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Piper KR, Ikhimiukor OO, Souza SSR, Garcia-Aroca T, Andam CP. Evolutionary dynamics of the accessory genomes of Staphylococcus aureus. mSphere 2024; 9:e0075123. [PMID: 38501935 PMCID: PMC11036810 DOI: 10.1128/msphere.00751-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/24/2024] [Indexed: 03/20/2024] Open
Abstract
Staphylococcus aureus is a ubiquitous commensal and opportunistic bacterial pathogen that can cause a wide gamut of infections, which are exacerbated by the presence of multidrug-resistant and methicillin-resistant S. aureus. S. aureus is genetically heterogeneous and consists of numerous distinct lineages. Using 558 complete genomes of S. aureus, we aim to determine how the accessory genome content among phylogenetic lineages of S. aureus is structured and has evolved. Bayesian hierarchical clustering identified 10 sequence clusters, of which seven contained major sequence types (ST 1, 5, 8, 30, 59, 239, and 398). The seven sequence clusters differed in their accessory gene content, including genes associated with antimicrobial resistance and virulence. Focusing on the two largest clusters, BAPS8 and BAPS10, and each consisting mostly of ST5 and ST8, respectively, we found that the structure and connected components in the co-occurrence networks of accessory genomes varied between them. These differences are explained, in part, by the variation in the rates at which the two sequence clusters gained and lost accessory genes, with the highest rate of gene accumulation occurring recently in their evolutionary histories. We also identified a divergent group within BAPS10 that has experienced high gene gain and loss early in its history. Together, our results show highly variable and dynamic accessory genomes in S. aureus that are structured by the history of the specific lineages that carry them.IMPORTANCEStaphylococcus aureus is an opportunistic, multi-host pathogen that can cause a variety of benign and life-threatening infections. Our results revealed considerable differences in the structure and evolution of the accessory genomes of major lineages within S. aureus. Such genomic variation within a species can have important implications on disease epidemiology, pathogenesis of infection, and interactions with the vertebrate host. Our findings provide important insights into the underlying genetic basis for the success of S. aureus as a highly adaptable and resistant pathogen, which will inform current efforts to control and treat staphylococcal diseases.
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Affiliation(s)
- Kathryn R. Piper
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Teddy Garcia-Aroca
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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2
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Fernández-Vázquez JL, Hernández-González IL, Castillo-Ramírez S, Jarillo-Quijada MD, Gayosso-Vázquez C, Mateo-Estrada VE, Morfín-Otero R, Rodríguez-Noriega E, Santos-Preciado JI, Alcántar-Curiel MD. Pandrug-resistant Acinetobacter baumannii from different clones and regions in Mexico have a similar plasmid carrying the blaOXA-72 gene. Front Cell Infect Microbiol 2023; 13:1278819. [PMID: 38192399 PMCID: PMC10773864 DOI: 10.3389/fcimb.2023.1278819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Background Multidrug-resistant Acinetobacter baumannii is a common hospital-acquired pathogen. The increase in antibiotic resistance is commonly due to the acquisition of mobile genetic elements carrying antibiotic resistance genes. To comprehend this, we analyzed the resistome and virulome of Mexican A. baumannii multidrug-resistant isolates. Methods Six clinical strains of A. baumannii from three Mexican hospitals were sequenced using the Illumina platform, the genomes were assembled with SPAdes and annotated with Prokka. Plasmid SPAdes and MobRecon were used to identify the potential plasmid sequences. Sequence Type (ST) assignation under the MLST Oxford scheme was performed using the PubMLST database. Homologous gene search for known virulent factors was performed using the virulence factor database VFDB and an in silico prediction of the resistome was conducted via the ResFinder databases. Results The six strains studied belong to different STs and clonal complexes (CC): two strains were ST208 and one was ST369; these two STs belong to the same lineage CC92, which is part of the international clone (IC) 2. Another two strains were ST758 and one was ST1054, both STs belonging to the same lineage CC636, which is within IC5. The resistome analysis of the six strains identified between 7 to 14 antibiotic resistance genes to different families of drugs, including beta-lactams, aminoglycosides, fluoroquinolones and carbapenems. We detected between 1 to 4 plasmids per strain with sizes from 1,800 bp to 111,044 bp. Two strains from hospitals in Mexico City and Guadalajara had a plasmid each of 10,012 bp pAba78r and pAba79f, respectively, which contained the bla OXA-72 gene. The structure of this plasmid showed the same 13 genes in both strains, but 4 of them were inverted in one of the strains. Finally, the six strains contain 49 identical virulence genes related to immune response evasion, quorum-sensing, and secretion systems, among others. Conclusion Resistance to carbapenems due to pAba78r and pAba79f plasmids in Aba pandrug-resistant strains from different geographic areas of Mexico and different clones was detected. Our results provide further evidence that plasmids are highly relevant for the horizontal transfer of antibiotic resistance genes between different clones of A. baumannii.
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Affiliation(s)
- José Luis Fernández-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Ismael Luis Hernández-González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ma Dolores Jarillo-Quijada
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Catalina Gayosso-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Eréndira Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara “Fray Antonio Alcalde” e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Eduardo Rodríguez-Noriega
- Hospital Civil de Guadalajara “Fray Antonio Alcalde” e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - José Ignacio Santos-Preciado
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María Dolores Alcántar-Curiel
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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3
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Bulach D, Carter GP, Li L, Al-Hashem G, Rotimi VO, Albert MJ. The whole-genome molecular epidemiology of sequential isolates of Acinetobacter baumannii colonizing the rectum of patients in an adult intensive care unit of a tertiary hospital. Microbiol Spectr 2023; 11:e0219123. [PMID: 37843271 PMCID: PMC10715177 DOI: 10.1128/spectrum.02191-23] [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: 05/24/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a multidrug-resistant nosocomial pathogen that colonizes and infects debilitated patients in the ICU. There is very little information on the genomic characteristics of colonizing strains. This information is important to understand the evolution of lineages of A. baumannii that develop resistance while patients receive antibiotic treatment in the ICU. Our study demonstrated different patterns of colonization of the rectum of ICU patients with different STs of A. baumannii while one ST colonized all patients. Some STs carried more antibiotic resistance genes compared to others. However, there was a correlation between ST and a particular resistance gene profile. Our results further elucidate the dynamics of enteric colonization of this opportunistic pathogen.
