Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia
The human, animal and environmental health are interconnected, since all of them can contribute to the emergence, evolution and spread of antibiotic resistance. Hence, this problem must be addressed through a One Health approach. Staphylococcus spp., both coagulase-positive (CoPS) and coagulase-nega...
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Universidad de La Rioja (España)
2021
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The human, animal and environmental health are interconnected, since all of them can contribute to the emergence, evolution and spread of antibiotic resistance. Hence, this problem must be addressed through a One Health approach. Staphylococcus spp., both coagulase-positive (CoPS) and coagulase-negative (CoNS), are commensal bacteria of the skin and mucous membranes of healthy humans and animals, but they can also act as opportunistic pathogens, causing diseases of diverse severity. The objective of this thesis was to analyze the frequency and diversity of species, and to perform the molecular characterization of Staphylococcus spp. of diverse origins, including animals and the environment, with special attention to emergent and unusual antibiotic resistance and virulence genes.
Staphylococcus spp. isolates recovered from tracheal samples of 242 wild birds were characterized. SCoP were recovered from 8.3% of wild birds tested, and the isolates were identified as S. aureus (n=9) and S. delphini (n=12). Most of S. aureus isolates (n=7) were methicillin-resistant (MRSA), mecC-positive and belonged to the lineage CC130, but a mecA-carrying CC398 isolate was also identified. The virulence gene etd2 was present in all MRSA-mecC isolates, and the human immune evasion cluster (IEC) type E was identified in two of them. S. delphini isolates were methicillin-susceptible but showed resistance to at least one of the antimicrobials tested, with high penicillin (75%) and tetracycline (58%) resistance rates. All S. delphini isolates carried the virulence genes lukS-I, siet and se-int. The 60% of birds tested were CoNS-carriers, and 173 isolates were recovered, which belonged to 11 different species with predominance of S. sciuri (68.2%) and S. lentus (14.5%). The 34% of CoNS showed a multidrug resistance phenotype, and 42 mecA-carrying methicillin-resistant CoNS (MRCoNS) were detected. Two S. sciuri isolates harbored the virulence gene tst.
Seventy-two staphylococci recovered from environmental samples (air and liquid manure tank) of two pig farms, with intensive production (IP) and semiextensive production (SEP), were analyzed. Four MRSA and MSSA (methicillin-susceptible S. aureus) isolates of lineage CC398 were recovered from the air of the PI farm. Regarding CoNS, multidrug resistance was observed in 59 of the 68 isolates (80%), and eight mecAMRCoNS isolates were identified. The rates of resistance for five groups of antimicrobial agents were significatively higher in CoNS isolates recovered from the IP farm in relation to those of SEP farm. One S. simulans isolate carrying the genes encoding the Panton-Valentine leukocidin (PVL) and three S. cohnii harboring the virulence gene eta were identified. Two S. equorum or S. arlettae isolates recovered from the IP farm showed linezolid resistance and carried the cfr gene.
The genetic lineages and the antibiotic resistance and virulence genes of 56 CoPS recovered from animals with signs of infection (pigs and companion animals), were investigated. Among the isolates recovered from diseased pigs (23 S. aureus), a great prevalence of MRSA CC398 was detected, but other livestock associated genetic lineages, such as MRSA CC9, were also identified, most of them (91%) multiresistant isolates. One MRSA CC398 isolate of porcine origin showed linezolid resistance mediated by the cfr gene, which was co-located with the fexA gene in a Tn558 variant. Among the isolates recovered from companion animals (five S. aureus and 28 S. pseudintermedius), nine methicillinresistant isolates (27%) carrying the mecA gene were detected, and the eight methicillin-resistant S. pseudintermedius (MRSP), belonged to the epidemic clones ST71, ST68 and ST258. The S. pseudintermedius isolates showed high penicillin, tetracycline and trimethoprimsulfamethoxazole resistance rates (>50%), and all of them carried the siet, se-int and lukS/F-I virulence genes. Among the S. aureus isolates, a MRSA isolate ascribed to CC398 and MSSA isolates of human-associated genetic lineages (CC22 and CC5) carrying the PVL and IEC encoding genes were detected; a t10576-ST1660 SASM isolate of potential equine origin, harboring the lukPQ and scneq genes, was also identified.
