101
|
El-Shazly S, Dashti A, Vali L, Bolaris M, Ibrahim AS. Molecular epidemiology and characterization of multiple drug-resistant (MDR) clinical isolates of Acinetobacter baumannii. Int J Infect Dis 2015; 41:42-9. [PMID: 26518066 DOI: 10.1016/j.ijid.2015.10.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVES The aim of this study was to identify the genetic relatedness of multiple drug-resistant (MDR) Acinetobacter baumannii clinical isolates recovered from a hospital in Los Angeles. METHODS Twenty-one MDR A. baumannii isolates were collected and their antibiotic susceptibilities determined according to Clinical and Laboratory Standards Institute guidelines. Genes coding for antibiotic resistance were identified by PCR, and their identities were confirmed by DNA sequencing. Clonal relationships were studied by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). RESULTS MDR consistently correlated with the presence of oxacillinases, mostly in the form of the plasmid-mediated OXA-23 enzyme, which was detected in 12 (57.1%) isolates. GES-type carbapenemases were found in 20 (95.2%) strains, AAC in all 21 (100%) strains, and PER in seven (33.3%) strains, and ISAba1 was detected in 16 (76.2%) isolates. The association between ISAba1 and resistance genes confirms insertion elements as a source of β-lactamase production. Of the 21 clinical isolates, five were found to be related to sequence type 1 (ST1) and 16 to ST2, as analyzed by MLST. PFGE demonstrated that the majority of clinical isolates were highly related (>85%). CONCLUSIONS This study supports a more complete understanding of genotyping of antibiotic resistance for better assessment of MDR strain transmission.
Collapse
Affiliation(s)
- Sherief El-Shazly
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Kuwait; Division of Adult Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-University of California Los Angeles (UCLA) Medical Center, 1124 West Carson St., St. John's Cardiovascular Research Center, Torrance, CA 90502, USA
| | - Ali Dashti
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Kuwait
| | - Leila Vali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Kuwait
| | - Michael Bolaris
- Division of Pediatric Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-University of California Los Angeles (UCLA) Medical Center, Torrance, California, USA
| | - Ashraf S Ibrahim
- Division of Adult Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-University of California Los Angeles (UCLA) Medical Center, 1124 West Carson St., St. John's Cardiovascular Research Center, Torrance, CA 90502, USA; David Geffen School of Medicine at UCLA, Los Angeles, California, USA.
| |
Collapse
|
102
|
Sahl JW, Del Franco M, Pournaras S, Colman RE, Karah N, Dijkshoorn L, Zarrilli R. Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage. Sci Rep 2015; 5:15188. [PMID: 26462752 PMCID: PMC4604477 DOI: 10.1038/srep15188] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/22/2015] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is a globally distributed nosocomial pathogen that has gained interest due to its resistance to most currently used antimicrobials. Whole genome sequencing (WGS) and phylogenetics has begun to reveal the global genetic diversity of this pathogen. The evolution of A. baumannii has largely been defined by recombination, punctuated by the emergence and proliferation of defined clonal lineages. In this study we sequenced seven genomes from the sequence type (ST)25 lineage and compared them to 12 ST25 genomes deposited in public databases. A recombination analysis identified multiple genomic regions that are homoplasious in the ST25 phylogeny, indicating active or historical recombination. Genes associated with antimicrobial resistance were differentially distributed between ST25 genomes, which matched our laboratory-based antimicrobial susceptibility typing. Differences were also observed in biofilm formation between ST25 isolates, which were demonstrated to produce significantly more extensive biofilm than an isolate from the ST1 clonal lineage. These results demonstrate that within A. baumannii, even a fairly recently derived monophyletic lineage can still exhibit significant genotypic and phenotypic diversity. These results have implications for associating outbreaks with sequence typing as well as understanding mechanisms behind the global propagation of successful A. baumannii lineages.
Collapse
Affiliation(s)
- Jason W. Sahl
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Spyros Pournaras
- Department of Microbiology, Medical School, University of Athens, Athens, Greece
| | | | - Nabil Karah
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Lenie Dijkshoorn
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples “Federico II”, Naples, Italy
| |
Collapse
|
103
|
Ruan Z, Feng Y. BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. Nucleic Acids Res 2015; 44:D682-7. [PMID: 26433226 PMCID: PMC4702769 DOI: 10.1093/nar/gkv1004] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/23/2015] [Indexed: 02/06/2023] Open
Abstract
Whole genome sequencing has become one of the routine methods in molecular epidemiological practice. In this study, we present BacWGSTdb (http://bacdb.org/BacWGSTdb), a bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. This database borrows the population structure from the current multi-locus sequence typing (MLST) scheme and adopts a hierarchical data structure: species, clonal complex and isolates. When users upload the pre-assembled genome sequences to BacWGSTdb, it offers the functionality of bacterial genotyping at both traditional MLST and whole-genome levels. More importantly, users are told which isolates in the public database are phylogenetically close to the query isolate, along with their clinical information such as host, isolation source, disease, collection time and geographical location. In this way, BacWGSTdb offers a rapid and convenient platform for worldwide users to address a variety of clinical microbiological issues such as source tracking bacterial pathogens.