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Affiliation(s)
- Dieter Bulach
- Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lucy Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ghayda Al-Hashem
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya, Kuwait
| | - Vincent O. Rotimi
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya, Kuwait
| | - M. John Albert
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya, Kuwait
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4
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Freitas JF, Silva DFL, Silva BS, Castro JNF, Felipe MBMC, Silva-Portela RCB, Minnicelli CF, Agnez-Lima LF. Genomic and phenotypic features of Acinetobacter baumannii isolated from oil reservoirs reveal a novel subspecies specialized in degrading hazardous hydrocarbons. Microbiol Res 2023; 273:127420. [PMID: 37270893 DOI: 10.1016/j.micres.2023.127420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/24/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023]
Abstract
The genus Acinetobacter encompasses biotechnologically relevant species and nosocomial pathogens. In this study, nine isolates recovered from different oil reservoir samples showed the ability to grow with petroleum as the only carbon source and possessed the ability to emulsify kerosene. The whole genomes of the nine strains were sequenced and analyzed. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of all strains were compared to the reference strains, and the results were below the reference values (<97.88 and 82, respectively), suggesting that the isolates belong to a new subspecies of Acinetobacter baumannii. The name Acinetobacter baumannii oleum ficedula is proposed. A comparison of the whole genome repertoire of 290 Acinetobacter species indicated that the strains in this study resemble non-pathogenic Acinetobacter strains. However, the new isolates resemble A. baumannii when comparing virulence factors. The isolates in this study carry many genes involved in hydrocarbon degradation, indicating the potential to degrade most toxic compounds listed by environmental regulatory agencies such as ATSDR, EPA, and CONAMA. In addition, despite the absence of known biosurfactant or bioemulsifier genes, the strains showed emulsifying activity, suggesting the presence of new pathways or genes related to this process. This study investigated the genomic, phenotypic, and biochemical features of the novel environmental subspecies A. baumannii oleum ficedula, revealing their potential to degrade hydrocarbons and to produce biosurfactants or bioemulsifiers. Applying these environmental subspecies in bioaugmentation strategies sheds light on future approaches to bioremediation. The study shows the importance of genomic analysis of environmental strains and their inclusion in metabolic pathways databases, highlighting unique enzymes/alternative pathways for consuming hazardous hydrocarbons.
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Affiliation(s)
- J F Freitas
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil
| | - D F L Silva
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil
| | - B S Silva
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil
| | - J N F Castro
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil
| | - M B M C Felipe
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil
| | - R C B Silva-Portela
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil
| | - C F Minnicelli
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil
| | - L F Agnez-Lima
- Laboratório de Biologia Molecular e Genômica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Brazil.
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5
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Zhang W, Yao Y, Zhou H, He J, Wang J, Li L, Gao M, Liu X, Shi Y, Lin J, Liu J, Chen H, Feng Y, Zhou Z, Yu Y, Hua X. Interactions between host epithelial cells and Acinetobacter baumannii promote the emergence of highly antibiotic resistant and highly mucoid strains. Emerg Microbes Infect 2022; 11:2556-2569. [PMID: 36227610 PMCID: PMC9621264 DOI: 10.1080/22221751.2022.2136534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Acinetobacter baumannii is an important nosocomial pathogen. Upon colonizing a host, A. baumannii are subjected to selective pressure by immune defenses as they adapt to the host environment. However, the mechanism of this pathoadaptation is unknown. Here, we established an in vitro system to evolve A. baumannii driven by the continuous selective pressure exerted by epithelial cells, and we used a combination of experimental evolution, phenotypic characterization and multi-omics analysis to address the underlying mechanism. When continuously exposed to selective pressure by pulmonary epithelial cells, A. baumannii showed ptk mutation-mediated mucoid conversion (reduced adhesion and increased anti-phagocytic ability) by enhancement of capsular exopolysaccharide chain length; rsmG mutation-mediated deficiency of 7-methylguanosine modification in the 524th nucleotide of 16S rRNA, which increased ribosome translation efficiency; and rnaseI mutation-mediated changes in outer membrane permeability and efflux pump expression. Together, these mutations altered susceptibility to a variety of antimicrobial agents, including the novel antibiotic cefiderocol, by regulating siderophore and siderophore-receptor biosynthesis. In conclusion, pulmonary epithelial cells modulate A. baumannii pathoadaptation, implicating the host–microbe interaction in the survival and persistence of A. baumannii.
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Affiliation(s)
- Wang Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yue Yao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Jingfen Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Li Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaochen Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Ya Shi
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, Zhejiang, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China.,Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huan Chen
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, Zhejiang, China
| | - Yu Feng
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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6
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Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa. Appl Environ Microbiol 2022; 88:e0122022. [PMID: 36094203 PMCID: PMC9499020 DOI: 10.1128/aem.01220-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Xylella fastidiosa infects several economically important crops in the Americas, and it also recently emerged in Europe. Here, using a set of Xylella genomes reflective of the genus-wide diversity, we performed a pan-genome analysis based on both core and accessory genes for two purposes: (i) to test associations between genetic divergence and plant host species and (ii) to identify positively selected genes that are potentially involved in arms-race dynamics. For the former, tests yielded significant evidence for the specialization of X. fastidiosa to plant host species. This observation contributes to a growing literature suggesting that the phylogenetic history of X. fastidiosa lineages affects the host range. For the latter, our analyses uncovered evidence of positive selection across codons for 5.3% (67 of 1,257) of the core genes and 5.4% (201 of 3,691) of the accessory genes. These genes are candidates to encode interacting factors with plant and insect hosts. Most of these genes had unknown functions, but we did identify some tractable candidates, including nagZ_2, which encodes a beta-glucosidase that is important for Neisseria gonorrhoeae biofilm formation; cya, which modulates gene expression in pathogenic bacteria, and barA, a membrane associated histidine kinase that has roles in cell division, metabolism, and pili formation. IMPORTANCEXylella fastidiosa causes devasting diseases to several critical crops. Because X. fastidiosa colonizes and infects many plant species, it is important to understand whether the genome of X. fastidiosa has genetic determinants that underlie specialization to specific host plants. We analyzed genome sequences of X. fastidiosa to investigate evolutionary relationships and to test for evidence of positive selection on specific genes. We found a significant signal between genome diversity and host plants, consistent with bacterial specialization to specific plant hosts. By screening for positive selection, we identified both core and accessory genes that may affect pathogenicity, including genes involved in biofilm formation.
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7
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Picazo DR, Werner A, Dagan T, Kupczok A. Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance. Genome Biol Evol 2022; 14:6613374. [PMID: 35731940 PMCID: PMC9260185 DOI: 10.1093/gbe/evac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained..
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Affiliation(s)
- Devani Romero Picazo
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Almut Werner
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
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8
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Beyond microbial core genomic epidemiology: towards pan genomic epidemiology. THE LANCET MICROBE 2022; 3:e244-e245. [DOI: 10.1016/s2666-5247(22)00058-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
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9
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Artuso I, Lucidi M, Visaggio D, Capecchi G, Lugli GA, Ventura M, Visca P. Genome diversity of domesticated Acinetobacter baumannii ATCC 19606 T strains. Microb Genom 2022; 8. [PMID: 35084299 PMCID: PMC8914354 DOI: 10.1099/mgen.0.000749] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Acinetobacter baumannii has emerged as an important opportunistic pathogen worldwide, being responsible for large outbreaks for nosocomial infections, primarily in intensive care units. A. baumannii ATCC 19606T is the species type strain, and a reference organism in many laboratories due to its low virulence, amenability to genetic manipulation and extensive antibiotic susceptibility. We wondered if frequent propagation of A. baumannii ATCC 19606T in different laboratories may have driven micro- and macro-evolutionary events that could determine inter-laboratory differences of genome-based data. By combining Illumina MiSeq, MinION and Sanger technologies, we generated a high-quality whole-genome sequence of A. baumannii ATCC 19606T, then performed a comparative genome analysis between A. baumannii ATCC 19606T strains from several research laboratories and a reference collection. Differences between publicly available ATCC 19606T genome sequences were observed, including SNPs, macro- and micro-deletions, and the uneven presence of a 52 kb prophage belonging to genus Vieuvirus. Two plasmids, pMAC and p1ATCC19606, were invariably detected in all tested strains. The presence of a putative replicase, a replication origin containing four 22-mer direct repeats, and a toxin-antitoxin system implicated in plasmid stability were predicted by in silico analysis of p1ATCC19606, and experimentally confirmed. This work refines the sequence, structure and functional annotation of the A. baumannii ATCC 19606T genome, and highlights some remarkable differences between domesticated strains, likely resulting from genetic drift.
