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Tseng YW, Huang CW, Chen CC, Er TK. Assessment of antibiotic resistance patterns in Central Taiwan during the COVID-19 pandemic: A retrospective study. J Infect Public Health 2024; 17:229-235. [PMID: 38118294 DOI: 10.1016/j.jiph.2023.11.026] [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: 10/07/2023] [Revised: 11/15/2023] [Accepted: 11/26/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a growing worldwide public health issue due to the overuse and inappropriate use of antibiotics. AMR has been more prevalent during the coronavirus pandemic of 2019 (COVID-19) compared to previous periods. Therefore, this study was conducted to evaluate the AMR profile of common bacteria that were isolated for routine analysis during the pandemic of COVID-19 in Central Taiwan. The main goal of this study was to examine and analyze the AMR patterns both before and after the start of the COVID-19 pandemic. METHODS We conducted a retrospective analysis of clinical samples collected from two different time periods: the 1-year period before the onset of the COVID-19 pandemic (January 2019 to December 2019) and the 2-year period following the start of the pandemic (September 2020 to September 2022). The data for this study were obtained from clinical records, and both bacterial identification and antibiotic susceptibility testing were performed using the Phoenix identification system. RESULTS Among the 8152 bacterial isolates obtained during the study period from September 2020 to September 2022, 4022 (49.3%) were Escherichia coli, 1346 (16.5%) were Klebsiella pneumoniae, 1156 (14.2%) were Staphylococcus aureus, 887 (10.9%) were Pseudomonas aeruginosa, 376 (4.6%) were Enterococcus faecium, and 365 (4.5%) were Acinetobacter baumannii. The overall prevalence of resistant bacteria during the COVID-19 pandemic was as follows: vancomycin-resistant Enterococcus, 69%; carbapenem-resistant A. baumannii, 65%; methicillin-resistant S. aureus, 49%; carbapenem-resistant K. pneumoniae, 29%; carbapenem-resistant P. aeruginosa, 17%; and carbapenem-resistant E. coli, 2%. Carbapenem-resistant A. baumannii, vancomycin-resistant Enterococcus, carbapenem-resistant K. pneumoniae, and carbapenem-resistant E. coli increased by 19%, 10%, 2%, and 1%, respectively. On the other hand, carbapenem-resistant P. aeruginosa and methicillin-resistant S. aureus decreased by 6%, respectively. CONCLUSION This study provides a comprehensive assessment of AMR during the COVID-19 pandemic in Central Taiwan. Understanding the prevalence of AMR is crucial for preventing infection and formulating disease prevention policies. Further research is warranted to elucidate the correlation between AMR and the severity of infection in COVID-19 patients.
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Affiliation(s)
- Yu-Wei Tseng
- Division of Laboratory Medicine, Asia University Hospital, Asia University, Taichung, Taiwan
| | - Chien-Wen Huang
- Division of Chest Medicine, Department of Internal Medicine, Asia University Hospital, Asia University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tze-Kiong Er
- Division of Laboratory Medicine, Asia University Hospital, Asia University, Taichung, Taiwan; Department of Nursing, Asia University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.
