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Castillo-Ramírez S. On the road to genomically defining bacterial intra-species units. mSystems 2024:e0058424. [PMID: 38940600 DOI: 10.1128/msystems.00584-24] [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: 06/29/2024] Open
Abstract
Over almost three decades, average nucleotide identity (ANI) analysis has been instrumental in operationally defining species in bacteria. However, barely any attention has been paid to soundly defining intra-species units employing ANI analyses until recently. Notably, some very recent publications are good steps forward in that direction. The level of granularity provided by these intra-species units will be relevant to understanding the eco-evolutionary dynamics and transmission of bacterial lineages and mobile genetic elements, antibiotic resistance, and virulence genes. These intra-species units will undoubtedly advance the genomic epidemiology of many bacterial pathogens. In the coming years, we anticipate that many studies will implement ANI-based definitions of different intra-species units, such as strains or sequence types, for many different bacterial species.
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Affiliation(s)
- Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
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Xu A, Li M, Hang Y, Zeng L, Zhang X, Hu Y, Guo Q, Wang M. Multicenter retrospective genomic characterization of carbapenemase-producing Acinetobacter baumannii isolates from Jiangxi patients 2021-2022: identification of a novel international clone, IC11. mSphere 2024; 9:e0027624. [PMID: 38832781 DOI: 10.1128/msphere.00276-24] [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: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
This study aimed to characterize carbapenem-resistant Acinetobacter baumannii (CRAB) isolates from Jiangxi patients using whole-genome sequencing (WGS). We subjected 100 clinical CRAB strains isolated from the three local largest teaching hospitals to WGS and antimicrobial susceptibility testing. Molecular epidemiology was investigated using multilocus sequence typing, core genome multilocus typing, core genome single-nucleotide polymorphism phylogeny, and pulsed-field gel electrophoresis. The most prevalent acquired carbapenemase was blaOXA-23, predominant in all isolates (100%). Isolates belonging to the dominating international clone IC2 accounted for 92% of all isolates. International IC11 (ST164Pas/ST1418Ox) clone was found in an additional 8% (eight isolates), with seven isolates (87.5%) carrying an acquired additional blaNDM-1 carbapenemase. The oxa23-associated Tn2009, either alone or in a tandem repeat structure containing four copies of blaOXA-23, was discovered in 62% (57 isolates) of IC2. The oxa23-associated Tn2006 was identified in 38% (35 isolates) of IC2 and all IC11 isolates. A putative conjugative RP-T1 (formerly RepAci6) plasmid with blaOXA-23 in Tn2006 within AbaR4, designated pSRM1.1, was found in IC2 A. baumannii strain SRM1. The blaNDM-1 gene found in seven IC11 isolates was located on a novel Tn6924-like transposon, a first-time report in IC11. These findings underscore the significant importance of real-time surveillance to prevent the further spread of CRAB. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii (CRAB) is notorious for causing difficult-to-treat infections. To elucidate the molecular and clinical epidemiology of CRAB in Jiangxi, clinical CRAB isolates were collected and underwent whole-genome sequencing and antibiotic susceptibility phenotyping. Key findings included the predominance of OXA-23-producing IC2 A. baumannii, marked by the emergence of OXA-23 and NDM-1-producing IC11 strains.
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Affiliation(s)
- An Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of People's Republic of China, Shanghai, China
| | - Min Li
- Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yaping Hang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Lingbing Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xuefei Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of People's Republic of China, Shanghai, China
| | - Yiyi Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of People's Republic of China, Shanghai, China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of People's Republic of China, Shanghai, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of People's Republic of China, Shanghai, China
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Bansal K, Saroha T, Patil PP, Kumar S, Kumar S, Singhal L, Gautam V, Patil PB. Evolutionary trends of carbapenem-resistant and susceptible Acinetobacter baumannii isolates in a major tertiary care setting from North India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105542. [PMID: 38122920 DOI: 10.1016/j.meegid.2023.105542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/09/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Emergence of carbapenem-resistant A. baumannii (CRAB) is a global, ongoing healthcare concern. CRAB is among the topmost priority pathogens, with various studies focusing on its global population structure and resistant allelic profiles. However, carbapenem-susceptible A. baumannii (CSAB) isolates are often overlooked due to their sensitivity to beta-lactams, which can provide important insights into origin of CRAB lineages and isolates. In the present study, we report genomic investigation of CRAB and CSAB coexisting in Indian hospital setting. MLST based population structure and phylogenomics suggest they mainly follow distinct evolutionary routes forming two phylogroups. PG-I exclusively for a successful clone (ST2) of CRAB and PG-II comprises diversified CSAB isolates except PG3373, which is CRAB. Additionally, there are few CRAB isolates not belonging to PG-I and sharing clonal relationship with CSAB isolates indicating role of genome plasticity towards extensive drug resistance in the nosocomial environment. Further, genealogical analysis depicts prominent role of recombination in emergence and evolution of a major CRAB lineage. Further, CRAB isolates are enriched in resistomes as compared to CSAB isolates, which were encoded on the genomic island. Such comparative genomic insights will aid in our understanding and localized management of rapidly evolving pandrug resistant nosocomial pathogens.
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Affiliation(s)
- Kanika Bansal
- CSIR- Institute of Microbial Technology, Chandigarh- 160036, India
| | - Tanu Saroha
- CSIR- Institute of Microbial Technology, Chandigarh- 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Prashant P Patil
- CSIR- Institute of Microbial Technology, Chandigarh- 160036, India
| | - Sanjeet Kumar
- CSIR- Institute of Microbial Technology, Chandigarh- 160036, India
| | - Sunil Kumar
- Postgraduate Institute of Medical Education and Research, Chandigarh- 160012, India; Department of Microbiology, Graphic Era Deemed to be University, Dehradun, Uttarakhand- 248002, India
| | - Lipika Singhal
- Government Medical College & Hospital, Chandigarh- 160047, India
| | - Vikas Gautam
- Postgraduate Institute of Medical Education and Research, Chandigarh- 160012, India.
