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Santos MDV, Barros MPS, Silveira-Filho VDM, Mendes-Marques CL, Lima AVA, Silva MVD, Leal-Balbino TC, Silva MDPCD, Paiva PMG, Oliveira MBMD. Genetic and Biochemical Diversity of Clinical Acinetobacter baumannii and Pseudomonas aeruginosa Isolates in a Public Hospital in Brazil. Microb Drug Resist 2020; 27:509-517. [PMID: 32882147 DOI: 10.1089/mdr.2020.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Life-threatening bacterial infections are a major concern in health care services worldwide. This retrospective study aimed to demonstrate genetic and biochemical diversity in isolates of Acinetobacter baumannii and Pseudomonas aeruginosa from a public hospital in Brazil. A total of 63 isolates collected from different sites of infection and hospital sectors were characterized, and their susceptibility profile to antibiotics was assessed for 18 drugs belonging to 8 antimicrobial categories using the automated BACTEC system. Genetic diversity was assessed using the multiple locus variable number tandem repeat analysis. Among the isolates of A. baumannii, 83% were classified as extensively drug resistant (XDR), and 17 genotypic profiles were identified. About 67% of P. aeruginosa isolates were susceptible to antimicrobials and were distributed into 37 genotypic profiles, revealing genetic heterogeneity. This study has demonstrated the multicolonization of investigated pathogens and the high frequency (95.8%) of multidrug-resistant and XDR, as well as high genetic diversity, among the isolates supporting the continuous need to monitor these species in the hospital environment.
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Affiliation(s)
| | | | | | | | | | - Marcia Vanusa da Silva
- Department of Biochemistry, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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Vogler AJ, Sahl JW, Leal NC, Sobreira M, Williamson CHD, Bollig MC, Birdsell DN, Rivera A, Thompson B, Nottingham R, Rezende AM, Keim P, Almeida AMP, Wagner DM. A single introduction of Yersinia pestis to Brazil during the 3rd plague pandemic. PLoS One 2019; 14:e0209478. [PMID: 30625164 PMCID: PMC6326411 DOI: 10.1371/journal.pone.0209478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/06/2018] [Indexed: 12/30/2022] Open
Abstract
Yersinia pestis was introduced to Brazil during the third plague pandemic and currently exists in several recognized foci. There is currently limited available phylogeographic data regarding Y. pestis in Brazil. We generated whole genome sequences for 411 Y. pestis strains from six Brazilian foci to investigate the phylogeography of Y. pestis in Brazil; these strains were isolated from 1966 to 1997. All 411 strains were assigned to a single monophyletic clade within the 1.ORI population, indicating a single Y. pestis introduction was responsible for the successful establishment of endemic foci in Brazil. There was a moderate level of genomic diversity but little population structure among the 411 Brazilian Y. pestis strains, consistent with a radial expansion wherein Y. pestis spread rapidly from the coast to the interior of Brazil and became ecologically established. Overall, there were no strong spatial or temporal patterns among the Brazilian strains. However, strains from the same focus tended to be more closely related and strains isolated from foci closer to the coast tended to fall in more basal positions in the whole genome phylogeny than strains from more interior foci. Overall, the patterns observed in Brazil are similar to other locations affected during the 3rd plague pandemic such as in North America and Madagascar.
