Genomic and phylogenomic characterization of carbapenem-resistant Pseudomonas aeruginosa 'high-risk' clone O4/ExoS+/ST654 circulating in Chilean hospitals.

INTRODUCTION: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a serious threat to public health. Globally, carbapenemases-producing CRPA isolates mainly belong to 'high-risk' clones; however, the molecular epidemiology of CRPA isolates circulating in Chile are scarce, where this pathogen is the main aetiological agent of ventilator-associated pneumonia. OBJECTIVES: To characterize the phylogenomics and molecular features of ST654 CRPA isolates collected in Chile between 2016 - 2022. METHODS: 89 CRPA isolates collected in different Chilean hospitals from clinical specimens between 2005 and 2022 were analyzed. Antibiotic susceptibility tests and carbapenemases production were carried out on the CRPA ST654 isolates. Also, they were subjected to whole-genome sequencing (WGS) from which in silico analyses were performed. RESULTS: Thirty-four strains (38.2%) belonged to the ST654 'high risk' clone, being the most predominant lineage of the collection. Most of these isolates belonged to a sub-clade including KPC-producers that also clustered with strains from Argentina and the USA, whereas few VIM and NDM co-producers clustered in two different smaller sub-clades. The isolates exhibited a broad resistome encompassing genes mediating resistance to several other clinically relevant drugs. Additionally, all the 34 ST654 isolates were ExoS+ as a virulence factor and associated to the O4-serotype. CONCLUSIONS: Our report represents the most comprehensive phylogenomic study of CRPA 'high risk' clone ST654 to date. Our analyses suggest that this lineage is undergoing a divergent evolutionary path in Chile, since most of the isolates were KPC-producers and were O4-serotype, differing from previous descriptions, which underline the relevance of performing molecular surveillance on this pathogen.

Isolation of an Extensively Drug-Resistant Pseudomonas aeruginosa exoS+/O4 Strain Belonging to the "High-Risk" Clone ST654 and Coproducer of NDM-1 and the Novel VIM-80.

The aim of this study was to investigate the genomic features of an extensively drug-resistant (XDR) Pseudomonas aeruginosa isolate (P-469) emerging in Chile. Antibiotic susceptibility was determined by disk diffusion and "colistin agar" test. Whole-genome sequencing (WGS) was performed by the Illumina NextSeq 2000 platform, and epidemiologically and clinically relevant data (i.e., sequence-type, serotype, mobile genetic elements, virulome, resistome, plasmidome, prophages, and CRISPR-Cas systems) were retrieved using multiple bioinformatic tools. The P-469 strain displayed an XDR profile, remaining susceptible to colistin. Genomic analysis revealed that this isolate belonged to the "high-risk" clone ST654 (CC654), serotype O4, and genotype exoS+. Strikingly, two CRISPR-Cas systems, five intact prophages sequences, and a broad resistome that included blaNDM-1 and the novel blaVIM-80 carbapenemase genes were predicted. Our results revealed the genomic characteristics of P. aeruginosa belonging to the high-risk clone ST654/O4 coproducing NDM-1 and VIM-80 in Chile, supporting that genomic surveillance is necessary to track the emergence and spread of epidemiologically successful WHO's critical priority pathogens in order to prevent their rapid dissemination.

High prevalence of CTX-M-1 group in ESBL-producing enterobacteriaceae infection in intensive care units in southern Chile.

