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Hattab S, Ma AH, Tariq Z, Vega Prado I, Drobish I, Lee R, Yee R. Rapid Phenotypic and Genotypic Antimicrobial Susceptibility Testing Approaches for Use in the Clinical Laboratory. Antibiotics (Basel) 2024; 13:786. [PMID: 39200086 PMCID: PMC11351821 DOI: 10.3390/antibiotics13080786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
The rapid rise in increasingly resistant bacteria has become a major threat to public health. Antimicrobial susceptibility testing (AST) is crucial in guiding appropriate therapeutic decisions and infection prevention practices for patient care. However, conventional culture-based AST methods are time-consuming and labor-intensive. Therefore, rapid AST approaches exist to address the delayed gap in time to actionable results. There are two main types of rapid AST technologies- phenotypic and genotypic approaches. In this review, we provide a summary of all commercially available rapid AST platforms for use in clinical microbiology laboratories. We describe the technologies utilized, performance characteristics, acceptable specimen types, types of resistance detected, turnaround times, limitations, and clinical outcomes driven by these rapid tests. We also discuss crucial factors to consider for the implementation of rapid AST technologies in a clinical laboratory and what the future of rapid AST holds.
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Affiliation(s)
- Siham Hattab
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA; (S.H.); (Z.T.); (I.V.P.)
| | - Adrienne H. Ma
- Department of Pharmacy, Valley View Hospital, Glenwood Springs, CO 81647, USA;
| | - Zoon Tariq
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA; (S.H.); (Z.T.); (I.V.P.)
| | - Ilianne Vega Prado
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA; (S.H.); (Z.T.); (I.V.P.)
| | - Ian Drobish
- Critical Care Medicine Department, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Rachel Lee
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA;
| | - Rebecca Yee
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA; (S.H.); (Z.T.); (I.V.P.)
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Sati NM, Card RM, Barco L, Muhammad M, Luka PD, Chisnall T, Fagbamila IO, Cento G, Nnadi NE, Kankya C, Rwego IB, Ikwap K, Mugisha L, Erume J, Mwiine FN. Antimicrobial Resistance and Phylogenetic Relatedness of Salmonella Serovars in Indigenous Poultry and Their Drinking Water Sources in North Central Nigeria. Microorganisms 2024; 12:1529. [PMID: 39203371 PMCID: PMC11356752 DOI: 10.3390/microorganisms12081529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 09/03/2024] Open
Abstract
There is scant information on Salmonella in indigenous poultry in Nigeria. We investigated the occurrence and characterized Salmonella serovars in indigenous poultry and their drinking water sources to enhance the monitoring of the infection in poultry and to promote public health. We collected 1208 samples, poultry droppings (n = 1108), and water (n = 100) across 15 markets in North Central Nigeria. Salmonella spp. were isolated following World Organisation for Animal Health guidelines. Salmonella spp., confirmed through invA gene detection by a polymerase chain reaction assay, were 6.8% (75/1108) droppings and 3% (3/100) water. Susceptibility testing against 13 antimicrobials showed 60.3% (47/78) susceptibility to all the antimicrobials tested while 14.1% (11/78) were multidrug resistant. Serotyping and whole-genome sequencing were carried out on 44 of the isolates, and 23 different serovars were identified. Genomes of serovars Luedinghausen, Laredo, Widemarsh, and Lansing are being documented in Africa for the first time. Twenty (20) antimicrobial resistance (AMR) gene markers encoding for resistance to aminoglycosides, tetracyclines, sulphonamides, quinolones, trimethoprim, penicillins and phenicols were found. Phylogenetic cluster analysis showed close relatedness among isolates from different sources. This study shows both low Salmonella prevalence and AMR, but since uncommon serovars are circulating, continuous monitoring is recommended so as to ensure food safety and poultry health.
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Affiliation(s)
- Nancy M. Sati
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7072, Uganda; (C.K.); (I.B.R.); (K.I.); (L.M.); (J.E.); (F.N.M.)
- National Veterinary Research Institute, Vom 930103, Nigeria; (M.M.); (I.O.F.)
| | - Roderick M. Card
- Animal and Plant Health Agency, Weybridge KT15 3NB, UK; (R.M.C.); (T.C.)
| | - Lisa Barco
- National and WOAH Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 10, 35020 Padova, Italy; (L.B.); (G.C.)
| | - Maryam Muhammad
- National Veterinary Research Institute, Vom 930103, Nigeria; (M.M.); (I.O.F.)
| | - Pam D. Luka
- National Veterinary Research Institute, Vom 930103, Nigeria; (M.M.); (I.O.F.)
| | - Thomas Chisnall
- Animal and Plant Health Agency, Weybridge KT15 3NB, UK; (R.M.C.); (T.C.)
| | - Idowu O. Fagbamila
- National Veterinary Research Institute, Vom 930103, Nigeria; (M.M.); (I.O.F.)
| | - Giulia Cento
- National and WOAH Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 10, 35020 Padova, Italy; (L.B.); (G.C.)
| | - Nnaemeka E. Nnadi
- Department of Microbiology, Plateau State University, Bokkos 932111, Nigeria;
| | - Clovice Kankya
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7072, Uganda; (C.K.); (I.B.R.); (K.I.); (L.M.); (J.E.); (F.N.M.)
| | - Innocent B. Rwego
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7072, Uganda; (C.K.); (I.B.R.); (K.I.); (L.M.); (J.E.); (F.N.M.)
| | - Kokas Ikwap
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7072, Uganda; (C.K.); (I.B.R.); (K.I.); (L.M.); (J.E.); (F.N.M.)
| | - Lawrence Mugisha
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7072, Uganda; (C.K.); (I.B.R.); (K.I.); (L.M.); (J.E.); (F.N.M.)
| | - Joseph Erume
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7072, Uganda; (C.K.); (I.B.R.); (K.I.); (L.M.); (J.E.); (F.N.M.)
| | - Frank N. Mwiine
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7072, Uganda; (C.K.); (I.B.R.); (K.I.); (L.M.); (J.E.); (F.N.M.)
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3
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Fahy S, O’Connor JA, Sleator RD, Lucey B. From Species to Genes: A New Diagnostic Paradigm. Antibiotics (Basel) 2024; 13:661. [PMID: 39061343 PMCID: PMC11274079 DOI: 10.3390/antibiotics13070661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.
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Affiliation(s)
- Sinead Fahy
- Department of Microbiology, Mercy University Hospital, T12 WE28 Cork, Ireland;
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
| | - James A. O’Connor
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
| | - Roy D. Sleator
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (J.A.O.); (B.L.)
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Young EL, Roach DJ, Martinsen MA, McGrath G, Holbrook NR, Cho HE, Seyoum EY, Pierce VM, Bhattacharyya RP. Clinical Pilot of Bacterial Transcriptional Profiling as a Combined Genotypic and Phenotypic Antimicrobial Susceptibility Test. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.10.24310021. [PMID: 39040176 PMCID: PMC11261942 DOI: 10.1101/2024.07.10.24310021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Antimicrobial resistance is a growing health threat, but standard methods for determining antibiotic susceptibility are slow and can delay optimal treatment, which is especially consequential in severe infections such as bacteremia. Novel approaches for rapid susceptibility profiling have emerged that characterize either bacterial response to antibiotics (phenotype) or detect specific resistance genes (genotype). GoPhAST-R is a novel assay, performed directly on positive blood cultures, that integrates rapid transcriptional response profiling with detection of key resistance gene transcripts, thereby providing simultaneous data on both phenotype and genotype. Here, we performed the first clinical pilot of GoPhAST-R on 42 positive blood cultures: 26 growing Escherichia coli, 15 growing Klebsiella pneumoniae, and 1 with both. An aliquot of each positive blood culture was exposed to 9 different antibiotics, lysed, then underwent rapid transcriptional profiling on the NanoString® platform; results were analyzed using an in-house susceptibility classification algorithm. GoPhAST-R achieved 95% overall agreement with standard antimicrobial susceptibility testing methods, with the highest agreement for beta-lactams (98%) and the lowest for fluoroquinolones (88%). Epidemic resistance genes including the extended spectrum beta-lactamase bla CTX-M-15 and the carbapenemase bla KPC were also detected within the population. This study demonstrates the clinical feasibility of using transcriptional response profiling for rapid resistance determination, although further validation with larger and more diverse bacterial populations will be essential in future work. GoPhAST-R represents a promising new approach for rapid and comprehensive antibiotic susceptibility testing in clinical settings.