| | - Prabhu B Patil
- CSIR- Institute of Microbial Technology, Chandigarh- 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
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Castillo-Ramírez S. Genomic epidemiology of Acinetobacter baumannii goes global. mBio 2023; 14:e0252023. [PMID: 37909743 PMCID: PMC10746248 DOI: 10.1128/mbio.02520-23] [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: 11/03/2023] Open
Abstract
Acinetobacter baumannii is a major public health concern, for which many genomic epidemiology studies have been conducted in the last decade. However, the vast majority of these are local studies focusing on hospitals from one or a few countries. Proper global genomic epidemiology studies are needed if we are to understand the worldwide dissemination of A. baumannii clones. In this regard, a recent study published in mBio is a good step forward. Müller et al. (mBio e2260-23, 2023, https://doi.org/10.1128/mbio.02260-23) sequenced the genomes of 313 carbapenem-resistant A. baumannii isolates from over 100 hospitals in almost 50 countries from Africa, Asia, Europe, and The Americas. With this data set the authors provide an updated view of the global distribution of the major international clones and their carbapenemase genes. Future global genomic epidemiology studies can be enhanced by considering not only human but also non-human isolates, and by considering isolates despite their antibiotic resistance profile.
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Affiliation(s)
- Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
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Müller C, Reuter S, Wille J, Xanthopoulou K, Stefanik D, Grundmann H, Higgins PG, Seifert H. A global view on carbapenem-resistant Acinetobacter baumannii. mBio 2023; 14:e0226023. [PMID: 37882512 PMCID: PMC10746149 DOI: 10.1128/mbio.02260-23] [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: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 10/27/2023] Open
Abstract
To give an update on the molecular epidemiology and global distribution of carbapenemase encoding genes, we subjected 313 carbapenem-resistant Acinetobacter baumannii isolated from 114 study centers in 47 countries in five world regions, Africa, Asia, Europe, Latin America, and North America, to whole genome sequencing. Numbers of isolates investigated were proportional to the population size of the contributing countries. Molecular epidemiology was investigated using seven-loci and core genome multilocus sequence typing, whole-genome single nucleotide polymorphism phylogenies, and the intrinsic blaOXA-51-like variant. Carbapenemase encoding genes were identified by multiplex PCR and ResFinder. Among the total of 313 isolates, 289 (92.3%) were assigned to A. baumannii international clones (IC) IC1-IC8. IC2 predominated with 196 isolates (62.6%) and was spread worldwide, followed by IC5 with 44 isolates (14.1%) mainly confined to Latin America. Six isolates (1.9%) originating from Belgium, Egypt, Italy, and Pakistan represent the novel IC9. Acquired OXA-type carbapenemase genes were found in 300 (96%) isolates with blaOXA-23-like and blaOXA-40-like predominating, which constitutes a significant increase compared to our findings from 2010. Metallo-beta-lactamases were rare with seven isolates (2.2%). The distribution of ICs and carbapenemase determinants can vary widely among different geographical regions. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii are of increasing public health importance, as they are resistant to last-line antibiotics. International clones with well-characterized resistance genes dominate globally; however, locally, other lineages with different properties may be of importance to consider. This study investigated isolates from a broad geographic origin from 114 hospitals in 47 countries and from five world regions ensuring the greatest possible diversity in an organism known for its propensity for clonal epidemic spread and reflecting the current global epidemiology of carbapenem-resistant A. baumannii. In Latin America, a lineage different from other geographic regions circulates, with a different resistance gene profile. This knowledge is important to adjust local infection prevention measures. In a global world with migration and increasing use of antimicrobials, multidrug-resistant bacteria will continue to adapt and challenge our healthcare systems worldwide.
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Affiliation(s)
- Carina Müller
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre–University of Freiburg, Freiburg, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Danuta Stefanik
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre–University of Freiburg, Freiburg, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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Moreno-Manjón J, Castillo-Ramírez S, Jolley KA, Maiden MCJ, Gayosso-Vázquez C, Fernández-Vázquez JL, Mateo-Estrada V, Giono-Cerezo S, Alcántar-Curiel MD. Acinetobacter baumannii IC2 and IC5 Isolates with Co-Existing blaOXA-143-like and blaOXA-72 and Exhibiting Strong Biofilm Formation in a Mexican Hospital. Microorganisms 2023; 11:2316. [PMID: 37764160 PMCID: PMC10536109 DOI: 10.3390/microorganisms11092316] [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: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with international clones are frequently unknown in low- and middle-income countries. Here, we analyze the phenotype and genotype of seventy-six HAIs and outbreak-causing A. baumannii isolates from a Mexican hospital over ten years, with special attention to the carbapenem resistome and biofilm formation. The isolates belonged to the global international clone (IC) 2 and the Latin America endemic IC5 and were predominantly extensively drug-resistant (XDR). Oxacillinases were identified as a common source of carbapenem resistance. We noted the presence of the blaOXA-143-like family (not previously described in Mexico), the blaOXA-72 and the blaOXA-398 found in both ICs. A low prevalence of efflux pump overexpression activity associated with carbapenem resistance was observed. Finally, strong biofilm formation was found, and significant biofilm-related genes were identified, including bfmRS, csuA/BABCDE, pgaABCD and ompA. This study provides a comprehensive profile of the carbapenem resistome of A. baumannii isolates belonging to the same pulse type, along with their significant biofilm formation capacity. Furthermore, it contributes to a better understanding of their role in the recurrence of infection and the endemicity of these isolates in a Mexican hospital.
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Affiliation(s)
- Julia Moreno-Manjón
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
- Laboratorio de Bacteriología Médica, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11350, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62209, Mexico; (S.C.-R.); (V.M.-E.)
| | - Keith A. Jolley
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK; (K.A.J.); (M.C.J.M.)
| | - Martin C. J. Maiden
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK; (K.A.J.); (M.C.J.M.)
| | - Catalina Gayosso-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
| | - José Luis Fernández-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62209, Mexico; (S.C.-R.); (V.M.-E.)
| | - Silvia Giono-Cerezo
- Laboratorio de Bacteriología Médica, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11350, Mexico
| | - María Dolores Alcántar-Curiel
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 06720, Mexico; (J.M.-M.); (C.G.-V.); (J.L.F.-V.)