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Affiliation(s)
- Irene Artuso
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Massimiliano Lucidi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Daniela Visaggio
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.,Santa Lucia Fundation IRCCS, Via Ardeatina 306-354, 00179 Rome, Italy
| | - Giulia Capecchi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.,Santa Lucia Fundation IRCCS, Via Ardeatina 306-354, 00179 Rome, Italy
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10
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Hernández-González IL, Mateo-Estrada V, Castillo-Ramirez S. The promiscuous and highly mobile resistome of Acinetobacter baumannii. Microb Genom 2022; 8. [PMID: 35075990 PMCID: PMC8914355 DOI: 10.1099/mgen.0.000762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the whole resistome of Acinetobacter baumannii, a very important nosocomial pathogen. Here we analyse 1450+ genomes (covering >40 countries and >4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii. We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae. Despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Our results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genomic epidemiology (and surveillance) of bacterial pathogens.
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Affiliation(s)
- Ismael L Hernández-González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Santiago Castillo-Ramirez,
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11
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Abstract
Acinetobacter baumannii has become one of the most important multidrug-resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages coexisting in hospital settings. Here, using whole-genome sequencing, epidemiological data, and antimicrobial susceptibility tests, we uncover the transmission dynamics of extensive and multidrug-resistant A. baumannii in a tertiary hospital over a decade. Our core genome phylogeny of almost 300 genomes suggests that there were several introductions of lineages from international clone 2 into the hospital. The molecular dating analysis shows that these introductions happened in 2006, 2007, and 2013. Furthermore, using the accessory genome, we show that these lineages were extensively disseminated across many wards in the hospital. Our results demonstrate that accessory genome variation can be a very powerful tool for conducting genomic epidemiology. We anticipate future studies employing the accessory genome along with the core genome as a powerful phylogenomic strategy to track bacterial transmissions over very short microevolutionary scales. IMPORTANCE Whole-genome sequencing for epidemiological investigations (genomic epidemiology) has been of paramount importance to understand the transmission dynamics of many bacterial (and nonbacterial) pathogens. Commonly, variation in the core genome, single nucleotide polymorphisms (SNPs), is employed to carry out genomic epidemiology. However, at very short periods of time, the core genome might not have accumulated enough variation (sufficient SNPs) to tell apart isolates. In this scenario, gene content variation in the accessory genome can be an option to conduct genomic epidemiology. Here, we used the accessory genome, as well as the core genome, to uncover the transmission dynamics of extensive and multidrug-resistant A. baumannii in a tertiary hospital for a decade. Our study shows that accessory genome variation can be a very powerful tool for conducting genomic epidemiology.
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12
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López-Leal G, Reyes-Muñoz A, Santamaria RI, Cevallos MA, Pérez-Monter C, Castillo-Ramírez S. A novel vieuvirus from multidrug-resistant Acinetobacter baumannii. Arch Virol 2021; 166:1401-1408. [PMID: 33635432 DOI: 10.1007/s00705-021-05010-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/16/2021] [Indexed: 11/26/2022]
Abstract
Bacteriophages are considered the most abundant biological entities on earth, and they are able to modulate the populations of their bacterial hosts. Although the potential of bacteriophages has been accepted as an alternative strategy to combat multidrug-resistant pathogenic bacteria, there still exists a considerable knowledge gap regarding their genetic diversity, which hinders their use as antimicrobial agents. In this study, we undertook a genomic and phylogenetic characterization of the phage Ab11510-phi, which was isolated from a multidrug-resistant Acinetobacter baumannii strain (Ab11510). We found that Ab11510-phi has a narrow host range and belongs to a small group of transposable phages of the genus Vieuvirus that have only been reported to infect Acinetobacter bacteria. Finally, we showed that Ab11510-phi (as well as other vieuvirus phages) has a high level of mosaicism. On a broader level, we demonstrate that comparative genomics and phylogenetic analysis are necessary tools for the proper characterization of phage diversity.
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Affiliation(s)
- Gamaliel López-Leal
- Grupo de Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, D.C., Colombia.
| | - Alejandro Reyes-Muñoz
- Grupo de Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, D.C., Colombia
| | - Rosa Isela Santamaria
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Carlos Pérez-Monter
- Departamento de Gastroenterología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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13
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Hwang SM, Cho HW, Kim TY, Park JS, Jung J, Song KH, Lee H, Kim ES, Kim HB, Park KU. Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii. Diagnostics (Basel) 2021; 11:diagnostics11020201. [PMID: 33573077 PMCID: PMC7910894 DOI: 10.3390/diagnostics11020201] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.
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Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Hee Won Cho
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Seoul 06351, Korea;
| | - Jeong Su Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Jongtak Jung
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Kyoung-Ho Song
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hyunju Lee
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Eu Suk Kim
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hong Bin Kim
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Correspondence: ; Tel.: +82-2740-8005
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14
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Richard D, Pruvost O, Balloux F, Boyer C, Rieux A, Lefeuvre P. Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen. Mol Ecol 2020; 30:1823-1835. [PMID: 33305421 DOI: 10.1111/mec.15770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 01/03/2023]
Abstract
Horizontal gene transfer is of major evolutionary importance as it allows for the redistribution of phenotypically important genes among lineages. Such genes with essential functions include those involved in resistance to antimicrobial compounds and virulence factors in pathogenic bacteria. Understanding gene turnover at microevolutionary scales is critical to assess the pace of this evolutionary process. Here, we characterized and quantified gene turnover for the epidemic lineage of a bacterial plant pathogen of major agricultural importance worldwide. Relying on a dense geographic sampling spanning 39 years of evolution, we estimated both the dynamics of single nucleotide polymorphism accumulation and gene content turnover. We identified extensive gene content variation among lineages even at the smallest phylogenetic and geographic scales. Gene turnover rate exceeded nucleotide substitution rate by three orders of magnitude. Accessory genes were found preferentially located on plasmids, but we identified a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. Whereas most changes in the gene content are probably transient, the rapid spread of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens illustrates how some accessory genes can become ubiquitous within a population over short timeframes.
