Phylogenetic analysis of the first four SARS-CoV-2 cases in Chile

The current pandemic caused by the new coronavirus is a worldwide public health concern. To aboard this emergency, and like never before, scientific groups around the world have been working in a fast and coordinated way to get the maximum of information about this virus when it has been almost 3 months since the first cases were detected in Wuhan province in China. The complete genome sequences of around 450 isolates are available, and studies about similarities and differences among them and with the close related viruses that caused similar epidemics in this century. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. Our findings reveal at least two different viral variants entries to Chilean territory, coming from Europe and Asia. We also sub‐classified the isolates into variants according to punctual mutations in the genome. Our work contributes to global information about transmission dynamics and the importance to take control measures to stop the spread of the infection.

First genetic study of the SARS‐CoV‐2 isolates in Chile.

At least two different viral variants were identified from Chilean travelers.

S and G Chilean variants are associated to European and Asian viral isolates.

Effect of chloride on the one step electrochemical treatment of an industrial textile wastewater with tin dioxide anodes. The case of trichromy procion HEXL

The resulting solutions from the cotton fabrics dyeing using the trichromy Procion HEXL, with NaCl as electrolyte, were electrochemically treated. These dyes have two azo groups as chromophores and two monochlorotriazinic groups as reactive groups in their structure. The combined oxidation/reduction at 125 mA cm^-2 in a filter-press cell without compartment separation was carried out using an anode of Ti/SnO₂-Sb-Pt and a cathode of stainless steel. This procedure has been effective in previous experiments using sulphate as electrolyte. A significant decrease in total organic carbon (TOC), chemical oxygen demand (COD), and total nitrogen (TN) was obtained. Moreover, the process took place efficiently. The average oxidation state (AOS) and the carbon oxidation state (COS) data confirmed the presence of stable oxidized intermediates in the electrolysed solution. The chromatography and the UV-Visible spectrophotometry assays indicated that full decolourisation is obtained at a loaded charge of around 0.81 Ah L^-1 which is associated with an electrical energy per order (EEO) of 1.20 kWh m^-3.

Tracing Listeria monocytogenes contamination in artisanal cheese to the processing environments in cheese producers in southern Chile

Artisanal cheese from southern Chile is made primarily by rural families who raise dairy cows and produce cheese as a way to add value to their milk. The most common cheese produced is chanco, a semi-hard cheese that is typically sold in unauthorized markets. The methods of chanco production do not always follow good manufacturing practices; however, the presence of Listeria monocytogenes contamination in this cheese has not been previously documented. To better understand production practices and L. monocytogenes contamination, 39 cheese producers were surveyed with regard to infrastructure, cleaning and sanitation, pest control, personal hygiene, training, raw materials, and manufacturing. During four sampling trips in 2016 (March, May, August, and November), 546 samples were collected (468 cheese samples and 78 milk samples). For producers that tested positive for L. monocytogenes, environmental monitoring was also conducted, for which 130 additional samples were collected. Presumptive L. monocytogenes isolates (N = 94) were further characterized and subtyped using standard techniques and qPCR-based species/subtype verification; a subset of 52 isolates were also subtyped by Pulsed Field Gel Electrophoresis (PFGE). L. monocytogenes was found in 19 cheeses (4.1%) from five producers (12.8%). The most frequent serotypes were 1/2b (48.9%), group 4B (4b, 4d, 4e) (45.7%), and serotype 1/2a (5.4%). Although no milk samples tested positive for L. monocytogenes, all cheese samples from two producers tested positive during two of the samplings. Distinct PFGE types were recovered from each facility, demonstrating persistence of certain subtypes of the pathogen that ultimately caused end-product contamination. Environmental monitoring of the five positive producers revealed a prevalence of L. monocytogenes ranging from 0 to 30%, with food contact surfaces having the highest incidence of this organism. The findings of this study contribute to the understanding of L. monocytogenes incidence in artisanal cheese in the region of southern Chile.

Genetic evolution of influenza viruses among selected countries in Latin America, 2017-2018

OBJECTIVE

Since the 2009 influenza pandemic, Latin American (LA) countries have strengthened their influenza surveillance systems. We analyzed influenza genetic sequence data from the 2017 through 2018 Southern Hemisphere (SH) influenza season from selected LA countries, to map the availability of influenza genetic sequence data from, and to describe, the 2017 through 2018 SH influenza seasons in LA.