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Fu Y, M’ikanatha NM, Dudley EG. Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds. J Clin Microbiol 2023; 61:e0184722. [PMID: 37249426 PMCID: PMC10281135 DOI: 10.1128/jcm.01847-22] [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: 12/14/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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Sharma T, Kumar R, Kalra JS, Singh S, Bhalla GS, Bhardwaj A. Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes. Front Microbiol 2023; 13:1041847. [PMID: 36817105 PMCID: PMC9933921 DOI: 10.3389/fmicb.2022.1041847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 12/21/2022] [Indexed: 01/28/2023] Open
Abstract
Introduction Antimicrobial susceptibility testing (AST) is used to determine the susceptibility of an organism to antibiotics. The determination of susceptibility is based on MIC breakpoints and is provided by EUCAST and CLSI. Likewise, phenotypic classification criteria developed by CDC/ECDC are used for the classification of pathogens into susceptible, multidrug-resistant, extremely drug-resistant, or totally drug-resistant categories. Whole-genome sequencing (WGS)-based diagnosis is now supplementing existing gold-standard microbiology methods for rapid and more precise AST, and therefore, EUCAST recommended quality criteria to assess whole-genome sequence for reporting the same. In this study, these three global standards, MIC breakpoints, phenotypic classification, and genome quality, are applied to the largest publicly available data for Acinetobacter baumannii (AB), the most critical priority pathogen identified by WHO. Materials and Methods The drug sensitivity profile and genomes for isolates of AB were obtained from PATRIC and evaluated with respect to AST standards (CLSI and EUCAST). Whole genome quality assessment and antimicrobial resistance mapping is performed with QUAST and ABRicate, respectively. Four in-house methods are developed for mapping standards and are integrated into a Galaxy workflow based system, Galaxy-ASIST. Analysis of the extent of agreement between CLSI 2022 and EUCAST 2022 for antibiotics was carried out using Cohen's kappa statistics. Results and Discussion An automated pipeline, Galaxy-ASIST, is designed and developed for the characterization of clinical isolates based on these standards. Evaluation of over 6,500 AB strains using Galaxy-ASIST indicated that only 10% of the publicly available datasets have metadata to implement these standards. Furthermore, given that CLSI and EUCAST have different MIC breakpoints, discrepancies are observed in the classification of resistant and susceptible isolates following these standards. It is, therefore, imperative that platforms are developed that allow the evaluation of ever increasing phenotypic and genome sequence datasets for AST. Galaxy-ASIST offers a centralized repository and a structured metadata architecture to provide a single globally acceptable framework for AST profiling of clinical isolates based on global standards. The platform also offers subsequent fine mapping of antimicrobial-resistant determinants. Galaxy-ASIST is freely available at https://ab-openlab.csir.res.in/asist.
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Affiliation(s)
- Tina Sharma
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rakesh Kumar
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Shreya Singh
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Anshu Bhardwaj
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Anshu Bhardwaj, ✉
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Castillo-Ramírez S. Zoonotic Acinetobacter baumannii: the need for genomic epidemiology in a One Health context. THE LANCET. MICROBE 2022; 3:e895-e896. [PMID: 36150399 PMCID: PMC9489090 DOI: 10.1016/s2666-5247(22)00255-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 01/14/2023]
Affiliation(s)
- Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, México
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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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Gao Y, Li H, Chen H, Zhang J, Wang R, Wang Z, Wang H. Origin, Phylogeny, and Transmission of the Epidemic Clone ST208 of Carbapenem-Resistant Acinetobacter baumannii on a Global Scale. Microbiol Spectr 2022; 10:e0260421. [PMID: 35638783 PMCID: PMC9241911 DOI: 10.1128/spectrum.02604-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) is an opportunistic pathogen that has become a global threat. The dissemination of global clone 2 (GC2) CRAB has been well documented. Oxford sequence type (ST) 208 is one of the most prevalent lineages of A. baumannii GC2; however, its evolution and phylogeny are unclear. We collected 45 representative ST208 isolates from 14 cities in China between 1999 and 2018. Moreover, 411 ST208 genome sequences were downloaded from the GenBank database for comparison. The global ST208 phylogeny showed that ST208 might have originated from North America and subsequently evolved into two clades. Notably, the widespread OXA-23-producing ST208 A. baumannii was correlated with the transposon structure and dynamics of replicative transposition, and the Tn2009 tandem structure of five copies of blaOXA-23 and potential circular intermediate of Tn2009 were first detected. Furthermore, 15 Chinese ST208 isolates carried GR25 pABTJ1-like plasmids, which contained blaOXA-23 and have only been found in China in the last decade. In conclusion, our work suggests that replicative transposition contributes to the evolution and transmission of OXA-23-producing ST208 A. baumannii and highlights the new challenges posed by the epidemiological surveillance of globally distributed clonal groups via whole genome sequencing. IMPORTANCE ST208 as one of the most prevalent lineages of CRAB has caused several difficult-to-treat infections and outbreaks around the world. However, few studies have focused on evaluating the genetic background differences of ST208 A. baumannii isolated from very distant geographic regions. A comprehensive genomic analysis of 456 clinical strains of ST208 A. baumannii from a wide temporal and geographic range was performed in this study. Moreover, the mechanisms leading to the horizontal transfer of blaOXA-23 in ST208 A. baumannii are poorly understood. We first describe experimental evidence of the potential circular intermediate of Tn2009, and the Tn2009 tandem structure of five copies of blaOXA-23 was first detected. The interbacterial transfer of genetic elements carrying resistance to last-line antibiotic carbapenems highlights the essential need to enhance epidemiologic surveillance.
