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Pei Y, Shum MHH, Liao Y, Leung VW, Gong YN, Smith DK, Yin X, Guan Y, Luo R, Zhang T, Lam TTY. ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences. MICROBIOME 2024; 12:84. [PMID: 38725076 PMCID: PMC11080312 DOI: 10.1186/s40168-024-01805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing. RESULTS In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG. CONCLUSIONS ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.
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Grants
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 31922087 National Natural Science Foundation of China's Excellent Young Scientists Fund (Hong Kong and Macau)
- Hong Kong Research Grants Council’s Theme-based Research Scheme
- Innovation and Technology Commission’s InnoHK funding (D24H), and the Government of Guangdong Province
- National Natural Science Foundation of China’s Excellent Young Scientists Fund (Hong Kong and Macau)
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Affiliation(s)
- Yao Pei
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yunshi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Vivian W Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yu-Nong Gong
- Division of Biotechnology, Research Center of Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Xiaole Yin
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China.
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China.
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
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2
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Scarpellini R, Vélez De Mendizábal LL, Quevedo-Caraballo S, Blanco JL, García ME, Pérez-Sancho M, Portero Fuentes M, Penelo S, Esposito E, Mondo E, Piva S. Active surveillance of antimicrobial resistance in companion animals: A pilot study in a Spanish Veterinary Teaching Hospital. Comp Immunol Microbiol Infect Dis 2024; 108:102169. [PMID: 38579648 DOI: 10.1016/j.cimid.2024.102169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/22/2024] [Accepted: 03/31/2024] [Indexed: 04/07/2024]
Abstract
The role of small animal veterinary hospitals in the onset and dissemination of antimicrobial-resistant organisms (AMROs) is still not clear, and the implementation of an internal surveillance systems is a cost-effective tool to better understand their impact. The aim of this study was to describe a pilot program of active surveillance in a Spanish Veterinary Teaching Hospital, developed to estimate the detection frequency of AMROs in the commensal flora of patients and in the environment. Surveillance was focused on Methicillin-resistant Staphylococci (MRS), third generation cephalosporins resistant gram-negative bacteria (3GCR-GNB), and carbapenems-resistant gram-negative bacteria (CR-GNB). Oral and perirectal swabs were collected in the same dogs and cats hospitalized > 48 h, at their admission and before their discharge. Out of 50 patients sampled, 24% (12/50) were carriers at admission of at least one of the three investigated AMROs. Twenty-eight percent of patients (14/50) acquired at least one AMRO during the hospital stay. MRS detection frequency at admission was 12% (6/50), while acquisition was 6% (3/50). 3GCR-GNB detection frequency was 14% at admission (7/50) and acquisition 22% (11/50), while CR-GNB detection frequency was 2% at admission (1/50) and acquisition 2% (1/50). Environmental surveillance (98 samples) showed a total detection frequency of 22.4% for MRS (22/98), 2% for 3GCR-GNB and CR-GNB (2/98). Clinical staff' shoe soles showed high detection frequency for MRS (50%). 3GCR Escherichia coli was the most isolated species in patients (n = 17). The results show how active surveillance can be used as a tool to assess the impact of AMROs in veterinary hospitals to subsequently build up tailored control plans based on specific issues.
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Affiliation(s)
- Raffaele Scarpellini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra 50, Ozzano Emilia (BO) 40006, Italy.
| | - Laura Leal Vélez De Mendizábal
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, av. Puerta de Hierro s/n, Madrid 28040, Spain; Complutense University of Madrid, Faculty of Veterinary Medicine, Veterinary Teaching Hospital, av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - Sergio Quevedo-Caraballo
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, av. Puerta de Hierro s/n, Madrid 28040, Spain; Complutense University of Madrid, Faculty of Veterinary Medicine, Veterinary Teaching Hospital, av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - José L Blanco
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, av. Puerta de Hierro s/n, Madrid 28040, Spain; Complutense University of Madrid, Faculty of Veterinary Medicine, Veterinary Teaching Hospital, av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - Marta E García
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, av. Puerta de Hierro s/n, Madrid 28040, Spain; Complutense University of Madrid, Faculty of Veterinary Medicine, Veterinary Teaching Hospital, av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - Marta Pérez-Sancho
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, av. Puerta de Hierro s/n, Madrid 28040, Spain; VISAVET Health Surveillance Centre, Complutense University of Madrid, av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - Miriam Portero Fuentes
- Complutense University of Madrid, Faculty of Veterinary Medicine, Veterinary Teaching Hospital, av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - Silvia Penelo
- Complutense University of Madrid, Faculty of Veterinary Medicine, Veterinary Teaching Hospital, av. Puerta de Hierro s/n, Madrid 28040, Spain
| | - Erika Esposito
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra 50, Ozzano Emilia (BO) 40006, Italy
| | - Elisabetta Mondo
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra 50, Ozzano Emilia (BO) 40006, Italy
| | - Silvia Piva
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra 50, Ozzano Emilia (BO) 40006, Italy
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3
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Liu Z, Li X, Zhang R, Ji L, Gong L, Ji Y, Zhou F, Yin Y, Li K, Sun P, Pu Z, Wang Q, Zou J. Identification of DNA variants at ultra-low variant allele frequencies via Taq polymerase cleavage of wild-specific blockers. Anal Bioanal Chem 2023; 415:6537-6549. [PMID: 37702773 DOI: 10.1007/s00216-023-04931-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Detecting mutations related to tumors holds immense clinical significance for cancer diagnosis and treatment. However, the presence of highly redundant wild DNA poses a challenge for the advancement of low-copy mutant ctDNA genotyping in cancer cases. To address this, a Taqman qPCR strategy to identify rare mutations at low variant allele fractions (VAFs) has been developed. This strategy combines mutant-specific primers with wild-specific blockers. Diverging from other blocker-mediated PCRs, which rely on primer-induced strand displacement or the use of modified oligos resistant to Taq polymerase, our innovation is built upon the cleavage of specific blockers by Taq polymerase. Given its unique design, which does not hinge on strand displacement or base modification, we refer to this novel method as unmodified-blocker cleavage PCR (UBC-PCR). Multiple experiments consistently confirmed that variant distinction was improved significantly by introduction of 5' unmatched blockers into the reaction. Moreover, UBC-PCR successfully detected mutant DNA at VAFs as low as 0.01% across six different variant contexts. Multiplex UBC-PCR was also performed to identify a reference target and three mutations with a sensitivity of 0.01% VAFs in one single tube. In profiling the gene status from 12 lung cancer ctDNA samples and 22 thyroid cancer FNA DNA samples, UBC-PCR exhibited a 100% concordance rate with ddPCR and a commercial ARMS kit, respectively. Our work demonstrates that UBC-PCR can identify low-abundance variants with high sensitivity in multiplex reactions, independent of strand displacement and base modification. This strategy holds the potential to significantly impact clinical practice and precision medicine.
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Affiliation(s)
- Zhaocheng Liu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Xiushuai Li
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China
| | - Rui Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Li Ji
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Lingli Gong
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Yong Ji
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Fengsheng Zhou
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ying Yin
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Koukou Li
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi, 214023, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Qing Wang
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China.
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China.
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China.
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4
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Maechler F, Schwab F, Hansen S, Behnke M, Bonten MJ, Canton R, Diaz Agero C, Fankhauser C, Harbarth S, Huttner BD, Kola A, Gastmeier P. Quantification of time delay between screening and subsequent initiation of contact isolation for carriers of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales: A post hoc subgroup analysis of the R-GNOSIS WP5 Trial. Infect Control Hosp Epidemiol 2023; 44:1410-1416. [PMID: 36912321 PMCID: PMC10507499 DOI: 10.1017/ice.2022.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 03/14/2023]
Abstract
OBJECTIVES The aim of this study was to quantify the time delay between screening and initiation of contact isolation for carriers of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E). METHODS This study was a secondary analysis of contact isolation periods in a cluster-randomized controlled trial that compared 2 strategies to control ESBL-E (trial no. ISRCTN57648070). Patients admitted to 20 non-ICU wards in Germany, the Netherlands, Spain, and Switzerland were screened for ESBL-E carriage on admission, weekly thereafter, and on discharge. Data collection included the day of sampling, the day the wards were notified of the result, and subsequent ESBL-E isolation days. RESULTS Between January 2014 and August 2016, 19,122 patients, with a length of stay ≥2 days were included. At least 1 culture was collected for 16,091 patients (84%), with a median duration between the admission day and the day of first sample collection of 2 days (interquartile range [IQR], 1-3). Moreover, 854 (41%) of all 2,078 ESBL-E carriers remained without isolation during their hospital stay. In total, 6,040 ESBL-E days (32% of all ESBL-E days) accrued for patients who were not isolated. Of 2,078 ESBL-E-carriers, 1,478 ESBL-E carriers (71%) had no previous history of ESBL-E carriage. Also, 697 (34%) were placed in contact isolation with a delay of 4 days (IQR, 2-5), accounting for 2,723 nonisolation days (15% of ESBL-E days). CONCLUSIONS Even with extensive surveillance screening, almost one-third of all ESBL-E days were nonisolation days. Limitations in routine culture-based ESBL-E detection impeded timely and exhaustive implementation of targeted contact isolation.