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Busby EJ, Doyle RM, Leboreiro Babe C, Harris KA, Mack D, Méndez-Cervantes G, O’Sullivan DM, Pang V, Sadouki Z, Solanki P, Huggett JF, McHugh TD, Wey EQ. Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Molecular Typing of Acinetobacter baumannii in Comparison with Orthogonal Methods. Microbiol Spectr 2023; 11:e0499522. [PMID: 37154773 PMCID: PMC10269802 DOI: 10.1128/spectrum.04995-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/23/2023] [Indexed: 05/10/2023] Open
Abstract
Colonization and subsequent health care-associated infection (HCAI) with Acinetobacter baumannii are a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multidrug-resistant strains are associated with increased patient morbidity and mortality and poorer overall outcomes. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks. In addition to methods deployed by reference laboratories, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) may assist by making initial in-house judgments on strain relatedness. However, limited studies on method reproducibility exist for this application. We applied MALDI-TOF MS typing to A. baumannii isolates associated with a nosocomial outbreak and evaluated different methods for data analysis. In addition, we compared MALDI-TOF MS with whole-genome sequencing (WGS) and Fourier transform infrared spectroscopy (FTIR) as orthogonal methods to further explore their resolution for bacterial strain typing. A related subgroup of isolates consistently clustered separately from the main outbreak group by all investigated methods. This finding, combined with epidemiological data from the outbreak, indicates that these methods identified a separate transmission event unrelated to the main outbreak. However, the MALDI-TOF MS upstream approach introduced measurement variability impacting method reproducibility and limiting its reliability as a standalone typing method. Availability of in-house typing methods with well-characterized sources of measurement uncertainty could assist with rapid and dependable confirmation (or denial) of suspected transmission events. This work highlights some of the steps to be improved before such tools can be fully integrated into routine diagnostic service workflows for strain typing. IMPORTANCE Managing the transmission of antimicrobial resistance necessitates reliable methods for tracking outbreaks. We compared the performance of MALDI-TOF MS with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates correlated with a health care-associated infection (HCAI) event. Combined with epidemiological data, all methods investigated identified a group of isolates that were temporally and spatially linked to the outbreak, yet potentially attributed to a separate transmission event. This may have implications for guiding infection control strategies during an outbreak. However, the technical reproducibility of MALDI-TOF MS needs to be improved for it to be employed as a standalone typing method, as different stages of the experimental workflow introduced bias influencing interpretation of biomarker peak data. Availability of in-house methods for strain typing of bacteria could improve infection control practices following increased reports of outbreaks of antimicrobial-resistant organisms during the COVID-19 pandemic, related to sessional usage of personal protective equipment (PPE).
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Affiliation(s)
- Eloise J. Busby
- National Measurement Laboratory, LGC, Teddington, Middlesex, United Kingdom
| | - Ronan M. Doyle
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Clara Leboreiro Babe
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Kathryn A. Harris
- Virology Department, ESEL Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Damien Mack
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | | | | | - Vicky Pang
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | - Zahra Sadouki
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Priya Solanki
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Jim F. Huggett
- National Measurement Laboratory, LGC, Teddington, Middlesex, United Kingdom
- School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, United Kingdom
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Emmanuel Q. Wey
- Centre for Clinical Microbiology, Royal Free Campus, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- Royal Free Hospital NHS Foundation Trust, London, United Kingdom
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3
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Treffon J, Heppner B, Eismann J, Bothe J, Omengo B, Mellmann A. Single Nucleotide Polymorphism-Based Real-Time PCR Screening Assay for Rapid Tracking of Bacterial Infection Clusters To Complement Whole-Genome Sequencing Efforts during Outbreak Investigations. Microbiol Spectr 2022; 10:e0303622. [PMID: 36250868 PMCID: PMC9769705 DOI: 10.1128/spectrum.03036-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/16/2022] [Indexed: 01/09/2023] Open
Abstract
