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Article ; Online: The enzymatic properties of Arabidopsis thaliana DNA polymerase λ suggest a role in base excision repair.

Morales-Ruiz, T / Beltrán-Melero, C / Ortega-Paredes, D / Luna-Morillo, J A / Martínez-Macías, M I / Roldán-Arjona, T / Ariza, R R / Córdoba-Cañero, D

Plant molecular biology

2024 Volume 114, Issue 1, Page(s) 3

Abstract: Base excision repair (BER) generates gapped DNA intermediates containing a 5'-terminal 2-deoxyribose-5-phosphate (5'-dRP) group. In mammalian cells, gap filling and dRP removal are catalyzed by Pol β, which belongs to the X family of DNA polymerases. In ... ...

Abstract	Base excision repair (BER) generates gapped DNA intermediates containing a 5'-terminal 2-deoxyribose-5-phosphate (5'-dRP) group. In mammalian cells, gap filling and dRP removal are catalyzed by Pol β, which belongs to the X family of DNA polymerases. In higher plants, the only member of the X family of DNA polymerases is Pol λ. Although it is generally believed that plant Pol λ participates in BER, there is limited experimental evidence for this hypothesis. Here we have characterized the biochemical properties of Arabidopsis thaliana Pol λ (AtPol λ) in a BER context, using a variety of DNA repair intermediates. We have found that AtPol λ performs gap filling inserting the correct nucleotide, and that the rate of nucleotide incorporation is higher in substrates containing a C in the template strand. Gap filling catalyzed by AtPol λ is most efficient with a phosphate at the 5'-end of the gap and is not inhibited by the presence of a 5'-dRP mimic. We also show that AtPol λ possesses an intrinsic dRP lyase activity that is reduced by mutations at two lysine residues in its 8-kDa domain, one of which is present in Pol λ exclusively and not in any Pol β homolog. Importantly, we also found that the dRP lyase activity of AtPol λ allows efficient completion of uracil repair in a reconstituted short-patch BER reaction. These results suggest that AtPol λ plays an important role in plant BER.
MeSH term(s)	Animals ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Excision Repair ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; DNA Repair ; Nucleotides ; Phosphates ; Mammals/metabolism ; DNA Polymerase beta
Chemical Substances	DNA polymerase beta2 (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Nucleotides ; Phosphates ; DNA Polymerase beta (EC 2.7.7.7)
Language	English
Publishing date	2024-01-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	778032-1
ISSN	1573-5028 ; 0167-4412
ISSN (online)	1573-5028
ISSN	0167-4412
DOI	10.1007/s11103-023-01407-8
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Zs.A 3458: Show issues

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Article ; Online: Ready-to-eat street food: a potential source for dissemination of multidrug-resistant Escherichia coli epidemic clones in Quito, Ecuador.

Zurita, J / Yánez, F / Sevillano, G / Ortega-Paredes, D / Paz Y Miño, A

Letters in applied microbiology

2020 Volume 70, Issue 3, Page(s) 203–209

Abstract: Ready-to-eat food contamination with ESBL-producing Escherichia coli is a growing health concern. Some of these strains also are epidemic clones and can cause community-associated infections that are difficult to treat. In this study, the occurrence of ... ...

Abstract	Ready-to-eat food contamination with ESBL-producing Escherichia coli is a growing health concern. Some of these strains also are epidemic clones and can cause community-associated infections that are difficult to treat. In this study, the occurrence of ESBL-producing E. coli contaminated ready-to-eat street food in Quito, Ecuador was evaluated. In total, 150 samples were collected randomly in the most crowded sites of the city. In all, 34 samples (34/150; 22·6%) were positive for total thermotolerant (44·5°C) coliforms resistant to cefotaxime. MALDI-TOF analysis identified that the E. coli was found in 20 food samples (20/34; 59%). ESBL gene bla
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Ecuador/epidemiology ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Escherichia coli Infections/epidemiology ; Escherichia coli Infections/transmission ; Fast Foods/microbiology ; Food Contamination/analysis ; Humans ; Multilocus Sequence Typing ; Phylogeny ; beta-Lactamases/genetics
Chemical Substances	Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2020-01-08
Publishing country	England
Document type	Journal Article
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.13263
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Article ; Online: Colistin-resistant Escherichia coli clinical isolate harbouring the mcr-1 gene in Ecuador.