Collapse
Affiliation(s)
- Zhi Ruan
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Ye Feng
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, 310029, China
| |
Collapse
|
104
|
Repizo GD, Gagné S, Foucault-Grunenwald ML, Borges V, Charpentier X, Limansky AS, Gomes JP, Viale AM, Salcedo SP. Differential Role of the T6SS in Acinetobacter baumannii Virulence. PLoS One 2015; 10:e0138265. [PMID: 26401654 PMCID: PMC4581634 DOI: 10.1371/journal.pone.0138265] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/27/2015] [Indexed: 02/07/2023] Open
Abstract
Gram-negative bacteria, such as Acinetobacter baumannii, are an increasing burden in hospitals worldwide with an alarming spread of multi-drug resistant (MDR) strains. Herein, we compared a type strain (ATCC17978), a non-clinical isolate (DSM30011) and MDR strains of A. baumannii implicated in hospital outbreaks (Ab242, Ab244 and Ab825), revealing distinct patterns of type VI secretion system (T6SS) functionality. The T6SS genomic locus is present and was actively transcribed in all of the above strains. However, only the A. baumannii DSM30011 strain was capable of killing Escherichia coli in a T6SS-dependent manner, unlike the clinical isolates, which failed to display an active T6SS in vitro. In addition, DSM30011 was able to outcompete ATCC17978 as well as Pseudomonas aeruginosa and Klebsiella pneumoniae, bacterial pathogens relevant in mixed nosocomial infections. Finally, we found that the T6SS of DSM30011 is required for host colonization of the model organism Galleria mellonella suggesting that this system could play an important role in A. baumannii virulence in a strain-specific manner.
Collapse
Affiliation(s)
- Guillermo D. Repizo
- Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086, Université Lyon 1, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Stéphanie Gagné
- Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086, Université Lyon 1, Institut de Biologie et Chimie des Protéines, Lyon, France
| | | | - Vitor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Xavier Charpentier
- Unité de Microbiologie, Adaptation et Pathogénie, CNRS UMR 5240, Université Lyon 1, Villeurbanne, France
| | - Adriana S. Limansky
- Instituto de Biologia Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiologia, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Alejandro M. Viale
- Instituto de Biologia Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiologia, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Suzana P. Salcedo
- Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086, Université Lyon 1, Institut de Biologie et Chimie des Protéines, Lyon, France
- * E-mail:
| |
Collapse
|
105
|
Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
Collapse
Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
| |
Collapse
|
106
|
Vali L, Dashti K, Opazo-Capurro AF, Dashti AA, Al Obaid K, Evans BA. Diversity of multi-drug resistant Acinetobacter baumannii population in a major hospital in Kuwait. Front Microbiol 2015; 6:743. [PMID: 26257720 PMCID: PMC4513246 DOI: 10.3389/fmicb.2015.00743] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/06/2015] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter baumannii is one of the most important opportunistic pathogens that causes serious health care associated complications in critically ill patients. In the current study we report on the diversity of the clinical multi-drug resistant (MDR) A. baumannii in Kuwait by molecular characterization. One hundred A. baumannii were isolated from one of the largest governmental hospitals in Kuwait. Following the identification of the isolates by molecular methods, the amplified blaOXA-51-like gene product of one isolate (KO-12) recovered from blood showed the insertion of the ISAba19 at position 379 in blaOXA-78. Of the 33 MDR isolates, 28 (85%) contained blaOXA-23, 2 (6%) blaOXA-24 and 6 (18%) blaPER-1 gene. We did not detect blaOXA-58, blaVIM, blaIMP, blaGES,blaVEB, and blaNDM genes in any of the tested isolates. In three blaPER-1 positive isolates the genetic environment of blaPER-1 consisted of two copies of ISPa12 (tnpiA1) surrounding the blaPER-1 gene on a highly stable plasmid of ca. 140-kb. Multilocus-sequence typing (MLST) analysis of the 33 A. baumannii isolates identified 20 different STs, of which six (ST-607, ST-608, ST-609, ST-610, ST-611, and ST-612) were novel. Emerging STs such as ST15 (identified for the first time in the Middle East), ST78 and ST25 were also detected. The predominant clonal complex was CC2. Pulsed-field gel electrophoresis and MLST defined the MDR isolates as multi-clonal with diverse lineages. Our results lead us to believe that A. baumannii is diverse in clonal origins and/or is undergoing clonal expansion continuously while multiple lineages of MDR A. baumannii circulate in hospital ward simultaneously.
Collapse
Affiliation(s)
- Leila Vali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University Sulaibekhat, Kuwait
| | - Khadija Dashti
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University Sulaibekhat, Kuwait
| | - Andrés F Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción Concepción, Chile
| | - Ali A Dashti
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University Sulaibekhat, Kuwait
| | | | - Benjamin A Evans
- Department of Biomedical and Forensic Sciences, Faculty of Science and Technology, Anglia Ruskin University Cambridge, UK
| |
Collapse
|
107
|
A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii. Genome Biol 2015. [PMID: 26195261 PMCID: PMC4507327 DOI: 10.1186/s13059-015-0701-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. baumannii pan-genomic studies used modest sample sizes of low diversity and comparisons to a single reference genome, limiting our understanding of gene order and content. A consensus representation of multiple genomes will provide a better framework for comparison. A large-scale comparative study will identify genomic determinants associated with their diversity and adaptation as a successful pathogen. Results We determine draft-level genomic sequence of 50 diverse military isolates and conduct the largest bacterial pan-genome analysis of 249 genomes. The pan-genome of A. baumannii is open when the input genomes are normalized for diversity with 1867 core proteins and a paralog-collapsed pan-genome size of 11,694 proteins. We developed a novel graph-based algorithm and use it to assemble the first consensus pan-chromosome, identifying both the order and orientation of core genes and flexible genomic regions. Comparative genome analyses demonstrate the existence of novel resistance islands and isolates with increased numbers of resistance island insertions over time, from single insertions in the 1950s to triple insertions in 2011. Gene clusters responsible for carbon utilization, siderophore production, and pilus assembly demonstrate frequent gain or loss among isolates. Conclusions The highly variable and dynamic nature of the A. baumannii genome may be the result of its success in rapidly adapting to both abiotic and biotic environments through the gain and loss of gene clusters controlling fitness. Importantly, some archaic adaptation mechanisms appear to have reemerged among recent isolates. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0701-6) contains supplementary material, which is available to authorized users.
