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Epidemiology of Aeromonas Species Bloodstream Infection in Queensland, Australia: Association with Regional and Climate Zones. Microorganisms 2022; 11:microorganisms11010036. [PMID: 36677328 PMCID: PMC9867365 DOI: 10.3390/microorganisms11010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Aeromonas species can cause severe bloodstream infection (BSI) however, few studies have examined their epidemiology in non-selected populations. The objective of this study was to describe the incidence and determinants of Aeromonas species BSI in Queensland, Australia. A retrospective population-based cohort study was conducted during 2000-2019. Aeromonas species BSI were identified by laboratory surveillance and clinical and outcome information through data linkages to statewide databases. A total of 407 incident Aeromonas species BSI were identified with an age- and sex-standardized incidence of 5.2 per million residents annually. No trend in annual incidence rate during two decades of surveillance was demonstrated. Significant variable monthly occurrences were observed with highest rates during warmer, wetter months, and lowest rates during winter and dry periods. There was significant variability in incidence accordingly to region and climate zones, with higher rates observed in tropical north regions and lowest in southeastern corner. The highest incidence was observed in very remote and hot areas in Queensland. Cases were infrequent in children and risk was highest in elderly and males. Seventy-eight patients died within 30 days with a case-fatality rate of 19%. Older age, non-focal infection, higher Charlson score, and monomicrobial bacteremia were independent risk factors for death. Demographic and climatic changes may increase the burden of these infections in future years.
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Dubey S, Ager-Wick E, Peng B, Evensen Ø, Sørum H, Munang’andu HM. Characterization of virulence and antimicrobial resistance genes of Aeromonas media strain SD/21-15 from marine sediments in comparison with other Aeromonas spp. Front Microbiol 2022; 13:1022639. [PMID: 36532448 PMCID: PMC9752117 DOI: 10.3389/fmicb.2022.1022639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/06/2022] [Indexed: 10/03/2023] Open
Abstract
Aeromonas media is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in A. media strain SD/21-15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several A. media strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21-15 with A. hydrophila, A. veronii, and A. salmonicida reference strains. We detected Msh pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found hylA, hylIII, and TSH hemolysin genes in all isolates responsible for virulence in all isolates while the aerA gene was not detected in all A. media isolates but was present in A. hydrophila, A. veronii, and A. salmonicida reference strains. In addition, we detected LuxS and mshA-Q responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (Fur), heme and siderophore genes responsible for iron acquisition in all A. media isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the vgrG1, vrgG3, hcp, and ats genes that form parts of the T6SS were detected in some isolates. Presence of bla MOX-9 and bla OXA-427 β-lactamases as well as crp and mcr genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all A. media isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that A. media has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of A. media in the spread of AMR genes.
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Affiliation(s)
- Saurabh Dubey
- Section for Experimental Biomedicine, Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Eirill Ager-Wick
- Section for Experimental Biomedicine, Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Bo Peng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Higher Education Mega Center, Guangzhou, China
| | - Øystein Evensen
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Henning Sørum
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Hetron Mweemba Munang’andu
- Section for Experimental Biomedicine, Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Aeromonas: the multifaceted middleman in the One Health world. Curr Opin Microbiol 2021; 65:24-32. [PMID: 34717260 DOI: 10.1016/j.mib.2021.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023]
Abstract
Aeromonas is at the interface of all the One Health components and represents an amazingly sound test case in the One Health approach, from economic loss in aquaculture tochallenges related to antibiotic-resistant bacteria selected from the environment. In human health, infections following leech therapy is an outstanding example of such One Health challenges. Aeromonads are not only ubiquitous environmental bacteria, able to rapidly colonize and cause opportunistic infections in humans and animals, they are also capable of promoting interactions and gene exchanges between the One Health components. This makes this genus a key amplifier of genetic transfer, especially of antibiotic resistance genes.
