Whole genome analysis of Gram-negative bacteria using the EPISEQ CS application and other bioinformatic platforms.

OBJECTIVES: To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa from medical centres of Mexico using whole genome sequencing data analysed with the EPISEQⓇ CS application and other bioinformatic platforms. METHODS: Clinical isolates collected from 28 centres in Mexico included carbapenem-non-susceptible K. pneumoniae (n = 22), E. coli (n = 24), A. baumannii (n = 16), and P. aeruginosa (n = 13). Isolates were subjected to whole genome sequencing using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQⓇ CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database was used for E. coli and A. baumannii. RESULTS: For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance, and the presence of blaNDM-1 explained carbapenem non-susceptibility in 18 strains and blaKPC-3 in four strains. Regarding E. coli, both EPISEQⓇ CS and bacterial whole genome sequence typing database analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried blaNDM, 3 of 24 (12.4%) carried blaOXA-232, and 1 carried blaOXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was blaOXA-72, followed by blaOXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, blaVIM, blaIMP, and blaGES were the more frequently detected. Multiple virulence genes were detected in all strains. CONCLUSION: Compared to the other available platforms, EPISEQⓇ CS enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of the virulome and resistome.

Bacterial incidence and drug resistance from pathogens recovered from blood, cerebrospinal and pleural fluids in 2019-2020. Results of the Invifar network.

Background: Antimicrobial resistance is a global concern. Analysis of sterile fluids is essential because microorganisms are defined as significant in most cases. Blood, cerebrospinal, and pleural fluids are frequently received in the microbiology lab because they are associated with considerable rates of morbi-mortality. Knowledge of epidemiology in these samples is needed to choose proper empirical treatments due to the importance of reducing selection pressure. Methods: We used retrospective laboratory data of blood, CSF, and pleural fluid collected from patients in Mexico between 2019 and 2020. Each laboratory identified the strains and tested susceptibility using its routine methods. For Streptococcus pneumoniae, a comparative analysis was performed with data from the broth microdilution method. Results: Forty-five centers participated in the study, with 30,746 clinical isolates from blood, 2,429 from pleural fluid, and 2,275 from CSF. For blood and CSF, Staphylococcus epidermidis was the most frequent. For blood, among gram negatives, the most frequent was Escherichia coli. Among Enterobacterales, 9.8% of K. pneumoniae were carbapenem-resistant. For S. pneumoniae, similar resistance percentages were observed for levofloxacin, cefotaxime, and vancomycin. For CSF, the most frequent gram-negative was E. coli. In Acinetobacter baumannii, carbapenem resistance was 71.4%. The most frequent species detected for pleural fluid was E. coli; in A. baumannii, carbapenem resistance was 96.3%. Conclusion: Gram-negative bacteria, with E. coli most prevalent, are frequently recovered from CSF, blood, and pleural fluid. In S. pneumoniae, the routine, conventional methods showed good agreement in detecting resistance percentages for erythromycin, levofloxacin, and vancomycin.

Active Surveillance of Antimicrobial Resistance and Carbapenemase-Encoding Genes According to Sites of Care and Age Groups in Mexico: Results from the INVIFAR Network.

We analyzed the antimicrobial resistance (AMR) data of 6519 clinical isolates of Escherichia coli (n = 3985), Klebsiella pneumoniae (n = 775), Acinetobacter baumannii (n = 163), Pseudomonas aeruginosa (n = 781), Enterococcus faecium (n = 124), and Staphylococcus aureus (n = 691) from 43 centers in Mexico. AMR assays were performed using commercial microdilution systems (37/43) and the disk diffusion susceptibility method (6/43). The presence of carbapenemase-encoding genes was assessed using PCR. Data from centers regarding site of care, patient age, and clinical specimen were collected. According to the site of care, the highest AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from ICU patients. In contrast, in A. baumannii, higher AMR was observed in isolates from hospitalized non-ICU patients. According to age group, the highest AMR was observed in the ≥60 years age group for E. coli, E. faecium, and S. aureus, and in the 19-59 years age group for A. baumannii and P. aeruginosa. According to clinical specimen type, a higher AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from blood specimens. The most frequently detected carbapenemase-encoding gene in E. coli was blaNDM (84%).

Increment Antimicrobial Resistance During the COVID-19 Pandemic: Results from the Invifar Network.

