1
|
Valdivia-Carrera CA, Ho-Palma AC, Munguia-Mercado A, Gonzalez-Pizarro K, Ibacache-Quiroga C, Dinamarca A, Stehlík M, Rusiñol M, Girones R, Lopez-Urbina MT, Basaldua Galarza A, Gonzales-Gustavson E. Surveillance of SARS-CoV-2, rotavirus, norovirus genogroup II, and human adenovirus in wastewater as an epidemiological tool to anticipate outbreaks of COVID-19 and acute gastroenteritis in a city without a wastewater treatment plant in the Peruvian Highlands. Sci Total Environ 2023; 905:167161. [PMID: 37730068 DOI: 10.1016/j.scitotenv.2023.167161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated that Wastewater Based Epidemiology is a fast and economical alternative for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the community level in high-income countries. In the present study, wastewater from a city in the Peruvian Highlands, which lacks a wastewater treatment plant, was monitored for one year to assess the relationship between the concentration of SARS-CoV-2 and the reported cases of COVID-19 in the community. Additionally, we compared the relationship between rotavirus (RV), norovirus genogroup II (NoV GGII), and human adenovirus (HAdV) with the number of reported cases of acute gastroenteritis. Before commencing the analysis of the samples, the viral recovery efficacy of three processing methods was determined in spiked wastewater with SARS-CoV-2. This evaluation demonstrated the highest recovery rate with direct analysis (72.2 %), as compared to ultrafiltration (50.8 %) and skimmed milk flocculation (5.6 %). Wastewater monitoring revealed that 72 % (36/50) of the samples tested positive for SARS-CoV-2, with direct analysis yielding the highest detection frequency and quantification of SARS-CoV-2. Furthermore, a strong correlation was observed between the concentration of SARS-CoV-2 in wastewater and the reported cases of COVID-19, mainly when we shift the concentration of SARS-CoV-2 by two weeks, which allows us to anticipate the onset of the fourth and fifth waves of the pandemic in Peru up to two weeks in advance. All samples processed using the skimmed milk flocculation method tested positive and showed high concentrations of RV, NoV GGII, and HAdV. In fact, the highest RV concentrations were detected up to four weeks before outbreaks of acute gastroenteritis reported in children under four years of age. In conclusion, the results of this study suggest that periodic wastewater monitoring is an excellent epidemiological tool for surveillance and can anticipate outbreaks of infectious diseases, such as COVID-19, in low- and middle-income countries.
Collapse
Affiliation(s)
- Cesar A Valdivia-Carrera
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru; Department of Animal Health and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| | - Ana C Ho-Palma
- Department of Human Medicine, School of Human Medicine, Universidad Nacional del Centro del Peru, Av. Mariscal Castilla 3909, Huancayo, Peru.
| | - Astrid Munguia-Mercado
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru.
| | - Karoll Gonzalez-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Claudia Ibacache-Quiroga
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile; Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Alejandro Dinamarca
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile; Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Milan Stehlík
- Institute of Statistics, Universidad de Valparaiso, Av. Gran Bretana 1111, Valparaiso, Chile; Linz Institute of Technology & Department of Applied Statistics, Johannes Kepler University in Linz, Altenberger Straße 69, 4040 Linz, Austria.
| | - Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Maria T Lopez-Urbina
- Laboratory of Veterinary Epidemiology and Economics, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| | - Anani Basaldua Galarza
- Department of Human Medicine, School of Human Medicine, Universidad Nacional del Centro del Peru, Av. Mariscal Castilla 3909, Huancayo, Peru; Dirección Ejecutiva de Epidemiología, Dirección Regional de Salud, Jr. Julio Cesar Tello 488, Huancayo 12004, Junin, Peru.
| | - Eloy Gonzales-Gustavson
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru; Department of Animal Health and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| |
Collapse
|
2
|
Contreras MJ, Leal K, Bruna P, Nuñez-Montero K, Goméz-Espinoza O, Santos A, Bravo L, Valenzuela B, Solis F, Gahona G, Cayo M, Dinamarca MA, Ibacache-Quiroga C, Zamorano P, Barrientos L. Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities. Front Microbiol 2023; 14:1197399. [PMID: 37538842 PMCID: PMC10395097 DOI: 10.3389/fmicb.2023.1197399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023] Open
Abstract
Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.