Collapse
|
108
|
A multidrug resistance plasmid contains the molecular switch for type VI secretion in Acinetobacter baumannii. Proc Natl Acad Sci U S A 2015; 112:9442-7. [PMID: 26170289 DOI: 10.1073/pnas.1502966112] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Infections with Acinetobacter baumannii, one of the most troublesome and least studied multidrug-resistant superbugs, are increasing at alarming rates. A. baumannii encodes a type VI secretion system (T6SS), an antibacterial apparatus of Gram-negative bacteria used to kill competitors. Expression of the T6SS varies among different strains of A. baumannii, for which the regulatory mechanisms are unknown. Here, we show that several multidrug-resistant strains of A. baumannii harbor a large, self-transmissible resistance plasmid that carries the negative regulators for T6SS. T6SS activity is silenced in plasmid-containing, antibiotic-resistant cells, while part of the population undergoes frequent plasmid loss and activation of the T6SS. This activation results in T6SS-mediated killing of competing bacteria but renders A. baumannii susceptible to antibiotics. Our data show that a plasmid that has evolved to harbor antibiotic resistance genes plays a role in the differentiation of cells specialized in the elimination of competing bacteria.
Collapse
|
109
|
Mahdian S, Sadeghifard N, Pakzad I, Ghanbari F, Soroush S, Azimi L, Rastegar-Lari A, Giannouli M, Taherikalani M. Acinetobacter baumannii clonal lineages I and II harboring different carbapenem-hydrolyzing-β-lactamase genes are widespread among hospitalized burn patients in Tehran. J Infect Public Health 2015; 8:533-42. [PMID: 26111484 DOI: 10.1016/j.jiph.2015.04.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 02/21/2015] [Accepted: 04/02/2015] [Indexed: 01/22/2023] Open
Abstract
The aim of this study was to analyze antimicrobial resistance patterns and their encoding genes and genotypic diversity of Acinetobacter baumannii isolated from burn patients in Tehran, Iran. The presence of extended-spectrum beta-lactamase- and blaOXA-encoding genes among 37 multidrug resistant (MDR) A. baumannii strains isolated from patients hospitalized in a teaching hospital in Tehran was evaluated. Susceptibility to 7 antibiotics was tested by disk agar diffusion and to polymyxin B and colistin was tested by E-test, according to CLSI guidelines. All isolates were then analyzed by PCR for the presence of blaIMP, blaVIM, blaSIMblaOXA-23, blaOXA-24, and blaOXA-58-like carbapenemase genes, and blaOXA-51-like, blaTEM, blaSHV, blaPER, blaVEB, and blaGIM genes. Genotyping of A. baumannii strains was performed by repetitive sequence-based (REP)-PCR and cluster analysis of REP-PCR profiles. A. baumannii isolates were assigned to international clones by multiplex PCR sequence group analysis. Twenty-five A. baumannii isolates were classified as MDR, and 12 were classified as extensively drug resistant. All isolates were susceptible to colistin and polymyxin B. Eighty-one percent of the isolates was resistant to imipenem or meropenem and harbored at least one or both of the blaOXA-23-like or blaOXA-24-like carbapenemase genes. Co-existence of different resistance genes was found among carbapenem-resistant isolates. Multiplex PCR sequence group analysis most commonly assigned A. baumannii isolates to international clones I (18/37; 48.6%) and II (18/37; 48.6%). An alarming increase in resistance to carbapenems and the spread of blaOXA-23-like and/or blaOXA-24-like carbapenemase genes was observed among A. baumannii strains belonging to clonal lineages I and II, isolated from burn patients in Tehran.
Collapse
Affiliation(s)
- Somayeh Mahdian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran; Department of Medical Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Iraj Pakzad
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Fatemeh Ghanbari
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Setareh Soroush
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran; Department of Medical Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Lila Azimi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abdolaziz Rastegar-Lari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maria Giannouli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Morovat Taherikalani
- Department of Microbiology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Lorestan, Iran.
| |
Collapse
|
110
|
Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii. J Bacteriol 2015; 197:2027-35. [PMID: 25845845 DOI: 10.1128/jb.00131-15] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/31/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for A. baumannii strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make A. baumannii a formidable public health threat. IMPORTANCE Acinetobacter baumannii is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of A. baumannii that is highly virulent and representative of current outbreak strains.
Collapse
|
111
|
Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat Commun 2015; 6:6560. [PMID: 25814293 PMCID: PMC4389252 DOI: 10.1038/ncomms7560] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 02/06/2015] [Indexed: 12/18/2022] Open
Abstract
Genome sequencing is revolutionizing clinical microbiology and our understanding of infectious diseases. Previous studies have largely relied on the sequencing of a single isolate from each individual. However, it is not clear what degree of bacterial diversity exists within, and is transmitted between individuals. Understanding this ‘cloud of diversity’ is key to accurate identification of transmission pathways. Here, we report the deep sequencing of methicillin-resistant Staphylococcus aureus among staff and animal patients involved in a transmission network at a veterinary hospital. We demonstrate considerable within-host diversity and that within-host diversity may rise and fall over time. Isolates from invasive disease contained multiple mutations in the same genes, including inactivation of a global regulator of virulence and changes in phage copy number. This study highlights the need for sequencing of multiple isolates from individuals to gain an accurate picture of transmission networks and to further understand the basis of pathogenesis. Populations of bacterial pathogens can be diverse within colonized individuals. Here, the authors sequence the genomes of methicillin-resistant Staphylococcus aureus isolated from staff and animal patients at a veterinary hospital and show considerable within-host diversity that can rise and fall over time.