Enterobacteria-producing extended-spectrum ß-lactamases (ESBL) play an important role in healthcare infections, increasing hospitalization time, morbidity and mortality rates. Among several ESBLs that emerge from these pathogens, CTX-M-type enzymes had the most successful global spread in different epidemiological settings. Latin America presents high prevalence of CTX-M-2 in ESBL-producing enterobacterial infections with local emergence of the CTX-M-1 group. However, this high prevalence of the CTX-M-1 group has not yet been reported in Chile. The aim of this study was to identify ESBLs among enterobacteria isolated from clinical samples of critically ill patients from southern Chile. One-hundred thirty seven ESBL-producing bacteria were isolated from outpatients from all critical patient units from Hernán Henríquez Aravena Hospital. Phenotype characterization was performed by antibiogram, screening of ESBL, and determination of minimum inhibitory concentration (MIC). PCR was used for genetic confirmation of resistance. Molecular typing was performed by ERIC-PCR. ESBL-producing isolates were identified as Klebsiella pneumoniae (n=115), Escherichia coli (n=18), Proteus mirabilis (n=3), and Enterobacter cloacae (n=1), presenting multidrug resistance profiles. PCR amplification showed that the strains were positive for blaSHV (n=111/81%), blaCTX-M-1 (n=116/84.7%), blaTEM (n=100/73%), blaCTX-M-2 (n=28/20.4%), blaCTX-M-9 (0.7%), blaPER-1 (0.7%), and blaGES-10 (0.7%). The multiple production of ESBL was observed in 93% of isolates, suggesting high genetic mobility independent of the clonal relationship. The high frequency of the CTX-M-1 group and a high rate of ESBL co-production are changing the epidemiology of the ESBL profile in Chilean intensive care units. This epidemiology is a constant and increasing challenge, not only in Chile, but worldwide.

Creación del primer biorrepositorio nacional de bacterias multirresistentes disponible para el estudio de la resistencia bacteriana en Chile

La disponibilidad de cepas bacteriana para el estudio de la resistencia bacteriana es clave para los avances en la investigación básica y clínica respecto del tema. Existen pocos biorrepositorios o bancos de bacterias con mecanismos de resistencia conocidos, aisladas de infecciones clínicamente significativas. Una revisión de la literatura revela que sólo en los Estados Unidos de América existe un biobanco de aislados resistentes disponibles para estudios. En esta publicación se cuenta cómo se creó el primer biorrepositorio de bacterias resistentes en Chile asociados a la Red de Laboratorios MICROB-R, con la participación de 11 centros distribuidos a lo largo del país, que a la fecha cuenta con más de 3.500 aislados bacterianos estudiados fenotípica y genotípicamente, disponibles para la comunidad científica chilena.

The availability of bacterial strains for the study of bacterial resistance is key to advances in basic and clinical research. There are few biobanks of bacteria with known resistance mechanisms, isolated from clinically significant infections. A review of the literature reveals that only in the United States of America is there a biobank of resistant isolates. This publication shows the creation of the first biorepository of resistant bacteria Chile associated with the MICROB-R Laboratory Network, with the participation of 11 centers distributed throughout the country, which to date has more than 3,500 bacterial isolates studied phenotypically and genotypically, available to the Chilean scientific community.

High prevalence of CTX-M-1 group in ESBL-producing enterobacteriaceae infection in intensive care units in southern Chile

ABSTRACT Enterobacteria-producing extended-spectrum β-lactamases (ESBL) play an important role in healthcare infections, increasing hospitalization time, morbidity and mortality rates. Among several ESBLs that emerge from these pathogens, CTX-M-type enzymes had the most successful global spread in different epidemiological settings. Latin America presents high prevalence of CTX-M-2 in ESBL-producing enterobacterial infections with local emergence of the CTX-M-1 group. However, this high prevalence of the CTX-M-1 group has not yet been reported in Chile. The aim of this study was to identify ESBLs among enterobacteria isolated from clinical samples of critically ill patients from southern Chile. One-hundred thirty seven ESBL-producing bacteria were isolated from outpatients from all critical patient units from Hernán Henríquez Aravena Hospital. Phenotype characterization was performed by antibiogram, screening of ESBL, and determination of minimum inhibitory concentration (MIC). PCR was used for genetic confirmation of resistance. Molecular typing was performed by ERIC-PCR. ESBL-producing isolates were identified as Klebsiella pneumoniae (n = 115), Escherichia coli (n = 18), Proteus mirabilis (n = 3), and Enterobacter cloacae (n = 1), presenting multidrug resistance profiles. PCR amplification showed that the strains were positive for blaSHV (n = 111/81%), blaCTX-M-1 (n = 116/84.7%), blaTEM (n = 100/73%), blaCTX-M-2 (n = 28/20.4%), blaCTX-M-9 (0.7%), blaPER-1 (0.7%), and blaGES-10 (0.7%). The multiple production of ESBL was observed in 93% of isolates, suggesting high genetic mobility independent of the clonal relationship. The high frequency of the CTX-M-1 group and a high rate of ESBL co-production are changing the epidemiology of the ESBL profile in Chilean intensive care units. This epidemiology is a constant and increasing challenge, not only in Chile, but worldwide.