Collapse
Affiliation(s)
- María José Contreras
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Karla Leal
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Pablo Bruna
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Kattia Nuñez-Montero
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
- Biotechnology Research Center, Instituto Tecnológico de Costa Rica, Cártago, Costa Rica
| | - Olman Goméz-Espinoza
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Andrés Santos
- Universitat Autònoma de Barcelona, Departament de Genètica i de Microbiologia, Institut Biotecnologia i de Biomedicina, Cerdanyola del Vallès, Barcelona, Spain
| | - León Bravo
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisco Solis
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Giovanni Gahona
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Mayra Cayo
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Leticia Barrientos
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
| |
Collapse
|
3
|
Ibacache-Quiroga C, González-Pizarro K, Charifeh M, Canales C, Díaz-Viciedo R, Schmachtenberg O, Dinamarca MA. Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods 2022; 11:foods11070900. [PMID: 35406987 PMCID: PMC8997647 DOI: 10.3390/foods11070900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.
Collapse
Affiliation(s)
- Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
| | - Karoll González-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Mariam Charifeh
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Christian Canales
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción 4080871, Chile;
| | - Rodrigo Díaz-Viciedo
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
| | - Oliver Schmachtenberg
- Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2360102, Chile;
- Centro Interdisciplinario de Neurociencias (CINV), Universidad de Valparaíso, Valparaíso 2381850, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
| |
Collapse
|
4
|
Julio-Pieper M, López-Aguilera A, Eyzaguirre-Velásquez J, Olavarría-Ramírez L, Ibacache-Quiroga C, Bravo JA, Cruz G. Gut Susceptibility to Viral Invasion: Contributing Roles of Diet, Microbiota and Enteric Nervous System to Mucosal Barrier Preservation. Int J Mol Sci 2021; 22:ijms22094734. [PMID: 33946994 PMCID: PMC8125429 DOI: 10.3390/ijms22094734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/08/2023] Open
Abstract
The gastrointestinal lumen is a rich source of eukaryotic and prokaryotic viruses which, together with bacteria, fungi and other microorganisms comprise the gut microbiota. Pathogenic viruses inhabiting this niche have the potential to induce local as well as systemic complications; among them, the viral ability to disrupt the mucosal barrier is one mechanism associated with the promotion of diarrhea and tissue invasion. This review gathers recent evidence showing the contributing effects of diet, gut microbiota and the enteric nervous system to either support or impair the mucosal barrier in the context of viral attack.
Collapse
Affiliation(s)
- Marcela Julio-Pieper
- Grupo de NeuroGastroBioquímica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (A.L.-A.); (J.E.-V.); (J.A.B.)
- Correspondence:
| | - Alejandra López-Aguilera
- Grupo de NeuroGastroBioquímica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (A.L.-A.); (J.E.-V.); (J.A.B.)
| | - Johana Eyzaguirre-Velásquez
- Grupo de NeuroGastroBioquímica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (A.L.-A.); (J.E.-V.); (J.A.B.)
| | | | - Claudia Ibacache-Quiroga
- Centro de Micro-Bioinnovación (CMBi), Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2340000, Chile;
| | - Javier A. Bravo
- Grupo de NeuroGastroBioquímica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile; (A.L.-A.); (J.E.-V.); (J.A.B.)
| | - Gonzalo Cruz
- Centro de Neurobiología y Fisiopatología Integrativa (CENFI), Instituto de Fisiología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2340000, Chile;
| |
Collapse
|
5
|
Rojas F, Ibacache-Quiroga C. A forecast model for prevention of foodborne outbreaks of non-typhoidal salmonellosis. PeerJ 2020; 8:e10009. [PMID: 33240587 PMCID: PMC7664469 DOI: 10.7717/peerj.10009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/31/2020] [Indexed: 11/20/2022] Open
Abstract
Background This work presents a forecast model for non-typhoidal salmonellosis outbreaks. Method This forecast model is based on fitted values of multivariate regression time series that consider diagnosis and estimation of different parameters, through a very flexible statistical treatment called generalized auto-regressive and moving average models (GSARIMA). Results The forecast model was validated by analyzing the cases of Salmonella enterica serovar Enteritidis in Sydney Australia (2014–2016), the environmental conditions and the consumption of high-risk food as predictive variables. Conclusions The prediction of cases of Salmonella enterica serovar Enteritidis infections are included in a forecast model based on fitted values of time series modeled by GSARIMA, for an early alert of future outbreaks caused by this pathogen, and associated to high-risk food. In this context, the decision makers in the epidemiology field can led to preventive actions using the proposed model.