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Vasquez I, Cao T, Hossain A, Valderrama K, Gnanagobal H, Dang M, Leeuwis RHJ, Ness M, Campbell B, Gendron R, Kao K, Westcott J, Gamperl AK, Santander J. Aeromonas salmonicida infection kinetics and protective immune response to vaccination in sablefish (Anoplopoma fimbria). FISH & SHELLFISH IMMUNOLOGY 2020; 104:557-566. [PMID: 32592927 DOI: 10.1016/j.fsi.2020.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Effective vaccine programs against Aeromonas salmonicida have been identified as a high priority area for the sablefish (Anoplopoma fimbria) aquaculture. In this study, we established an A. salmonicida infection model in sablefish to evaluate the efficacy of commercial vaccines and an autogenous vaccine preparation. Groups of 40 fish were intraperitoneally (ip) injected with different doses of A. salmonicida J410 isolated from infected sablefish to calculate the median lethal dose (LD50). Samples of blood, head kidney, spleen, brain, and liver were also collected at different time points to determine the infection kinetics. The LD50 was estimated as ~3 × 105 CFU/dose. To evaluate the immune protection provided by an autogenous vaccine and two commercial vaccines in a common garden experimental design, 140 fish were PIT-tagged, vaccinated and distributed equally into 4 tanks (35 fish for each group, including a control group). Blood samples were taken every 2 weeks to evaluate IgM titers. At 10 weeks post-immunization, all groups were ip challenged with 100 times the calculated LD50 for A. salmonicida J410. A. salmonicida was detected after 5 days post-infection (dpi) in all collected tissues. At 30 days post-challenge the relative percentage survival (RPS) with respect to the control group was calculated for each vaccine. The RPS for the bacterin mix was 65.22%, for Forte Micro 4® vaccine was 56.52% and for Alpha Ject Micro 4® was 30.43%, and these RPS values were reflected by A. salmonicida tissue colonization levels at 10 days post-challenge. Total IgM titers peaked at 6-8 weeks post-immunization, where the autogenous vaccine group showed the highest IgM titers and these values were consistent with the RPS data. Also, we determined that the A. salmonicida A-layer binds to immunoglobulins F(ab)' in a non-specific fashion, interfering with immune assays and potentially vaccine efficacy. Our results indicate that vaccine design influences sablefish immunity and provide a guide for future sablefish vaccine programs.
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Affiliation(s)
- Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Katherinne Valderrama
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - My Dang
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Robine H J Leeuwis
- Fish Physiology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | | | - Robert Gendron
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Kenneth Kao
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jillian Westcott
- Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, NL, Canada
| | - A Kurt Gamperl
- Fish Physiology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada.
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Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities. mSystems 2019; 4:4/5/e00252-19. [PMID: 31641046 PMCID: PMC6811364 DOI: 10.1128/msystems.00252-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections.IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.
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Talagrand-Reboul E, Latif-Eugenín F, Beaz-Hidalgo R, Colston S, Figueras MJ, Graf J, Jumas-Bilak E, Lamy B. Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads. PLoS One 2018; 13:e0201428. [PMID: 30110345 PMCID: PMC6093642 DOI: 10.1371/journal.pone.0201428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Many virulence factors have been described for opportunistic pathogens within the genus Aeromonas. Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas from the environment to host, but their performances have never been thoroughly evaluated. We aimed to determine diagnostic sensitivity and specificity of PCR assays for the detection of virulence-associated genes in a collection of Aeromonas isolates representative for the genetic diversity in the genus. Thirty-nine Aeromonas strains belonging to 27 recognized species were screened by published PCR assays for virulence-associated genes (act, aerA, aexT, alt, ascFG, ascV, ast, lafA, lip, ser, stx1, stx2A). In parallel, homologues of the 12 putative virulence genes were searched from the genomes of the 39 strains. Of the 12 published PCR assays for virulence factors, the comparison of PCR results and genome analysis estimated diagnostic sensitivities ranging from 34% to 100% and diagnostic specificities ranged from 71% to 100% depending upon the gene. To improve the detection of virulence-associated genes in aeromonads, we have designed new primer pairs for aerA/act, ser, lafA, ascFG and ascV, which showed excellent diagnostic sensitivity and specificity. Altogether, the analysis of high quality genomic data, which are more and more easy to obtain, provides significant improvements in the genetic detection of virulence factors in bacterial strains.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Laboratoire de Bactériologie, Hôpitaux universitaires de Strasbourg, Strasbourg, France