Ortega-Paredes, D / Barba, P / Zurita, J

Epidemiology and infection

2016 Volume 144, Issue 14, Page(s) 2967–2970

Abstract: Colistin resistance mediated by the mcr-1 gene has been reported worldwide, but to date not from the Andean region, South America. We report the first clinical isolate of Escherichia coli harbouring the mcr-1 gene in Ecuador. The strain was isolated from ...

Abstract	Colistin resistance mediated by the mcr-1 gene has been reported worldwide, but to date not from the Andean region, South America. We report the first clinical isolate of Escherichia coli harbouring the mcr-1 gene in Ecuador. The strain was isolated from peritoneal fluid from a 14-year-old male with acute appendicitis, and subjected to molecular analysis. The minimum inhibitory concentration of colistin for the strain was 8 mg/ml and it was susceptible to carbapenems but resistant to tigecycline. The strain harboured mcr-1 and bla CTX-M-55 genes and was of sequence type 609. The recognition of an apparently commensal strain of E. coli harbouring mcr-1 serves as an alert to the presence in the region of this recently described resistance mechanism to one of the last line of drugs available for the treatment of multi-resistant Gram-negative infections.
MeSH term(s)	Acute Disease ; Adolescent ; Anti-Bacterial Agents/pharmacology ; Appendicitis/microbiology ; Colistin/pharmacology ; Drug Resistance, Bacterial ; Ecuador ; Escherichia coli/genetics ; Escherichia coli/physiology ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/genetics ; Humans ; Male ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents ; Escherichia coli Proteins ; MCR-1 protein, E coli ; Colistin (Z67X93HJG1)
Language	English
Publishing date	2016-06-22
Publishing country	England
Document type	Journal Article
ZDB-ID	632982-2
ISSN	1469-4409 ; 0950-2688
ISSN (online)	1469-4409
ISSN	0950-2688
DOI	10.1017/S0950268816001369
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Article ; Online: Dominance of ST131, B2, blaCTX-M-15, and papA-papC-kpsMII-uitA among ESBL Escherichia coli isolated from bloodstream infections in Quito, Ecuador: a 10-year surveillance study (2009-2019).

Zurita, Jeannete / Sevillano, Gabriela / Paz Y Miño, Ariane / Haro, Nathalí / Larrea-Álvarez, Marco / Alcocer, Iliana / Ortega-Paredes, David

Journal of applied microbiology

2023 Volume 134, Issue 11

Abstract: Aims: This study aimed to examine antibiotic resistance and the epidemiology of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli associated with bloodstream infections over a period of 10 years.: Methods and results: Isolates were ... ...

Abstract	Aims: This study aimed to examine antibiotic resistance and the epidemiology of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli associated with bloodstream infections over a period of 10 years. Methods and results: Isolates were collected from January 2009 to December 2019 and those testing for E. coli were included. Antibiotic susceptibility was tested using the VITEK® system. Selected isolates were further characterized by amplification of marker genes (virulence traits, phylogroups, and sequence types). A total of 166 ESBL-producing E. coli were recovered. The blaCTX-M-15 allele was the most abundant. Most of the isolates were resistant to ceftriaxone, cefepime, ceftazidime, ampicillin/sulbactam, piperacillin/tazobactam, and ciprofloxacin. No resistance to carbapenems was registered. More than 80% of bacteria were classified as extraintestinal pathogenic E. coli (ExPEC), and the combination of virulence traits:papA-papC-kpsMII-uitA was the most common. Phylogroup B2 was the most prevalent, and bacteria predominantly belonged to ST131. Conclusions: There was an increase in the ExPEC ESBL-E coli in bloodstream infections and the relationship between the isolates found in these infections during these 10 years.
MeSH term(s)	Humans ; Escherichia coli ; Escherichia coli Infections/epidemiology ; Escherichia coli Infections/microbiology ; Ecuador/epidemiology ; beta-Lactamases/genetics ; Sepsis/microbiology ; Extraintestinal Pathogenic Escherichia coli ; Anti-Bacterial Agents/pharmacology
Chemical Substances	beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-11-16
Publishing country	England
Document type	Journal Article
ZDB-ID	1358023-1
ISSN	1365-2672 ; 1364-5072
ISSN (online)	1365-2672
ISSN	1364-5072
DOI	10.1093/jambio/lxad269
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Zs.A 259: Show issues

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Article: In Silico Detection of Antimicrobial Resistance Integrons in

Torres-Elizalde, Lilibeth / Ortega-Paredes, David / Loaiza, Karen / Fernández-Moreira, Esteban / Larrea-Álvarez, Marco

Antibiotics (Basel, Switzerland)

2021 Volume 10, Issue 11

Abstract: Antimicrobial resistance genes are often associated with integrons, which promote their movement between and within DNA molecules. IntFinder 1.0 and I-VIP v1.2 were used for the detection of integrons and their associated resistance genes in assembled ... ...