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Affiliation(s)
- Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Sonja Hansen
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Marc J. Bonten
- Department of Medical Microbiology and Infection Control, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid
| | - Cristina Diaz Agero
- Servicio de Medicina Preventiva y Salud Pública Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid
| | - Carolina Fankhauser
- Infection Control Program, Geneva University Hospitals and Medical School, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program, Geneva University Hospitals and Medical School, Geneva, Switzerland
| | - Benedikt D. Huttner
- Infection Control Program, Geneva University Hospitals and Medical School, Geneva, Switzerland
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Universitätsmedizin – CharitéBerlin, Germany
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5
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Bou G, Calbo E, Crespo M, Cantón R, Álvarez de Luna FF, García Rodríguez J, Ángel Goenaga M, González-García J, Gonzàlez J, Larrosa N, Martínez-Martínez L, Navarro D, Ramón Paño J, Rivero A, Carlos Rodríguez J, Tomás M, Vilaj J. Justification for 24/7 clinical microbiology services. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2021.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Bou G, Calbo E, Crespo M, Cantón R, Álvarez de Luna FF, García Rodríguez J, Ángel Goenaga M, González-García J, Gonzàlez J, Larrosa N, Martínez-Martínez L, Navarro D, Ramón Paño J, Rivero A, Carlos Rodríguez J, Tomás M, Vilaj J. Justification for 24/7 clinical microbiology services. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:1-4. [PMID: 34991847 DOI: 10.1016/j.eimce.2021.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/12/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Germán Bou
- Servicio de Microbiología, Complejo Hospitalario Universitario La Coruña e Instituto Investigación Biomédica A Coruña (INIBIC), La Coruña, Spain
| | - Esther Calbo
- Unidad de Enfermedades Infecciosas, Hospital Mutua de Terrassa, Universidad Internacional de Cataluña, Barcelona, Spain
| | - Manuel Crespo
- Servicio de Medicina Interna, Instituto de Investigación Galicia Sur, Hospital Universitario Álvaro Cunqueiro, Vigo, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal e Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | - Julio García Rodríguez
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPaz, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Goenaga
- Servicio Enfermedades Infecciosas, Hospital Donostia, OSI Donostialdea, Donostia, Spain
| | - Juan González-García
- Servicio de Medicina Interna, Hospital Universitario La Paz, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain; Instituto de Investigación Hospital Universitario La Paz (IdiPaz), Madrid, Spain
| | - Julià Gonzàlez
- Servicio de Microbiología, Hospital Clínic, Facultad de Medicina, Universidad de Barcelona, Barcelona, Spain; Instituto de Salud Global (ISGlobal) de Barcelona, Barcelona, Spain
| | - Nieves Larrosa
- Servicio de Microbiología, Hospital Universitario Vall d'Hebron, VHIR, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luis Martínez-Martínez
- Unidad de Microbiología Clínica, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, Córdoba, Spain
| | - David Navarro
- Servicio de Microbiología, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - José Ramón Paño
- Servicio de Enfermedades Infecciosas, Hospital Clínico Universitario "Lozano Blesa", IIS Aragón, Zaragoza, Spain
| | - Antonio Rivero
- Servicio de Enfermedades Infecciosas, Hospital Universitario Reina Sofía, Universidad de Córdoba, IMIBIC, Córdoba, Spain
| | - Juan Carlos Rodríguez
- Servicio de Microbiología, Hospital General Universitario de Alicante-ISABIAL, Universidad Miguel Hernández, Alicante, Spain
| | - María Tomás
- Servicio de Microbiología, Complejo Hospitalario Universitario La Coruña e Instituto Investigación Biomédica A Coruña (INIBIC), La Coruña, Spain
| | - Jordi Vilaj
- Instituto de Salud Global (ISGlobal) de Barcelona, Barcelona, Spain.
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7
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Seo SM, Jeong IS. [External Validation of Carbapenem-Resistant Enterobacteriaceae Acquisition Risk Prediction Model in a Medium Sized Hospital]. J Korean Acad Nurs 2021; 50:621-630. [PMID: 32895347 DOI: 10.4040/jkan.20137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE This study was aimed to evaluate the external validity of a carbapenem-resistant Enterobacteriaceae (CRE) acquisition risk prediction model (the CREP-model) in a medium-sized hospital. METHODS This retrospective cohort study included 613 patients (CRE group: 69, no-CRE group: 544) admitted to the intensive care units of a 453-beds secondary referral general hospital from March 1, 2017 to September 30, 2019 in South Korea. The performance of the CREP-model was analyzed with calibration, discrimination, and clinical usefulness. RESULTS The results showed that those higher in age had lower presence of multidrug resistant organisms (MDROs), cephalosporin use ≥ 15 days, Acute Physiology and Chronic Health Evaluation II (APACHE II) score ≥ 21 points, and lower CRE acquisition rates than those of CREP-model development subjects. The calibration-in-the-large was 0.12 (95% CI: - 0.16~0.39), while the calibration slope was 0.87 (95% CI: 0.63~1.12), and the concordance statistic was .71 (95% CI: .63~.78). At the predicted risk of .10, the sensitivity, specificity, and correct classification rates were 43.5%, 84.2%, and 79.6%, respectively. The net true positive according to the CREP-model were 3 per 100 subjects. After adjusting the predictors' cutting points, the concordance statistic increased to .84 (95% CI: .79~.89), and the sensitivity and net true positive was improved to 75.4%. and 6 per 100 subjects, respectively. CONCLUSION The CREP-model's discrimination and clinical usefulness are low in a medium sized general hospital but are improved after adjusting for the predictors. Therefore, we suggest that institutions should only use the CREP-model after assessing the distribution of the predictors and adjusting their cutting points.
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Affiliation(s)
- Su Min Seo
- Infection Control Unit, Dongeui Medical Center, Busan, Korea
| | - Ihn Sook Jeong
- College of Nursing, Pusan National University, Yangsan, Korea.
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8
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Abstract
Advances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multiomics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances toward such diagnostics. However, the inability to squeeze light with several hundred nanometer wavelengths into angstrom-scale volume for single-nucleotide measurements has hindered further progress. This limitation has been circumvented by analyzing the relative nucleobase content with Raman spectroscopy, in an optical sequencing method. Here, we performed optical sequencing measurements on positively charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in label-free DNA k-mer blocks (where k = 10) as well as measurements on RNA and chemically modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy measurements were then used with a content-scoring database searching algorithm to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 block content measurements (<15% coverage) of the gene. These results prove the feasibility of an optical sequencing platform as a diagnostic method. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to the ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.
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9
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Korshoj LE, Nagpal P. BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage. Comput Biol Med 2019; 110:196-206. [PMID: 31173943 DOI: 10.1016/j.compbiomed.2019.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/10/2023]
Abstract
A single, inexpensive diagnostic test capable of rapidly identifying a wide range of genetic biomarkers would prove invaluable in precision medicine. Previous work has demonstrated the potential for high-throughput, label-free detection of A-G-C-T content in DNA k-mers, providing an alternative to single-letter sequencing while also having inherent lossy data compression and massively parallel data acquisition. Here, we apply a new bioinformatics algorithm - block optical content scoring (BOCS) - capable of using the high-throughput content k-mers for rapid, broad-spectrum identification of genetic biomarkers. BOCS uses content-based sequence alignment for probabilistic mapping of k-mer contents to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes, even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and >90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Simulations for detecting multiple resistance genes within a methicillin-resistant Staphylococcus aureus (MRSA) strain showed 100% accuracy at an average gene coverage of merely 0.515, when the k-mer lengths were variable and with 4% sequencing error within the k-mer blocks. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes. Combined with a high-throughput content-based sequencing technique, the BOCS algorithm potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases.
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Affiliation(s)
- Lee E Korshoj
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Prashant Nagpal
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA.