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Affiliation(s)
- Damien Richard
- Cirad, UMR PVBMT, Réunion, France.,ANSES, Plant Health Laboratory, Réunion, France.,Université de la Réunion, UMR PVBMT, Réunion, France
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15
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Mancilla-Rojano J, Ochoa SA, Reyes-Grajeda JP, Flores V, Medina-Contreras O, Espinosa-Mazariego K, Parra-Ortega I, Rosa-Zamboni DDL, Castellanos-Cruz MDC, Arellano-Galindo J, Cevallos MA, Hernández-Castro R, Xicohtencatl-Cortes J, Cruz-Córdova A. Molecular Epidemiology of Acinetobacter calcoaceticus- Acinetobacter baumannii Complex Isolated From Children at the Hospital Infantil de México Federico Gómez. Front Microbiol 2020; 11:576673. [PMID: 33178158 PMCID: PMC7593844 DOI: 10.3389/fmicb.2020.576673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
The Acinetobacter calcoaceticus-baumannii (Acb) complex is regarded as a group of phenotypically indistinguishable opportunistic pathogens responsible for mainly causing hospital-acquired pneumonia and bacteremia. The aim of this study was to determine the frequency of isolation of the species that constitute the Acb complex, as well as their susceptibility to antibiotics, and their distribution at the Hospital Infantil de Mexico Federico Gomez (HIMFG). A total of 88 strains previously identified by Vitek 2®, 40 as Acinetobacter baumannii and 48 as Acb complex were isolated from 52 children from 07, January 2015 to 28, September 2017. A. baumannii accounted for 89.77% (79/88) of the strains; Acinetobacter pittii, 6.82% (6/88); and Acinetobacter nosocomialis, 3.40% (3/88). Most strains were recovered mainly from patients in the intensive care unit (ICU) and emergency wards. Blood cultures (BC) provided 44.32% (39/88) of strains. The 13.63% (12/88) of strains were associated with primary bacteremia, 3.4% (3/88) with secondary bacteremia, and 2.3% (2/88) with pneumonia. In addition, 44.32% (39/88) were multidrug-resistant (MDR) strains and, 11.36% (10/88) were extensively drug-resistant (XDR). All strains amplified the blaOXA-51 gene; 51.13% (45/88), the blaOXA-23 gene; 4.54% (4/88), the blaOXA-24 gene; and 2.27% (2/88), the blaOXA-58 gene. Plasmid profiles showed that the strains had 1–6 plasmids. The strains were distributed in 52 pulsotypes, and 24 showed identical restriction patterns, with a correlation coefficient of 1.0. Notably, some strains with the same pulsotype were isolated from different patients, wards, or years, suggesting the persistence of more than one clone. Twenty-seven sequence types (STs) were determined for the strains based on a Pasteur multilocus sequence typing (MLST) scheme using massive sequencing; the most prevalent was ST 156 (27.27%, 24/88). The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas I-Fb system provided amplification in A. baumannii and A. pittii strains (22.73%, 20/88). This study identified an increased number of MDR strains and the relationship among strains through molecular typing. The data suggest that more than one strain could be causing an infection in some patient. The implementation of molecular epidemiology allowed the characterization of a set of strains and identification of different attributes associated with its distribution in a specific environment.
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Affiliation(s)
- Jetsi Mancilla-Rojano
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico.,Facultad de Medicina, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Juan Pablo Reyes-Grajeda
- Subdirección de Desarrollo de Aplicaciones Clínicas, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
| | - Víctor Flores
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Irapuato, Mexico
| | - Oscar Medina-Contreras
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Karina Espinosa-Mazariego
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Israel Parra-Ortega
- Departamento de Laboratorio Clínico, Laboratorio Central, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | | | | | - José Arellano-Galindo
- Unidad de investigación en Enfermedades Infecciosas, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Miguel A Cevallos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, CDMX, Mexico
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16
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López-Leal G, Santamaria RI, Cevallos MÁ, Gonzalez V, Castillo-Ramírez S. Letter to the Editor: Prophages Encode Antibiotic Resistance Genes in Acinetobacter baumannii. Microb Drug Resist 2020; 26:1275-1277. [DOI: 10.1089/mdr.2019.0362] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Gamaliel López-Leal
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Grupo de Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, District of Colombia
| | - Rosa Isela Santamaria
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Miguel Ángel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Victor Gonzalez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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17
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High mortality in an outbreak of multidrug resistant Acinetobacter baumannii infection introduced to an oncological hospital by a patient transferred from a general hospital. PLoS One 2020; 15:e0234684. [PMID: 32702006 PMCID: PMC7377454 DOI: 10.1371/journal.pone.0234684] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 06/01/2020] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE To describe the clinical features, outcomes, and molecular epidemiology of an outbreak of multidrug resistant (MDR) A. baumannii. METHODS We performed a retrospective analysis of all MDR A. baumannii isolates recovered during an outbreak from 2011 to 2015 in a tertiary care cancer hospital. Cases were classified as colonized or infected. We determined sequence types following the Bartual scheme and plasmid profiles. RESULTS There were 106 strains of A. baumannii isolated during the study period. Sixty-six (62.3%) were considered as infection and 40 (37.7%) as colonization. The index case, identified by molecular epidemiology, was a patient with a drain transferred from a hospital outside Mexico City. Ninety-eight additional cases had the same MultiLocus Sequence Typing (MLST) 758, of which 94 also had the same plasmid profile, two had an extra plasmid, and two had a different plasmid. The remaining seven isolates belonged to different MLSTs. Fifty-three patients (50%) died within 30 days of A. baumanniii isolation: 28 (20%) in colonized and 45 (68.2%) in those classified as infection (p<0.001). In multivariate regression analysis, clinical infection and patients with hematologic neoplasm, predicted 30-day mortality. The molecular epidemiology of this outbreak showed the threat posed by the introduction of MDR strains from other institutions in a hospital of immunosuppressed patients and highlights the importance of adhering to preventive measures, including contact isolation, when admitting patients with draining wounds who have been hospitalized in other institutions.
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Farajzadeh Sheikh A, Savari M, Abbasi Montazeri E, Khoshnood S. Genotyping and molecular characterization of clinical Acinetobacter baumannii isolates from a single hospital in Southwestern Iran. Pathog Glob Health 2020; 114:251-261. [PMID: 32552452 PMCID: PMC7480470 DOI: 10.1080/20477724.2020.1765124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
ACINETOBACTER BAUMANNII (A. baumannii) is a pathogen responsible for nosocomial infections among the hospitalized patients. The aim of this study was to investigate genotyping and molecular characterization and to examine the biofilm formation ability of A. baumannii isolates. In total, 70 A. baumannii isolates were collected from patients admitted to Imam Khomeini Hospital in Ahvaz, Southwestern Iran. Minimum inhibitory concentrations (MIC) test was performed using Vitek 2 system. The presence of genes encoding metallo-β-lactamases, oxacillinases, and integrase and the biofilm formation ability were then evaluated. Multiple locus variable-number tandem repeat (VNTR) analysis (MLVA) typing and multiplex PCR were performed to determine the genetic relationships. The blaOXA-23-like gene had the highest prevalence. The frequency of genes encoding blaSPM, blaIMP, and blaVIM among MDR A. baumannii isolates were 12 (17.1%), 18 (25.7%), and 22 (31.4%), respectively. Moreover, 46 isolates (75.4%) harbored class I integron and 10 isolates (16.39%) carried class II integron. The number of weak, moderate and strong biofilm-producing isolates were 3 (4.3%), 7 (10%), and 55 (78.5%), respectively. The results showed that 70 A. baumannii isolates were grouped into 12 distinct MLVA types with five clusters and four singleton genotypes. In addition, 25 (35.7%) isolates were assigned to international clone (IC) variants, 37 (52.8%) isolates belonged to group 1 (IC II), and 8 (11.4%) isolates belonged to group 2 (IC I). Our findings revealed that the population structure of the A. baumannii isolates was genetically diverse. More focus on genetic variation and antibiotic resistance of A. baumannii isolates are recommended.
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Affiliation(s)
- Ahmad Farajzadeh Sheikh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Effat Abbasi Montazeri
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeed Khoshnood
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical
Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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19
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Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni. Proc Natl Acad Sci U S A 2020; 117:11018-11028. [PMID: 32366649 PMCID: PMC7245135 DOI: 10.1073/pnas.1917168117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.