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Affiliation(s)
- E L Young
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - D J Roach
- The Broad Institute of MIT and Harvard, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - M A Martinsen
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Geg McGrath
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - N R Holbrook
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - H E Cho
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - E Y Seyoum
- The Broad Institute of MIT and Harvard, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - V M Pierce
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Current address: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - R P Bhattacharyya
- The Broad Institute of MIT and Harvard, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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5
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Truong TT, Lu J, Dien Bard J. Blood Cultures in Children: Maximizing Their Usefulness. Pediatr Infect Dis J 2024:00006454-990000000-00932. [PMID: 38985997 DOI: 10.1097/inf.0000000000004453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Affiliation(s)
- Thao T Truong
- From the Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Jacky Lu
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
- Keck School of Medicine, University of Southern California, Los Angeles, CA
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Chang THW, Pourtois JD, Haddock N, Furkuawa D, Hong T, Amanatullah D, Burgener E, Bollyky P. Using Genomic Tools to Predict Antimicrobial Resistance and Markers in Clinical Bacterial Samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.595912. [PMID: 38895396 PMCID: PMC11185549 DOI: 10.1101/2024.06.02.595912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Antimicrobial resistance (AMR) poses a critical threat to hospital infections particularly in the context of hospital-acquired infections (HAIs). This study leverages genomic tools to predict AMR and identify resistance markers in clinical bacterial samples associated with HAIs. Using comprehensive genomic and phenotypic analyses, we evaluated the genetic profiles of Pseudomonas aeruginosa and Staphylococcus aureus to uncover resistance mechanisms. Our results demonstrate that genomic tools, such as CARD-RGI and the Solu platform, can accurately identify resistance genes and predict AMR phenotypes in nosocomial pathogens. These findings underscore the potential of integrating genomic approaches into clinical practice to enhance the management of resistant infections in hospital settings and inform the development of novel antimicrobial strategies. Importance This study investigates the impact of prophages on antibiotic resistance in two clinically significant bacteria, Pseudomonas aeruginosa and Staphylococcus aureus. Understanding how prophages influence resistance mechanisms in these pathogens is crucial, as Pseudomonas aeruginosa is known for its role in chronic infections in cystic fibrosis patients, while Staphylococcus aureus, including MRSA strains, is a leading cause of hospital-acquired infections. By exploring the relationship between prophage presence and resistance, this research provides insights that could inform the development of more effective treatment strategies and enhance our ability to combat antibiotic-resistant infections, ultimately improving patient outcomes and public health.
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Rahmeh R, Akbar A, Almutairi B, Kishk M, Jordamovic NB, Al-Ateeqi A, Shajan A, Al-Sherif H, Esposito A, Al-Momin S, Piazza S. Camel Milk Resistome in Kuwait: Genotypic and Phenotypic Characterization. Antibiotics (Basel) 2024; 13:380. [PMID: 38786109 PMCID: PMC11117293 DOI: 10.3390/antibiotics13050380] [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: 03/28/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the major global health and economic threats. There is growing concern about the emergence of AMR in food and the possibility of transmission of microorganisms possessing antibiotic resistance genes (ARGs) to the human gut microbiome. Shotgun sequencing and in vitro antimicrobial susceptibility testing were used in this study to provide a detailed characterization of the antibiotic resistance profile of bacteria and their ARGs in dromedary camel milk. Eight pooled camel milk samples, representative of multiple camels distributed in the Kuwait desert, were collected from retail stores and analyzed. The genotypic analysis showed the presence of ARGs that mediate resistance to 18 classes of antibiotics in camel milk, with the highest resistance to fluoroquinolones (12.48%) and disinfecting agents and antiseptics (9%). Furthermore, the results pointed out the possible transmission of the ARGs to other bacteria through mobile genetic elements. The in vitro antimicrobial susceptibility testing indicated that 80% of the isolates were resistant to different classes of antibiotics, with the highest resistance observed against three antibiotic classes: penicillin, tetracyclines, and carbapenems. Multidrug-resistant pathogens including Klebsiella pneumoniae, Escherichia coli, and Enterobacter hormaechei were also revealed. These findings emphasize the human health risks related to the handling and consumption of raw camel milk and highlight the necessity of improving the hygienic practices of farms and retail stores to control the prevalence of ARGs and their transmission.
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Affiliation(s)
- Rita Rahmeh
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Abrar Akbar
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Batlah Almutairi
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Mohamed Kishk
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Naida Babic Jordamovic
- Computational Biology, International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (N.B.J.); (S.P.)
| | - Abdulaziz Al-Ateeqi
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Anisha Shajan
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Heba Al-Sherif
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Alfonso Esposito
- Faculty of Agricultural Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy;
| | - Sabah Al-Momin
- Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait; (A.A.); (B.A.); (M.K.); (A.A.-A.); (A.S.); (H.A.-S.); (S.A.-M.)
| | - Silvano Piazza
- Computational Biology, International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy; (N.B.J.); (S.P.)
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Zhang H, Mou J, Ding J, Qin W. Rapid antibiotic screening based on E. coli apoptosis using a potentiometric sensor array. Anal Chim Acta 2024; 1297:342378. [PMID: 38438244 DOI: 10.1016/j.aca.2024.342378] [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: 01/03/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024]
Abstract
Phenotypic antimicrobial susceptibility testing enables reliable antibiotic screening but requires multiple strategies to identify each phenotypic change induced by different bactericidal mechanisms. Bacteria apoptosis with typical phenotypic features has never been explored for antibiotic screening. Herein, we developed an antibiotic screening method based on the measurement of antibiotic-induced phosphatidylserine (PS) exposure of apoptotic bacteria. Phosphatidylserine externalization of E. coli that can be widely used as an apoptosis marker for antibiotics with different antibacterial mechanisms was explored. A positively charged PS-binding peptide was immobilized on magnetic beads (MBs) to recognize and capture apoptotic E. coli with PS externalization. Apoptotic E. coli binding led to the charge or charge density change of MBs-peptide, resulting in a potential change on a magneto-controlled polymeric membrane potentiometric sensor. Based on the detection of apoptotic E. coli killed by antibiotics, antibiotic screening for different classes of antibiotics and silver nanoparticles was achieved within 1.5 h using a potentiometric sensor array. This approach enables sensitive, general, and time-saving antibiotic screening, and may open up a new path for antibiotic susceptibility testing.
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Affiliation(s)
- Han Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Junsong Mou
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jiawang Ding
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266071, PR China.
| | - Wei Qin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266071, PR China
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9
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Hurtado O, Timbrook TT, Hommel B. Systematic review and meta-analysis on Staphylococcus aureus methicillin resistance detection performance and discrepancy analysis with the BIOFIRE® FILMARRAY® Pneumonia Panel. Anaesth Crit Care Pain Med 2024; 43:101352. [PMID: 38355043 DOI: 10.1016/j.accpm.2024.101352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Affiliation(s)
| | - Tristan T Timbrook
- bioMérieux, Salt Lake City, USA; University of Utah College of Pharmacy, Salt Lake City, USA
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André C, Van Camp AG, Ung L, Gilmore MS, Bispo PJM. Characterization of the resistome and predominant genetic lineages of Gram-positive bacteria causing keratitis. Antimicrob Agents Chemother 2024; 68:e0124723. [PMID: 38289077 PMCID: PMC10916405 DOI: 10.1128/aac.01247-23] [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: 09/27/2023] [Accepted: 12/03/2023] [Indexed: 02/04/2024] Open
Abstract
Bacterial keratitis is a vision-threatening infection mainly caused by Gram-positive bacteria (GPB). Antimicrobial therapy is commonly empirical using broad-spectrum agents with efficacy increasingly compromised by the emergence of antimicrobial resistance. We used a combination of phenotypic tests and genome sequencing to identify the predominant lineages of GPB causing keratitis and to characterize their antimicrobial resistance patterns. A total of 161 isolates, including Staphylococcus aureus (n = 86), coagulase-negative staphylococci (CoNS; n = 34), Streptococcus spp. (n = 34), and Enterococcus faecalis (n = 7), were included. The population of S. aureus isolates consisted mainly of clonal complex 5 (CC5) (30.2%). Similarly, the population of Staphylococcus epidermidis was homogenous with most of them belonging to CC2 (78.3%). Conversely, the genetic population of Streptococcus pneumoniae was highly diverse. Resistance to first-line antibiotics was common among staphylococci, especially among CC5 S. aureus. Methicillin-resistant S. aureus was commonly resistant to fluoroquinolones and azithromycin (78.6%) and tobramycin (57%). One-third of the CoNS were resistant to fluoroquinolones and 53% to azithromycin. Macrolide resistance was commonly caused by erm genes in S. aureus, mphC and msrA in CoNS, and mefA and msr(D) in streptococci. Aminoglycoside resistance in staphylococci was mainly associated with genes commonly found in mobile genetic elements and that encode for nucleotidyltransferases like ant(4')-Ib and ant(9)-Ia. Fluroquinolone-resistant staphylococci carried from 1 to 4 quinolone resistance-determining region mutations, mainly in the gyrA and parC genes. We found that GPB causing keratitis are associated with strains commonly resistant to first-line topical therapies, especially staphylococcal isolates that are frequently multidrug-resistant and associated with major hospital-adapted epidemic lineages.