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10
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11
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Park SH. Management of multi-drug resistant organisms in healthcare settings. JOURNAL OF THE KOREAN MEDICAL ASSOCIATION 2018. [DOI: 10.5124/jkma.2018.61.1.26] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Sun Hee Park
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Seoul, Korea
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12
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Computational and biological profile of boronic acids for the detection of bacterial serine- and metallo-β-lactamases. Sci Rep 2017; 7:17716. [PMID: 29255163 PMCID: PMC5735191 DOI: 10.1038/s41598-017-17399-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/16/2017] [Indexed: 12/21/2022] Open
Abstract
β-Lactamases (BLs) able to hydrolyze β-lactam antibiotics and more importantly the last resort carbapenems, represent a major mechanism of resistance in Gram-negative bacteria showing multi-drug or extensively drug resistant phenotypes. The early detection of BLs responsible of resistant infections is challenging: approaches aiming at the identification of new BLs inhibitors (BLI) can thus serve as the basis for the development of highly needed diagnostic tools. Starting from benzo-[b]-thiophene-2-boronic acid (BZB), a nanomolar inhibitor of AmpC β-lactamase (K i = 27 nM), we have identified and characterized a set of BZB analogues able to inhibit clinically-relevant β-lactamases, including AmpC, Extended-Spectrum BLs (ESBL), KPC- and OXA-type carbapenemases and metallo-β-lactamases (MBL). A multiligand set of boronic acid (BA) β-lactamase inhibitors was obtained using covalent molecular modeling, synthetic chemistry, enzyme kinetics and antibacterial susceptibility testing. Data confirmed the possibility to discriminate between clinically-relevant β-lactamases on the basis of their inhibition profile. Interestingly, this work also allowed the identification of potent KPC-2 and NDM-1 inhibitors able to potentiate the activity of cefotaxime (CTX) and ceftazidime (CAZ) against resistant clinical isolates (MIC reduction, 32-fold). Our results open the way to the potential use of our set of compounds as a diagnostic tool for the sensitive detection of clinically-relevant β-lactamases.
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13
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Cantón R, Gómez G. de la Pedrosa E. Impacto económico de los métodos de diagnóstico rápido en Microbiología Clínica: precio de la prueba o impacto clínico global. Enferm Infecc Microbiol Clin 2017; 35:659-666. [DOI: 10.1016/j.eimc.2017.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 09/13/2017] [Indexed: 12/19/2022]
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14
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Buchanan CM, Wood RL, Hoj TR, Alizadeh M, Bledsoe CG, Wood ME, McClellan DS, Blanco R, Hickey CL, Ravsten TV, Husseini GA, Robison RA, Pitt WG. Rapid separation of very low concentrations of bacteria from blood. J Microbiol Methods 2017; 139:48-53. [PMID: 28495585 PMCID: PMC5533616 DOI: 10.1016/j.mimet.2017.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/05/2017] [Accepted: 05/05/2017] [Indexed: 12/20/2022]
Abstract
A rapid and accurate diagnosis of the species and antibiotic resistance of bacteria in septic blood is vital to increase survival rates of patients with bloodstream infections, particularly those with carbapenem-resistant enterobacteriaceae (CRE) infections. The extremely low levels in blood (1 to 100CFU/ml) make rapid diagnosis difficult. In this study, very low concentrations of bacteria (6 to 200CFU/ml) were separated from 7ml of whole blood using rapid sedimentation in a spinning hollow disk that separated plasma from red and white cells, leaving most of the bacteria suspended in the plasma. Following less than a minute of spinning, the disk was slowed, the plasma was recovered, and the bacteria were isolated by vacuum filtration. The filters were grown on nutrient plates to determine the number of bacteria recovered from the blood. Experiments were done without red blood cell (RBC) lysis and with RBC lysis in the recovered plasma. While there was scatter in the data from blood with low bacterial concentrations, the mean average recovery was 69%. The gender of the blood donor made no statistical difference in bacterial recovery. These results show that this rapid technique recovers a significant amount of bacteria from blood containing clinically relevant low levels of bacteria, producing the bacteria in minutes. These bacteria could subsequently be identified by molecular techniques to quickly identify the infectious organism and its resistance profile, thus greatly reducing the time needed to correctly diagnose and treat a blood infection.
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Affiliation(s)
- Clara M Buchanan
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Ryan L Wood
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Taalin R Hoj
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Mahsa Alizadeh
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Colin G Bledsoe
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Madison E Wood
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Daniel S McClellan
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Rae Blanco
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Caroline L Hickey
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Tanner V Ravsten
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Ghaleb A Husseini
- Chemical Engineering Department, American University of Sharjah, Sharjah, United Arab Emirates
| | - Richard A Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - William G Pitt
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA.
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Djibré M, Fedun S, Le Guen P, Vimont S, Hafiani M, Fulgencio JP, Parrot A, Denis M, Fartoukh M. Universal versus targeted additional contact precautions for multidrug-resistant organism carriage for patients admitted to an intensive care unit. Am J Infect Control 2017; 45:728-734. [PMID: 28285725 DOI: 10.1016/j.ajic.2017.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although additional contact precautions (ACPs) are routinely used to reduce cross-transmission of multidrug-resistant organisms (MDROs), the relevance of isolation precautions remains debated. We hypothesized that the collection of recognized risk factors for MDRO carriage on intensive care unit (ICU) admission might be helpful to target ACPs without increasing MDRO acquisition during ICU stays, compared with universal ACPs. MATERIALS AND METHODS This is a sequential single-center observational study performed in consecutive patients admitted to a French medical and surgical ICU. During the first 6-month period, screening for MDRO carriage and ACPs were performed in all patients. During the second 6-month period, screening was maintained, but ACP use was guided by the presence of at least 1 defined risk factor for MDRO. RESULTS During both periods, 33 (10%) and 30 (10%) among 327 and 297 admissions were, respectively, associated with a positive admission MDRO carriage. During both periods, a second screening was performed in 147 (45%) and 127 (43%) patients. Altogether, the rate of acquired MDRO (positive screening or clinical specimen) was similar during both periods (10% [n = 15] and 11.8% [n = 15], respectively; P = .66). CONCLUSIONS The results of our study contribute to support the safety of an isolation-targeted screening policy on ICU admission compared with universal screening and isolation regarding the rate of ICU-acquired MDRO colonization or infection.
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Exner M, Bhattacharya S, Christiansen B, Gebel J, Goroncy-Bermes P, Hartemann P, Heeg P, Ilschner C, Kramer A, Larson E, Merkens W, Mielke M, Oltmanns P, Ross B, Rotter M, Schmithausen RM, Sonntag HG, Trautmann M. Antibiotic resistance: What is so special about multidrug-resistant Gram-negative bacteria? GMS HYGIENE AND INFECTION CONTROL 2017; 12:Doc05. [PMID: 28451516 PMCID: PMC5388835 DOI: 10.3205/dgkh000290] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In the past years infections caused by multidrug-resistant Gram-negative bacteria have dramatically increased in all parts of the world. This consensus paper is based on presentations, subsequent discussions and an appraisal of current literature by a panel of international experts invited by the Rudolf Schülke Stiftung, Hamburg. It deals with the epidemiology and the inherent properties of Gram-negative bacteria, elucidating the patterns of the spread of antibiotic resistance, highlighting reservoirs as well as transmission pathways and risk factors for infection, mortality, treatment and prevention options as well as the consequences of their prevalence in livestock. Following a global, One Health approach and based on the evaluation of the existing knowledge about these pathogens, this paper gives recommendations for prevention and infection control measures as well as proposals for various target groups to tackle the threats posed by Gram-negative bacteria and prevent the spread and emergence of new antibiotic resistances.
