Increasing trend of antimicrobial resistance in Shigella associated with MSM transmission in Barcelona, 2020-21: outbreak of XRD Shigella sonnei and dissemination of ESBL-producing Shigella flexneri.

BACKGROUND: Several countries have recently reported the detection of ESBL-producing Shigella sonnei associated with transmission among MSM. In a previous study by our group, 2.8% of Shigella spp. obtained from MSM in Barcelona between 2015 and 2019 were ESBL producers. OBJECTIVES: To describe and characterize the emerging ESBL-producing Shigella spp. associated with sexual transmission among MSM detected from 2020 to 2021 in Barcelona, elucidating their connectivity with contemporaneous ESBL-producing Shigella spp. from other countries. RESULTS: From 2020 to 2021, we identified that among MSM, 68% of S. sonnei were XDR harbouring blaCTX-M-27 and 14% of Shigella flexneri were MDR harbouring blaCTX-M-27. WGS analysis showed that the ESBL-producing S. sonnei were part of a monophyletic cluster, which included isolates responsible for the prolonged outbreak occurring in the UK. Our data also reveal the first emergence and clonal dissemination of ESBL-producing and fluoroquinolone-resistant S. flexneri 2a among MSM. CONCLUSIONS: We report an increasing trend of antimicrobial resistance in Shigella spp. among MSM in Barcelona since 2021, mainly as a consequence of the dissemination of XDR ESBL-producing S. sonnei, previously reported in the UK. These results highlight the importance of international collaborative surveillance of MDR/XDR S. sonnei and S. flexneri for rapid identification of their emergence and the prevention of the transmission of these pathogens.

Time to decision in sepsis / Tiempo para la toma de decisiones en sepsis

Introduction: This study aimed to identify the common barriers leading to delayed initial management, microbiological diagnosis, and appropriate empirical antimicrobial treatment in sepsis. Patients and methods: A cross-sectional study was performed by the application of a population-based survey. Four different surveys were designed, targeting the healthcare personnel located in main hospital areas [emergency department (SEMES); infectious diseases and clinical microbiology-microbiological diagnosis (SEIMC-M); intensive care and infectious diseases, (SEMICYUC-GTEIS); and infectious diseases and clinical microbiology-clinical diagnosis, (SEIMC-C)]. Results: A total of 700 valid surveys were collected from June to November 2019: 380 (54.3%) of SEMES, 127 (18.1%) of SEIMC-M, 97 (13.9%) de SEMICYUC-GTEIS and 96 (13.7%) of SEIMC-C, in 270 hospitals of all levels of care. The qSOFA score was used as a screening tool. The most used biomarker was procalcitonin (n=92, 39.8%). The sepsis code was implemented in 157 of 235 participating centers (66.2%), particularly in tertiary level hospitals. The mean frequency of contaminated blood cultures was 8.9% (8.7). In 85 (78.7%) centers, positive results of blood cultures were available within the first 72 hours and were communicated to the treating physician effectively by phone or e-mail in 76 (81.7%) cases. The main reason for escalating treatment was clinical deterioration, and the reason for de-escalating antimicrobials was significantly different between the specialties. Quality indicators were not frequently monitored among the different participating centers. Conclusion: There are significant barriers that hinder adequate management processes in sepsis in Spanish hospitals. (AU)

Introducción: Este estudio tuvo como objetivo identificar las barreras comunes que conducen al retraso en el manejo inicial, el diagnóstico microbiológico y el tratamiento antimicrobiano empírico adecuado en la sepsis. Pacientes y métodos: Se realizó un estudio transversal mediante la aplicación de una encuesta de base poblacional. Se diseñaron cuatro encuestas diferentes, dirigidas al personal de salud ubicado en las principales áreas hospitalarias [urgencias (SEMES); enfermedades infecciosas y microbiología clínica-diagnóstico microbiológico (SEIMC-M); cuidados intensivos y enfermedades infecciosas (SEMICYUC-GTEIS); y enfermedades infecciosas y microbiología clínica-diagnóstico clínico, (SEIMC-C)]. Resultados: Se recogieron un total de 700 encuestas válidas de junio a noviembre de 2019: 380 (54,3%) de SEMES, 127 (18,1%) de SEIMC-M, 97 (13,9%) de SEMICYUC-GTEIS y 96 (13,7%) de la SEIMC-C, en 270 hospitales de todos los niveles de atención. El qSOFA se utilizó principalmente como herramienta de detección. El biomarcador más utilizado fue la procalcitonina (n=92, 39,8%). El código sepsis estaba implementado en 157 de 235 centros participantes (66,2%), particularmente en hospitales de tercer nivel. La frecuencia media de hemocultivos contaminados fue del 8,9% (8,7). En 85 (78,7%) de los centros, los resultados de los hemocultivos positivos estuvieron disponibles en las primeras 72 horas y se comunicaron al médico responsable del paciente por teléfono o correo electrónico en 76 casos (81,7%). El motivo principal de la escalada del tratamiento fue el deterioro clínico y el motivo de la desescalada de los antimicrobianos fue significativamente diferente entre las especialidades. Los indicadores de calidad no se monitorizaban con frecuencia en los diferentes centros. Conclusión: Existen importantes barreras que dificultan los procesos de manejo adecuado de la sepsis en los hospitales españoles. (AU)