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Affiliation(s)
- Yue Gao
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Henan Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Jiangang Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Zhiren Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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12
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Kadhom HA, Ali MR. Epidemiological Molecular Analysis of Acinetobacter baumannii isolates using a multilocus sequencing typing and Global lineage. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.01.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Multilocus sequence typing MLST method was used to recognize outbreaks of hospitals distinct clonal lineages of A. baumannii; these schemes appeared to provide largely concordant classifications that have been tools to evaluate the population structures of bacterial pathogens. One hundred fifty samples were collected from different specimens of patients within Baghdad hospitals (blood 40%, CSF 5%, urine 5%) between July 2019 to February 2020. Then identification all isolated as phenotypic detection and performed using PCR amplification of 16srRNA and blaOXA-51-like as genotypic detections. According to clinical and laboratory standards institute (CLSI) guidelines, Susceptibility testing was performed. Clonally analysis was performed by global lineage ICs correlated with multilocus sequence typing (MLST) when our data showed a very high rate of antimicrobial resistance in all hospital isolates, especially against colistin (8%) which determined the PDR isolates from other types also recorded 70% of isolates standing for carbapenems antibiotics (IMI 32%, MER70%& DOR 64%). Then already clustered into four groups according to multiplex PCR for two groups of three genes (ompA, csuE & blaOXA-51-like) where IC II was predominant in Iraq but in our strains founding ICI (38%) more prevalence one followed by IC0 (26%) then ICII and ICIII (20% &16% respectively). MLST used for detected the common sequence types (STs) of our selected 8 A. baumannii strains (IC0/A11, ICI/A6,48, ICII/A33,50,19 and ICIII/A1,36) were performed by using 7 housekeeping genes than were submitted in the MLST Pasteur scheme dataset (ID 5098, 5099, 5100, 5101, 5102, 5103, 5482 & 5483) followed by statistical eBurst analysis was done to study Clonal complexes (CCs). Identified 5 new STs (8, 444, 346, 1587 & 621) within Iraq and new one ST (1830) worldwide.
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Affiliation(s)
- Heba A. Kadhom
- Department of Biomedical Engineering, University of Technology, Baghdad, Iraq
| | - Munim R. Ali
- College of Science, Mustansiriyah University, Baghdad, Iraq
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13
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Hernández-González IL, Mateo-Estrada V, Castillo-Ramirez S. The promiscuous and highly mobile resistome of Acinetobacter baumannii. Microb Genom 2022; 8. [PMID: 35075990 PMCID: PMC8914355 DOI: 10.1099/mgen.0.000762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the whole resistome of Acinetobacter baumannii, a very important nosocomial pathogen. Here we analyse 1450+ genomes (covering >40 countries and >4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii. We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae. Despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Our results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genomic epidemiology (and surveillance) of bacterial pathogens.
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Affiliation(s)
- Ismael L Hernández-González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Santiago Castillo-Ramirez,
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14
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A High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA. Appl Environ Microbiol 2021; 87:e0139921. [PMID: 34586910 DOI: 10.1128/aem.01399-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Molecular typing methods are used to characterize the relatedness between bacterial isolates involved in infections. These approaches rely mostly on discrete loci or whole-genome sequencing (WGS) analyses of pure cultures. On the other hand, their application to environmental DNA profiling to evaluate epidemiological relatedness among patients and environments has received less attention. We developed a specific, high-throughput short sequence typing (HiSST) method for the opportunistic human pathogen Serratia marcescens. Genes displaying the highest polymorphism were retrieved from the core genome of 60 S. marcescens strains. Bioinformatics analyses showed that use of only three loci (within bssA, gabR, and dhaM) distinguished strains with a high level of efficiency. This HiSST scheme was applied to an epidemiological survey of S. marcescens in a neonatal intensive care unit (NICU). In a first case study, a strain responsible for an outbreak in the NICU was found in a sink drain of this unit, by using HiSST scheme and confirmed by WGS. The HiSST scheme was also applied to environmental DNA extracted from sink-environment samples. Diversity of S. marcescens was modest, with 11, 6, and 4 different sequence types (ST) of gabR, bssA, and dhaM loci among 19 sink drains, respectively. Epidemiological relationships among sinks were inferred on the basis of pairwise comparisons of ST profiles. Further research aimed at relating ST distribution patterns to environmental features encompassing sink location, utilization, and microbial diversity is needed to improve the surveillance and management of opportunistic pathogens. IMPORTANCE Serratia marcescens is an important opportunistic human pathogen, often multidrug resistant and involved in outbreaks of nosocomial infections in neonatal intensive care units. Here, we propose a quick and user-friendly method to select the best typing scheme for nosocomial outbreaks in relating environmental and clinical sources. This method, named high-throughput short sequence typing (HiSST), allows to distinguish strains and to explore the diversity profile of nonculturable S. marcescens. The application of HiSST profile analysis for environmental DNA offers new possibilities to track opportunistic pathogens, identify their origin, and relate their distribution pattern with environmental features encompassing sink location, utilization, and microbial diversity. Adaptation of the method to other opportunistic pathogens is expected to improve knowledge regarding their ecology, which is of significant interest for epidemiological risk assessment and elaborate outbreak mitigation strategies.
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15
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Lombardo D, Cordovana M, Deidda F, Pane M, Ambretti S. Application of Fourier transform infrared spectroscopy for real-time typing of Acinetobacter baumannii outbreak in intensive care unit. Future Microbiol 2021; 16:1239-1250. [PMID: 34674538 DOI: 10.2217/fmb-2020-0276] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Acinetobacter baumannii is a pathogen of serious concern, often exhibiting multiple antibiotic resistance, frequently associated with hospital outbreaks in intensive care units. A prompt detection and tracking of these isolates is crucial. Reference methods for typing (pulsed-field gel electrophoresis, whole-genome sequencing) are accurate, but expensive and time-consuming, therefore limited to retrospective analysis. Materials & methods: In this study, the application of the FTIR-based IR Biotyper® (IRBT) to track and monitor in real-time the spread of a multidrug-resistant A. baumannii outbreak was investigated. The index case and the multidrug-resistant A. baumannii isolates collected in the following 3 weeks were investigated. Results: IR Biotyper® clustering results were fully confirmed by pulsed-field gel electrophoresis results. Conclusions: IR Biotyper represent a promising tool for real-time hospital hygiene, enabling a prompt and reliable typing.
