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Chatzimichail S, Turner P, Feehily C, Farrar A, Crook D, Andersson M, Oakley S, Barrett L, El Sayyed H, Kyropoulos J, Nellåker C, Stoesser N, Kapanidis AN. Rapid identification of bacterial isolates using microfluidic adaptive channels and multiplexed fluorescence microscopy. LAB ON A CHIP 2024; 24:4843-4858. [PMID: 39291847 PMCID: PMC11409657 DOI: 10.1039/d4lc00325j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 09/04/2024] [Indexed: 09/19/2024]
Abstract
We demonstrate the rapid capture, enrichment, and identification of bacterial pathogens using Adaptive Channel Bacterial Capture (ACBC) devices. Using controlled tuning of device backpressure in polydimethylsiloxane (PDMS) devices, we enable the controlled formation of capture regions capable of trapping bacteria from low cell density samples with near 100% capture efficiency. The technical demands to prepare such devices are much lower compared to conventional methods for bacterial trapping and can be achieved with simple benchtop fabrication methods. We demonstrate the capture and identification of seven species of bacteria with bacterial concentrations lower than 1000 cells per mL, including common Gram-negative and Gram-positive pathogens such as Escherichia coli and Staphylococcus aureus. We further demonstrate that species identification of the trapped bacteria can be undertaken in the order of one-hour using multiplexed 16S rRNA-FISH with identification accuracies of 70-98% with unsupervised classification methods across 7 species of bacteria. Finally, by using the bacterial capture capabilities of the ACBC chip with an ultra-rapid antimicrobial susceptibility testing method employing fluorescence imaging and convolutional neural network (CNN) classification, we demonstrate that we can use the ACBC chip as an imaging flow cytometer that can predict the antibiotic susceptibility of E. coli cells after identification.
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Affiliation(s)
- Stelios Chatzimichail
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Piers Turner
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Conor Feehily
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Alison Farrar
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Monique Andersson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Sarah Oakley
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lucinda Barrett
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Hafez El Sayyed
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jingwen Kyropoulos
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
| | - Christoffer Nellåker
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Big Data Institute, Oxford, OX3 7LF, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Achillefs N Kapanidis
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Fang X, Ding H, Chen Y, Wang Q, Yuan X, Zhang C, Huang J, Huang J, Lv J, Hu H, Huang C, Hu X, Lin Y, Zhang N, Zhou W, Huang Y, Li W, Niu S, Wu Z, Lin J, Yang B, Yuan T, Zhang W. Wireless Optogenetic Targeting Nociceptors Helps Host Cells Win the Competitive Colonization in Implant-Associated Infections. SMALL METHODS 2024:e2400216. [PMID: 39087367 DOI: 10.1002/smtd.202400216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/20/2024] [Indexed: 08/02/2024]
Abstract
The role of nociceptive nerves in modulating immune responses to harmful stimuli via pain or itch induction remains controversial. Compared to conventional surgery, various implant surgeries are more prone to infections even with low bacterial loads. In this study, an optogenetic technique is introduced for selectively activating peripheral nociceptive nerves using a fully implantable, wirelessly rechargeable optogenetic device. By targeting nociceptors in the limbs of awake, freely moving mice, it is found that activation induces anticipatory immunity in the innervated territory and enhances the adhesion of various host cells to the implant surface. This effect mediates acute immune cell-mediated killing of Staphylococcus aureus on implants and enables the host to win "implant surface competition" against Staphylococcus aureus. This finding provides new strategies for preventing and treating implant-associated infections.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Haiqi Ding
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Yang Chen
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Qijin Wang
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedics, Affiliated Mindong Hospital of Fujian Medical University, Fu'an, 355000, China
| | - Xuhui Yuan
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Chaofan Zhang
