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Article: What Does 16S rRNA Gene-Targeted Next Generation Sequencing Contribute to the Study of Infective Endocarditis in Heart-Valve Tissue?

Santibáñez, Paula / García-García, Concepción / Portillo, Aránzazu / Santibáñez, Sonia / García-Álvarez, Lara / de Toro, María / Oteo, José A.

Pathogens. 2021 Dec. 29, v. 11, no. 1

2021

Abstract: Infective endocarditis (IE) is a severe and life-threatening disease. Identification of infectious etiology is essential for establishing the appropriate antimicrobial treatment and decreasing mortality. The aim of this study was to explore the potential ...

Abstract	Infective endocarditis (IE) is a severe and life-threatening disease. Identification of infectious etiology is essential for establishing the appropriate antimicrobial treatment and decreasing mortality. The aim of this study was to explore the potential utility of metataxonomics for improving microbiological diagnosis of IE. Here, next-generation sequencing (NGS) of the V3–V4 region of the 16S rRNA gene was performed in 27 heart valve tissues (18 natives, 5 intravascular devices, and 4 prosthetics) from 27 patients diagnosed with IE (4 of them with negative blood cultures). Metataxonomics matched with conventional diagnostic techniques in 24/27 cases (88.9%). The same bacterial family was assigned to 24 cases; the same genus, to 23 cases; and the same species, to 13 cases. In 22 of them, the etiological agent was represented by percentages > 99% of the reads and in two cases, by ~70%. Staphylococcus aureus was detected in a previously microbiological undiagnosed patient. Thus, microbiological diagnosis with 16S rRNA gene targeted-NGS was possible in one more sample than using traditional techniques. The remaining two patients showed no coincidence between traditional and 16S rRNA gene-targeted NGS microbiological diagnoses. In addition, 16S rRNA gene-targeted NGS allowed us to suggest coinfections that were supported by clinical data in one patient, and minority records also verified mixed infections in three cases. In our series, metataxonomics was valid for the identification of the causative agents, although more studies are needed before implementation of 16S rRNA gene-targeted NGS for the diagnosis of IE.
Keywords	Staphylococcus aureus ; blood ; endocarditis ; genes ; heart ; mortality ; patients
Language	English
Dates of publication	2021-1229
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11010034
Database	NAL-Catalogue (AGRICOLA)

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Article: What Does 16S rRNA Gene-Targeted Next Generation Sequencing Contribute to the Study of Infective Endocarditis in Heart-Valve Tissue?

Santibáñez, Paula / García-García, Concepción / Portillo, Aránzazu / Santibáñez, Sonia / García-Álvarez, Lara / de Toro, María / Oteo, José A

Pathogens (Basel, Switzerland)

2021 Volume 11, Issue 1

Abstract	Infective endocarditis (IE) is a severe and life-threatening disease. Identification of infectious etiology is essential for establishing the appropriate antimicrobial treatment and decreasing mortality. The aim of this study was to explore the potential utility of metataxonomics for improving microbiological diagnosis of IE. Here, next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene was performed in 27 heart valve tissues (18 natives, 5 intravascular devices, and 4 prosthetics) from 27 patients diagnosed with IE (4 of them with negative blood cultures). Metataxonomics matched with conventional diagnostic techniques in 24/27 cases (88.9%). The same bacterial family was assigned to 24 cases; the same genus, to 23 cases; and the same species, to 13 cases. In 22 of them, the etiological agent was represented by percentages > 99% of the reads and in two cases, by ~70%.
Language	English
Publishing date	2021-12-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11010034
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Article: Epidemiological, Clinical, and Microbiological Characteristics in a Large Series of Patients Affected by

Santibáñez, Sonia / Portillo, Aránzazu / Ibarra, Valvanera / Santibáñez, Paula / Metola, Luís / García-García, Concepción / Palomar, Ana M / Cervera-Acedo, Cristina / Alba, Jorge / Blanco, José R / Oteo, José A

Pathogens (Basel, Switzerland)

2022 Volume 11, Issue 5

Abstract: During recent decades, a tick-borne rickettsial syndrome, characterized by eschar and painful lymphadenopathy ... ...