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Affiliation(s)
- Martin Exner
- Institute of Hygiene and Public Health, Bonn University, Bonn, Germany
| | | | - Bärbel Christiansen
- Department of Internal Hygiene, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Jürgen Gebel
- Institute of Hygiene and Public Health, Bonn University, Bonn, Germany
| | | | - Philippe Hartemann
- Departement Environnement et Santé Publique S.E.R.E.S., Faculté de Médecine, Nancy, France
| | - Peter Heeg
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany
| | - Carola Ilschner
- Institute of Hygiene and Public Health, Bonn University, Bonn, Germany
| | - Axel Kramer
- Institute of Hygiene and Environmental Medicine, University Medicine Greifswald, Germany
| | - Elaine Larson
- School of Nursing, Columbia University, New York, USA.,Mailman School of Public Health, Columbia University, New York, USA
| | | | | | | | - Birgit Ross
- Hospital Hygiene, Essen University Hospital, Essen, Germany
| | | | | | - Hans-Günther Sonntag
- Institute of Hygiene and Medical Microbiology, University of Heidelberg, Germany
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17
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Wang HY, Yoo G, Kim J, Uh Y, Song W, Kim JB, Lee H. Development of a Rapid Reverse Blot Hybridization Assay for Detection of Clinically Relevant Antibiotic Resistance Genes in Blood Cultures Testing Positive for Gram-Negative Bacteria. Front Microbiol 2017; 8:185. [PMID: 28232823 PMCID: PMC5299004 DOI: 10.3389/fmicb.2017.00185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/25/2017] [Indexed: 01/11/2023] Open
Abstract
Rapid and accurate identification of the causative pathogens of bloodstream infections is crucial for the prompt initiation of appropriate antimicrobial therapy to decrease the related morbidity and mortality rates. The aim of this study was to evaluate the performance of a newly developed PCR-reverse blot hybridization assay (REBA) for the rapid detection of Gram-negative bacteria (GNB) and their extended-spectrum β-lactamase (ESBL), AmpC β-lactamase, and carbapenemase resistance genes directly from the blood culture bottles. The REBA-EAC (ESBL, AmpC β-lactamase, carbapenemase) assay was performed on 327 isolates that were confirmed to have an ESBL producer phenotype, 200 positive blood culture (PBCs) specimens, and 200 negative blood culture specimens. The concordance rate between the results of REBA-EAC assay and ESBL phenotypic test was 94.2%. The sensitivity, specificity, positive predictive value, and negative predictive value of the REBA-EAC assay for GNB identification in blood culture specimens were 100% (95% CI 0.938–1.000, P < 0.001), 100% (95% CI 0.986–1.000, P < 0.001), 100% (95% CI 0.938–1.000, P < 0.001), and 100% (95% CI 0.986–1.000, P < 0.001), respectively. All 17 EAC-producing GNB isolates from the 73 PBCs were detected by the REBA-EAC assay. The REBA-EAC assay allowed easy differentiation between EAC and non-EAC genes in all isolates. Moreover, the REBA-EAC assay was a rapid and reliable method for identifying GNB and their β-lactamase resistance genes in PBCs. Thus, this assay may provide essential information for accelerating therapeutic decisions to achieve earlier appropriate antibiotic treatment during the acute phase of bloodstream infection.
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Affiliation(s)
- Hye-Young Wang
- Optipharm M&D, Inc., Wonju Eco Environmental Technology Center Wonju, Gangwon, South Korea
| | - Gilsung Yoo
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine Wonju, South Korea
| | - Juwon Kim
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine Wonju, South Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine Wonju, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine Seoul, South Korea
| | - Jong Bae Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University Wonju, South Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University Wonju, South Korea
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Decousser JW, Poirel L, Nordmann P. Recent advances in biochemical and molecular diagnostics for the rapid detection of antibiotic-resistant Enterobacteriaceae: a focus on ß-lactam resistance. Expert Rev Mol Diagn 2017; 17:327-350. [DOI: 10.1080/14737159.2017.1289087] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jean-Winoc Decousser
- Department of Virology, Bacteriology - Infection Control, Parasitology - Mycology, Assistance Publique - Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
- IAME, UMR 1137, INSERM, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
- Institute for Microbiology, University of Lausanne and University hospital Center, Lausanne, Switzerland
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19
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Zhang L, Wang J, Liu F, Xiong Y, Liu Z, Jiang D, Li Y, Tu D, Wang Y, Pu X. Rapid detection of blaNDM-1 in multidrug-resistant organisms using a novel electrochemical biosensor. RSC Adv 2017. [DOI: 10.1039/c6ra27916c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The traditional detection methods of multidrug-resistant organisms (MDROs) are costly and comprise multiple steps. In this study, we successfully established a fast electrochemical method for blaNDM-1 in MDROs based on the LNA probes.
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Cortegiani A, Russotto V, Graziano G, Geraci D, Saporito L, Cocorullo G, Raineri SM, Mammina C, Giarratano A. Use of Cepheid Xpert Carba-R® for Rapid Detection of Carbapenemase-Producing Bacteria in Abdominal Septic Patients Admitted to Intensive Care Unit. PLoS One 2016; 11:e0160643. [PMID: 27490684 PMCID: PMC4973873 DOI: 10.1371/journal.pone.0160643] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/24/2016] [Indexed: 01/22/2023] Open
Abstract
Early institution of effective antibiotic therapy and source control are pivotal to improve survival of abdominal septic patients. Xpert® Carba-R is a real time polymerase chain reaction assay for rapid detection and differentiation of five genes (blaKPC, blaVIM, blaOXA-48, blaIMP-1, blaNDM) responsible for carbapenem resistance. We performed an observational study investigating the clinical usefulness and applicability of Xpert® Carba-R to detect carbapenem resistance in abdominal septic patients admitted to intensive care unit. We compared the results of Xpert® Carba-R with standard microbiological culture. We collected a set of two rectal/stomia swabs and two swabs from abdominal drainage fluid for each patient. We included 20 patients for a total of 45 comparisons between the two methods. In our clinical setting, the overall performance of Xpert® Carba-R for detection of carbapenem resistance in the presence of genes detectable and non-detectable by the method was: sensitivity 50% (95% CI 24.6-75.3); specificity 93.1% (95% CI 77.2-99.1); positive predictive value (PPV) 80% (95% CI 44.4-97.5); negative predictive value (NPV) 77.1% (95% CI 56.9-89.6). The inter-rater agreement was 0.47 (SE 0.14; 95% CI 0.20-0.74). When considering the only 5 mechanisms of resistance detected by both methods, the overall diagnostic performance was: sensitivity 100% (95% CI 69.1-100), specificity 94.2 (95% CI 80.8-99.3), PPV 83.3 (95% CI 59.6-97.9) and NPV 100% (95% CI 89.4-100). The inter-rater agreement was 0.88 (SE 0.08; 95% CI 0.71-1). Xpert® Carba-R may be considered an additional diagnostic tool for early diagnosis of carbapenem resistance in abdominal septic patients. Clinicians should be aware of their epidemiology before its introduction in the diagnostic protocol of their intensive care units.
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Affiliation(s)
- Andrea Cortegiani
- Department of Biopathology and Medical Biotechnologies (DIBIMED), Section of Anesthesia, Analgesia, Intensive Care and Emergency, Policlinico P. Giaccone, University of Palermo, Via del Vespro 129, 90127, Palermo, Italy
| | - Vincenzo Russotto
- Department of Biopathology and Medical Biotechnologies (DIBIMED), Section of Anesthesia, Analgesia, Intensive Care and Emergency, Policlinico P. Giaccone, University of Palermo, Via del Vespro 129, 90127, Palermo, Italy
| | - Giorgio Graziano
- Department of Sciences for Health Promotion and Mother-Child Care, University of Palermo, Palermo, Italy
| | - Daniela Geraci
- Department of Sciences for Health Promotion and Mother-Child Care, University of Palermo, Palermo, Italy
| | - Laura Saporito
- Department of Sciences for Health Promotion and Mother-Child Care, University of Palermo, Palermo, Italy
| | - Gianfranco Cocorullo
- Department of General Surgery, Urgency and Organ Transplantation, University of Palermo, Italy
| | - Santi Maurizio Raineri
- Department of Biopathology and Medical Biotechnologies (DIBIMED), Section of Anesthesia, Analgesia, Intensive Care and Emergency, Policlinico P. Giaccone, University of Palermo, Via del Vespro 129, 90127, Palermo, Italy
| | - Caterina Mammina
- Department of Sciences for Health Promotion and Mother-Child Care, University of Palermo, Palermo, Italy
| | - Antonino Giarratano
- Department of Biopathology and Medical Biotechnologies (DIBIMED), Section of Anesthesia, Analgesia, Intensive Care and Emergency, Policlinico P. Giaccone, University of Palermo, Via del Vespro 129, 90127, Palermo, Italy
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Palanisami A, Khan S, Erdem SS, Hasan T. Guiding Empiric Treatment for Serious Bacterial Infections via Point of Care [Formula: see text]-Lactamase Characterization. IEEE JOURNAL OF TRANSLATIONAL ENGINEERING IN HEALTH AND MEDICINE 2016; 4:2800410. [PMID: 27602307 PMCID: PMC5003167 DOI: 10.1109/jtehm.2016.2573305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/31/2016] [Accepted: 04/26/2016] [Indexed: 01/21/2023]
Abstract
Fever is one of the most common symptoms of illness in infants and represents a clinical challenge due to the potential for serious bacterial infection. As delayed treatment for these infections has been correlated with increased morbidity and mortality, broad-spectrum [Formula: see text]-lactam antibiotics are often prescribed while waiting for microbiological lab results (1-3 days). However, the spread of antibiotic resistance via the [Formula: see text]-lactamase enzyme, which can destroy [Formula: see text]-lactam antibiotics, has confounded this paradigm; empiric antibiotic regimens are increasingly unable to cover all potential bacterial pathogens, leaving some infants effectively untreated until the pathogen is characterized. This can lead to lifelong sequela or death. Here, we introduce a fluorescent, microfluidic assay that can characterize [Formula: see text]-lactamase derived antibiotic susceptibility in 20 min with a sensitivity suitable for direct human specimens. The protocol is extensible, and the antibiotic spectrum investigated can be feasibly adapted for the pathogens of regional relevance. This new assay fills an important need by providing the clinician with hitherto unavailable point of care information for treatment guidance in an inexpensive and simple diagnostic format.