Infection clusters of multidrug-resistant bacteria increase mortality and entail expensive infection control measures. Whereas whole-genome sequencing (WGS) is the current gold standard to confirm infection clusters, PCR-based assays targeting cluster-specific signatures, such as single nucleotide polymorphisms (SNPs) derived from WGS data, are more suitable to initially screen for cluster isolates within large sample sizes. Here, we evaluated four software tools (SeqSphere+, RUCS, Gegenees, and Find Differential Primers) regarding their efficiency to find SNPs within WGS data sets that were specific for two bacterial monospecies infection clusters but were absent from a WGS reference data set comprising several hundred diverse genotypes of the same bacterial species. Cluster-specific SNPs were subsequently used to establish a probe-based real-time PCR screening assay for in vitro differentiation between cluster and noncluster isolates. SeqSphere+ and RUCS found 2 and 24 SNPs for clusters 1 and 14 and 24 SNPs for cluster 2, respectively. However, some signatures detected by RUCS were not cluster specific. Interestingly, all SNPs identified by SeqSphere+ were also detected by RUCS. In contrast, analyses with the remaining tools either resulted in no SNPs (with Find Differential Primers) or failed (Gegenees). Design of six cluster-specific real-time PCR assays enabled reliable cluster screening in vitro. Our evaluation revealed that SeqSphere+ and RUCS identified cluster-specific SNPs that could be used for large-scale screening in surveillance samples via real-time PCR, thereby complementing WGS efforts. This faster and simplified approach for the surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians. IMPORTANCE Infection clusters of multidrug-resistant bacteria threaten medical facilities worldwide and cause immense health care costs. In recent years, whole-genome sequencing (WGS) has been increasingly applied to detect and to further control bacterial clusters. However, as WGS is still expensive and time-consuming, its exclusive application for screening and confirmation of bacterial infection clusters contributes to high costs and enhanced turnaround times, which many hospitals cannot afford. Therefore, there is need for alternative methods that can enable further surveillance of bacterial clusters that are initially detected by WGS in a faster and more cost-efficient way. Here, we established a system based on real-time PCR that enables rapid large-scale sample screening for bacterial cluster isolates within 7 days after the initial detection of an infection cluster, thereby complementing WGS efforts. This faster and simplified surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians.
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Affiliation(s)
- Janina Treffon
- University Hospital Münster, Institute of Hygiene, Münster, Germany
| | - Bianca Heppner
- University Hospital Münster, Institute of Hygiene, Münster, Germany
| | | | - Julia Bothe
- inno-train Diagnostik GmbH, Kronberg, Germany
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Jiang Y, Ding Y, Wei Y, Jian C, Liu J, Zeng Z. Carbapenem-resistant Acinetobacter baumannii: A challenge in the intensive care unit. Front Microbiol 2022; 13:1045206. [PMID: 36439795 PMCID: PMC9684325 DOI: 10.3389/fmicb.2022.1045206] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) has become one of the leading causes of healthcare-associated infections globally, particularly in intensive care units (ICUs). Cross-transmission of microorganisms between patients and the hospital environment may play a crucial role in ICU-acquired CRAB colonization and infection. The control and treatment of CRAB infection in ICUs have been recognized as a global challenge because of its multiple-drug resistance. The main concern is that CRAB infections can be disastrous for ICU patients if currently existing limited therapeutic alternatives fail in the future. Therefore, the colonization, infection, transmission, and resistance mechanisms of CRAB in ICUs need to be systematically studied. To provide a basis for prevention and control countermeasures for CRAB infection in ICUs, we present an overview of research on CRAB in ICUs, summarize clinical infections and environmental reservoirs, discuss the drug resistance mechanism and homology of CRAB in ICUs, and evaluate contemporary treatment and control strategies.
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Havenga B, Reyneke B, Ndlovu T, Khan W. Genotypic and phenotypic comparison of clinical and environmental Acinetobacter baumannii strains. Microb Pathog 2022; 172:105749. [PMID: 36087691 DOI: 10.1016/j.micpath.2022.105749] [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: 05/26/2022] [Revised: 07/20/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022]
Abstract
The genotypic and phenotypic characteristics and antibiotic resistance (antibiogram) profiles of clinical (n = 13) and environmental (n = 7) Acinetobacter baumannii isolates were compared. Based on the Repetitive Extragenic Palindromic Sequence-based PCR (REP-PCR) analysis, the clinical and environmental A. baumannii isolates shared low genetic relatedness (∼60%). Multilocus sequence typing (MLST, Oxford scheme) indicated that the clinical A. baumannii were assigned to three sequence types (ST231, ST945 and ST848), while the environmental A. baumannii (excluding AB 14) were categorised into the novel ST2520. The majority of the clinical (excluding AB 5, CAB 11, CAC 37) and environmental (excluding AB 14 and AB 16) A. baumannii strains were then capable of phase variation with both the translucent (71.4%; 15/21) and opaque (95.2%; 20/21) colony phenotypes detected. The clinical isolates however, exhibited significantly (p < 0.05) higher biofilm formation capabilities (OD570: 2.094 ± 0.497). Moreover, the clinical isolates exhibited significantly (p < 0.05) higher resistance to first line antibiotics, with 92.3% (12/13) characterised as extensively drug resistant (XDR), whereas environmental A. baumannii exhibited increased antibiotic susceptibility with only 57.1% (4/7) characterised as multidrug resistant (MDR). The environmental isolate AB 14 was however, characterised as XDR. In addition, only five clinical A. baumannii isolates exhibited colistin resistance (38.5%; 5/13). The current study highlighted the differences in the genotypic, phenotypic, and antibiotic resistance profiles of clinical and environmental A. baumannii. Moreover, the environmental strains were assigned to the novel ST2520, which substantiates the existence of this opportunistic pathogen in extra-hospital reservoirs.
