Zika virus (ZIKV) is an emerging mosquitoborne flavivirus circulating in Asia and Africa. In 2013, a large outbreak was reported on the archipelago of French Polynesia. In this study, we report the detection and molecular characterization of Zika virus for the first time in Chile from an outbreak among the inhabitants of Easter Island. A total of 89 samples from patients suspected of having ZIKV infection were collected between the period from January to May, 2014. Molecular diagnosis of the virus was performed by RT-PCR followed by the sequencing of the region containing the NS5 gene. A comparison of the viral nucleic acid sequence with those of other strains of ZIKA virus was performed using the MEGA software. Fifty-one samples were found positive for ZIKV by RT-PCR analysis. Further analysis of the NS5 gene revealed that the ZIKV strains identified in Easter Island were most closely related to those found in French Polynesia (99.8 to 99.9 % nt and 100 % aa sequence identity). These results strongly suggest that the transmission pathway leading to the introduction of Zika virus on Easter Island has its origin in French Polynesia.Keywords Zika virus Á Easter Island Á Outbreak Á South Pacific Á ZIKV Zika virus (ZIKV) is a mosquito-borne virus belonging to the family Flaviviridae and the genus Flavivirus. The Flaviviruses also include yellow fever, dengue, St. Louis encephalitis, West Nile, and Japanese encephalitis viruses [6]. ZIKV was first isolated from the blood of a sentinel rhesus monkey inhabiting the Zika Forest in Uganda [6]. Later on, ZIKV was isolated from a mosquito of the species Aedes africanus, obtained from the same locality of the Zika Forest. ZIKV has been isolated from several species of Aedes mosquito, notably, A. aegypti and A. albopictus [10]. A. aegypti is widely distributed in tropical and subtropical regions of the world [6,11,12].Clinically diagnosed ZIKV infections in human cases have been reported to include self-limiting acute febrile illnesses with fever, headache, myalgia, retro-orbital pain, arthralgia, conjunctivitis, and rash. These clinical presentations closely resemble those that are caused by dengue virus (DENV) and Chikungunya virus [6]. Serological studies and isolation of ZIKV strains have subsequently indicated that the virus has a wide geographical distribution, including regions in East and West Africa, South and South East Asia, and Micronesia [6], where an outbreak of Zika fever was reported on Yap Island [4]. In 2013, a Zika fever outbreak in French Polynesia was the largest ever reported for an arbovirus other than DENV at this location. Following this, there was a report of a Zika outbreak on the Cook Islands of New Caledonia [3,12].In Chile, at the end of 2000, the presence of A. aegypti on Easter Island was reported; the island is located on the east edge of the Polynesian Triangle, in the south Pacific Ocean, with a latitude of 27°9 0 10'' S, and a longitude of 109°27 0 17'' W [13]. The closest continental point from this island is the Chilean coast, l...

ObjectivesShigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic.MethodsWe applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants.ResultsS. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins.ConclusionsLatin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.

Clostridium difficile infection has gained importance in recent years as a result of the rapid spread of epidemic strains, including hypervirulent strains. This study reports the molecular epidemiology of C. difficile obtained from hospitalized patients in Chile. Seven hundred and nineteen isolates of toxigenic C. difficile from 45 hospitals across the country were characterized through toxin profile, pulsed-field gel electrophoresis (PFGE), and sequencing of the tcdC gene. In addition, polymerase chain reaction (PCR) ribotyping and multilocus sequence typing (MLST) were performed on a subset of selected strains. PFGE typing of 719 isolates of C. difficile produced 60 PFGE patterns (subtypes). Subtype 1 was predominant (79% of isolates) and related to the hypervirulent strain (NAP1). Subtype 1 showed 73% relatedness with nine other subtypes, which had a similar tcdC deletion. Subtype 1 corresponded to ribotype 027 and ST1. This report shows the wide dissemination of the hypervirulent strain NAP1/027/ST1 in Chile.

BackgroundAcanthamoeba spp. are the causative agents of a severe keratitis occurring mainly in contact lens wearers. The genus comprises more than 24 species that are currently divided into 20 different genotypes (T1-T20) according to sequence variations in the 18S rRNA gene. The objective of this study was to identify the genotypes and sub-genotypes of Acanthamoeba isolates collected at the Parasitology Laboratory of the Public Health Institute of Chile, the only laboratory in the country where Acanthamoeba screening is performed. This is the first report of genotypic identification of clinical isolates of Acanthamoeba in Chile and one of the few in South America.ResultsIn this study, 114 Acanthamoeba isolates from 76 Acanthamoeba keratitis patients, obtained between 2005–2016, were genotyped. T4 was the predominant genotype; T2 and T11 genotypes, which are scarcely reported worldwide, were also identified in Chilean patients (one and two patients, respectively). This is the first report of T2 and T11 genotypes isolated from Acanthamoeba keratitis patients in South America. It is also the first report of the T2 genotype circulating in this continent. Analysis of the diagnostic fragment 3 region of the 18S rRNA gene showed 24 T4 variants, with a predominance of the sub-genotype T4/A, followed by T4/B, T4/G, T4/C and T4/D. Bayesian analysis revealed three groups among the T4 variants: two well supported groups that included 12 and 7 sub-genotypes, respectively, and a weakly supported group that included 5 sub-genotypes. Most of the predominant T4 sub-genotypes belonged to the same group, which included 71.3% of the patients, while some minority variants lied mainly in the other two clusters.ConclusionsT2, T4 and T11 genotypes were predominantly isolated from the Acanthamoeba keratitis patients in Chile. Chilean predominant T4 sub-genotypes, which have also been reported worldwide, formed a separate cluster of the minority T4 variants. This study provides useful information about the predominant genotypes and subgenotypes that would be useful in selecting suitable strains to develop immunological and/or molecular diagnostic assays in Chile.Electronic supplementary materialThe online version of this article (10.1186/s13071-019-3302-5) contains supplementary material, which is available to authorized users.

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