Abstract	During recent decades, a tick-borne rickettsial syndrome, characterized by eschar and painful lymphadenopathy after
Language	English
Publishing date	2022-04-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11050528
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Article ; Online: Importance of Lid Hygiene Before Ocular Surgery: Qualitative and Quantitative Analysis of Eyelid and Conjunctiva Microbiota.

Peral, Assumpta / Alonso, Jose / García-García, Concepción / Niño-Rueda, Cristina / Calvo Del Bosque, Patricia

Eye & contact lens

2016 Volume 42, Issue 6, Page(s) 366–370

Abstract: Objective: To evaluate the efficacy of a cleansing eyelid wipe in reducing the microbiota present on the ocular surface before cataract surgery.: Methods: A single-center, prospective, single-blind phase IV study was conducted at the University ... ...

Abstract	Objective: To evaluate the efficacy of a cleansing eyelid wipe in reducing the microbiota present on the ocular surface before cataract surgery. Methods: A single-center, prospective, single-blind phase IV study was conducted at the University Complutense of Madrid. Forty-five adult patients who were scheduled for ocular surgery after treatment with commercially available eyelid wipes were consecutively enrolled. The study lasted 5 days and the patients were examined at day 0 (D0), day 3 (D3), and day 5 (D5). They received instructions to apply the eyelid wipe only to the eye subject to surgery, using the other eye as a control with no treatment. Lid and conjunctival swabs were taken on each day and microbes identified. Ocular surface microbiota was estimated by measuring the area of the agar plate occupied by the grown colonies with respect to the total available area. Results: Measurements at D3 and D5 showed a percent reduction of 58% and 63%, respectively, in the microbial load on the eyelid in the treated eyes (P=0.0011). There was also a reduction, although nonsignificant, in the microbiota of the conjunctiva of 72% and 69% on D3 and D5, respectively. Conclusions: The degree of microbiota reduction was comparable with that obtained after topical application of antibiotics in other studies. The results suggest the use of these eyelid wipes as a complementary prophylactic method before any ocular surgery.
MeSH term(s)	Aged ; Anti-Bacterial Agents/administration & dosage ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Bacteria/isolation & purification ; Conjunctiva/microbiology ; Disinfectants/administration & dosage ; Disinfectants/pharmacology ; Disinfection/methods ; Eyelids/microbiology ; Female ; Humans ; Hygiene ; Male ; Microbiota/drug effects ; Middle Aged ; Ophthalmologic Surgical Procedures ; Preoperative Care/methods ; Prospective Studies
Chemical Substances	Anti-Bacterial Agents ; Disinfectants
Language	English
Publishing date	2016-11
Publishing country	United States
Document type	Clinical Trial, Phase IV ; Journal Article
ZDB-ID	2103049-2
ISSN	1542-233X ; 1542-2321
ISSN (online)	1542-233X
ISSN	1542-2321
DOI	10.1097/ICL.0000000000000221
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Article ; Online: Calvarial tuberculosis with parenchymal involvement.

García-García, Concepción / Ibarra, Valvanera / Azcona-Gutiérrez, José M / Oteo, José A

Travel medicine and infectious disease

2013 Volume 11, Issue 5, Page(s) 329–331

Abstract: Tuberculosis is an infectious disease caused by the acid-fast bacilli Mycobacterium tuberculosis that usually affects the lungs although it may affect any organ. Tuberculous osteitis of the cranial bones is an uncommon manifestation of disseminated ... ...