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Affiliation(s)
- Camille André
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew G. Van Camp
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael S. Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Paulo J. M. Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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11
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Jose Lucar, Rebecca Yee. Diagnostic Stewardship for Multiplex Respiratory Testing: What We Know and What Needs to Be Done. Clin Lab Med 2024; 44:45-61. [PMID: 38280797 DOI: 10.1016/j.cll.2023.10.001] [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: 01/29/2024]
Abstract
Syndromic respiratory panels are now widely available in clinical microbiology laboratories and health care institutions. These panels can rapidly diagnose infections and detect antimicrobial resistance genes allowing for more rapid therapeutic optimization compared to standard microbiology approaches. However, given reimbursement concerns and limitations of multiplex molecular testing and results interpretation, maximum clinical utility and positive clinical outcomes depend on active diagnostic stewardship. Here, the authors review clinical outcomes of both upper and lower respiratory panels and present diagnostic stewardship strategies for optimal use of respiratory panels.
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Affiliation(s)
- Jose Lucar
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue Northeast, Washington, DC 20037, USA
| | - Rebecca Yee
- Department of Pathology, George Washington University School of Medicine and Health Sciences, 900 23rd Street Northwest, Washington, DC 20037, USA.
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Al-Kadmy IMS, Aziz SN, Hussein NH, El-Shafeiy SN, Hamzah IH, Suhail A, Alhomaidi E, Algammal AM, El-Saber Batiha G, ElBadre HM, Hetta HF. Sequencing analysis and efficient biodiesel production by lipase from Pseudomonas aeruginosa. Mol Biol Rep 2024; 51:323. [PMID: 38393680 DOI: 10.1007/s11033-023-09156-z] [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: 03/12/2023] [Accepted: 12/12/2023] [Indexed: 02/25/2024]
Abstract
BACKGROUND Recently, lipase processing for biodiesel production has shown a global increase as it is considered a potential alternative clean-fuel source. The current study's objective is to investigate of lipolytic activity of lipase produced from different strains of Pseudomonas aeruginosa (P. aeruginosa) in biodiesel production using edible plant oils. The goal is to develop an efficient and cost-effective method for producing inexpensive and environmentally friendly biodiesel. METHODS AND RESULTS Four P. aeruginosa isolates were obtained from different environmental sources (soil), phenotypically identified, and it was confirmed by the PCR detection of the 16SrRNA gene. The isolated P. aeruginosa strains were screened for lipase production, and the recovered lipase was purified. Besides, the lipase (lip) gene was detected by PCR, and the purified PCR products were sequenced and analyzed. The production of biofuel was conducted using gas chromatography among tested oils. It was found that castor oil was the best one that enhances lipase production in-vitro.
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Affiliation(s)
- Israa M S Al-Kadmy
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, Baghdad, 10422, Iraq.
| | - Sarah Naji Aziz
- Branch of'Microbiology, Department of Biology, College of Science, Mustansiriyah University, Baghdad, 10422, Iraq
| | - Nadheema Hammood Hussein
- Branch of'Microbiology, Department of Biology, College of Science, Mustansiriyah University, Baghdad, 10422, Iraq
| | - Samah N El-Shafeiy
- Plant Protection Research Institute, Agricultural Research Center, Dokki, Giza, 44516, Egypt
| | - Israa Hussein Hamzah
- Branch of Zoology, Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Ahmed Suhail
- Department of physics, College of science, Mosul University, Mosul, Iraq
| | - Eman Alhomaidi
- Department of biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, 41522, Ismailia, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicines, Damanhour University, 22511, Damanhour, Egypt
| | - Hala M ElBadre
- Department of Medical Biochemistry, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
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13
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Turbett SE, Banach DB, Bard JD, Gandhi RG, Letourneau AR, Azar MM. Rapid antimicrobial resistance detection methods for bloodstream infection in solid organ transplantation: Proposed clinical guidance, unmet needs, and future directions. Transpl Infect Dis 2023; 25:e14113. [PMID: 37594214 DOI: 10.1111/tid.14113] [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: 06/06/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/19/2023]
Abstract
Recent advances in antimicrobial resistance detection have spurred the development of multiple assays that can accurately detect the presence of bacterial resistance from positive blood cultures, resulting in faster institution of effective antimicrobial therapy. Despite these advances, there are limited data regarding the use of these assays in solid organ transplant (SOT) recipients and there is little guidance on how to select, implement, and interpret them in clinical practice. We describe a practical approach to the implementation and interpretation of these assays in SOT recipients using the best available data and expert opinion. These findings were part of a consensus conference sponsored by the American Society of Transplantation held on December 7, 2021 and represent the collaboration between experts in transplant infectious diseases, pharmacy, antimicrobial and diagnostic stewardship, and clinical microbiology. Areas of unmet need and recommendations for future investigation are also presented.
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Affiliation(s)
- Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - David B Banach
- Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ronak G Gandhi
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pharmacy, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alyssa R Letourneau
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Marwan M Azar
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
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14
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Ruiz-Ramos J, Escolà-Vergé L, Monje-López ÁE, Herrera-Mateo S, Rivera A. The Interventions and Challenges of Antimicrobial Stewardship in the Emergency Department. Antibiotics (Basel) 2023; 12:1522. [PMID: 37887223 PMCID: PMC10604141 DOI: 10.3390/antibiotics12101522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
Over the last decades, we have witnessed a constant increase in infections caused by multi-drug-resistant strains in emergency departments. Despite the demonstrated effectiveness of antimicrobial stewardship programs in antibiotic consumption and minimizing multi-drug-resistant bacterium development, the characteristics of emergency departments pose a challenge to their implementation. The inclusion of rapid diagnostic tests, tracking microbiological results upon discharge, conducting audits with feedback, and implementing multimodal educational interventions have proven to be effective tools for optimizing antibiotic use in these units. Nevertheless, future multicenter studies are essential to determine the best way to proceed and measure outcomes in this scenario.
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Affiliation(s)
- Jesus Ruiz-Ramos
- Pharmacy Department, Hospital Santa Creu i Sant Pau, 08025 Barcelona, Spain;
- Sant Pau Institute of Biomedical Research (IIb Sant Pau), 08025 Barcelona, Spain (A.R.)
| | - Laura Escolà-Vergé
- Infectious Diseases Department, Hospital Santa Creu i Sant Pau, 08025 Barcelona, Spain;
- CIBERINFEC, ISCIII—CIBER, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Álvaro Eloy Monje-López
- Pharmacy Department, Hospital Santa Creu i Sant Pau, 08025 Barcelona, Spain;
- Sant Pau Institute of Biomedical Research (IIb Sant Pau), 08025 Barcelona, Spain (A.R.)
| | - Sergio Herrera-Mateo
- Sant Pau Institute of Biomedical Research (IIb Sant Pau), 08025 Barcelona, Spain (A.R.)
- Emergency Department, Hospital Santa Creu i Sant Pau, 08025 Barcelona, Spain
| | - Alba Rivera
- Sant Pau Institute of Biomedical Research (IIb Sant Pau), 08025 Barcelona, Spain (A.R.)
- Microbiology Department, Hospital Santa Creu i Sant Pau, 08025 Barcelona, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain
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15
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Zaghen F, Sora VM, Meroni G, Laterza G, Martino PA, Soggiu A, Bonizzi L, Zecconi A. Epidemiology of Antimicrobial Resistance Genes in Staphyloccocus aureus Isolates from a Public Database in a One Health Perspective-Sample Characteristics and Isolates' Sources. Antibiotics (Basel) 2023; 12:1225. [PMID: 37508321 PMCID: PMC10376612 DOI: 10.3390/antibiotics12071225] [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: 06/30/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023] Open
Abstract
Staphylococcus aureus is considered one of the most widespread bacterial pathogens for both animals and humans, being the causative agent of various diseases like food poisoning, respiratory tract infections, nosocomial bacteremia, and surgical site and cardiovascular infections in humans, as well as clinical and subclinical mastitis, dermatitis, and suppurative infections in animals. Thanks to their genetic flexibility, several virulent and drug-resistant strains have evolved mainly due to horizontal gene transfer and insurgence of point mutations. Infections caused by the colonization of such strains are particularly problematic due to frequently occurring antibiotic resistance, particulary methicillin-resistant S. aureus (MRSA), and are characterized by increased mortality, morbidity, and hospitalization rates compared to those caused by methicillin-sensitive S. aureus (MSSA). S. aureus infections in humans and animals are a prime example of a disease that may be managed by a One Health strategy. In fact, S. aureus is a significant target for control efforts due to its zoonotic potential, the frequency of its illnesses in both humans and animals, and the threat posed by S. aureus antibiotic resistance globally. The results of an epidemiological analysis on a worldwide public database (NCBI Pathogen Detection Isolate Browser; NPDIB) of 35,026 S. aureus isolates were described. We considered the diffusion of antibiotic resistance genes (ARGs), in both human and animal setting, and the results may be considered alarming. The result of this study allowed us to identify the presence of clusters with specific ARG patterns, and that these clusters are associated with different sources of isolation (e.g., human, non-human).