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Affiliation(s)
- Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Thando Ndlovu
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB, 0022, Gaborone, Botswana
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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Acinetobacter baumannii Genomic Sequence-Based Core Genome Multilocus Sequence Typing Using Ridom SeqSphere+ and Antimicrobial Susceptibility Prediction in ARESdb. J Clin Microbiol 2022; 60:e0053322. [PMID: 35862760 PMCID: PMC9383114 DOI: 10.1128/jcm.00533-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Whole-genome sequencing (WGS) is rapidly replacing traditional typing methods for the investigation of infectious disease outbreaks. Additionally, WGS data are being used to predict phenotypic antimicrobial susceptibility. Acinetobacter baumannii, which is often multidrug-resistant, is a significant culprit in outbreaks in health care settings. A well-characterized collection of A. baumannii was studied using core genome multilocus sequence typing (cgMLST). Seventy-two isolates previously typed by PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) provided by the Antimicrobial Resistance Leadership Group (ARLG) were analyzed using a clinical microbiology laboratory developed workflow for cgMLST with genomic susceptibility prediction performed using the ARESdb platform. Previously performed PCR/ESI-MS correlated with cgMLST using relatedness thresholds of allelic differences of ≤9 and ≤200 allelic differences in 78 and 94% of isolates, respectively. Categorical agreement between genotypic and phenotypic antimicrobial susceptibility across a panel of 11 commonly used drugs was 89%, with minor, major, and very major error rates of 8%, 11%, and 1%, respectively.
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7
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Naing SY, Hordijk J, Duim B, Broens EM, van der Graaf-van Bloois L, Rossen JW, Robben JH, Leendertse M, Wagenaar JA, Zomer AL. Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands. Pathogens 2022; 11:pathogens11020123. [PMID: 35215067 PMCID: PMC8875366 DOI: 10.3390/pathogens11020123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/27/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes a pressing public health threat. Two MDR A. baumannii outbreaks occurred in 2012 and 2014 in a companion animal intensive care unit (caICU) in the Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), environmental isolates (n = 5), and human reference strains (n = 3) to investigate if the isolates of the two outbreaks were related. All clinical isolates shared identical resistance phenotypes displaying multidrug resistance. Multi-locus Sequence Typing (MLST) revealed that all clinical isolates belonged to sequence type ST2. The core genome MLST (cgMLST) results confirmed that the isolates of the two outbreaks were not related. Comparative genome analysis showed that the outbreak isolates contained different gene contents, including mobile genetic elements associated with antimicrobial resistance genes (ARGs). The time-measured phylogenetic reconstruction revealed that the outbreak isolates diverged approximately 30 years before 2014. Our study shows the importance of WGS analyses combined with molecular clock investigations to reduce transmission of MDR A. baumannii infections in companion animal clinics.