Abstract	Tuberculosis is an infectious disease caused by the acid-fast bacilli Mycobacterium tuberculosis that usually affects the lungs although it may affect any organ. Tuberculous osteitis of the cranial bones is an uncommon manifestation of disseminated tuberculosis known as calvarial tuberculosis. Cases with parenchymal involvement are infrequent in the literature. We report a case of a patient with multiple osteolytic cranial lesions and a tuberculoma.
MeSH term(s)	Brain Diseases/diagnostic imaging ; Brain Diseases/metabolism ; Brain Diseases/pathology ; Elbow/microbiology ; Female ; Frontal Bone/diagnostic imaging ; Frontal Bone/pathology ; Humans ; Middle Aged ; Mycobacterium tuberculosis/isolation & purification ; Pakistan ; Scalp/diagnostic imaging ; Scalp/pathology ; Tomography, X-Ray Computed ; Tuberculosis, Osteoarticular/diagnostic imaging ; Tuberculosis, Osteoarticular/microbiology ; Tuberculosis, Osteoarticular/pathology
Language	English
Publishing date	2013-09
Publishing country	Netherlands
Document type	Case Reports ; Journal Article
ZDB-ID	2170891-5
ISSN	1873-0442 ; 1477-8939
ISSN (online)	1873-0442
ISSN	1477-8939
DOI	10.1016/j.tmaid.2012.11.008
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Article: Bartonella

García-Álvarez, Lara / García-García, Concepción / Muñoz, Patricia / Fariñas-Álvarez, María Del Carmen / Cuadra, Manuel Gutiérrez / Fernández-Hidalgo, Nuria / García-Vázquez, Elisa / Moral-Escudero, Encarnación / Alonso-Socas, María Del Mar / García-Rosado, Dácil / Hidalgo-Tenorio, Carmen / Domínguez, Fernando / Goikoetxea-Agirre, Josune / Gainzarain, Juan Carlos / Rodríguez-Esteban, María Ángeles / Bosch-Guerra, Xerach / Oteo, José A / On Behalf Of Grupo de Apoyo Al Manejo de la Endocarditis Infecciosa En España Games

Pathogens (Basel, Switzerland)

2022 Volume 11, Issue 5

Abstract: Blood culture negative endocarditis (BCNE) is frequent in infective endocarditis (IE). One of the causes of BCNE is fastidious microorganisms, such ... ...

Abstract	Blood culture negative endocarditis (BCNE) is frequent in infective endocarditis (IE). One of the causes of BCNE is fastidious microorganisms, such as
Language	English
Publishing date	2022-05-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11050561
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Article ; Online: Spinal cord toxoplasmosis in human immunodeficiency virus infection/acquired immunodeficiency syndrome.

García-García, Concepción / Castillo-Álvarez, Federico / Azcona-Gutiérrez, José M / Herraiz, María J / Ibarra, Valvanera / Oteo, José A

Infectious diseases (London, England)

2015 Volume 47, Issue 5, Page(s) 277–282

Abstract: Neurological complications in patients with human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) are still common, even in the era of highly active antiretroviral therapy. Opportunistic infections, immune reconstitution, ... ...

Abstract	Neurological complications in patients with human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) are still common, even in the era of highly active antiretroviral therapy. Opportunistic infections, immune reconstitution, the virus itself, antiretroviral drugs and neurocognitive disorders have to be considered when establishing the differential diagnosis. Toxoplasmic encephalitis remains the major cause of space-occupying lesions in the brain of patients with HIV/AIDS; however, spinal cord involvement has been reported infrequently. Here, we review spinal cord toxoplasmosis in HIV infection and illustrate the condition with a recent case from our hospital. We suggest that most patients with HIV/AIDS and myelitis with enhanced spine lesions, multiple brain lesions and positive serology for Toxoplasma gondii should receive immediate empirical treatment for toxoplasmosis, and a biopsy should be performed in those cases without clinical improvement or with deterioration.
MeSH term(s)	AIDS-Related Opportunistic Infections/complications ; AIDS-Related Opportunistic Infections/diagnosis ; AIDS-Related Opportunistic Infections/therapy ; Acquired Immunodeficiency Syndrome/complications ; Antiretroviral Therapy, Highly Active ; HIV Infections/complications ; Humans ; Male ; Middle Aged ; Myelitis/complications ; Myelitis/diagnosis ; Myelitis/therapy ; Nervous System Diseases/pathology ; Spinal Cord/pathology ; Toxoplasma/isolation & purification ; Toxoplasmosis/complications ; Toxoplasmosis/diagnosis ; Toxoplasmosis/therapy ; Toxoplasmosis, Cerebral/complications ; Toxoplasmosis, Cerebral/diagnosis ; Toxoplasmosis, Cerebral/therapy
Language	English
Publishing date	2015-05
Publishing country	England
Document type	Case Reports ; Journal Article ; Review
ZDB-ID	2839775-7
ISSN	2374-4243 ; 2374-4235
ISSN (online)	2374-4243
ISSN	2374-4235
DOI	10.3109/00365548.2014.993421
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Article ; Online: Molecular diversity and frequency of the diarrheagenic enteric protozoan Giardia duodenalis and Cryptosporidium spp. in a hospital setting in Northern Spain.