METHODS

We analyzed influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata hemagglutinin sequences from clinical samples from 12 National Influenza Centers (NICs) in ten countries (Argentina, Brazil, Chile, Colombia, Costa Rica, Ecuador, Mexico, Paraguay, Peru and Uruguay) with a collection date from epidemiologic week (EW) 18, 2017 through EW 43, 2018. These sequences were generated by the NIC or the WHO Collaborating Center (CC) at the U.S Centers for Disease Control and Prevention, uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) platform, and used for phylogenetic reconstruction.

FINDINGS

Influenza hemagglutinin sequences from the participating countries (A/H1pdm09 n = 326, A/H3 n = 636, B n = 433) were highly concordant with the genetic groups of the influenza vaccine-recommended viruses for influenza A/H1pdm09 and influenza B. For influenza A/H3, the concordance was variable.

CONCLUSIONS

Considering the constant evolution of influenza viruses, high-quality surveillance data-specifically genetic sequence data, are important to allow public health decision makers to make informed decisions about prevention and control strategies, such as influenza vaccine composition. Countries that conduct influenza genetic sequencing for surveillance in LA should continue to work with the WHO CCs to produce high-quality genetic sequence data and upload those sequences to open-access databases.

A diet based on cured acorn-fed ham with oleic acid content promotes anti-inflammatory gut microbiota and prevents ulcerative colitis in an animal model

Background

Diets based on meat products are not recommended in the case of ulcerative colitis (UC). The objective here is to test if some traditional cured meat products, as acorn-fed ham (high levels of oleic acid), may be useful for controlling inflammatory diseases as UC in animal models, which could represent a new dietary complementary intervention in the prevention of this inflammatory disease in humans.

Methods

Two rat cohorts have been used: conventional vegetable rat feed and acorn-fed ham. UC was induced with DSS in drinking water ad libitum for 1 week. Short-chain fatty acids (SCFAs) and 16S rRNA metagenomics from bacterial populations were analyzed in cecum samples. Colon samples were analyzed for histological parameters.

Results

Acorn-fed ham diet induced changes in gut microbiota composition, with pronounced enrichments in anti-inflammatory bacterial genera (Alistipes, Blautia, Dorea, Parabacteroides). The animals with this diet showed a strong reduction in most parameters associated to ulcerative colitis: disease activity index, macroscopic score of colitis, epitelium alteration in colon mucosa, inflammatory cell density in colon, myeloperoxidase titers in colon, proinflammatory cytokines (IL-17, IFN-γ). Also, acorn-fed ham diet animals showed increased total antioxidant activity an oleic acid levels in plasma, as well as higher short-chain fatty acid concentrations in cecum (isobutyric, isovaleric and valeric).

Conclusions

In the acorn-fed ham cohort, as a result of the dietary intake of oleic acid and low intake of omega-6 fatty acids, a strong preventive effect against UC symptoms was observed.

[Genetic characterization of Listeria monocytogenes strains isolated during 2007-2014 in Chile]

BACKGROUND

Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a disease that can present as febrile gastroenteritis or as an invasive form that has high mortality rates. So far, the genetic diversity of strains of L. monocytogenes isolated from patients, foods and environmental sources in Chile has been poorly studied.

AIM

To characterize genetically L. monocytogenes strains received by the Institute of Public Health of Chile (ISP) between 2007 and 2014.

METHODS

We selected 94 strains of L. monocytogenes corresponding to 94 different pulsotypes identified by pulsed field gel electrophoresis (PFGE), DNA was extracted and serotyping was performed by polymerase chain reaction (PCR) and multilocus sequence typing (MLST).

RESULTS

The most common serotype was 4b (55.3%), followed by serotypes 1/2a (25.5%), 1/2b (17%) and 1/2c (2.2%). 32 sequence-type (ST) were identified, of which 4 were new, and the predominant ones were ST1 (28.7%) and ST2 (13.8%). All the strains of L. monocytogenes were grouped in Lineages I and II.

CONCLUSIONS

A great genetic variability was observed in the strains of L. monocytogenes analyzed, being predominant the ST1 and ST2, both belonging to Lineage I. Our results contribute to know the population structure of this pathogen in Chile and its presence in clinical samples, food and the environment.