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Affiliation(s)
- Amy J. Vogler
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nilma C. Leal
- Institute Aggeu Magalhães, Recife, Pernambuco, Brazil
| | | | - Charles H. D. Williamson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Molly C. Bollig
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Dawn N. Birdsell
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Andrew Rivera
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Brian Thompson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne Nottingham
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
| | | | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail: (DMW); (AMPA)
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Leal NC, Sobreira M, Araújo AFQ, Magalhães JLO, Vogler AJ, Bollig MC, Nottingham R, Keim P, Wagner DM, Almeida AMP. Viability of Yersinia pestis subcultures in agar stabs. Lett Appl Microbiol 2015; 62:91-5. [PMID: 26524218 DOI: 10.1111/lam.12519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 12/01/2022]
Abstract
UNLABELLED Since its identification as the causative agent of plague in 1894, thousands of Yersinia pestis strains have been isolated and stored. Here, we report the ability of Y. pestis to survive up to 47 years in agar stabs, in rubber-stoppered tubes, under refrigeration (+4 to +10°C), although overall subculture recovery rates were poor and inversely related to the length of time stored. Genetic characterization of virulence gene presence among these subcultures was suggestive of significant variation in the genomic stability of Y. pestis subcultures stored under these conditions. Specifically, we found variation in the presence of plasmid and chromosomal virulence markers (genes pla, lcrV, caf1 and irp2) among multiple subcultures of Y. pestis strains in the 'Collection of Yersinia pestis' (Fiocruz-CYP) maintained by the SRP of FIOCRUZ-PE in Brazil. This variation, together with all of the inherent temporal, geographic and other genetic variation represented by all of the recoverable strains in this historical collection was preserved in new frozen culture stocks stored at -70°C as a result of this study. These frozen culture stocks represent a valuable resource for future comparative studies of Y. pestis. SIGNIFICANCE AND IMPACT OF THE STUDY We report the ability of Yersinia pestis to survive up to 47 years in agar stabs, in rubber-stoppered tubes, under refrigeration (+4 to +10°C), although overall subculture recovery rates were poor and inversely related to the length of time stored. Genetic characterization of virulence gene presence among these subcultures was suggestive of significant variation in the genomic stability of Y. pestis subcultures stored under these conditions. This variation, together with all of the inherent temporal, geographic and other genetic variation represented by all of the recoverable strains in the historical 'Collection of Yersinia pestis' (Fiocruz-CYP) maintained by the SRP of FIOCRUZ-PE in Brazil was preserved in new frozen culture stocks stored at -70°C as a result of this study. These frozen culture stocks represent a valuable resource for future comparative studies of Y. pestis.
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Affiliation(s)
- N C Leal
- Centro de Pesquisa Aggeu Magalhães (CPqAM) - FIOCRUZ/PE, Recife, Brazil
| | - M Sobreira
- Centro de Pesquisa Aggeu Magalhães (CPqAM) - FIOCRUZ/PE, Recife, Brazil
| | - A F Q Araújo
- Centro de Pesquisa Aggeu Magalhães (CPqAM) - FIOCRUZ/PE, Recife, Brazil
| | - J L O Magalhães
- Centro de Pesquisa Aggeu Magalhães (CPqAM) - FIOCRUZ/PE, Recife, Brazil
| | - A J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - M C Bollig
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - R Nottingham
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - P Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.,Translational Genomics Research Institute North, Flagstaff, AZ, USA
| | - D M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - A M P Almeida
- Centro de Pesquisa Aggeu Magalhães (CPqAM) - FIOCRUZ/PE, Recife, Brazil
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Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2015; 37:21-36. [PMID: 26518910 DOI: 10.1016/j.meegid.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/28/2022]
Abstract
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA.
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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Barros MPS, França CT, Lins RHFB, Santos MDV, Silva EJ, Oliveira MBM, Silveira-Filho VM, Rezende AM, Balbino VQ, Leal-Balbino TC. Dynamics of CRISPR loci in microevolutionary process of Yersinia pestis strains. PLoS One 2014; 9:e108353. [PMID: 25265542 PMCID: PMC4180756 DOI: 10.1371/journal.pone.0108353] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 08/27/2014] [Indexed: 12/19/2022] Open
Abstract
The potential use of CRISPR loci genotyping to elucidate population dynamics and microevolution of 146 Yersinia pestis strains from different biovars and locations was investigated in this work. The majority of strains from the Orientalis biovar presented specific spacer arrays, allowing for the establishment of a CRISPR signature for their respective isolates. Twenty-one new spacers were found in the Y. pestis strains from plague foci in Brazil. Ninety-three (64%) strains were grouped in the G1 genotype, whereas the others were distributed in 35 genotypes. This study allowed observing a microevolutionary process in a group of Y. pestis isolated from Brazil. We also identified specific genotypes of Y. pestis that were important for the establishment of the bacteria in plague foci in Brazil. The data have provided supporting evidence for the diversity and dynamics of CRISPR loci present in the genome of Y. pestis strains from plague foci in Brazil.