A side-by-side comparison of the performance and time-and-motion data of VITEK MS.

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry systems are designed for rapid and reliable microbial identification. VITEK MS PRIME is the bioMérieux's new generation instrument equipped with a continuous load-and-go sample loading system, urgent slide prioritization for critical patient samples and new internal components for faster identification. The aim of this study was to assess the performance of VITEK MS PRIME and to compare it to that of the VITEK MS system. In addition, at two sites, we performed a time-and-motion study to evaluate the efficiency of sample analysis from colony picking to slide removal from the instrument. We analyzed by VITEK MS and VITEK MS PRIME a total of 1413 isolates (1320 bacterial and 76 yeast) deriving from routine diagnostic samples that came into four laboratories in Canada, France, Italy, and Spain. VITEK MS PRIME and VITEK MS were concordant to the species and genus level for 1354/1413 (95.8%) and to the species level for 1341/1413 (94.9%). The identification and concordance rates in individual centers were largely homogenous. Overall, VITEK MS PRIME identified 1370/1413 (97.0%) of isolates compared to 1367/1413 (96.7%) identified by VITEK MS. Identification rates were consistently high for all microorganism categories. A time-and-motion study showed that the use of VITEK MS PRIME was associated with significant time saving. VITEK MS PRIME performs as well as VITEK MS and reduces the time necessary for pathogen identification. To fully optimize the laboratory process and obtain maximum efficiency, VITEK MS PRIME must be integrated into the laboratory workflow.

Pertactin-Deficient Bordetella pertussis with Unusual Mechanism of Pertactin Disruption, Spain, 1986-2018.

Bordetella pertussis not expressing pertactin has increased in countries using acellular pertussis vaccines (ACV). The deficiency is mostly caused by pertactin gene disruption by IS481. To assess the effect of the transition from whole-cell vaccine to ACV on the emergence of B. pertussis not expressing pertactin in Spain, we studied 342 isolates collected during 1986-2018. We identified 93 pertactin-deficient isolates. All were detected after introduction of ACV and represented 38% of isolates collected during the ACV period; 58.1% belonged to a genetic cluster of isolates carrying the unusual prn::del(-292, 1340) mutation. Pertactin inactivation by IS481 insertion was identified in 23.7% of pertactin-deficient isolates, arising independently multiple times and in different phylogenetic branches. Our findings support the emergence and dissemination of a cluster of B. pertussis with an infrequent mechanism of pertactin disruption in Spain, probably resulting from introduction of ACV.

Circulation of multi-drug-resistant Shigella sonnei and Shigella flexneri among men who have sex with men in Barcelona, Spain, 2015-2019.