- * E-mail: (BL); (ETR)
| | - Fadua Latif-Eugenín
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Roxana Beaz-Hidalgo
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Sophie Colston
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Maria-Jose Figueras
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Département d’Hygiène Hospitalière, CHRU de Montpellier, Montpellier, France
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Département de Bactériologie, CHU de Nice, Nice, France
- * E-mail: (BL); (ETR)
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Navarro A, Martínez-Murcia A. Phylogenetic analyses of the genusAeromonasbased on housekeeping gene sequencing and its influence on systematics. J Appl Microbiol 2018; 125:622-631. [DOI: 10.1111/jam.13887] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/14/2018] [Accepted: 04/11/2018] [Indexed: 11/27/2022]
Affiliation(s)
- A. Navarro
- Genetic Analysis Strategies S.L.; CEEI; Elche, Alicante Spain
| | - A. Martínez-Murcia
- Genetic Analysis Strategies S.L.; CEEI; Elche, Alicante Spain
- Area de Microbiología; EPSO; Universidad Miguel Hernández; Orihuela, Alicante Spain
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van Zwetselaar M, Nyombi B, Sonda T, Kumburu H, Chamba N, Dekker MCJ, Kilonzo KG, Urasa SJ, Mmbaga BT. Aeromonas caviae mimicking Vibrio cholerae infectious enteropathy in a cholera-endemic region with possible public health consequences: two case reports. J Med Case Rep 2018; 12:71. [PMID: 29548295 PMCID: PMC5857081 DOI: 10.1186/s13256-018-1603-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/02/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aeromonas species have been documented to yield false positive results in microbiological tests for Vibrio cholerae. They share many biochemical properties with Vibrio species, with which they were jointly classified in the family Vibrionaceae until genotypic information provided new insights. Aeromonas species are increasingly associated with gastrointestinal infections, albeit with great apparent variation in pathogenicity and virulence both between and within species of the genus. We report two cases with clinically mild cholera-like symptoms, at a time when a cholera outbreak was unfolding in other regions of the country (Tanzania). These are the first cases to be reported with Aeromonas mimicking cholera in our area. CASE PRESENTATION Two patients were admitted at the isolation unit designated by the Kilimanjaro Christian Medical Centre for emerging infectious diseases and provided informed consent about regular stool analysis and culture under the provisional diagnosis of gastroenteritis. The first patient was a 23-year-old black African woman with a 2-day history of watery diarrhea and vomiting associated with a temperature of 39.7 °C. The second patient was a 47-year-old black African woman with a 2-day history of diarrhea and vomiting with a temperature of 37.7 °C, and she was hemodynamically stable. Both patients were isolated in a specific area for infection control and treated with fluids and orally administered rehydration solution, ciprofloxacin, metronidazole, and paracetamol. Stool culture was done. The isolated colonies were reported as V. cholerae and transferred to the research laboratory of Kilimanjaro Clinical Research Institute for confirmation using whole genome sequencing. Microbiological testing determined colonies isolated from stool to be V. cholerae, and warranted the conclusion "presumptive cholera." Whole genome sequencing, however, established the presence of Aeromonas caviae rather than V. cholerae. CONCLUSIONS The co-existence of Aeromonas species with V. cholerae in cholera-endemic regions suggests the possibility that a proportion of suspected cholera cases may be Aeromonas infections. However, with close to no epidemiological data available on Aeromonas infection in cases of diarrhea and dysentery in Sub-Saharan Africa, it is not currently possible to establish the extent of misdiagnosis to any degree of certainty. Whole genome sequencing was shown to readily exclude V. cholerae as the etiological agent and establish the presence of Aeromonas species.