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Affiliation(s)
- Soe Yu Naing
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Els M. Broens
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - John W. Rossen
- Department of Medical Microbiology, University Medical Center, University of Groningen, 9700 AB Groningen, The Netherlands;
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joris H. Robben
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands;
| | - Masja Leendertse
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
- Correspondence:
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Shelenkov A. Whole-Genome Sequencing of Pathogenic Bacteria-New Insights into Antibiotic Resistance Spreading. Microorganisms 2021; 9:2624. [PMID: 34946225 PMCID: PMC8708895 DOI: 10.3390/microorganisms9122624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023] Open
Abstract
In recent years, the acquisition of antimicrobial resistance (AMR) by both pathogenic and opportunistic bacteria has become a major problem worldwide, which was already noticed as a global healthcare threat by the World Health Organization [...].
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Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Rospotrebnadzor, 111123 Moscow, Russia
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9
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Diversity of International High-Risk Clones of Acinetobacter baumannii Revealed in a Russian Multidisciplinary Medical Center during 2017-2019. Antibiotics (Basel) 2021; 10:antibiotics10081009. [PMID: 34439060 PMCID: PMC8389025 DOI: 10.3390/antibiotics10081009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Acinetobacter baumannii is a dangerous bacterial pathogen possessing the ability to persist on various surfaces, especially in clinical settings, and to rapidly acquire the resistance to a broad spectrum of antibiotics. Thus, the epidemiological surveillance of A. baumannii within a particular hospital, region, and across the world is an important healthcare task that currently usually includes performing whole-genome sequencing (WGS) of representative isolates. During the past years, the dissemination of A. baumannii across the world was mainly driven by the strains belonging to two major groups called the global clones or international clones (ICs) of high risk (IC1 and IC2). However, currently nine ICs are already considered. Although some clones were previously thought to spread in particular regions of the world, in recent years this is usually not the case. In this study, we determined five ICs, as well as three isolates not belonging to the major ICs, in one multidisciplinary medical center within the period 2017-2019. We performed WGS using both short- and long-read sequencing technologies of nine representative clinical A. baumannii isolates, which allowed us to determine the antibiotic resistance and virulence genomic determinants, reveal the CRISPR/Cas systems, and obtain the plasmid structures. The phenotypic and genotypic antibiotic resistance profiles are compared, and the possible ways of isolate and resistance spreading are discussed. We believe that the data obtained will provide a better understanding of the spreading and resistance acquisition of the ICs of A. baumannii and further stress the necessity for continuous genomic epidemiology surveillance of this problem-causing bacterial species.
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Meschiari M, Lòpez-Lozano JM, Di Pilato V, Gimenez-Esparza C, Vecchi E, Bacca E, Orlando G, Franceschini E, Sarti M, Pecorari M, Grottola A, Venturelli C, Busani S, Serio L, Girardis M, Rossolini GM, Gyssens IC, Monnet DL, Mussini C. A five-component infection control bundle to permanently eliminate a carbapenem-resistant Acinetobacter baumannii spreading in an intensive care unit. Antimicrob Resist Infect Control 2021; 10:123. [PMID: 34412693 PMCID: PMC8376111 DOI: 10.1186/s13756-021-00990-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/07/2021] [Indexed: 12/18/2022] Open
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) infection outbreaks are difficult to control and sometimes require cohorting of CRAB-positive patients or temporary ward closure for environmental cleaning. We aimed at controlling the deadly 2018 CRAB outbreak in a 12 bed- intensive care unit (ICU) including 9 beds in a 220 m2 open space. We implemented a new multimodal approach without ward closure, cohorting or temporarily limiting admissions. Methods A five-component bundle was introduced in 2018 including reinforcement of hand hygiene and sample extension of screening, application of contact precautions to all patients, enhanced environmental sampling and the one-time application of a cycling radical environmental cleaning and disinfection procedure of the entire ICU. The ICU-CRAB incidence density (ID), ICU alcohol-based hand rub consumption and antibiotic use were calculated over a period of 6 years and intervention time series analysis was performed. Whole genome sequencing analysis (WGS) was done on clinical and environmental isolates in the study period. Results From January 2013, nosocomial ICU-CRAB ID decreased from 30.4 CRAB cases per 1000 patients-days to zero cases per 1000 patients-days. Our intervention showed a significant impact (-2.9 nosocomial ICU-CRAB cases per 1000 bed-days), while no influence was observed for antibiotic and alcohol-based hand rub (AHR) consumption. WGS demonstrated that CRAB strains were clonally related to an environmental reservoir which confirms the primary role of the environment in CRAB ICU spreading. Conclusion A five-component bundle of continuous hand hygiene improvement, extended sampling at screening including the environment, universal contact precautions and a novel cycling radical environmental cleaning and disinfection procedure proved to be effective for permanently eliminating CRAB spreading within the ICU. Cohorting, admission restriction or ICU closure were avoided. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-00990-z.
