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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [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] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Blomfeldt A, Jørgensen SB, Helmersen K, Eskonsipo PKJ, Aamot HV. Is increased Staphylococcus aureus colonization during military service caused by specific genotypes? Molecular examination of long-term carriage in a prospective cohort study. APMIS 2021; 129:170-177. [PMID: 33336455 DOI: 10.1111/apm.13106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/15/2020] [Indexed: 11/28/2022]
Abstract
A 22% increase in Staphylococcus aureus colonization was observed in Norwegian recruits during first year of military service. The aim was to determine whether specific genotypes caused the increase and to examine carriage status based on genotyping. Characterization of S. aureus from nose, throat and perineum sampled at enrolment and discharge included spa typing, MLVA, detection of PVL genes and antimicrobial susceptibility testing. spa typing demonstrated high and stable genetic diversity. The three most frequent spa types were found in 15% of recruits at enrolment and in 29% at discharge. Only t084 increased significantly (p = 0.02). Subtyping revealed that t084, t065 and t002 consisted of 13, 6 and 11 different MLVA types, respectively, at discharge. The military cohort (n = 265) consisted of S. aureus carriers of identical genotype (n = 99, 38%), carriers of non-identical genotype (n = 52, 20%), intermittent carriers (n = 86, 33%) and non-carriers (n = 27, 10%). Carrier status was indefinable for one recruit due to unavailable isolates for genotyping. Antibiotic resistance towards erythromycin, fusidic acid and clindamycin increased significantly and above national surveillance levels. The observed increase in S. aureus colonization during military service was caused by many different genotypes implying many transmission routes. Genotype did not correlate with colonization niche or carriage status.
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Affiliation(s)
- Anita Blomfeldt
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Silje Bakken Jørgensen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Karin Helmersen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | | | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway
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Lunha K, Leangapichart T, Jiwakanon J, Angkititrakul S, Sunde M, Järhult JD, Ström Hallenberg G, Hickman RA, Van Boeckel T, Magnusson U. Antimicrobial Resistance in Fecal Escherichia coli from Humans and Pigs at Farms at Different Levels of Intensification. Antibiotics (Basel) 2020; 9:E662. [PMID: 33008077 PMCID: PMC7650604 DOI: 10.3390/antibiotics9100662] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/02/2022] Open
Abstract
The overall aim of the current study was to test the hypotheses that (i) antibiotic resistance in bacteria were more frequent in clinically health pigs in intensified company owned, medium-scale farms (MSFs) (100-500 sows) than in pigs in family-owned, small-scale farms (SSFs) (1-50 sows) and (ii) that farmers working at the MSFs were more prone to attain antibiotic resistant bacteria than farmers working at SSFs. The study was conducted in North-Eastern Thailand, comprising fecal Escherichia coli isolates from pigs, farmers working with the pigs (contact humans) and persons living in the same household as the farmer (non-contact humans) at 51 MSFs and 113 SSFs. Samples from all farms were also screened for methicillin-resistant staphylococcus aureus (MRSA), which was not detected in pig samples, but was found in one human sample. Susceptibility was tested by disc-diffusion for seven antibiotics commonly used in the study area. Resistance in pig isolates from MSFs were more frequent for chloramphenicol which (P < 0.001), trimethoprim/sulfamethoxazole (P < 0.001) and gentamicin (P < 0.05) compared with isolates from SSFs, whereas the opposite was true for tetracycline (P < 0.01). Resistance in the human isolates was lower than those in the isolates from pigs for tetracycline, trimethoprim/sulfamethoxazole and chloramphenicol (P < 0.001). The frequency of resistance in the contact human samples from SSFs and MSFs did not differ. There was no difference between isolates from contact and non-contact humans for any of the tested antibiotics. Multidrug resistance in isolates from pigs was 26%, significantly higher (P < 0.01) than the 13% from humans. The data indicate that (i) resistance to antibiotics, including those critical and highly important for human medicine, were more common in fecal E. coli from pigs at the MSFs than at the SSFs, whereas (ii) the resistance in fecal E. coli from pig farmers seemed not to be influenced by the level of intensification of the farm they were working at.
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Affiliation(s)
- Kamonwan Lunha
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden; (K.L.); (G.S.H.)
| | - Thongpan Leangapichart
- Section for Food Safety and AMR, Norwegian Veterinary Institute, N-0106 Oslo, Norway; (T.L.); (M.S.)
| | - Jatesada Jiwakanon
- Research Group for Animal Health Technology, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (S.A.)
| | - Sunpetch Angkititrakul
- Research Group for Animal Health Technology, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (S.A.)
| | - Marianne Sunde
- Section for Food Safety and AMR, Norwegian Veterinary Institute, N-0106 Oslo, Norway; (T.L.); (M.S.)
| | - Josef D. Järhult
- Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden;
| | - Gunilla Ström Hallenberg
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden; (K.L.); (G.S.H.)
| | - Rachel A. Hickman
- Department of Biomedical Chemistry and Microbiology, Uppsala University, SE-752 37 Uppsala, Sweden;
| | - Thomas Van Boeckel
- Institute for Environmental Decisions, ETH, 8092 Zurich, Switzerland;
- Center for Diseases Dynamics Economics and Policy, Washington, DC 20005, USA
| | - Ulf Magnusson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden; (K.L.); (G.S.H.)