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Affiliation(s)
- Maria Paloma S. Barros
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
- * E-mail:
| | - Camila T. França
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
| | - Rosanny Holanda F. B. Lins
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
- Departamento de Genética, Universidade Federal de Pernambuco (UFPE), Recife, PE, Brasil
| | - Milena Danda V. Santos
- Departamento de Bioquímica, Universidade Federal de Pernambuco (UFPE), Recife, PE, Brasil
| | - Ednaldo J. Silva
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
| | | | | | - Antônio M. Rezende
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
| | - Valdir Q. Balbino
- Departamento de Genética, Universidade Federal de Pernambuco (UFPE), Recife, PE, Brasil
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Lv G, Xu B, Wei P, Song J, Zhang H, Zhao C, Qin L, Zhao B. Molecular characterization of foodborne-associated Staphylococcus aureus strains isolated in Shijiazhuang, China, from 2010 to 2012. Diagn Microbiol Infect Dis 2013; 78:462-8. [PMID: 24582576 DOI: 10.1016/j.diagmicrobio.2013.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/07/2013] [Accepted: 12/08/2013] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen commonly identified from food poisoning-associated foodstuffs. From 1996 to the present, S. aureus isolates have been found to exhibit increasing resistance to antimicrobial drugs. The aim of this study was to assess the molecular epidemiology properties of various S. aureus isolates through molecular typing and to investigate their characterization based on their production of enterotoxins and hemolysins and their resistance to antibiotics. A total of 78 coagulase-positive staphylococcal strains isolated from food or clinical samples were analyzed. Eight VNTR loci were used to genotype the 78 isolates, and this analysis resulted in 39 different multilocus variable number tandem repeat analysis (MLVA) profiles. The isolates recovered from a single outbreak exhibited the same MLVA profile. According to CLSI, 97.4% of the isolates were resistant to penicillin, whereas only 3.8% were methicillin-resistant Staphylococcus aureus strains. Through multiplex PCR, 87.2% of the isolates were shown to be enterotoxigenic (SEs), and the most common genes present were sea, sem, seg, seu, and sek. In conclusion, this study demonstrates the prevalence of staphylococcal enterotoxins, the contents of virulent factors, and the characteristics of β-lactam antibiotic resistance in 78 S. aureus isolates. These findings emphasize the need to prevent the presence of S. aureus strains and SE production in foods. Our results also demonstrate that MLVA is a useful and powerful method for epidemiological studies of S. aureus. In contrast to multilocus sequence typing, the MLVA method is a simpler and more rapid method for epidemiological typing with a higher discriminatory power.
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Affiliation(s)
- GuoPing Lv
- College of Life Science, Hebei Normal University, Shijiazhuang 050000, China; Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - BaoHong Xu
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - PeiNan Wei
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - Jie Song
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - HongYing Zhang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - Chuan Zhao
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - LiYun Qin
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China.
| | - BaoHua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang 050000, China.
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Barros MPS, Silveira-Filho VM, Lins RHFB, Oliveira MBM, Almeida AMP, Leal-Balbino TC. Subtyping Brazilian Yersinia pestis strains by pulsed-field gel electrophoresis. GENETICS AND MOLECULAR RESEARCH 2013; 12:1294-302. [PMID: 23315882 DOI: 10.4238/2013.january.4.23] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We subtyped Brazilian Yersinia pestis strains by pulsed-field gel electrophoresis (PFGE). This was done with 22 Brazilian Y. pestis strains: 17 from an outbreak and 5 from endemic routine surveillance. The strains were divided into 2 groups (I and II), 8 subgroups (A-H) and 19 PFGE profiles or pulsotypes. PFGE did not separate outbreak from non-outbreak strains, as identical pulsotype patterns were found among outbreak strains and strains obtained from surveillance. However, it was able to detect intraspecific genetic diversity among Brazilian strains. This PFGE technique was able to differentiate a homogeneous group of Brazilian Y. pestis strains.
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Affiliation(s)
- M P S Barros
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães, FIOCRUZ, Recife, PE, Brasil
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