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Affiliation(s)
- Francesca Zaghen
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
- Department of Clinical and Community Sciences, School of Medicine, University of Milan, Via Celoria 22, 20133 Milan, Italy
| | - Valerio Massimo Sora
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
- Department of Clinical and Community Sciences, School of Medicine, University of Milan, Via Celoria 22, 20133 Milan, Italy
| | - Gabriele Meroni
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Giulia Laterza
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
- Department of Clinical and Community Sciences, School of Medicine, University of Milan, Via Celoria 22, 20133 Milan, Italy
| | - Piera Anna Martino
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Alessio Soggiu
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Luigi Bonizzi
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Alfonso Zecconi
- Department of Biomedical, Surgical and Dental Sciences-One Health Unit, School of Medicine, University of Milan, Via Pascal 36, 20133 Milan, Italy
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16
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Hess KA, Kooda K, Shirley JD, Schuetz AN, Abu Saleh O, Stevens RW. Failure of mecA/mecC PCR Testing to Accurately Predict Oxacillin Resistance in a Patient with Staphylococcus aureus Infective Endocarditis. Antimicrob Agents Chemother 2023; 67:e0043723. [PMID: 37341623 PMCID: PMC10583684 DOI: 10.1128/aac.00437-23] [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: 03/31/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023] Open
Abstract
Genotypic testing for mecA/mecC is heavily relied upon for rapid optimization of antimicrobial therapy in infections due to Staphylococcus aureus. Little is known regarding optimal reporting and/or therapy for patients demonstrating lack of genotypic evidence of mecA or mecC but phenotypic oxacillin resistance. We report a case of a 77-year-old patient with S. aureus bloodstream infection and infective endocarditis with discordance between mecA/mecC genotypic results and phenotypic susceptibility testing.
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Affiliation(s)
- Kyle A. Hess
- Department of Pharmacy, Mayo Clinic, Rochester, Minnesota, USA
| | - Kirstin Kooda
- Department of Pharmacy, Mayo Clinic, Rochester, Minnesota, USA
| | - Joshua D. Shirley
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Audrey N. Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Omar Abu Saleh
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryan W. Stevens
- Department of Pharmacy, Mayo Clinic, Rochester, Minnesota, USA
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17
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Everhart J, Henshaw NG. Updates in Molecular Diagnostics in Solid Organ Transplantation Recipients. Infect Dis Clin North Am 2023:S0891-5520(23)00038-7. [PMID: 37244805 DOI: 10.1016/j.idc.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Advances in molecular diagnostics have the potential to improve patient care among solid organ transplant recipients by reducing time to pathogen identification and informing directed therapy. Although cultures remain the cornerstone of traditional microbiology, advanced molecular diagnostics, such as metagenomic next-generation sequencing (mNGS), may increase detection of pathogens. This is particularly true in the settings of prior antibiotic exposure, and when causative organisms are fastidious. mNGS also offers a hypothesis-free diagnostic method of testing. This is useful in situations whereby the differential is broad or when the infectious agent is unlikely to be detected by routine methods.
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Affiliation(s)
- James Everhart
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA.
| | - Nancy G Henshaw
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA
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18
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Saeki M, Nirasawa S, Aung MS, Ono M, Urushibara N, Kobayashi N, Takahashi S. Detecting the performance of methicillin-resistant Staphylococcus aureus by a molecular diagnostic assay in positive blood culture: Influence of coexistence of mecA-positive bacteria and diversity in orfX-SCCmec junction region in methicillin-susceptible S. aureus. J Infect Chemother 2023:S1341-321X(23)00116-2. [PMID: 37178974 DOI: 10.1016/j.jiac.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/23/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND In blood cultures that test positive for staphylococcal bacteria, rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) or methicillin-susceptible Staphylococcus aureus (MSSA) by molecular assay is useful for appropriate antimicrobial treatment of bloodstream infections. Although the Xpert MRSA/SA BC assay is widely available in clinical settings in Japan, its efficacy has not yet evaluated thoroughly. METHODS We retrospectively studied 100 blood culture cases positive for S. aureus at Sapporo Medical University Hospital between March 2019 to May 2022. Cycle threshold (CT) values for target genes from the Xpert MRSA/SA BC assay were compared to phenotypic results. Genotyping and genetic analysis of the orfX-SCCmec junction region was performed for selected isolates. RESULTS We analyzed 25 and 75 isolates assigned to MRSA and MSSA, respectively, using the Xpert MRSA/SA BC assay. Of these, 99 isolates from agar cultures showed compatible susceptibility to oxacillin. One genetically misidentified case of MRSA was found to be caused by the mixed growth of MSSA and methicillin-resistant S. hominis on agar culture. Of the 73 MSSA with pure growth on agar culture, 45 (61.6%) were found to be orfX-SCCmec-positive, spa-positive, and mecA-negative in this assay. These MSSA belong to diverse spa and coa types. CONCLUSION The Xpert MRSA/SA BC assay accurately identified MRSA and MSSA in positive blood cultures. However, over half of the MSSA isolates showed positive results for orfX-SCCmec, presumably due to genetic diversity in the orfX-associated region of MSSA. Therefore, the coexistence of MSSA and mecA-harboring coagulase-negative staphylococci may cause confusion about identification of MRSA.
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Affiliation(s)
- Masachika Saeki
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Shinya Nirasawa
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mayumi Ono
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Satoshi Takahashi
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan; Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.
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19
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Simner PJ, Dien Bard J, Doern C, Kristie Johnson J, Westblade L, Yenokyan G, Patel R, Hanson KE. Reporting of Antimicrobial Resistance from Blood Cultures, an Antibacterial Resistance Leadership Group Survey Summary: Resistance Marker Reporting Practices from Positive Blood Cultures. Clin Infect Dis 2023; 76:1550-1558. [PMID: 36533704 PMCID: PMC10411935 DOI: 10.1093/cid/ciac952] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/23/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We assessed how laboratories use and handle reporting of results of rapid diagnostics performed on positive blood culture broths, with a focus on antimicrobial resistance (AMR) markers. METHODS A survey assembled by the Antibacterial Resistance Leadership Group Diagnostics Committee was circulated from December 2020 to May 2021. The survey was sent to local hospitals, shared on the ClinMicroNet and Division C listservs, and included in a College of American Pathologists proficiency testing survey. RESULTS Ninety-six laboratories of various sizes across the United States (95%) and outside of the United States (5%) participated. Of the laboratories that had at least 1 rapid diagnostic in place (94%), significant heterogeneity in methods used and reporting practices was found across community (52%) and academic (40%) laboratories serving hospitals of various sizes. Respondents had implemented 1 to 6 different panels/platforms for a total of 31 permutations. Methods of reporting rapid organism identification and AMR results varied from listing all targets as "detected"/"not detected" (16-22%) without interpretive guidance, to interpreting results (23-42%), or providing therapeutic guidance comments to patient-facing healthcare teams (3-17%). CONCLUSIONS Current approaches to reporting molecular AMR test results from positive blood culture vary significantly across clinical laboratories. Providing interpretative comments with therapeutic guidance alongside results reported may assist clinicians who are not well-versed in genetic mechanisms of AMR. However, this is currently not being done in all clinical laboratories. Standardized strategies for AMR gene result reporting are needed.
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Affiliation(s)
- Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Christopher Doern
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, Virginia, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Gayane Yenokyan
- Johns Hopkins Biostatistics Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kimberly E Hanson
- Department of Medicine, Infectious Diseases Division, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Department of Pathology, Clinical Microbiology Division, University of Utah Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, Utah, USA
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20
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Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
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21
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Pennone V, Prieto M, Álvarez-Ordóñez A, Cobo-Diaz JF. Antimicrobial Resistance Genes Analysis of Publicly Available Staphylococcus aureus Genomes. Antibiotics (Basel) 2022; 11:1632. [PMID: 36421276 PMCID: PMC9686812 DOI: 10.3390/antibiotics11111632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 07/30/2023] Open
Abstract
Staphylococcus aureus is a pathogen that can cause severe illness and express resistance to multiple antimicrobial agents. It is part of the ESKAPE organisms and it has been included by the Centers for Disease Control and Prevention (CDC) of USA in the list of serious threats to humans. Many antimicrobial mechanisms have been identified, and, in particular, antimicrobial resistance genes (ARGs) can be determined by whole genome sequencing. Mobile genetic elements (MGEs) can determine the spread of these ARGs between strains and species and can be identified with bioinformatic analyses. The scope of this work was to analyse publicly available genomes of S. aureus to characterise the occurrence of ARGs present in chromosomes and plasmids in relation to their geographical distribution, isolation sources, clonal complexes, and changes over time. The results showed that from a total of 29,679 S. aureus genomes, 24,765 chromosomes containing 73 different ARGs, and 21,006 plasmidic contigs containing 47 different ARGs were identified. The most abundant ARG in chromosomes was mecA (84%), while blaZ was the most abundant in plasmidic contigs (30%), although it was also abundant in chromosomes (42%). A total of 13 clonal complexes were assigned and differences in ARGs and CC distribution were highlighted among continents. Temporal changes during the past 20 years (from 2001 to 2020) showed that, in plasmids, MRSA and macrolide resistance occurrence decreased, while the occurrence of ARGs associated with aminoglycosides resistance increased. Despite the lack of metadata information in around half of the genomes analysed, the results obtained enable an in-depth analysis of the distribution of ARGs and MGEs throughout different categories to be undertaken through the design and implementation of a relatively simple pipeline, which can be also applied in future works with other pathogens, for surveillance and screening purposes.
