Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa
Staphylococcus spp., especially S. aureus species, are part of the normal microbiota of healthy humans and animals, but it can also be opportunistic pathogens. Methicillin-resistant S. aureus (MRSA) is a serious health problem since it shows resistance to almost all β-lactam antibiotics. In 2005, fo...
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Universidad de La Rioja (España)
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Staphylococcus spp., especially S. aureus species, are part of the normal microbiota of healthy humans and animals, but it can also be opportunistic pathogens. Methicillin-resistant S. aureus (MRSA) is a serious health problem since it shows resistance to almost all β-lactam antibiotics. In 2005, for the first time, a genetic MRSA clonal complex CC398 was detected associated with livestock (MRSA-LA), whose main reservoir are pigs. Since then, it has been observed a large dissemination of this genetic lineage, as well as the transmission to people in direct or indirect contact with farm animals. In 2011, a new mec gene (mecC) was described associated with genetic lineages of S. aureus adapted to animals, especially CC130. MRSA-mecC is an emerging problem, detected in production and free-living animals, and also sporadically in people. The human, animal, and environmental ecosystems, are interconnected allowing a flow of bacteria and genes between them. The study of bacterial molecular epidemiology requires a global and integrating approach (one world, one health), such as the one proposed in this thesis.
Environmental samples [surface water, treated and untreated sewage water from waste water treatment plants (WWTP)], and free-living animals [small mammals, red deer and white storks] have been studied for the isolation and characterization of Staphylococcus. Likewise, using the whole genome sequencing, a comparison of CC130 strains of different origins and of CC398 strains was made, both clonal complexes being emerging in the animal-human interface.
A high variability of species was detected in wastewater and surface waters: S. aureus, S. equorum, S. vitulinis, S. lentus and S. sciuri being the most abundant in WWTP waters, and S. aureus, S. epidermidis, S. vitulinis, S. sciuri and S. fleurettii the most frequent ones in surface waters. A MRSA-ST398-t011 strain which with a multiresistant phenotype (scn-negative) was detected in treated wastewater. The remanding S. aureus strains from WWTP were susceptible to methicillin but some of them contained numerous enterotoxin genes. In surface waters, no MRSA strains were detected, and the isolated S. aureus belonged to CCs associated with humans (CC5) or adapted to animals (CC130, CC133). The 21.8% of coagulase-negative Staphylococcus (CoNS) isolated from the WWTP contained the mecA gene, and 15.6% presented a multiresistance antimicrobial phenotype. These percentages raised to 30.5% and 23.7%, respectively, in CoNS of surface waters.
Coagulase positive Staphylococcus (CoPS) strains of free-living animals were characterized, and detected prevalences for S. aureus were as follows: small mammals (13%), red deer (24.6%), and white storks (34.8%); a big difference was detected in storks, depending on where they were fed: areas with human influence (55.8%) or natural areas (16.3%). Moreover, 2% of small mammals and 17% of deers animal samples obtained from the same farm) were carriers of MRSA strains, all of them mecC-positive, typed as ST1945 and carrying genes of IEC system (type E). This is the first description of MRSA-mecC-IEC-positive strains. To date, no IEC-positive strain belonging to CC130 has been described. The similarity of these strains in the analysis carried out suggests an animal-animal transmission. The remaining S. aureus of red deer and small mammals were susceptible to methicillin and to the other antimicrobials tested, being described as CC5 and CC1956 (in small mammals) and CC133 (in red deer). On the other hand, the clonal diversity of S. aureus isolated from white storks was very high, highlighting the detection of three MRSA strains, one mecC-IEC-negative (ST3061-CC130), and two mecA-positive (one CC5 and another CC398-LA). Among the MSSA strains, CC398 lineage with different spa-types was detected (between them: t571, IEC type C, and erm(T)-positive, associated with invasive infections in humans). Other lineages detected were: CC5, CC7, CC22, CC30, CC45, CC59 and CC133.
