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Al-Asadi SA, Abdul Wahhab BH, Bootwala J, Alwatar WMA, Al-Kahachi RES. Unraveling antibiotic resistance in Achromobacter mucicolens IA strain: genomic insights, structural analysis, and prospects for targeted therapeutics. Microbiol Spectr 2024; 12:e0392623. [PMID: 39472000 PMCID: PMC11619425 DOI: 10.1128/spectrum.03926-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 09/18/2024] [Indexed: 12/08/2024] Open
Abstract
The mortality rate of infectious diseases caused by Achromobacter mucicolens is increasing. The enhanced antibiotic resistance among bacterial species through genetic transfer and mutations in the efflux mediating genes has made the treatment quite challenging. A. mucicolens is an aerobic, gram-negative, and non-fermenting opportunistic pathogen found in immunocompromised patients. A. mucicolens shows resistance against beta-lactams and other antibiotics through intrinsic resistance mechanisms, including multi-drug efflux pumps and beta-lactamases. In this study, the clinical isolate whole genome sequencing of A. mucicolens data was analyzed to identify the genes and mutations responsible for antimicrobial resistance. The identified genes and their mutants were then subjected to structural analysis to better understand the impact of mutations on the protein structure, and domain analysis was performed to investigate the role of domains in antibiotic resistance. A total of 4 genes, acrR, macB, msbA, and tolC, were identified with significant mutations, whereas macB was shortlisted for further analysis based on the conserved regions, sequence alignment, and the maximum number of mutations. All the mutants of the macB gene contain the two common domains, the ABC transporter-like ATP-binding domain and the AAA + ATPase domain. These domains are crucial in efflux mediating drug transport and can be targeted to design novel drugs for treating infections caused by A. mucicolens.IMPORTANCEAchromobacter species represent a significant threat as opportunistic pathogens, particularly in healthcare settings. Their resilience to antibiotics, demonstrated by strains like A. mucicolens, poses a serious challenge in treating infections, especially in immunocompromised patients. This study emphasizes the critical need for heightened vigilance among healthcare professionals regarding Achromobacter infections. By analyzing the whole genome sequencing data of A. mucicolens, the study sheds light on the genetic basis of antimicrobial resistance, aiding in more targeted treatment strategies. Furthermore, structural and domain analyses offer insights into how mutations impact protein structure and function, crucial for developing effective interventions. Ultimately, implementing rigorous sanitation measures and antibiotic stewardship protocols is needed to mitigate the spread of Achromobacter and safeguard vulnerable patient populations.
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Affiliation(s)
- Sura Ali Al-Asadi
- Department of Molecular and Medical Techniques, Biotechnology Research Centre, Al Nahrain University, Baghdad, Iraq
| | | | | | - Wifaq M. Ali Alwatar
- Unit of Clinical and Communicable diseases, College of medicine, Baghdad University, Baghdad, Iraq
| | - Rusul Emaduldeen S. Al-Kahachi
- Department of scholarships and cultural relationship, Republic of Iraq Ministry of Higher Education and Scientific Research, Baghdad, Iraq
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2
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Turton K, Parks HJ, Zarodkiewicz P, Hamad MA, Dwane R, Parau G, Ingram RJ, Coll RC, Bryant CE, Valvano MA. The Achromobacter type 3 secretion system drives pyroptosis and immunopathology via independent activation of NLRC4 and NLRP3 inflammasomes. Cell Rep 2023; 42:113012. [PMID: 37598340 PMCID: PMC7614980 DOI: 10.1016/j.celrep.2023.113012] [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: 02/07/2023] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
How the opportunistic Gram-negative pathogens of the genus Achromobacter interact with the innate immune system is poorly understood. Using three Achromobacter clinical isolates from two species, we show that the type 3 secretion system (T3SS) is required to induce cell death in human macrophages by inflammasome-dependent pyroptosis. Macrophages deficient in the inflammasome sensors NLRC4 or NLRP3 undergo pyroptosis upon bacterial internalization, but those deficient in both NLRC4 and NLRP3 do not, suggesting either sensor mediates pyroptosis in a T3SS-dependent manner. Detailed analysis of the intracellular trafficking of one isolate indicates that the intracellular bacteria reside in a late phagolysosome. Using an intranasal mouse infection model, we observe that Achromobacter damages lung structure and causes severe illness, contingent on a functional T3SS. Together, we demonstrate that Achromobacter species can survive phagocytosis by promoting macrophage cell death and inflammation by redundant mechanisms of pyroptosis induction in a T3SS-dependent manner.
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Affiliation(s)
- Keren Turton
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Hannah J Parks
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Paulina Zarodkiewicz
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Mohamad A Hamad
- Department of Medical Laboratory Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Rachel Dwane
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Georgiana Parau
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Rebecca J Ingram
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Rebecca C Coll
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Clare E Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; Department of Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK.
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3
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Olbrecht M, Echahidi F, Piérard D, Peeters C, Vandamme P, Wybo I, Demuyser T. In Vitro Susceptibility of Achromobacter Species Isolated from Cystic Fibrosis Patients: a 6-Year Survey. Antimicrob Agents Chemother 2023; 67:e0037923. [PMID: 37310234 PMCID: PMC10353363 DOI: 10.1128/aac.00379-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/17/2023] [Indexed: 06/14/2023] Open
Abstract
We conducted in vitro antimicrobial susceptibility testing of 267 Achromobacter isolates for 16 antibiotics from 2017 to 2022. The highest susceptibility was found for piperacillin-tazobactam (70%) and ceftazidime-avibactam (62%). Between 30% and 49% of strains were susceptible to tigecycline, ceftazidime, and meropenem. We applied species-specific Achromobacter xylosoxidans breakpoints for piperacillin-tazobactam, meropenem, and trimethoprim-sulfamethoxazole and EUCAST pharmacokinetic/pharmacodynamic (PK/PD) breakpoints for the others. A. xylosoxidans was the most frequently isolated species, followed by Achromobacter insuavis and Achromobacter ruhlandii.
