Publications and Projects

D’Andreano S, Cuscó A, Francino O. (2020) Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples. Biol Methods Protoc. 2020 Dec 23;6(1):bpaa026. doi: 10.1093/ biomethods/bpaa026. PMID: 33506108; PMCID: PMC7820110.

García-Fonticoba, R., Ferrer, L., Francino, O. Cusco, A. (2020) The microbiota of the surface, dermis and subcutaneous tissue of dog skin. anim microbiome 2, 34 (2020).

Cusco A, Perez D, Viñes J et al. (2020) Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces, 19 August 2020, PREPRINT (Version 1) available at Research Square [ 10.21203/] – Submitted to BMC Genomics (December 2020)

Cuscó A, Salas A, Torre C, Francino O. (2019) Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage. bioRxiv. doi:

Cuscó A, Catozzi C, Viñes J, Sanchez A, Francino O. (2019) Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon [version 2; peer review: 2 approved, 3 approved with reservations]. F1000Research 2019, 7:1755 (

Catozzi C, Cusco A, Lecchi C, Talenti A, Martuciello A, Cappelli G, Sanchez A, Francino O, Ceciliani F. (2019) Intra- and inter-individual milk microbiota variability in healthy and infected water buffalo udder quarters. Journal of Dairy Science 102:7476-7482. DOI: 10.3168/jds.2019-16352

Catozzi C, Cusco A, Lecchi C, De Carlo E, Vecchio D, Martuciello A, D’Angelo L, Francino O, Sanchez A, Ceciliani F. (2019) Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis. PLoS ONE 14:1 DOI: 10.1371/journal.pone.0210204

Cuscó A, Catozzi C, Viñes J, Sánchez A, Francino O. Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon. bioRxiv 2018; doi:

Soler C, Goossens T, Bermejo A, Migura- García L, Cusco A, Francino O, et al. Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period. PLoS ONE 2018, 13(5): e0197353. doi:

Cusco A, Belanger JM, Gershony L, Islas-Trejo A, Levy K, Medrano JF, Sánchez A, Oberbauer AM, Francino O. Individual signatures and environmental factors shape skin microbiota on healthy dogs. Microbiome. 2017, 5(1):139. doi:

Catozzi C, Sanchez Bonastre A, Francino O, Lecchi C, De Carlo E, Vecchio D, Martucciello A, Fraulo P, Bronzo V, Cuscó A, D’Andreano S, Ceciliani F. The microbiota of water buffalo milk during mastitis. PLoS One. 2017, 12(9): e0184710. doi:

Cusco A, Vines J, D’Andreano S, Riva F, Casellas J, Sanchez A, Francino O. Using MinION to characterize dog skin microbiota through full-length 16S rRNA gene sequencing approach. bioRxiv 2017, doi:

Cuscó A, Sanchez A, Altet L, Ferrer L, Francino O. Individual Signatures Define Canine Skin Microbiota Composition and Variability. Front. Vet. Sci. 2017, doi:

Cuscó A, Sánchez A, Altet L, Ferrer L, Francino O. Corrigendum: Individual Signatures Define Canine Skin Microbiota Composition and Variability. Front Vet Sci. 2017, 4:119. doi:

D’Andreano S, Sànchez A, Francino O, Cuscó A, Lecchi C, Grilli G, Giovanardi D, Ceciliani F. Gastrointestinal microbial population of turkey (Meleagris gallopavo) affected by Haemorrhagic Enteritis virus. Poult Sci. 2017, 96(10): 3550-3558. doi:

Francino O, Viñes J, D’Andreano S. Whole-genome sequencing and de novo assembly of Malassezia pachydermatis isolated from the ear canal of a dog with otitis. Microbial Resource Announcement (MRA00205-21) (in press)

Francino O, Pérez D, Viñes J, Fonticoba R, Madroñero S, Meroni G, Martino A, Martínez S, Cusco A, Fabregas N, Migura-García L, Ferrer L. (2021) Whole genome sequencing and de novo assembly of 61 Staphylococcus pseudintermedius isolated from healthy dogs and dogs with pyoderma. Microbial Resource Announcement (MRA00152-21) (in press)

Ferrer, L; García-Fonticoba, R; Perez, D; Viñes, J; Fabregas, N; Madroñero, S; Meroni, G; Martino, P; Martínez, S; Cusco, A; Migura, L; Francino, Olga. (2021) Whole genome sequencing and de novo assembly of Staphylococcus pseudintermedius: a pangenome approach to unravelling pathogenesis of canine pyoderma. Vet Dermatology (submitted)

Viñes J, Cuscó A, Napp S, Alvarez J, Saez-Llorente JL, Rosàs-Rodoreda M, Francino O, Migura-Garcia L. (2021) Transmission of similar mcr-1 carrying plasmids among different Escherichia coli lineages isolated from livestock and the farmer. 2021. Antibiotics (in press)