Collapse
|
112
|
Wright MS, Stockwell TB, Beck E, Busam DA, Bajaksouzian S, Jacobs MR, Bonomo RA, Adams MD. SISPA-Seq for rapid whole genome surveys of bacterial isolates. INFECTION GENETICS AND EVOLUTION 2015; 32:191-8. [PMID: 25796360 DOI: 10.1016/j.meegid.2015.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 01/17/2023]
Abstract
Whole genome sequencing (WGS) of large isolate collections has many applications, yet sequencing costs are still significant. We sought to develop a rapid and cost efficient WGS method to address fundamental questions in clinical microbiology. We evaluated the performance of SISPA (Sequence-Independent, Single-Primer Amplification) combined with next-generation sequencing (SISPA-Seq) of 75 clinical isolates of Acinetobacter baumannii to establish whether SISPA-Seq resulted in sufficient coverage and quality to (1) determine strain phylogenetic placement and (2) and carriage of known antibiotic resistance (AbR) genes. Strains for which whole genome sequences were available were included for validation. Two libraries for each strain were constructed from separate SISPA reactions with different barcoded primers, using genomic DNA prepared from either high quality or rapid heat-lysis preparations. SISPA-Seq resulted in a median of 65× genome coverage when reads from both primer sets were combined. Coverage and quality were sufficient for detection of AbR genes by comparison of reads to the ARG-ANNOT database and were often sufficient to distinguish between different allelic variants of the same gene. kSNP and RAxML were used to construct a robust phylogeny based on single-nucleotide variants (SNVs) that showed that the SISPA-Seq data was sufficient for sensitive and accurate phylogenetic placement. Advantages of the SISPA-Seq method include inexpensive and rapid DNA preparation and a typical total cost less than one-half that of standard genome sequencing. In summary, SISPA-Seq can be used to survey whole genomes of a large strain collection and identify strains that should be targeted for additional sequencing.
Collapse
Affiliation(s)
| | | | - Erin Beck
- J. Craig Venter Institute, Rockville, MD, USA
| | | | | | - Michael R Jacobs
- University Hospitals Case Medical Center, USA; Case Western Reserve University, USA
| | - Robert A Bonomo
- Case Western Reserve University, USA; Louis Stokes Cleveland Veterans Affairs Medical Center, USA
| | | |
Collapse
|
113
|
Senchenkova SN, Shashkov AS, Popova AV, Shneider MM, Arbatsky NP, Miroshnikov KA, Volozhantsev NV, Knirel YA. Structure elucidation of the capsular polysaccharide of Acinetobacter baumannii AB5075 having the KL25 capsule biosynthesis locus. Carbohydr Res 2015; 408:8-11. [PMID: 25816997 DOI: 10.1016/j.carres.2015.02.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/03/2015] [Accepted: 02/25/2015] [Indexed: 11/17/2022]
Abstract
Capsular polysaccharide was isolated by the phenol-water extraction of Acinetobacter baumannii AB5075 and studied by 1D and 2D (1)H and (13)C NMR spectroscopy. The following structure of the linear trisaccharide repeating unit was established: → 3)-β-D-ManpNAcA-(1 → 4)-β-D-ManpNAcA-(1 → 3)-α-D-QuipNAc4NR-(1 → where R indicates (S)-3-hydroxybutanoyl or acetyl in the ratio ∼ 2.5:1. The genes in the polysaccharide biosynthesis locus designated KL25 are appropriate to the established CPS structure.
Collapse
Affiliation(s)
- Sof'ya N Senchenkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya V Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Mikhail M Shneider
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin A Miroshnikov
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay V Volozhantsev
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
114
|
Ou HY, Kuang SN, He X, Molgora BM, Ewing PJ, Deng Z, Osby M, Chen W, Xu HH. Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors. Sci Rep 2015; 5:8643. [PMID: 25728466 PMCID: PMC4345345 DOI: 10.1038/srep08643] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/29/2015] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors. Compared with 20 other complete genomes of A. baumannii, LAC-4 genome harbors at least 12 copies of five distinct insertion sequences. It contains 12 and 14 copies of two novel IS elements, ISAba25 and ISAba26, respectively. Additionally, three novel composite transposons were identified: Tn6250, Tn6251 and Tn6252, two of which contain resistance genes. The antibiotic resistance genetic determinants on the LAC-4 genome correlate well with observed antimicrobial susceptibility patterns. Moreover, twelve genomic islands (GI) were identified in LAC-4 genome. Among them, the 33.4-kb GI12 contains a large number of genes which constitute the K (capsule) locus. LAC-4 harbors several unique putative virulence factor loci. Furthermore, LAC-4 and all 19 other outbreak isolates were found to harbor a heme oxygenase gene (hemO)-containing gene cluster. The sequencing of the first complete genome of an ST10 A. baumannii clinical strain should accelerate our understanding of the epidemiology, mechanisms of resistance and virulence of A. baumannii.
Collapse
Affiliation(s)
- Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism and School of Life Sciences &Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Shan N Kuang
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, California, USA
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism and School of Life Sciences &Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Brenda M Molgora
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, California, USA
| | - Peter J Ewing
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, California, USA
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences &Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Melanie Osby
- Department of Pathology, LAC+USC Medical Center, Los Angeles, California, USA
| | - Wangxue Chen
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - H Howard Xu
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, California, USA
| |
Collapse
|
115
|
Patel G, Perez F, Hujer AM, Rudin SD, Augustine JJ, Jacobs GH, Jacobs MR, Bonomo RA. Fulminant endocarditis and disseminated infection caused by carbapenem-resistant Acinetobacter baumannii in a renal-pancreas transplant recipient. Transpl Infect Dis 2015; 17:289-96. [PMID: 25661804 DOI: 10.1111/tid.12351] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/13/2014] [Accepted: 12/11/2014] [Indexed: 01/23/2023]
Abstract
Acinetobacter baumannii is an important cause of healthcare-associated infections, and is particularly problematic among patients who undergo organ transplantation. We describe a case of fulminant sepsis caused by carbapenem-resistant A. baumannii harboring the blaOXA-23 carbapenemase gene and belonging to international clone II. This isolate led to the death of a patient 6 days after simultaneous kidney-pancreas transplantation. Autopsy findings revealed acute mitral valve endocarditis, myocarditis, splenic and renal emboli, peritonitis, and pneumonia. This case highlights the severe nature of certain A. baumannii infections and the vulnerability of transplanted patients to the increasingly intractable "high-risk" clones of multidrug-resistant organisms.
