Foliar transcriptomes reveal candidate genes for late blight resistance in cultivars of diploid potato Solanum tuberosum L. Andigenum Group.

Characterization of major resistance (R) genes to late blight (LB) -caused by the oomycete Phytophthora infestans- is very important for potato breeding. The objective of this study was to identify novel genes for resistance to LB from diploid Solanum tuberosum L. Andigenum Group (StAG) cultivar accessions. Using comparative analysis with a edgeR bioconductor package for differential expression analysis of transcriptomes, two of these accessions with contrasting levels of resistance to LB were analyzed using digital gene expression data. As a result, various differentially expressed genes (P ≤ 0.0001, Log2FC ≥ 2, FDR < 0.001) were noted. The combination of transcriptomic analysis provided 303 candidate genes that are overexpressed and underexpressed, thereby giving high resistance to LB. The functional analysis showed differential expression of R genes and their corresponding proteins related to disease resistance, NBS-LRR domain proteins, and specific disease resistance proteins. Comparative analysis of specific tissue transcriptomes in resistant and susceptible genotypes can be used for rapidly identifying candidate R genes, thus adding novel genes from diploid StAG cultivar accessions for host plant resistance to P. infestans in potato.

Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery.

DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be limited for understudied taxa or regions. One such region is Antarctica, where, despite the importance of lichens and lichenized fungi identification, their genetic diversity is far from characterized. The aim of this exploratory study was to survey the lichenized fungi diversity of King George Island using a fungal barcode marker as an initial identification tool. Samples were collected unrestricted to specific taxa in coastal areas near Admiralty Bay. Most samples were identified using the barcode marker and verified up to the species or genus level with a high degree of similarity. A posterior morphological evaluation focused on samples with novel barcodes allowed for the identification of unknown Austrolecia, Buellia, and Lecidea s.l. species. These results contribute to better represent the lichenized fungi diversity in understudied regions such as Antarctica by increasing the richness of the nucleotide databases. Furthermore, the approach used in this study is valuable for exploratory surveys in understudied regions to guide taxonomic efforts towards species recognition and discovery.

Pneumocystis primary infection in non-immunosuppressed infants in Lima, Peru.

OBJECTIVES: To provide original data on Pneumocystis primary infection in non-immunosuppressed infants from Peru. METHODS: A cross sectional study was performed. Infants less than seven months old, without any underlying medical conditions attending the "well baby" outpatient clinic at one hospital in Lima, Peru were prospectively enrolled during a 15-month period from November 2016 to February 2018. All had a nasopharyngeal aspirate (NPA) for detection of P. jirovecii DNA using a PCR assay, regardless of respiratory symptoms. P. jirovecii DNA detection was considered to represent pulmonary colonization contemporaneous with Pneumocystis primary infection. Associations between infants' clinical and demographic characteristics and results of P. jirovecii DNA detection were analyzed. RESULTS: P. jirovecii DNA was detected in 45 of 146 infants (30.8%) and detection was not associated with concurrent respiratory symptoms in 40 of 45 infants. Infants with P. jirovecii had a lower mean age when compared to infants not colonized (p <0.05). The highest frequency of P. jirovecii was observed in 2-3-month-old infants (p < 0.01) and in the cooler winter and spring seasons (p <0.01). Multivariable analysis showed that infants living in a home with ≤ 1 bedroom were more likely to be colonized; Odds Ratio =3.03 (95%CI 1.31-7.00; p = 0.01). CONCLUSION: Pneumocystis primary infection in this single site in Lima, Peru, was most frequently observed in 2-3-month-old infants, in winter and spring seasons, and with higher detection rates being associated with household conditions favoring close inter-individual contacts and potential transmission of P. jirovecii.

Liver abscess caused by Candida haemulonii var. vulnera. First case report in Peru.

BACKGROUND: Liver abscesses caused by Candida species are mainly found in immunocompromised hosts, associated with conditions (such as neutropenia and mucositis) that facilitate the spreading of microorganisms from the gastrointestinal tract. CASE REPORT: We present the case of a non-immunocompromised 72-year-old woman with a liver abscess caused by Candida haemulonii var. vulnera, in whom potential associated conditions could be polycystic kidney disease and renal replacement therapy. The patient experienced clinical resolution after percutaneous drainage and treatment with caspofungin. CONCLUSIONS: To our knowledge, this is the first case reported in Peru of a liver abscess due to Candida haemulonii var. vulnera, a clinical presentation that has not been described previously. This finding should prompt us to establish active surveillance of causal agents of systemic candidiasis.

