Pub Date : 2024-03-01DOI: 10.1099/acmi.0.000766.v3
Ashma Chakrawarti, Korin M. Eckstrom, Pheobe Laaguiby, John W. Barlow
Antimicrobial resistance (AMR) in Staphylococcus aureus is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of S. aureus, this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline. Our analyses showcased the hybrid-assembled genome’s superior completeness compared to Oxford Nanopore (R9.4.1)-only or Illumina-only assembled genomes. Furthermore, the hybrid assembly accurately determined multilocus sequence typing (MLST) strain types across all isolates. The comprehensive probe for antibiotic resistance genes (ARGs) using databases like CARD, Resfinder, and MEGARES 2.0 characterized AMR in S. aureus isolates from Vermont dairy farms, and revealed the presence of notable resistance genes, including beta-lactam genes blaZ, blaI, and blaR. In conclusion, the hybrid assembly approach emerged as a tool for uncovering the genomic nuances of S. aureus isolates collected from multiple sources on dairy farms. Our findings offer a pathway for detecting AMR gene prevalence and shaping AMR management strategies crucial for safeguarding human and animal health.
{"title":"Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies","authors":"Ashma Chakrawarti, Korin M. Eckstrom, Pheobe Laaguiby, John W. Barlow","doi":"10.1099/acmi.0.000766.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000766.v3","url":null,"abstract":"Antimicrobial resistance (AMR) in Staphylococcus aureus is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of S. aureus, this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline.\u0000 Our analyses showcased the hybrid-assembled genome’s superior completeness compared to Oxford Nanopore (R9.4.1)-only or Illumina-only assembled genomes. Furthermore, the hybrid assembly accurately determined multilocus sequence typing (MLST) strain types across all isolates. The comprehensive probe for antibiotic resistance genes (ARGs) using databases like CARD, Resfinder, and MEGARES 2.0 characterized AMR in S. aureus isolates from Vermont dairy farms, and revealed the presence of notable resistance genes, including beta-lactam genes blaZ, blaI, and blaR. In conclusion, the hybrid assembly approach emerged as a tool for uncovering the genomic nuances of S. aureus isolates collected from multiple sources on dairy farms. Our findings offer a pathway for detecting AMR gene prevalence and shaping AMR management strategies crucial for safeguarding human and animal health.","PeriodicalId":502145,"journal":{"name":"Access Microbiology","volume":"2 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140404234","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 : 2024-03-01DOI: 10.1099/acmi.0.000648.v3
Alveera Alam, Hiba Sami, S. Z. A. Hashmi, K. Gururaj, Mohammad Azam Khan, P. Khan, Haleema Ahmad, Nazish Fatima, Haris M. Khan
Introduction. Brucellosis, a globally distributed zoonotic disease, is caused by the Gram-negative bacteria known as Brucella. Humans acquire infection through direct contact with the blood, urine and placenta of animals, inhalation of dust or aerosols at infected animal farms, and raw milk and meat intake. This study aimed to assess the prevalence of brucellosis in dairy farmers in and around the Aligarh region of North India, to document various clinical signs and symptoms in Brucella-positive individuals, and to create awareness in dairy farmers concerning brucellosis and ways to prevent it. Methods. This was an observational study that included 125 dairy farmers in and around the Aligarh region. Serum samples were taken from this high-risk group after obtaining informed consent. Further, a pre-designed proforma was used to collect information about their knowledge, attitude and practices (KAP) concerning brucellosis and assess the risk factors for the disease. The Rose Bengal test (RBT), serum agglutination test (SAT) and enzyme-linked immunosorbent assay (ELISA) were performed to detect the seroprevalence of brucellosis. Result. Brucella infection was diagnosed in 64 (51.20 %) cases by indirect ELISA (IgM+IgG), 41 (32.8 %) by RBT and 4 (3.2 %) by SAT. Significant clustering of patients was seen in the 20–55 years age group. The most common symptoms in ELISA IgM-positive patients were joint pain (16.07 %), fatigue (14.28 %), anorexia (12.50 %), weight loss (8.92 %), malaise (5.35 %), undulant fever (3.57 %), night sweats (3.57 %) and headache (1.78 %). The findings of this study indicate that ELISA (IgM+IgG) exhibits great sensitivity as compared to SAT and RBT. KAP was very poor among dairy farmers. Conclusion. In India, Brucella is a frequent but severely underreported illness. ELISA is the most sensitive serological test for diagnosing brucellosis. No potential vaccine has yet been introduced for humans against brucellosis. Thus, it is necessary to impart awareness and sensitize high-risk groups concerning brucellosis.