Collapse
Affiliation(s)
- G Patel
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | | | | | | | | |
Collapse
|
116
|
Kirkup BC. Bacterial Strain Diversity Within Wounds. Adv Wound Care (New Rochelle) 2015; 4:12-23. [PMID: 25566411 DOI: 10.1089/wound.2014.0560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 06/23/2014] [Indexed: 12/17/2022] Open
Abstract
Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.
Collapse
Affiliation(s)
- Benjamin C. Kirkup
- FE Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| |
Collapse
|
117
|
Liu F, Zhu Y, Yi Y, Lu N, Zhu B, Hu Y. Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants. BMC Genomics 2014; 15:1163. [PMID: 25534766 PMCID: PMC4367897 DOI: 10.1186/1471-2164-15-1163] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/16/2014] [Indexed: 01/19/2023] Open
Abstract
Background Acinetobacter baumannii is an important nosocomial pathogen that poses a serious health threat to immune-compromised patients. Due to its rapid ability to develop multidrug resistance (MDR), A. baumannii has increasingly become a focus of attention worldwide. To better understand the genetic variation and antibiotic resistance mechanisms of this bacterium at the genomic level, we reported high-quality draft genome sequences of 8 clinical isolates with various sequence types and drug susceptibility profiles. Results We sequenced 7 MDR and 1 drug-sensitive clinical A. baumannii isolates and performed comparative genomic analysis of these draft genomes with 16 A. baumannii complete genomes from GenBank. We found a high degree of variation in A. baumannii, including single nucleotide polymorphisms (SNPs) and large DNA fragment variations in the AbaR-like resistance island (RI) regions, the prophage and the type VI secretion system (T6SS). In addition, we found several new AbaR-like RI regions with highly variable structures in our MDR strains. Interestingly, we found a novel genomic island (designated as GIBJ4) in the drug-sensitive strain BJ4 carrying metal resistance genes instead of antibiotic resistance genes inserted into the position where AbaR-like RIs commonly reside in other A. baumannii strains. Furthermore, we showed that diverse antibiotic resistance determinants are present outside the RIs in A. baumannii, including antibiotic resistance-gene bearing integrons, the blaOXA-23-containing transposon Tn2009, and chromosomal intrinsic antibiotic resistance genes. Conclusions Our comparative genomic analysis revealed that extensive genomic variation exists in the A. baumannii genome. Transposons, genomic islands and point mutations are the main contributors to the plasticity of the A. baumannii genome and play critical roles in facilitating the development of antibiotic resistance in the clinical isolates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1163) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | - Baoli Zhu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | | |
Collapse
|
118
|
Evolution of carbapenem-resistant Acinetobacter baumannii revealed through whole-genome sequencing and comparative genomic analysis. Antimicrob Agents Chemother 2014; 59:1168-76. [PMID: 25487793 DOI: 10.1128/aac.04609-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Acinetobacter baumannii is a globally important nosocomial pathogen characterized by an evolving multidrug resistance. A total of 35 representative clinical A. baumannii strains isolated from 13 hospitals in nine cities in China from 1999 to 2011, including 32 carbapenem-resistant and 3 carbapenem-susceptible A. baumannii strains, were selected for whole-genome sequencing and comparative genomic analysis. Phylogenetic analysis revealed that the earliest strain, strain 1999BJAB11, and two strains isolated in Zhejiang Province in 2004 were the founder strains of carbapenem-resistant A. baumannii. Ten types of AbaR resistance islands were identified, and a previously unreported AbaR island, which comprised a two-component response regulator, resistance-related proteins, and RND efflux system proteins, was identified in two strains isolated in Zhejiang in 2004. Multiple transposons or insertion sequences (ISs) existed in each strain, and these gradually tended to diversify with evolution. Some of these IS elements or transposons were the first to be reported, and most of them were mainly found in strains from two provinces. Genome feature analysis illustrated diversified resistance genes, surface polysaccharides, and a restriction-modification system, even in strains that were phylogenetically and epidemiologically very closely related. IS-mediated deletions were identified in the type VI secretion system region, the csuE region, and core lipooligosaccharide (LOS) loci. Recombination occurred in the heme utilization region, and intrinsic resistance genes (blaADC and blaOXA-51-like variants) and three novel blaOXA-51-like variants (blaOXA-424, blaOXA-425, and blaOXA-426) were identified. Our results could improve the understanding of the evolutionary processes that contribute to the emergence of carbapenem-resistant A. baumannii strains and help elucidate the molecular evolutionary mechanism in A. baumannii.
Collapse
|
119
|
Nigro SJ, Holt KE, Pickard D, Hall RM. Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid. J Antimicrob Chemother 2014; 70:1259-61. [PMID: 25433005 PMCID: PMC4356202 DOI: 10.1093/jac/dku486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Steven J Nigro
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Ruth M Hall
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
120
|
Eijkelkamp BA, Stroeher UH, Hassan KA, Paulsen IT, Brown MH. Comparative analysis of surface-exposed virulence factors of Acinetobacter baumannii. BMC Genomics 2014; 15:1020. [PMID: 25422040 PMCID: PMC4256060 DOI: 10.1186/1471-2164-15-1020] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/14/2014] [Indexed: 01/19/2023] Open
Abstract
Background Acinetobacter baumannii is a significant hospital pathogen, particularly due to the dissemination of highly multidrug resistant isolates. Genome data have revealed that A. baumannii is highly genetically diverse, which correlates with major variations seen at the phenotypic level. Thus far, comparative genomic studies have been aimed at identifying resistance determinants in A. baumannii. In this study, we extend and expand on these analyses to gain greater insight into the virulence factors across eight A. baumannii strains which are clonally, temporally and geographically distinct, and includes an isolate considered non-pathogenic and a community-acquired A. baumannii. Results We have identified a large number of genes in the A. baumannii genomes that are known to play a role in virulence in other pathogens, such as the recently studied proline-alanine-alanine-arginine (PAAR)-repeat domains of the type VI secretion systems. Not surprising, many virulence candidates appear to be part of the A. baumannii core genome of virulent isolates but were often found to be insertionally disrupted in the avirulent A. baumannii strain SDF. Our study also reveals that many known or putative virulence determinants are restricted to specific clonal lineages, which suggests that these virulence determinants may be crucial for the success of these widespread common clones. It has previously been suggested that the high level of intrinsic and adaptive resistance has enabled the widespread presence of A. baumannii in the hospital environment. This appears to have facilitated the expansion of its repertoire of virulence traits, as in general, the nosocomial strains in this study possess more virulence genes compared to the community-acquired isolate. Conclusions Major genetic variation in known or putative virulence factors was seen across the eight strains included in this study, suggesting that virulence mechanisms are complex and multifaceted in A. baumannii. Overall, these analyses increase our understanding of A. baumannii pathogenicity and will assist in future studies determining the significance of virulence factors within clonal lineages and/or across the species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1020) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | - Melissa H Brown
- School of Biological Sciences, Flinders University, Adelaide, Australia.
