patients were included, which were predominately male (62.5%) and white (52.5%), with a median age of 8.7 [IQR, 4.4–16.0] years. DAP was used for a wide range of infections, including central line-associated bloodstream infections (CLABSIs; 32.5%), infective endocarditis (15.0%), surgical-site infections (12.5%), and osteomyelitis (12.5%). The most common pathogen isolated was MRSA (37.5%), and most patients were bacteremic (60.0%). The median DAP dose was 8 [IQR, 6–10] mg/kg, and the median duration of the DAP therapy was 11.5 [IQR, 4.8–18.8] days. Most patients achieved composite clinical success (75.0%). An adverse effect occurred in 5.0% of the patients. DAP was prescribed the most for its ease of use/ability to facilitate discharge (40.0%) and/or for issues with alternative therapies (37.5%). Conclusion: Most pediatric patients that received DAP demonstrated clinical success with a low incidence of adverse effects. Larger, real-world studies of DAP use are necessary to further assess clinical outcomes.
{"title":"Real-World Clinical Characteristics and Outcomes with Daptomycin Use in Pediatric Patients: A Retrospective Case Series","authors":"Hanna Persha, Stephen A. Thacker, Krutika Mediwala Hornback, Gustavo R. Alvira-Arill, Richard Lueking, Taylor Morrisette","doi":"10.3390/antibiotics13090833","DOIUrl":"https://doi.org/10.3390/antibiotics13090833","url":null,"abstract":"Introduction: Daptomycin (DAP) is a cyclic lipopeptide that exhibits potent in vitro activity against many drug-resistant gram-positive organisms, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Despite substantial reports evaluating the clinical outcomes of DAP within the adult population, real-world data are lacking in children. The primary goal of this evaluation was to describe the clinical characteristics and outcomes of DAP use in pediatric patients across a wide range of infections. Methods: This retrospective evaluation included patients < 18 years of age who were treated with DAP from January 2014 to May 2023. The primary objective was to evaluate the composite clinical success, which was defined as a 30-day survival, the lack of a 30-day microbiological recurrence, and the resolution of signs and symptoms of an acute infection without therapy modifications based on clinical failures. Secondary objectives included adverse effects potentially attributable to DAP and reasons for DAP utilization. Results: Forty patients were included, which were predominately male (62.5%) and white (52.5%), with a median age of 8.7 [IQR, 4.4–16.0] years. DAP was used for a wide range of infections, including central line-associated bloodstream infections (CLABSIs; 32.5%), infective endocarditis (15.0%), surgical-site infections (12.5%), and osteomyelitis (12.5%). The most common pathogen isolated was MRSA (37.5%), and most patients were bacteremic (60.0%). The median DAP dose was 8 [IQR, 6–10] mg/kg, and the median duration of the DAP therapy was 11.5 [IQR, 4.8–18.8] days. Most patients achieved composite clinical success (75.0%). An adverse effect occurred in 5.0% of the patients. DAP was prescribed the most for its ease of use/ability to facilitate discharge (40.0%) and/or for issues with alternative therapies (37.5%). Conclusion: Most pediatric patients that received DAP demonstrated clinical success with a low incidence of adverse effects. Larger, real-world studies of DAP use are necessary to further assess clinical outcomes.","PeriodicalId":8151,"journal":{"name":"Antibiotics","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}