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Affiliation(s)
- Marianna Meschiari
- Infectious Disease Clinic, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy.
| | | | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | | | - Elena Vecchi
- Hospital Hygiene and Infection Control, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy
| | - Erica Bacca
- Infectious Disease Clinic, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy
| | - Gabriella Orlando
- Infectious Disease Clinic, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy
| | - Erica Franceschini
- Infectious Disease Clinic, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy
| | - Mario Sarti
- Clinical Microbiology Laboratory, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy
| | - Monica Pecorari
- Laboratory of Virology and Molecular Biology, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy
| | - Antonella Grottola
- Laboratory of Virology and Molecular Biology, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy
| | - Claudia Venturelli
- Clinical Microbiology Laboratory, Azienda Ospedaliero-Universitaria Policlinico of Modena, Modena, Italy
| | - Stefano Busani
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy
| | - Lucia Serio
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy
| | - Massimo Girardis
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy
| | - Gian Maria Rossolini
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Inge C Gyssens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Dominique L Monnet
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Cristina Mussini
- Infectious Disease Clinic, Azienda Ospedaliero-Universitaria Policlinico and University of Modena and Reggio Emilia, Modena, Italy
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11
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Stracquadanio S, Torti E, Longshaw C, Henriksen AS, Stefani S. In vitro activity of cefiderocol and comparators against isolates of Gram-negative pathogens from a range of infection sources: SIDERO-WT-2014-2018 studies in Italy. J Glob Antimicrob Resist 2021; 25:390-398. [PMID: 34020073 DOI: 10.1016/j.jgar.2021.04.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/12/2021] [Accepted: 04/24/2021] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES Antimicrobial resistance, particularly carbapenem resistance, in Gram-negative pathogens poses a significant healthcare threat. Carbapenem resistance rates in Italy are among the highest in Europe. We report the in vitro activity of cefiderocol, a novel siderophore cephalosporin, and comparator antibiotics against Gram-negative isolates from Italy as part of the SIDERO-WT studies. METHODS Isolates were collected between 2014 and 2018. Minimum inhibitory concentrations (MICs) were determined using International Organization for Standardization and EUCAST guidelines. Antimicrobial susceptibilities were interpreted using EUCAST breakpoints; pharmacodynamic/pharmacokinetic breakpoints were used if EUCAST breakpoints were not specified. RESULTS The 2472 isolates [1545 (62.5%) Enterobacterales and 927 (37.5%) non-fermenters] represented a range of infection sources, including nosocomial pneumonia (902; 36.5%), complicated urinary tract infection (374; 15.1%), bloodstream infection (596; 24.1%), complicated intra-abdominal infection (257; 10.4%) and other infection sources (343; 13.9%). Cefiderocol was active against the majority of isolates, regardless of infection source (susceptibility, 94.2-97.3%). A high proportion of non-fermenters (97.6%) and Enterobacterales (95.6%) were cefiderocol-susceptible, although susceptibility was lower in Klebsiella pneumoniae (88.1%). Susceptibility to cefiderocol was significantly (P < 0.01) greater than comparators overall (96.4% vs. 71.3-81.6%) and in non-fermenters (97.6% vs. 44.3-90.3%) across infection sources. Overall 612/2472 isolates (24.8%) were meropenem-resistant (MIC > 8 mg/L), comprising 516/927 (55.7%) non-fermenters and 96/1545 (6.2%) Enterobacterales. Cefiderocol (499/516; 96.7%) activity was greater than colistin (440/516; 85.3%), ceftazidime/avibactam (123/516; 23.8%) and ceftolozane/tazobactam (89/516; 17.2%) in meropenem-resistant non-fermenter isolates. CONCLUSION Susceptibility to cefiderocol was significantly greater than meropenem, colistin, ceftazidime/avibactam and ceftolozane/tazobactam overall, regardless of infection source.