Marí-Almirall M, Cosgaya C, Pitart C et al. (2020) Dissemination of NDM-producing Klebsiella pneumoniae and Escherichia coli high-risk clones in Catalan healthcare institutions, Journal of Antimicrobial Chemotherapy dkaa459,

Viñes J, Cuscó A, Francino O.  (2020) Hybrid Assembly from a Pathogenic Methicillin- and Multidrug-Resistant Staphylococcus pseudintermedius Strain Isolated from a Case of Canine Otitis in Spain. Microbiology Resource Announcements. DOI: 10.1128/MRA.01121-19

Viñes J, Cuscó A, Napp S, Gonzalez J, Perez de Rozas A, Francino O, Migura-García L.  (2019) Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer. bioRxiv. doi:

Vila A, Estrada-Peña A, Altet L, Cusco A, Dandreano S, Francino O, Halos L, Roura X. (2019) Endosymbionts carried by ticks feeding on dogs in Spain, Ticks and Tick-borne Diseases.

Roura X, Santamarina G, Tabar M-D, Francino O, Altet L. Polymerase chain reaction detection of Bartonella spp. in dogs from Spain with blood culture-negative infectious endocarditis, Journal of Veterinary Cardiology 2018. doi:

Sastre N, Calvete O, Martínez-Vargas J, Medarde N, Casellas J, Altet L, Sánchez A, Francino O, Ventura J. Skin mites in mice (Mus musculus): high prevalence of Myobia sp. (Acari, Arachnida) in Robertsonian mice. Parasitology Research 2018, 117: 2139–2148. doi: 10.1007/s00436-018-5901-z.

Nashat M, Ricart Arbona R, Riedel ER, Francino O, Ferrer L, Luchins KR, Lipman NS. A comparison of diagnostic methods and sampling sites for the detection of Demodex musculi. Journal of the American Association for Laboratory Animal Science.2018, 57(2):173-185.

Tabar MD, Movilla R, Serrano L, Altet L, Francino O, Roura X. PCR evaluation of selected vector-borne pathogens in dogs with pericardial effusion. J Small Anim Pract. 2018, 59(4): 248-252. doi:

Cevidanes A, Altet L, Chirife AD, Proboste T, Millán J. Drivers of Bartonella infection in micromammals and their fleas in a Mediterranean peri-urban area. Veterinary Microbiology 2017. doi:

Movilla R, Altet L, Serrano L, Tabar MD, Roura X. Molecular detection of vector-borne pathogens in blood and splenic samples from dogs with splenic disease. Parasit Vectors. 2017, 13;10(1):131. doi:

Tabar MD, Altet L, Maggi RG, Altimira J, Roura X. First description of Bartonella koehlerae infection in a Spanish dog with infective endocarditis. Parasit Vectors. 2017, 10(1): 247. doi:

Zewe CM, Altet L, Lam ATH, Ferrer L. Afoxolaner and fluralaner treatment do not impact on cutaneous Demodex populations of healthy dogs. Vet Dermatol. 2017, 28(5):468-e107. doi:

Sastre N, Francino O, Curti JN, Armenta TC, Fraser DL, Kelly RM, Hunt E, Silbermayr K, Zewe C, Sánchez A, Ferrer L. Detection, Prevalence and Phylogenetic Relationships of Demodex spp and further Skin Prostigmata Mites (Acari, Arachnida) in Wild and Domestic Mammals. PLoS One. 2016 1;11(11): e0165765. doi:

Maia C, Altet L, Serrano L, Cristóvão JM, Tabar MD, Francino O, Cardoso L, Campino L, Roura X. Molecular detection of Leishmania infantum, filariae and Wolbachia spp. in dogs from southern Portugal. Parasites & Vectors. 2016, 9(1):170. doi:

Solano-Gallego L., Di Filippo L., Ordeix L., Planellas M., Roura X., Altet L., Martínez-Orellana P, Montserrat S. Early reduction of Leishmania infantum-specific antibodies and blood parasitemia during treatment in dogs with moderate or severe disease. Parasites & Vectors. 2016, 9:235. doi:

Millán J, Proboste T, Fernández de Mera IG, Chirife AD, de la Fuente J, Altet L. Molecular detection of vector-borne pathogens in wild and domestic carnivores and their ticks at the human-wildlife interface. Ticks Tick Borne Dis. 2016, 7(2): 284-90. doi:

Millán J, Chirife AD, Altet L. Serum chemistry reference values for the common genet (Genetta genetta): variations associated with Leishmania infantum infection. Vet Q. 2015, 35(1): 43-7. doi:

