Methicilin-resistant Staphylococcus aureus: evolution of endemic clones and emergence of community clones in the hospital environment

Abstract

Infections by methicillin-resistant Staphylococcus aureus (MRSA) are still an important cause of morbidity and mortality worldwide. Health-care associated infections, especially bacteremia, often represent a clinical challenge because of the severity of the infection, the associated high mortality (close to 30% in some series) and the difficulty to initiate a correct empirical (o guided) antibiotic therapy. MRSA has spread throughout Hospital Universitari de Bellvitge (HUB) for more than 20 years and, in spite of preventive measures, the percentage of methicillin resistance among S. aureus is currently close to 24%. This figure is similar to that found in many other hospitals around Spain. The epidemiology of MRSA infection has been changing over the years with the evolution of endemic clones and the emergence of new genetic lineages of MRSA with distinct virulence attributes and with the ability to spread within the community. The identification of new reservoirs and the knowledge of the MRSA genetic content will help on one hand, to better understand the pathogenesis of the disease and to facilitate the adequate therapy; and, on the other hand, to limit the spread of epidemic lineages.

The aim of the work presented in this Thesis was to provide an integrated analysis of the genetic background of successive MRSA populations causing infection in the HUB since the beginning of the endemia (1990-2014), linked to the phenotypic expression of antibiotic resistance. In addition, we were the reference Microbiology Laboratory for a multicentre study that allowed us to have access to MRSA bacteremic isolates from 23 different hospitals in Spain obtained in 2008-2009.

The results of the studies addressed in this Thesis showed that, on average, 20% of all S. aureus isolated in Hospital Universitari de Bellvitge (HUB) from 1990 to 2014, were methicillin resistant. Over the last 10 years, methicillin resistance percentage was around 24%. This figure is similar to other hospitals in Spain (25%).

The dominant lineage in HUB for the first decade (the multiresistant Iberian clone, ST247-SCCmecI-agrI) was considered extinct. Currently, Clonal Complex 5, related to the Pediatric clone (ST5-SCCmecIV-agrII), was the dominant lineage in the HUB, as it was in other Spanish hospitals. In the HUB, clone ST8-SCCmecIV-agrI has become the second most frequent lineage in 2014. Antibiotic resistance determinants as well as genetic determinants of virulence properties were specific of particular clones.

The dominant lineage in HUB for the first decade (the multiresistant Iberian clone, ST247-SCCmecI-agrI) was considered extinct. Currently, Clonal Complex 5, related to the Pediatric clone (ST5-SCCmecIV-agrII), was the dominant lineage in the HUB, as it was in other Spanish hospitals. In the HUB, clone ST8-SCCmecIV-agrI has become the second most frequent lineage in 2014. Antibiotic resistance determinants as well as genetic determinants of virulence properties were specific of particular clones.

The presence of community-acquired MRSA lineages was detected in both MRSA collections (MRSA isolated from HUB and MRSA from different Spanish hospitals), being the most important clone USA300 (with positive and negative ACME) and the livestock related clone MRSA-ST398. However, the number of isolates belonging to these clones was scarce and in most cases corresponded to hospital-onset infections, caused by bacteria acquired in the community. No significant nosocomial transmission of community-acquired clones was detected.

Vancomycin tolerance was only detected among isolates belonging to clone ST247-SCCmecI-agrI (Iberian clone). In addition, we could not detect any influence on vancomycin susceptibility expression of agr polymorphism or rpoB mutations.

SARM se ha diseminado en el Hospital Universitari de Bellvitge (HUB) durante más de 20 años y a pesar de la aplicación de medidas preventivas, actualmente el porcentaje de resistencia a meticilina entre los aislamientos de SARM está cerca al 24%. Esta situación es similar a muchos otros hospitales españoles. El objetivo del trabajo presentado en esta tesis fue realizar un análisis integrado del perfil genético de las sucesivas poblaciones de SARM que han causado infección en el HUB desde el principio de la endemia (1990-2014), y un estudio de la expresión fenotípica de la resistencia antibiótica. En, este trabajo, se incluye también los resultados de un estudio multicéntrico en el que el Servicio de Microbiología del HUB actuó como centro de referencia, para el estudio de aislamientos procedentes de pacientes con bacteriemia por SARM ingresados en 23 hospitales españoles aislados durante el período 2008-2009.

Los resultados de los estudios presentados en esta tesis muestran que la resistencia media a meticilina en S. aureus alcanzó un valor del 20% en el HUB en el período 1990-2014. Durante los últimos 10 años, el porcentaje de resistencia a meticilina fue próximo al 24%. Esta situación fue similar en los demás hospitales (25%). El linaje dominante en el HUB durante la primera década del estudio (el clon multiresistente — clon Ibérico, ST247-SCCmecl-agr1), desapareció posteriormente. Actualmente el complejo clonal 5, relacionado con el clon Pediátrico (ST5-SCCmecIV-agrIII) es el linaje dominante en el HUB, así como en los demás hospitales en España. En el HUB, el clon ST8-SCCmecIV-agrl se ha convertido en el segundo clon más frecuente en 2014. Los determinantes de resistencia antibiótica así como los determinantes genéticos de virulencia fueron específicos para cada clon. La presencia de linajes de origen comunitaria se detectó en ambas colecciones de SARM (SARM aislado en el HUB y SARM aislado de diferentes hospitales españoles), siendo los más importantes los clones USA300 (ACME positivo y negativo) y el clon SARM asociado al ganado - SARM-ST398. Sin embargo, el número de aislados que pertenecieron a estos clones fue bajo y en la mayoría de los casos se asociaron a infecciones que debutaron en el hospital, causadas por bacterias adquiridas en la comunidad. No se detectó transmisión nosocomial de los clones asociados a la comunidad.