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Affiliation(s)
- Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, Università di Catania, Via Santa Sofia 97, I-95123 Catania, Italy.
| | | | | | | | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, Università di Catania, Via Santa Sofia 97, I-95123 Catania, Italy
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12
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Lötsch F, Albiger B, Monnet DL, Struelens MJ, Seifert H, Kohlenberg A. Epidemiological situation, laboratory capacity and preparedness for carbapenem-resistant Acinetobacter baumannii in Europe, 2019. ACTA ACUST UNITED AC 2021; 25. [PMID: 33183407 PMCID: PMC7667627 DOI: 10.2807/1560-7917.es.2020.25.45.2001735] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
To update information on the epidemiological situation and national capacity for detection, surveillance and containment of carbapenem-resistant Acinetobacter baumannii (CRAb) in Europe, we performed a survey in 37 countries. Nine countries reported regional or inter-regional spread and seven an endemic situation. Laboratories with a reference function, surveillance systems, and a national containment plan for CRAb existed in 30, 23 and eight countries, respectively. A pan-European molecular survey would provide in-depth understanding of the CRAb epidemiology.
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Affiliation(s)
- Felix Lötsch
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Barbara Albiger
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Dominique L Monnet
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Marc J Struelens
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Harald Seifert
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Anke Kohlenberg
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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- The EURGen-Net carbapenem-resistant Acinetobacter baumannii capacity survey group members are listed below
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13
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Chen L, Tan P, Zeng J, Yu X, Cai Y, Liao K, Guo P, Chen Y, Wu Z, Qu P, Cai R, Chen C, Huang B. Impact of an Intervention to Control Imipenem-Resistant Acinetobacter baumannii and Its Resistance Mechanisms: An 8-Year Survey. Front Microbiol 2021; 11:610109. [PMID: 33664711 PMCID: PMC7921317 DOI: 10.3389/fmicb.2020.610109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/24/2020] [Indexed: 01/09/2023] Open
Abstract
Background This study aimed to examine the impact of an intervention carried out in 2011 to combat multi-drug resistance and outbreaks of imipenem-resistant Acinetobacter baumannii (IRAB), and to explore its resistance mechanism. Methods A total of 2572 isolates of A. baumannii, including 1673 IRAB isolates, were collected between 2007 and 2014. An intervention was implemented to control A. baumannii resistance and outbreaks. Antimicrobial susceptibility was tested by calculating minimal inhibitory concentrations (MICs), and outbreaks were typed using pulsed-field gel electrophoresis (PFGE). Resistance mechanisms were explored by polymerase chain reaction (PCR) and whole genome sequencing (WGS). Results Following the intervention in 2011, the resistance rates of A. baumannii to almost all tested antibiotics decreased, from 85.3 to 72.6% for imipenem, 100 to 80.8% for ceftriaxone, and 45.0 to 6.9% for tigecycline. The intervention resulted in a decrease in the number (seven to five), duration (8–3 months), and departments (five to three) affected by outbreaks; no outbreaks occurred in 2011. After the intervention, only blaAMPC (76.47 to 100%) and blaTEM–1 (75.74 to 96.92%) increased (P < 0.0001); whereas blaGES–1 (32.35 to 3.07%), blaPER–1 (21.32 to 1.54%), blaOXA–58 (60.29 to 1.54%), carO (37.50 to 7.69%), and adeB (9.56 to 3.08%) decreased (P < 0.0001). Interestingly, the frequency of class B β-lactamase genes decreased from 91.18% (blaSPM–1) and 61.03% (blaIMP–1) to 0%, while that of class D blaOXA–23 increased to 96.92% (P < 0.0001). WGS showed that the major PFGE types causing outbreaks each year (type 01, 11, 18, 23, 26, and 31) carried the same resistance genes (blaKPC–1, blaADC–25, blaOXA–66, and adeABC), AdeR-S mutations (G186V and A136V), and a partially blocked porin channel CarO. Meanwhile, plasmids harboring blaOXA–23 were found after the intervention. Conclusion The intervention was highly effective in reducing multi-drug resistance of A. baumannii and IRAB outbreaks in the long term. The resistance mechanisms of IRAB may involve genes encoding β-lactamases, efflux pump overexpression, outer membrane porin blockade, and plasmids; in particular, clonal spread of blaOXA–23 was the major cause of outbreaks. Similar interventions may also help reduce bacterial resistance rates and outbreaks in other hospitals.