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20
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Pang R, Wu S, Zhang F, Huang J, Wu H, Zhang J, Li Y, Ding Y, Zhang J, Chen M, Wei X, Zhang Y, Gu Q, Zhou Z, Liang B, Li W, Wu Q. The Genomic Context for the Evolution and Transmission of Community-Associated Staphylococcus aureus ST59 Through the Food Chain. Front Microbiol 2020; 11:422. [PMID: 32256477 PMCID: PMC7090029 DOI: 10.3389/fmicb.2020.00422] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/27/2020] [Indexed: 12/16/2022] Open
Abstract
Sequence type 59 (ST59) is a predominant clonal lineage of community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) in Asia. Despite its increasing clinical relevance in China, the evolution and geographic expansion of ST59 has been relatively uncared for. Previous study has shown that ST59 was the predominant clone in food-related MRSA in China. This study compared the genomes of 87 clonal complex (CC) 59 S. aureus isolates sourced from food chain and infection cases to reconstruct the molecular evolution and geographical spread of ST59. Accordingly, three major sub-clades of ST59 were identified and these did not correlate with isolation source or location. Phylogenetic analysis estimated that ST59 in mainland China diverged from a most common recent ancestor around 1974, and most of the cases of cross-country transmission occurred between 1987 and 2000. Notably, two recent events of cross-country transmission through the food chain were observed, the isolates from these events diverged within relatively short time intervals. These isolates also showed high similarity in terms of their core genome, accessory genes, and antibiotic resistance patterns. These findings provide a valuable insight into the potential route of ST59 expansion in China and indicate a need for robust food chain surveillance to prevent the spread of this pathogen.
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Affiliation(s)
- Rui Pang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shi Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Feng Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiahui Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haoming Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Junhui Zhang
- Department of Food Science and Technology, Jinan University, Guangzhou, China
| | - Yanping Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Department of Food Science and Technology, Jinan University, Guangzhou, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qihui Gu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhenwen Zhou
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Bingshao Liang
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wenzhi Li
- Infinitus (China) Company Ltd., Jiangmen, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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21
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Mateo-Estrada V, Graña-Miraglia L, López-Leal G, Castillo-Ramírez S. Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter. Genome Biol Evol 2020; 11:2531-2541. [PMID: 31406982 PMCID: PMC6740150 DOI: 10.1093/gbe/evz178] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2019] [Indexed: 12/22/2022] Open
Abstract
The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.
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Affiliation(s)
- Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Lucía Graña-Miraglia
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Gamaliel López-Leal
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
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22
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Origin of OXA-23 Variant OXA-239 from a Recently Emerged Lineage of Acinetobacter baumannii International Clone V. mSphere 2020; 5:5/1/e00801-19. [PMID: 31915222 PMCID: PMC6952199 DOI: 10.1128/msphere.00801-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes. Over the last few decades, carbapenemase-producing Acinetobacter baumannii has become a major cause of nosocomial infections all over the world. However, the genome identity of lineages of this species in Latin America has not been studied as much as in developed countries. Here, through a population genomics approach considering the whole genomes of 148 isolates (almost 40 from Mexico and Honduras), we describe the recent emergence of the lineage sequence type 758 (ST758), which belongs to the international clone V and has spread out to Canada, Mexico, Honduras, and Colombia. Notably, this lineage was found to coexist with other A. baumannii lineages in hospitals in Mexico and Honduras. Isolates from this lineage show considerable variation in antibiotic resistance profiles, but most of them are resistant to carbapenems. Moreover, we found a variety of acquired oxacillinase (OXA) families within this lineage and tracked the very recent inception, and subsequent horizontal transmission, of the OXA-239 carbapenemase. This work highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes. IMPORTANCEA. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.
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23
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Yeong EK, Huang WL. Risk Factors for Multidrug-Resistant Acinetobacter baumannii Infections in a Mass Burn Casualty Incident. J Burn Care Res 2019; 40:823-827. [PMID: 31197367 DOI: 10.1093/jbcr/irz092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
They investigated the risk factors of multidrug-resistant Acinetobacter baumannii infections in 33 burn patients in a mass burn casualty. The independent variables included sex, burn size, vancomycin, ampicillin/sulbactam, cefazolin, meropenem, third-/fourth-generation cephalosporin, the number of classes of antibiotic used, and the number of days of antibiotic use. Multidrug-resistant A. baumannii infection was the outcome variable. Logistic regressions and structural equation model were used for statistical analysis. The average age was 21.7 years (range, 17-32 years; M = 11 [33%], F = 22 [67%]; mean burn area, 42% of the total body surface area; study period, June 28, 2015 to July 31, 2015). The incidence of infection was 39% (n = 13/33). For every percent increase in burn size, the odds of developing A. baumannii infections increased by 1.1 (P < .05). Similarly, the odds increased by 2.5 in every number increase in the classes of antibiotic used, by 1.2 in everyday increase in the days of antibiotic used, and by 12 in patients treated with vancomycin (P < .05). The correlations of these risk factors were demonstrated in a hypothetical structural equation model (P-value of chi-squared test > .05 and root mean square error of approximation < 0.05) in which burn size was the fundamental risk factor of multidrug-resistant A. baumannii infections. The model did not predict the emergence of multidrug-resistant A. baumannii infections. Conclusively, the risks of multidrug-resistant A. baumannii infections in burns are correlated with burn size, the number of classes of antibiotic used, the number of days of antibiotic use, and the prior use of vancomycin.
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Affiliation(s)
- Eng-Kean Yeong
- Department of Surgery, National Taiwan University Hospital, National Taiwan.,Department of Surgery, National Taiwan University Hospital Yunlin Branch, Douliou City of Yunlin County, Douliu City, Yunlin County, Taiwan
| | - Wei-Lieh Huang
- Department of Psychiatry, National Taiwan University Hospital, Yun-Lin Branch, Douliu City, Yunlin County, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei City, Taiwan
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24
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Alcántar-Curiel MD, Rosales-Reyes R, Jarillo-Quijada MD, Gayosso-Vázquez C, Fernández-Vázquez JL, Toledano-Tableros JE, Giono-Cerezo S, Garza-Villafuerte P, López-Huerta A, Vences-Vences D, Morfín-Otero R, Rodríguez-Noriega E, López-Álvarez MDR, Espinosa-Sotero MDC, Santos-Preciado JI. Carbapenem-Resistant Acinetobacter baumannii in Three Tertiary Care Hospitals in Mexico: Virulence Profiles, Innate Immune Response and Clonal Dissemination. Front Microbiol 2019; 10:2116. [PMID: 31616391 PMCID: PMC6764332 DOI: 10.3389/fmicb.2019.02116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/28/2019] [Indexed: 01/08/2023] Open
Abstract
Acinetobacter baumannii is one of the most important nosocomial pathogens distributed worldwide. Due to its multidrug-resistance and the propensity for the epidemic spread, the World Health Organization includes this bacterium as a priority health issue for development of new antibiotics. The aims of this study were to investigate the antimicrobial resistance profile, the clonal relatedness, the virulence profiles, the innate host immune response and the clonal dissemination of A. baumannii in Hospital Civil de Guadalajara (HCG), Hospital Regional General Ignacio Zaragoza (HRGIZ) and Pediatric ward of the Hospital General de México Eduardo Liceaga (HGM-P). A total of 252 A. baumannii clinical isolates were collected from patients with nosocomial infections in these hospitals between 2015 and 2016. These isolates showed a multidrug-resistant profile and most of them only susceptible to colistin. Furthermore, 83.3 and 36.9% of the isolates carried the blaOXA–24 and blaTEM–1 genes for resistance to carbapenems and β-lactam antibiotics, respectively. The clonal relatedness assessed by pulsed-field gel electrophoresis (PFGE) and by multi-locus sequence typing (MLST) demonstrated a genetic diversity. Remarkably, the ST136, ST208 and ST369 that belonged to the clonal complex CC92 and ST758 and ST1054 to the CC636 clonal complex were identified. The ST136 was a high-risk persistent clone involved in an outbreak at HCG and ST369 were related to the first carbapenem-resistant A. baumannii outbreak in HRGIZ. Up to 58% isolates were able to attach to A549 epithelial cells and 14.5% of them induced >50% of cytotoxicity. A549 cells infected with A. baumannii produced TNFα, IL-6 and IL-1β and the oxygen and nitrogen reactive species that contributes to the development of an inflammatory immune response. Up to 91.3% of clinical isolates were resistant to normal human serum activity. Finally, 98.5% of the clinical isolates were able to form biofilm over polystyrene tubes. In summary, these results demonstrate the increasingly dissemination of multidrug-resistant A. baumannii clones in three hospitals in Mexico carrying diverse bacterial virulence factors that could contribute to establishment of the innate immune response associated to the fatality risks in seriously ill patients.