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Affiliation(s)
- Donatella Lombardo
- Operative Unit of Microbiology, University Hospital Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | - Miriam Cordovana
- Operative Unit of Microbiology, University Hospital Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
| | - Simone Ambretti
- Operative Unit of Microbiology, University Hospital Policlinico Sant'Orsola-Malpighi, Bologna, Italy
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16
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Acinetobacter baumannii strains isolated from cerebrospinal fluid (CSF) and bloodstream analysed by cgMLST: the dominance of clonal complex CC92 in CSF infections. Int J Antimicrob Agents 2021; 58:106404. [PMID: 34298091 DOI: 10.1016/j.ijantimicag.2021.106404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 06/29/2021] [Accepted: 07/03/2021] [Indexed: 11/22/2022]
Abstract
A total of 54 unique clinical Acinetobacter baumannii strains isolated from cerebrospinal fluid (CSF) together with 21 bloodstream isolates collected from five tertiary hospitals in East China between April 2013 and November 2016 were studied for antimicrobial susceptibility patterns and the prevalence of antimicrobial resistance genes. Molecular epidemiological characteristics of CSF isolates and the phylogenetic relationship of isolates from different sources were assessed using multilocus sequence typing (MLST) and core genome MLST (cgMLST). Of the 54 CSF isolates, 51 (94.4%) were blaOXA-23-carrying carbapenem-resistant A. baumannii. Their average resistance rate to different classes of antibiotics was extremely high (>90%), except for tigecycline and colistin. According to the Oxford MLST scheme, all CSF isolates fell into 10 defined sequence types (STs) and 4 novel STs. ST195 and ST208 were the leading STs in isolates from either source. A total of 50 CSF isolates and 20 bloodstream isolates were assigned to clonal complex 92 (CC92), revealing a wild distribution of CC92 in the hospitals of East China. In combination with epidemiological data linked in time and space, cgMLST results elucidated intrahospital and interhospital polyclonal dissemination of A. baumannii causing meningitis. Based on cgMLST, there was no correlation between phylogeny and the source of isolation of A. baumannii. These results emphasise that the genetic potential of this pathogen is vast enough to infect multiple human body sites.
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17
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Abstract
Acinetobacter baumannii has become one of the most important multidrug-resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages coexisting in hospital settings. Here, using whole-genome sequencing, epidemiological data, and antimicrobial susceptibility tests, we uncover the transmission dynamics of extensive and multidrug-resistant A. baumannii in a tertiary hospital over a decade. Our core genome phylogeny of almost 300 genomes suggests that there were several introductions of lineages from international clone 2 into the hospital. The molecular dating analysis shows that these introductions happened in 2006, 2007, and 2013. Furthermore, using the accessory genome, we show that these lineages were extensively disseminated across many wards in the hospital. Our results demonstrate that accessory genome variation can be a very powerful tool for conducting genomic epidemiology. We anticipate future studies employing the accessory genome along with the core genome as a powerful phylogenomic strategy to track bacterial transmissions over very short microevolutionary scales. IMPORTANCE Whole-genome sequencing for epidemiological investigations (genomic epidemiology) has been of paramount importance to understand the transmission dynamics of many bacterial (and nonbacterial) pathogens. Commonly, variation in the core genome, single nucleotide polymorphisms (SNPs), is employed to carry out genomic epidemiology. However, at very short periods of time, the core genome might not have accumulated enough variation (sufficient SNPs) to tell apart isolates. In this scenario, gene content variation in the accessory genome can be an option to conduct genomic epidemiology. Here, we used the accessory genome, as well as the core genome, to uncover the transmission dynamics of extensive and multidrug-resistant A. baumannii in a tertiary hospital for a decade. Our study shows that accessory genome variation can be a very powerful tool for conducting genomic epidemiology.
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18
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Lavrinenko A, Sheck E, Kolesnichenko S, Azizov I, Turmukhambetova A. Antibiotic Resistance and Genotypes of Nosocomial Strains of Acinetobacter baumannii in Kazakhstan. Antibiotics (Basel) 2021; 10:antibiotics10040382. [PMID: 33916831 PMCID: PMC8065490 DOI: 10.3390/antibiotics10040382] [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: 02/08/2021] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 12/17/2022] Open
Abstract
The aim of this study was to determine the prevalence of A. baumannii antibiotic-resistant strains in Kazakhstan and to characterize genotypes related to epidemic “high-risk” clones. Two hundred and twenty four A. baumannii isolates from four cities of Kazakhstan in 2011–2019 were studied. Antibiotic susceptibility testing was performed by using broth microdilutions method according to EUCAST (v 11.0) recommendations. The presence of blaOXA-23-like, blaOXA-24/40-like,blaOXA-58-like,blaVIM,blaIMP, and blaNDM genes was determined by PCR. Genotyping was performed using high-throughput real-time PCR detection of 21 SNPs at 10 chromosomal loci used in existing MLST schemes. Resistance rates to imipenem, meropenem, amikacin, gentamicin, and ciprofloxacin were 81.3%, 78.6%, 79.9%, 65.2%, and 89.3%, respectively. No colistin resistant isolates were detected. The values of the MIC 50% and the MIC 90% of tigecycline were 0.125 mg/L, only four isolates (1.8%) had the ECOFF value >0.5 mg/L. The presence of acquired carbapenemase genes was found in 82.2% strains, including blaOXA-23-like (78.6%) or blaOXA-58-like (3.6%) genes. The spreading of carbapenem resistant A. baumannii strains in Kazakhstan was associated with epidemic “high-risk” clonal groups, predominantly, CG208(92)OXF/CG2PAS (80.8%) and less often CG231(109)OXF/CG1PAS (1.8%).
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Affiliation(s)
- Alyona Lavrinenko
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
| | - Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214014 Smolensk, Russia; (E.S.); (I.A.)
| | - Svetlana Kolesnichenko
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
- Correspondence: ; Tel.: +7-721-251-3479
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214014 Smolensk, Russia; (E.S.); (I.A.)
| | - Anar Turmukhambetova
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
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19
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Acinetobacter baumannii: An Ancient Commensal with Weapons of a Pathogen. Pathogens 2021; 10:pathogens10040387. [PMID: 33804894 PMCID: PMC8063835 DOI: 10.3390/pathogens10040387] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is regarded as a life-threatening pathogen associated with community-acquired and nosocomial infections, mainly pneumonia. The rise in the number of A. baumannii antibiotic-resistant strains reduces effective therapies and increases mortality. Bacterial comparative genomic studies have unraveled the innate and acquired virulence factors of A. baumannii. These virulence factors are involved in antibiotic resistance, environmental persistence, host-pathogen interactions, and immune evasion. Studies on host–pathogen interactions revealed that A. baumannii evolved different mechanisms to adhere to in order to invade host respiratory cells as well as evade the host immune system. In this review, we discuss current data on A. baumannii genetic features and virulence factors. An emphasis is given to the players in host–pathogen interaction in the respiratory tract. In addition, we report recent investigations into host defense systems using in vitro and in vivo models, providing new insights into the innate immune response to A. baumannii infections. Increasing our knowledge of A. baumannii pathogenesis may help the development of novel therapeutic strategies based on anti-adhesive, anti-virulence, and anti-cell to cell signaling pathways drugs.