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Affiliation(s)
- Margo Olbrecht
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Fedoua Echahidi
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Denis Piérard
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Ingrid Wybo
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Thomas Demuyser
- Department Microbiology and Infection Control, National Reference Center for Burkholderia Cepacia Complex and other Gram negative non fermenters (NRC), Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- AIMS lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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4
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Achromobacter spp. prevalence and adaptation in cystic fibrosis lung infection. Microbiol Res 2022; 263:127140. [DOI: 10.1016/j.micres.2022.127140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
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Pickrum AM, Riegert MO, Wells C, Brockman K, Frank DW. The In Vitro Replication Cycle of Achromobacter xylosoxidans and Identification of Virulence Genes Associated with Cytotoxicity in Macrophages. Microbiol Spectr 2022; 10:e0208322. [PMID: 35856670 PMCID: PMC9430717 DOI: 10.1128/spectrum.02083-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Achromobacter xylosoxidans is an opportunistic pathogen implicated in a wide variety of human infections including the ability to colonize the lungs of cystic fibrosis (CF) patients. The role of A. xylosoxidans in human pathology remains controversial due to the lack of optimized in vitro and in vivo model systems to identify and test bacterial gene products that promote a pathological response. We have previously identified macrophages as a target host cell for A. xylosoxidans-induced cytotoxicity. By optimizing our macrophage infection model, we determined that A. xylosoxidans enters macrophages and can reside within a membrane bound vacuole for extended periods of time. Intracellular replication appears limited with cellular lysis preceding an enhanced, mainly extracellular replication cycle. Using our optimized in vitro model system along with transposon mutagenesis, we identified 163 genes that contribute to macrophage cytotoxicity. From this list, we characterized a giant RTX adhesin encoded downstream of a type one secretion system (T1SS) that mediates bacterial binding and entry into host macrophages, an important first step toward cellular toxicity and inflammation. The RTX adhesin is encoded by other human isolates and is recognized by antibodies present in serum isolated from CF patients colonized by A. xylosoxidans, indicating this virulence factor is produced and deployed in vivo. This study represents the first characterization of A. xylosoxidans replication during infection and identifies a variety of genes that may be linked to virulence and human pathology. IMPORTANCE Patients affected by CF develop chronic bacterial infections characterized by inflammatory exacerbations and tissue damage. Advancements in sequencing technologies have broadened the list of opportunistic pathogens colonizing the CF lung. A. xylosoxidans is increasingly recognized as an opportunistic pathogen in CF, yet our understanding of the bacterium as a contributor to human disease is limited. Genomic studies have identified potential virulence determinants in A. xylosoxidans isolates, but few have been mechanistically studied. Using our optimized in vitro cell model, we identified and characterized a bacterial adhesin that mediates binding and uptake by host macrophages leading to cytotoxicity. A subset of serum samples from CF patients contains antibodies that recognize the RTX adhesion, suggesting, for the first time, that this virulence determinant is produced in vivo. This work furthers our understanding of A. xylosoxidans virulence factors at a mechanistic level.
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Affiliation(s)
- Adam M. Pickrum
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Molly O. Riegert
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Clive Wells
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kenneth Brockman
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Dara W. Frank
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Achromobacter spp. Adaptation in Cystic Fibrosis Infection and Candidate Biomarkers of Antimicrobial Resistance. Int J Mol Sci 2022; 23:ijms23169265. [PMID: 36012535 PMCID: PMC9409262 DOI: 10.3390/ijms23169265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/29/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Achromobacter spp. can establish occasional or chronic lung infections in patients with cystic fibrosis (CF). Chronic colonization has been associated with worse prognosis highlighting the need to identify markers of bacterial persistence. To this purpose, we analyzed phenotypic features of 95 Achromobacter spp. isolates from 38 patients presenting chronic or occasional infection. Virulence was tested in Galleria mellonella larvae, cytotoxicity was tested in human bronchial epithelial cells, biofilm production in static conditions was measured by crystal violet staining and susceptibility to selected antibiotics was tested by the disk diffusion method. The presence of genetic loci associated to the analyzed phenotypic features was evaluated by a genome-wide association study. Isolates from occasional infection induced significantly higher mortality of G. mellonella larvae and showed a trend for lower cytotoxicity than chronic infection isolates. No significant difference was observed in biofilm production among the two groups. Additionally, antibiotic susceptibility testing showed that isolates from chronically-infected patients were significantly more resistant to sulfonamides and meropenem than occasional isolates. Candidate genetic biomarkers associated with antibiotic resistance or sensitivity were identified. Achromobacter spp. strains isolated from people with chronic and occasional lung infection exhibit different virulence and antibiotic susceptibility features, which could be linked to persistence in CF lungs. This underlines the possibility of identifying predictive biomarkers of persistence that could be useful for clinical purposes.
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Zhang J, Gao S, Zheng F, Wang N. Intestinal Bacterial Diversity and Functional Analysis of Three Lepidopteran Corn Ear Worm Larvae. INSECTS 2022; 13:740. [PMID: 36005365 PMCID: PMC9409944 DOI: 10.3390/insects13080740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Insects, as the most abundant animal group on earth, and their symbionts help their hosts to adapt to various environments. Conogethes punctiferalis, Ostrinia furnacalis and Helicoverpa armigera are three main pests co-occurring in the ear stage of corn, which significantly affect the yield and quality of corn. The purpose of this study was to compare the diversity and function of the intestinal bacteria of the three co-occurring lepidopteran pests, C. punctiferalis, O. furnacalis and H. armigera, and to explore the reason of their prevalence from the microbiota's view. Our results showed the difference of diversity and abundance of the gut bacteria of three co-occurring lepidopteran pests at the ear stage. Proteobacteria and Firmicutes were the dominant phyla, and the Enterobacteriaceae and Enterococcaceae were the dominant families in the three pests. Compared with the other two pests, Bacteroidetes was found much more in C. punctiferalis. In addition, C. punctiferalis showed more correlation and similarity in bacteria composition with corn endophytic bacteria, as well as had obvious advantages in metabolic, environmental information processing, cellular processes and organic systems function pathways. Our findings may provide insight into the prevalence of corn earworm larvae from the perspective of gut microbiota and function prediction.
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8
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Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance. mSystems 2022; 7:e0138421. [PMID: 35695507 PMCID: PMC9238379 DOI: 10.1128/msystems.01384-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation. IMPORTANCE Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 clinical bacterial isolates collected from hospitalized patients at a large medical center over a 2-year period. We identified nearly 100 different bacterial species, which we divided into 14 different groups of related species. When we examined how genetic relatedness differed between species, we found that different species were likely evolving at different rates within our hospital. This is significant because the identification of bacterial outbreaks in the hospital currently relies on genetic similarity cutoffs, which are often applied uniformly across organisms. Finally, we found that antibiotic resistance genes and mobile genetic elements were abundant and were shared among the bacterial isolates we sampled. Overall, this study provides an in-depth view of the genomic diversity and evolutionary processes of bacteria sampled from hospitalized patients, as well as genetic similarity estimates that can inform hospital outbreak detection and prevention efforts.
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Le Goff M, Vastel M, Lebrun R, Mansuelle P, Diarra A, Grandjean T, Triponney P, Imbert G, Gosset P, Dessein R, Garnier F, Durand E. Characterization of the Achromobacter xylosoxidans Type VI Secretion System and Its Implication in Cystic Fibrosis. Front Cell Infect Microbiol 2022; 12:859181. [PMID: 35782124 PMCID: PMC9245596 DOI: 10.3389/fcimb.2022.859181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Achromobacter are environmental germs, with an unknown reservoir. It can become opportunistic pathogens in immunocompromised patients, causing bacteremia, meningitis, pneumonia, or peritonitis. In recent years, Achromobacter xylosoxidans has emerged with increasing incidence in patients with cystic fibrosis (CF). Recent studies showed that A. xylosoxidans is involved in the degradation of the respiratory function of patients with CF. The respiratory ecosystem of patients with CF is colonized by bacterial species that constantly fight for space and access to nutrients. The type VI secretion system (T6SS) empowers this constant bacterial antagonism, and it is used as a virulence factor in several pathogenic bacteria. This study aimed to investigate the prevalence of the T6SS genes in A. xylosoxidans isolated in patients with CF. We also evaluated clinical and molecular characteristics of T6SS-positive A. xylosoxidans strains. We showed that A. xylosoxidans possesses a T6SS gene cluster and that some environmental and clinical isolates assemble a functional T6SS nanomachine. A. xylosoxidans T6SS is used to target competing bacteria, including other CF-specific pathogens. Finally, we demonstrated the importance of the T6SS in the internalization of A. xylosoxidans in lung epithelial cells and that the T6SS protein Hcp is detected in the sputum of patients with CF. Altogether, these results suggest for the first time a role of T6SS in CF-lung colonization by A. xylosoxidans and opens promising perspective to target this virulence determinant as innovative theranostic options for CF management.