| |
Collapse
|
121
|
Powers RA, Swanson HC, Taracila MA, Florek NW, Romagnoli C, Caselli E, Prati F, Bonomo RA, Wallar BJ. Biochemical and structural analysis of inhibitors targeting the ADC-7 cephalosporinase of Acinetobacter baumannii. Biochemistry 2014; 53:7670-9. [PMID: 25380506 PMCID: PMC4263437 DOI: 10.1021/bi500887n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
β-Lactam
resistance in Acinetobacter baumannii presents one
of the greatest challenges to contemporary antimicrobial chemotherapy.
Much of this resistance to cephalosporins derives from the expression
of the class C β-lactamase enzymes, known as Acinetobacter-derived cephalosporinases (ADCs). Currently, β-lactamase inhibitors
are structurally similar to β-lactam substrates and are not
effective inactivators of this class C cephalosporinase. Herein, two boronic acid transition state inhibitors
(BATSIs S02030 and SM23) that are chemically distinct from β-lactams
were designed and tested for inhibition of ADC enzymes. BATSIs SM23
and S02030 bind with high affinity to ADC-7, a chromosomal cephalosporinase
from Acinetobacter baumannii (Ki = 21.1 ± 1.9 nM and 44.5 ± 2.2 nM, respectively).
The X-ray crystal structures of ADC-7 were determined in both the
apo form (1.73 Å resolution) and in complex with S02030 (2.0
Å resolution). In the complex, S02030 makes several canonical
interactions: the O1 oxygen of S02030 is bound in the oxyanion hole,
and the R1 amide group makes key interactions with conserved residues
Asn152 and Gln120. In addition, the carboxylate group of the inhibitor
is meant to mimic the C3/C4 carboxylate found
in β-lactams. The C3/C4 carboxylate recognition
site in class C enzymes is comprised of Asn346 and Arg349 (AmpC numbering),
and these residues are conserved in ADC-7. Interestingly, in the ADC-7/S02030
complex, the inhibitor carboxylate group is observed to interact with
Arg340, a residue that distinguishes ADC-7 from the related class
C enzyme AmpC. A thermodynamic analysis suggests that ΔH driven compounds may be optimized to generate
new lead agents. The ADC-7/BATSI complex provides insight into recognition
of non-β-lactam inhibitors by ADC enzymes and offers a starting
point for the structure-based optimization of this class of novel
β-lactamase inhibitors against a key resistance target.
Collapse
Affiliation(s)
- Rachel A Powers
- Department of Chemistry, Grand Valley State University , 1 Campus Drive, Allendale, Michigan 49401, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
122
|
Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Med 2014; 6:70. [PMID: 25414729 PMCID: PMC4237759 DOI: 10.1186/s13073-014-0070-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/08/2014] [Indexed: 01/23/2023] Open
Abstract
Background Multidrug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within an outbreak, it can be difficult to identify the routes of cross-infection rapidly and accurately enough to inform infection control. Here, we describe a protracted hospital outbreak of multidrug-resistant A. baumannii, in which whole-genome sequencing (WGS) was used to obtain a high-resolution view of the relationships between isolates. Methods To delineate and investigate the outbreak, we attempted to genome-sequence 114 isolates that had been assigned to the A. baumannii complex by the Vitek2 system and obtained informative draft genome sequences from 102 of them. Genomes were mapped against an outbreak reference sequence to identify single nucleotide variants (SNVs). Results We found that the pulsotype 27 outbreak strain was distinct from all other genome-sequenced strains. Seventy-four isolates from 49 patients could be assigned to the pulsotype 27 outbreak on the basis of genomic similarity, while WGS allowed 18 isolates to be ruled out of the outbreak. Among the pulsotype 27 outbreak isolates, we identified 31 SNVs and seven major genotypic clusters. In two patients, we documented within-host diversity, including mixtures of unrelated strains and within-strain clouds of SNV diversity. By combining WGS and epidemiological data, we reconstructed potential transmission events that linked all but 10 of the patients and confirmed links between clinical and environmental isolates. Identification of a contaminated bed and a burns theatre as sources of transmission led to enhanced environmental decontamination procedures. Conclusions WGS is now poised to make an impact on hospital infection prevention and control, delivering cost-effective identification of routes of infection within a clinically relevant timeframe and allowing infection control teams to track, and even prevent, the spread of drug-resistant hospital pathogens.