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20
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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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21
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Nodari CS, Cayô R, Streling AP, Lei F, Wille J, Almeida MS, de Paula AI, Pignatari ACC, Seifert H, Higgins PG, Gales AC. Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates Belonging to Major Endemic Clones in South America. Front Microbiol 2020; 11:584603. [PMID: 33329450 PMCID: PMC7734285 DOI: 10.3389/fmicb.2020.584603] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) are emerging worldwide. In South America, clinical isolates presenting such a phenotype usually do not belong to the globally distributed international clone 2 (IC2). The majority of these isolates are also resistant to multiple other antimicrobials and are often designated extremely drug-resistant (XDR). The aim of this study was to characterize the resistance mechanisms presented by 18 carbapenem-resistant A. baumannii isolates from five different Brazilian hospitals. Species identification was determined by rpoB sequencing, and antimicrobial susceptibility was determined by broth microdilution. Isolates were submitted to whole genome sequencing using Illumina platform and genetic similarity was determined by PFGE, MLST, and cgMLST. Genome analysis was used to identify intrinsic and acquired resistance determinants, including mutations in the AdeRSABC efflux system and in outer membrane proteins (OMPs). All isolates were identified as A. baumannii and grouped into 4 pulsotypes by PFGE, which belonged to clonal complexes (CC) 15Pas/103Ox (n = 4) and 79Pas/113Ox (n = 14), corresponding to IC4 and IC5, respectively. High MIC values to carbapenems, broad-spectrum cephalosporins, amikacin, and ciprofloxacin were observed in all isolates, while MICs of ampicillin/sulbactam, gentamicin, and tigecycline varied among the isolates. Minocycline was the most active antimicrobial agent tested. Moreover, 12 isolates (66.7%) were considered resistant to polymyxins. Besides intrinsic OXA-51 and ADC variants, all isolates harbored an acquired carbapenem-hydrolyzing class D β-lactamase (CHDL) encoding gene, either blaOXA–23 or blaOXA–72. A diversity of aminoglycoside modifying enzymes and resistance determinants to other antimicrobial classes were found, as well as mutations in gyrA and parC. Non-synonymous mutations have also been identified in the AdeRSABC efflux system and in most OMPs, but they were considered natural polymorphisms. Moreover, resistance to polymyxins among isolates belonging to IC5 were associated to non-synonymous mutations in pmrB, but no known polymyxin resistance mechanism was identified in isolates belonging to IC4. In conclusion, A. baumannii clinical isolates belonging to South America’s major clones present a myriad of antimicrobial resistance determinants. Special attention should be paid to natural polymorphisms observed in each clonal lineage, especially regarding non-synonymous mutations in constitutive genes associated with distinct resistance phenotypes.
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Affiliation(s)
- Carolina Silva Nodari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Rodrigo Cayô
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil.,Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia - Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, Brazil
| | - Ana Paula Streling
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Felipe Lei
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Myriam S Almeida
- Laboratório de Microbiologia, Hospital Universitário Cassiano Antônio de Moraes, Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | - Alexandre Inacio de Paula
- Setor de Microbiologia - Serviço de Análises Clínicas, Hospital do Servidor Público Estadual (IAMSPE), São Paulo, Brazil
| | - Antonio Carlos Campos Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil.,Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
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22
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Mancilla-Rojano J, Ochoa SA, Reyes-Grajeda JP, Flores V, Medina-Contreras O, Espinosa-Mazariego K, Parra-Ortega I, Rosa-Zamboni DDL, Castellanos-Cruz MDC, Arellano-Galindo J, Cevallos MA, Hernández-Castro R, Xicohtencatl-Cortes J, Cruz-Córdova A. Molecular Epidemiology of Acinetobacter calcoaceticus- Acinetobacter baumannii Complex Isolated From Children at the Hospital Infantil de México Federico Gómez. Front Microbiol 2020; 11:576673. [PMID: 33178158 PMCID: PMC7593844 DOI: 10.3389/fmicb.2020.576673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
The Acinetobacter calcoaceticus-baumannii (Acb) complex is regarded as a group of phenotypically indistinguishable opportunistic pathogens responsible for mainly causing hospital-acquired pneumonia and bacteremia. The aim of this study was to determine the frequency of isolation of the species that constitute the Acb complex, as well as their susceptibility to antibiotics, and their distribution at the Hospital Infantil de Mexico Federico Gomez (HIMFG). A total of 88 strains previously identified by Vitek 2®, 40 as Acinetobacter baumannii and 48 as Acb complex were isolated from 52 children from 07, January 2015 to 28, September 2017. A. baumannii accounted for 89.77% (79/88) of the strains; Acinetobacter pittii, 6.82% (6/88); and Acinetobacter nosocomialis, 3.40% (3/88). Most strains were recovered mainly from patients in the intensive care unit (ICU) and emergency wards. Blood cultures (BC) provided 44.32% (39/88) of strains. The 13.63% (12/88) of strains were associated with primary bacteremia, 3.4% (3/88) with secondary bacteremia, and 2.3% (2/88) with pneumonia. In addition, 44.32% (39/88) were multidrug-resistant (MDR) strains and, 11.36% (10/88) were extensively drug-resistant (XDR). All strains amplified the blaOXA-51 gene; 51.13% (45/88), the blaOXA-23 gene; 4.54% (4/88), the blaOXA-24 gene; and 2.27% (2/88), the blaOXA-58 gene. Plasmid profiles showed that the strains had 1–6 plasmids. The strains were distributed in 52 pulsotypes, and 24 showed identical restriction patterns, with a correlation coefficient of 1.0. Notably, some strains with the same pulsotype were isolated from different patients, wards, or years, suggesting the persistence of more than one clone. Twenty-seven sequence types (STs) were determined for the strains based on a Pasteur multilocus sequence typing (MLST) scheme using massive sequencing; the most prevalent was ST 156 (27.27%, 24/88). The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas I-Fb system provided amplification in A. baumannii and A. pittii strains (22.73%, 20/88). This study identified an increased number of MDR strains and the relationship among strains through molecular typing. The data suggest that more than one strain could be causing an infection in some patient. The implementation of molecular epidemiology allowed the characterization of a set of strains and identification of different attributes associated with its distribution in a specific environment.