Collapse
Affiliation(s)
- Fernando Rojas
- Centro de Micro-Bio Innovación, Universidad de Valparaíso, Valparaíso, Chile.,Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | - Claudia Ibacache-Quiroga
- Centro de Micro-Bio Innovación, Universidad de Valparaíso, Valparaíso, Chile.,Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| |
Collapse
|
6
|
González D, Huber KJ, Tindall B, Hedrich S, Rojas-Villalobos C, Quatrini R, Dinamarca MA, Ibacache-Quiroga C, Schwarz A, Canales C, Nancucheo I. Acidiferrimicrobium australe gen. nov., sp. nov., an acidophilic and obligately heterotrophic, member of the Actinobacteria that catalyses dissimilatory oxido-reduction of iron isolated from metal-rich acidic water in Chile. Int J Syst Evol Microbiol 2020; 70:3348-3354. [PMID: 32375942 DOI: 10.1099/ijsem.0.004179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel acidophilic member of the phylum Actinobacteria was isolated from an acidic, metal-contaminated stream draining from an abandoned underground coal mine (Trongol mine), situated close to Curanilahue, Biobío Region, Chile. The isolate (USS-CCA1T) was demonstrated to be a heterotroph that catalysed under aerobic conditions the oxidation of ferrous iron and the reduction of ferric iron under anaerobic conditions, but not the oxidation of sulfur nor hydrogen. USS-CCA1T is a Gram-positive, motile, short rod-shaped, mesophilic bacterium with a temperature growth optimum at 30 °C (range 20-39 °C). It was categorized as an extreme acidophile growing between 1.7 and 4.5 and optimally at pH 3.0. The G+C content of the chromosomal DNA of the isolate was 74.1 mol%, which is highly related to Aciditerrimonas ferrireducens IC-180T , (the most closely related genus; 94.4 % 16S rRNA gene identity), and higher than other acidophilic actinobacteria. The isolate (USS-CCA1T) was shown to form a distinct 16S rRNA clade from characterized acidophilic actinobacteria, well separated from the genera Acidimicrobium, Ferrimicrobium, Ferrithrix, 'Acidithrix' and Aciditerrimonas. Genomic indexes (ANIb, DDH, AAI, POCP) derived from the USS-CCA1T draft genome sequence (deposited at DDBJ/ENA/GenBank under the accession WJHE00000000) support assignment of the isolate to a new species and a new genus within the Acidimicrobiaceae family. Isolate USS-CCA1T is the designated type strain of the novel species Acidiferrimicrobium australe (=DSM 106828T,=RGM 2506T).
Collapse
Affiliation(s)
- Daniella González
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| | - Katharina J Huber
- Leibniz Institute DSMZ-German Collection of Microorganism and Cell Culture GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Brian Tindall
- Leibniz Institute DSMZ-German Collection of Microorganism and Cell Culture GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Sabrina Hedrich
- Federal Institute for Geosciences and Natural Resources, Resource Geochemistry, Stilleweg 2, 30655 Hannover, Germany
| | - Camila Rojas-Villalobos
- Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
- Fundación Ciencia y Vida, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Santiago, Chile
- Universidad San Sebastián, Santiago, Chile
- Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - M Alejandro Dinamarca
- Centro de Micro-Bioinnovación (CMBi), Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | - Claudia Ibacache-Quiroga
- Centro de Micro-Bioinnovación (CMBi), Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | - Alex Schwarz
- Departamento de Ingeniería Civil y Centro de Recursos Hídricos para el Agua y la Minería (CRHIAM), Universidad de Concepción, Chile
| | - Christian Canales
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| | - Ivan Nancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| |
Collapse
|
7
|
Elabed H, González-Tortuero E, Ibacache-Quiroga C, Bakhrouf A, Johnston P, Gaddour K, Blázquez J, Rodríguez-Rojas A. Seawater salt-trapped Pseudomonas aeruginosa survives for years and gets primed for salinity tolerance. BMC Microbiol 2019; 19:142. [PMID: 31234794 PMCID: PMC6591848 DOI: 10.1186/s12866-019-1499-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Background In nature, microorganisms have to adapt to long-term stressful conditions often with growth limitations. However, little is known about the evolution of the adaptability of new bacteria to such environments. Pseudomonas aeruginosa, an opportunistic pathogen, after natural evaporation of seawater, was shown to be trapped in laboratory-grown halite crystals and to remain viable after entrapment for years. However, how this bacterium persists and survives in such hypersaline conditions is not understood. Results In this study, we aimed to understand the basis of survival, and to characterise