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Jiagu Huang
- Department of Orthopedic Surgery, Ningde municipal Hospital, Ningde, 352000, China
| | - Jiexin Huang
- Department of Orthopedic Surgery, Nanping First Hospital, Nanping, 353000, China
| | - Jianhua Lv
- Department of Orthopedic Surgery, Affiliated Hospital of Putian University, Putian, 351100, China
| | - Hongxin Hu
- Department of Orthopedic Surgery, Affiliated Hospital of Putian University, Putian, 351100, China
| | - Changyu Huang
- Department of Orthopedic Surgery, Quanzhou Orthopedic-traumatological Hospital, Quanzhou, 362000, China
| | - Xueni Hu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Yiming Lin
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Nanxin Zhang
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Wei Zhou
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Ying Huang
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Wenbo Li
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Susheng Niu
- Key Laboratory of Orthopedics & Traumatology of Traditional Chinese Medicine and Rehabilitation Ministry of Education, Fujian university of Traditional Chinese Medicine, Fuzhou, 350000, China
| | - Zhaoyang Wu
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Jianhua Lin
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Tifei Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Brain Health Institute, National Center for Mental Disorders, Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200000, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350000, China
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Tian PP, Su SS, Zhu LS, Wang T, Yang H, Du MY, Ding CZ, Wang L, Fan W, Yi HW. Short-term culture for rapid identification by mass spectrometry and automated antimicrobial susceptibility testing from positive bottles. BMC Infect Dis 2024; 24:566. [PMID: 38844852 PMCID: PMC11157804 DOI: 10.1186/s12879-024-09475-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Early and appropriate antibiotic treatment improves the clinical outcome of patients with sepsis. There is an urgent need for rapid identification (ID) and antimicrobial susceptibility testing (AST) of bacteria that cause bloodstream infection (BSI). Rapid ID and AST can be achieved by short-term incubation on solid medium of positive blood cultures using MALDI-TOF mass spectrometry (MS) and the BD M50 system. The purpose of this study is to evaluate the performance of rapid method compared to traditional method. METHODS A total of 124 mono-microbial samples were collected. Positive blood culture samples were short-term incubated on blood agar plates and chocolate agar plates for 5 ∼ 7 h, and the rapid ID and AST were achieved through Zybio EXS2000 MS and BD M50 System, respectively. RESULTS Compared with the traditional 24 h culture for ID, this rapid method can shorten the cultivation time to 5 ∼ 7 h. Accurate organism ID was achieved in 90.6% of Gram-positive bacteria (GP), 98.5% of Gram-negative bacteria (GN), and 100% of fungi. The AST resulted in the 98.5% essential agreement (EA) and 97.1% category agreements (CA) in NMIC-413, 99.4% EA and 98.9% CA in PMIC-92, 100% both EA and CA in SMIC-2. Besides, this method can be used for 67.2% (264/393) of culture bottles during routine work. The mean turn-around time (TAT) for obtaining final results by conventional method is approximately 72.6 ± 10.5 h, which is nearly 24 h longer than the rapid method. CONCLUSIONS The newly described method is expected to provide faster and reliable ID and AST results, making it an important tool for rapid management of blood cultures (BCs). In addition, this rapid method can be used to process most positive blood cultures, enabling patients to receive rapid and effective treatment.
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Affiliation(s)
- Peng-Peng Tian
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Shan-Shan Su
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Li-Sha Zhu
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Tian Wang
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Hui Yang
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Meng-Yao Du
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Cai-Zhi Ding
- Laboratory Department, The People's Hospital of Songzi, Jingzhou, Hubei, China
| | - Li Wang
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Wen Fan
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China.
| | - Hua-Wei Yi
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China.
- Hubei Provincial Clinical Research Center for Individualized Diagnosis and Treatment of Cancer, The First People's Hospital of Jingzhou, Jingzhou, Hubei, China.