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Affiliation(s)
- Vincenzo Pennone
- Department of Food and Drug, Università degli Studi di Parma, 43121 Parma, Italy
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Institute of Food Science and Technology, Universidad de León, 24071 León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Institute of Food Science and Technology, Universidad de León, 24071 León, Spain
| | - José F. Cobo-Diaz
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
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22
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Antimicrobial Resistance and Virulence Factors of Proteus mirabilis Isolated from Dog with Chronic Otitis Externa. Pathogens 2022; 11:pathogens11101215. [PMID: 36297273 PMCID: PMC9612330 DOI: 10.3390/pathogens11101215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022] Open
Abstract
Otitis externa is among the most prevalent diseases in dogs. If the underlying cause is not addressed, bacterial reinfection becomes frequent, necessitating antibiotic administration for an extended period of time. Prolonged treatment promotes the emergence of antibiotic-resistant bacteria and increases the risk of their transmission from animals to humans. This study aimed to analyze the antibiotic resistance pattern of the emerging pathogen Proteus mirabilis to identify bacterial virulence and antibiotic selection. Samples were collected from randomly encountered dogs with chronic otitis externa. Thirty-two strains of P. mirabilis were isolated and identified, using MALDI-TOF. The Kirby-Bauer disk diffusion method was used to assess the antibiotic susceptibility of P. mirabilis to 11 antibiotics. The isolates (n = 32) were most resistant to cefazolin (75%), trimethoprim–sulfamethoxazole (72%), chloramphenicol (72%), amoxicillin–clavulanate (63%), ampicillin (59%), cefepime (56%), ciprofloxacin (53%), aztreonam (50%), ceftazidime avibactam (50%), gentamicin (22%), and amikacin (16%). Moreover, 75% of isolates were found to be multidrug-resistant bacteria. P. mirabilis was found to have a high resistance-pattern ratio. Although the exact cause is unknown, continuous antibiotic use is thought to be a major factor. We concluded that antibiotic use must be prudent and selective to prevent antibiotic resistance.
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23
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Abstract
A vast amount of antimicrobial susceptibility test (AST) data is generated from routine testing in diagnostic laboratories for the primary purpose of guiding clinicians in antimicrobial therapy decisions for their patients. However, there is additional value for these data when they are compiled at the local, regional, national, and global levels. Cumulative AST data can be used to prepare antibiograms at the individual health care facility level. These reports can be used to gain insight into appropriate empirical therapy options prior to the availability of AST results on an individual patient's isolate. Different types of cumulative AST data reports can also be compiled at the regional, national, and global levels to estimate susceptibility rates in geographic regions, document trends in evolving microbial populations, and recognize the appearance and spread of emerging antimicrobial resistance threats. The first CLSI M39 Guideline for Analysis and Presentation of Cumulative AST Data was published in 2000. Since that time, there have been changes to AST and reporting recommendations as well as the introduction of advanced informatics technologies to analyze and present data. The 5th edition of M39 has taken into consideration these changes to assist those who analyze, present, and utilize routine antibiograms and other types of cumulative AST data reports as well as those who design information systems for the capturing and analyzing of AST data. Furthermore, antimicrobial stewardship programs (ASPs) have expanded considerably, and uses of the antibiogram by ASPs have been addressed. This minireview will remind users of the basic recommendations for analysis and presentation of antibiograms and provide new suggestions to enhance these reports.
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Jitmuang A, Puttinad S, Hemvimol S, Pansasiri S, Horthongkham N. A multiplex pneumonia panel for diagnosis of hospital-acquired and ventilator-associated pneumonia in the era of emerging antimicrobial resistance. Front Cell Infect Microbiol 2022; 12:977320. [PMID: 36310855 PMCID: PMC9597303 DOI: 10.3389/fcimb.2022.977320] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
Background Antimicrobial resistance (AMR), including multidrug (MDR) and extensively drug-resistant (XDR) bacteria, is an essential consideration in the prevention and management of hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). In the AMR era, the clinical utility of the BioFire FilmArray Pneumonia Panel Plus (BFPP) to diagnose HAP/VAP has not been thoroughly evaluated. Methods We enrolled adult hospitalized patients with HAP or VAP at Siriraj Hospital and Saraburi Hospital from July 2019–October 2021. Respiratory samples were collected for standard microbiological assays, antimicrobial susceptibility testing (AST), and the BFPP analysis. Results Of 40 subjects, 21 were men. The median duration of HAP/VAP diagnoses was 10.5 (5, 21.5) days, and 36 endotracheal aspirate and 4 sputum samples were collected. Standard cultures isolated 54 organisms—A. baumannii (37.0%), P. aeruginosa (29.6%), and S. maltophilia (16.7%). 68.6% of Gram Negatives showed an MDR or XDR profile. BFPP detected 77 bacterial targets—A. baumannii 32.5%, P. aeruginosa 26.3%, and K. pneumoniae 17.5%. Of 28 detected AMR gene targets, CTX-M (42.5%), OXA-48-like (25%), and NDM (14.3%) were the most common. Compared with standard testing, the BFPP had an overall sensitivity of 98% (88-100%), specificity of 81% (74-87%), positive predictive value of 60% (47-71%), negative predictive value of 99% (96-100%), and kappa (κ) coefficient of 0.64 (0.53-0.75). The concordance between phenotypic AST and detected AMR genes in Enterobacterales was 0.57. There was no concordance among A. baumannii, P. aeruginosa, and S. aureus Conclusions The BFPP has excellent diagnostic sensitivity to detect HAP/VAP etiology. The absence of S. maltophilia and discordance of AMR gene results limit the test performance.
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Affiliation(s)
- Anupop Jitmuang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- *Correspondence: Anupop Jitmuang,
| | - Soravit Puttinad
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Siri Pansasiri
- Saraburi Hospital Research Center, Saraburi Hospital, Saraburi, Thailand
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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25
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Abstract
Enterococci are major, recalcitrant nosocomial pathogens with a wide repertoire of intrinsic and acquired resistance determinants and the potential of developing resistance to all clinically available antimicrobials. As such, multidrug-resistant enterococci are considered a serious public health threat. Due to limited treatment options and rapid emergence of resistance to all novel agents, the clinical microbiology laboratory plays a critical role in deploying accurate, reproducible, and feasible antimicrobial susceptibility testing methods to guide appropriate treatment of patients with deep-seated enterococcal infections. In this review, we provide an overview of the advantages and disadvantages of existing manual and automated methods that test susceptibility of Enterococcus faecium and Enterococcus faecalis to β-lactams, aminoglycosides, vancomycin, lipoglycopeptides, oxazolidinones, novel tetracycline-derivatives, and daptomycin. We also identify unique problems and gaps with the performance and clinical utility of antimicrobial susceptibility testing for enterococci, provide recommendations for clinical laboratories to circumvent select problems, and address potential future innovations that can bridge major gaps in susceptibility testing.
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26
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Papaleo S, Alvaro A, Nodari R, Panelli S, Bitar I, Comandatore F. The red thread between methylation and mutation in bacterial antibiotic resistance: How third-generation sequencing can help to unravel this relationship. Front Microbiol 2022; 13:957901. [PMID: 36188005 PMCID: PMC9520237 DOI: 10.3389/fmicb.2022.957901] [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: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an important mechanism involved in bacteria limiting foreign DNA acquisition, maintenance of mobile genetic elements, DNA mismatch repair, and gene expression. Changes in DNA methylation pattern are observed in bacteria under stress conditions, including exposure to antimicrobial compounds. These changes can result in transient and fast-appearing adaptive antibiotic resistance (AdR) phenotypes, e.g., strain overexpressing efflux pumps. DNA methylation can be related to DNA mutation rate, because it is involved in DNA mismatch repair systems and because methylated bases are well-known mutational hotspots. The AdR process can be the first important step in the selection of antibiotic-resistant strains, allowing the survival of the bacterial population until more efficient resistant mutants emerge. Epigenetic modifications can be investigated by third-generation sequencing platforms that allow us to simultaneously detect all the methylated bases along with the DNA sequencing. In this scenario, this sequencing technology enables the study of epigenetic modifications in link with antibiotic resistance and will help to investigate the relationship between methylation and mutation in the development of stable mechanisms of resistance.