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Affiliation(s)
- María Dolores Alcántar-Curiel
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ma Dolores Jarillo-Quijada
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Catalina Gayosso-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José Luis Fernández-Vázquez
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José Eduardo Toledano-Tableros
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Silvia Giono-Cerezo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Paola Garza-Villafuerte
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Arath López-Huerta
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniela Vences-Vences
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara Fray Antonio Alcalde, Instituto de Patología Infecciosa y Experimental, UDG, Guadalajara, Mexico
| | - Eduardo Rodríguez-Noriega
- Hospital Civil de Guadalajara Fray Antonio Alcalde, Instituto de Patología Infecciosa y Experimental, UDG, Guadalajara, Mexico
| | | | | | - José Ignacio Santos-Preciado
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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25
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Coppens J, Xavier BB, Loens K, Lammens C, Ieven M, Matheeussen V, Goossens H, Malhotra-Kumar S. Remarkable Genome Stability among emm1 Group A Streptococcus in Belgium over 19 Years. Genome Biol Evol 2019; 11:1432-1439. [PMID: 31065672 PMCID: PMC6521816 DOI: 10.1093/gbe/evz093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2019] [Indexed: 12/30/2022] Open
Abstract
During the last two decades, there has been a public health concern of severe invasive infections caused by Group A Streptococcus (GAS) of the emm1 genotype. This study investigated the dynamics of emm1 GAS during 1994–2013 in Belgium. emm1 GAS isolated from blood, tissue, and wounds of patients with invasive infections (n = 23, S1–S23), and from patients with uncomplicated pharyngitis (n = 15, NS1–NS15) were subjected to whole-genome mapping (WGM; kpn) (Opgen). Whole-genome sequencing was performed on 25 strains (WGS; S1–S23 and NS6–NS7) (Illumina Inc.). Belgian GAS belonged to the M1T1 clone typified by the 36-kb chromosomal region encoding extracellular toxins, NAD+-glycohydrolase and streptolysin O. Strains from 1994–1999 clustered together with published strains (MGAS5005 and M1476). From 2001 onward, invasive GAS showed higher genomic divergence in the accessory genome and harbored on average 7% prophage content. Low evolutionary rate (2.49E-008; P > 0.05) was observed in this study, indicating a highly stable genome. The studied invasive and pharyngitis isolates were no genetically distinct populations based on the WGM and core genome phylogeny analyses. Two copies of the speJ superantigen were present in the 1999 and 2010 study strains (n = 3), one being chromosomal and one being truncated and associated with phage remnants. This study showed that emm1 GAS in Belgium, compared with Canada and UK M1 strains, were highly conserved by harboring a remarkable genome stability over a 19-year period with variations observed in the accessory genome.
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Affiliation(s)
- Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Katherine Loens
- Belgian Reference Centre for Group A Streptococcus, Antwerp University Hospital, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Margareta Ieven
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium.,Belgian Reference Centre for Group A Streptococcus, Antwerp University Hospital, Antwerp, Belgium
| | - Veerle Matheeussen
- Belgian Reference Centre for Group A Streptococcus, Antwerp University Hospital, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium.,Belgian Reference Centre for Group A Streptococcus, Antwerp University Hospital, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
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26
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Rafei R, Osman M, Dabboussi F, Hamze M. Update on the epidemiological typing methods for Acinetobacter baumannii. Future Microbiol 2019; 14:1065-1080. [DOI: 10.2217/fmb-2019-0134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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27
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Castillo-Ramírez S, Graña-Miraglia L. Inaccurate Multilocus Sequence Typing of Acinetobacter baumannii. Emerg Infect Dis 2019; 25:186-187. [PMID: 30561303 PMCID: PMC6302598 DOI: 10.3201/eid2501.180374] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing has been useful for genotyping pathogens in surveillance and epidemiologic studies. However, it cannot reflect the true relationships of isolates for species with very dynamic genomes. Using a robust genome phylogeny, we demonstrated the limitations of this method for typing Acinetobacter baumannii.
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28
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Parajuli P, Deimel LP, Verma NK. Genome Analysis of Shigella flexneri Serotype 3b Strain SFL1520 Reveals Significant Horizontal Gene Acquisitions Including a Multidrug Resistance Cassette. Genome Biol Evol 2019; 11:776-785. [PMID: 30715343 PMCID: PMC6424224 DOI: 10.1093/gbe/evz026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2019] [Indexed: 11/23/2022] Open
Abstract
Shigella flexneri is a major etiological agent of shigellosis in developing countries, primarily occurring in children under 5 years of age. We have sequenced, for the first time, the complete genome of S. flexneri serotype 3b (strain SFL1520). We used a hybrid sequencing method––both long-read MinION Flow (Oxford Nanopore Technologies) and short-read MiSeq (Illumina) sequencing to generate a high-quality reference genome. The SFL1520 chromosome was found to be ∼4.58 Mb long, with 4,729 coding sequences. Despite sharing a substantial number of genes with other publicly available S. flexneri genomes (2,803), the SFL1520 strain contains 1,926 accessory genes. The phage-related genes accounted for 8% of the SFL1520 genome, including remnants of the Sf6 bacteriophage with an intact O-acetyltransferase gene specific to serotype 3b. The SFL1520 chromosome was also found to contain a multiple-antibiotic resistance cassette conferring resistance to ampicillin, chloramphenicol, streptomycin, and tetracycline, which was potentially acquired from a plasmid via transposases. The phylogenetic analysis based on core genes showed a high level of similarity of SFL1520 with other S. flexneri serotypes; however, there were marked differences in the accessory genes of SFL1520. In particular, a large number of unique genes were identified in SFL1520 suggesting significant horizontal gene acquisition in a relatively short time period. The major virulence traits of SFL1520 (such as serotype conversion and antimicrobial resistance) were associated with horizontal gene acquisitions highlighting the role of horizontal gene transfer in S. flexneri diversity and evolution.