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Affiliation(s)
- Jetsi Mancilla-Rojano
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico.,Facultad de Medicina, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Juan Pablo Reyes-Grajeda
- Subdirección de Desarrollo de Aplicaciones Clínicas, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
| | - Víctor Flores
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Irapuato, Mexico
| | - Oscar Medina-Contreras
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Karina Espinosa-Mazariego
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Israel Parra-Ortega
- Departamento de Laboratorio Clínico, Laboratorio Central, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | | | | | - José Arellano-Galindo
- Unidad de investigación en Enfermedades Infecciosas, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Miguel A Cevallos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
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López-Leal G, Santamaria RI, Cevallos MÁ, Gonzalez V, Castillo-Ramírez S. Letter to the Editor: Prophages Encode Antibiotic Resistance Genes in Acinetobacter baumannii. Microb Drug Resist 2020; 26:1275-1277. [DOI: 10.1089/mdr.2019.0362] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Gamaliel López-Leal
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Grupo de Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, District of Colombia
| | - Rosa Isela Santamaria
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Miguel Ángel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Victor Gonzalez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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24
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Hua X, Zhang L, He J, Leptihn S, Yu Y. Population Biology and Epidemiological Studies of Acinetobacter baumannii in the Era of Whole Genome Sequencing: Is the Oxford Scheme Still Appropriate? Front Microbiol 2020; 11:775. [PMID: 32411113 PMCID: PMC7201049 DOI: 10.3389/fmicb.2020.00775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/31/2020] [Indexed: 12/03/2022] Open
Affiliation(s)
- Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Linyue Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Sebastian Leptihn
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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25
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Molecular characterisation of an Acinetobacter baumannii outbreak. Infect Prev Pract 2020; 2:100040. [PMID: 34368692 PMCID: PMC8336282 DOI: 10.1016/j.infpip.2020.100040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background Acinetobacter baumannii are problematic hospital pathogens, and the increased incidence of multi drug resistance has significantly limited treatment options. The global epidemiology is not fully characterised due to large data gaps from low- and middle-income countries. This study characterised the molecular epidemiology of an A. baumanniii outbreak in Egypt. Methods Fifty-four A. baumannii isolates were recovered from a 4-month-outbreak at Tanta University Hospitals (TUH). Associated clinical and demographic data, and the antibiograms were analysed, and Carbapenem resistant isolates were screened for acquired carbapenemase genes by PCR and sequencing. Epidemiological typing was performed by single-locus sequencing of blaOXA-51-like and Multi Locus Sequence Typing (MLST), and sequence types (STs) were analysed based on maximum-likelihood phylogeny (PhyML) to identify relatedness. Findings Immune suppression and ICU admission were the most common co-morbidity and risk factor. Carbapenem resistance accounted for 81%, and correlated with the presence of OXA-23, NDM-1 and -2, and VIM-1 and -2 carbapenemases. Nine different blaOXA-51-like genes were identified which corresponded to 22 different Sequence Types (STs), including 10 novel. International clone (IC2) was the predominant clone. PhyML analysis revealed the presence of 2 distinct clones with multiple sub-lineages. Conclusion Given the short duration of the study, there was a rare heterogeneous population in the hospital. Carbapenem resistance is mediated by acquired carbapenemases in diverse lineages indicating the possibility of horizontal gene transfer. The diversity indicates the influx of multiple lineages of IC2 into TUH from unknown sources. Molecular epidemiological studies are essential for infection prevention and control measures.
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26
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Origin of OXA-23 Variant OXA-239 from a Recently Emerged Lineage of Acinetobacter baumannii International Clone V. mSphere 2020; 5:5/1/e00801-19. [PMID: 31915222 PMCID: PMC6952199 DOI: 10.1128/msphere.00801-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes. Over the last few decades, carbapenemase-producing Acinetobacter baumannii has become a major cause of nosocomial infections all over the world. However, the genome identity of lineages of this species in Latin America has not been studied as much as in developed countries. Here, through a population genomics approach considering the whole genomes of 148 isolates (almost 40 from Mexico and Honduras), we describe the recent emergence of the lineage sequence type 758 (ST758), which belongs to the international clone V and has spread out to Canada, Mexico, Honduras, and Colombia. Notably, this lineage was found to coexist with other A. baumannii lineages in hospitals in Mexico and Honduras. Isolates from this lineage show considerable variation in antibiotic resistance profiles, but most of them are resistant to carbapenems. Moreover, we found a variety of acquired oxacillinase (OXA) families within this lineage and tracked the very recent inception, and subsequent horizontal transmission, of the OXA-239 carbapenemase. This work highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes. IMPORTANCEA. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.