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Affiliation(s)
- Stella Papaleo
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Alessandro Alvaro
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Bioscience, University of Milan, Milan, Italy
| | - Riccardo Nodari
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Simona Panelli
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Francesco Comandatore
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- *Correspondence: Francesco Comandatore
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Miller KM, Lamagni T, Cherian T, Cannon JW, Parks T, Adegbola RA, Pickering J, Barnett T, Engel ME, Manning L, Bowen AC, Carapetis JR, Moore HC, Barth DD, Kaslow DC, Van Beneden CA. Standardization of Epidemiological Surveillance of Invasive Group A Streptococcal Infections. Open Forum Infect Dis 2022; 9:S31-S40. [PMID: 36128405 PMCID: PMC9474937 DOI: 10.1093/ofid/ofac281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Invasive group A streptococcal (Strep A) infections occur when Streptococcus pyogenes, also known as beta-hemolytic group A Streptococcus, invades a normally sterile site in the body. This article provides guidelines for establishing surveillance for invasive Strep A infections. The primary objective of invasive Strep A surveillance is to monitor trends in rates of infection and determine the demographic and clinical characteristics of patients with laboratory-confirmed invasive Strep A infection, the age- and sex-specific incidence in the population of a defined geographic area, trends in risk factors, and the mortality rates and rates of nonfatal sequelae caused by invasive Strep A infections.
This article includes clinical descriptions followed by case definitions, based on clinical and laboratory evidence, and case classifications (confirmed or probable, if applicable) for invasive Strep A infections and for 3 Strep A syndromes: streptococcal toxic shock syndrome, necrotizing fasciitis, and pregnancy-associated Strep A infection.
Considerations of the type of surveillance are also presented, noting that most people who have invasive Strep A infections will present to hospital and that invasive Strep A is a notifiable disease in some countries. Minimal surveillance necessary for invasive Strep A infection is facility-based, passive surveillance. A resource-intensive but more informative approach is active case finding of laboratory-confirmed Strep A invasive infections among a large (eg, state-wide) and well defined population.
Participant eligibility, surveillance population, and additional surveillance components such as the use of International Classification of Disease diagnosis codes, follow-up, period of surveillance, seasonality, and sample size are discussed. Finally, the core data elements to be collected on case report forms are presented.
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Affiliation(s)
- Kate M Miller
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
| | | | | | - Jeffrey W Cannon
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health , Boston, Massachusetts , USA
| | - Tom Parks
- Department of Infectious Disease, Imperial College London, Hammersmith Hospital , London , United Kingdom
| | | | - Janessa Pickering
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
| | - Tim Barnett
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
| | - Mark E Engel
- AFROStrep Research Initiative, Department of Medicine, University of Cape Town , Cape Town , South Africa
| | - Laurens Manning
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
- Infectious Diseases Department, Fiona Stanley Hospital , Perth, Western Australia , Australia
- Medical School, University of Western Australia , Perth, Western Australia , Australia
| | - Asha C Bowen
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
- Perth Children’s Hospital , Nedlands, Western Australia
- Faculty of Health and Medicine, University of Western Australia , Nedlands, Western Australia
| | - Jonathan R Carapetis
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
- Faculty of Health and Medicine, University of Western Australia , Nedlands, Western Australia
| | - Hannah C Moore
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
| | - Dylan D Barth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia , Nedlands, Western Australia
- Faculty of Health and Medicine, University of Western Australia , Nedlands, Western Australia
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28
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Wang H, Jia C, Li H, Yin R, Chen J, Li Y, Yue M. Paving the way for precise diagnostics of antimicrobial resistant bacteria. Front Mol Biosci 2022; 9:976705. [PMID: 36032670 PMCID: PMC9413203 DOI: 10.3389/fmolb.2022.976705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 12/26/2022] Open
Abstract
The antimicrobial resistance (AMR) crisis from bacterial pathogens is frequently emerging and rapidly disseminated during the sustained antimicrobial exposure in human-dominated communities, posing a compelling threat as one of the biggest challenges in humans. The frequent incidences of some common but untreatable infections unfold the public health catastrophe that antimicrobial-resistant pathogens have outpaced the available countermeasures, now explicitly amplified during the COVID-19 pandemic. Nowadays, biotechnology and machine learning advancements help create more fundamental knowledge of distinct spatiotemporal dynamics in AMR bacterial adaptation and evolutionary processes. Integrated with reliable diagnostic tools and powerful analytic approaches, a collaborative and systematic surveillance platform with high accuracy and predictability should be established and implemented, which is not just for an effective controlling strategy on AMR but also for protecting the longevity of valuable antimicrobials currently and in the future.
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Affiliation(s)
- Hao Wang
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Chenhao Jia
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hongzhao Li
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Rui Yin
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Jiang Chen
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
| | - Yan Li
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
| | - Min Yue
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
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29
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Serpa PH, Deng X, Abdelghany M, Crawford E, Malcolm K, Caldera S, Fung M, McGeever A, Kalantar KL, Lyden A, Ghale R, Deiss T, Neff N, Miller SA, Doernberg SB, Chiu CY, DeRisi JL, Calfee CS, Langelier CR. Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections. Genome Med 2022; 14:74. [PMID: 35818068 PMCID: PMC9275031 DOI: 10.1186/s13073-022-01072-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 06/15/2022] [Indexed: 12/14/2022] Open
Abstract
Background Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing. Methods We studied 88 patients with acute respiratory failure between 07/2013 and 9/2018, enrolled through a previous observational study of LRTI. Inclusion criteria were age ≥ 18, need for mechanical ventilation, and respiratory specimen collection within 72 h of intubation. Exclusion criteria were decline of study participation, unclear LRTI status, or no matched RNA and DNA mNGS data from a respiratory specimen. Patients with LRTI were identified by clinical adjudication. mNGS was performed on lower respiratory tract specimens. The primary outcome was mNGS performance for predicting phenotypic antimicrobial susceptibility and was assessed in patients with LRTI from culture-confirmed bacterial pathogens with clinical antimicrobial susceptibility testing (n = 27 patients, n = 32 pathogens). Secondary outcomes included the association between hospital exposure and AMR gene burden in the respiratory microbiome (n = 88 patients), and AMR gene detection using Cas9 targeted enrichment and nanopore sequencing (n = 10 patients). Results Compared to clinical antimicrobial susceptibility testing, the performance of respiratory mNGS for predicting AMR varied by pathogen, antimicrobial, and nucleic acid type sequenced. For gram-positive bacteria, a combination of RNA + DNA mNGS achieved a sensitivity of 70% (95% confidence interval (CI) 47–87%) and specificity of 95% (CI 85–99%). For gram-negative bacteria, sensitivity was 100% (CI 87–100%) and specificity 64% (CI 48–78%). Patients with hospital-onset LRTI had a greater AMR gene burden in their respiratory microbiome versus those with community-onset LRTI (p = 0.00030), or those without LRTI (p = 0.0024). We found that Cas9 targeted sequencing could enrich for low abundance AMR genes by > 2500-fold and enabled their rapid detection using a nanopore platform. Conclusions mNGS has utility for the detection and surveillance of resistant bacterial LRTI pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01072-4.
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Affiliation(s)
- Paula Hayakawa Serpa
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Mazin Abdelghany
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Katherine Malcolm
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Monica Fung
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Rajani Ghale
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Thomas Deiss
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Steven A Miller
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Sarah B Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Charles R Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Mushtaq A, Chasan R, Nowak MD, Rana M, Ilyas S, Paniz-Mondolfi AE, Sordillo EM, Patel G, Gitman MR. Correlation between Identification of β-Lactamase Resistance Genes and Antimicrobial Susceptibility Profiles in Gram-Negative Bacteria: a Laboratory Data Analysis. Microbiol Spectr 2022; 10:e0148521. [PMID: 35254140 PMCID: PMC9045321 DOI: 10.1128/spectrum.01485-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/05/2022] [Indexed: 11/20/2022] Open
Abstract
We reported the frequency of resistance gene detection in Gram-negative blood culture isolates and correlated these findings with corresponding antibiograms. Data were obtained from 1045 isolates tested on the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panels at the Mount Sinai Hospital Clinical Microbiology Laboratory in New York from March 2019 to February 2021. Susceptibilities were performed using Vitek 2 (bioMérieux Clinical Diagnostics) or Microscan (Beckman Coulter Inc.). blaCTX-M was detected in 26.4% Klebsiella pneumoniae, 23.5% Escherichia coli, and 16.4% Proteus mirabilis isolates. As would be expected, both blaCTX-M and blaCTX-M negative isolates were likely to be susceptible to newer agents while blaCTX-M positive isolates were more likely to be resistant to earlier generations of beta-lactam antibiotics. 3/204 blaCTX-M-positive isolates were found to be ceftriaxone-susceptible. Conversely, 2.8% ceftriaxone nonsusceptible strains were negative for all β-lactamase genes on the ePlex BCID-GN panel, including blaCTX-M. The prevalence of CTX-M-producing Enterobacterales remains high in the United States. A small number of blaCTX-M-positive isolates were susceptible to ceftriaxone, and a small number of ceftriaxone nonsusceptible isolates were negative for blaCTX-M. Further studies are needed to determine the optimal management when an isolate is phenotypically susceptible to ceftriaxone, but blaCTX-M is detected. IMPORTANCE There is limited literature on corresponding results obtained from rapid molecular diagnostics with the antibiotic susceptibility profile. We reported a correlation between the results obtained from ePlex and the antibiograms against a large collection of Gram-negative bacteria. We reported that there can be a discrepancy in a small number of cases, but the clinical significance of that is unknown.