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Affiliation(s)
- Akilan Palanisami
- Wellman Center for PhotomedicineMassachusetts General HospitalBostonMA02114USA
| | - Shazia Khan
- Wellman Center for PhotomedicineMassachusetts General HospitalBostonMA02114USA
- Current Address: ElsevierCambridgeMA02139USA
| | - Sultan Sibel Erdem
- Wellman Center for PhotomedicineMassachusetts General HospitalBostonMA02114USA
- Current Address: International School of Medicine and Regenerative and Restorative Medicine Research Centerİstanbul Medipol UniversityIstanbul34810Turkey
| | - Tayyaba Hasan
- Wellman Center for PhotomedicineMassachusetts General HospitalBostonMA02114USA
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Pitt WG, Alizadeh M, Husseini GA, McClellan DS, Buchanan CM, Bledsoe CG, Robison RA, Blanco R, Roeder BL, Melville M, Hunter AK. Rapid separation of bacteria from blood-review and outlook. Biotechnol Prog 2016; 32:823-39. [PMID: 27160415 DOI: 10.1002/btpr.2299] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/03/2016] [Indexed: 12/11/2022]
Abstract
The high morbidity and mortality rate of bloodstream infections involving antibiotic-resistant bacteria necessitate a rapid identification of the infectious organism and its resistance profile. Traditional methods based on culturing the blood typically require at least 24 h, and genetic amplification by PCR in the presence of blood components has been problematic. The rapid separation of bacteria from blood would facilitate their genetic identification by PCR or other methods so that the proper antibiotic regimen can quickly be selected for the septic patient. Microfluidic systems that separate bacteria from whole blood have been developed, but these are designed to process only microliter quantities of whole blood or only highly diluted blood. However, symptoms of clinical blood infections can be manifest with bacterial burdens perhaps as low as 10 CFU/mL, and thus milliliter quantities of blood must be processed to collect enough bacteria for reliable genetic analysis. This review considers the advantages and shortcomings of various methods to separate bacteria from blood, with emphasis on techniques that can be done in less than 10 min on milliliter-quantities of whole blood. These techniques include filtration, screening, centrifugation, sedimentation, hydrodynamic focusing, chemical capture on surfaces or beads, field-flow fractionation, and dielectrophoresis. Techniques with the most promise include screening, sedimentation, and magnetic bead capture, as they allow large quantities of blood to be processed quickly. Some microfluidic techniques can be scaled up. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:823-839, 2016.
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Affiliation(s)
- William G Pitt
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Mahsa Alizadeh
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Ghaleb A Husseini
- Dept. of Chemical Engineering, American University of Sharjah, Sharjah, UAE
| | | | - Clara M Buchanan
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Colin G Bledsoe
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Richard A Robison
- Dept. of Microbiology and Molecular Biology, Brigham Young University, Provo, UT
| | - Rae Blanco
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | | | - Madison Melville
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Alex K Hunter
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
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Giuffrè M, Geraci DM, Bonura C, Saporito L, Graziano G, Insinga V, Aleo A, Vecchio D, Mammina C. The Increasing Challenge of Multidrug-Resistant Gram-Negative Bacilli: Results of a 5-Year Active Surveillance Program in a Neonatal Intensive Care Unit. Medicine (Baltimore) 2016; 95:e3016. [PMID: 26962817 PMCID: PMC4998898 DOI: 10.1097/md.0000000000003016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Colonization and infection by multidrug-resistant gram-negative bacilli (MDR GNB) in neonatal intensive care units (NICUs) are increasingly reported.We conducted a 5-year prospective cohort surveillance study in a tertiary NICU of the hospital "Paolo Giaccone," Palermo, Italy. Our objectives were to describe incidence and trends of MDR GNB colonization and the characteristics of the most prevalent organisms and to identify the risk factors for colonization. Demographic, clinical, and microbiological data were prospectively collected. Active surveillance cultures (ASCs) were obtained weekly. Clusters of colonization by extended spectrum β-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae were analyzed by conventional and molecular epidemiological tools.During the study period, 1152 infants were enrolled in the study. Prevalences of colonization by MDR GNB, ESBL-producing GNB and multiple species/genera averaged, respectively, 28.8%, 11.7%, and 3.7%. Prevalence and incidence density of colonization by MDR GNB and ESBL-producing GNB showed an upward trend through the surveillance period. Rates of ESBL-producing E coli and K pneumoniae colonization showed wide fluctuations peaking over the last 2 years. The only independent variables associated with colonization by MDR GNB and ESBL-producing organisms and multiple colonization were, respectively, the days of NICU stay (odds ratio [OR] 1.041), the days of exposure to ampicillin-sulbactam (OR 1.040), and the days of formula feeding (OR 1.031). Most clusters of E coli and K pneumoniae colonization were associated with different lineages. Ten out of 12 clusters had an outborn infant as their index case.Our study confirms that MDR GNB are an increasing challenge to NICUs. The universal once-a-week approach allowed us to understand the epidemiology of MDR GNB, to timely detect new clones and institute contact precautions, and to assess risk factors. Collection of these data can be an important tool to optimize antimicrobials use and control the emergence and dissemination of resistances in NICU.
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Affiliation(s)
- Mario Giuffrè
- From the Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo, Palermo, Italy; the Azienda Ospedaliera-Universitaria Policlinico "Paolo Giaccone" (MG, CB, VI, CM), Palermo, Italy; Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro" (DMG, AA), University of Palermo, Palermo, Italy; Post-Graduate Residency School in Hygiene and Preventive Medicine (LS, GG), University of Palermo, Palermo, Italy; Post-Graduate Residency School in Pediatrics (DV), University of Palermo, Palermo, Italy
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Li J, Zrazhevskiy P, Gao X. Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:1035-1043. [PMID: 26749053 PMCID: PMC4815929 DOI: 10.1002/smll.201503101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/30/2015] [Indexed: 05/21/2023]
Abstract
Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes.
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Affiliation(s)
- Junwei Li
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Pavel Zrazhevskiy
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
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Evaluation of the Check-Points Check MDR CT103 and CT103 XL Microarray Kits by Use of Preparatory Rapid Cell Lysis. J Clin Microbiol 2016; 54:1368-71. [PMID: 26888905 DOI: 10.1128/jcm.03302-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/09/2016] [Indexed: 12/22/2022] Open
Abstract
Using a rapid bacterial lysis method, the Check MDR CT103 and CT103 XL microarrays demonstrated accuracies of 98.1% and 94.2%, respectively, for detection of known resistance genes in 108 multidrug-resistant Gram-negative bacilli. In 45 isolates, 49 previously unrecognized extended-spectrum β-lactamase or plasmid AmpC targets were detected and confirmed by conventional PCR.
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26
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Luo J, Wang J, Mathew AS, Yau ST. Ultrasensitive Detection of Shigella Species in Blood and Stool. Anal Chem 2016; 88:2010-4. [PMID: 26879365 DOI: 10.1021/acs.analchem.5b04242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A modified immunosensing system with voltage-controlled signal amplification was used to detect Shigella in stool and blood matrixes at the single-digit CFU level. Inactivated Shigella was spiked in these matrixes and detected directly. The detection was completed in 78 min. Detection limits of 21 CFU/mL and 18 CFU/mL were achieved in stool and blood, respectively, corresponding to 2-7 CFUs immobilized on the detecting electrode. The outcome of the detection of extremely low bacterium concentration, i.e., below 100 CFU/mL, blood samples show a random nature. An analysis of the detection probabilities indicates the correlation between the sample volume and the success of detection and suggests that sample volume is critical for ultrasensitive detection of bacteria. The calculated detection limit is qualitatively in agreement with the empirically determined detection limit. The demonstrated ultrasensitive detection of Shigella on the single-digit CFU level suggests the feasibility of the direct detection of the bacterium in the samples without performing a culture.
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Affiliation(s)
- Jieling Luo
- Department of Electrical and Computer Engineering, Cleveland State University , Cleveland, Ohio 44115, United States
| | - Jiapeng Wang
- Department of Electrical and Computer Engineering, Cleveland State University , Cleveland, Ohio 44115, United States
| | - Anup S Mathew
- Department of Electrical and Computer Engineering, Cleveland State University , Cleveland, Ohio 44115, United States
| | - Siu-Tung Yau
- Department of Electrical and Computer Engineering, Cleveland State University , Cleveland, Ohio 44115, United States.,The Applied Bioengineering Program, Cleveland State University , Cleveland, Ohio 44115, United States
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Zhou J, Li G, Ma X, Yang Q, Yi J. Outbreak of colonization by carbapenemase-producing Klebsiella pneumoniae in a neonatal intensive care unit: Investigation, control measures and assessment. Am J Infect Control 2015; 43:1122-4. [PMID: 26149749 DOI: 10.1016/j.ajic.2015.05.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 05/24/2015] [Accepted: 05/27/2015] [Indexed: 10/23/2022]
Abstract
We describe an outbreak of carbapenemase-producing Klebsiella pneumoniae in a neonatal intensive care unit and assess the effect of infection control measures. Our assessment indicates that active surveillance culture is very useful in identifying multidrug-resistant organisms and its prevention from transmission. Besides contact precaution, environment disinfection, good compliance of hand hygiene, and single-room isolation is very important for preventing transmission of carbapenemase-producing K pneumoniae isolates.
