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  1. Article ; Online: Pseudomonas aeruginosa strains isolated from animal with high virulence genes content and highly sensitive to antimicrobials.

    Morales-Espinosa, Rosario / Delgado, Gabriela / Espinosa-Camacho, Fernando / Flores-Alanis, Alejandro / Rodriguez, Cristina / Mendez, Jose L / Gonzalez-Pedraza, Alberto / Cravioto, Alejandro

    Journal of global antimicrobial resistance

    2024  Volume 37, Page(s) 75–80

    Abstract: Objectives: P. aeruginosa is one of the most metabolically versatile bacteria having the ability to survive in multiple environments through its accessory genome. An important hallmark of P. aeruginosa is the high level of antibiotic resistance, which ... ...

    Abstract Objectives: P. aeruginosa is one of the most metabolically versatile bacteria having the ability to survive in multiple environments through its accessory genome. An important hallmark of P. aeruginosa is the high level of antibiotic resistance, which often makes eradication difficult and sometimes impossible. Evolutionary forces have led to this bacterium to develop high antimicrobial resistance with a variety of elements contributing to both intrinsic and acquired resistance. The objectives were to genetically and phenotypically characterizer P. aeruginosa strains isolated from companion animals of different species.
    Methods: We characterized a collection of 39 P. aeruginosa strains isolated from infected animals. The genetic characterization was in relation to chromosomal profile by PFGE; content of virulence gene; presence of genomic islands (GIs); genes of the cytotoxins exported by T3SS: exoU, exoS, exoT and exoY; and type IV pili allele. The phenotypic characterization was based on patterns of susceptibility to different antimicrobials.
    Results: Each strain had a PFGE profile, a high virulence genes content, and a large accessory genome. However, most of the strains presented high sensitivity to almost all antimicrobials tested, showing no acquired resistance (no β-lactamases). The exception to this lack of resistance was seen with penicillin.
    Conclusions: P. aeruginosa could be a naturally sensitive bacterium to standard antimicrobials but could rapidly develop intrinsic and acquired resistance when the bacterium is exposed to pressure exerted by antibiotics, as observed in hospital settings.
    Language English
    Publishing date 2024-03-06
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2710046-7
    ISSN 2213-7173 ; 2213-7173
    ISSN (online) 2213-7173
    ISSN 2213-7173
    DOI 10.1016/j.jgar.2024.02.023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Spatiotemporal Changes in

    Flores-Alanis, Alejandro / González-Cerón, Lilia / Santillán-Valenzuela, Frida / Ximenez, Cecilia / Sandoval-Bautista, Marco A / Cerritos, Rene

    Microorganisms

    2022  Volume 10, Issue 1

    Abstract: For 20 years, ...

    Abstract For 20 years,
    Language English
    Publishing date 2022-01-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10010186
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Spatiotemporal Changes in Plasmodium vivax msp142 Haplotypes in Southern Mexico: From the Control to the Pre-Elimination Phase

    Flores-Alanis, Alejandro / González-Cerón, Lilia / Santillán-Valenzuela, Frida / Ximenez, Cecilia / Sandoval-Bautista, Marco A. / Cerritos, Rene

    Microorganisms. 2022 Jan. 15, v. 10, no. 1

    2022  

    Abstract: For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to ... ...

    Abstract For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp1₄₂ fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R² index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.
    Keywords B-lymphocytes ; Plasmodium vivax ; epitopes ; genetic variation ; geographical distribution ; haplotypes ; malaria ; monitoring ; parasites ; Central America ; Mexico
    Language English
    Dates of publication 2022-0115
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10010186
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789.

    Flores-Alanis, Alejandro / Sandner-Miranda, Luisa / Delgado, Gabriela / Cravioto, Alejandro / Morales-Espinosa, Rosario

    BMC research notes

    2020  Volume 13, Issue 1, Page(s) 398

    Abstract: Objective: In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a ... ...

    Abstract Objective: In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans.
    Results: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.
    MeSH term(s) Adaptation, Biological/genetics ; Angiotensin-Converting Enzyme 2 ; Animals ; Betacoronavirus/genetics ; Binding Sites/genetics ; Chiroptera/virology ; Coronaviridae/genetics ; Eutheria/virology ; Evolution, Molecular ; Furin/metabolism ; Host Specificity ; Humans ; Peptidyl-Dipeptidase A/metabolism ; Phylogeny ; Recombination, Genetic ; SARS-CoV-2 ; Selection, Genetic ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Furin (EC 3.4.21.75)
    Keywords covid19
    Language English
    Publishing date 2020-08-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2413336-X
    ISSN 1756-0500 ; 1756-0500
    ISSN (online) 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-020-05242-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern.

    Flores-Alanis, Alejandro / Delgado, Gabriela / Espinosa-Camacho, Luis F / Rodríguez-Gómez, Flor / Cruz-Rangel, Armando / Sandner-Miranda, Luisa / Cravioto, Alejandro / Morales-Espinosa, Rosario

    Frontiers in microbiology

    2022  Volume 13, Page(s) 886585

    Abstract: Background: The advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of ... ...