The analysis of the complete genome sequences of 18 S. aureus isolated from multiple animal species belonging to 6 sequences type ascribed to CC130 (14 MRSA and 4 MSSA) allowed to establish possible phylogeny relationships. The obtained results show that, except for the ST700 lineage, the core genome did not present differential characteristics that allowed to group the strains according to the animal species or the geographical origin area, although there seems to be a certain clustering depending on the methicillin resistance phenotype and the sequence type.
The study of comparative genomics of two strains ST398-t011, one MSSA and another MRSA, isolated from a swine driving men, showed that both belonged to the animal clade and that they had a very high clonal relationship. The results obtained suggest the evolutionary change from MRSA to MSSA due to the loss of the mecA gene (associated with the loss of a 17342pb fragment), probably due to the recombination of putative primase which caused a SCCmec remnant. |
| author2 |
Torres Manrique, Carmen (null) |
| author_facet |
Torres Manrique, Carmen (null) Gómez Villaescusa, Paula |
| format |
text (thesis) |
| author |
Gómez Villaescusa, Paula |
| spellingShingle |
Gómez Villaescusa, Paula Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa |
| author_sort |
Gómez Villaescusa, Paula |
| title |
Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa |
| title_short |
Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa |
| title_full |
Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa |
| title_fullStr |
Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa |
| title_full_unstemmed |
Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa |
| title_sort |
staphylococcus aureus en animales de vida libre y medioambiente. resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativa |
| publisher |
Universidad de La Rioja (España) |
| publishDate |
2019 |
| url |
https://dialnet.unirioja.es/servlet/oaites?codigo=221322 |
| work_keys_str_mv |
AT gomezvillaescusapaula staphylococcusaureusenanimalesdevidalibreymedioambienteresistenciaaantimicrobianosvirulencialineasgeneticascirculantesygenomicacomparativa |
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1718346677038874624 |
| spelling |
oai-TES00000228902019-05-15Staphylococcus aureus en animales de vida libre y medioambiente. Resistencia a antimicrobianos, virulencia, líneas genéticas circulantes y genómica comparativaGómez Villaescusa, PaulaStaphylococcus spp., especially S. aureus species, are part of the normal microbiota of healthy humans and animals, but it can also be opportunistic pathogens. Methicillin-resistant S. aureus (MRSA) is a serious health problem since it shows resistance to almost all β-lactam antibiotics. In 2005, for the first time, a genetic MRSA clonal complex CC398 was detected associated with livestock (MRSA-LA), whose main reservoir are pigs. Since then, it has been observed a large dissemination of this genetic lineage, as well as the transmission to people in direct or indirect contact with farm animals. In 2011, a new mec gene (mecC) was described associated with genetic lineages of S. aureus adapted to animals, especially CC130. MRSA-mecC is an emerging problem, detected in production and free-living animals, and also sporadically in people. The human, animal, and environmental ecosystems, are interconnected allowing a flow of bacteria and genes between them. The study of bacterial molecular epidemiology requires a global and integrating approach (one world, one health), such as the one proposed in this thesis. Environmental samples [surface water, treated and untreated sewage water from waste water treatment plants (WWTP)], and free-living animals [small mammals, red deer and white storks] have been studied for the isolation and characterization of Staphylococcus. Likewise, using the whole genome sequencing, a comparison of CC130 strains of different origins and of CC398 strains was made, both clonal complexes being emerging in the animal-human interface. A high variability of species was detected in wastewater and surface waters: S. aureus, S. equorum, S. vitulinis, S. lentus and S. sciuri being the most abundant in WWTP waters, and S. aureus, S. epidermidis, S. vitulinis, S. sciuri and S. fleurettii the most frequent ones in surface waters. A MRSA-ST398-t011 strain which with a multiresistant phenotype (scn-negative) was detected in treated wastewater. The