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Pfaller MA, Castanheira M. Nosocomial Candidiasis: Antifungal Stewardship and the Importance of Rapid Diagnosis. Med Mycol 2015; 54:1-22. [PMID: 26385381 DOI: 10.1093/mmy/myv076] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/20/2015] [Indexed: 01/12/2023] Open
Abstract
Candidemia and other forms of candidiasis are associated with considerable excess mortality and costs. Despite the addition of several new antifungal agents with improved spectrum and potency, the frequency of Candida infection and associated mortality have not decreased in the past two decades. The lack of rapid and sensitive diagnostic tests has led to considerable overuse of antifungal agents resulting in increased costs, selection pressure for resistance, unnecessary drug toxicity, and adverse drug interactions. Both the lack of timely diagnostic tests and emergence of antifungal resistance pose considerable problems for antifungal stewardship. Whereas antifungal stewardship with a focus on nosocomial candidiasis should be able to improve the administration of antifungal therapy in terms of drug selection, proper dose and duration, source control and de-escalation therapy, an important parameter, timeliness of antifungal therapy, remains a victim of slow and insensitive diagnostic tests. Fortunately, new proteomic and molecular diagnostic tools are improving the time to species identification and detection. In this review we will describe the potential impact that rapid diagnostic testing and antifungal stewardship can have on the management of nosocomial candidiasis.
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Affiliation(s)
- Michael A Pfaller
- T2Biosystems, Lexington, Massachusetts JMI Laboratories, North Liberty, Iowa University of Iowa College of Medicine College of Public Health, Iowa City, Iowa
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Chavada R, Maley M. Evaluation of a Commercial Multiplex PCR for Rapid Detection of Multi Drug Resistant Gram Negative Infections. Open Microbiol J 2015; 9:125-35. [PMID: 26464612 PMCID: PMC4598387 DOI: 10.2174/1874285801509010125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 11/22/2022] Open
Abstract
Introduction: Community and healthcare associated infections caused by multi-drug resistant gram negative organisms (MDR GN) represent a worldwide threat. Nucleic Acid Detection tests are becoming more common for their detection; however they can be expensive requiring specialised equipment and local expertise. This study was done to evaluate the utility of a commercial multiplex tandem (MT) PCR for detection of MDR GN. Methods: The study was done on stored laboratory MDR GN isolates from sterile and non-sterile specimens (n=126, out of stored 567 organisms). Laboratory validation of the MT PCR was done to evaluate sensitivity, specificity and agreement with the current phenotypic methods used in the laboratory. Amplicon sequencing was also done on selected isolates for assessing performance characteristics. Workflow and cost implications of the MT PCR were evaluated. Results: The sensitivity and specificity of the MT PCR were calculated to be 95% and 96.7% respectively. Agreement with the phenotypic methods was 80%. Major lack of agreement was seen in detection of AmpC beta lactamase in enterobacteriaceae and carbapenemase in non-fermenters. Agreement of the MT PCR with another multiplex PCR was found to be 87%. Amplicon sequencing confirmed the genotype detected by MT PCR in 94.2 % of cases tested. Time to result was faster for the MT PCR but cost per test was higher. Conclusion: This study shows that with carefully chosen targets for detection of resistance genes in MDR GN, rapid and efficient identification is possible. MT PCR was sensitive and specific and likely more accurate than phenotypic methods.
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Affiliation(s)
- Ruchir Chavada
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services(SSWPS), Corner Goulburn and Forbes Street, Liverpool Hospital, Liverpool, NSW-2170, Sydney, Australia
| | - Michael Maley
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services(SSWPS), Corner Goulburn and Forbes Street, Liverpool Hospital, Liverpool, NSW-2170, Sydney, Australia
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Application of Culture-Independent Rapid Diagnostic Tests in the Management of Invasive Candidiasis and Cryptococcosis. J Fungi (Basel) 2015; 1:217-251. [PMID: 29376910 PMCID: PMC5753112 DOI: 10.3390/jof1020217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 12/26/2022] Open
Abstract
The diagnosis of invasive candidiasis (IC) and cryptococcosis is often complicated by slow and insensitive culture-based methods. Such delay results in poor outcomes due to the lack of timely therapeutic interventions. Advances in serological, biochemical, molecular and proteomic approaches have made a favorable impact on this process, improving the timeliness and accuracy of diagnosis with resultant improvements in outcome. This paper will serve as an overview of recent developments in the diagnostic approaches to infections due to these important yeast-fungi.
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Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data. PLoS One 2015. [PMID: 26197475 PMCID: PMC4510569 DOI: 10.1371/journal.pone.0133492] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. Results Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR’s application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. Conclusions We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.
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Bilir SP, Ferrufino CP, Pfaller MA, Munakata J. The economic impact of rapid Candida species identification by T2Candida among high-risk patients. Future Microbiol 2015; 10:1133-44. [DOI: 10.2217/fmb.15.29] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT Introduction: This study estimates the cost–effectiveness and hospital budget impact of rapid candidemia identification using T2Candida, a novel diagnostic panel with same-day species-specific results. Materials & Methods: A 1-year decision-tree model estimates hospital costs (2013 US$) and effects (candidemia-related deaths) for faster diagnostics versus blood culture (BC), accounting for disease prevalence, distribution of Candida species, test characteristics (sensitivity/specificity/time to result), antifungal medication and differential length-of-stay and mortality by appropriate treatment timing. Results: The model estimates a hospital with 5100 annual high-risk patients could possibly save $5,858,448 with T2Candida versus BC, a 47.6% decrease in candidemia diagnosis and treatment budget ($1149/patient tested), while averting 60.6% of candidemia-related mortality. Conclusion: Hospitals may observe lower candidemia-related inpatient costs and mortality with rapid Candida diagnosis.
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Affiliation(s)
- Sara Pinar Bilir
- Health Economics & Outcomes Research, 425 Market Street, 7th Floor, IMS Health, San Francisco, CA 94105, USA
| | - Cheryl P Ferrufino
- Health Economics & Outcomes Research, 425 Market Street, 7th Floor, IMS Health, San Francisco, CA 94105, USA
| | - Michael A Pfaller
- T2Biosystems, 101 Hartwell Ave, Lexington, MA 02421, USA
- University of Iowa College of Medicine & College of Public Health, Iowa City, IA 52242, USA
| | - Julie Munakata
- Health Economics & Outcomes Research, 425 Market Street, 7th Floor, IMS Health, San Francisco, CA 94105, USA
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34
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Kim YA, Lee K. Active Surveillance of Multidrug-Resistant Organisms with Rapid Detection Methods for Infection Control. ANNALS OF CLINICAL MICROBIOLOGY 2015. [DOI: 10.5145/acm.2015.18.4.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Young Ah Kim
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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Mthethwa NS, Oyedeji BAO, Obi LC, Aiyegoro OA. Anti-staphylococcal, anti-HIV and cytotoxicity studies of four South African medicinal plants and isolation of bioactive compounds from Cassine transvaalensis (Burtt. Davy) codd. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 14:512. [PMID: 25522685 PMCID: PMC4320432 DOI: 10.1186/1472-6882-14-512] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 12/02/2014] [Indexed: 11/17/2022]
Abstract
Background Medicinal plants represent an important opportunity to rural communities in Africa, as a source of affordable medicine and as a source of income. Increased patient awareness about safe usage is important as well as more training with regards to traditional medicine. The aim of this study was to evaluate the ethnomedicinal prowess of some indigenous South African plants commonly used in Eastern Cape Province of South Africa for the treatment of skin and respiratory tract infections, HIV and their toxicity potential. Methods Cassine transvaalensis, Vangueria infausta, Croton gratissimus and Vitex ferruginea were tested for antibacterial activities against Staphylococcus aureus and Staphylococcus epidermidis using Kirby-Bauer disk diffusion and minimum inhibition concentration (MIC). Cytotoxic and anti-HIV-1 activities of plants were tested using MTT Assay (3- (Dimethylthiozole-2-yl-2,5-diphenyltetrazolium bromide)) and anti- HIV-1iib assay. In search of bioactive lead compounds, Cassine transvaalensis which was found to be the most active plant extract against the two Staphylocoous bacteria was subjected to various chromatographic. Thin layer chromatography, Column chromatography and Nuclear Magnetic Resonance (NMR), (1H-1H, 13C-13C, in DMSO_d6, Bruker 600 MHz) were used to isolate and characterize 3-Oxo-28-hydroxylbetuli-20(29)-ene and 3,28-dihydroxylbetuli-20(29)-ene bioactive compounds from C. transvaalensis. Results The four plants studied exhibited bioactive properties against the test isolates. The zones of inhibition ranged between 16 mm to 31 mm for multi-drug resistant staphylococci species. MIC values varied between 0.6 and 0.02 μg/ml. C. gratissimus and C. transvaalensis exhibited the abilities to inhibit HIV-1iib. Two bioactive compounds were isolated from C. transvaalensis. Conclusion Data from this study reveals the use of these plant by traditional healers in the Eastern Cape. Furthermore, C. transvaalensis and C. gratissimus were found to be more active as against HIV-1iib. While C. transvaalensis was most active against the two Staphylococcus bacteria.