Collapse
|
123
|
Bruhn KW, Pantapalangkoor P, Nielsen T, Tan B, Junus J, Hujer KM, Wright MS, Bonomo RA, Adams MD, Chen W, Spellberg B. Host fate is rapidly determined by innate effector-microbial interactions during Acinetobacter baumannii bacteremia. J Infect Dis 2014; 211:1296-305. [PMID: 25378635 DOI: 10.1093/infdis/jiu593] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii is one of the most antibiotic-resistant pathogens. Defining mechanisms driving pathogenesis is critical to enable new therapeutic approaches. METHODS We studied virulence differences across a diverse panel of A. baumannii clinical isolates during murine bacteremia to elucidate host-microbe interactions that drive outcome. RESULTS We identified hypervirulent strains that were lethal at low intravenous inocula and achieved very high early, and persistent, blood bacterial densities. Virulent strains were nonlethal at low inocula but lethal at 2.5-fold higher inocula. Finally, relatively avirulent (hypovirulent) strains were nonlethal at 20-fold higher inocula and were efficiently cleared by early time points. In vivo virulence correlated with in vitro resistance to complement and macrophage uptake. Depletion of complement, macrophages, and neutrophils each independently increased bacterial density of the hypovirulent strain but insufficiently to change lethality. However, disruption of all 3 effector mechanisms enabled early bacterial densities similar to hypervirulent strains, rendering infection 100% fatal. CONCLUSIONS The lethality of A. baumannii strains depends on distinct stages. Strains resistant to early innate effectors are able to establish very high early bacterial blood density, and subsequent sustained bacteremia leads to Toll-like receptor 4-mediated hyperinflammation and lethality. These results have important implications for translational efforts to develop therapies that modulate host-microbe interactions.
Collapse
Affiliation(s)
| | | | | | - Brandon Tan
- Department of Molecular Microbiology and Immunology
| | - Justin Junus
- Department of Molecular Microbiology and Immunology
| | - Kristine M Hujer
- Department of Medicine Department of Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio
| | | | - Robert A Bonomo
- Department of Medicine Department of Pharmacology Department of Molecular Biology and Microbiology, Case Western Reserve University Department of Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Ohio
| | - Mark D Adams
- Department of J. Craig Venter Institute, La Jolla, California
| | - Wangxue Chen
- Department of Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario
| | - Brad Spellberg
- Department of Medicine, Division of Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles
| |
Collapse
|
124
|
Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC, Murphy C, Feldgarden M, Wortman J, Clermont D, Lambert T, Grillot-Courvalin C, Nemec A, Courvalin P, Rocha EPC. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol 2014; 6:2866-82. [PMID: 25313016 PMCID: PMC4224351 DOI: 10.1093/gbe/evu225] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens.
Collapse
Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France CNRS, UMR3525, Paris, France
| | - Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France CNRS, UMR3525, Paris, France
| | - Eun-Jeong Yoon
- Unité des Agents Antibactériens, Institut Pasteur, Paris, France
| | - Lenka Krizova
- Laboratory of Bacterial Genetics, National Institute of Public Health, Prague, Czech Republic
| | | | - Cheryl Murphy
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | | | | | - Thierry Lambert
- Unité des Agents Antibactériens, Institut Pasteur, Paris, France
| | | | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Prague, Czech Republic.
| | | | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France CNRS, UMR3525, Paris, France
| |
Collapse
|
125
|
Dunne WM, van Belkum A. More Timely Antimicrobial Susceptibility Testing as a Tool in Combatting Antimicrobial Resistance in Clinically Relevant Microorganisms: Is There More than One Way to Skin a Cat? ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.clinmicnews.2014.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
126
|
Rafei R, Kempf M, Eveillard M, Dabboussi F, Hamze M, Joly-Guillou ML. Current molecular methods in epidemiological typing of Acinetobacter baumannii. Future Microbiol 2014; 9:1179-94. [DOI: 10.2217/fmb.14.63] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ABSTRACT The emergence of Acinetobacter baumannii during recent decades as an important nosocomial pathogen responsible of worldwide, intensively documented, outbreaks has resulted in a need for effective epidemiological typing methods. Throughout the years, many typing methods for A. baumannii epidemiological studies have been proposed from phenotypic to molecular methods. Currently, the use of phenotypic typing methods have declined considerably and been progressively replaced by molecular methods. In this review, we introduce the current molecular methods available for A. baumannii typing. Each method has its own advantages and disadvantages, and the selection of an appropriate genotyping method depends on studied objectives. This review sheds light on questions in different epidemiological settings and most molecular methods used to fit these objectives.
Collapse
Affiliation(s)
- Rayane Rafei
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Microbiologie Santé et Environnement (LMSE), Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Marie Kempf
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, 4 rue Larrey, 49933 Angers cedex, France
| | - Matthieu Eveillard
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, 4 rue Larrey, 49933 Angers cedex, France
| | - Fouad Dabboussi
- Laboratoire de Microbiologie Santé et Environnement (LMSE), Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Monzer Hamze
- Laboratoire de Microbiologie Santé et Environnement (LMSE), Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Marie-Laure Joly-Guillou
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, 4, rue Larrey, 49933 Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, 4 rue Larrey, 49933 Angers cedex, France
| |
Collapse
|
127
|
In vitro potential of Lycosin-I as an alternative antimicrobial drug for treatment of multidrug-resistant Acinetobacter baumannii infections. Antimicrob Agents Chemother 2014; 58:6999-7002. [PMID: 25199777 DOI: 10.1128/aac.03279-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The resistance of multidrug-resistant Acinetobacter baumannii (MDRAB) isolates to most traditional antibiotics results in huge challenges for infection therapy. We investigated the in vitro activities of both l- and d-lycosin-I against MDRAB. These two compounds displayed high antibacterial activities and rapid bactericidal effects against MDRAB. Moreover, the compounds retained their activity even at high salt (Mg(2+) or Ca(2+)) concentrations. These results demonstrate the potential of lycosin-I to be developed as a new antibiotic.