Azcona-Gutiérrez, José Manuel / de Lucio, Aida / Hernández-de-Mingo, Marta / García-García, Concepción / Soria-Blanco, Luis Miguel / Morales, Lucía / Aguilera, María / Fuentes, Isabel / Carmena, David

PloS one

2017 Volume 12, Issue 6, Page(s) e0178575

Abstract: Background: Human giardiosis and cryptosporidiosis are caused by the enteric protozoan parasites Giardia duodenalis and Cryptosporidium spp. Both pathogens are major contributors to the global burden of diarrhoeal disease, affecting primarily children ... ...

Abstract	Background: Human giardiosis and cryptosporidiosis are caused by the enteric protozoan parasites Giardia duodenalis and Cryptosporidium spp. Both pathogens are major contributors to the global burden of diarrhoeal disease, affecting primarily children and immunodebilitated individuals in resource-poor settings. Giardiosis and cryptosporidiosis also represent an important, often underestimate, public health threat in developed countries. In Spain only limited information is currently available on the epidemiology of these infections. Molecular data on the diversity, frequency, geographical distribution, and seasonality of G. duodenalis assemblages/sub-assemblages and Cryptosporidium species/sub-genotypes are particularly scarce. Methods: A longitudinal molecular epidemiological survey was conducted between July 2015 to September 2016 in patients referred to or attended at the Hospital San Pedro (La Rioja, Northern Spain) that tested positive for G. duodenalis (N = 106) or Cryptosporidium spp. (N = 103) by direct microscopy and/or a rapid lateral flow immunochromatographic assay. G. duodenalis infections were subsequently confirmed by real-time PCR and positive isolates assessed by multi-locus sequence genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. Cryptosporidium species and sub-genotypes were investigated at the 60 kDa glycoprotein or the small subunit ribosomal RNA genes of the parasite. Sociodemographic and clinical parameters of infected patients were also gathered and analysed. Principal findings: Out of 90 G. duodenalis-positive isolates by real-time PCR a total of 16 isolates were successfully typed. AII (44%, 7/16) was the most prevalent sub-assemblage found, followed by BIV (31%, 5/16) and BIII (19%, 3/16). A discordant genotype result AII/AIII was identified in an additional (6%, 1/16) isolate. No mixed infections A+B were detected. Similarly, a total of 81 Cryptosporidium spp. isolates were successfully typed, revealing the presence of C. hominis (81%, 66/81) and C. parvum (19%, 15/81). Obtained GP60 sequences were assigned to sub-type families Ib (73%, 59/81) within C. hominis, and IIa (7%, 6/81) and IId (2%, 2/81) within C. parvum. A marked inter-annual variation in Cryptosporidium cases was observed. Conclusions: Human giardiasis and cryptosporidiosis are commonly identified in patients seeking medical care in Northern Spain and represent a more important health concern than initially thought. Assemblage A within G. duodenalis and sub-genotype IbA10G2 within C. hominis were the genetic variants of these parasite species more frequently found circulating in the population under study. Molecular data presented here seem to suggest that G. duodenalis and Cryptosporidium infections arise through anthroponotic rather than zoonotic transmission in this Spanish region.
MeSH term(s)	Adolescent ; Adult ; Child ; Child, Preschool ; Cryptosporidiosis/diagnosis ; Cryptosporidium/classification ; Cryptosporidium/genetics ; Cryptosporidium/isolation & purification ; DNA, Protozoan/genetics ; Female ; Giardia lamblia/classification ; Giardia lamblia/genetics ; Giardia lamblia/isolation & purification ; Giardiasis/diagnosis ; Hospitals ; Humans ; Infant ; Longitudinal Studies ; Male ; Middle Aged ; Multilocus Sequence Typing ; Prevalence ; Spain ; Young Adult
Chemical Substances	DNA, Protozoan
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0178575
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Serum IFN-γ and RNAemia temporal profiles as biomarkers of severe COVID-19 in solid organ transplant and immunocompetent patients.

