Jorge Fernández

First Human Isolate of Hantavirus (Andes virus) in the Americas

We isolated Andes virus (formal name: Andes virus [ANDV], a species in the genus Hantavirus), from serum of an asymptomatic 10-year-old Chilean boy who died 6 days later of hantavirus pulmonary syndrome (HPS). The serum was obtained 12 days after his grandmother died from HPS and 2 days before he became febrile. No hantavirus immunoglobulin (Ig) G or IgM antibodies were detected in the serum sample. After three blind passages, ANDV antigens were detected in Vero E6 cells by immunofluorescence assay and enzyme-linked immunosorbent assay, and ANDV RNA was detected by reverse transcription-polymerase chain reaction. A fragment of the virus genome showed 96.2% nucleotide identity with that of prototype ANDV. To our knowledge, this is the first isolation of any agent of hemorrhagic fever with renal syndrome from a human and the first such isolation of hantavirus before symptoms of that syndrome or HPS began.

Analysis of Molecular Epidemiology of Chilean Salmonella enterica Serotype Enteritidis Isolates by Pulsed-Field Gel Electrophoresis and Bacteriophage Typing

ABSTRACT Human Salmonella enterica serotype Enteritidis infections emerged in Chile in 1994. S. enterica serotype Enteritidis phage type 1 isolates predominated in the north, and phage type 4 isolates predominated in the central and southern regions. A study was planned to characterize this epidemic using the best discriminatory typing technique. Research involved 441 S. enterica serotype Enteritidis isolates, including clinical preepidemic samples (n = 74; 1975 to 1993) and epidemic (n = 199), food (n = 72), poultry (n = 57), and some Latin American (n = 39) isolates. The best method was selected based on a sample of preepidemic isolates, analyzing the discriminatory power (DP) obtained by phage typing and randomly amplified polymorphic DNA and pulsed-field gel electophoresis (PFGE) analysis. The highest DP was associated with BlnI PFGE-bacteriophage typing analysis (0.993). A total of 38 BlnI patterns (B patterns) were identified before the epidemic period, 19 since 1994, and only 4 in both periods. Two major clusters were identified by phylogenetic analysis, and the predominant B patterns clustered in the same branch. Combined analysis revealed that specific B pattern-phage type combinations (subtypes) disappeared before 1994, that different genotypes associated with S. enterica serotype Enteritidis phage type 4 had been observed since 1988, and that strain diversity increased before the expansion of S. enterica serotype Enteritidis in 1994. Predominant subtype B3-phage type 4 was associated with the central and southern regions, and subtype B38-phage type 1 was associated with the north (P < 0.0001). Food and poultry isolates matched the predominant S. enterica serotype Enteritidis subtypes, but isolates identified in neighboring countries (Peru and Bolivia) did not match S. enterica serotype Enteritidis subtypes identified in the north of Chile. The results of this work demonstrate that genetic diversity, replacement, and expansion of specific S. enterica serotype Enteritidis subtypes were associated with epidemic changes.

Pandemic (H1N1) 2009 in breeding turkeys, Valparaiso, Chile.

Pandemic (H1N1) 2009 virus was detected in breeding turkeys on 2 farms in Valparaiso, Chile. Infection was associated with measurable declines in egg production and shell quality. Although the source of infection is not yet known, the outbreak was controlled, and the virus was eliminated from the birds.

Molecular characterization of invasive Neisseria meningitidis strains isolated in Chile during 2010-2011.

Background With the upcoming licensure of Outer Membrane Protein-based vaccines against meningococcal disease, data on disease incidence and molecular characteristic of circulating N. meningitidis strains in Latin American countries is needed. Chile is, to date, one of the few countries in the region that has performed this type of work in a comprehensive collection of disease-associated strains from two consecutive years, 2010–2011. Methods A total of 119 N. meningitidis strains isolated from patients with invasive disease in Chile in 2010–2011 were characterized by the National Reference Laboratory. Serogroup determination, MLST and porA typing were performed. Results Serogroup B was predominant in both study years, but W135 experienced a noticeable increase in 2011 compared to 2010. ST-11 complex, ST-41/44 complex ST-32 complex were the most prevalent among the isolates, and were strongly associated with serogroups W135 (ST-11 Complex) and B (ST-41/44 and ST-32 complexes). Likewise, the major porA types detected were strongly associated with these three clonal complexes: P1.5,2 was found exclusively among W135:ST-11 isolates, whereas P1.7, 2–3 was only detected in C:ST-11. ST-41/44 isolates mainly had P1.10-8, and ST-32 complex were associated with a P1.18-8 porA. Conclusions Our data show disease-associated N. meningitidis circulating in Chile are similar to those found in other parts of the world. The increase on W135:ST-11 isolates observed in 2011 foretold the unusual epidemiological situation experienced in the country in 2012, and MLST data show that this strain is indistinguishable from the one linked to the global Hajj 2000-related outbreak that occurred in 2001. Finally, this work demonstrates the importance of maintaining a strong national surveillance program integrating clinical, epidemiological and laboratory data and incorporating gold standard diagnostic and characterization techniques that allow the data to be compared all over the world.