Molecular Epidemiology Reveals Low Genetic Diversity among Cryptococcus neoformans Isolates from People Living with HIV in Lima, Peru, during the Pre-HAART Era.

Cryptococcosis, a mycosis presenting mostly as meningoencephalitis, affecting predominantly human immunodeficiency virus (HIV)-infected people, is mainly caused by Cryptococcus neoformans. The genetic variation of 48 C. neoformans isolates, recovered from 20 HIV-positive people in Lima, Peru, during the pre-highly active antiretroviral therapy (HAART) era, was studied retrospectively. The mating type of the isolates was determined by PCR, and the serotype by agglutination and CAP59-restriction fragment length polymorphism (RFLP). Genetic diversity was assessed by URA5-RFLP, PCR-fingerprinting, amplified fragment length polymorphism (AFLP), and multilocus sequence typing (MLST). All isolates were mating type alpha, with 39 molecular type VNI, seven VNII, corresponding to C. neoformans var. grubii serotype A, and two VNIII AD hybrids. Overall, the cryptococcal population from HIV-positive people in Lima shows a low degree of genetic diversity. In most patients with persistent cryptococcal infection, the same genotype was recovered during the follow-up. In four patients with relapse and one with therapy failure, different genotypes were found in isolates from the re-infection and from the isolate recovered at the end of the treatment. In one patient, two genotypes were found in the first cryptococcosis episode. This study contributes data from Peru to the ongoing worldwide population genetic analysis of Cryptococcus.

Colonización por Pneumocystis jirovecii en mujeres gestantes y recién nacidos en Lima, Perú / neumocystis jirovecii colonisation in pregnant women and newborns in Lima, Peru

ANTECEDENTES: La primoinfección por Pneumocystis jirovecii ocurre de forma asintomática antes de los 6 meses de edad, lo que sugiere que la infección se adquiere muy precozmente en la vida. Se ha descrito también la presencia de neumonía por Pneumocystis en recién nacidos, lo que indica la necesidad de estudiar la colonización en el binomio madre-hijo. OBJETIVOS: Evaluar la prevalencia de colonización de Pneumocystis en gestantes y explorar la potencial transmisión transplacentaria. MÉTODOS: Estudio transversal que incluyó a mujeres gestantes mayores de 18 años con 37 o más semanas de gestación y negativas para el VIH que acudieron al Hospital Cayetano Heredia en los años 2016-2017. Se obtuvo información clínica y demográfica de la gestante y del recién nacido. Se tomaron muestras de lavado orofaríngeo/hisopado nasal de la gestante, de placenta y de aspirado nasofaríngeo/hisopado nasal del recién nacido. Todas las muestras respiratorias fueron analizadas mediante PCR anidada. En el caso de las muestras de placenta solo fueron analizadas aquellas procedentes de mujeres con resultados positivos de PCR para Pneumocystis en las muestras respiratorias. RESULTADOS: De las 92 gestantes incluidas en el estudio cinco presentaban colonización por Pneumocystis (5,43%). Se evaluaron las muestras de 87 recién nacidos y las placentas de las cinco madres con PCR positiva, no encontrándose ADN de Pneumocystis en ninguna de ellas. CONCLUSIONES: Aunque el 5,43% de las mujeres gestantes estuvieran colonizadas por Pneumocystis no pudo determinarse el rol de esta colonización en la transmisión a sus recién nacidos, ya que en ninguno de ellos se demostró la presencia de Pneumocystis

BACKGROUND: Pneumocystisjirovecii primary infection occurs asymptomatically before 6 months of age, suggesting that the infection is acquired very early in life. Furthermore, Pneumocystis pneumonia has been described in newborns, which emphasizes the importance of studying Pneumocystis colonization in mother-infant pairs. AIMS: To evaluate the prevalence of Pneumocystis colonization among pregnant women and to determine the potential transplacental transmission. METHODS: A cross-sectional study was carried out on HIV-negative women over 18 years-old, and 37 or more weeks of pregnancy attending Hospital Cayetano Heredia Maternity unit during 2016-2017. Clinical and demographical information was collected on them and their newborns. Oropharyngeal washes, nasal swabs, and placenta samples were collected from women, as well as a nasopharyngeal aspirate and nasal swab from newborns. All respiratory samples were analysed by nested-PCR for the detection of Pneumocystis. Placenta samples from women with a positive PCR result in their respiratory samples were also analysed by nested-PCR. RESULTS: Of the 92 pregnant women included, five of them (5.43%) were colonized by Pneumocystis. Pneumocystis DNA was not found in any of the 87 available newborn samples or in the placentas of the five women who had a positive result by PCR in their upper respiratory samples. CONCLUSIONS: It was found that 5.43% of the pregnant women were colonized by Pneumocystis, there was no evidence of any role of this colonization in the transmission to their newborns, since none of them tested positive for Pneumocystis

[Pneumocystis jirovecii colonisation in pregnant women and newborns in Lima, Peru]. / Colonización por Pneumocystis jirovecii en mujeres gestantes y recién nacidos en Lima, Perú.