Collapse
|
128
|
Huang H, Dong Y, Yang ZL, Luo H, Zhang X, Gao F. Complete sequence of pABTJ2, a plasmid from Acinetobacter baumannii MDR-TJ, carrying many phage-like elements. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:172-7. [PMID: 25046542 PMCID: PMC4411360 DOI: 10.1016/j.gpb.2014.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/14/2014] [Accepted: 05/26/2014] [Indexed: 12/24/2022]
Abstract
Acinetobacter baumannii is an important opportunistic pathogen in hospital, and the multidrug-resistant isolates of A. baumannii have been increasingly reported in recent years. A number of different mechanisms of resistance have been reported, some of which are associated with plasmid-mediated acquisition of genes. Therefore, studies on plasmids in A. baumannii have been a hot issue lately. We have performed complete genome sequencing of A. baumannii MDR-TJ, which is a multidrug-resistant isolate. Finalizing the remaining large scaffold of the previous assembly, we found a new plasmid pABTJ2, which carries many phage-like elements. The plasmid pABTJ2 is a circular double-stranded DNA molecule, which is 110,967bp in length. We annotated 125 CDSs from pABTJ2 using IMG ER and ZCURVE_V, accounting for 88.28% of the whole plasmid sequence. Many phage-like elements and a tRNA-coding gene were detected in pABTJ2, which is rarely reported among A. baumannii. The tRNA gene is specific for asparagine codon GTT, which may be a small chromosomal sequence picked up through incorrect excision during plasmid formation. The phage-like elements may have been acquired during the integration process, as the GC content of the region carrying phage-like elements was higher than that of the adjacent regions. The finding of phage-like elements and tRNA-coding gene in pABTJ2 may provide a novel insight into the study of A. baumannii pan-plasmidome.
Collapse
Affiliation(s)
- He Huang
- MOE Key Laboratory of Systems Bioengineering, Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Dong
- MOE Key Laboratory of Systems Bioengineering, Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhi-Liang Yang
- MOE Key Laboratory of Systems Bioengineering, Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Xi Zhang
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China.
| |
Collapse
|
129
|
Population dynamics of an Acinetobacter baumannii clonal complex during colonization of patients. J Clin Microbiol 2014; 52:3200-8. [PMID: 24951812 DOI: 10.1128/jcm.00921-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Acinetobacter baumannii has emerged as one of the leading pathogens causing hospital-acquired infection. The success of A. baumannii as a pathogen has to a large extent been attributed to its capacity to remodel its genome. Several major epidemic clonal complexes of A. baumannii spread across different health care facilities around the world, each of which contains a subset of diversified strains. However, little is known about the population dynamics during colonization of A. baumannii within hosts. Here, whole-genome sequencing was used to analyze population dynamics of A. baumannii strains isolated from a group of patients at different time points as well as from different sites of a particular patient. Seven out of nine of the sampled A. baumannii strains belonged to the international clone II (CC92 clonal complex). While the A. baumannii strains were found to be stable in three patients, there was a change of A. baumannii strains in one patient. Comparative genomic analysis revealed that the accessory genome of these strains contained a large set of virulence-encoding genes and these virulence factors might play a role in determining population dynamics. Microscale genome modification has been revealed by analysis of single nucleotide polymorphisms (SNPs) between A. baumannii strains isolated from the same patient. Parallel evolutionary traits have been observed during genome diversification when A. baumannii colonize in different patients. Our study suggested that both antibiotic usage and host environment might impose selective forces that drive the rapid adaptive evolution in colonizing A. baumannii.
Collapse
|
130
|
Senchenkova SN, Shashkov AS, Shneider MM, Arbatsky NP, Popova AV, Miroshnikov KA, Volozhantsev NV, Knirel YA. Structure of the capsular polysaccharide of Acinetobacter baumannii ACICU containing di-N-acetylpseudaminic acid. Carbohydr Res 2014; 391:89-92. [DOI: 10.1016/j.carres.2014.04.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/26/2014] [Accepted: 04/01/2014] [Indexed: 01/22/2023]
|
131
|
Premkumar L, Kurth F, Duprez W, Grøftehauge MK, King GJ, Halili MA, Heras B, Martin JL. Structure of the Acinetobacter baumannii dithiol oxidase DsbA bound to elongation factor EF-Tu reveals a novel protein interaction site. J Biol Chem 2014; 289:19869-80. [PMID: 24860094 DOI: 10.1074/jbc.m114.571737] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The multidrug resistant bacterium Acinetobacter baumannii is a significant cause of nosocomial infection. Biofilm formation, that requires both disulfide bond forming and chaperone-usher pathways, is a major virulence trait in this bacterium. Our biochemical characterizations show that the periplasmic A. baumannii DsbA (AbDsbA) enzyme has an oxidizing redox potential and dithiol oxidase activity. We found an unexpected non-covalent interaction between AbDsbA and the highly conserved prokaryotic elongation factor, EF-Tu. EF-Tu is a cytoplasmic protein but has been localized extracellularly in many bacterial pathogens. The crystal structure of this complex revealed that the EF-Tu switch I region binds to the non-catalytic surface of AbDsbA. Although the physiological and pathological significance of a DsbA/EF-Tu association is unknown, peptides derived from the EF-Tu switch I region bound to AbDsbA with submicromolar affinity. We also identified a seven-residue DsbB-derived peptide that bound to AbDsbA with low micromolar affinity. Further characterization confirmed that the EF-Tu- and DsbB-derived peptides bind at two distinct sites. These data point to the possibility that the non-catalytic surface of DsbA is a potential substrate or regulatory protein interaction site. The two peptides identified in this work together with the newly characterized interaction site provide a novel starting point for inhibitor design targeting AbDsbA.
Collapse
Affiliation(s)
- Lakshmanane Premkumar
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Fabian Kurth
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Wilko Duprez
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Morten K Grøftehauge
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Gordon J King
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Maria A Halili
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Begoña Heras
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Jennifer L Martin
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| |
Collapse
|
132
|
Perez F, Bonomo RA. Vaccines for Acinetobacter baumannii: thinking "out of the box". Vaccine 2014; 32:2537-9. [PMID: 24662709 DOI: 10.1016/j.vaccine.2014.03.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/27/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Federico Perez
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, United States.
| | - Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, United States.
| |
Collapse
|