Proboste T, Kalema-Zikusoka G, Altet L, Solano-Gallego L, Isabel G. de Mera F, Chirife AD, Muro J, Bach E, Piazza A, Cevidanes A, Blanda V, Mugisha L, de la Fuente J, Caracappa S, Millán J. Infection and exposure to vector-borne pathogens in rural dogs and their ticks, Uganda. Parasites & Vectors 2015, 8(1):306. doi:

Pennisi M-G, Persichetti M-F, Serrano L, Altet L, Reale S, Gulotta L, et al. Ticks and associated pathogens collected from cats in Sicily and Calabria (Italy). Parasit Vectors. 2015;8:512. doi:

Ferreira D, Sastre N, Ravera I, Altet L, Francino O, Bardagí M, Ferrer L. Identification of a third feline Demodex species through partial sequencing of the 16S rDNA and frequency of Demodex species in 74 cats using a PCR assay. Veterinary Dermatology 2015, 26(4):239-e53. doi:

Fernandez M, Altet L, Martinez-Diaz VL, Tabar M-D, Silvestrini P, Francino O, Roura X. Assessment of PCR status of vector-borne pathogens in dogs presenting arrhythmias. Comp Clin Pathol 2014, 23(5): 1447–1452. doi:

Ravera I, Altet L, Francino O, Sánchez A, Roldán W, Villanueva S, Bardagí M, Ferrer L. Small Demodex populations colonize most parts of the skin of healthy dogs. Veterinary Dermatology 2013, 24: 168-173. doi:

Vilhena H, Martínez-Díaz VL, Cardoso L, Vieira L, Altet L, Francino O, Pastor J and Silvestre-Ferreira AC. Feline vector-borne pathogens in the north and centre of Portugal. Parasites & Vectors 2013, 6:99. doi:

Tabar M.D, Altet L, Martínez V, Roura X. Wolbachia, filariae and Leishmania coinfection in dogs from a Mediterranean area. Journal of Small Animal Practice 2013, 54(4): 174-178. doi:

Martínez-Díaz VL, Silvestre-Ferreira AC, Vilhena H, Pastor J, Francino O, Altet L. Prevalence and co-infection of haemotropic mycoplasmas in Portuguese cats by real-time polymerase chain reaction. Journal of Feline Medicine and Surgery 2013. doi:

Sastre N, Ravera I, Ferreira D, Altet L, Sanchez A, Bardagí M, Francino O, Ferrer L.  Development of a PCR technique specific for Demodex injai in biological specimens. Parasitol Res 2013, 112(9): 3369-72. doi: 10.1007/s00436-013-3531-z.

Cabello J, Altet L, Napolitano C, Sastre N, Hidalgo E, Dávila JA, Millán J. Survey of infectious agents in the endangered Darwin’s fox (Lycalopex fulvipes): High prevalence and diversity of hemotrophic mycoplasmas. Veterinary Microbiology 2013, 167: 448–454. doi:

Ravera I, Altet L, Francino O, Sánchez A, Roldán W, Villanueva S, Bardagí M, Ferrer L. Small Demodex populations colonize most parts of the skin of healthy dogs. Veterinary Dermatology 2013, 24: 168-173. doi:

Sastre N, Ravera I, Villanueva S, Altet L, Bardagí M, Sánchez A, Francino O, Ferrer L. Phylogenetic relationships in three species of canine Demodex mite based on partial sequences of mitochondrial 16S rDNA. Veterinary Dermatology 2012, 23: 509-516. doi:

Naranjo C, Fondevila D, Altet L, Francino O, Ríos J, Roura X, Peña T. Evaluation of the presence of Leishmania spp. by real-time PCR in the lacrimal glands of dogs with leishmaniosis. The Veterinary Journal 2012, 193: 168–173. doi:

Ravera I, Altet L, Francino O, Bardagí M, Sánchez A, Ferrer L. Development of a real-time PCR to detect Demodex canis DNA in different tissue samples. Parasitol Res. 2011, 108(2): 305-8. doi: 10.1007/s00436-010-2062-0.

Martínez V, Quilez J, Sanchez A, Roura X, Francino O, Altet L. Canine leishmaniasis: the key points for qPCR result interpretation. Parasites & Vectors 2011, 4:57. doi:

Salinas M, Francino O, Sánchez A, Altet L. Mycoplasma and herpesvirus PCR detection in tortoises with rhinitis-stomatitis complex in Spain. J Wildl Dis. 2011; 47(1): 195-200. doi:

Tabar M-D, Maggi RG, Altet L, Vilafranca M, Francino O, Roura X. Gammopathy in a Spanish dog infected with Bartonella henselae. Journal of Small Animal Practice 2011, 52: 209–212. doi:

Ravera I, Altet L, Francino O, Bardagí M, Sánchez A, Ferrer L. Development of a real-time PCR to detect Demodex canis DNA in different tissue samples. Parasitol Res 2011, 108: 305–308. doi: 10.1007/s00436-010-2062-0.