remanding S. aureus strains from WWTP were susceptible to methicillin but some of them contained numerous enterotoxin genes. In surface waters, no MRSA strains were detected, and the isolated S. aureus belonged to CCs associated with humans (CC5) or adapted to animals (CC130, CC133). The 21.8% of coagulase-negative Staphylococcus (CoNS) isolated from the WWTP contained the mecA gene, and 15.6% presented a multiresistance antimicrobial phenotype. These percentages raised to 30.5% and 23.7%, respectively, in CoNS of surface waters. Coagulase positive Staphylococcus (CoPS) strains of free-living animals were characterized, and detected prevalences for S. aureus were as follows: small mammals (13%), red deer (24.6%), and white storks (34.8%); a big difference was detected in storks, depending on where they were fed: areas with human influence (55.8%) or natural areas (16.3%). Moreover, 2% of small mammals and 17% of deers animal samples obtained from the same farm) were carriers of MRSA strains, all of them mecC-positive, typed as ST1945 and carrying genes of IEC system (type E). This is the first description of MRSA-mecC-IEC-positive strains. To date, no IEC-positive strain belonging to CC130 has been described. The similarity of these strains in the analysis carried out suggests an animal-animal transmission. The remaining S. aureus of red deer and small mammals were susceptible to methicillin and to the other antimicrobials tested, being described as CC5 and CC1956 (in small mammals) and CC133 (in red deer). On the other hand, the clonal diversity of S. aureus isolated from white storks was very high, highlighting the detection of three MRSA strains, one mecC-IEC-negative (ST3061-CC130), and two mecA-positive (one CC5 and another CC398-LA). Among the MSSA strains, CC398 lineage with different spa-types was detected (between them: t571, IEC type C, and erm(T)-positive, associated with invasive infections in humans). Other lineages detected were: CC5, CC7, CC22, CC30, CC45, CC59 and CC133. The analysis of the complete genome sequences of 18 S. aureus isolated from multiple animal species belonging to 6 sequences type ascribed to CC130 (14 MRSA and 4 MSSA) allowed to establish possible phylogeny relationships. The obtained results show that, except for the ST700 lineage, the core genome did not present differential characteristics that allowed to group the strains according to the animal species or the geographical origin area, although there seems to be a certain clustering depending on the methicillin resistance phenotype and the sequence type. The study of comparative genomics of two strains ST398-t011, one MSSA and another MRSA, isolated from a swine driving men, showed that both belonged to the animal clade and that they had a very high clonal relationship. The results obtained suggest the evolutionary change from MRSA to MSSA due to the loss of the mecA gene (associated with the loss of a 17342pb fragment), probably due to the recombination of putative primase which caused a SCCmec remnant.Staphylococcus spp., y muy especialmente la especie S. aureus, forman parte de la microbiota normal de personas y animales sanos, pero pueden ser tambien patógenos oportunistas. S. aureus resistente a meticilina (SARM), supone un grave problema de salud, ya que muestra resistencia a casi todos los antibióticos β-lactámicos. En el año 2005, se detectó por primera vez una línea genética SARM del complejo clonal CC398 asociado a ganado (SARM-AG), cuyo principal reservorio es el porcino. Desde entonces, se viene observando una gran diseminación de esta línea y también su transferencia a personas en contacto directo o indirecto con animales. En el año 2011 se describió un nuevo gen mec (mecC), asociado a líneas genéticas de S. aureus adaptadas a animales, especialmente CC130. SARM-mecC es un problema emergente detectado en animales de producción y de vida libre y esporádicamente en personas. Los ecosistemas humano, animal y ambiental están interconectados, permitiendo un flujo de bacterias y de genes entre ellos. El estudio de la epidemiología molecular bacteriana requiere indiscutiblemente un enfoque global e integrador (un mundo, una salud) como el planteado en esta tesis. Se han estudiado muestras ambientales [aguas superficiales, aguas de estaciones depuradoras de aguas residuales (EDAR) tratadas y no tratadas] y de animales de vida libre [micromamíferos, ciervos y cigüeñas] para el aislamiento y caracterización de