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Affiliation(s)
- Pawan Parajuli
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Lachlan P Deimel
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Naresh K Verma
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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29
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López-Leal G, Zuniga-Moya JC, Castro-Jaimes S, Graña-Miraglia L, Pérez-Oseguera Á, Reyes-García HS, Gough-Coto SD, Pavón-Madrid R, Bejarano SA, Ferrera A, Castillo-Ramírez S, Cevallos MA. Unexplored Genetic Diversity of Multidrug- and Extremely Drug-Resistant Acinetobacter baumannii Isolates from Tertiary Hospitals in Honduras. Microb Drug Resist 2019; 25:690-695. [DOI: 10.1089/mdr.2018.0311] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Gamaliel López-Leal
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Semiramis Castro-Jaimes
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Lucía Graña-Miraglia
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Ángeles Pérez-Oseguera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | | | - René Pavón-Madrid
- Campus San Pedro y San Pablo, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Suyapa Aurora Bejarano
- Campus San Pedro y San Pablo, Universidad Católica de Honduras, San Pedro Sula, Honduras
- Liga Contra el Cancer, San Pedro Sula, Honduras
| | - Annabelle Ferrera
- Universidad Nacional Autónoma de Honduras, Escuela de Microbiologia, Edificio E1, 2da planta, Ciudad Universitaria Tegucigalpa, Tegucigalpa M.D.C., Honduras
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Miguel A. Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
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30
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Adams MD, Wright MS, Karichu JK, Venepally P, Fouts DE, Chan AP, Richter SS, Jacobs MR, Bonomo RA. Rapid Replacement of Acinetobacter baumannii Strains Accompanied by Changes in Lipooligosaccharide Loci and Resistance Gene Repertoire. mBio 2019; 10:e00356-19. [PMID: 30914511 PMCID: PMC6437055 DOI: 10.1128/mbio.00356-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
The population structure of health care-associated pathogens reflects patterns of diversification, selection, and dispersal over time. Empirical data detailing the long-term population dynamics of nosocomial pathogens provide information about how pathogens adapt in the face of exposure to diverse antimicrobial agents and other host and environmental pressures and can inform infection control priorities. Extensive sequencing of clinical isolates from one hospital spanning a decade and a second hospital in the Cleveland, OH, metropolitan area over a 3-year time period provided high-resolution genomic analysis of the Acinetobacter baumannii metapopulation. Genomic analysis demonstrated an almost complete replacement of the predominant strain groups with a new, genetically distinct strain group during the study period. The new group, termed clade F, differs from other global clone 2 (GC2) strains of A. baumannii in several ways, including its antibiotic resistance and lipooligosaccharide biosynthesis genes. Clade F strains are part of a large phylogenetic group with broad geographic representation. Phylogenetic analysis of single-nucleotide variants in core genome regions showed that although the Cleveland strains are phylogenetically distinct from those isolated from other locations, extensive intermixing of strains from the two hospital systems was apparent, suggesting either substantial exchange of strains or a shared, but geographically restricted, external pool from which infectious isolates were drawn. These findings document the rapid evolution of A. baumannii strains in two hospitals, with replacement of the predominant clade by a new clade with altered lipooligosaccharide loci and resistance gene repertoires.IMPORTANCE Multidrug-resistant (MDR) A. baumannii is a difficult-to-treat health care-associated pathogen. Knowing the resistance genes present in isolates causing infection aids in empirical treatment selection. Furthermore, knowledge of the genetic background can assist in tracking patterns of transmission to limit the spread of infections in hospitals. The appearance of a new genetic background in A. baumannii strains with a different set of resistance genes and cell surface structures suggests that strong selective pressures exist, even in highly MDR pathogens. Because the new strains have levels of antimicrobial resistance similar to those of the strains that were displaced, we hypothesize that other features, including host colonization and infection, may confer additional selective advantages and contribute to their increased prevalence.
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Affiliation(s)
- Mark D Adams
- The J. Craig Venter Institute, La Jolla, California, USA
| | | | - James K Karichu
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | | | - Agnes P Chan
- The J. Craig Venter Institute, Rockville, Maryland, USA
| | - Sandra S Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michael R Jacobs
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Center for Proteomics, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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31
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Mancilla-Rojano J, Castro-Jaimes S, Ochoa SA, Bobadilla Del Valle M, Luna-Pineda VM, Bustos P, Laris-González A, Arellano-Galindo J, Parra-Ortega I, Hernández-Castro R, Cevallos MA, Xicohtencatl-Cortes J, Cruz-Córdova A. Whole-Genome Sequences of Five Acinetobacter baumannii Strains From a Child With Leukemia M2. Front Microbiol 2019; 10:132. [PMID: 30787915 PMCID: PMC6372515 DOI: 10.3389/fmicb.2019.00132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/21/2019] [Indexed: 01/05/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen and is one of the primary etiological agents of healthcare-associated infections (HAIs). A. baumannii infections are difficult to treat due to the intrinsic and acquired antibiotic resistance of strains of this bacterium, which frequently limits therapeutic options. In this study, five A. baumannii strains (810CP, 433H, 434H, 483H, and A-2), all of which were isolated from a child with leukemia M2, were characterized through antibiotic susceptibility profiling, the detection of genes encoding carbapenem hydrolyzing oxacillinases, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), adherence and invasion assays toward the A549 cell line, and the whole-genome sequence (WGS). The five strains showed Multidrug resistant (MDR) profiles and amplification of the blaOXA-23 gene, belonging to ST758 and grouped into two PFGE clusters. WGS of 810CP revealed the presence of a circular chromosome and two small plasmids, pAba810CPa and pAba810CPb. Both plasmids carried genes encoding the Sp1TA system, although resistance genes were not identified. A gene-by-gene comparison analysis was performed among the A. baumannii strains isolated in this study and others A. baumannii ST758 strains (HIMFG and INCan), showing that 86% of genes were present in all analyzed strains. Interestingly, the 433H, 434H, and 483H strains varied by 8–10 single-nucleotide variants (SNVs), while the A2 and 810CP strains varied by 46 SNVs. Subsequently, an analysis using BacWGSTdb showed that all of our strains had the same resistance genes and were ST758. However, some variations were observed in relation to virulence genes, mainly in the 810CP strain. The genes involved in the synthesis of hepta-acylated lipooligosaccharides, the pgaABCD locus encoding poly-β-1-6-N-acetylglucosamine, the ompA gene, Csu pili, bap, the two-component system bfms/bfmR, a member of the phospholipase D family, and two iron-uptake systems were identified in our A. baumannii strains genome. The five A. baumannii strains isolated from the child were genetically different and showed important characteristics that promote survival in a hospital environment. The elucidation of their genomic sequences provides important information for understanding their epidemiology, antibiotic resistance, and putative virulence factors.