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Affiliation(s)
- Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania
| | - Balthazar Nyombi
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Nyasatu Chamba
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania
| | - Marieke C. J. Dekker
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania
| | - Kajiru G. Kilonzo
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Sarah J. Urasa
- 0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 072Xgrid.415218.bKilimanjaro Christian Medical Centre, Moshi, Kilimanjaro United Republic of Tanzania ,0000 0004 0648 0439grid.412898.eKilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania
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Tong W, Li X, Huo Y, Zhang L, Cao Y, Wang E, Chen W, Tao S, Wei G. Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris. Syst Appl Microbiol 2018; 41:300-310. [PMID: 29576402 DOI: 10.1016/j.syapm.2018.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA. The bean rhizobia were found in 16 defined species and nine putative novel species; in addition, 35 strains previously described as Rhizobium etli, Rhizobium phaseoli, Rhizobium vallis, Rhizobium gallicum, Rhizobium leguminosarum and Rhizobium spp. should be renamed. The phylogenetic patterns of symbiotic genes nodC and nifH were highly host-specific and inconsistent with the genomic phylogeny. Multiple symbiovars (sv.) within the Rhizobium species were found as a common feature: sv. phaseoli, sv. trifolii and sv. viciae in Rhizobium anhuiense; sv. phaseoli and sv. mimosae in Rhizobium sophoriradicis/R. etli/Rhizobium sp. III; sv. phaseoli and sv. trifolii in Rhizobium hidalgonense/Rhizobium acidisoli; sv. phaseoli and sv. viciae in R. leguminosarum/Rhizobium sp. IX; sv. trifolii and sv. viciae in Rhizobium laguerreae. Thus, genomic comparison revealed great species diversity in bean rhizobia, corrected the species definition of some previously misnamed strains, and demonstrated the MLSA a valuable and simple method for defining Rhizobium species.
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Affiliation(s)
- Wenjun Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunyun Huo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Talagrand-Reboul E, Roger F, Kimper JL, Colston SM, Graf J, Latif-Eugenín F, Figueras MJ, Petit F, Marchandin H, Jumas-Bilak E, Lamy B. Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case. Front Microbiol 2017; 8:621. [PMID: 28458658 PMCID: PMC5394120 DOI: 10.3389/fmicb.2017.00621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/27/2017] [Indexed: 11/13/2022] Open
Abstract
Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and isDDH (in silico DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species Aeromonas media and Aeromonas rivipollensis. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside A. media species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the A. media complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département d'Hygiène Hospitalière, CHRU de MontpellierMontpellier, France
| | - Frédéric Roger
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France
| | - Jean-Luc Kimper
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France
| | - Sophie M Colston
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Fadua Latif-Eugenín
- Unidad de Microbiologia, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i VirgiliReus, Spain
| | - Maria José Figueras
- Unidad de Microbiologia, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i VirgiliReus, Spain
| | - Fabienne Petit
- Normandie Univ, UNIROUEN, UNICAEN, Centre National de la Recherche Scientifique, M2CRouen, France.,Sorbonne Universités, UPMC, Centre National de la Recherche Scientifique, EPHE, UMR 7619 METISParis, France
| | - Hélène Marchandin
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département de Bactériologie, CHRU de MontpellierMontpellier, France
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département d'Hygiène Hospitalière, CHRU de MontpellierMontpellier, France
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France.,Département de Bactériologie, CHU de NiceNice, France
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11
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Talagrand-Reboul E, Jumas-Bilak E, Lamy B. The Social Life of Aeromonas through Biofilm and Quorum Sensing Systems. Front Microbiol 2017; 8:37. [PMID: 28163702 PMCID: PMC5247445 DOI: 10.3389/fmicb.2017.00037] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/06/2017] [Indexed: 01/25/2023] Open
Abstract