Staphylococcus. Asimismo, mediante la secuenciación completa del genoma, se ha realizado la comparativa de cepas CC130 de distintos orígenes y de cepas CC398, ambas líneas genéticas emergentes en la interfaz animal-hombre. Tanto en las aguas residuales como en las superficiales se detectó una elevada variabilidad de especies, siendo S. aureus, S. equorum, S. vitulinis, S. lentus y S. sciuri, las más abundantes en aguas de EDAR y S. aureus, S. epidermidis, S. vitulinis, S. sciuri y S. fleurettii las más frecuentes en aguas superficiales. En aguas residuales tratadas se detectó un SARM-ST398-t011 (scn-negativo), que además presentó un fenotipo de multiresistencia. El resto de cepas S. aureus procedentes de EDAR fueron sensibles a meticilina pero algunas de ellas contenían numerosos genes de enterotoxinas. En aguas superficiales no se detectaron cepas SARM, y los S. aureus aislados pertenecían a CCs asociados con humanos (CC5) o adaptados a animales (CC130, CC133). El 21,8% de los Staphylococcus coagulasa negativo (SCoN) aislados de EDAR contenían el gen mecA y el 15,6% presentaron un fenotipo de multiresistencia a antimicrobianos. En los SCoN de aguas superficiales, estos porcentajes ascienden hasta el 30,5 y 23,7%, respectivamente. En los animales de vida libre se caracterizaron las cepas de Staphylococcus coagulasa positivo (SCoP). Las prevalencias detectadas de S. aureus fueron: micromamíferos (13%), ciervos (24,6%) y cigüeñas (34,8%), existiendo una gran diferencia en este último caso en función de si se alimentaban en zonas con influencia humana (55,8%) o en parajes naturales (16,3%). El 2% de los micromamíferos y el 17% de los ciervos analizados (los animales procedían de la misma finca) fueron portadores de cepas SARM, siendo todas ellas mecC‑positivas, tipadas como ST1945 y portadoras de genes del sistema IEC (tipo E). Se trata de la primera descripción de cepas SARM-mecC-IEC-positivas; tampoco se había descrito hasta la fecha ninguna cepa IEC-positiva perteneciente al CC130. La similitud de estas cepas en los análisis realizados, sugiere una transmisión animal-animal. El resto de S. aureus de ciervos y micromamíferos fueron sensibles a meticilina y al resto de antimicrobianos testados, tipándose como CC5 y CC1956 (en micromamíferos) y CC133 (en ciervos). Por otro lado la diversidad clonal de S. aureus aislados de cigüeñas fue muy elevada, destacando la detección de tres cepas SARM, una mecC-IEC-negativa (ST3061-CC130) y dos mecA-positivas (una CC5 y otra CC398-AG). Entre las cepas SASM se detectó el linaje CC398 con diferentes spa-tipos (entre ellos t571, IEC tipo-C y erm(T)-positivo, asociado con infecciones invasivas en humanos); otros linajes detectados fueron: CC5, CC7, CC22, CC30, CC45, CC59 y CC133. El análisis de las secuencias completas del genoma de 18 S.aureus aislados de múltiples especies animales, pertenecientes a 6 secuencias tipo adscritas al CC130 (14 SARM y 4 SASM), permitió establecer posibles relaciones de filogenia. Los resultados obtenidos muestran que, salvo para la línea ST700, el genoma-núcleo no presentaba secuencias características diferenciales que permitieran agrupar las cepas en función de la especie animal o del área geográfica de origen, aunque si parece existir una cierta agrupación en función del fenotipo de resistencia a meticilina y de la secuencia tipo. El estudio de genómica comparativa de dos cepas ST398-t011, una SASM y otra SARM, aisladas de un transportista en contacto con ganado porcino, mostró que ambas pertenecían al clado animal y que presentaban una relación clonal muy elevada. Los resultados obtenidos sugieren el cambio evolutivo de SARM a SASM por la pérdida del gen mecA (asociado a un fragmento de 17342pb), probablemente debido a la recombinación de unas primasas putativas, que originó un SCCmec remanente.Universidad de La Rioja (España)Torres Manrique, Carmen (null)Zarazaga Chamorro, Myriam (null)2019text (thesis)application/pdfhttps://dialnet.unirioja.es/servlet/oaites?codigo=221322spaLICENCIA DE USO: Los documentos a texto completo incluidos en Dialnet son de acceso libre y propiedad de sus autores y/o editores. Por tanto, cualquier acto de reproducción, distribución, comunicación pública y/o transformación total o parcial requiere el consentimiento expreso y escrito de aquéllos. Cualquier enlace al texto completo de estos documentos deberá hacerse a través de la URL oficial de éstos en Dialnet. 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