the physiological changes required to develop salt tolerance using P. aeruginosa as a model. Several clones of P. aeruginosa were rescued after 14 years in naturally evaporated marine salt crystals. Incubation of samples in nutrient-rich broth allowed re-growth and subsequent plating yielded observable colonies. Whole genome sequencing of the P. aeruginosa isolates confirmed the recovery of the original strain. The re-grown strains, however, showed a new phenotype consisting of an enhanced growth in growing salt concentration compared to the ancestor strain. The intracellular accumulation of K+ was elicited by high concentration of Na+ in the external medium to maintain the homeostasis. Whole transcriptomic analysis by microarray indicated that 78 genes had differential expression between the parental strain and its derivative clones. Sixty-one transcripts were up-regulated, while 17 were down-regulated. Based on a collection of single-gene knockout mutants and gene ontology analysis, we suggest that the adaptive response in P. aeruginosa to hyper-salinity relies on multiple gene product interactions. Conclusions The individual gene contributions build up the observed phenotype, but do not ease the identification of salinity-related metabolic pathways. The long-term inclusion of P. aeruginosa in salt crystals primes the bacteria, mediating a readjustment of the bacterial physiology to growth in higher salt concentrations. Our findings provide a starting point to understand how P. aeruginosa, a relevant environmental and pathogenic bacterium, survives to long-term salt stress. Electronic supplementary material The online version of this article (10.1186/s12866-019-1499-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hamouda Elabed
- Laboratory of Contagious Diseases and Biologically Active Substances LR99-ES27 Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.,Department of Microbial Biotechnology, Spanish National Center for Biotechnology (CNB), Madrid, Spain
| | - Enrique González-Tortuero
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Ibacache-Quiroga
- Department of Microbial Biotechnology, Spanish National Center for Biotechnology (CNB), Madrid, Spain.,Centro de Micro-Bioinnovación, Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | - Amina Bakhrouf
- Laboratory of Analysis, Treatment and Valorization of Environmental Polluants and products, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Paul Johnston
- Institute of Biology, FreieUniversität Berlin, Berlin, Germany
| | - Kamel Gaddour
- Laboratory of Analysis, Treatment and Valorization of Environmental Polluants and products, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Jesús Blázquez
- Department of Microbial Biotechnology, Spanish National Center for Biotechnology (CNB), Madrid, Spain
| | | |
Collapse
|
8
|
Ibacache-Quiroga C, Oliveros JC, Couce A, Blázquez J. Parallel Evolution of High-Level Aminoglycoside Resistance in Escherichia coli Under Low and High Mutation Supply Rates. Front Microbiol 2018; 9:427. [PMID: 29615988 PMCID: PMC5867336 DOI: 10.3389/fmicb.2018.00427] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/22/2018] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance is a major concern in public health worldwide, thus there is much interest in characterizing the mutational pathways through which susceptible bacteria evolve resistance. Here we use experimental evolution to explore the mutational pathways toward aminoglycoside resistance, using gentamicin as a model, under low and high mutation supply rates. Our results show that both normo and hypermutable strains of Escherichia coli are able to develop resistance to drug dosages > 1,000-fold higher than the minimal inhibitory concentration for their ancestors. Interestingly, such level of resistance was often associated with changes in susceptibility to other antibiotics, most prominently with increased resistance to fosfomycin. Whole-genome sequencing revealed that all resistant derivatives presented diverse mutations in five common genetic elements: fhuA, fusA and the atpIBEFHAGDC, cyoABCDE, and potABCD operons. Despite the large number of mutations acquired, hypermutable strains did not pay, apparently, fitness cost. In contrast to recent studies, we found that the mutation supply rate mainly affected the speed (tempo) but not the pattern (mode) of evolution: both backgrounds acquired the mutations in the same order, although the hypermutator strain did it faster. This observation is compatible with the adaptive landscape for high-level gentamicin resistance being relatively smooth, with few local maxima; which might be a common feature among antibiotics for which resistance involves multiple loci.