导言。布鲁氏菌病是一种遍布全球的人畜共患疾病，由革兰氏阴性菌布鲁氏菌引起。人类通过直接接触动物的血液、尿液和胎盘，吸入受感染动物农场的灰尘或气溶胶，以及摄入生牛奶和肉类而感染。本研究旨在评估北印度阿利加尔地区及周边地区奶农的布鲁氏菌病患病率，记录布鲁氏菌阳性者的各种临床症状和体征，并提高奶农对布鲁氏菌病的认识和预防方法。 研究方法这是一项观察性研究，包括阿利加尔地区及其周边的 125 名奶农。在获得知情同意后，从这一高风险群体中采集了血清样本。此外，研究人员还使用事先设计好的表格收集有关布鲁氏菌病的知识、态度和做法 (KAP) 的信息，并评估该疾病的风险因素。研究人员采用玫瑰红试验（RBT）、血清凝集试验（SAT）和酶联免疫吸附试验（ELISA）检测布鲁氏菌病的血清流行率。 结果。通过间接酶联免疫吸附试验（IgM+IgG）确诊的布鲁氏菌感染病例为 64 例（51.20%），通过 RBT 确诊的病例为 41 例（32.8%），通过 SAT 确诊的病例为 4 例（3.2%）。患者主要集中在 20-55 岁年龄组。ELISA IgM 阳性患者最常见的症状是关节疼痛（16.07%）、疲劳（14.28%）、厌食（12.50%）、体重减轻（8.92%）、乏力（5.35%）、发热（3.57%）、盗汗（3.57%）和头痛（1.78%）。本研究结果表明，与 SAT 和 RBT 相比，ELISA（IgM+IgG）的灵敏度更高。奶农的 KAP 非常低。 结论在印度，布鲁氏菌是一种常见疾病，但报告严重不足。ELISA 是诊断布鲁氏菌病最灵敏的血清学检测方法。目前还没有针对人类的布鲁氏菌病疫苗。因此，有必要提高高危人群对布鲁氏杆菌病的认识和敏感性。
{"title":"Seroprevalence and risk factor analysis of brucellosis among dairy farmers in Aligarh region, North India: creating awareness of a neglected disease","authors":"Alveera Alam, Hiba Sami, S. Z. A. Hashmi, K. Gururaj, Mohammad Azam Khan, P. Khan, Haleema Ahmad, Nazish Fatima, Haris M. Khan","doi":"10.1099/acmi.0.000648.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000648.v3","url":null,"abstract":"\u0000 Introduction. Brucellosis, a globally distributed zoonotic disease, is caused by the Gram-negative bacteria known as Brucella. Humans acquire infection through direct contact with the blood, urine and placenta of animals, inhalation of dust or aerosols at infected animal farms, and raw milk and meat intake. This study aimed to assess the prevalence of brucellosis in dairy farmers in and around the Aligarh region of North India, to document various clinical signs and symptoms in Brucella-positive individuals, and to create awareness in dairy farmers concerning brucellosis and ways to prevent it.\u0000 \u0000 Methods. This was an observational study that included 125 dairy farmers in and around the Aligarh region. Serum samples were taken from this high-risk group after obtaining informed consent. Further, a pre-designed proforma was used to collect information about their knowledge, attitude and practices (KAP) concerning brucellosis and assess the risk factors for the disease. The Rose Bengal test (RBT), serum agglutination test (SAT) and enzyme-linked immunosorbent assay (ELISA) were performed to detect the seroprevalence of brucellosis.\u0000 \u0000 Result.\u0000 Brucella infection was diagnosed in 64 (51.20 %) cases by indirect ELISA (IgM+IgG), 41 (32.8 %) by RBT and 4 (3.2 %) by SAT. Significant clustering of patients was seen in the 20–55 years age group. The most common symptoms in ELISA IgM-positive patients were joint pain (16.07 %), fatigue (14.28 %), anorexia (12.50 %), weight loss (8.92 %), malaise (5.35 %), undulant fever (3.57 %), night sweats (3.57 %) and headache (1.78 %). The findings of this study indicate that ELISA (IgM+IgG) exhibits great sensitivity as compared to SAT and RBT. KAP was very poor among dairy farmers.\u0000 \u0000 Conclusion. In India, Brucella is a frequent but severely underreported illness. ELISA is the most sensitive serological test for diagnosing brucellosis. No potential vaccine has yet been introduced for humans against brucellosis. Thus, it is necessary to impart awareness and sensitize high-risk groups concerning brucellosis.","PeriodicalId":502145,"journal":{"name":"Access Microbiology","volume":"6 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140407569","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}
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