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Affiliation(s)
- Lida Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Blood Transfusion, China-Japan Friendship Hospital, Beijing, China
| | - Pinghai Tan
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianming Zeng
- Department of Laboratory Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xuegao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yimei Cai
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Penghao Guo
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zongwen Wu
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Pinghua Qu
- Department of Laboratory Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Renxin Cai
- Department of Laboratory Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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14
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Hwang SM, Cho HW, Kim TY, Park JS, Jung J, Song KH, Lee H, Kim ES, Kim HB, Park KU. Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii. Diagnostics (Basel) 2021; 11:diagnostics11020201. [PMID: 33573077 PMCID: PMC7910894 DOI: 10.3390/diagnostics11020201] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.
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Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Hee Won Cho
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Seoul 06351, Korea;
| | - Jeong Su Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Jongtak Jung
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Kyoung-Ho Song
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hyunju Lee
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Eu Suk Kim
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hong Bin Kim
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Correspondence: ; Tel.: +82-2740-8005
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15
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Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY 2021; 1:e62. [PMID: 36168472 PMCID: PMC9495627 DOI: 10.1017/ash.2021.233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/12/2022]
Abstract
Background: Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms. Objective: To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital. Design: Cost-effectiveness study. Setting: Intensive care unit and burn unit of large metropolitan hospital. Patients: Simulated intensive care unit and burn unit patients. Methods: We built a complex simulation model to estimate pathogen transmission, associated hospital costs, and quality-adjusted life years (QALYs) during a 32-month outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB). Model parameters were determined using microbiology surveillance data, genome sequencing results, hospital admission databases, and local clinical knowledge. The model was calibrated to the actual pathogen spread within the intensive care unit and burn unit (scenario 1) and compared with early use of WGS (scenario 2) and early use of WGS and metagenomics (scenario 3) to determine their respective cost-effectiveness. Sensitivity analyses were performed to address model uncertainty. Results: On average compared with scenario 1, scenario 2 resulted in 14 fewer patients with CRAB, 59 additional QALYs, and $75,099 cost savings. Scenario 3, compared with scenario 1, resulted in 18 fewer patients with CRAB, 74 additional QALYs, and $93,822 in hospital cost savings. The likelihoods that scenario 2 and scenario 3 were cost-effective were 57% and 60%, respectively. Conclusions: The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes.
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16
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Rafei R, Osman M, Dabboussi F, Hamze M. Update on the epidemiological typing methods for Acinetobacter baumannii. Future Microbiol 2019; 14:1065-1080. [DOI: 10.2217/fmb-2019-0134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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17
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Muthuirulandi Sethuvel DP, Devanga Ragupathi NK, Bakthavatchalam YD, Vijayakumar S, Varghese R, Shankar C, Jacob JJ, Vasudevan K, Elangovan D, Balaji V. Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens. Indian J Med Microbiol 2019; 37:147-162. [PMID: 31745014 DOI: 10.4103/ijmm.ijmm_19_396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.
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Affiliation(s)
| | | | | | - Saranya Vijayakumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Divyaa Elangovan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Veeraraghavan Balaji
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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