BACKGROUND: Pneumocystisjirovecii primary infection occurs asymptomatically before 6 months of age, suggesting that the infection is acquired very early in life. Furthermore, Pneumocystis pneumonia has been described in newborns, which emphasizes the importance of studying Pneumocystis colonization in mother-infant pairs. AIMS: To evaluate the prevalence of Pneumocystis colonization among pregnant women and to determine the potential transplacental transmission. METHODS: A cross-sectional study was carried out on HIV-negative women over 18 years-old, and 37 or more weeks of pregnancy attending Hospital Cayetano Heredia Maternity unit during 2016-2017. Clinical and demographical information was collected on them and their newborns. Oropharyngeal washes, nasal swabs, and placenta samples were collected from women, as well as a nasopharyngeal aspirate and nasal swab from newborns. All respiratory samples were analysed by nested-PCR for the detection of Pneumocystis. Placenta samples from women with a positive PCR result in their respiratory samples were also analysed by nested-PCR. RESULTS: Of the 92 pregnant women included, five of them (5.43%) were colonized by Pneumocystis. Pneumocystis DNA was not found in any of the 87 available newborn samples or in the placentas of the five women who had a positive result by PCR in their upper respiratory samples. CONCLUSIONS: It was found that 5.43% of the pregnant women were colonized by Pneumocystis, there was no evidence of any role of this colonization in the transmission to their newborns, since none of them tested positive for Pneumocystis.

Transcriptomic profiling against Globodera pallida in resistant and susceptible potato roots / Perfil del transcriptoma de raíz de papa resistente y susceptible a Globodera pallida

Abstract Globodera pallida is a white potato cyst nematode present in the Andes, which causes huge losses to Peruvian farmers. An RNA-seq analysis allowed the identification of candidate genes that could mediate resistance against this pathogen. Two varieties, "María Huanca" (Solanum andigena) clone resistant (CIP 279142.12) and "Chimbina Colorada" (Solanum chaucha) (CIP 701013) clone susceptible to G. pallida, were used to identify differentially expressed genes. Total RNA from roots was extracted 72 hours post inoculation with second stage juveniles. Sequencing was done using the Illumina Hiseq 2500 platform. Reads were screened for quality issues and then mapped to the reference potato genome (clone DM1-3516 R44 v4.03). Here, we report 27717 and 27750 genes expressed in the resistant and susceptible variety respectively. The comparative analysis of expression identified 100 candidate genes. 91 genes were associated with resistance to G. pallida with Fold Change ≥ 2 (p <0.05). The remaining 9 R genes had Fold Change ≤ 1. We show differences in the expression of an NBS-LRR protein similar to Gro1-8, genes linked to late blight and TMV virus resistance.

Resumen Globodera pallida es un nemátodo formador de quistes. En la papa (Solanum tuberosum) ocasiona daños atrofiando las raíces. En los Andes peruanos ocasiona grandes pérdidas económicas a los agricultores. A través del análisis por RNA-seq, se identificaron genes candidatos que podrían mediar la resistencia contra este nemátodo. Dos variedades de papa: "María Huanca" (S. andigena) clon resistente (CIP 279142.12) y "Chimbina Colorada" (S. chaucha) clon susceptible (CIP 701013) a G. pallida, fueron utilizados para identificar genes expresados diferencialmente. Las raíces fueron inoculadas con G. pallida en segundo estadío juvenil (J2). El ARN total fue extraído a 72 horas post inoculación. El secuenciamiento fue realizado en plataforma Illumina HiSeq 2500. Las lecturas de buena calidad fueron mapeadas al genoma de referencia de S. tuberosum (clon DM1-3516 R44 v4.03). Reportamos 27717 y 27750 genes expresados en la variedad resistente y susceptible, respectivamente. El análisis comparativo identificó 100 genes candidatos, de ellos 91 genes fueron asociados con la resistencia a G. pallida (Fold Change ≥ 2 , p <0.05) y los 9 restantes con genes R ( Fold Change ≤ 1). En este último grupo se observaron diferencias en la expresión de genes NBS-LRR similar a Gro 1-8, genes relacionados a late blight y resistencia al Virus TMV.

Identification and characterization of compounds from Chrysosporium multifidum, a fungus with moderate antimicrobial activity isolated from Hermetia illucens gut microbiota.