Lastly, a comparative study on the mechanisms of linezolid resistance among the animal and environmental isolates, and those recovered from clinical samples of different Spanish hospitals, was performed. The cfr gene was detected in two clinical mecA-MRSA isolates: 1) one MRSA CC398 isolate, recovered from the nasal sample of a pig farmer, with the cfr and fexA genes located in a Tn558 variant; 2) one MRSA isolate, from a pharyngeal sample, with the cfr gene identified together with the fexA gene in a conjugative 38864 bp plasmid. In the remaining clinical isolates (one MSSA and 17 CoNS), linezolid resistance was mediated by point mutations in the rRNA 23S (G2576T or C2534T) and/or amino acid changes in the ribosomal proteins L3 and L4.
This thesis brings a One Health approach in order to understand the population dynamics of Staphylococcus spp., the antibiotic resistance and virulence genes flow, as well as the interaction among the bacteria of this genus in the human, animal and environmental settings. |
| author2 |
Torres Manrique, Carmen (Universidad de La Rioja) |
| author_facet |
Torres Manrique, Carmen (Universidad de La Rioja) Ruiz Ripa, Laura |
| format |
text (thesis) |
| author |
Ruiz Ripa, Laura |
| spellingShingle |
Ruiz Ripa, Laura Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia |
| author_sort |
Ruiz Ripa, Laura |
| title |
Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia |
| title_short |
Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia |
| title_full |
Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia |
| title_fullStr |
Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia |
| title_full_unstemmed |
Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia |
| title_sort |
epidemiología molecular de staphylococcus spp. desde un enfoque one health: genes emergentes e inusuales de resistencia a antibióticos y de virulencia |
| publisher |
Universidad de La Rioja (España) |
| publishDate |
2021 |
| url |
https://dialnet.unirioja.es/servlet/oaites?codigo=286288 |
| work_keys_str_mv |
AT ruizripalaura epidemiologiamoleculardestaphylococcussppdesdeunenfoqueonehealthgenesemergenteseinusualesderesistenciaaantibioticosydevirulencia |
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1718346693294948352 |
| spelling |
oai-TES00000229832021-03-06Epidemiología molecular de Staphylococcus spp. desde un enfoque One Health: genes emergentes e inusuales de resistencia a antibióticos y de virulenciaRuiz Ripa, LauraThe human, animal and environmental health are interconnected, since all of them can contribute to the emergence, evolution and spread of antibiotic resistance. Hence, this problem must be addressed through a One Health approach. Staphylococcus spp., both coagulase-positive (CoPS) and coagulase-negative (CoNS), are commensal bacteria of the skin and mucous membranes of healthy humans and animals, but they can also act as opportunistic pathogens, causing diseases of diverse severity. The objective of this thesis was to analyze the frequency and diversity of species, and to perform the molecular characterization of Staphylococcus spp. of diverse origins, including animals and the environment, with special attention to emergent and unusual antibiotic resistance and virulence genes. Staphylococcus spp. isolates recovered from tracheal samples of 242 wild birds were characterized. SCoP were recovered from 8.3% of wild birds tested, and the isolates were identified as S. aureus (n=9) and S. delphini (n=12). Most of S. aureus isolates (n=7) were methicillin-resistant (MRSA), mecC-positive and belonged to the lineage CC130, but a mecA-carrying CC398 isolate was also identified. The virulence gene etd2 was present in all MRSA-mecC isolates, and the human immune evasion cluster (IEC) type E was identified in two of them. S. delphini isolates were methicillin-susceptible but showed resistance to at least one of the antimicrobials tested, with high penicillin (75%) and tetracycline (58%) resistance rates. All S. delphini isolates carried the virulence genes lukS-I, siet and se-int. The 60% of birds tested were CoNS-carriers, and 173 isolates were recovered, which belonged to 11 different species with predominance of S. sciuri (68.2%) and S. lentus (14.5%). The 34% of CoNS showed a multidrug resistance phenotype, and 42 mecA-carrying methicillin-resistant CoNS (MRCoNS) were detected. Two S. sciuri isolates harbored the virulence gene tst. Seventy-two