Complete sequence of the genome of the human isolate of Andes virus CHI-7913: comparative sequence and protein structure analysis

We report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 amino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of 34 to 103 amino acids. The encoded proteins have greater than 98% overall similarity with the proteins of Andes virus isolates AH-1 and Chile R123. Among other sequenced Hantavirus, CHI-7913 is more closely related to Sin Nombre virus, with an overall protein similarity of 92%. The characteristics of the encoded proteins of this isolate, such as hydrophobic domains, glycosylation sites, and conserved amino acid motifs shared with other Hantavirus and other members of the Bunyaviridae family, are identified and discussed.

Standardization and international multicenter validation of a PulseNet pulsed-field gel electrophoresis protocol for subtyping Shigella flexneri isolates.

Shigella flexneri is one of the agents most frequently linked to diarrheal illness in developing countries and often causes outbreaks in settings with poor hygiene or sanitary conditions. Travel is one of the means by which S. flexneri can be imported into developed countries, where this pathogen is not commonly seen. A robust and discriminatory subtyping method is needed for the surveillance of S. flexneri locally and regionally, and to aid in the detection and investigation of outbreaks. The PulseNet International network utilizes standardized pulsed-field gel electrophoresis (PFGE) protocols to carry out laboratory-based surveillance of foodborne pathogens in combination with epidemiologic data. A multicenter validation was carried out in nine PulseNet laboratories located in North and South America, Europe, and Asia, and it demonstrated that a new protocol is highly robust and reproducible for subtyping of S. flexneri. This protocol, already approved for PulseNet laboratories, applies NotI and XbaI as primary and secondary restriction enzymes, respectively, under electrophoresis conditions of initial switch time of 5 s to final switch time of 35 s, at 6 volts/cm.

Neisseria meningitidis ST-11 Clonal Complex, Chile 2012

Serogroup W Neisseria meningitidis was the main cause of invasive meningococcal disease in Chile during 2012. The case-fatality rate for this disease was higher than in previous years. Genotyping of meningococci isolated from case-patients identified the hypervirulent lineage W:P1.5,2:ST-11, which contained allele 22 of the fHbp gene.

Rubella Outbreaks Following Virus Importations: The Experience of Chile

BACKGROUND Strategies for accelerated control of rubella and congenital rubella syndrome (CRS) in Chile included mass vaccination of women of childbearing age in 1999 but did not include vaccination of adult men. METHODS We reviewed data from Chiles integrated surveillance system for measles, rubella, and CRS from 2004 through 2009 and describe the epidemiology of rubella outbreaks and implementation of control measures in 2005 and 2007 following mass vaccination of women. Population estimates from census data were used to calculate rubella incidence rates. The age distribution of rubella cases during 2007 was compared with rubella vaccination opportunities by birth cohort to orient mass vaccination of adult men. RESULTS In 2005, an institutional outbreak of rubella occurred among male naval recruits 18-22 years of age, with 46 confirmed cases over a 5-month period. Beginning in March 2007, rubella outbreaks among young adults in the capital of Santiago spread throughout Chile, resulting in >4000 confirmed rubella cases. Delayed control measures and rapid dissemination among young adults led to widespread transmission. From 2007 through 2009, rubella incidence was highest among adult men not included in previous vaccination strategies. Mass vaccination of men 19-29 years of age was conducted in November 2007 to interrupt rubella transmission. CONCLUSIONS Chiles experience suggests that vaccination strategies for rubella and CRS elimination need to include both men and women.

Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections.

Next-generation technologies and bioinformatics enabled source attribution and implementation of effective control strategies.

Vigilancia de laboratorio de enfermedad meningocóccica invasora en Chile, 2006-2012

Introduccion: La vigilancia de laboratorio de enfermedad meningococica invasora (EMI) que realiza el Instituto de Salud Publica de Chile, confirma, seroagrupa y estudia el perfil genetico de las cepas de Neisseria meningitidis provenientes de los laboratorios del pais. Objetivo: En este articulo se muestra los resultados de esta vigilancia entre los anos 2006 a 2012. Materiales y Metodos: Se realizo un analisis descriptivo de los casos confirmados de EMI, caracterizacion serologica, el analisis de susceptibilidad antimicrobiana y el estudio de subtipo genetico de la cepa. El analisis se desagrego por serogrupo, edad y region. Resultados: En el periodo 2006-2012 fue confirmado un total de 486 cepas de N. meningitidis. A partir del ano 2011 se observo un alza en la tasa de EMI dado por el numero de casos del serogrupo W, afectando principalmente a ninos bajo 5 anos de edad. El W se transformo en el serogrupo prevalente el ano 2012 (58,3%), desplazando al serogrupo B, el cual historicamente habia sido prevalente. Predominaron principalmente las cepas pertenecientes al complejo clonal ST-32 complex/ET-5 complex (40,4% de las muestras) y el ST-41/44 complex/Lineage 3 (45,9% de las muestras). Conclusiones: El sistema de vigilancia de laboratorio ha permitido la identificacion del serogrupo W, emergente en Chile. Esta informacion nos ha obligado a estar en permanente alerta y monitoreo de casos diarios, mediante la participacion activa de todos los laboratorios clinicos del pais.