    Abstract Background: The advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs).
    Objective: This study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs.
    Methods: 30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed.
    Results: 148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes.
    Conclusion: The COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.
    Language English
    Publishing date 2022-07-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.886585
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789

    Alejandro Flores-Alanis / Luisa Sandner-Miranda / Gabriela Delgado / Alejandro Cravioto / Rosario Morales-Espinosa

    BMC Research Notes, Vol 13, Iss 1, Pp 1-

    2020  Volume 6

    Abstract: Abstract Objective In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed ...

    Abstract Abstract Objective In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. Results Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.
    Keywords SARS-CoV-2 ; Spike glycoprotein ; Recombination ; Natural selection ; Genealogy ; Molecular evolution ; Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390 ; covid19
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Spatiotemporal Changes in Plasmodium vivax msp1 42 Haplotypes in Southern Mexico

    Alejandro Flores-Alanis / Lilia González-Cerón / Frida Santillán-Valenzuela / Cecilia Ximenez / Marco A. Sandoval-Bautista / Rene Cerritos

    Microorganisms, Vol 10, Iss 186, p

    From the Control to the Pre-Elimination Phase

    2022  Volume 186

    Abstract: For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to ... ...

    Abstract For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax -infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp1 42 fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R 2 index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.
    Keywords Plasmodium vivax ; merozoite surface protein 1 (42 kD) ; pvmsp1 42 ; haplotype diversity ; haplogroups ; B-cell epitopes ; Biology (General) ; QH301-705.5
    Subject code 616
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789

    Flores-Alanis, Alejandro / Sandner-Miranda, Luisa / Delgado, Gabriela / Cravioto, Alejandro / Morales-Espinosa, Rosario

    BMC Research Notes

    2020  Volume 13, Issue 1

    Keywords General Biochemistry, Genetics and Molecular Biology ; General Medicine ; covid19
    Language English
    Publisher Springer Science and Business Media LLC
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2413336-X
    ISSN 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-020-05242-8
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Pseudotyped Vesicular Stomatitis Virus-Severe Acute Respiratory Syndrome-Coronavirus-2 Spike for the Study of Variants, Vaccines, and Therapeutics Against Coronavirus Disease 2019.

    Salazar-García, Marcela / Acosta-Contreras, Samyr / Rodríguez-Martínez, Griselda / Cruz-Rangel, Armando / Flores-Alanis, Alejandro / Patiño-López, Genaro / Luna-Pineda, Victor M

    Frontiers in microbiology

    2022  Volume 12, Page(s) 817200

    Abstract: World Health Organization (WHO) has prioritized the infectious emerging diseases such as Coronavirus Disease (COVID-19) in terms of research and development of effective tests, vaccines, antivirals, and other treatments. Severe Acute Respiratory Syndrome- ...

    Abstract World Health Organization (WHO) has prioritized the infectious emerging diseases such as Coronavirus Disease (COVID-19) in terms of research and development of effective tests, vaccines, antivirals, and other treatments. Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2), the etiological causative agent of COVID-19, is a virus belonging to risk group 3 that requires Biosafety Level (BSL)-3 laboratories and the corresponding facilities for handling. An alternative to these BSL-3/-4 laboratories is to use a pseudotyped virus that can be handled in a BSL-2 laboratory for study purposes. Recombinant Vesicular Stomatitis Virus (VSV) can be generated with complementary DNA from complete negative-stranded genomic RNA, with deleted G glycoprotein and, instead, incorporation of other fusion protein, like SARS-CoV-2 Spike (S protein). Accordingly, it is called pseudotyped VSV-SARS-CoV-2 S. In this review, we have described the generation of pseudotyped VSV with a focus on the optimization and application of pseudotyped VSV-SARS-CoV-2 S. The application of this pseudovirus has been addressed by its use in neutralizing antibody assays in order to evaluate a new vaccine, emergent SARS-CoV-2 variants (delta and omicron), and approved vaccine efficacy against variants of concern as well as in viral fusion-focused treatment analysis that can be performed under BSL-2 conditions.
    Language English
    Publishing date 2022-01-14
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.817200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging.

    Flores-Alanis, Alejandro / Cruz-Rangel, Armando / Rodríguez-Gómez, Flor / González, James / Torres-Guerrero, Carlos Alberto / Delgado, Gabriela / Cravioto, Alejandro / Morales-Espinosa, Rosario

    Pathogens (Basel, Switzerland)

    2021  Volume 10, Issue 2

    Abstract: In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study ... ...

    Abstract In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (
    Language English
    Publishing date 2021-02-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2695572-6
    ISSN 2076-0817
    ISSN 2076-0817
    DOI 10.3390/pathogens10020184
    Database MEDical Literature Analysis and Retrieval System OnLINE

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