Laparoscopic Cholecystectomy with a Mixed Approach in a Patient with Kartagener Syndrome: Technical Report and Review of Literature

Kartagener syndrome (KS) is a rare autosomal recessive disease. The disease is characterized by three typical symptoms: chronic sinusitis, situs viscerum inversus (SVI), and bronchiectasis. The laparoscopic cholecystectomy (LC) is the standard procedure in most cases of cholelithiasis, but in SVI patients it can be difficult, especially for right-handed surgeons. We report the case of a 24-year-old female affected by KS, presenting with a history of symptomatic cholelithiasis. Ultrasound and magnetic resonance cholangiopancreatography confirmed SVI totalis and cholelithiasis. The patient underwent a laparoscopic cholecystectomy by a right-handed surgeon performed with a mixed approach without complications. Laparoscopic cholecystectomy in SVI patients can be a safe and reliable technique especially for a left-handed surgeon. The described technique is also easy for a right-handed surgeon. However, it is considered a technically challenging procedure and often requires technical modification

Escherichia coli, Salmonella spp., Hepatitis A Virus and Norovirus in bivalve molluscs in Southern Italy

European Legislation has fixed microbiological, chemical and biotoxicological limits for shellfish but no limits for viruses. In the present study we report the results of an investigation on Salmonella spp., Escherichia coli, Hepatitis A virus (HAV) and Norovirus (NoV) contamination in 59 bivalve shellfish collected during the years 2011-2012 in Southern Italy. All the samples of Mytilus galloprovincialis and of Solen marginatus were negative for HAV whereas 6.8% of them were positive for Norovirus GI (NoVGI) and 11.9% positive for Norovirus GII (NoVGII). Samples were also negative for Salmonella spp., while 16 of them (27%) were positive for E. coli. No correlation was found between E. coli and NoV contamination in bivalve molluscs. Moreover, the Competent Authorities are advised to take into serious consideration additional measures for the legislation in force in order to guarantee the consumer's health

Multiplex PCR to detect bacteriophages from natural whey cultures of buffalo milk and characterisation of two phages active against Lactococcus lactis, фApr-1 and фApr-2

This work investigated bacteriophage induced starter failures in artisanal buffalo Mozzarella production plants in Southern Italy. Two hundred and ten samples of whey starter cultures were screened for bacteriophage infection. Multiplex polymerase chain reaction (PCR) revealed phage infection in 28.56% of samples, all showing acidification problems during cheese making. Based on DNA sequences, bacteriophages for Lactococcus lactis (L. lactis), Lactobacillus delbruekii (L. delbruekii) and Streptococcus thermophilus (S. thermophilus) were detected. Two phages active against L.  lactis, фApr-1 and фApr-2, were isolated and characterised. The genomes, approximately 31.4 kb and 31 kb for фApr-1 and фApr-2 respectively, consisted of double-stranded linear DNA with pac-type system. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed one major structural protein of approximately 32.5 kDa and several minor proteins. This is the first report of phage isolation in buffalo milk and of the use of multiplex PCR to screen and study the diversity of phages against Lactic Acid Bacteria (LAB) strains in artisanal Water Buffalo Mozzarella starters

Management of pheochromocytoma during pregnancy from diagnosis to laparoscopic adrenalectomy. A case report and review of literature