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Alós JI. [Antibiotic resistance: A global crisis]. Enferm Infecc Microbiol Clin 2014; 33:692-9. [PMID: 25475657 DOI: 10.1016/j.eimc.2014.10.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/06/2014] [Accepted: 10/17/2014] [Indexed: 12/31/2022]
Abstract
The introduction of antibiotics into clinical practice represented one of the most important interventions for the control of infectious diseases. Antibiotics have saved millions of lives and have also brought a revolution in medicine. However, an increasing threat has deteriorated the effectiveness of these drugs, that of bacterial resistance to antibiotics, which is defined here as the ability of bacteria to survive in antibiotic concentrations that inhibit/kill others of the same species. In this review some recent and important examples of resistance in pathogens of concern for mankind are mentioned. It is explained, according to present knowledge, the process that led to the current situation in a short time, evolutionarily speaking. It begins with the resistance genes, continues with clones and genetic elements involved in the maintenance and dissemination, and ends with other factors that contribute to its spread. Possible responses to the problem are also reviewed, with special reference to the development of new antibiotics.
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Affiliation(s)
- Juan-Ignacio Alós
- Servicio de Microbiología, Hospital Universitario de Getafe, Getafe, Madrid, España; Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Villaviciosa de Odón, Madrid, España.
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Strauss C, Endimiani A, Perreten V. A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria. J Microbiol Methods 2014; 108:25-30. [PMID: 25451460 DOI: 10.1016/j.mimet.2014.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/12/2014] [Accepted: 11/12/2014] [Indexed: 01/21/2023]
Abstract
A rapid and simple DNA labeling system has been developed for disposable microarrays and has been validated for the detection of 117 antibiotic resistance genes abundant in Gram-positive bacteria. The DNA was fragmented and amplified using phi-29 polymerase and random primers with linkers. Labeling and further amplification were then performed by classic PCR amplification using biotinylated primers specific for the linkers. The microarray developed by Perreten et al. (Perreten, V., Vorlet-Fawer, L., Slickers, P., Ehricht, R., Kuhnert, P., Frey, J., 2005. Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J.Clin.Microbiol. 43, 2291-2302.) was improved by additional oligonucleotides. A total of 244 oligonucleotides (26 to 37 nucleotide length and with similar melting temperatures) were spotted on the microarray, including genes conferring resistance to clinically important antibiotic classes like β-lactams, macrolides, aminoglycosides, glycopeptides and tetracyclines. Each antibiotic resistance gene is represented by at least 2 oligonucleotides designed from consensus sequences of gene families. The specificity of the oligonucleotides and the quality of the amplification and labeling were verified by analysis of a collection of 65 strains belonging to 24 species. Association between genotype and phenotype was verified for 6 antibiotics using 77 Staphylococcus strains belonging to different species and revealed 95% test specificity and a 93% predictive value of a positive test. The DNA labeling and amplification is independent of the species and of the target genes and could be used for different types of microarrays. This system has also the advantage to detect several genes within one bacterium at once, like in Staphylococcus aureus strain BM3318, in which up to 15 genes were detected. This new microarray-based detection system offers a large potential for applications in clinical diagnostic, basic research, food safety and surveillance programs for antimicrobial resistance.
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Affiliation(s)
- Christian Strauss
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility. Antimicrob Agents Chemother 2014; 59:427-36. [PMID: 25367914 DOI: 10.1128/aac.03954-14] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many clinical isolates of Pseudomonas aeruginosa cause infections that are difficult to eradicate due to their resistance to a wide variety of antibiotics. Key genetic determinants of resistance were identified through genome sequences of 390 clinical isolates of P. aeruginosa, obtained from diverse geographic locations collected between 2003 and 2012 and were related to microbiological susceptibility data for meropenem, levofloxacin, and amikacin. β-Lactamases and integron cassette arrangements were enriched in the established multidrug-resistant lineages of sequence types ST111 (predominantly O12) and ST235 (O11). This study demonstrates the utility of next-generation sequencing (NGS) in defining relevant resistance elements and highlights the diversity of resistance determinants within P. aeruginosa. This information is valuable in furthering the design of diagnostics and therapeutics for the treatment of P. aeruginosa infections.
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Macesic N, Morrissey CO, Cheng AC, Spencer A, Peleg AY. Changing microbial epidemiology in hematopoietic stem cell transplant recipients: increasing resistance over a 9-year period. Transpl Infect Dis 2014; 16:887-96. [PMID: 25298044 DOI: 10.1111/tid.12298] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 06/03/2014] [Accepted: 07/12/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Infections remain important contributors to mortality in hematopoietic stem cell transplantation (HSCT). METHOD We studied the evolving epidemiology and trends in susceptibility of bacterial and Candida isolates at an Australian HSCT center. A total of 528 HSCTs in 508 patients were performed from April 2001 to May 2010. A total of 605 isolates were eligible for study inclusion; 318 (53%) were gram-positive, 268 (44%) were gram-negative, and 19 (3%) were Candida species. RESULTS The most common site for isolates was blood (380 isolates, 63%). Staphylococcus aureus was the most common gram-positive organism (n = 107, 34%), but trends to increasing coagulase-negative staphylococci (P = 0.002) and vancomycin-resistant Enterococcus (P < 0.001) were observed. Escherichia coli was the most common gram-negative isolate (n = 74, 28%). Fluoroquinolone resistance increased with widespread use of protocol fluoroquinolone prophylaxis (P = 0.001). Carbapenem resistance was found in 44% of Pseudomonas or Acinetobacter isolates. Bloodstream infection with a multidrug-resistant organism (odds ratio 3.61, 95% confidence interval: 1.40-9.32, P = 0.008) was an independent predictor of mortality at 7 days after a positive blood culture. CONCLUSIONS Antimicrobial resistance is an increasing problem in this vulnerable patient population, and not only has an impact on choice of empiric therapy for febrile neutropenia but also on mortality.
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Affiliation(s)
- N Macesic
- Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia
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Lowman W, Marais M, Ahmed K, Marcus L. Routine active surveillance for carbapenemase-producing Enterobacteriaceae from rectal swabs: diagnostic implications of multiplex polymerase chain reaction. J Hosp Infect 2014; 88:66-71. [DOI: 10.1016/j.jhin.2014.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/27/2014] [Indexed: 11/29/2022]
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Kafshgari MH, Cavallaro A, Delalat B, Harding FJ, McInnes SJP, Mäkilä E, Salonen J, Vasilev K, Voelcker NH. Nitric oxide-releasing porous silicon nanoparticles. NANOSCALE RESEARCH LETTERS 2014; 9:333. [PMID: 25114633 PMCID: PMC4109794 DOI: 10.1186/1556-276x-9-333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/24/2014] [Indexed: 05/28/2023]
Abstract
In this study, the ability of porous silicon nanoparticles (PSi NPs) to entrap and deliver nitric oxide (NO) as an effective antibacterial agent is tested against different Gram-positive and Gram-negative bacteria. NO was entrapped inside PSi NPs functionalized by means of the thermal hydrocarbonization (THC) process. Subsequent reduction of nitrite in the presence of d-glucose led to the production of large NO payloads without reducing the biocompatibility of the PSi NPs with mammalian cells. The resulting PSi NPs demonstrated sustained release of NO and showed remarkable antibacterial efficiency and anti-biofilm-forming properties. These results will set the stage to develop antimicrobial nanoparticle formulations for applications in chronic wound treatment.