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Affiliation(s)
- Jetsi Mancilla-Rojano
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.,Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Semiramis Castro-Jaimes
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Miriam Bobadilla Del Valle
- Departamento de Enfermedades Infecciosas Instituto Nacional de Ciencias Médicas y de Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Victor M Luna-Pineda
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Almudena Laris-González
- Departamento de Epidemiología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - José Arellano-Galindo
- Laboratorio de Infectología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Israel Parra-Ortega
- Laboratorio Central, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos Hospital General "Dr. Manuel Gea González", Mexico City, Mexico
| | - Miguel A Cevallos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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32
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Kim SJ, Kim YJ, Ko KS. Genomic Analysis of Consecutive Acinetobacter baumannii Strains From a Single Patient. Front Microbiol 2018; 9:2840. [PMID: 30542330 PMCID: PMC6277775 DOI: 10.3389/fmicb.2018.02840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/05/2018] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter baumannii is one of the most important nosocomial pathogens, and thus it is required to investigate how it disseminate in hospitals and infect patients. We performed whole genome sequencing for 24 A. baumannii strains isolated successively from the blood of a single patient to evaluate whether repeated infections were due to re-infection or relapse infection and to investigate within-host evolution. The whole genome of the first strain, BL1, was sequenced de novo using the PacBio RSII system. BL2-BL24, were sequenced with an Illumina Hiseq4000 and mapped to the genome sequences of BL1. We identified 42 single-nucleotide variations among the strains. The SNVs differentiated the strains into three groups, BL1, BL2-BL16, and BL17-BL24, indicating that the patient suffered from re-infections or co-infections by similar, but different strains. The results also showed that A. baumannii strains in each group were rather stable at the genomic level. Our study emphasizes the importance of intensive infection control.
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Affiliation(s)
- Sun Ju Kim
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Yae-Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, South Korea
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33
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Linz B, Mukhtar N, Shabbir MZ, Rivera I, Ivanov YV, Tahir Z, Yaqub T, Harvill ET. Virulent Epidemic Pneumonia in Sheep Caused by the Human Pathogen Acinetobacter baumannii. Front Microbiol 2018; 9:2616. [PMID: 30459734 PMCID: PMC6232368 DOI: 10.3389/fmicb.2018.02616] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/12/2018] [Indexed: 01/12/2023] Open
Abstract
The human pathogen Acinetobacter baumannii has emerged as a frequent cause of hospital-acquired infections, but infection of animals has rarely been observed. Here we analyzed an outbreak of epidemic pneumonia killing hundreds of sheep on a farm in Pakistan and identified A. baumannii as the infecting agent. A pure culture of strain AbPK1 isolated from lungs of sick animals was inoculated into healthy sheep, which subsequently developed similar disease symptoms. Bacteria re-isolated from the infected animals were shown to be identical to the inoculum, fulfilling Koch’s postulates. Comparison of the AbPK1 genome against 2283 A. baumannii genomes from the NCBI database revealed that AbPK1 carries genes for unusual surface structures, including a unique composition of iron acquisition genes, genes for O-antigen synthesis and sialic acid-specific acetylases of cell-surface carbohydrates that could enable immune evasion. Several of these unusual and otherwise rarely present genes were also identified in genomes of phylogenetically unrelated A. baumannii isolates from combat-wounded US military from Afghanistan indicating a common gene pool in this geographical region. Based on core genome MLST this virulent isolate represents a newly emerging lineage of Global Clone 2, suggesting a human source for this disease outbreak. The observed epidemic, direct transmission from sheep to sheep, which is highly unusual for A. baumannii, has important consequences for human and animal health. First, direct animal-to-animal transmission facilitates fast spread of pathogen and disease in the flock. Second, it may establish a stable ecological niche and subsequent spread in a new host. And third, it constitutes a serious risk of transmission of this hyper-virulent clone from sheep back to humans, which may result in emergence of contagious disease amongst humans.
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Affiliation(s)
- Bodo Linz
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Nadia Mukhtar
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Zubair Shabbir
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Israel Rivera
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Yury V Ivanov
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Zarfishan Tahir
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Yaqub
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Eric T Harvill
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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34
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Graña-Miraglia L, Arreguín-Pérez C, López-Leal G, Muñoz A, Pérez-Oseguera A, Miranda-Miranda E, Cossío-Bayúgar R, Castillo-Ramírez S. Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus. PeerJ 2018; 6:e5839. [PMID: 30386709 PMCID: PMC6203942 DOI: 10.7717/peerj.5839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/28/2018] [Indexed: 12/21/2022] Open
Abstract
Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylogeny of the species within the genus Staphylococcus; with the idea that those who cannot afford whole genome sequencing can use these loci to carry out species assignation confidently. We retrieved 177 orthologous groups (OGs) by using a genome-based phylogeny and an average nucleotide identity analysis. The top 26 OGs showed topologies similar to the species tree and the concatenation of them yielded a topology almost identical to that of the species tree. Furthermore, a phylogeny of just the top seven OGs could be used for species assignment. We sequenced four staphylococcus isolates to test the 26 OGs and found that these OGs were far superior to commonly used markers for this genus. On the whole, our procedure allowed identification of the most adequate markers for inferring the phylogeny within the genus Staphylococcus. We anticipate that this approach will be employed for the identification of the most suitable markers for other bacterial genera and can be very helpful to sort out poorly classified genera.
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Affiliation(s)
- Lucia Graña-Miraglia
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - César Arreguín-Pérez
- Centro Nacional de Investigación Disciplinaria en Parasitología Veterinaria del Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Jiutepec, Morelos, Mexico
| | - Gamaliel López-Leal
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alan Muñoz
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Angeles Pérez-Oseguera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Estefan Miranda-Miranda
- Centro Nacional de Investigación Disciplinaria en Parasitología Veterinaria del Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Jiutepec, Morelos, Mexico
| | - Raquel Cossío-Bayúgar
- Centro Nacional de Investigación Disciplinaria en Parasitología Veterinaria del Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Jiutepec, Morelos, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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35
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Zhang X, Liu Z, Wei G, Yang F, Liu X. In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle. Front Microbiol 2018; 9:1255. [PMID: 29937764 PMCID: PMC6002666 DOI: 10.3389/fmicb.2018.01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/24/2018] [Indexed: 12/27/2022] Open
Abstract
The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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36
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Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. Sci Rep 2018; 8:2523. [PMID: 29410443 PMCID: PMC5802823 DOI: 10.1038/s41598-018-20847-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/25/2018] [Indexed: 01/14/2023] Open
Abstract
In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit (ICU) in 2000 (9 strains referred to collectively as Ab_GEIH-2000) and 2010 (9 strains referred to collectively as Ab_GEIH-2010), during the GEIH-REIPI project (Umbrella BioProject PRJNA422585). We observed two main molecular differences between the Ab_GEIH-2010 and the Ab_GEIH-2000 collections, acquired over the course of the decade long sampling interval and involving the mobilome: i) a plasmid harbouring genes for blaOXA 24/40 ß-lactamase and abKA/abkB proteins of a toxin-antitoxin system; and ii) two temperate bacteriophages, Ab105-1ϕ (63 proteins) and Ab105-2ϕ (93 proteins), containing important viral defence proteins. Moreover, all Ab_GEIH-2010 strains contained a Quorum functional network of Quorum Sensing (QS) and Quorum Quenching (QQ) mechanisms, including a new QQ enzyme, AidA, which acts as a bacterial defence mechanism against the exogenous 3-oxo-C12-HSL. Interestingly, the infective capacity of the bacteriophages isolated in this study (Ab105-1ϕ and Ab105-2ϕ) was higher in the Ab_GEIH-2010 strains (carrying a functional Quorum network) than in the Ab_GEIH-2000 strains (carrying a deficient Quorum network), in which the bacteriophages showed little or no infectivity. This is the first study about the evolution of the Quorum network and the mobilome in clinical strains of Acinetobacter baumannii during a decade.
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