Bacteria of the genus Aeromonas display multicellular behaviors herein referred to as “social life”. Since the 1990s, interest has grown in cell-to-cell communication through quorum sensing signals and biofilm formation. As they are interconnected, these two self-organizing systems deserve to be considered together for a fresh perspective on the natural history and lifestyles of aeromonads. In this review, we focus on the multicellular behaviors of Aeromonas, i.e., its social life. First, we review and discuss the available knowledge at the molecular and cellular levels for biofilm and quorum sensing. We then discuss the complex, subtle, and nested interconnections between the two systems. Finally, we focus on the aeromonad multicellular coordinated behaviors involved in heterotrophy and virulence that represent technological opportunities and applied research challenges.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France; Département d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire (CHRU) de MontpellierMontpellier, France
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France; Département d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire (CHRU) de MontpellierMontpellier, France
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de MontpellierMontpellier, France; Département de Bactériologie, Centre Hospitalier Universitaire (CHU) de NiceNice, France
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12
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Chen PL, Lamy B, Ko WC. Aeromonas dhakensis, an Increasingly Recognized Human Pathogen. Front Microbiol 2016; 7:793. [PMID: 27303382 PMCID: PMC4882333 DOI: 10.3389/fmicb.2016.00793] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/11/2016] [Indexed: 12/18/2022] Open
Abstract
Aeromonas dhakensis was first isolated from children with diarrhea in Dhaka, Bangladesh and described in 2002. In the past decade, increasing evidence indicate this species is widely distributed in the environment and can cause a variety of infections both in human and animals, especially in coastal areas. A. dhakensis is often misidentified as A. hydrophila, A. veronii, or A. caviae by commercial phenotypic tests in the clinical laboratory. Correct identification relies on molecular methods. Increasingly used matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) may be able to identify Aeromonas specie rapidly and accurately. A. dhakensis has shown its potent virulence in different animal models and clinical infections. Although several virulence factors had been reported, no single mechanism is conclusive. Characteristically A. dhakensis is the principal species causing soft tissue infection and bacteremia, especially among patients with liver cirrhosis or malignancy. Of note, A. dhakensis bacteremia is more lethal than bacteremia due to other Aeromonas species. The role of this species in gastroenteritis remains controversial. Third generation cephalosporins and carbapenems should be used cautiously in the treatment of severe A. dhakensis infection due to the presence of AmpC ββ-lactamase and metallo-β-lactamase genes, and optimal regimens may be cefepime or fluoroquinolones. Studies of bacterial virulence factors and associated host responses may provide the chance to understand the heterogeneous virulence between species. The hypothesis A. dhakensis with varied geographic prevalence and enhanced virulence that compared to other Aeromonas species warrants more investigations.
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Affiliation(s)
- Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainan, Taiwan; Center for Infection Control, National Cheng Kung University HospitalTainan, Taiwan
| | - Brigitte Lamy
- Laboratoire de Bactériologie-Virologie, Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HydroSciences Montpellier, Université de MontpellierMontpellier, France; Laboratoire de Bactériologie, Centre Hospitalier Régional Universitaire de MontpellierMontpellier, France
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainan, Taiwan; Center for Infection Control, National Cheng Kung University HospitalTainan, Taiwan
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13
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Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L, Shao Z. Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 2015; 5:14082. [PMID: 26373441 PMCID: PMC4571650 DOI: 10.1038/srep14082] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 08/17/2015] [Indexed: 02/01/2023] Open
Abstract
The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments.