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Helmersen K, Aamot HV. DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing. Sci Rep 2020; 10:2985. [PMID: 32076089 PMCID: PMC7031281 DOI: 10.1038/s41598-020-59957-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/08/2020] [Indexed: 01/10/2023] Open
Abstract
Identification of bacteria causing tissue infections can be comprehensive and, in the cases of non- or slow-growing bacteria, near impossible with conventional methods. Performing shotgun metagenomic sequencing on bacterial DNA extracted directly from the infected tissue may improve time to diagnosis and targeted treatment considerably. However, infected tissue consists mainly of human DNA (hDNA) which hampers bacterial identification. In this proof of concept study, we present a modified version of the Ultra-Deep Microbiome Prep kit for DNA extraction procedure, removing additional human DNA. Tissue biopsies from 3 patients with orthopedic implant-related infections containing varying degrees of Staphylococcus aureus were included. Subsequent DNA shotgun metagenomic sequencing using Oxford Nanopore Technologies' (ONT) MinION platform and ONTs EPI2ME WIMP and ARMA bioinformatic workflows for microbe and antibiotic resistance genes identification, respectively. The modified DNA extraction protocol led to an additional ~10-fold reduction of human DNA while preserving S. aureus DNA. Including the DNA sequencing and bioinformatics analyses, the presented protocol has the potential of identifying the infection-causing pathogen in infected tissue within 7 hours after biopsy. However, due to low number of S. aureus reads, positive identification of antibiotic resistance genes was not possible.
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Affiliation(s)
- Karin Helmersen
- Akershus University Hospital, Department of Microbiology and Infection Control, Lørenskog, 1478, Norway
| | - Hege Vangstein Aamot
- Akershus University Hospital, Department of Microbiology and Infection Control, Lørenskog, 1478, Norway.
- Akershus University Hospital and University of Oslo, Department of Clinical Molecular Biology (Epigen), Lørenskog, 1478, Norway.
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Tunsjø HS, Kalyanasundaram S, Charnock C, Leegaard TM, Moen AEF. Challenges in the identification of methicillin-resistantStaphylococcus argenteusby routine diagnostics. APMIS 2018; 126:533-537. [DOI: 10.1111/apm.12843] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/04/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Hege Smith Tunsjø
- Department of Health Sciences; OsloMet - Oslo Metropolitan University; Oslo Norway
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
| | - Sumana Kalyanasundaram
- Department of Core Facilities; Bioinformatics Core Facility; Institute of Cancer Research; Radium Hospital; Oslo University Hospital; Oslo Norway
- Department of Clinical Molecular Biology (EpiGen); Akershus University Hospital; Lørenskog Norway
| | - Colin Charnock
- Department of Health Sciences; OsloMet - Oslo Metropolitan University; Oslo Norway
| | - Truls Michael Leegaard
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
- Institute of Clinical Medicine; University of Oslo; Oslo Norway
| | - Aina E. F. Moen
- Department of Clinical Molecular Biology (EpiGen); Akershus University Hospital; Lørenskog Norway
- Institute of Clinical Medicine; University of Oslo; Oslo Norway
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Tunsjø HS, Kalyanasundaram S, Worren MM, Leegaard TM, Moen AEF. High frequency of occupied attB regions in Norwegian Staphylococcus aureus isolates supports a two-step MRSA screening algorithm. Eur J Clin Microbiol Infect Dis 2016; 36:65-74. [PMID: 27638009 DOI: 10.1007/s10096-016-2771-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/25/2016] [Indexed: 01/10/2023]
Abstract
Rapid nucleic acid amplification tests for methicillin-resistant Staphylococcus aureus (MRSA) diagnostics commonly target the mec resistance gene, genes specific for S. aureus, and the integration site for the SCCmec resistance cassette, orfX. Due to poor specificity when these target genes are used individually, additional culture is required to verify positive results. The combination of these targets is useful, but the optimal algorithm may depend on the presence of the genetic markers in S. aureus isolates, as well as the prevalence of MRSA in a population. The aim of the present study was to identify a rapid, low-cost, and functional screening algorithm in order to reduce the response time for MRSA diagnostics. An in-house orfX-SCCmec polymerase chain reaction (PCR) assay was established and evaluated. The results were compared with an existing mec/nuc PCR assay and traditional culture. Methicillin-sensitive S. aureus (MSSA) that tested false-positive in the orfX-SCCmec PCR assay were further investigated with full genome sequencing using the Ion PGM™ System to verify results and causality. Based on these data, a two-step screening algorithm with initial mec/nuc PCR followed by orfX-SCCmec PCR on positive samples was suggested and tested on 1443 patient samples. 22.5 % of MSSA isolates tested false-positive with the orfX-SCCmec PCR. Full genome sequencing of these isolates identified genetic variation in the attB region of S. aureus, including empty cassette variants and non-mec SCC. The suggested two-step MRSA screening algorithm allowed us to report MRSA results for 95.6 % of all samples and 99 % of MRSA-negative samples after one day.
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Affiliation(s)
- H S Tunsjø
- Department of Health Sciences, Oslo and Akershus University College, Oslo, Norway. .,Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
| | - S Kalyanasundaram
- Bioinformatics Core Facility, Department of Core Facilities, Institute of Cancer Research, Radium Hospital, part of Oslo University Hospital, Oslo, Norway
| | - M M Worren
- Institute for Cancer Genetics and Informatics, Radium Hospital, part of Oslo University Hospital, Oslo, Norway
| | - T M Leegaard
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - A E F Moen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Clinical Molecular Biology and Laboratory Sciences (EpiGen), Akershus University Hospital, Lørenskog, Norway
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