Aim: This study aims to assess the changes in antimicrobial resistance among some critical and high-priority microorganisms collected previously and during the coronavirus disease 2019 (COVID-19) pandemic in Mexico. Methods: We collected antimicrobial susceptibility data for critical and high-priority microorganisms from blood, urine, respiratory samples, and from all specimens, in which the pathogen may be considered a causative agent. Data were stratified and compared for two periods: 2019 versus 2020 and second semester 2019 (prepandemic) versus the second semester 2020 (pandemic). Results: In the analysis of second semester 2019 versus the second semester 2020, in blood samples, increased resistance to oxacillin (15.2% vs. 36.9%), erythromycin (25.7% vs. 42.8%), and clindamycin (24.8% vs. 43.3%) (p ≤ 0.01) was detected for Staphylococcus aureus, to imipenem (13% vs. 23.4%) and meropenem (11.2% vs. 21.4) (p ≤ 0.01), for Klebsiella pneumoniae. In all specimens, increased ampicillin and tetracycline resistance was detected for Enterococcus faecium (p ≤ 0.01). In cefepime, meropenem, levofloxacin, and gentamicin (p ≤ 0.01), resistance was detected for Escherichia coli; and in piperacillin-tazobactam, cefepime, imipenem, meropenem, ciprofloxacin, levofloxacin, and gentamicin (p ≤ 0.01), resistance was detected for Pseudomonas aeruginosa. Conclusion: Antimicrobial resistance increased in Mexico during the COVID-19 pandemic. The increase in oxacillin resistance for S. aureus and carbapenem resistance for K. pneumoniae recovered from blood specimens deserves special attention. In addition, an increase in erythromycin resistance in S. aureus was detected, which may be associated with high azithromycin use. In general, for Acinetobacter baumannii and P. aeruginosa, increasing resistance rates were detected.

Drug resistance phenotypes and genotypes in Mexico in representative gram-negative species: Results from the infivar network.

AIM: This report presents phenotypic and genetic data on the prevalence and characteristics of extended-spectrum ß-lactamases (ESBLs) and representative carbapenemases-producing Gram-negative species in Mexico. MATERIAL AND METHODS: A total of 52 centers participated, 43 hospital-based laboratories and 9 external laboratories. The distribution of antimicrobial resistance data for Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae complex, Acinetobacter baumannii complex, and Pseudomonas aeruginosa in selected clinical specimens from January 1 to March 31, 2020 was analyzed using the WHONET 5.6 platform. The following clinical isolates recovered from selected specimens were included: carbapenem-resistant Enterobacteriaceae, ESBL or carbapenem-resistant E. coli, and K. pneumoniae, carbapenem-resistant A. baumannii complex, and P. aeruginosa. Strains were genotyped to detect ESBL and/or carbapenemase-encoding genes. RESULTS: Among blood isolates, A. baumannii complex showed more than 68% resistance for all antibiotics tested, and among Enterobacteria, E. cloacae complex showed higher resistance to carbapenems. A. baumannii complex showed a higher resistance pattern for respiratory specimens, with only amikacin having a resistance lower than 70%. Among K. pneumoniae isolates, blaTEM, blaSHV, and blaCTX were detected in 68.79%, 72.3%, and 91.9% of isolates, respectively. Among E. coli isolates, blaTEM, blaSHV, and blaCTX were detected in 20.8%, 4.53%, and 85.7% isolates, respectively. For both species, the most frequent genotype was blaCTX-M-15. Among Enterobacteriaceae, the most frequently detected carbapenemase-encoding gene was blaNDM-1 (81.5%), followed by blaOXA-232 (14.8%) and blaoxa-181(7.4%), in A. baumannii was blaOXA-24 (76%) and in P. aeruginosa, was blaIMP (25.3%), followed by blaGES and blaVIM (13.1% each). CONCLUSION: Our study reports that NDM-1 is the most frequent carbapenemase-encoding gene in Mexico in Enterobacteriaceae with the circulation of the oxacillinase genes 181 and 232. KPC, in contrast to other countries in Latin America and the USA, is a rare occurrence. Additionally, a high circulation of ESBL blaCTX-M-15 exists in both E. coli and K. pneumoniae.

Implementation results of the assessment and management of pain guideline within Best Practice Spotlight Organisations (BPSO®). / Resultados de la implantación de la Guía de valoración y manejo del dolor en Centros Comprometidos con la Excelencia en Cuidados (CCEC®) en España.