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Affiliation(s)
- Ammara Mushtaq
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Rachel Chasan
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael D. Nowak
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Meenakshi Rana
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sahrish Ilyas
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alberto E. Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia M. Sordillo
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gopi Patel
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Melissa R. Gitman
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Tenover FC, Tickler IA. Detection of Methicillin-Resistant Staphylococcus aureus Infections Using Molecular Methods. Antibiotics (Basel) 2022; 11:antibiotics11020239. [PMID: 35203841 PMCID: PMC8868555 DOI: 10.3390/antibiotics11020239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
The application of molecular detection methods for bacterial pathogens has dramatically improved the outcomes of septic patients, including those with methicillin-resistant Staphylococcus aureus (MRSA) infections. Molecular methods can be applied to a variety of clinical specimens including nasal swabs, growth in blood culture bottles, and wounds. While data show that the overall accuracy of molecular tests for MRSA is high, results can be confounded by the presence of multiple staphylococcal species in a specimen, insertions and deletions of DNA in and around the Staphylococcal Cassette Chromosome mec (SCCmec) element, and point mutations in mecA. Herein, we explore the complexities of molecular approaches to MRSA detection and the instances where phenotypic methods should be pursued to resolve discrepancies between genotypic and phenotypic results.
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Multicenter Evaluation of the Acuitas ® AMR Gene Panel for Detection of an Extended Panel of Antimicrobial Resistance Genes among Bacterial Isolates. J Clin Microbiol 2022; 60:e0209821. [PMID: 35138924 DOI: 10.1128/jcm.02098-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The Acuitas® AMR Gene Panel is a qualitative, multiplex nucleic acid-based in vitro diagnostic test for detection and differentiation of 28 antimicrobial resistance (AMR) markers associated with not susceptible results (NS, i.e., intermediate or resistant) to one or more antimicrobial agents among cultured isolates of select Enterobacterales, Pseudomonas aeruginosa and Enterococcus faecalis. Methods: This study was conducted at four sites and included testing of 1,224 de-identified stocks created from 584 retrospectively collected isolates and 83 prospectively collected clinical isolates. The Acuitas results were compared with a combined reference standard including whole genome sequencing, organism identification and phenotypic antimicrobial susceptibility testing. Results: Positive percent agreement (PPA) for FDA-cleared AMR targets ranged from 94.4% for MCR-1 to 100% for armA, CTX-M-2, DHA, IMP, OXA-9, SHV, vanA and VEB. The negative percent agreement (NPA) for the majority of targets was ≥99%, except for AAC, AAD, CMY-41, P. aeruginosa gyrA mutant, Sul1, Sul2 and TEM targets (range: 96.5% to 98.5%). Three AMR markers did not meet FDA inclusion criteria (GES, SPM & MCR-2). For each organism, 1 to 22 AMR targets met the minimum reportable PPA/NPA and correlated with ≥80% positive predictive value with associated NS results for at least one agent (i.e., the probability of an organism carrying an AMR marker testing NS to the associated agent). Conclusion: We demonstrate that the Acuitas® AMR Gene Panel is an accurate method to detect a broad array of AMR markers among cultured isolates. The AMR markers were further associated with expected NS results for specific agent-organism combinations.
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Fatoba DO, Amoako DG, Akebe ALK, Ismail A, Essack SY. Genomic analysis of antibiotic-resistant Enterococcus spp. reveals novel enterococci strains and the spread of plasmid-borne Tet(M), Tet(L) and Erm(B) genes from chicken litter to agricultural soil in South Africa. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114101. [PMID: 34800768 DOI: 10.1016/j.jenvman.2021.114101] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Manure from food animals exposed to antibiotics is often used as soil fertiliser, potentially releasing antibiotic-resistant bacteria (ARB) with diverse antibiotic-resistance genes (ARGs) into the soil. To determine the impact of chicken litter application on the soil resistome, Enterococcus spp. isolated from chicken litter and soil samples collected before and after the soil amendment were characterised, using whole-genome sequencing and bioinformatics tools. Nineteen Enterococcus spp. isolates from the three sources were sequenced on Illumina Miseq platform to ascertain the isolates' resistome, mobilome, virulome, clonality, and phylogenomic relationships. Multilocus sequence typing (MLST) analysis revealed eight novel sequence types (STs) (ST1700, ST1752, ST1753, ST1754, ST1755, ST1756, ST1004, and ST1006). The isolates harboured multiple resistance genes including those conferring resistance to inter alia macrolides-lincosamide-streptogramin (erm(B), lnu(B), lnu(G), lsaA, lsaE, eat(A), msr(C)), tetracycline (tet(M), tet(L), tet(S)), aminoglycosides (aac(6')-Ii, aac(6')-Iih, ant(6)-Ia, aph(3')-III, ant(9)-Ia), fluoroquinolones (efmA, and emeA), vancomycin (VanC {VanC-2, VanXY, VanXYC-3, VanXYC-4, VanRC}), and chloramphenicol (cat). The litter-amended soil harboured new ARB (particularly E. faecium) and ARGs (ant(6)-Ia, aac(6')-Ii, aph(3')-III), lnu(G), msr(C), and eat(A), efmA) that were not previously detected in the soil. The identified ARGs were associated with diverse mobile genetic elements (MGEs) such as insertion sequences (IS6, ISL3, IS256, IS30), transposons (Tn3 and Tn916) and plasmids (repUS43, repUS1, rep9b, and rep 22). Twenty-eight virulence genes encoding adherence/biofilm formation (ebpA, ebpB, ebpC), antiphagocytosis (elrA) and bacterial sex pheromones (Ccf10, cOB1, cad, and camE), were detected in the genomes of the isolates. Phylogenomic analysis revealed a close relationship between a few isolates from litter-amended soil and the chicken litter isolates. The differences in the ARG and ARB profiles in the soil before and after the litter amendment and their association with diverse MGEs indicate the mobilisation and transmission of ARGs and ARB from the litter to the soil.
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Affiliation(s)
- Dorcas Oladayo Fatoba
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa.
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa; Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Abia Luther King Akebe
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
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Datar R, Orenga S, Pogorelcnik R, Rochas O, Simner PJ, van Belkum A. Recent Advances in Rapid Antimicrobial Susceptibility Testing. Clin Chem 2021; 68:91-98. [DOI: 10.1093/clinchem/hvab207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/17/2021] [Indexed: 12/30/2022]
Abstract
Abstract
Background
Antimicrobial susceptibility testing (AST) is classically performed using growth-based techniques that essentially require viable bacterial matter to become visible to the naked eye or a sophisticated densitometer.
Content
Technologies based on the measurement of bacterial density in suspension have evolved marginally in accuracy and rapidity over the 20th century, but assays expanded for new combinations of bacteria and antimicrobials have been automated, and made amenable to high-throughput turn-around. Over the past 25 years, elevated AST rapidity has been provided by nucleic acid-mediated amplification technologies, proteomic and other “omic” methodologies, and the use of next-generation sequencing. In rare cases, AST at the level of single-cell visualization was developed. This has not yet led to major changes in routine high-throughput clinical microbiological detection of antimicrobial resistance.
Summary
We here present a review of the new generation of methods and describe what is still urgently needed for their implementation in day-to-day management of the treatment of infectious diseases.