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraβe 7B, 38124, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraβe 7B, 38124, Braunschweig, Germany
| | - Meng Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Yamin Sun
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
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14
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Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 2014; 5:e02136. [PMID: 25406383 PMCID: PMC4251997 DOI: 10.1128/mbio.02136-14] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Prokaryotic taxonomy is the underpinning of microbiology, as it provides a framework for the proper identification and naming of organisms. The “gold standard” of bacterial species delineation is the overall genome similarity determined by DNA-DNA hybridization (DDH), a technically rigorous yet sometimes variable method that may produce inconsistent results. Improvements in next-generation sequencing have resulted in an upsurge of bacterial genome sequences and bioinformatic tools that compare genomic data, such as average nucleotide identity (ANI), correlation of tetranucleotide frequencies, and the genome-to-genome distance calculator, or in silico DDH (isDDH). Here, we evaluate ANI and isDDH in combination with phylogenetic studies using Aeromonas, a taxonomically challenging genus with many described species and several strains that were reassigned to different species as a test case. We generated improved, high-quality draft genome sequences for 33 Aeromonas strains and combined them with 23 publicly available genomes. ANI and isDDH distances were determined and compared to phylogenies from multilocus sequence analysis of housekeeping genes, ribosomal proteins, and expanded core genes. The expanded core phylogenetic analysis suggested relationships between distant Aeromonas clades that were inconsistent with studies using fewer genes. ANI values of ≥96% and isDDH values of ≥70% consistently grouped genomes originating from strains of the same species together. Our study confirmed known misidentifications, validated the recent revisions in the nomenclature, and revealed that a number of genomes deposited in GenBank are misnamed. In addition, two strains were identified that may represent novel Aeromonas species. Improvements in DNA sequencing technologies have resulted in the ability to generate large numbers of high-quality draft genomes and led to a dramatic increase in the number of publically available genomes. This has allowed researchers to characterize microorganisms using genome data. Advantages of genome sequence-based classification include data and computing programs that can be readily shared, facilitating the standardization of taxonomic methodology and resolving conflicting identifications by providing greater uniformity in an overall analysis. Using Aeromonas as a test case, we compared and validated different approaches. Based on our analyses, we recommend cutoff values for distance measures for identifying species. Accurate species classification is critical not only to obviate the perpetuation of errors in public databases but also to ensure the validity of inferences made on the relationships among species within a genus and proper identification in clinical and veterinary diagnostic laboratories.
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15
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Aravena-Román M, Beaz-Hidalgo R, Inglis TJJ, Riley TV, Martínez-Murcia AJ, Chang BJ, Figueras MJ. Aeromonas australiensis sp. nov., isolated from irrigation water. Int J Syst Evol Microbiol 2013; 63:2270-2276. [DOI: 10.1099/ijs.0.040162-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, facultatively anaerobic bacillus, designated strain 266T, was isolated from an irrigation water system in the south-west of Western Australia. Analysis of the 16S rRNA gene sequence confirmed that strain 266T belonged to the genus
Aeromonas
, with the nearest species being
Aeromonas fluvialis
(99.6 % similarity to the type strain, with 6 nucleotide differences) followed by
Aeromonas veronii
and
Aeromonas allosaccharophila
(both 99.5 %). Analysis of gyrB and rpoD sequences suggested that strain 266T formed a phylogenetic line independent of other species in the genus. This was confirmed using the concatenated sequences of six housekeeping genes (gyrB, rpoD, recA, dnaJ, gyrA and dnaX) that also indicated that
A. veronii
and
A. allosaccharophila
were the nearest relatives. DNA–DNA reassociation experiments and phenotypic analysis further supported the conclusion that strain 266T represents a novel species, for which the name Aeromonas australiensis sp. nov. is proposed, with type strain 266T ( = CECT 8023T = LMG 2670T).
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Affiliation(s)
- Max Aravena-Román
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Nedlands, WA, Australia
- School of Pathology and Laboratory Medicine, the University of Western Australia, Crawley, WA, Australia
| | - Roxana Beaz-Hidalgo
- Unitat de Microbiologia, Department de Ciènces Mèdiques Básiques, Facultat de Medicina i Ciènces de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Timothy J. J. Inglis
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Nedlands, WA, Australia
- School of Pathology and Laboratory Medicine, the University of Western Australia, Crawley, WA, Australia
| | - Thomas V. Riley
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Nedlands, WA, Australia
- School of Pathology and Laboratory Medicine, the University of Western Australia, Crawley, WA, Australia
| | - Antonio J. Martínez-Murcia
- Departamento de Producción Vegetal y Microbiología, EPSO, Universidad Miguel Hernández, Orihuela 03312 (Alicante), Spain
| | - Barbara J. Chang
- School of Pathology and Laboratory Medicine, the University of Western Australia, Crawley, WA, Australia
| | - Maria Jose Figueras
- Unitat de Microbiologia, Department de Ciènces Mèdiques Básiques, Facultat de Medicina i Ciènces de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
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16
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de Morais OO, Gomes CM. Reply: is it really Aeromonas hydrophila? Infection 2012; 41:281. [PMID: 23135799 DOI: 10.1007/s15010-012-0365-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 10/30/2012] [Indexed: 11/27/2022]
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