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Affiliation(s)
- Mélanie Le Goff
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Marseille, France
| | - Manon Vastel
- Université de Limoges, INSERM, Centre Hospitalier Universitaire (CHU) Limoges, Unité Mixte de Recherche (UMR) 1092, Limoges, France
| | - Régine Lebrun
- Plateforme Protéomique de l’Institut de Microbiologie de la Méditerranée, Marseille Protéomique, Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS) FR 3479, Marseille, France
| | - Pascal Mansuelle
- Plateforme Protéomique de l’Institut de Microbiologie de la Méditerranée, Marseille Protéomique, Aix Marseille Université, Centre National de la Recherche Scientifique (CNRS) FR 3479, Marseille, France
| | - Ava Diarra
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Teddy Grandjean
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Pauline Triponney
- Centre National de Référence de la Résistance aux Antibiotiques , Centre Hospitalier Universitaire de Besançon, Besançon, France
| | | | - Philippe Gosset
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Rodrigue Dessein
- Université de Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017-CIIL-Centre d’Infection et d’Immunité de Lille, University of Lille, Lille, France
| | - Fabien Garnier
- Université de Limoges, INSERM, Centre Hospitalier Universitaire (CHU) Limoges, Unité Mixte de Recherche (UMR) 1092, Limoges, France
- *Correspondence: Eric Durand, ; ; Fabien Garnier,
| | - Eric Durand
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Marseille, France
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Unité Mixte de Recherche (UMR) 7255, INSERM, Marseille, France
- *Correspondence: Eric Durand, ; ; Fabien Garnier,
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Bonis BM, Hunter RC. JMM Profile: Achromobacter xylosoxidans: the cloak-and-dagger opportunist. J Med Microbiol 2022; 71. [PMID: 35587447 DOI: 10.1099/jmm.0.001505] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Achromobacter xylosoxidans is associated with resilient nosocomial infections, with bacteraemia, pneumonia and chronic cystic fibrosis lung infection being the most common clinical presentations. Innate multi-drug resistance and a suite of virulence factors select for A. xylosoxidans infection during long-term antibiotic therapy, contributing to its persistence, treatment recalcitrance, association with poor clinical outcomes and emergence as a problematic pathogen. Horizontal gene transfer and maintenance of large genomes underpin the resilience and cosmopolitan lifestyle of A. xylosoxidans, and complicate its phylogenetic characterization.
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Affiliation(s)
- Benjamin M Bonis
- Department of Microbiology & Immunology, University of Minnesota Medical School, 689 23rd Ave. SE, Minneapolis, MN 55455, USA
| | - Ryan C Hunter
- Department of Microbiology & Immunology, University of Minnesota Medical School, 689 23rd Ave. SE, Minneapolis, MN 55455, USA
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11
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Ben Khedher M, Ghedira K, Rolain JM, Ruimy R, Croce O. Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies. Int J Mol Sci 2022; 23:1395. [PMID: 35163319 PMCID: PMC8835973 DOI: 10.3390/ijms23031395] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biological questions. This revolution has enabled advances in areas ranging from genome composition to how proteins interact with nucleic acids. This has created unprecedented opportunities through the integration of genomic data into clinics for the diagnosis of genetic traits associated with disease. Since then, these technologies have continued to evolve, and recently, long-read sequencing has overcome previous limitations in terms of accuracy, thus expanding its applications in genomics, transcriptomics and metagenomics. In this review, we describe a brief history of the bacterial genome sequencing revolution and its application in public health and molecular epidemiology. We present a chronology that encompasses the various technological developments: whole-genome shotgun sequencing, high-throughput sequencing, long-read sequencing. We mainly discuss the application of next-generation sequencing to decipher bacterial genomes. Secondly, we highlight how long-read sequencing technologies go beyond the limitations of traditional short-read sequencing. We intend to provide a description of the guiding principles of the 3rd generation sequencing applications and ongoing improvements in the field of microbial medical research.
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Affiliation(s)
- Mariem Ben Khedher
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur of Tunis, Tunis 1002, Tunisia;
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, 13005 Marseille, France;
| | - Raymond Ruimy
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), INSERM, Université Côte D’Azur, 06108 Nice, France
| | - Olivier Croce
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
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Ronin E, Derancourt C, Cabié A, Marion-Sanchez K. Achromobacter spp. Surgical Site Infections: A Systematic Review of Case Reports and Case Series. Microorganisms 2021; 9:microorganisms9122471. [PMID: 34946073 PMCID: PMC8704055 DOI: 10.3390/microorganisms9122471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Achromobacter species are isolated from rare but severe healthcare-associated infections, including surgical site infections. They are considered to preferentially infect immunocompromised patients but so far with limited evidence. We conducted a systematic review on Achromobacter spp. surgical site infections (SSIs) to determine if such infections were indeed more commonly associated with immunocompromised patients. The secondary objective was to describe the characteristics of infected patients. Eligible articles had to be published before 30 September 2020 and to report Achromobacter spp. SSIs across all surgical specialties excluding ophthalmology. Analyses were performed on individual data without meta-analysis. Cases were divided into 2 subgroups: one group which had either prosthesis or implant and the other group which did not. A first selection led to a review of 94 articles, of which 37 were analyzed. All were case reports or case series and corresponded to 49 infected patients. Most of the patients were under 65 years of age and had undergone a heart or digestive surgery followed by deep infection with no co-infecting pathogens. Nine out of the 49 cases were immunocompromised, with similar distribution between the two subgroups (16.6% and 20%, respectively). This review suggests that Achromobacter spp. SSIs do not preferentially target immunocompromised patients.