staphylococci recovered from environmental samples (air and liquid manure tank) of two pig farms, with intensive production (IP) and semiextensive production (SEP), were analyzed. Four MRSA and MSSA (methicillin-susceptible S. aureus) isolates of lineage CC398 were recovered from the air of the PI farm. Regarding CoNS, multidrug resistance was observed in 59 of the 68 isolates (80%), and eight mecAMRCoNS isolates were identified. The rates of resistance for five groups of antimicrobial agents were significatively higher in CoNS isolates recovered from the IP farm in relation to those of SEP farm. One S. simulans isolate carrying the genes encoding the Panton-Valentine leukocidin (PVL) and three S. cohnii harboring the virulence gene eta were identified. Two S. equorum or S. arlettae isolates recovered from the IP farm showed linezolid resistance and carried the cfr gene. The genetic lineages and the antibiotic resistance and virulence genes of 56 CoPS recovered from animals with signs of infection (pigs and companion animals), were investigated. Among the isolates recovered from diseased pigs (23 S. aureus), a great prevalence of MRSA CC398 was detected, but other livestock associated genetic lineages, such as MRSA CC9, were also identified, most of them (91%) multiresistant isolates. One MRSA CC398 isolate of porcine origin showed linezolid resistance mediated by the cfr gene, which was co-located with the fexA gene in a Tn558 variant. Among the isolates recovered from companion animals (five S. aureus and 28 S. pseudintermedius), nine methicillinresistant isolates (27%) carrying the mecA gene were detected, and the eight methicillin-resistant S. pseudintermedius (MRSP), belonged to the epidemic clones ST71, ST68 and ST258. The S. pseudintermedius isolates showed high penicillin, tetracycline and trimethoprimsulfamethoxazole resistance rates (>50%), and all of them carried the siet, se-int and lukS/F-I virulence genes. Among the S. aureus isolates, a MRSA isolate ascribed to CC398 and MSSA isolates of human-associated genetic lineages (CC22 and CC5) carrying the PVL and IEC encoding genes were detected; a t10576-ST1660 SASM isolate of potential equine origin, harboring the lukPQ and scneq genes, was also identified. Lastly, a comparative study on the mechanisms of linezolid resistance among the animal and environmental isolates, and those recovered from clinical samples of different Spanish hospitals, was performed. The cfr gene was detected in two clinical mecA-MRSA isolates: 1) one MRSA CC398 isolate, recovered from the nasal sample of a pig farmer, with the cfr and fexA genes located in a Tn558 variant; 2) one MRSA isolate, from a pharyngeal sample, with the cfr gene identified together with the fexA gene in a conjugative 38864 bp plasmid. In the remaining clinical isolates (one MSSA and 17 CoNS), linezolid resistance was mediated by point mutations in the rRNA 23S (G2576T or C2534T) and/or amino acid changes in the ribosomal proteins L3 and L4. This thesis brings a One Health approach in order to understand the population dynamics of Staphylococcus spp., the antibiotic resistance and virulence genes flow, as well as the interaction among the bacteria of this genus in the human, animal and environmental settings.La salud humana, animal y ambiental están interconectadas, ya que todas ellas contribuyen a la emergencia, evolución y diseminación de la resistencia a los antibióticos. Por lo tanto, este problema debe ser abordado desde un enfoque “One Health”. Staphylococcus spp., tanto coagulasa positivo (SCoP) como coagulasa negativo (SCoN), son bacterias comensales de la piel y mucosas de humanos y animales sanos, pero también pueden actuar como patógenos oportunistas, causando infecciones de diversa severidad. El objetivo de esta tesis fue analizar la frecuencia y diversidad de especies, y realizar la caracterización molecular de Staphylococcus spp. de diversos orígenes, incluyendo animales y medio ambiente, con especial atención a genes de resistencia a antibióticos y de virulencia emergentes o inusuales. Se caracterizaron las cepas de Staphylococcus spp. aisladas de muestras traqueales de 242 aves silvestres. Se detectó SCoP en el 8,3% de las aves estudiadas, y los aislados fueron identificados como S. aureus (n=9) y S. delphini (n=12). La gran mayoría de los S. aureus (n=7) fueron resistentes a meticilina (SARM), mecC positivos y del linaje CC130, pero se