Ten-year surveillance of pneumococcal infections in Temuco, Chile: implications for vaccination strategies.

We monitored Streptococcus pneumoniae serotypes causing invasive infections in patients admitted to one hospital in southern Chile during a 10-year period (1994 to 2004). All specimens isolated from patients with invasive S. pneumoniae infections were serotyped at the CDC in Atlanta, GA. A total of 508 isolates belonged to 58 serotypes. There were 95 infections in patients <2 years old, 33 infections in patients 2 to 4 years old, 61 infections in patients 5 to 14 years old, 66 infections in patients 15 to 44 years old, 134 infections in patients 45 to 64 years old, and 120 infections in patients >or=65 years old. The 10 serotypes isolated with the highest frequency in all groups were, in decreasing order, 1, 3, 14, 5, 19F, 6B, 7F, 12F, 23F, and 6A. The 10 most frequent isolates in children under 2 years of age were 1, 6B, 14, 19F, 5, 23F, 6A, 9V, and 7F. In patients >or=65 years old, the most common serotypes were 3, 7F, 1, 14, 19A, 23F, 19F, 35B, 4, and 5. Penicillin resistance was detected in 14 (2.7%) clinical specimens isolated since 1998, with 13 resistant strains identified since 2001. Vaccine coverage for the 7-valent conjugate vaccine was 42% for children <2 years of age. This study is important for the design of vaccines for this region and to evaluate public health measures to decrease pneumococcal infections.

[Comparison of Shigella susceptibility to commonly used antimicrobials in the Temuco Regional Hospital, Chile 1990 - 2001]. / Comparación de susceptibilidad de especies de Shigella a antimicrobianos de uso habitual en el Hospital Regional de Temuco, Chile 1990-2001.

BACKGROUND: The permanent surveillance of antimicrobial susceptibility of Shigella sp in the Temuco Regional Hospital, allowed us to define the empirical use of antimicrobials in dysenteric syndrome. AIM: To study antimicrobial susceptibility of Shigella strains collected from 1997 to May 2001 and compare the results with those reported in 1990. MATERIAL AND METHODS: Two hundred and seventeen Shigella strains, coming from stool cultures of pediatric patients, were studied. RESULTS: In the period 1989-1990 Shigella flexneri was the main species isolated (83%) whereas, in the period 1997-2001, Shigella sonnei (55.8%) predominated. In the second period, an increase of antimicrobial resistance, as compared with the period 1989-1990, was observed for ampicillin (74.5 and 42% respectively), for cotrimoxazol (57.5 and 45% respectively) and tetracycline (64 and 8% respectively). Chloramphenicol resistance increased from 0 to 57.5%. In the second period no resistance to ciprofloxacin was detected. There was simultaneous resistance to four drugs in 30% of the strains, predominating multiresistance in S flexneri (52.1%). CONCLUSIONS: In the two periods studied, a significant increase was detected in the resistance of Shigella strains to antimicrobials.

Diagnóstico etiológico de meningitis bacteriana (M.B.) por pruebas de aglutinación del látex / Etiologic diagnosis of bacterial meningitis by latex agglutination tests

Se analizan 14 casos de pacientes hospitalizados con diagnóstico de M.B. en el Servicio de Pediatría del Hospital Regional Temuco, durante el período Mayo-Septiembre de 1985, para evaluar la utilidad de la prueba de Aglutinación del Látex en relación al cultivo y Gram en Líquido Celaforraquídeo (LCR). Las edades de los niños fluctuaron entre 3 meses y 8 años; el 53% fueron mujeres y 91% eutróficos. En 2 casos que se descartó el diagnóstico de M.B. por examen citoquímico, Gram y cultivo de LCR, el Látex también fue negativo. 10 niños tuvieron reacción del Látex(-), 8 cultivos (-) y en 6 la tinción de Gram fue (-). La sensibilidad de la reacción del Látex fue del 90,0%, en tanto que la del cultivo y Gram 66,6% y 54,5% respectivamente. La especificidad del método en estudio fue 100%, no registrándose falsos positivos ni negativos. El látex fue el único método de pesquisa etiológica en 3 niños (25%)