Prospective multicentre study of rectal carriage of multidrug-resistant Enterobacteriaceae among health-care workers in Spain

OBJECTIVES

To investigate the rectal carriage of multidrug-resistant Enterobacteriaceae (colistin-resistant, extended-spectrum β-lactamase (ESBL) -producers and/or carbapenemase-producers) among health-care workers (HCWs) from six Spanish hospitals.

METHODS

Rectal swabs from 258 HCWs, employed in intensive care units, haematology wards and clinical microbiology laboratories from six hospitals in northern Spain were studied. They were cultured in selective media for Gram-negative resistant bacteria. Detection of antimicrobial resistance genes and multilocus sequence typing were performed by PCR and further sequencing. A questionnaire including data related to risk factors of colonization/infection by resistant bacteria (age, gender, chronic diseases, immunosuppressive therapies, invasive procedures or antimicrobial treatments) was given to each participant.

RESULTS

No carbapenemase-producing Enterobacteriaceae were recovered. However, 8/258 HCWs (3.1%) were positive for ESBL-producing isolates. This rate was not higher than the colonization rate previously reported in Spain for healthy people in the community. Five isolates showed high-level resistance to colistin (MICs ranging from 8 to 128 mg/L) but all of them were negative for the mcr genes tested. No statistically significant risk factors for gut colonization by ESBL-producing or colistin-resistant Enterobacteriaceae were identified among the HCWs participating in the study.

CONCLUSIONS

Our data suggest that working in hospitals does not represent a risk for rectal carriage of multidrug-resistant Enterobacteriaceae.

Vibroequilibria in microgravity: Comparison of experiments and theory

Experiments on vibrated fluids confined in cylindrical and cuboidal containers were performed under the reduced gravity conditions of a parabolic flight. The results constitute a systematic quantitative investigation of the vibroequilibria effect, which refers to the reorientation of vibrated fluids in response to the inhomogeneous oscillatory velocity field and the accompanying dynamic pressure. This effect is amplified in microgravity where the restoring force of gravity is small or absent. Here the vibrations are transmitted via a pair of piezoelectric ceramics and a cantilever beam, excited in a resonant mode. The first and second resonances exhibit different types of motion and lead to different types of vibroequilibria surfaces, one with a dip or crater in the interior and the other flattened compared to the unforced reference experiment. The general tendency for interfaces to orient more perpendicular, on average, to the vibrational axis is confirmed. In the case of water in a cuboidal container, a quantitative comparison is made with vibroequilibria theory and with direct simulations of the Navier-Stokes equations. The good agreement confirms the predictions of vibroequilibria theory and suggests the capacity of this phenomenon to manipulate and position fluids in space environments through the choice of frequency and resonant mode.

Long-term endemic situation caused by a linezolid- and meticillin-resistant clone of Staphylococcus epidermidis in a tertiary hospital

BACKGROUND

Linezolid (LZD)-resistant Staphylococcus epidermidis (LRSE) are increasing, and are mainly associated with outbreaks in hospital wards with high LZD consumption.

AIM

To investigate the frequency of LRSE in a tertiary hospital in the context of LZD use.

METHODS

The frequency of LRSE and the data on LZD usage [expressed as defined daily dose (DDD) per 100 patient-days], from 2011 to 2017, were analysed retrospectively. Selected LRSE were typed by pulsed-field gel electrophoresis (PFGE) and screened for transferable LZD resistance genes. Representative isolates were typed by multi-locus sequence typing, and ribosomal mechanisms of LZD resistance were investigated.

FINDINGS

In total, 435 LRSE were detected, with frequencies ranging from 13.56% to 32.93% in the intensive care unit (ICU) where LZD consumption was high (6.34-8.10 DDDs), and from 2.48 to 6.80% in the remaining wards where LZD use was considerably lower (0.63-2.49 DDDs). The first 44 LRSE isolates recovered (June 2013-June 2014) were closely related according to PFGE patterns, and all except one were resistant to meticillin due to mecA production. Selected isolates belonged to ST2, carried SCCmec III, and had the G2576T mutation in the V domain of each of the six copies of the 23S rRNA gene. Five of the 44 isolates (11.36%) were positive for the cfr gene.