AIM: to analyse the progress of implementing the process recommendations of the RNAO Assessment and Management of Pain guideline and health outcomes. METHOD: An observational, longitudinal, retrospective study conducted in 3tertiary-level hospitals in Spain. All patients discharged over the last 5 days of each month from the units selected in the implementation process were included. We evaluated structural data, mean hospital stay, implementation strategy and degree of implementation of the process recommendations of the RNAO guideline over the first 3 years of implementation, and outcomes. A descriptive analysis was performed by calculating means and absolute and relative frequencies in periods: baseline (T0), annual, over the 3first years of implementation (T1, T2 and T3 respectively), and inferential. RESULTS: 8128 patients were included in the study. Hypotheses were contrasted between the different periods. The initial pain assessment in the first 24h following admission or post-surgery increased after the baseline period in all the hospitals, especially those that did not meet the guidelines from the outset. It continued to rise progressively up to 3 years following implementation (reaching 94.6% in hospital 2). By contrast, implementation of the care plan did not exceed 37.5% and 38.5% in hospitals 1 and 3 respectively. With regard to the outcome indicators, the prevalence of pain at 24hours and intense pain generally decreased in the 3hospitals from T0 or T1 to T3, however no conclusive statistically significant differences were obtained. CONCLUSIONS: Implementation of the process recommendations improved from the outset, as did patient outcomes. A decrease in the prevalence and intensity of pain was achieved, although no conclusive data were obtained; all of which leads to better nursing practice with more recording, continuity of care and improved pain management for patients.

Application and evaluation of the best practice guideline: Breastfeeding. / Aplicación y evaluación de la Guía de buenas prácticas: lactancia materna.

OBJECTIVE: To analyse the progress of care in the promotion of breastfeeding and describe breastfeeding results following the implementation of the RNAO guideline in various types of national health centres. METHOD: Quantitative descriptive longitudinal study of the results of implementing the recommendations of the RNAO-Breastfeeding guideline in 9 national health centres following the implementation methodology of the programme of the Best Practice Spotlight Organization®. Process and result variables are collected at hospital level and in primary care by registering on the CAREVID platform. The weighted mean was calculated as a summary statistic. RESULTS: The implementation of the recommendations of the Breastfeeding guideline was associated with a relative increase in: skin-to-skin contact 57,7% (p < 0,000), exclusive breastfeeding in the 1st intake 47,8% (p < 0,000), exclusive breastfeeding on hospital discharge 18,4% (p < 0,000) and prenatal education 63,95% (p < 0,00). CONCLUSION: The implementation of the RNAO-Breastfeeding guideline in different national health centres has increased the application of the recommendations based on scientific evidence, generalising appropriate breastfeeding care (such as prenatal education, application of skin-to-skin contact and exclusive breastfeeding in the first intake) and is consequently significantly approaching the international recommendations on breastfeeding.

Resultados de la implantación de la Guía de valoración y manejo del dolor en Centros Comprometidos con la Excelencia en Cuidados (CCEC) en España / Implementation results of the assessment and management of pain guideline within Best Practice Spotlight Organisations (BPSO)

OBJETIVO: Analizar la evolución de la implantación de las recomendaciones de proceso de la guía RNAO Valoración y manejo del dolor y de los resultados en salud. MÉTODO: Estudio observacional, longitudinal, retrospectivo, realizado en 3hospitales de tercer nivel de España. Se incluyó a todos los pacientes dados de alta los últimos 5 días de cada mes de las unidades seleccionadas en el proceso de implantación. Se evaluaron datos estructurales, estancia media, estrategia de implantación y grado de implantación de recomendaciones de proceso según la guía RNAO durante los 3primeros años de implantación y resultados. Se realizó un análisis descriptivo mediante el cálculo de medias y frecuencias absolutas y relativas por periodos: basal (T0) y anual durante los 3primeros años de implantación (T1, T2 y T3, respectivamente) e inferencial. RESULTADOS: Se ha incluido a 8.128 pacientes. Se ha realizado contraste de hipótesis entre los diferentes periodos. La valoración inicial del dolor en las primeras 24h de ingreso o poscirugía se incrementó tras el periodo basal en todos los hospitales, especialmente en aquellos en los que no se cumplían los requisitos de la guía al inicio, y continuó creciendo de forma progresiva hasta a los 3 años de implantación (alcanzando un 94,6% en el hospital 2). En cambio, la implantación del plan de cuidados no ha llegado a superar el 37,5 o el 38,5% de los hospitales 1 y 3, respectivamente. Respecto a los indicadores de resultado, la prevalencia de dolor a las 24 h e intenso disminuyó en los 3hospitales de forma general desde T0 o T1 a T3; sin embargo, no se obtuvieron diferencias estadísticamente significativas concluyentes. CONCLUSIONES: La evolución de la implantación de las recomendaciones de proceso ha mejorado desde el inicio, al igual que los resultados sobre los pacientes, consiguiendo una disminución de la prevalencia y la intensidad del dolor, aunque no se obtuvieron datos concluyentes; todo esto conlleva una mejor práctica enfermera con mayores registros, continuidad asistencial y mejora de la gestión del dolor en los pacientes