The gut microbiota of insects is composed of a wide range of microorganisms which produce bioactive compounds that protect their host from pathogenic attack. In the present study, we isolate and identify the fungus Chrysosporium multifidum from the gut of Hermetia illucens larvae. Extract from C. multifidum culture broth supernatant showed moderate activity against a strain of methicillin-resistant Staphylococcus aureus (MRSA). Bioguided isolation of the extract resulted in the characterization of six α-pyrone derivatives (1-6) and one diketopiperazine (7). Of these compounds, 5,6-dihydro-4-methoxy-6-(1-oxopentyl)-2H-pyran-2-one (4) showed the greatest activity (IC50 = 11.4 ± 0.7 µg/mL and MIC = 62.5 µg/mL) against MRSA.

Multi-environment multi-QTL association mapping identifies disease resistance QTL in barley germplasm from Latin America.

KEY MESSAGE: Multi-environment multi-QTL mixed models were used in a GWAS context to identify QTL for disease resistance. The use of mega-environments aided the interpretation of environment-specific and general QTL. Diseases represent a major constraint for barley (Hordeum vulgare L.) production in Latin America. Spot blotch (caused by Cochliobolus sativus), stripe rust (caused by Puccinia striiformis f.sp. hordei) and leaf rust (caused by Puccinia hordei) are three of the most important diseases that affect the crop in the region. Since fungicide application is not an economically or environmentally sound solution, the development of durably resistant varieties is a priority for breeding programs. Therefore, new resistance sources are needed. The objective of this work was to detect genomic regions associated with field level plant resistance to spot blotch, stripe rust, and leaf rust in Latin American germplasm. Disease severities measured in multi-environment trials across the Americas and 1,096 SNPs in a population of 360 genotypes were used to identify genomic regions associated with disease resistance. Optimized experimental design and spatial modeling were used in each trial to estimate genotypic means. Genome-Wide Association Mapping (GWAS) in each environment was used to detect Quantitative Trait Loci (QTL). All significant environment-specific QTL were subsequently included in a multi-environment-multi-QTL (MEMQ) model. Geographical origin and inflorescence type were the main determinants of population structure. Spot blotch severity was low to intermediate while leaf and stripe rust severity was high in all environments. Mega-environments were defined by locations for spot blotch and leaf rust. Significant marker-trait associations for spot blotch (9 QTL), leaf (6 QTL) and stripe rust (7 QTL) and both global and environment-specific QTL were detected that will be useful for future breeding efforts.

Evaluation of cats as the source of endemic sporotrichosis in Peru.

Although contact with domestic cats has been shown to be a risk factor for sporotrichosis in endemic areas, systematic evaluation of apparently unaffected cats as possible reservoirs for infection has not been explored. The goals of this study were to identify the following aspects of sporotrichosis in the endemic area of Abancay, Peru: (i) the overall prevalence of sporotrichosis in the cat population, (ii) the most common site where the fungus can be isolated from these cats, and (iii) whether cats without identifiable skin lesions may be carriers of the fungus in the oral mucosa, nasal mucosa, or nails. One household cat in each of 85 neighborhoods within the endemic area of Abancay, Peru was randomly selected. Oral and nasal swabs, as well as nail clippings were taken from 84 of the cats. In addition, samples from skin lesions that were suspected to be due to sporotrichosis were collected from cats or members of families that owned the pets. Cultures inoculated with two nasal swabs and one set of nail clippings from two different cats yielded Sporothrix schenckii, the identity of which were confirmed by rDNA sequencing. The overall prevalence of Sporothrix schenckii colonization was 2.38% (95% CI 0.41-9.14) in this cat population. None of the skin lesion samples from the cats and only one such sample from a family member were positive for Sporothrix schenckii in culture. These results suggest a role for domestic cats as a possible reservoir for sporotrichosis infection in Abancay.

Epidemiology of human sporotrichosis investigated by amplified fragment length polymorphism.

Amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity of Peruvian strains of Sporothrix schenckii and to compare them to a panel of non-Peruvian strains. AFLP analysis suggests that the Peruvian strains can be divided into two homogeneous clusters with no reference to geographical origin or the clinical form of sporotrichosis. The strains from abroad present heterogeneous profiles, with the Bolivian strain and the Colombian strains related to one of the Peruvian population. Sequencing of internal transcribed spacer 2, used to examine the relationships over a longer distance, confirmed the division of Peruvian strains into two populations that can be identified on the basis of a single but specific sequence divergence. This paper introduces automated AFLP analysis as a valuable tool for further investigation of the epidemiology and ecology of S. schenckii.