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Affiliation(s)
- Eve Ronin
- Department of Hospital Hygiene, CHU Martinique, F-97200 Fort-de-France, Martinique;
| | | | - André Cabié
- Department of Infectious Diseases, CHU Martinique, F-97200 Fort-de-France, Martinique;
- Unité Mixte de Recherche 1058 : Pathogenesis and Control of Chronic and Emerging Infections, 34000 Montpellier, France
| | - Karine Marion-Sanchez
- Department of Hospital Hygiene, CHU Martinique, F-97200 Fort-de-France, Martinique;
- Unité Mixte de Recherche 1058 : Pathogenesis and Control of Chronic and Emerging Infections, 34000 Montpellier, France
- Correspondence: ; Tel.: +596-596-55-97-42
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13
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Veschetti L, Sandri A, Patuzzo C, Melotti P, Malerba G, Lleo MM. Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients. Microb Genom 2021; 7. [PMID: 34292148 PMCID: PMC8477391 DOI: 10.1099/mgen.0.000606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Achromobacter species are increasingly being detected in cystic fibrosis (CF) patients, where they can establish chronic infections by adapting to the lower airway environment. To better understand the mechanisms contributing to a successful colonization by Achromobacter species, we sequenced the whole genome of 54 isolates from 26 patients with occasional and early/late chronic lung infection. We performed a phylogenetic analysis and compared virulence and resistance genes, genetic variants and mutations, and hypermutability mechanisms between chronic and occasional isolates. We identified five Achromobacter species as well as two non-affiliated genogroups (NGs). Among them were the frequently isolated Achromobacter xylosoxidans and four other species whose clinical importance is not yet clear: Achromobacter insuavis, Achromobacter dolens, Achromobacter insolitus and Achromobacter aegrifaciens. While A. insuavis and A. dolens were isolated only from chronically infected patients and A. aegrifaciens only from occasionally infected patients, the other species were found in both groups. Most of the occasional isolates lacked functional genes involved in invasiveness, chemotaxis, type 3 secretion system and anaerobic growth, whereas the great majority (>60%) of chronic isolates had these genomic features. Interestingly, almost all (n=22/23) late chronic isolates lacked functional genes involved in lipopolysaccharide production. Regarding antibiotic resistance, we observed a species-specific distribution of blaOXA genes, confirming what has been reported in the literature and additionally identifying blaOXA-2 in some A. insolitus isolates and observing no blaOXA genes in A. aegrifaciens or NGs. No significant difference in resistance genes was found between chronic and occasional isolates. The results of the mutator genes analysis showed that no occasional isolate had hypermutator characteristics, while 60% of early chronic (<1 year from first colonization) and 78% of late chronic (>1 year from first colonization) isolates were classified as hypermutators. Although all A. dolens, A. insuavis and NG isolates presented two different mutS genes, these seem to have a complementary rather than compensatory function. In conclusion, our results show that Achromobacter species can exhibit different adaptive mechanisms and some of these mechanisms might be more useful than others in establishing a chronic infection in CF patients, highlighting their importance for the clinical setting and the need for further studies on the less clinically characterized Achromobacter species.
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Affiliation(s)
- Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Angela Sandri
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Paola Melotti
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Maria M Lleo
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy
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14
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Scoffone VC, Trespidi G, Barbieri G, Irudal S, Perrin E, Buroni S. Role of RND Efflux Pumps in Drug Resistance of Cystic Fibrosis Pathogens. Antibiotics (Basel) 2021; 10:863. [PMID: 34356783 PMCID: PMC8300704 DOI: 10.3390/antibiotics10070863] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 01/21/2023] Open
Abstract
Drug resistance represents a great concern among people with cystic fibrosis (CF), due to the recurrent and prolonged antibiotic therapy they should often undergo. Among Multi Drug Resistance (MDR) determinants, Resistance-Nodulation-cell Division (RND) efflux pumps have been reported as the main contributors, due to their ability to extrude a wide variety of molecules out of the bacterial cell. In this review, we summarize the principal RND efflux pump families described in CF pathogens, focusing on the main Gram-negative bacterial species (Pseudomonas aeruginosa, Burkholderia cenocepacia, Achromobacter xylosoxidans, Stenotrophomonas maltophilia) for which a predominant role of RND pumps has been associated to MDR phenotypes.
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Affiliation(s)
- Viola Camilla Scoffone
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Gabriele Trespidi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Giulia Barbieri
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Samuele Irudal
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Elena Perrin
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
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15
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Gabrielaite M, Nielsen FC, Johansen HK, Marvig RL. Achromobacter spp. genetic adaptation in cystic fibrosis. Microb Genom 2021; 7:000582. [PMID: 34232117 PMCID: PMC8477396 DOI: 10.1099/mgen.0.000582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/12/2021] [Indexed: 11/23/2022] Open
Abstract
Achromobacter spp. are emerging pathogens in patients with cystic fibrosis (CF) and Achromobacter spp. caused infections are associated with more severe disease outcomes and high intrinsic antibiotic resistance. While conventional CF pathogens are studied extensively, little is known about the genetic determinants leading to antibiotic resistance and the genetic adaptation in Achromobacter spp. infections. Here, we analysed 101 Achromobacter spp. genomes from 51 patients with CF isolated during the course of up to 20 years of infection to identify within-host adaptation, mutational signatures and genetic variation associated with increased antibiotic resistance. We found that the same regulatory and inorganic ion transport genes were frequently mutated in persisting clone types within and between Achromobacter species, indicating convergent genetic adaptation. Genome-wide association study of six antibiotic resistance phenotypes revealed the enrichment of associated genes involved in inorganic ion transport, transcription gene enrichment in β-lactams, and energy production and translation gene enrichment in the trimethoprim/sulfonamide group. Overall, we provide insights into the pathogenomics of Achromobacter spp. infections in patients with CF airways. Since emerging pathogens are increasingly recognized as an important healthcare issue, our findings on evolution of antibiotic resistance and genetic adaptation can facilitate better understanding of disease progression and how mutational changes have implications for patients with CF.
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Affiliation(s)
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Helle K. Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
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16
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Khademi SMH, Gabrielaite M, Paulsson M, Knulst M, Touriki E, Marvig RL, Påhlman LI. Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis. mSystems 2021; 6:e0052321. [PMID: 34184916 PMCID: PMC8269239 DOI: 10.1128/msystems.00523-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial pathogens evolve during chronic colonization of the human host by selection for pathoadaptive mutations. One of the emerging and understudied bacterial species causing chronic airway infections in patients with cystic fibrosis (CF) is Achromobacter xylosoxidans. It can establish chronic infections in patients with CF, but the genetic and phenotypic changes associated with adaptation during these infections are not completely understood. In this study, we analyzed the whole-genome sequences of 55 clinical A. xylosoxidans isolates longitudinally collected from the sputum of 6 patients with CF. Four genes encoding regulatory proteins and two intergenic regions showed convergent evolution, likely driven by positive selection for pathoadaptive mutations, across the different clones of A. xylosoxidans. Most of the evolved isolates had lower swimming motility and were resistant to multiple classes of antibiotics, while fewer of the evolved isolates had slower growth or higher biofilm production than the first isolates. Using a genome-wide association study method, we identified several putative genetic determinants of biofilm formation, motility and β-lactam resistance in this pathogen. With respect to antibiotic resistance, we discovered that a combination of mutations in pathoadaptive genes (phoQ and bigR) and two other genes encoding regulatory proteins (spoT and cpxA) were associated with increased resistance to meropenem and ceftazidime. Altogether, our results suggest that genetic changes within regulatory loci facilitate within-host adaptation of A. xylosoxidans and the emergence of adaptive phenotypes, such as antibiotic resistance or biofilm formation. IMPORTANCE A thorough understanding of bacterial pathogen adaptation is essential for the treatment of chronic bacterial infections. One unique challenge in the analysis and interpretation of genomics data is identifying the functional impact of mutations accumulated in the bacterial genome during colonization in the human host. Here, we investigated the genomic and phenotypic evolution of A. xylosoxidans in chronic airway infections of patients with CF and identified several mutations associated with the phenotypic evolution of this pathogen using genome-wide associations. Identification of phenotypes under positive selection and the associated mutations can enlighten the adaptive processes of this emerging pathogen in human infections and pave the way for novel therapeutic interventions.