identificó también una cepa portadora del gen mecA perteneciente al CC398. El gen de virulencia etd2 estuvo presente todas las cepas SARM-mecC, y el clúster de evasión del sistema inmune humano (IEC) tipo-E se identificó en dos de ellas. Las cepas S. delphini fueron sensibles a meticilina, pero todas mostraron resistencia al menos a uno de los antibióticos analizados, con tasas altas de resistencia a penicilina (75%) y tetraciclina (58%). Todos los aislados S. delphini portaban los genes de virulencia lukS-I, siet, y se-int. El 60% de las aves estudiadas eran portadoras de SCoN, y se recuperaron 173 cepas que pertenecían a 11 especies diferentes, con predominancia de S. sciuri (68,2%) y S. lentus (14,5%). El 34% de los SCoN mostraron un fenotipo de multiresistencia y se detectaron 42 cepas resistentes a meticilina (SCoNRM), portadoras del gen mecA. Dos cepas S. sciuri albergaban el gen de virulencia tst. Se analizaron 72 cepas de Staphylococcus aisladas de muestras ambientales (aire y tanque de purines) de dos granjas porcinas, con producción intensiva (PI) y semiextensiva (PSE). Se aislaron cuatro cepas SARM y S. aureus sensible a meticilina (SASM) del linaje CC398, de las muestras de aire de la granja PI. Respecto a los SCoN, 59 de las 68 cepas obtenidas (80%) fueron multiresistentes, y ocho cepas fueron SCoNRM, portadores del gen mecA. Las tasas de resistencia a 5 familias de antibióticos fueron significativamente más altas entre los aislados SCoN de la granja PI que en los de la granja PSE. Se identificó una cepa S. simulans portadora de los genes de la leucocidina de Panton-Valentine (LPV) y tres cepas S. cohnii que albergaban el gen de virulencia eta. Dos cepas S. equroum o S. arlettae aisladas de la granja PI fueron resistentes a linezolid, y potaban portadoras el gen cfr. Se investigaron las líneas genéticas y los genes de virulencia y de resistencia a antibióticos 56 SCoP aislados de animales con signos de infección (cerdos y animales de compañía). Entre las cepas obtenidas de cerdos enfermos (23 S. aureus), se detectaron mayoritariamente cepas SARM-CC398, pero también otros clones asociados a ganado como SARM-CC9, siendo en su mayoría cepas multiresistentes (91%). Una cepa SARM CC398 resistente a linezolid de origen porcino portaba el gen cfr, colocalizado con fexA en una variante del Tn558. Entre las cepas de animales de compañía (cinco S. aureus y 28 S. pseudintermedius) se detectaron nueve cepas resistentes a meticilina mecA positivas y entre las ocho cepas de S. pseudintermedius resistentes a meticilina se identificaron los clones epidémicos ST71, ST68 y ST258. Las cepas S. pseudintermedius presentaron altas tasas de resistencia a penicilina, tetraciclina y trimetoprim-sulfametoxazol (>50%), y todas ellas contenían los genes de virulencia siet, se-int y lukS/F-I. Entre las cinco cepas S. aureus se detectó una cepa SARM del linaje CC398 y cepas SASM de líneas genéticas asociadas a humanos (CC22 y CC5), portadoras de los genes de la LPV y el IEC; también se identificó una cepa SASM con un posible origen equino portadora de los genes lukPQ y scneq. Por último, se realizó un estudio comparativo de los mecanismos de resistencia a linezolid en las cepas de origen animal y ambiental, con los presentes en muestras de origen clínico procedentes de distintos hospitales españoles. El gen cfr se detectó en dos cepas clínicas SARM portadoras del gen mecA: 1) una cepa SARM-CC398, aislada de una muestra nasal de un granjero, con los genes cfr y fexA localizados en una variante del transposón Tn558; 2) una cepa SARM, de una muestra faríngea, en la que se identificó el gen cfr junto con fexA en un plásmido conjugativo de 38864 pb. En el resto de las cepas clínicas (1 SASM Y 17 SCoN) la resistencia a linezolid estuvo mediada por mutaciones puntuales en el ARNr 23S (G2576T o C2534T) y/o cambios aminoacídicos en las proteínas ribosomales L3 y L4. Esta tesis supone una aproximación One Health para entender la dinámica poblacional de Staphylococcus spp., así como el flujo de genes de resistencia y de virulencia, y la interacción de las bacterias de este género en los ámbitos humano, animal y ambiental.Universidad de La Rioja (España)Torres Manrique, Carmen (Universidad de La Rioja)2021text (thesis)application/pdfhttps://dialnet.unirioja.es/servlet/oaites?codigo=286288spaLICENCIA 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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