Abstract	Antimicrobial resistance genes are often associated with integrons, which promote their movement between and within DNA molecules. IntFinder 1.0 and I-VIP v1.2 were used for the detection of integrons and their associated resistance genes in assembled sequences and raw reads. A dataset comprising 1688 sequenced
Language	English
Publishing date	2021-11-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics10111388
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Article ; Online: Evidence of SARS-CoV-2 reinfection within the same clade in Ecuador: A case study.

Sevillano, Gabriela / Ortega-Paredes, David / Loaiza, Karen / Zurita-Salinas, Camilo / Zurita, Jeannete

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2021 Volume 108, Page(s) 53–56

Abstract: Objectives: To date, reported SARS-CoV-2 reinfection cases are mainly from strains belonging to different clades. As the pandemic advances, a few lineages have become dominant in certain areas leading to reinfections by similar strains. Here, we report ... ...

Abstract	Objectives: To date, reported SARS-CoV-2 reinfection cases are mainly from strains belonging to different clades. As the pandemic advances, a few lineages have become dominant in certain areas leading to reinfections by similar strains. Here, we report a reinfection case within the same clade of the initial infection in a symptomatic 28-year-old-male in Quito-Ecuador. Methods: Infection was detected by reverse transcription-polymerase chain reaction, and immune response evaluated by antibody testing. Whole-genome sequencing was performed and phylogenetic analysis conducted to determine relatedness. Results: Both the infection and the reinfection strains were assigned as Nextstrain 20B, Pangolin lineage B.1.1 and GISAID clade O. Our analysis indicated 4-6 fold more nucleotide changes than are expected for reactivation or persistence compared with the natural rate of SARS-CoV-2 mutation (∼2-3 nucleotide changes per month), thus supporting reinfection. Furthermore, approximately 3 months after the second infection, COVID-19 antibodies were not detectable in the patient, suggesting potential vulnerability to a third infection. Conclusions: Our results showed evidence of SARS-CoV-2 reinfection within the same clade in Ecuador, indicating that previous exposure to SARS-CoV-2 does not guarantee immunity in all cases.
MeSH term(s)	Adult ; COVID-19 ; Ecuador/epidemiology ; Humans ; Male ; Phylogeny ; Reinfection ; SARS-CoV-2
Language	English
Publishing date	2021-04-27
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2021.04.073
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Article: Ready‐to‐eat street food: a potential source for dissemination of multidrug‐resistant Escherichia coli epidemic clones in Quito, Ecuador

Zurita, J / Yánez, F / Sevillano, G / Ortega‐Paredes, D / Paz y Miño, A

Letters in applied microbiology. 2020 Mar., v. 70, no. 3

2020

Abstract: Ready‐to‐eat food contamination with ESBL‐producing Escherichia coli is a growing health concern. Some of these strains also are epidemic clones and can cause community‐associated infections that are difficult to treat. In this study, the occurrence of ... ...

Abstract	Ready‐to‐eat food contamination with ESBL‐producing Escherichia coli is a growing health concern. Some of these strains also are epidemic clones and can cause community‐associated infections that are difficult to treat. In this study, the occurrence of ESBL‐producing E. coli contaminated ready‐to‐eat street food in Quito, Ecuador was evaluated. In total, 150 samples were collected randomly in the most crowded sites of the city. In all, 34 samples (34/150; 22·6%) were positive for total thermotolerant (44·5°C) coliforms resistant to cefotaxime. MALDI‐TOF analysis identified that the E. coli was found in 20 food samples (20/34; 59%). ESBL gene blaCTX‐M‐55 was identified in nine isolates, blaCTX‐M‐15 in six isolates, blaCTX‐M‐14 in two isolates, and one isolate each harboured blaCTX‐M‐24, blaCTX‐M‐65, blaCTX‐M‐55 and blaCTX‐M‐8. Phylogenetic groups like A and B1 were the most common, followed by groups D and B2. MLST analysis identified 12 different sequence types (STs), the most common was ST162. Recognized epidemic clonal groups ST410, ST131 and ST744 were encountered. Ready‐to‐eat street food is a potential way of spreading ESBL‐producing E. coli epidemic clones in Quito, Ecuador. SIGNIFICANCE AND IMPACT OF THE STUDY: This study identified ESBL‐producing Escherichia coli epidemic clones: ST131, ST410 and ST744 in ready‐to‐eat street food samples. Street food is a possible way to spread harm multidrug‐resistant (MDR) E. coli strains in the community. Studies to identify the contamination sources of this kind of food are needed to tackle MDR E. coli dissemination.
Keywords	Escherichia coli ; antibiotic resistance ; beta-lactamase bacteria ; cefotaxime ; clones ; coliform bacteria ; food contamination ; genes ; heat tolerance ; matrix-assisted laser desorption-ionization mass spectrometry ; multiple drug resistance ; phylogeny ; ready-to-eat foods ; street foods ; Ecuador
Language	English
Dates of publication	2020-03
Size	p. 203-209.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.13263
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genetic diversity and drug resistance of