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Affiliation(s)
- S. M. Hossein Khademi
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | | | - Magnus Paulsson
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
- Division of Infectious Diseases, Skåne University Hospital Lund, Lund, Sweden
| | - Mattis Knulst
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Eleni Touriki
- Clinical Microbiology, Labmedicin Skåne, Lund, Sweden
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Lisa I. Påhlman
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
- Division of Infectious Diseases, Skåne University Hospital Lund, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
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17
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Menetrey Q, Sorlin P, Jumas-Bilak E, Chiron R, Dupont C, Marchandin H. Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients' Lung. Genes (Basel) 2021; 12:610. [PMID: 33919046 PMCID: PMC8142972 DOI: 10.3390/genes12050610] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection-inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.
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Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Pauline Sorlin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Raphaël Chiron
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Chloé Dupont
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France
- UMR 5151 HydroSciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université de Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
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18
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Ng RN, Tai AS, Chang BJ, Stick SM, Kicic A. Overcoming Challenges to Make Bacteriophage Therapy Standard Clinical Treatment Practice for Cystic Fibrosis. Front Microbiol 2021; 11:593988. [PMID: 33505366 PMCID: PMC7829477 DOI: 10.3389/fmicb.2020.593988] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
Individuals with cystic fibrosis (CF) are given antimicrobials as prophylaxis against bacterial lung infection, which contributes to the growing emergence of multidrug resistant (MDR) pathogens isolated. Pathogens such as Pseudomonas aeruginosa that are commonly isolated from individuals with CF are armed with an arsenal of protective and virulence mechanisms, complicating eradication and treatment strategies. While translation of phage therapy into standard care for CF has been explored, challenges such as the lack of an appropriate animal model demonstrating safety in vivo exist. In this review, we have discussed and provided some insights in the use of primary airway epithelial cells to represent the mucoenvironment of the CF lungs to demonstrate safety and efficacy of phage therapy. The combination of phage therapy and antimicrobials is gaining attention and has the potential to delay the onset of MDR infections. It is evident that efforts to translate phage therapy into standard clinical practice have gained traction in the past 5 years. Ultimately, collaboration, transparency in data publications and standardized policies are needed for clinical translation.
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Affiliation(s)
- Renee N. Ng
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Wal-yan Respiratory Research Center, Telethon Kids Institute, The University of Western Australia, Crawley, WA, Australia
| | - Anna S. Tai
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
- Institute for Respiratory Health, School of Medicine, The University of Western Australia, Perth, WA, Australia
| | - Barbara J. Chang
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Stephen M. Stick
- Wal-yan Respiratory Research Center, Telethon Kids Institute, The University of Western Australia, Crawley, WA, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA, Australia
- Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Anthony Kicic
- Wal-yan Respiratory Research Center, Telethon Kids Institute, The University of Western Australia, Crawley, WA, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Perth, WA, Australia
- Center for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, WA, Australia
- Occupation and the Environment, School of Public Health, Curtin University, Perth, WA, Australia
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19
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Veschetti L, Sandri A, Patuzzo C, Melotti P, Malerba G, Lleò MM. Mobilome Analysis of Achromobacter spp. Isolates from Chronic and Occasional Lung Infection in Cystic Fibrosis Patients. Microorganisms 2021; 9:microorganisms9010130. [PMID: 33430044 PMCID: PMC7826576 DOI: 10.3390/microorganisms9010130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Achromobacter spp. is an opportunistic pathogen that can cause lung infections in patients with cystic fibrosis (CF). Although a variety of mobile genetic elements (MGEs) carrying antimicrobial resistance genes have been identified in clinical isolates, little is known about the contribution of Achromobacter spp. mobilome to its pathogenicity. To provide new insights, we performed bioinformatic analyses of 54 whole genome sequences and investigated the presence of phages, insertion sequences (ISs), and integrative and conjugative elements (ICEs). Most of the detected phages were previously described in other pathogens and carried type II toxin-antitoxin systems as well as other pathogenic genes. Interestingly, the partial sequence of phage Bcep176 was found in all the analyzed Achromobacter xylosoxidans genome sequences, suggesting the integration of this phage in an ancestor strain. A wide variety of IS was also identified either inside of or in proximity to pathogenicity islands. Finally, ICEs carrying pathogenic genes were found to be widespread among our isolates and seemed to be involved in transfer events within the CF lung. These results highlight the contribution of MGEs to the pathogenicity of Achromobacter species, their potential to become antimicrobial targets, and the need for further studies to better elucidate their clinical impact.
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Affiliation(s)
- Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Angela Sandri
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy;
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Paola Melotti
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy;
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Maria M. Lleò
- Department of Diagnostics and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy;
- Correspondence:
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20
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Crettaz-Minaglia M, Fallico M, Aranda O, Juarez I, Pezzoni M, Costa C, Andrinolo D, Giannuzzi L. Effect of temperature on microcystin-LR removal and lysis activity on Microcystis aeruginosa (cyanobacteria) by an indigenous bacterium belonging to the genus Achromobacter. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44427-44439. [PMID: 32767213 DOI: 10.1007/s11356-020-09901-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Microcystis is a frequent cyanobacterium bloom-forming with cosmopolitan distribution which can produce a hepatotoxin group called microcystins (MCs). These MCs are resistant to the traditional processes employed in the water treatment plants and they are often detected after conventional treatments. Because of this, the bio-removal studies have obtained a great interest in the last decades. In this work, a bacterial strain namely LG1 with the ability to remove microcystin-LR (MC-LR) under laboratory conditions was isolated from Rio de la Plata River and it was identified as Achromobacter spp. This ubiquitous bacterium was able to remove 79.5% MC-LR in 7 days with average removal time of 3.33 ± 0.08, 3.06 ± 0.05, and 2.77 ± 0.05 days at 28, 32, and 36 ± 1 °C, being higher at high temperature (36 °C) with an activation energy = 16.79 ± 1.99 kJ mol-1. LG1 grew better at higher temperature (from 28 to 36 ± 1 °C) increasing the specific growth rate (μ) and reducing 2-fold the lag phase duration (LPD) without significant differences (p > 0.05) between maximum population density (MPD). In addition, LG1 showed a lysis activity on two M. aeruginosa native strains in 7 days measured as chlorophyll a (Chl-a) concentration. The lysis activity increased around 2-fold when increasing the temperature from 28 to 36 ± 1 °C. This is the first report of an indigenous bacterium belonging to the genus Achromobacter spp. isolated from the Rio de la Plata River with the capacity to remove MC-LR and lysis activity on M. aeruginosa.
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Affiliation(s)
- Melina Crettaz-Minaglia
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina.