Salto-Alejandre, Sonsoles / Carretero-Ledesma, Marta / Camacho-Martínez, Pedro / Berastegui-Cabrera, Judith / Infante, Carmen / Rodríguez-Álvarez, Regino / Alba, Jorge / Pérez-Palacios, Patricia / García-Díaz, Emilio / Roca, Cristina / Praena, Julia / Blanco-Vidal, María José / Santibáñez, Sonia / Valverde-Ortiz, Rocío / Nieto-Arana, Javier / García-García, Concepción / Gutiérrez-Campos, David / Maldonado, Natalia / Bernal, Gabriel /

Gómez-Bravo, Miguel Ángel / Sobrino, José Manuel / Aguilar-Guisado, Manuela / Álvarez-Marín, Rocío / Goikoetxea-Aguirre, Josune / Oteo, José Antonio / Palacios-Baena, Zaira R / Pascual, Álvaro / Lepe, José Antonio / Rodríguez-Baño, Jesús / Cisneros, José Miguel / Pachón, Jerónimo / Sánchez-Céspedes, Javier / Cordero, Elisa

The Journal of infection

2023 Volume 86, Issue 5, Page(s) 529–533

MeSH term(s)	Humans ; COVID-19 ; Organ Transplantation/adverse effects ; Biomarkers ; Transplant Recipients
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-01-21
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2023.01.019
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Article ; Online: A confirmed case of Rickettsia parkeri infection in a traveler from Uruguay.

Portillo, Aránzazu / García-García, Concepción / Sanz, M Mercedes / Santibáñez, Sonia / Venzal, José M / Oteo, José A

The American journal of tropical medicine and hygiene

2013 Volume 89, Issue 6, Page(s) 1203–1205

Abstract: The first confirmed case of Rickettsia parkeri infection in Uruguay is reported. To date, in South America, molecularly confirmed cases of human infection have been found in Argentina and probably, Brazil. Our patient returned to Spain after a 7-day trip ...

Abstract	The first confirmed case of Rickettsia parkeri infection in Uruguay is reported. To date, in South America, molecularly confirmed cases of human infection have been found in Argentina and probably, Brazil. Our patient returned to Spain after a 7-day trip to Colonia Suiza (Southwestern Uruguay). He presented fever (39°C), chills, and two eschars (tache noire-like) surrounded by an indurated, erythematous halo on the inner side of the left ankle besides a maculopapular rash on the legs. After treatment with doxycycline for 7 days, he fully recovered. R. parkeri infection was diagnosed by molecular-based detection of the microorganism in a swab specimen of the eschar. Diagnosis was supported by seroconversion between acute- and convalescent-phase sera specimens.
MeSH term(s)	Anti-Bacterial Agents/therapeutic use ; Antibodies, Bacterial/blood ; DNA Primers/genetics ; Doxycycline/therapeutic use ; Fever ; Humans ; Male ; Middle Aged ; Polymerase Chain Reaction ; Rickettsia/classification ; Rickettsia/genetics ; Rickettsia/immunology ; Rickettsia/isolation & purification ; Rickettsia Infections/diagnosis ; Rickettsia Infections/drug therapy ; Rickettsia Infections/microbiology ; Spain ; Travel ; Treatment Outcome ; Uruguay
Chemical Substances	Anti-Bacterial Agents ; Antibodies, Bacterial ; DNA Primers ; Doxycycline (N12000U13O)
Language	English
Publishing date	2013-10-28
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	2942-7
ISSN	1476-1645 ; 0002-9637
ISSN (online)	1476-1645
ISSN	0002-9637
DOI	10.4269/ajtmh.13-0436
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