CONCLUSION

An ST2 LZD- and meticillin-resistant clone was found in the ICU and also in wards with low consumption of LZD. This highlights the need to implement and maintain infection control measures as well as antimicrobial stewardship programmes in all hospital units in order to preserve the efficacy of LZD.

Tunable upconversion emission in NaLuF4-glass-ceramic fibers doped with Er3+ and Yb3

Novel glass-ceramic optical fibers containing NaLuF4 nanocrystals doped with 0.5ErF3 and 2YbF3 (mol%) have been prepared by the rod-in-tube method and controlled crystallization. NaLuF4 nanocrystals with a size around 20 nm are obtained after heat treatment at 600 °C. Intense upconverted green and red emissions due to (2H11/2, 4S3/2) → 4I15/2 and 4F9/2 → 4I15/2 transitions, respectively, together with a blue emission due to 2H9/2 → 4I15/2 transition have been observed under excitation at 980 nm. The intensity of the green and red upconversion bands shows a nearly linear dependence on the excitation power which can be explained by saturation effects in the intermediate energy states and proves that a sensitized energy transfer upconversion process is responsible for the population of the emitting levels of Er3+ ions. The upconversion emission color changes from yellow to green by increasing the excitation power density which allows to manipulate the color output of the Er3+ emission in the glass-ceramic fibers. The tunable emission color is easily detected with the naked eye. This interesting characteristic makes these glass-ceramic fibers promising materials for photonic applications.

[Outbreak of fungemias by Sarocladium kiliense in eight public hospitals per intrinsic contamination of ondansetron intravenous]

Sarocladium kiliense is a saprophyte fungus that can cause opportunistic infections associated to invasive procedures. We report a multi-hospital nosocomial outbreak of fungemias due to this agent. Patients with positive blood culture to this agent were studied after six bloodstream infections identified in three Chilean hospitals in July 2013 were reported to Ministry of Health National Infection and Prevention Control Program. In general, there were mild clinical manifestations, without deaths attributable to the infection. Epidemiological and micro-biological study identified 65 cases in 8 hospitals, mostly pediatric patients in chemotherapy. Initial studies of 94 different drugs and medical devices had negative results, until a second analysis of specific blisters and their pharmaceutical matrix selected by epidemiological criteria identified an intrinsic contamination of ondansetron blisters from a specific producer used in all the patients. A recall of contaminated ondansetron blisters was performed in all the country, after which the outbreak was contained. Surveillance and response of local and national infection prevention and control programs and laboratory support were key to control of a national multi-hospital common source outbreak due to contamination of a drug by an unusual fungus.

Input/output energy in solid state dye random lasers

A new approach to the problem of energy in solid state dye random lasers is presented. The measurements performed in terms of absolute energy show that the slope efficiency depends on the measurement conditions. In particular, in lasers with pumping in the picoseconds range, the result is really different if measured by recording the emission in the same time range or in a longer one (nanoseconds range). In the last case, no energy threshold is observed. A previously developed model has been applied to the solid state dye random laser. It is a rate-equations model, based on a distribution of paths with different lengths, which partially share population inversion. The results of the model are satisfactory and show that the dynamic behavior is pretty similar in solid state dye random lasers and in inorganic powders.

Organochlorine pesticides air monitoring near a historical lindane production site in Spain

The landfilling and dumping of persistent organic pollutants (POPs) and other persistent hazardous chemicals, such as hexachlorocyclohexane (HCH) isomers can have significantly adverse environmental consequences and cause contamination in soil, water, and atmosphere systems. Approximately 115,000 t of HCH wastes were generated by INQUINOSA Factory located in Sabiñánigo (Aragón, Spain) from 1975 to 1992, and were mainly dumped at Bailín and Sardas landfills. Under the frame of the project plan approved by the Government of Aragón, remediation and containment measures were implemented at the derelict production facility and landfill sites. To protect and assess the local environment, the concentrations of HCH isomers, pentachlorobenzene (PeCB) and hexachlorobenzene (HCB) in air were periodically monitored in the Sardas landfills and surroundings by passive sampling devices. The influence of meteorological parameters was evaluated, showing positive correlations between temperature and HCH and HCB concentrations. The highest HCH levels were detected in Sardas landfill and INQUINOSA Factory sites. PeCB values were statistically higher in Sardas landfill than in Sabiñánigo urban core, nevertheless, HCB concentrations were similar in both sampling points. Statistically positive correlations were found among HCH isomers in all sampling points, showing a major common source. The chlorobenzenes also correlated positively with each other. The α-/γ-HCH ratios were calculated (1.46 ± 1.25; mean ± S.D.), corroborating that concentrations detected were mainly originated from the historical production, storage and waste disposal of technical HCH.