BACKGROUND: In high-income countries, shigellosis is mainly found in travellers to high-risk regions or in men who have sex with men (MSM). This study investigated the genomic characteristics and the features of antimicrobial resistance of MSM-associated Shigella flexneri and Shigella sonnei circulating in Barcelona, Spain, elucidating their connectivity with contemporaneous Shigella spp. from other countries. METHODS: Antimicrobial susceptibility, whole-genome sequencing, genomic characterization and phylogenetic analysis were performed in MSM-associated Shigella spp. recovered from 2015 to 2019. Reference genomes of MSM-associated Shigella spp. were included for contextualization and to determine their connection with international outbreaks. RESULTS: In total, 44 S. flexneri and 26 S. sonnei were identified among MSM. Overall, 80% showed resistance to azithromycin, 65.7% showed resistance to trimethoprim-sulphamethoxazole and 32.8% showed resistance to ciprofloxacin; 27.1% were resistant to all three antimicrobials. mphA and/or ermB, and qnrS and mutations in the quinolone resistance determining regions were found in the azithromycin- and ciprofloxacin-resistant isolates, respectively. Additionally, two isolates carried blaCTX-M-27. Single-nucleotide-polymorphism-based analysis revealed that the isolates were organized into different lineages, most of which were closely related to dominant MSM-associated lineages described previously in the UK and Australia. CONCLUSIONS: This study investigated the circulation of lineages of S. flexneri and S. sonnei among MSM in Spain that were mainly resistant to first-/second-line oral treatments, and closely related to dominant MSM-associated lineages described previously in the UK and Australia. These data reinforce the urgent need for the implementation of public health measures focusing on the early detection and prevention of transmission of this emerging pathogen, which is contributing to the antimicrobial resistance crisis in sexually transmitted infections.

Comprehensive clinical and epidemiological assessment of colonisation and infection due to carbapenemase-producing Enterobacteriaceae in Spain.

BACKGROUND: Most available information on carbapenemase-producing Enterobacteriaceae (CPE) is usually associated with specific types of infection or patient or with descriptions of outbreaks. The aim of this study was to comprehensively analyse the clinical epidemiology, clinical features and outcomes of colonisation and infections due to CPE in Spain. METHODS: A multicentre prospective cohort study was carried out in 34 Spanish hospitals from February to May 2013. All new patients testing positive for CPE in clinical samples were included. Logistic regression was used to identify predictors of mortality. RESULTS: Overall, 245 cases were included. The most frequent organism was Klebsiella pneumoniae (74%) and the carbapenemases belonged to the OXA-48 (74%), metallo-ß-lactamase (MBL) (24%) and KPC (2%) groups. Acquisition was nosocomial in 145 cases (60%) and healthcare-associated (HCA) in 91 (37%); 42% of the latter were nursing home residents, in whom OXA-48-producing K. pneumoniae ST405 predominated. MBLs and OXA-48 predominated in ICU and medical patients, respectively. Overall, 67% of patients had infections. The most frequent infections identified in this study were urinary tract (43%) and skin structure (21%) infections, and 10% of infections were bacteraemic. Crude mortality was 20%. Inappropriate antibiotic therapy was independently associated with an increased risk of death (OR = 3.30; 95% CI: 1.34-8.11). CONCLUSIONS: We found some differences in the epidemiology of CPE depending on the type of carbapenemase produced. Although a low proportion of CPE infections were bacteraemic, active antibiotic therapy was a protective factor for reducing mortality.

[Empirical antimicrobial therapy in ICU admitted patients. Influence of microbiological confirmation on the length of treatment]. / Influencia de la confirmación microbiológica en la duración y adaptación del tratamiento antimicrobiano empírico de los pacientes ingresados en UCI.

Introduction. Most patients admitted to the Intensive Care Units (ICU) receive antimicrobial treatment. A proper therapeutic strategy may be useful in decreasing inappropriate empirical antibiotic treatments. When the infection is not microbiologically confirmed, the antimicrobial streamlining may be difficult. Nevertheless, there is scant information about the influence of the microbiological confirmation of the infections on empirical antimicrobial treatment duration. Method. Post-hoc analysis of prospective data (ENVIN-UCI register) and observational study of patients admitted (> 24 hours) in a medico-surgical ICU, through the three-months annual surveillance interval for a period of ten years, receiving antimicrobial treatment for treating an infection. Demographic, infection and microbiological data were collected as well as empirical antimicrobial treatment and causes of adaptation. The main goal was to establish the influence of microbiological confirmation on empirical antimicrobial treatment duration. Results. During the study period 1,526 patients were included, 1,260 infections were diagnosed and an empirical antibiotic treatment was started in 1,754 cases. Infections were microbiologically confirmed in 1,073 (62.2%) of the empirical antibiotic treatment. In 593 (55.3%) cases, the antimicrobial treatment was considered appropriate. The main cause of treatment adaptation in the microbiologically confirmed infections was streamlining (39%). The microbiological confirmation of the infection was not associated with significantly shorter empirical antibiotic treatments (6.6 ± 5.2 VS. 6.8 ± 4.5 days). Conclusion. The microbiological confirmation of infections in patients admitted to UCI was associated with a higher reduction of antimicrobial spectrum, although had no effect on the length of empirical antimicrobial therapy.