- CONICET, Buenos Aires, Argentina.
| | - Maximiliano Fallico
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina
| | - Oswaldo Aranda
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina
| | - Ivan Juarez
- CONICET, Buenos Aires, Argentina
- Centro de Investigaciones y Desarrollo en Criotecnología de Alimentos, UNLP-CONICET, La Plata, Argentina
| | - Magdalena Pezzoni
- Departamento de Radiobiología, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Cristina Costa
- Departamento de Radiobiología, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Dario Andrinolo
- Laboratorio de Toxicología General, Facultad de Ciencias Exactas, UNLP, La Plata, Argentina
- CONICET, Buenos Aires, Argentina
| | - Leda Giannuzzi
- CONICET, Buenos Aires, Argentina
- Centro de Investigaciones y Desarrollo en Criotecnología de Alimentos, UNLP-CONICET, La Plata, Argentina
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21
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Isler B, Kidd TJ, Stewart AG, Harris P, Paterson DL. Achromobacter Infections and Treatment Options. Antimicrob Agents Chemother 2020; 64:e01025-20. [PMID: 32816734 PMCID: PMC7577122 DOI: 10.1128/aac.01025-20] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Achromobacter is a genus of nonfermenting Gram-negative bacteria under order Burkholderiales Although primarily isolated from respiratory tract of people with cystic fibrosis, Achromobacter spp. can cause a broad range of infections in hosts with other underlying conditions. Their rare occurrence and ever-changing taxonomy hinder defining their clinical features, risk factors for acquisition and adverse outcomes, and optimal treatment. Achromobacter spp. are intrinsically resistant to several antibiotics (e.g., most cephalosporins, aztreonam, and aminoglycosides), and are increasingly acquiring resistance to carbapenems. Carbapenem resistance is mainly caused by multidrug efflux pumps and metallo-β-lactamases, which are not expected to be overcome by new β-lactamase inhibitors. Among the other new antibiotics, cefiderocol, and eravacycline were used as salvage therapy for a limited number of patients with Achromobacter infections. In this article, we aim to give an overview of the antimicrobial resistance in Achromobacter species, highlighting the possible place of new antibiotics in their treatment.
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Affiliation(s)
- Burcu Isler
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
| | - Timothy J Kidd
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
- University of Queensland, Faculty of Science, School of Chemistry and Molecular Biosciences, Brisbane, Australia
| | - Adam G Stewart
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Patrick Harris
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - David L Paterson
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, Australia
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22
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Price EP, Soler Arango V, Kidd TJ, Fraser TA, Nguyen TK, Bell SC, Sarovich DS. Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp. Microb Genom 2020; 6:mgen000406. [PMID: 32667877 PMCID: PMC7478622 DOI: 10.1099/mgen.0.000406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/26/2020] [Indexed: 01/10/2023] Open
Abstract
Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans. Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans, with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non-Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.
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Affiliation(s)
- Erin P. Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Valentina Soler Arango
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, St Lucia, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Tamieka A. Fraser
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thuy-Khanh Nguyen
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Scott C. Bell
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Derek S. Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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Achromobacter xylosoxidans Cellular Pathology Is Correlated with Activation of a Type III Secretion System. Infect Immun 2020; 88:IAI.00136-20. [PMID: 32366575 DOI: 10.1128/iai.00136-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Achromobacter xylosoxidans is increasingly recognized as a colonizer of cystic fibrosis (CF) patients, but the role that A. xylosoxidans plays in pathology remains unknown. This knowledge gap is largely due to the lack of model systems available to study the toxic potential of this bacterium. Recently, a phospholipase A2 (PLA2) encoded by a majority of A. xylosoxidans genomes, termed AxoU, was identified. Here, we show that AxoU is a type III secretion system (T3SS) substrate that induces cytotoxicity to mammalian cells. A tissue culture model was developed showing that a subset of A. xylosoxidans isolates from CF patients induce cytotoxicity in macrophages, suggestive of a pathogenic or inflammatory role in the CF lung. In a toxic strain, cytotoxicity is correlated with transcriptional activation of axoU and T3SS genes, demonstrating that this model can be used as a tool to identify and track expression of virulence determinants produced by this poorly understood bacterium.
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Anani H, Zgheib R, Hasni I, Raoult D, Fournier PE. Interest of bacterial pangenome analyses in clinical microbiology. Microb Pathog 2020; 149:104275. [PMID: 32562810 DOI: 10.1016/j.micpath.2020.104275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Issam Hasni
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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25
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Essoh C, Vernadet JP, Vergnaud G, Coulibaly A, Kakou-N'Douba A, N'Guetta ASP, Ouassa T, Pourcel C. Characterization of sixteen Achromobacter xylosoxidans phages from Abidjan, Côte d'Ivoire, isolated on a single clinical strain. Arch Virol 2020; 165:725-730. [PMID: 31897726 DOI: 10.1007/s00705-019-04511-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/28/2019] [Indexed: 01/21/2023]
Abstract
Sixteen bacteriophages of Achromobacter xylosoxidans distributed into four genera have been isolated from sewage water in Abidjan, Côte d'Ivoire, using a single clinical strain, and their genomes have been sequenced. Three podoviruses belonged to the genus Phikmvvirus, and these represent the first A. xylosoxidans phages of this genus. Seven podoviruses, distributed into three groups, belonged to the genus Jwalphavirus. Among the siphoviruses, three revealed similarities to Pseudomonas phage 73 and members of the genus Septimatrevirus, and three were YuA-like phages. The virulence of these phages toward a panel of 10 genetically diverse strains was tested, with the phiKMV-like phages showing the broadest host range.
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Affiliation(s)
- Christiane Essoh
- Département de Biochimie-Génétique, UFR des Sciences Biologiques, Université Peleforo Gon- Coulibaly, Korhogo, Côte d'Ivoire
| | - Jean-Philippe Vernadet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Adama Coulibaly
- Département de Biochimie-Génétique, UFR des Sciences Biologiques, Université Peleforo Gon- Coulibaly, Korhogo, Côte d'Ivoire
| | - Adèle Kakou-N'Douba
- Laboratoire de Bactériologie-Virologie, Département de Microbiologie, UFR des Sciences Médicales, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Assavo S-P N'Guetta
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Thimotée Ouassa
- Laboratoire de Microbiologie, UFR des Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France. .,Université Paris-Sud, I2BC, Bât 400, 91405, Orsay cedex, France.
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26
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Staphylococcus arlettae Genomics: Novel Insights on Candidate Antibiotic Resistance and Virulence Genes in an Emerging Opportunistic Pathogen. Microorganisms 2019; 7:microorganisms7110580. [PMID: 31752379 PMCID: PMC6920755 DOI: 10.3390/microorganisms7110580] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022] Open
Abstract
Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical relevance, annotation of genes potentially involved in pathogenicity and/or antibiotic resistance in the CoNS species Staphylococcus arlettae (SAR) is currently very limited. In the current work we describe the genome of a novel methicillin resistant isolate of SAR, which we named Bari, and present a comprehensive analysis of predicted antibiotic resistance profiles and virulence determinants for all the 22 currently available SAR genomes. By comparing predicted antibiotic resistance and virulence-associated genes with those obtained from a manual selection of 148 bacterial strains belonging to 14 different species of staphylococci and to two “outgroup” species, Bacillus subtilis (BS) and Macrococcus caseoliticus (MC), we derived some interesting observations concerning the types and number of antibiotic resistance-related and virulence-like genes in SAR. Interestingly, almost 50% of the putative antibiotic resistance determinants identified in this work, which include the clinically relevant mec, van, and cls genes, were shared among all the SAR strains herein considered (Bari included). Moreover, comparison of predicted antibiotic resistance profiles suggest that SAR is closely related to well-known pathogenic Staphylococcus species, such as Staphylococcus aureus (SA) and Staphylococcus epidermidis (SE). A similar analysis of predicted virulence factors, revealed that several genes associated with pathogenesis (including, for example, ica, nuc, and ssp), which are commonly found in the genomes of pathogenic staphylococci such as Staphylococcus haemolyticus (SH) and Staphylococcus saprophyticus (SS), are observed also in the SAR strains for which a genomic sequence is available. All in all, we believe that the analyses presented in the current study, by providing a consistent and comprehensive annotation of virulence and antibiotic resistance-related genes in SAR, can constitute a valuable resource for the study of molecular mechanisms of opportunistic pathogenicity in this species.