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Affiliation(s)
- Rucha Datar
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | - Sylvain Orenga
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | | | - Olivier Rochas
- bioMérieux, Corporate Business Development, Marcy l'Etoile, France
| | - Patricia J Simner
- Department of Pathology, Bacteriology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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Tenover FC. Using Molecular Diagnostics to Develop Therapeutic Strategies for Carbapenem-Resistant Gram-Negative Infections. Front Cell Infect Microbiol 2021; 11:715821. [PMID: 34650933 PMCID: PMC8505994 DOI: 10.3389/fcimb.2021.715821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/20/2021] [Indexed: 12/23/2022] Open
Abstract
Infections caused by multidrug-resistant Gram-negative organisms have become a global threat. Such infections can be very difficult to treat, especially when they are caused by carbapenemase-producing organisms (CPO). Since infections caused by CPO tend to have worse outcomes than non-CPO infections, it is important to identify the type of carbapenemase present in the isolate or at least the Ambler Class (i.e., A, B, or D), to optimize therapy. Many of the newer beta-lactam/beta-lactamase inhibitor combinations are not active against organisms carrying Class B metallo-enzymes, so differentiating organisms with Class A or D carbapenemases from those with Class B enzymes rapidly is critical. Using molecular tests to detect and differentiate carbapenem-resistance genes (CRG) in bacterial isolates provides fast and actionable results, but utilization of these tests globally appears to be low. Detecting CRG directly in positive blood culture bottles or in syndromic panels coupled with bacterial identification are helpful when results are positive, however, even negative results can provide guidance for anti-infective therapy for key organism-drug combinations when linked to local epidemiology. This perspective will focus on the reluctance of laboratories to use molecular tests as aids to developing therapeutic strategies for infections caused by carbapenem-resistant organisms and how to overcome that reluctance.
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Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California. Antibiotics (Basel) 2021; 10:antibiotics10091042. [PMID: 34572624 PMCID: PMC8471271 DOI: 10.3390/antibiotics10091042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
The objectives of this study were to characterize overall genomic antibiotic resistance profiles of fecal Escherichia coli and Enterococcus spp. from dairy cattle at different production stages using whole-genome sequencing and to determine the association between antimicrobial resistance (AMR) phenotypes and their corresponding genotypes. The Comprehensive Antibiotic Resistance Database (CARD) and ResFinder, two publicly available databases of antimicrobial resistance genes, were used to annotate isolates. Based on the ResFinder database, 27.5% and 20.0% of tested E. coli isolates (n = 40) harbored single and ≥3 antimicrobial resistance genes, respectively; for Enterococcus spp., we observed 87.8% and 8.2%, respectively. The highest prevalence of AMR genes in E. coli was for resistance to tetracycline (27.5%), followed by sulphonamide (22.5%) and aminoglycoside (20.0%); the predominant antimicrobial resistance genes in Enterococcus spp. targeted macrolide drugs (77.6%). Based on the CARD database, resistance to ≥3 antimicrobial classes was observed in all E. coli and 77.6% in Enterococcus spp. isolates. A high degree of agreement existed between the resistance phenotype and the presence of resistance genes for various antimicrobial classes for E. coli but much less so for isolates of Enterococcus. Consistent with prior work, fecal E. coli and Enterococcus spp. isolates from calves harbored a wide spectrum of resistance genes, compared to those from cattle at other production stages, based on the cross-sectional samples from the studied farm.
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Elevated MICs of Susceptible Anti-Pseudomonal Cephalosporins in Non-Carbapenemase-Producing, Carbapenem-Resistant Pseudomonas aeruginosa: Implications for Dose Optimization. Antimicrob Agents Chemother 2021; 65:e0120421. [PMID: 34398670 DOI: 10.1128/aac.01204-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present study evaluated the in vitro potency of ceftazidime and cefepime amongst carbapenem-resistant Pseudomonas aeruginosa collected as part of a global surveillance program and assessed the pharmacodynamic implications using previously published population pharmacokinetics. When susceptible, MICs resulted at the high end of distribution for both ceftazidime and cefepime, thus 6 g/day was required to achieve optimal pharmacodynamic profiles. These findings should be considered in the clinic and for the application of CLSI susceptibility breakpoints.
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Golden AR, Karlowsky JA, Walkty A, Baxter MR, Denisuik AJ, McCracken M, Mulvey MR, Adam HJ, Bay D, Zhanel GG. Comparison of phenotypic antimicrobial susceptibility testing results and WGS-derived genotypic resistance profiles for a cohort of ESBL-producing Escherichia coli collected from Canadian hospitals: CANWARD 2007-18. J Antimicrob Chemother 2021; 76:2825-2832. [PMID: 34378044 DOI: 10.1093/jac/dkab268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/05/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine whether the genotypic resistance profile inferred from WGS could accurately predict phenotypic resistance for ESBL-producing Escherichia coli isolated from patient samples in Canadian hospital laboratories. METHODS As part of the ongoing CANWARD study, 671 E. coli were collected and phenotypically confirmed as ESBL producers using CLSI M100 disc testing criteria. Isolates were sequenced using the Illumina MiSeq platform, resulting in 636 high-quality genomes for comparison. Using a rules-based approach, the genotypic resistance profile was compared with the phenotypic resistance interpretation generated using the CLSI broth microdilution method for ceftriaxone, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole. RESULTS The most common genes associated with non-susceptibility to ceftriaxone, gentamicin and trimethoprim/sulfamethoxazole were CTX-M-15 (n = 391), aac(3)-IIa + aac(6')-Ib-cr (n = 121) and dfrA17 + sul1 (n = 169), respectively. Ciprofloxacin non-susceptibility was most commonly attributed to alterations in both gyrA (S83L + D87N) and parC (S80I + E84V), with (n = 187) or without (n = 197) aac(6')-Ib-cr. Categorical agreement (susceptible or non-susceptible) between actual and predicted phenotype was 95.6%, 98.9%, 97.6% and 88.8% for ceftriaxone, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole, respectively. Only ciprofloxacin results (susceptible or non-susceptible) were predicted with major error (ME) and very major error (VME) rates of <3%: ciprofloxacin (ME, 1.5%; VME, 1.1%); gentamicin (ME, 0.8%-31.7%; VME, 4.8%); ceftriaxone (ME, 81.8%; VME, 3.0%); and trimethoprim/sulfamethoxazole (ME, 0.9%-23.0%; VME, 5.2%-8.5%). CONCLUSIONS Our rules-based approach for predicting a resistance phenotype from WGS performed well for ciprofloxacin, with categorical agreement of 98.9%, an ME rate of 1.5% and a VME rate of 1.1%. Although high categorical agreements were also obtained for gentamicin, ceftriaxone and trimethoprim/sulfamethoxazole, ME and/or VME rates were ≥3%.
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Affiliation(s)
- Alyssa R Golden
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Department of Clinical Microbiology, Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Andrew Walkty
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Department of Clinical Microbiology, Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Andrew J Denisuik
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Melissa McCracken
- National Microbiology Laboratory-Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2 Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,National Microbiology Laboratory-Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2 Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Department of Clinical Microbiology, Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Denice Bay
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
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Impact of Accelerate Pheno and BacT/Alert Virtuo on Clinical Processes and Outcomes in Patients with Sepsis and Concurrent Gram-Negative Bacteremia. Antimicrob Agents Chemother 2021; 65:AAC.02364-20. [PMID: 33753337 DOI: 10.1128/aac.02364-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/14/2021] [Indexed: 12/14/2022] Open
Abstract
The Accelerate Pheno and BacT/Alert Virtuo systems may improve bacteremia management. Here, we evaluated the impact of both devices on outcomes in patients with sepsis and concurrent Gram-negative bacteremia. This quasiexperimental study included a retrospective preimplementation and a prospective postimplementation group. Patients ≥18 years old with Gram-negative bacteremia were included. Patients with neutropenia, pregnant patients, those who were transferred from an outside hospital with active bloodstream infections, and those with polymicrobial bacteremia were excluded. Blood culture incubation in the BacT/Alert 3D device and microdilution antimicrobial susceptibility testing from culture plate growth were used prior to implementation of the BacT/Alert Virtuo and Accelerate Pheno systems. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identification directly from blood culture was used pre- and postimplementation. Time to Gram stain results, identification, susceptibility reporting, initiation of narrow-spectrum Gram-negative therapy at 72 h, 30-day inpatient mortality, sepsis resolution, and length of hospital stay were evaluated. A total of 116 patients were included (63 preimplementation, 53 postimplementation). Median times to Gram stain and susceptibility results were significantly shorter postimplementation (P < 0.001). The postimplementation group had an improved hazard ratio for narrow-spectrum Gram-negative therapy at 72 h (hazard ratio [HR], 2.685 [95% confidence interval {CI}, 1.348 to 5.349]), a reduced hazard ratio for 30-day inpatient mortality (adjusted HR [aHR], 0.150 [95% CI, 0.026 to 0.846]), and improved sepsis resolution (92.5% versus 77.8% [P = 0.030]). The length of hospital stay was unchanged after implementation. We conclude that implementation of the BacT/Alert Virtuo and Accelerate Pheno systems improved microbiology laboratory processes, antibiotic utilization processes, and clinical outcomes. These data support the use of rapid diagnostics in sepsis with concurrent Gram-negative bacteremia.
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