Collapse
Affiliation(s)
- Claudia Ibacache-Quiroga
- Centro Nacional de Biotecnología, Madrid, Spain.,Centro de Micro-Bioinnovación, Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | | | - Alejandro Couce
- Unité Mixte de Recherche 1137, Infection, Antimicrobiens, Modélisation, Evolution, INSERM, Université Paris Diderot, Paris, France
| | - Jesus Blázquez
- Centro Nacional de Biotecnología, Madrid, Spain.,Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| |
Collapse
|
9
|
Genovese F, Lazzari S, Venturi E, Costantino L, Blazquez J, Ibacache-Quiroga C, Costi MP, Tondi D. Design, synthesis and biological evaluation of non-covalent AmpC β-lactamases inhibitors. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1809-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
10
|
Ibacache-Quiroga C, Dinamarca MA, Ojeda J, Troncoso JM. A Salmo salar diet based on a marine biosurfactant for the profilaxis and treatment of Pisciricketsia salmonis. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
11
|
Dinamarca MA, Romo N, Ibacache-Quiroga C. Biosurfactant produced by marine bacteria interacts with diffusible pyoverdine produced by Pseudomonas aeruginosa. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
12
|
Ibacache-Quiroga C, Ojeda J, Espinoza-Vergara G, Olivero P, Cuellar M, Dinamarca MA. The hydrocarbon-degrading marine bacterium Cobetia sp. strain MM1IDA2H-1 produces a biosurfactant that interferes with quorum sensing of fish pathogens by signal hijacking. Microb Biotechnol 2013; 6:394-405. [PMID: 23279885 PMCID: PMC3917474 DOI: 10.1111/1751-7915.12016] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/12/2012] [Accepted: 11/14/2012] [Indexed: 11/27/2022] Open
Abstract
Biosurfactants are produced by hydrocarbon-degrading marine bacteria in response to the presence of water-insoluble hydrocarbons. This is believed to facilitate the uptake of hydrocarbons by bacteria. However, these diffusible amphiphilic surface-active molecules are involved in several other biological functions such as microbial competition and intra-or inter-species communication. We report the isolation and characterization of a marine bacterial strain identified as Cobetia sp. MM1IDA2H-1, which can grow using the sulfur-containing heterocyclic aromatic hydrocarbon dibenzothiophene (DBT). As with DBT, when the isolated strain is grown in the presence of a microbial competitor, it produces a biosurfactant. Because the obtained biosurfactant was formed by hydroxy fatty acids and extracellular lipidic structures were observed during bacterial growth, we investigated whether the biosurfactant at its critical micelle concentration can interfere with bacterial communication systems such as quorum sensing. We focused on Aeromonas salmonicida subsp. salmonicida, a fish pathogen whose virulence relies on quorum sensing signals. Using biosensors for quorum sensing based on Chromobacterium violaceum and Vibrio anguillarum, we showed that when the purified biosurfactant was mixed with N-acyl homoserine lactones produced by A. salmonicida, quorum sensing was inhibited, although bacterial growth was not affected. In addition, the transcriptional activities of A. salmonicida virulence genes that are controlled by quorum sensing were repressed by both the purified biosurfactant and the growth in the presence of Cobetia sp. MM1IDA2H-1. We propose that the biosurfactant, or the lipid structures interact with the N-acyl homoserine lactones, inhibiting their function. This could be used as a strategy to interfere with the quorum sensing systems of bacterial fish pathogens, which represents an attractive alternative to classical antimicrobial therapies in fish aquaculture.
Collapse
Affiliation(s)
- C Ibacache-Quiroga
- Laboratorio de Biotecnología Microbiana, Universidad de Valparaíso, Valparaíso, Chile
| | | | | | | | | | | |
Collapse
|
13
|
Dinamarca MA, Ibacache-Quiroga C, Baeza P, Galvez S, Villarroel M, Olivero P, Ojeda J. Biodesulfurization of gas oil using inorganic supports biomodified with metabolically active cells immobilized by adsorption. Bioresour Technol 2010; 101:2375-8. [PMID: 20034786 DOI: 10.1016/j.biortech.2009.11.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 11/18/2009] [Accepted: 11/19/2009] [Indexed: 05/23/2023]
Abstract
The immobilization of Pseudomonas stutzeri using adsorption on different inorganic supports was studied in relation to the number of adsorbed cells, metabolic activity and biodesulfurization (BDS). The electrophoretic migration (EM) measurements and Tetrazolioum (TTC) method were used to evaluate adsorption and metabolic activity. Results indicate that maximal immobilization was obtained with an initial load of 14 x 10(8) cells mL(-1) for Al and Sep, whereas Ti requires 20 x 10(8) cells mL(-1). The highest interaction was observed in the P. stutzeri/Si and P. stutzeri/Sep biocatalysts. The IEP values and metabolic activities indicate that P. stutzeri change the surface of supports and maintains metabolic activity. A direct relation between BDS activity and the adsorption capacity of the bacterial cells was observed at the adsorption/desorption equilibrium level. The biomodification of inorganic supports by the adsorption process increases the bioavailability of sulphur substrates for bacterial cells, improving BDS activity.
Collapse
Affiliation(s)
- M Alejandro Dinamarca
- Laboratorio de Biotecnología Microbiana, Facultad de Farmacia, Universidad de Valparaíso, Casilla 5001, Valparaíso, Chile
| | | | | | | | | | | | | |
Collapse
|