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27
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Richards VP, Velsko IM, Alam MT, Zadoks RN, Manning SD, Pavinski Bitar PD, Hassler HB, Crestani C, Springer GH, Probert BM, Town CD, Stanhope MJ. Population Gene Introgression and High Genome Plasticity for the Zoonotic Pathogen Streptococcus agalactiae. Mol Biol Evol 2019; 36:2572-2590. [PMID: 31350563 PMCID: PMC6805230 DOI: 10.1093/molbev/msz169] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/04/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023] Open
Abstract
The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacterial populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here, we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated 12 major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of 11 populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation.
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Affiliation(s)
- Vincent P Richards
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
| | - Irina M Velsko
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Md Tauqeer Alam
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL
| | - Ruth N Zadoks
- Pentlands Science Park, Moredun Research Institute, Penicuik, United Kingdom
- Institute for Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, E. Lansing, MI
| | - Paulina D Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Hayley B Hassler
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
| | - Chiara Crestani
- Pentlands Science Park, Moredun Research Institute, Penicuik, United Kingdom
| | - Garrett H Springer
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
| | - Brett M Probert
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
| | | | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY
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28
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Marion-Sanchez K, Pailla K, Olive C, Le Coutour X, Derancourt C. Achromobacter spp. healthcare associated infections in the French West Indies: a longitudinal study from 2006 to 2016. BMC Infect Dis 2019; 19:795. [PMID: 31500579 PMCID: PMC6734299 DOI: 10.1186/s12879-019-4431-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/30/2019] [Indexed: 01/14/2023] Open
Abstract
Background Bacteria of the Achromobacter genus, more particularly xylosoxidans species, are responsible for various healthcare associated infections (HAI) which are increasingly described since the last decade. Cystic fibrosis (CF) patients are considered as potential reservoirs in hospitals. We performed a retrospective study to estimate the frequencies of Achromobacter spp. HAI among patients from French West Indies, to determine characteristics of infected patients and establish a possible link between CF and infections. Methods All adults with at least one Achromobacter spp. positive sample and infection criteria in accordance with European official definitions of HAI, hospitalized in University Hospital of Martinique from 2006 to 2016 for more than 48 h, were included. Patient clinical features, immune status and underlying diseases were obtained from medical files. A list of CF patients was given by clinicians. Antibiotic-susceptibility profiles of the strains were determined using an automated method. Results Mean incidence density was 0.038/1000 days of hospitalization. Achromobacter spp. HAI evolved as an endemic situation with a low but pretty much stable incidence rate over the 11-year observation period. An epidemic peak was noticed in 2013. Among the 66 included patients, 56.1% were immunocompetent and no one had CF. Pneumonia and bacteraemia were the two main HAI. Among the 79 isolated strains, 92.4% were resistant to at least 1 major antibiotic and 16.4% met the definition of multidrug-resistant bacteria. Conclusions This microorganism, little known in our country because of the scarcity of CF patients, represents a threat for both immunosuppressed and immunocompetent patients and a therapeutic challenge because of its high resistance.
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Affiliation(s)
- Karine Marion-Sanchez
- Department of Hospital Hygiene, CHU Martinique, Fort-de-France, Martinique. .,Unité de Surveillance et de Prévention des Infections Nosocomiales, CHU de Martinique, Site Pierre-Zobda-Quitman, CS 90632, 97290, Fort-de-France Cedex, Martinique.
| | - Karine Pailla
- Bacteriology Laboratory, CHU Martinique, Fort-de-France, Martinique
| | - Claude Olive
- Bacteriology Laboratory, CHU Martinique, Fort-de-France, Martinique
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29
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Marion-Sanchez K, Pailla K, Cesarine M, Platon MG, Derancourt C, Olive C. Achromobacter xylosoxidans resistance to antiseptics and disinfectants is far from obvious. Trans R Soc Trop Med Hyg 2019; 113:356-358. [PMID: 30892650 DOI: 10.1093/trstmh/trz016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Achromobacter xylosoxidans is described as being resistant to antiseptics and disinfectants. We studied in vitro the ability of five strains to survive and grow in such solutions, with and without starvation. METHODS Bacterial suspensions in rich media and in distilled water were inoculated into eight antiseptics or disinfectants under conditions of use. RESULTS All strains from cultures in distilled water survived in aqueous chlorhexidine and only environmental strains survived in a quaternary ammonium-based disinfectant. Survival did not exceed 30 min and no growth was observed. CONCLUSIONS This study highlights a relationship between starvation and survival in antiseptics and disinfectants.
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Affiliation(s)
| | - Karine Pailla
- CHU Martinique, Bacteriology Laboratory, Fort-de-France, Martinique
| | - Myriam Cesarine
- CHU Martinique, Bacteriology Laboratory, Fort-de-France, Martinique
| | | | | | - Claude Olive
- CHU Martinique, Bacteriology Laboratory, Fort-de-France, Martinique
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30
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The Pseudomonas aeruginosa Population among Cystic Fibrosis Patients in Quebec, Canada: a Disease Hot Spot without Known Epidemic Isolates. J Clin Microbiol 2019; 57:JCM.02019-18. [PMID: 30944192 DOI: 10.1128/jcm.02019-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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31
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Theis KR, Romero R, Winters AD, Greenberg JM, Gomez-Lopez N, Alhousseini A, Bieda J, Maymon E, Pacora P, Fettweis JM, Buck GA, Jefferson KK, Strauss JF, Erez O, Hassan SS. Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics. Am J Obstet Gynecol 2019; 220:267.e1-267.e39. [PMID: 30832984 PMCID: PMC6733039 DOI: 10.1016/j.ajog.2018.10.018] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND The human placenta has been traditionally viewed as sterile, and microbial invasion of this organ has been associated with adverse pregnancy outcomes. Yet, recent studies that utilized sequencing techniques reported that the human placenta at term contains a unique microbiota. These conclusions are largely based on the results derived from the sequencing of placental samples. However, such an approach carries the risk of capturing background-contaminating DNA (from DNA extraction kits, polymerase chain reaction reagents, and laboratory environments) when low microbial biomass samples are studied. OBJECTIVE To determine whether the human placenta delivered at term in patients without labor who undergo cesarean delivery harbors a resident microbiota ("the assemblage of microorganisms present in a defined niche or environment"). STUDY DESIGN This cross-sectional study included placentas from 29 women who had a cesarean delivery without labor at term. The study also included technical controls to account for potential background-contaminating DNA, inclusive in DNA extraction kits, polymerase chain reaction reagents, and laboratory environments. Bacterial profiles of placental tissues and background technical controls were characterized and compared with the use of bacterial culture, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and metagenomic surveys. RESULTS (1) Twenty-eight of 29 placental tissues had a negative culture for microorganisms. The microorganisms retrieved by culture from the remaining sample were likely contaminants because corresponding 16S ribosomal RNA genes were not detected in the same sample. (2) Quantitative real-time polymerase chain reaction did not indicate greater abundances of bacterial 16S ribosomal RNA genes in placental tissues than in technical controls. Therefore, there was no evidence of the presence of microorganisms above background contamination from reagents in the placentas. (3) 16S ribosomal RNA gene sequencing did not reveal consistent differences in the composition or structure of bacterial profiles between placental samples and background technical controls. (4) Most of the bacterial sequences obtained from metagenomic surveys of placental tissues were from cyanobacteria, aquatic bacteria, or plant pathogens, which are microbes unlikely to populate the human placenta. Coprobacillus, which constituted 30.5% of the bacterial sequences obtained through metagenomic sequencing of placental samples, was not identified in any of the 16S ribosomal RNA gene surveys of these samples. These observations cast doubt as to whether this organism is really present in the placenta of patients at term not in labor. CONCLUSION With the use of multiple modes of microbiologic inquiry, a resident microbiota could not be identified in human placentas delivered at term from women without labor. A consistently significant difference in the abundance and/or presence of a microbiota between placental tissue and background technical controls could not be found. All cultures of placental tissue, except 1, did not yield bacteria. Incorporating technical controls for potential sources of background-contaminating DNA for studies of low microbial biomass samples, such as the placenta, is necessary to derive reliable conclusions.