Zurita, J / Espinel, N / Barba, P / Ortega-Paredes, D / Zurita-Salinas, C / Rojas, Y / Alcocer, I

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

2019 Volume 23, Issue 2, Page(s) 166–173

Abstract: Background: The genetic diversity of : Objective: To investigate mutations related to drug resistance and bacterial genotypes in : Design: This was a retrospective study of : Results: Isolates showed mutations in the : Conclusion: This is ... ...

Abstract	Background: The genetic diversity of Objective: To investigate mutations related to drug resistance and bacterial genotypes in Design: This was a retrospective study of Results: Isolates showed mutations in the Conclusion: This is the first report from Ecuador; it describes five new mutations in
MeSH term(s)	Antitubercular Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ecuador ; Genetic Variation ; Genotype ; Humans ; Isoniazid/pharmacology ; Minisatellite Repeats/genetics ; Mutation ; Mycobacterium tuberculosis/drug effects ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/isolation & purification ; Phenotype ; Retrospective Studies ; Rifampin/pharmacology ; Tuberculosis, Multidrug-Resistant/drug therapy ; Tuberculosis, Multidrug-Resistant/epidemiology ; Tuberculosis, Multidrug-Resistant/microbiology
Chemical Substances	Antitubercular Agents ; Isoniazid (V83O1VOZ8L) ; Rifampin (VJT6J7R4TR)
Language	English
Publishing date	2019-02-26
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1385624-8
ISSN	1815-7920 ; 1027-3719
ISSN (online)	1815-7920
ISSN	1027-3719
DOI	10.5588/ijtld.18.0095
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Article: High quantities of multidrug-resistant Escherichia coli are present in the Machángara urban river in Quito, Ecuador.

Ortega-Paredes, David / Barba, Pedro / Mena-López, Santiago / Espinel, Nathaly / Crespo, Verónica / Zurita, Jeannete

Journal of water and health

2020 Volume 18, Issue 1, Page(s) 67–76

Abstract: Urban river pollution by multidrug-resistant (MDR) bacteria constitutes an important public health concern. Epidemiologically important strains of MDR Escherichia coli transmissible at the human-animal-environment interfaces are especially worrying. ... ...

Abstract	Urban river pollution by multidrug-resistant (MDR) bacteria constitutes an important public health concern. Epidemiologically important strains of MDR Escherichia coli transmissible at the human-animal-environment interfaces are especially worrying. Quantifying and characterizing MDR E. coli at a molecular level is thus imperative for understanding its epidemiology in natural environments and its role in the spread of resistance in precise geographical areas. Cefotaxime-resistant E. coli was characterized along the watercourse of the major urban river in Quito. Our results showed high quantities of cefotaxime-resistant E. coli (2.7 × 10
MeSH term(s)	Animals ; Anti-Bacterial Agents ; Drug Resistance, Multiple, Bacterial ; Ecuador ; Environmental Monitoring ; Escherichia coli ; Escherichia coli Infections ; Humans ; Microbial Sensitivity Tests ; Rivers/microbiology ; Water Microbiology
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2020-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2123845-5
ISSN	1996-7829 ; 1477-8920
ISSN (online)	1996-7829
ISSN	1477-8920
DOI	10.2166/wh.2019.195
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Article: Effects of

Šefcová, Miroslava Anna / Ortega-Paredes, David / Larrea-Álvarez, César Marcelo / Mina, Iván / Guapás, Victoria / Ayala-Velasteguí, David / Leoro-Garzón, Paula / Molina-Cuasapaz, Gabriel / Vinueza-Burgos, Christian / Revajová, Viera / Larrea-Álvarez, Marco

Microorganisms

2023 Volume 11, Issue 2

Abstract: There are no studies reporting the effects ... ...

Abstract	There are no studies reporting the effects of
Language	English
Publishing date	2023-01-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms11020256
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