Genetic variability of human papillomavirus type 66 L1 gene among women presenting for cervical cancer screening in Chile

The high-risk human papillomaviruses (HR-HPVs) are involved in the development of cervical cancer. Nevertheless, there are differences in the oncogenic potential among them. HPV-16 and HPV-18 are associated with approximately 70% of cancer worldwide, and both types are the most extensively studied HR-HPV. Great variations in the prevalence of HR-HPV have been described in different countries. The impact of these variations on the epidemiology of lesions and cervical cancer is currently unknown. A high prevalence of HPV-66 has been detected in Chile. Here, we have analyzed the genetic variability of the L1 gene from HPV-66-infected Chilean women. Higher order interactions between identified mutations were analyzed by co-variation and cluster analyses. Antigenic-index alterations following L1 mutations and B-cell epitopes were predicted by BcePred algorithm. HPV-66 L1 sequences clustered phylogenetically into two main clades. The genetic variability in the HPV-66 L1 gene involved thirty nucleotide changes. Four of these were for the first time identified in this study. Some of these variants are embedded in the B-cell epitope regions. Amino acid homology in the immunodominant epitopes of HPV-66 L1 protein (DE, FG and H1 loops) was 42.9-59.1% and 28.6-68.9% compared with HPV-16 and HPV-18, respectively. The results of this research suggest that the neutralizing epitopes of HPV-66 are antigenically different compared to HPV-16 and HPV-18. Our findings show the need to perform new structural and immunological studies on HPV-66 L1 protein to evaluate the cross-protection conferred by current HPV vaccines.

Investigating the Role of Easter Island in Migration of Zika Virus from South Pacific to Americas

The role of Easter Island in the dissemination of Zika virus from the Pacific islands into the Americas remains unclear. We analyzed new Zika virus sequences from Eastern Island and found that Zika virus was independently disseminated from French Polynesia into the Americas and Easter Island at around the same time.

Nuevos táxones animales descritos en la península Ibérica y Macaronesia desde 1994 (XXI)

La lista anual incluye en esta ocasión 580 táxones nuevos aparecidos en 309 referencias bibliográficas publicadas principalmente en 2017 y 2018. Comprende 463 especies, 69 géneros o subgéneros, 35 categorías supragenéricas, 12 subespecies y una categoría infrasubespecífica procedentes del área considerada.

Epidemiologic and Histopathologic Characterization of Cutaneous Metastases in Patients Who Visited 2 Hospitals in Santiago de Chile Between 2005 and 2017

BACKGROUND AND OBJECTIVE

Cutaneous metastases (CMs) account for 2% of skin tumors and their incidence varies between 0.7% and 9% in patients with cancer. The objective of this study was to describe and analyze the demographic, clinical, and histopathologic characteristics of CM in patients who visited 2 hospitals in the Santiago de Chile metropolitan region.

MATERIAL AND METHOD

We performed a retrospective, descriptive, analytical, observational, cross-sectional study. We reviewed the pathology reports, patient records, pathology slides, and dates of death for diagnosed cases of CM from the anatomic pathology departments of 2 hospitals in the Santiago de Chile metropolitan region between 2015 and 2017.

RESULTS

Ninety-six patients with CM were included in the study; 60.42% were women and 39.58% were men. The mean (SD) age was 67.95 (13.74) years, with a range of 28 to 96 years. The most common primary tumor was melanoma in 27.08% of cases (n=26), followed by breast cancer (18.75%, n=18), and adenocarcinoma (15.63%, n=15). The median time between diagnosis of the tumor and cutaneous metastasis was 9 months. Patients with CM of melanoma had a higher survival rate than patients with metastasis of other primary tumors (P<.05). A histopathologic study of 91 slides showed that diffuse infiltration of the tissue with tumor cells was the most common pattern and vascular invasion was rare.

CONCLUSIONS

The results are similar to those found worldwide. CM is a rare manifestation of internal tumors. It presents mainly at an advanced age and is equally prevalent in both sexes.