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Affiliation(s)
- Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI; Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI.
| | - Roberto Romero
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI.
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI; Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, MI
| | - Jonathan M Greenberg
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI; Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, MI
| | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI; Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Ali Alhousseini
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI; Department of Physiology, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Janine Bieda
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Eli Maymon
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Percy Pacora
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Jennifer M Fettweis
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA; Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA
| | - Gregory A Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA; Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA
| | - Kimberly K Jefferson
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA
| | - Offer Erez
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Maternity Department "D" and Obstetrical Day Care Center, Division of Obstetrics and Gynecology, Soroka University Medical Center, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Sonia S Hassan
- Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI; Department of Physiology, Wayne State University School of Medicine, Detroit, MI; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, and Detroit, MI
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Freschi L, Vincent AT, Jeukens J, Emond-Rheault JG, Kukavica-Ibrulj I, Dupont MJ, Charette SJ, Boyle B, Levesque RC. The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity. Genome Biol Evol 2019; 11:109-120. [PMID: 30496396 PMCID: PMC6328365 DOI: 10.1093/gbe/evy259] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/25/2022] Open
Abstract
The huge increase in the availability of bacterial genomes led us to a point in which we can investigate and query pan-genomes, for example, the full set of genes of a given bacterial species or clade. Here, we used a data set of 1,311 high-quality genomes from the human pathogen Pseudomonas aeruginosa, 619 of which were newly sequenced, to show that a pan-genomic approach can greatly refine the population structure of bacterial species, provide new insights to define species boundaries, and generate hypotheses on the evolution of pathogenicity. The 665-gene P. aeruginosa core genome presented here, which constitutes only 1% of the entire pan-genome, is the first to be in the same order of magnitude as the minimal bacterial genome and represents a conservative estimate of the actual core genome. Moreover, the phylogeny based on this core genome provides strong evidence for a five-group population structure that includes two previously undescribed groups of isolates. Comparative genomics focusing on antimicrobial resistance and virulence genes showed that variation among isolates was partly linked to this population structure. Finally, we hypothesized that horizontal gene transfer had an important role in this respect, and found a total of 3,010 putative complete and fragmented plasmids, 5% and 12% of which contained resistance or virulence genes, respectively. This work provides data and strategies to study the evolutionary trajectories of resistance and virulence in P. aeruginosa.
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Affiliation(s)
- Luca Freschi
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Antony T Vincent
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Québec City, Quebec, Canada.,Département de Biochimie, De Microbiologie et de Bio-informatique, Université Laval, Québec City, Quebec, Canada
| | - Julie Jeukens
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Jean-Guillaume Emond-Rheault
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Irena Kukavica-Ibrulj
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Marie-Josée Dupont
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Steve J Charette
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Québec City, Quebec, Canada.,Département de Biochimie, De Microbiologie et de Bio-informatique, Université Laval, Québec City, Quebec, Canada
| | - Brian Boyle
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Roger C Levesque
- Département de microbiologie-infectiologie et immunologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
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33
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Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Front Microbiol 2018; 9:771. [PMID: 29765358 PMCID: PMC5938378 DOI: 10.3389/fmicb.2018.00771] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
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Affiliation(s)
- Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas, Zaragoza, Spain.,Fundación Agencia Aragonesa para la Investigacion y el Desarrollo (ARAID), Zaragoza, Spain
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34
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Emond-Rheault JG, Jeukens J, Freschi L, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Colavecchio A, Barrere V, Cadieux B, Arya G, Bekal S, Berry C, Burnett E, Cavestri C, Chapin TK, Crouse A, Daigle F, Danyluk MD, Delaquis P, Dewar K, Doualla-Bell F, Fliss I, Fong K, Fournier E, Franz E, Garduno R, Gill A, Gruenheid S, Harris L, Huang CB, Huang H, Johnson R, Joly Y, Kerhoas M, Kong N, Lapointe G, Larivière L, Loignon S, Malo D, Moineau S, Mottawea W, Mukhopadhyay K, Nadon C, Nash J, Ngueng Feze I, Ogunremi D, Perets A, Pilar AV, Reimer AR, Robertson J, Rohde J, Sanderson KE, Song L, Stephan R, Tamber S, Thomassin P, Tremblay D, Usongo V, Vincent C, Wang S, Weadge JT, Wiedmann M, Wijnands L, Wilson ED, Wittum T, Yoshida C, Youfsi K, Zhu L, Weimer BC, Goodridge L, Levesque RC. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Front Microbiol 2017. [PMID: 28626454 PMCID: PMC5454079 DOI: 10.3389/fmicb.2017.00996] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.
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Affiliation(s)
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | | | | | | | - Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Travis K Chapin
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - France Daigle
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Michelle D Danyluk
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - Ken Dewar
- McGill University, MontréalQC, Canada.,Génome Québec Innovation Center, MontréalQC, Canada
| | | | | | - Karen Fong
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Eelco Franz
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | | | - Alexander Gill
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | - Linda Harris
- UC Davis Food Science and Technology, DavisCA, United States
| | - Carol B Huang
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Yann Joly
- McGill University, MontréalQC, Canada
| | - Maud Kerhoas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Nguyet Kong
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | | | | | | | | | - Walid Mottawea
- McGill University, MontréalQC, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | | | - Céline Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Ann Perets
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | - Aleisha R Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Rohde
- Department of Microbiology and Immunology, Dalhousie University, HalifaxNS, Canada
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | | | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Caroline Vincent
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Siyun Wang
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Joel T Weadge
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Martin Wiedmann
- Department of Food Science, Cornell University, IthacaNY, United States
| | - Lucas Wijnands
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Emily D Wilson
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Thomas Wittum
- College of Veterinary Medicine, The Ohio State University, ColumbusOH, United States
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Khadija Youfsi
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Lei Zhu
- McGill University, MontréalQC, Canada
| | - Bart C Weimer
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
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