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Demir M, Hazırolan G. Rapid Bacterial Identification from Positive Blood Cultures by MALDI-TOF MS Following Short-Term Incubation on Solid Media. INFECTIOUS DISEASES & CLINICAL MICROBIOLOGY 2024; 6:141-146. [PMID: 39005699 PMCID: PMC11243770 DOI: 10.36519/idcm.2024.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/08/2024] [Indexed: 07/16/2024]
Abstract
This study aimed to assess the performance of the MALDI-TOF MS short incubation method for bacterial identification at short-term incubation times to improve the reporting of blood cultures. MALDI-TOF MS analysis was conducted at intervals of 2, 4, and 6 hours during the development of microbial biomass on solid media until successful identification was achieved, with a final assessment at 24 hours for conventional identification. Species-level identification rates at the 2nd, 4th, 6th, and 24th hours were 57.5%, 83.6%, 93.1%, and 93.1% for Gram-negative bacilli; 12.5%, 42.7%, 76.1%, 97.8% for Gram-positive cocci and 0%, 11.8%, 17.6%, 58.8% for Gram-positive bacilli, respectively. The species-level identification rate was 76.5% for all monomicrobial cultures at the 6th hour. Our results have led us to implement this method into our routine laboratory workflow, and we have started to report rapid identification results for Gram-negative bacteria on the day of blood culture positivity.
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Affiliation(s)
- Mervenur Demir
- Department of Medical Microbiology, Hacettepe University School of Medicine, Ankara, Türkiye
| | - Gülşen Hazırolan
- Department of Medical Microbiology, Hacettepe University School of Medicine, Ankara, Türkiye
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Tsai YW, Zhang B, Chou HY, Chen HJ, Hsu YC, Shiue YL. Clinical impacts of the rapid diagnostic method on positive blood cultures. Lab Med 2024; 55:179-184. [PMID: 37352545 DOI: 10.1093/labmed/lmad057] [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] [Indexed: 06/25/2023] Open
Abstract
OBJECTIVE This study aimed to evaluate the impact of short-term incubation (STI) protocol on clinical outcomes of bloodstream infection (BSI) patients. METHODS A total of 1363 positive blood culture records from January 2019 to December 2021 were included. The main clinical outcomes included pathogen identification turnaround time (TAT), antimicrobial susceptibility testing (AST) TAT, and length of total hospital stay. RESULTS The TAT of pathogen identification and AST significantly decreased after implementing the STI protocol (2.2 vs 1.4 days and 3.4 vs 2.5 days, respectively, with P < .001 for both). Moreover, for patients with Gram-negative bacteria (GNB)-infected BSIs, the length of total hospital stay decreased from 31.9 days to 27.1 days, indicating that these patients could be discharged 5 days earlier after implementing the STI protocol (P < .01). CONCLUSION The protocol led to a significant reduction in TAT and improved clinical outcomes, particularly for GNB organisms. The findings suggest that the STI protocol can improve patient outcomes and hospital resource utilization in the management of BSIs.
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Affiliation(s)
- Ya-Wen Tsai
- Center for Integrative Medicine, Tainan City, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Bin Zhang
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, US
| | - Hsiu-Yin Chou
- Center for Integrative Medicine, Tainan City, Taiwan
| | - Hung-Jui Chen
- Division of Infectious Diseases, Department of Internal Medicine, Tainan City, Taiwan
| | - Yu-Chi Hsu
- Information Systems Office, Chi Mei Medical Center, Tainan City, Taiwan
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
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Tetteh FKM, Fatchu R, Ackah K, Philips TJ, Shewade HD, Fenny AP, Timire C, Edwards JK, Parbie EA. Sepsis among Neonates in a Ghanaian Tertiary Military Hospital: Culture Results and Turnaround Times. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11659. [PMID: 36141932 PMCID: PMC9517560 DOI: 10.3390/ijerph191811659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 06/16/2023]
Abstract
In this study, we described the bacterial profile, antibiotic resistance pattern, and laboratory result turnaround time (TAT) in neonates with suspected sepsis from a tertiary-level, military hospital in Accra, Ghana (2017-2020). This was a cross-sectional study using secondary data from electronic medical records. Of 471 neonates clinically diagnosed with suspected sepsis in whom blood samples were collected, the median TAT from culture request to report was three days for neonates who were culture-positive and five days for neonates who were culture-negative. There were 241 (51%) neonates discharged before the receipt of culture reports, and of them, 37 (15%) were culture-positive. Of 471 neonates, twenty-nine percent (n = 139) were bacteriologically confirmed, of whom 61% (n = 85) had late-onset sepsis. Gram-positive bacterial infection (89%, n = 124) was the most common cause of culture-positive neonatal sepsis. The most frequent Gram-positive pathogen was coagulase-negative Staphylococcus (55%, n = 68) followed by Staphylococcus aureus (36%, n = 45), of which one in two were multidrug resistant. The reasons for large numbers being discharged before the receipt of culture reports need to be further explored. There is a need for improved infection prevention and control, along with ongoing local antimicrobial resistance surveillance and antibiotic stewardship to guide future empirical treatment.