AIM: to analyse the progress of implementing the process recommendations of the RNAO Assessment and Management of Pain guideline and health outcomes. METHOD: An observational, longitudinal, retrospective study conducted in 3tertiary-level hospitals in Spain. All patients discharged over the last 5 days of each month from the units selected in the implementation process were included. We evaluated structural data, mean hospital stay, implementation strategy and degree of implementation of the process recommendations of the RNAO guideline over the first 3 years of implementation, and outcomes. A descriptive analysis was performed by calculating means and absolute and relative frequencies in periods: baseline (T0), annual, over the 3first years of implementation (T1, T2 and T3 respectively), and inferential. RESULTS: 8128 patients were included in the study. Hypotheses were contrasted between the different periods. The initial pain assessment in the first 24h following admission or post-surgery increased after the baseline period in all the hospitals, especially those that did not meet the guidelines from the outset. It continued to rise progressively up to 3 years following implementation (reaching 94.6% in hospital 2). By contrast, implementation of the care plan did not exceed 37.5% and 38.5% in hospitals 1 and 3 respectively. With regard to the outcome indicators, the prevalence of pain at 24hours and intense pain generally decreased in the 3hospitals from T0 or T1 to T3, however no conclusive statistically significant differences were obtained. CONCLUSIONS: Implementation of the process recommendations improved from the outset, as did patient outcomes. A decrease in the prevalence and intensity of pain was achieved, although no conclusive data were obtained; all of which leads to better nursing practice with more recording, continuity of care and improved pain management for patients

Aplicación y evaluación de la Guía de buenas prácticas: lactancia materna / Application and evaluation of the best practice guideline: Breastfeeding

OBJETIVO: Analizar la evolución de los cuidados para favorecer la lactancia materna (LM) y describir los resultados de la lactancia materna tras la implantación de la guía RNAO en diversos tipos de centros sanitarios nacionales. MÉTODO: Estudio descriptivo cuantitativo longitudinal de los resultados de la aplicación de las recomendaciones de la guía RNAO-LM en 9 centros sanitarios nacionales siguiendo la metodología del programa Best Practice Spotlight Organization®. Se recogen variables de proceso y resultado en el ámbito hospitalario y en atención primaria mediante el registro en la plataforma CAREVID. Los resultados globales se expresan como media ponderada de los centros participantes. RESULTADOS: La implantación de las recomendaciones de la guía de LM se asoció a un incremento relativo de: contacto piel con piel 57,7% (p < 0,000), LM exclusiva (LME) en la 1ª toma 47,8% (p < 0,000), LME al alta hospitalaria 18,4% (p < 0,000) y educación prenatal 63,95% (p < 0,00). CONCLUSIÓN: La implantación de la guía RNAO-LM en diversos centros en el ámbito nacional ha incrementado la aplicación de las recomendaciones, consiguiendo generalizar los cuidados adecuados en LM (como educación prenatal, aplicación del contacto piel con piel y LME en la primera toma), aproximándose significativamente a las recomendaciones internacionales sobre LM

OBJECTIVE: To analyse the progress of care in the promotion of breastfeeding and describe breastfeeding results following the implementation of the RNAO guideline in various types of national health centres. METHOD: Quantitative descriptive longitudinal study of the results of implementing the recommendations of the RNAO-Breastfeeding guideline in 9 national health centres following the implementation methodology of the programme of the Best Practice Spotlight Organization®. Process and result variables are collected at hospital level and in primary care by registering on the CAREVID platform. The weighted mean was calculated as a summary statistic. RESULTS: The implementation of the recommendations of the Breastfeeding guideline was associated with a relative increase in: skin-to-skin contact 57,7% (p < 0,000), exclusive breastfeeding in the 1st intake 47,8% (p < 0,000), exclusive breastfeeding on hospital discharge 18,4% (p < 0,000) and prenatal education 63,95% (p < 0,00). CONCLUSION: The implementation of the RNAO-Breastfeeding guideline in different national health centres has increased the application of the recommendations based on scientific evidence, generalising appropriate breastfeeding care (such as prenatal education, application of skin-to-skin contact and exclusive breastfeeding in the first intake) and is consequently significantly approaching the international recommendations on breastfeeding