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Affiliation(s)
- Morteza Hasanzadeh Kafshgari
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology,
Mawson Institute, University of South Australia, GPO Box 2471 Adelaide, SA
5001, Australia
| | - Alex Cavallaro
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology,
Mawson Institute, University of South Australia, GPO Box 2471 Adelaide, SA
5001, Australia
| | - Bahman Delalat
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology,
Mawson Institute, University of South Australia, GPO Box 2471 Adelaide, SA
5001, Australia
| | - Frances J Harding
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology,
Mawson Institute, University of South Australia, GPO Box 2471 Adelaide, SA
5001, Australia
| | - Steven JP McInnes
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology,
Mawson Institute, University of South Australia, GPO Box 2471 Adelaide, SA
5001, Australia
| | - Ermei Mäkilä
- Department of Physics and Astronomy, University of Turku, Turku FI-20014,
Finland
| | - Jarno Salonen
- Department of Physics and Astronomy, University of Turku, Turku FI-20014,
Finland
| | - Krasimir Vasilev
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology,
Mawson Institute, University of South Australia, GPO Box 2471 Adelaide, SA
5001, Australia
| | - Nicolas H Voelcker
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology,
Mawson Institute, University of South Australia, GPO Box 2471 Adelaide, SA
5001, Australia
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Tuite N, Reddington K, Barry T, Zumla A, Enne V. Rapid nucleic acid diagnostics for the detection of antimicrobial resistance in Gram-negative bacteria: is it time for a paradigm shift? J Antimicrob Chemother 2014; 69:1729-33. [PMID: 24677160 DOI: 10.1093/jac/dku083] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A key component for tackling the ever more serious antimicrobial resistance problem in Gram-negative bacteria is the introduction of rapid nucleic acid diagnostics. Successful incorporation of new diagnostic technologies has the potential benefit of improving not only patient treatment but also infection control and antimicrobial stewardship. However, there are still many hurdles to overcome, such as the complexity of resistance mechanisms in Gram-negative bacteria, the discrepancy between phenotype and genotype and the difficulty in distinguishing pathogens from background commensals. A small number of manufacturers have introduced tests to the market that concentrate partly or specifically on resistance determinants in Gram-negative bacteria. These are currently predominantly based on different types of PCR technology. The development of new technologies, such as whole-genome sequencing and the combination of MALDI-TOF with PCR, holds much promise for the introduction of improved diagnostics for the future.
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Affiliation(s)
- Nina Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Alimuddin Zumla
- Department for Clinical Microbiology, 2nd Floor Royal Free Hospital, University College London, Rowland Hill St., London NW3 2PF, UK
| | - Virve Enne
- Department for Clinical Microbiology, 2nd Floor Royal Free Hospital, University College London, Rowland Hill St., London NW3 2PF, UK
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Low N, Unemo M, Skov Jensen J, Breuer J, Stephenson JM. Molecular diagnostics for gonorrhoea: implications for antimicrobial resistance and the threat of untreatable gonorrhoea. PLoS Med 2014; 11:e1001598. [PMID: 24503544 PMCID: PMC3913554 DOI: 10.1371/journal.pmed.1001598] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
This Essay from Nicola Low and colleagues discusses the importance of the nucleic acid amplification tests for rapid detection of N. gonorrhoeae and its resistance determinants, as well as the importance of ensuring their rational use, as priorities for controlling both gonorrhoea and antimicrobial resistance. Please see later in the article for the Editors' Summary
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Affiliation(s)
- Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Örebro University Hospital, Örebro, Sweden
| | - Jørgen Skov Jensen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Judith Breuer
- MRC-UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
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Leung GH, Gray TJ, Cheong EY, Haertsch P, Gottlieb T. Persistence of related bla-IMP-4 metallo-beta-lactamase producing Enterobacteriaceae from clinical and environmental specimens within a burns unit in Australia - a six-year retrospective study. Antimicrob Resist Infect Control 2013; 2:35. [PMID: 24345195 PMCID: PMC3878348 DOI: 10.1186/2047-2994-2-35] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/07/2013] [Indexed: 11/25/2022] Open
Abstract
Background To describe the clinical epidemiology, environmental surveillance and infection control interventions undertaken in a six-year persistence of bla-IMP-4 metallo-beta-lactamase (MBL) producing Enterobacteriaceae within a separately confined hospital burns unit in a tertiary hospital in Sydney, Australia. Methods MBL positive clinical and environmental isolates were collected from the Burns Unit, from the first detection of isolates in September 2006 to August 2012. Unit-acquired clinical isolates were included, and patient outcomes analyzed amongst those who acquired clinically significant infections. Environmental isolates were analyzed with regard to relationship to clinical isolates, bacterial species, and persistence despite cleaning efforts. Results Thirty clinical isolates detected from 23 patients were identified. Clinically significant infection developed in 7 (30%) patients – 2 bacteremias, 2 central venous catheter tip infections without bacteremia, and 3 wound infections. All patients survived at 30 days. Seventy-one environmental isolates were confirmed to be MBL-positive, with 85% sourced from shower facilities or equipment. MBL organisms persisted at these sites despite both usual hospital cleaning, and following targeted environmental disinfection interventions. Conclusions Clear association exists between environmental Burns Unit contamination by MBLs and subsequent patient colonization. Clinical infection occurred in a small proportion of patients colonized by MBLs, and with generally favorable outcomes. Its persistence in the Burns Unit environment, despite concerted infection control measures, pose concern for ongoing clinical transmission.
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Affiliation(s)
| | | | | | | | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Sydney Local Health District Concord Hospital Human Research Ethics Committee, Hospital Rd, Concord, Sydney, NSW 2139, Australia.
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Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, Vlieghe E, Hara GL, Gould IM, Goossens H, Greko C, So AD, Bigdeli M, Tomson G, Woodhouse W, Ombaka E, Peralta AQ, Qamar FN, Mir F, Kariuki S, Bhutta ZA, Coates A, Bergstrom R, Wright GD, Brown ED, Cars O. Antibiotic resistance-the need for global solutions. THE LANCET. INFECTIOUS DISEASES 2013; 13:1057-98. [PMID: 24252483 DOI: 10.1016/s1473-3099(13)70318-9] [Citation(s) in RCA: 2558] [Impact Index Per Article: 232.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The causes of antibiotic resistance are complex and include human behaviour at many levels of society; the consequences affect everybody in the world. Similarities with climate change are evident. Many efforts have been made to describe the many different facets of antibiotic resistance and the interventions needed to meet the challenge. However, coordinated action is largely absent, especially at the political level, both nationally and internationally. Antibiotics paved the way for unprecedented medical and societal developments, and are today indispensible in all health systems. Achievements in modern medicine, such as major surgery, organ transplantation, treatment of preterm babies, and cancer chemotherapy, which we today take for granted, would not be possible without access to effective treatment for bacterial infections. Within just a few years, we might be faced with dire setbacks, medically, socially, and economically, unless real and unprecedented global coordinated actions are immediately taken. Here, we describe the global situation of antibiotic resistance, its major causes and consequences, and identify key areas in which action is urgently needed.
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Affiliation(s)
- Ramanan Laxminarayan
- Center for Disease Dynamics, Economics and Policy, Washington, DC, USA; Princeton University, Princeton NJ, USA; Public Health Foundation of India, New Delhi, India
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Detection of colonization by carbapenemase-producing Gram-negative Bacilli in patients by use of the Xpert MDRO assay. J Clin Microbiol 2013; 51:3780-7. [PMID: 24006011 DOI: 10.1128/jcm.01092-13] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detecting colonization of patients with carbapenemase-producing bacteria can be difficult. This study compared the sensitivity and specificity of a PCR-based method (Xpert MDRO) for detecting blaKPC, blaNDM, and blaVIM carbapenem resistance genes using GeneXpert cartridges to the results of culture with and without a broth enrichment step on 328 rectal, perirectal, and stool samples. The culture method included direct inoculation of a MacConkey agar plate on which a 10-μg meropenem disk was placed and plating on MacConkey agar after overnight enrichment of the sample in MacConkey broth containing 1 μg/ml of meropenem. Forty-three (13.1%) samples were positive by PCR for blaKPC and 11 (3.4%) were positive for blaVIM; none were positive for blaNDM. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the PCR assay for blaKPC were 100%, 99.0%, 93.0%, and 100%, respectively, compared to broth enrichment culture and sequencing of target genes. The sensitivity, specificity, PPV, and NPV of the assay for blaVIM were 100%, 99.4%, 81.8%, and 100%, respectively. Since none of the clinical samples contained organisms with blaNDM, 66 contrived stool samples were prepared at various dilutions using three Klebsiella pneumoniae isolates containing blaNDM. The PCR assay showed 100% positivity at dilutions from 300 to 1,800 CFU/ml and 93.3% at 150 CFU/ml. The Xpert MDRO PCR assay required 2 min of hands-on time and 47 min to complete. Rapid identification of patients colonized with carbapenemase-producing organisms using multiplex PCR may help hospitals to improve infection control activities.
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