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Affiliation(s)
| | - Raymond Fatchu
- Pathology Division, 37 Military Hospital, Neghelli Barracks, Accra GA 01, Ghana
| | - Kingsley Ackah
- Pathology Division, 37 Military Hospital, Neghelli Barracks, Accra GA 01, Ghana
| | - Trudy Janice Philips
- Clinical Pathology Department, Noguchi Memorial Institute for Medical Research, P.O. Box LG 581, Accra GA 01, Ghana
| | - Hemant Deepak Shewade
- Division of Health System Research, ICMR-National Institute of Epidemiology (ICMR-NIE), Chennai 600077, India
| | - Ama Pokuaa Fenny
- Institute of Statistical, Social and Economic Research, University of Ghana, P.O. Box LG 1181, Accra GA 01, Ghana
| | - Collins Timire
- International Union against Tuberculosis and Lung Disease (The Union), 75006 Paris, France
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Kong PH, Chiang CH, Lin TC, Kuo SC, Li CF, Hsiung CA, Shiue YL, Chiou HY, Wu LC, Tsou HH. Discrimination of Methicillin-resistant Staphylococcus aureus by MALDI-TOF Mass Spectrometry with Machine Learning Techniques in Patients with Staphylococcus aureus Bacteremia. Pathogens 2022; 11:pathogens11050586. [PMID: 35631107 PMCID: PMC9143686 DOI: 10.3390/pathogens11050586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022] Open
Abstract
Early administration of proper antibiotics is considered to improve the clinical outcomes of Staphylococcus aureus bacteremia (SAB), but routine clinical antimicrobial susceptibility testing takes an additional 24 h after species identification. Recent studies elucidated matrix-assisted laser desorption/ionization time-of-flight mass spectra to discriminate methicillin-resistant strains (MRSA) or even incorporated with machine learning (ML) techniques. However, no universally applicable mass peaks were revealed, which means that the discrimination model might need to be established or calibrated by local strains’ data. Here, a clinically feasible workflow was provided. We collected mass spectra from SAB patients over an 8-month duration and preprocessed by binning with reference peaks. Machine learning models were trained and tested by samples independently of the first six months and the following two months, respectively. The ML models were optimized by genetic algorithm (GA). The accuracy, sensitivity, specificity, and AUC of the independent testing of the best model, i.e., SVM, under the optimal parameters were 87%, 75%, 95%, and 87%, respectively. In summary, almost all resistant results were truly resistant, implying that physicians might escalate antibiotics for MRSA 24 h earlier. This report presents an attainable method for clinical laboratories to build an MRSA model and boost the performance using their local data.
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Affiliation(s)
- Po-Hsin Kong
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (P.-H.K.); (Y.-L.S.)
- Center for Precision Medicine, Chi Mei Medical Center, Tainan 71004, Taiwan;
| | - Cheng-Hsiung Chiang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
| | - Ting-Chia Lin
- Center for Precision Medicine, Chi Mei Medical Center, Tainan 71004, Taiwan;
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan;
| | - Chien-Feng Li
- Department of Medical Research, Chi Mei Medical Center, Tainan 71004, Taiwan;
| | - Chao A. Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (P.-H.K.); (Y.-L.S.)
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Hung-Yi Chiou
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
- School of Public Health, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
- Master’s Program in Applied Epidemiology, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
| | - Li-Ching Wu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (P.-H.K.); (Y.-L.S.)
- Center for Precision Medicine, Chi Mei Medical Center, Tainan 71004, Taiwan;
- Correspondence: (L.-C.W.); (H.-H.T.)
| | - Hsiao-Hui Tsou
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
- Graduate Institute of Biostatistics, College of Public Health, China Medical University, Taichung 40402, Taiwan
- Correspondence: (L.-C.W.); (H.-H.T.)
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