Influencia de la confirmación microbiológica en la duración y adaptación del tratamiento antimicrobiano empírico de los pacientes ingresados en UCI / Empirical antimicrobial therapy in ICU admitted patients. Influence of microbiological confirmation on the length of treatment

Introducción. Un elevado porcentaje de pacientes que ingresan en las Unidades de Cuidados intensivos (UCI) reciben tratamiento antimicrobiano. Inicialmente, éste ha de ser empírico, en espera de la confirmación microbiológica. Sin embargo, la adaptación y la duración del tratamiento empírico inicial son dificultosas en los casos en los que no se existe confirmación microbiológica de la infección. Además, existe escasa información sobre la influencia de la confirmación microbiológica en la duración y adaptación del tratamiento empírico. Método. Estudio post-hoc de datos prospectivos (registro ENVIN-UCI), observacional de pacientes ingresados (> 24 horas), en una UCI médico-quirúrgica durante los cortes de 3 meses anuales de 2001 a 2011, y que recibieron tratamiento antimicrobiano para el tratamiento de una infección. Se recogieron datos demográficos, de las infecciones, de la microbiología, del tratamiento antimicrobiano empírico y de las causas de adaptación del mismo, con el objetivo de determinar la influencia de la información microbiológica en la duración y adaptación del tratamiento empírico inicial. Resultados. Durante el periodo de estudio se incluyeron 1.516 pacientes y 1.260 infecciones que condicionaron 1.754 indicaciones de tratamiento empírico. En 1.073 (62,2%) de las indicaciones realizadas como tratamiento empírico se obtuvo confirmación microbiológica de la infección. En 593 (55,3%) casos los antibióticos prescritos se consideraron adecuados. La principal causa de adaptación del tratamiento en las infecciones con confirmación microbiológica fue la reducción de espectro (39%). La confirmación microbiológica no se asoció a diferencias significativas en la duración del tratamiento antimicrobiano en su indicación empírica (6,6 ± 5,2 vs. 6,8 ± 4,5 días). Conclusión. La confirmación microbiológica de las infecciones en pacientes ingresados en UCI permitió la reducción del espectro aunque no modificó de forma significativa la duración del tratamiento antimicrobiano en las indicaciones realizadas como tratamiento empírico (AU)

Introduction. Most patients admitted to the Intensive Care Units (ICU) receive antimicrobial treatment. A proper therapeutic strategy may be useful in decreasing inappropriate empirical antibiotic treatments. When the infection is not microbiologically confirmed, the antimicrobial streamlining may be difficult. Nevertheless, there is scant information about the influence of the microbiological confirmation of the infections on empirical antimicrobial treatment duration. Method. Post-hoc analysis of prospective data (ENVIN-UCI register) and observational study of patients admitted (> 24 hours) in a medico-surgical ICU, through the three-months annual surveillance interval for a period of ten years, receiving antimicrobial treatment for treating an infection. Demographic, infection and microbiological data were collected as well as empirical antimicrobial treatment and causes of adaptation. The main goal was to establish the influence of microbiological confirmation on empirical antimicrobial treatment duration. Results. During the study period 1,526 patients were included, 1,260 infections were diagnosed and an empirical antibiotic treatment was started in 1,754 cases. Infections were microbiologically confirmed in 1,073 (62.2%) of the empirical antibiotic treatment. In 593 (55.3%) cases, the antimicrobial treatment was considered appropriate. The main cause of treatment adaptation in the microbiologically confirmed infections was streamlining (39%). The microbiological confirmation of the infection was not associated with significantly shorter empirical antibiotic treatments (6.6 ± 5.2 VS. 6.8 ± 4.5 days). Conclusion. The microbiological confirmation of infections in patients admitted to UCI was associated with a higher reduction of antimicrobial spectrum, although had no effect on the length of empirical antimicrobial therapy (AU)

ESBL-producing Salmonella enterica serovar Typhi in traveler returning from Guatemala to Spain.

We report a case of typhoid fever in a traveler returning to Spain from Guatemala that was caused by Salmonella enterica serovar Typhi which produced an extended-spectrum ß-lactamase (ESBL). This finding demonstrates the presence of ESBL-producing S. enterica ser. Typhi strains in the Americas. Enhanced surveillance is necessary to prevent further spread.