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27
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Chen Y, Hong J, Chen Y, Wang H, Yu Y, Qu T. Characterization of a community-acquired methicillin-resistant sequence type 338 Staphylococcus aureus strain containing a staphylococcal cassette chromosome mec type V T. Int J Infect Dis 2019; 90:181-187. [PMID: 31682959 DOI: 10.1016/j.ijid.2019.10.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES To determine the molecular characteristics of a sequence type 338 community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strain and the relationship among MRSA strains from various lineages and areas. METHODS Whole-genome sequencing, genomic comparison, antimicrobial susceptibility testing, and hemolysis analysis were performed to identify the resistance determinants and virulence factors of strain ZY05 and the relationships among CC59 clones. RESULTS MRSA strain ZY05 was resistant to tetracycline, erythromycin, and clindamycin, and the resistance genes erm(B) and tet(K) were detected in the genome. ZY05 harbors the genomic islands νSaα, νSaβ, νSaγ, and ΦSa2, the pathogenicity island νSa1, and virulence factors such as Panton-Valentine leukocidin, phenol-soluble modulins, alpha-hemolysin, enterotoxin B, enterotoxin K, and enterotoxin Q, which are the same as those present in ST59 strains. In addition, the virulence potential of ST338 did not differ from that of ST59. This strain contains the staphylococcal cassette chromosome mec (SCCmec) type VT, a distinct SCCmec type previously reported from Taiwan. The results of core genome multilocus sequence typing (cgMLST) analysis showed that the gene distances between ST59 and ST338 were close among CC59 isolates, while strains from Taiwan were identical to isolates from the Chinese mainland with respect to these two sequence types. CONCLUSIONS The ST338 strain ZY05, which has a close genetic relationship to ST59 strains, is multidrug-resistant and highly virulent. Strains of two identical lineages, ST59 and ST338, from Taiwan and the Chinese mainland may have the same genetic background.
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Affiliation(s)
- Yiyi Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jinjing Hong
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Infectious Disease Department, The First People's Hospital of Wenling, Wenling, Zhejiang Province, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Haiping Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China.
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China.
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28
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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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29
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Martak D, Valot B, Sauget M, Cholley P, Thouverez M, Bertrand X, Hocquet D. Fourier-Transform InfraRed Spectroscopy Can Quickly Type Gram-Negative Bacilli Responsible for Hospital Outbreaks. Front Microbiol 2019; 10:1440. [PMID: 31293559 PMCID: PMC6606786 DOI: 10.3389/fmicb.2019.01440] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
The typing of epidemic bacterial pathogens in hospitals relies on DNA-based, expensive, and time-consuming techniques, that are often limited to retrospective studies. However, the quick identification of epidemic pathogens in the routine of the microbiology laboratories would expedite infection control procedures that limit the contamination of new patients. IR Biotyper (Bruker Daltonics GmbH) is a new typing machine based on Fourier-transform infrared (FTIR) spectroscopy which generates spectra, aiming at typing the micro-organisms within 3 h. This technique discriminates the isolates by exploring the differences of the surface cell polysaccharides. In this work, we evaluated the ability of the FTIR spectroscopy to recognize Gram-negative bacilli clones responsible for hospital outbreaks. Isolates of Pseudomonas aeruginosa (n = 100), Klebsiella pneumoniae (n = 16), Enterobacter cloacae (n = 23), and Acinetobacter baumannii (n = 20) were typed by the reference methods Multi-Locus Sequence Typing (defining sequence types – STs) along with or without pulsed field gel electrophoresis (PFGE) (defining pulsotypes), and by FTIR spectroscopy. The congruence of FTIR spectroscopy clustering was compared to those of MLST and PFGE by Adjusted Rand index and Adjusted Wallace coefficient. We found that FTIR spectroscopy accurately clustered P. aeruginosa, K. pneumoniae, and E. cloacae isolates belonging to the same ST. The performance of the FTIR spectroscopy was slightly lower for A. baumannii. Furthermore, FTIR spectroscopy also correctly clustered P. aeruginosa isolates having a similar pulsotype. Overall, the IR Biotyper can quickly (in less than 3 h) detect the spread of clones of P. aeruginosa, K. pneumoniae, E. cloacae, and A. baumannii. The use of this technique by clinical microbiology laboratories may help to tackle the spread of epidemic clones by the quick implementation of infection control measures.
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Affiliation(s)
- Daniel Martak
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Benoît Valot
- UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Marlène Sauget
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Pascal Cholley
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Michelle Thouverez
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
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30
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Gaiarsa S, Batisti Biffignandi G, Esposito EP, Castelli M, Jolley KA, Brisse S, Sassera D, Zarrilli R. Comparative Analysis of the Two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes. Front Microbiol 2019; 10:930. [PMID: 31130931 PMCID: PMC6510311 DOI: 10.3389/fmicb.2019.00930] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 01/22/2023] Open
Abstract
Acinetobacter species assigned to the Acinetobacter calcoaceticus-baumannii (Acb) complex, are Gram-negative bacteria responsible for a large number of human infections. The population structure of Acb has been studied using two 7-gene MLST schemes, introduced by Bartual and coworkers (Oxford scheme) and by Diancourt and coworkers (Pasteur scheme). The schemes have three genes in common but underlie two coexisting nomenclatures of sequence types and clonal complexes, which complicates communication on A. baumannii genotypes. The aim of this study was to compare the characteristics of the two schemes to make a recommendation about their usage. Using genome sequences of 730 strains of the Acb complex, we evaluated the phylogenetic congruence of MLST schemes, the correspondence between sequence types, their discriminative power and genotyping reliability from genomic sequences. In silico ST re-assignments highlighted the presence of a second copy of the Oxford gdhB locus, present in 553/730 genomes that has led to the creation of artefactual profiles and STs. The reliability of the two MLST schemes was tested statistically comparing MLST-based phylogenies to two reference phylogenies (core-genome genes and genome-wide SNPs) using topology-based and likelihood-based tests. Additionally, each MLST gene fragment was evaluated by correlating the pairwise nucleotide distances between each pair of genomes calculated on the core-genome and on each single gene fragment. The Pasteur scheme appears to be less discriminant among closely related isolates, but less affected by homologous recombination and more appropriate for precise strain classification in clonal groups, which within this scheme are more often correctly monophyletic. Statistical tests evaluate the tree deriving from the Oxford scheme as more similar to the reference genome trees. Our results, together with previous work, indicate that the Oxford scheme has important issues: gdhB paralogy, recombination, primers sequences, position of the genes on the genome. While there is no complete agreement in all analyses, when considered as a whole the above results indicate that the Pasteur scheme is more appropriate for population biology and epidemiological studies of A. baumannii and related species and we propose that it should be the scheme of choice during the transition toward, and in parallel with, core genome MLST.
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Affiliation(s)
- Stefano Gaiarsa
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - Eliana Pia Esposito
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | - Michele Castelli
- Romeo and Enrica Invernizzi Pediatric Research Center, Department of Biosciences, University of Milan, Milan, Italy
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples "Federico II", Naples, Italy
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31
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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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