Khater M, Escosura-Muñiz A, Altet L, Merkoçi  (2019) In Situ Plant Virus Nucleic Acid Isothermal Amplification Detection on Gold Nanoparticle-Modified Electrodes. A.Anal Chem. Apr 2;91(7):4790-4796. doi: 10.1021/acs.analchem.9b00340.

De la Escosura-Muñiz A, Baptista-Pire L, Serrano L, Altet L, Francino O, Sánchez A, Merkoçi A. Magnetic Bead/Gold Nanoparticle Double-Labeled Primers for Electrochemical Detection of Isothermal Amplified Leishmania DNA. Small 2016, 12(2): 205-13. doi:

Mayorga-Martinez CC, Chamorro-García A, Serrano L, Rivas L, Quesada D, Altet L, Francino O, Sánchez A, Merkoçi A. Iridium oxide nanoparticles and polythionine thin film based platform for sensitive Leishmania DNA detection. Journal of Materials Chemistry B 2015, 3: 5166-5171.

Rivas L, de la Escosura-Muñiz A, Serrano L, Altet L, Francino O, Sánchez A, Merkoçi A. Triple lines gold nanoparticle-based lateral flow for enhanced and simultaneous Leishmania DNA detection and endogenous control. Nano Research November 2015, 8(11): 3704–3714.

Gómez-Sánchez D, Olalde I, Sastre N, Enseñat C, Carrasco R, Marques-Bonet T, Lalueza-Fox C, Leonard JA, Vilà C, Ramírez O. On the path to extinction: Inbreeding and admixture in a declining grey wolf population. Mol Ecol 2018, 27(18): 3599-3612. doi:

Bartolomé N, Segarra S, Artieda M, Francino O, Sánchez E, Szczypiorska M, Casellas J, Tejedor D, Cerdeira J, Martínez A, Velasco A, Sánchez A. A Genetic Predictive Model for Canine Hip Dysplasia: Integration of Genome Wide Association Study (GWAS) and Candidate Gene Approaches. PLoS ONE 2015, 10(4):e0122558. doi:

Cuscó A, Sánchez A, Altet L, Ferrer L, Francino O. Non-synonymous genetic variation in exonic regions of canine Toll-like receptors. Canine Genetics and Epidemiology 2014, 1:11. doi:

Quilez J, Martinez V, Woolliams JA, Sanchez A, Pong-Wong R, Kennedy LJ, Quinnell RJ, Ollier WER, Roura X, Ferrer L, Altet L, Francino O. Genetic Control of Canine Leishmaniasis: Genome-Wide Association Study and Genomic Selection Analysis. PLoS ONE 2012, 7 (4): e35349. doi:

Sastre N, Vilá C, Salinas M, Bologov VV, Urios V, Sanchez A, Francino O, Ramírez O, Signatures of demographic bottlenecks in European wolf populations Conservation Genetics 2011, 12(3): 701–712.

Quilez J, Short A, Martínez V, Kennedy L, Ollier W, Sanchez A, Altet L, Francino O. A selective sweep of >8 Mb on chromosome 26 in the Boxer genome. BMC Genomics 2011, 12: 339. doi:

Salinas M, Altet L, Clavel C, Almela RM, Bayón A, Burguete I, Sánchez A. Genetic assessment, illegal trafficking and management of the Mediterranean spur-thighed tortoise in Southern Spain and Northern Africa. Conservation Genetics 2011, 12: 1-13.

2018-2021 -Systems biology to identify biomarkers of the skin microbiome in dog pyoderma. Line INNCORPORA – TORRES QUEVEDO (PTQ2018-009961)

2018-2020 – Pathogens And Antimicrobial Resistance: Metagenomics Applied To Personalized Medicine (2017 DI 037 Industrial Doctorate, AGAUR, Generalitat de Catalunya) 27 360 €

2016-2019 – Host genomics and functional metagenomics: homeostasis and resilience in the dog  (2015 DI 044 Industrial Doctorate, AGAUR, Generalitat de Catalunya) 27 360 €

2014-2017 – Genome, microbiome and environment: keeping the homeostasis in a variable world (2013 DI 011 Industrial Doctorate, AGAUR, Generalitat de Catalunya) 27 360 €

2014-2016 – Development and commercialization of a chip for individual identification and detection of parasites in canine feces (can-ID). Line INNCORPORA – TORRES QUEVEDO (PTQ-13-06514).

2012-2014 – Project POC4PETS (FP7-SME-2012-315653-POC4PETS).

2012-2014 – Development of a point of care device for the diagnosis of infectious diseases: canine leishmaniasis as a proof of concept. INNCORPORA-TORRES QUEVEDO (PTQ-11-04766).

2011-2012- Biosensor for the detection of Leishmania infantum DNA. INNOEMPRESA, Ajuts a la innovació per a empreses, ACCIÓ (IEDES-11-1-0063).