INTRODUCTION: Pheochromocytoma is an endocrine tumour of chromaffin cells. It can be diagnosed either sporadically or in the context of hereditary syndromes (e.g. Von Hippel Lindau, Neurofibromatosis type 1 and multiple neuroendocrine neoplasia type 2). During pregnancy, its frequency is very low (about 0,007%). This tumour causes paroxysmal hypertension in 0,1-0,6% pregnant women, because of an overproduction of catecholamines. If undiagnosed and nontreated, it's associated with high maternal and fetal mortality (40-50%). We report the case of a 30-year-old female diagnosed with pheochromocytoma during pregnancy at week 31 of gestation. In a multidisciplinary team made of surgeons, gynaecologists, anaesthetists, geneticists and endocrinologists we evaluated the case and according to literature, we choose a surgical approach after childbirth: performing a laparoscopic right adrenalectomy. DISCUSSION: In pregnancy, pheochromocytoma is a rare clinical condition. Gold standard treatment is laparoscopic adrenalectomy. However, the optimum timing of surgery is a challenge. CONCLUSION: Timely diagnosis of pheochromocytoma in pregnant women with hypertension and appropriate therapeutic management can lead to improve maternal, fetal and neonatal outcomes. The multidisciplinary team is necessary to recognize the symptoms and to adopt the right pre - and post - operative treatment. Laparoscopic adrenalectomy after delivery is safe and feasible even though the surgical procedure should be performed by an experienced surgeon. KEY WORDS: Pheochromocytoma, Pregnancy, Laparoscopic adrenalectomy and pregnancy, Management of pheochromocytoma, Laparoscopic adrenalectomy, Adrenalectomy, Pregnancy and pheochromocytoma

Campylobacter bacteriophage DA10: An excised temperate bacteriophage targeted by CRISPR-cas

Background: Lytic bacteriophages that infect Campylobacter spp. have been utilized to develop therapeutic/decontamination techniques. However, the association of Campylobacter spp. and bacteriophages has been the focus of several strands of research aimed at understanding the complex relationships that have developed between predators and prey over evolutionary time. The activities of endogenous temperate bacteriophages have been used to evaluate genomic rearrangements and differential protein expression in host cells, and mechanisms of resistance to bacteriophage infection in campylobacters such as phase variation and CRISPR-mediated immunity. Results: Temperate bacteriophage DA10 represents a novel excised and infective virus capable of replication in a restricted set of C. jejuni and C. coli hosts. Whole genome sequencing reveals that DA10 (35,379 bp) forms part of a novel group of temperate bacteriophages that have limited distribution among database host genome sequences. Analysis of potential host genomes reveals a robust response against DA10 and DA10-like bacteriophages is driven by CRISPR-mediated immunity with 75% of DA10 ORFs represented as ~ 30 bp spacer sequences in numerous Campylobacter Type II-C CRISPR arrays. Several DA10-like homologues have been identified in a small sub-set of C. jejuni and C. coli genome sequences (ranging from near complete integrated prophage sequences to fragments recognisable in the sequence read archive). Conclusions: A complete intact DA10-like prophage in C. jejuni CJ677CC520 provides evidence that the associations between host and DA10-like bacteriophages are long-standing in evolutionary timescales. Extensive nucleotide substitution and loss can be observed in the integrated DA10-like prophage of CJ677CC520 compared to other relatives as observed through pairwise genome comparisons. Examining factors that have limited the population expansion of the prophage, while others appear to have thrived and prospered (Mu-like, CJIE-like, and lytic Campylobacter bacteriophages) will assist in identifying the underlying evolutionary processes in the natural environment

Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

[EN] Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks.This work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under the grant agreement number 677379 (G2P-SOL project: Linking genetic resources, genomes, and phenotypes of solanaceous crops).Barchi, L.; Acquadro, A.; Alonso-Martín, D.; Aprea, G.; Bassolino, L.; Demurtas, O.; Ferrante, P.... (2019). Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. Frontiers in Plant Science. 10:1-17. https://doi.org/10.3389/fpls.2019.01005S11710Acquadro, A., Barchi, L., Gramazio, P., Portis, E., Vilanova, S., Comino, C., … Lanteri, S. (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLOS ONE, 12(7), e0180774. doi:10.1371/journal.pone.0180774Anderson, J. A., Churchill, G. A., Autrique, J. E., Tanksley, S. D., & Sorrells, M. E. (1993). Optimizing parental selection for genetic linkage maps. Genome, 36(1), 181-186. doi:10.1139/g93-024Barchi, L., Pietrella, M., Venturini, L., Minio, A., Toppino, L., Acquadro, A., … Rotino, G. L. (2019). A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Scientific Reports, 9(1). doi:10.1038/s41598-019-47985-wBeddows, I., Reddy, A., Kloesges, T., & Rose, L. E. (2017). Population Genomics in Wild Tomatoes—The Interplay of Divergence and Admixture. Genome Biology and Evolution, 9(11), 3023-3038. doi:10.1093/gbe/evx224Blanca, J., Montero-Pau, J., Sauvage, C., Bauchet, G., Illa, E., Díez, M. J., … Cañizares, J. (2015). Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics, 16(1). doi:10.1186/s12864-015-1444-1Caicedo, A. L., & Schaal, B. A. (2004). Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Ecology, 13(7), 1871-1882. doi:10.1111/j.1365-294x.2004.02191.xCastle, J. C. (2011). SNPs Occur in Regions with Less Genomic Sequence Conservation. PLoS ONE, 6(6), e20660. doi:10.1371/journal.pone.0020660Cericola, F., Portis, E., Toppino, L., Barchi, L., Acciarri, N., Ciriaci, T., … Lanteri, S. (2013). The Population Structure and Diversity of Eggplant from Asia and the Mediterranean Basin. PLoS ONE, 8(9), e73702. doi:10.1371/journal.pone.0073702Chen, K.-Y., Cong, B., Wing, R., Vrebalov, J., & Tanksley, S. D. (2007). Changes in Regulation of a Transcription Factor Lead to Autogamy in Cultivated Tomatoes. Science, 318(5850), 643-645. doi:10.1126/science.1148428Chen, K.-Y., & Tanksley, S. D. (2004). High-Resolution Mapping and Functional Analysis ofse2.1. Genetics, 168(3), 1563-1573. doi:10.1534/genetics.103.022558Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., … DePristo, M. A. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. doi:10.1093/bioinformatics/btr330Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., & Blaxter, M. L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12(7), 499-510. doi:10.1038/nrg3012Del Fabbro, C., Scalabrin, S., Morgante, M., & Giorgi, F. M. (2013). An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis. PLoS ONE, 8(12), e85024. doi:10.1371/journal.pone.0085024DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., … Daly, M. J. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43(5), 491-498. doi:10.1038/ng.806Dodsworth, S., Chase, M. W., Särkinen, T., Knapp, S., & Leitch, A. R. (2015). Using genomic repeats for phylogenomics: a case study in wild tomatoes (SolanumsectionLycopersicon: Solanaceae). Biological Journal of the Linnean Society, 117(1), 96-105. doi:10.1111/bij.12612Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011). A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE, 6(5), e19379. doi:10.1371/journal.pone.0019379Flint-Garcia, S. A. (2013). Genetics and Consequences of Crop Domestication. Journal of Agricultural and Food Chemistry, 61(35), 8267-8276. doi:10.1021/jf305511dGramazio, P., Prohens, J., Borràs, D., Plazas, M., Herraiz, F. J., & Vilanova, S. (2017). Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants. Euphytica, 213(12). doi:10.1007/s10681-017-2057-3Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2017). UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2), 518-522. doi:10.1093/molbev/msx281Hoheisel, J. D. (2006). Microarray technology: beyond transcript profiling and genotype analysis. Nature Reviews Genetics, 7(3), 200-210. doi:10.1038/nrg1809Huerta-Cepas, J., Serra, F., & Bork, P. (2016). ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Molecular Biology and Evolution, 33(6), 1635-1638. doi:10.1093/molbev/msw046Isshiki, S., Iwata, N., & Khan, M. M. R. (2008). ISSR variations in eggplant (Solanum melongena L.) and related Solanum species. Scientia Horticulturae, 117(3), 186-190. doi:10.1016/j.scienta.2008.04.003Kamenetzky, L., Asís, R., Bassi, S., de Godoy, F., Bermúdez, L., Fernie, A. R., … Carrari, F. (2010). Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits. Plant Physiology, 152(4), 1772-1786. doi:10.1104/pp.109.150532Kouassi, B., Prohens, J., Gramazio, P., Kouassi, A. B., Vilanova, S., Galán-Ávila, A., … Plazas, M. (2016). Development of backcross generations and new interspecific hybrid combinations for introgression breeding in eggplant ( Solanum melongena ). Scientia Horticulturae, 213, 199-207. doi:10.1016/j.scienta.2016.10.039Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., … Huang, S. (2014). Genomic analyses provide insights into the history of tomato breeding. Nature Genetics, 46(11), 1220-1226. doi:10.1038/ng.3117Lynch, V. J., & Wagner, G. P. (2010). DID EGG-LAYING BOAS BREAK DOLLO’S LAW? PHYLOGENETIC EVIDENCE FOR REVERSAL TO OVIPARITY IN SAND BOAS (ERYX: BOIDAE). Evolution, 64(1), 207-216. doi:10.1111/j.1558-5646.2009.00790.xMammadov, J., Aggarwal, R., Buyyarapu, R., & Kumpatla, S. (2012). SNP Markers and Their Impact on Plant Breeding. International Journal of Plant Genomics, 2012, 1-11. doi:10.1155/2012/728398Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), 10. doi:10.14806/ej.17.1.200Mason, A. S., Zhang, J., Tollenaere, R., Vasquez Teuber, P., Dalton-Morgan, J., Hu, L., … Batley, J. (2015). High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources, 15(5), 1091-1101. doi:10.1111/1755-0998.12379Meyer, R. S., Karol, K. G., Little, D. P., Nee, M. H., & Litt, A. (2012). Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication. Molecular Phylogenetics and Evolution, 63(3), 685-701. doi:10.1016/j.ympev.2012.02.006Miz, R. B., Mentz, L. A., & Souza-Chies, T. T. (2007). Overview of the phylogenetic relationships of some southern Brazilian species from section Torva and related sections of «spiny Solanum» (Solanum subgenus Leptostemonum, Solanaceae). Genetica, 132(2), 143-158. doi:10.1007/s10709-007-9156-3Nairismägi, M.-L., Tan, J., Lim, J. Q., Nagarajan, S., Ng, C. C. Y., Rajasegaran, V., … Ong, C. K. (2016). JAK-STAT and G-protein-coupled receptor signaling pathways are frequently altered in epitheliotropic intestinal T-cell lymphoma. Leukemia, 30(6), 1311-1319. doi:10.1038/leu.2016.13Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2014). IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution, 32(1), 268-274. doi:10.1093/molbev/msu300Pailles, Y., Ho, S., Pires, I. S., Tester, M., Negrão, S., & Schmöckel, S. M. (2017). Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.00138Herraiz, F. J., Blanca, J., Ziarsolo, P., Gramazio, P., Plazas, M., Anderson, G. J., … Vilanova, S. (2016). The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato. BMC Genomics, 17(1). doi:10.1186/s12864-016-2656-8Plazas, M., Andújar, I., Vilanova, S., Gramazio, P., Herraiz, F. J., & Prohens, J. (2014). Conventional and phenomics characterization provides insight into the diversity and relationships of hypervariable scarlet (Solanum aethiopicum L.) and gboma (S. macrocarpon L.) eggplant complexes. Frontiers in Plant Science, 5. doi:10.3389/fpls.2014.00318Plazas, M., Vilanova, S., Gramazio, P., Rodríguez-Burruezo, A., Fita, A., Herraiz, F. J., … Prohens, J. (2016). Interspecific Hybridization between Eggplant and Wild Relatives from Different Genepools. Journal of the American Society for Horticultural Science, 141(1), 34-44. doi:10.21273/jashs.141.1.34Poplin, R., Ruano-Rubio, V., DePristo, M. A., Fennell, T. J., Carneiro, M. O., Van der Auwera, G. A., … Banks, E. (2017). Scaling accurate genetic variant discovery to tens of thousands of samples. doi:10.1101/201178Razali, R., Bougouffa, S., Morton, M. J. L., Lightfoot, D. J., Alam, I., Essack, M., … Negrão, S. (2018). The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.01402Robinson, D. F., & Foulds, L. R. (1981). Comparison of phylogenetic trees. Mathematical Biosciences, 53(1-2), 131-147. doi:10.1016/0025-5564(81)90043-2Rodriguez, F., Wu, F., Ané, C., Tanksley, S., & Spooner, D. M. (2009). Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evolutionary Biology, 9(1), 191. doi:10.1186/1471-2148-9-191Sakata, Y., & Lester, R. N. (1997). Euphytica, 97(3), 295-301. doi:10.1023/a:1003000612441Sakata, Y., Nishio, T., & Matthews, P. J. (1991). Chloroplast DNA analysis of eggplant (Solanum melongena) and related species for their taxonomic affinity. Euphytica, 55(1), 21-26. doi:10.1007/bf00022555Särkinen, T., Bohs, L., Olmstead, R. G., & Knapp, S. (2013). A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evolutionary Biology, 13(1), 214. doi:10.1186/1471-2148-13-214Scaglione, D., Pinosio, S., Marroni, F., Di Centa, E., Fornasiero, A., Magris, G., … Morgante, M. (2019). Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize. Annals of Botany, 124(4), 543-551. doi:10.1093/aob/mcz054Scheben, A., Batley, J., & Edwards, D. (2017). Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnology Journal, 15(2), 149-161. doi:10.1111/pbi.12645Scolnick, J. A., Dimon, M., Wang, I.-C., Huelga, S. C., & Amorese, D. A. (2015). An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples. PLOS ONE, 10(7), e0128916. doi:10.1371/journal.pone.0128916Semagn, K., Babu, R., Hearne, S., & Olsen, M. (2013). Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Molecular Breeding, 33(1), 1-14. doi:10.1007/s11032-013-9917-xSim, S.-C., Van Deynze, A., Stoffel, K., Douches, D. S., Zarka, D., Ganal, M. W., … Francis, D. M. (2012). High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding. PLoS ONE, 7(9), e45520. doi:10.1371/journal.pone.0045520Syfert, M. M., Castañeda-Álvarez, N. P., Khoury, C. K., Särkinen, T., Sosa, C. C., Achicanoy, H. A., … Knapp, S. (2016). Crop wild relatives of the brinjal eggplant (Solanum melongena): Poorly represented in genebanks and many species at risk of extinction. American Journal of Botany, 103(4), 635-651. doi:10.3732/ajb.1500539(2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635-641. doi:10.1038/nature11119Thomson, R. C., & Shaffer, H. B. (2010). Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles. Systematic Biology, 59(1), 42-58. doi:10.1093/sysbio/syp075Tranchida-Lombardo, V., Mercati, F., Avino, M., Punzo, P., Fiore, M. C., Poma, I., … Grillo, S. (2018). Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, 153(2), 288-297. doi:10.1080/11263504.2018.1478900Vilanova, S., Manzur, J. P., & Prohens, J. (2011). Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins. Molecular Breeding, 30(2), 647-660. doi:10.1007/s11032-011-9650-2Vorontsova, M. S., Stern, S., Bohs, L., & Knapp, S. (2013). African spinySolanum(subgenusLeptostemonum, Solanaceae): a thorny phylogenetic tangle. Botanical Journal of the Linnean Society, 173(2), 176-193. doi:10.1111/boj.12053Weese, T. L., & Bohs, L. (2010). Eggplant origins: Out of Africa, into the Orient. TAXON, 59(1), 49-56. doi:10.1002/tax.591006Tan, M. H., Gan, H. M., Schultz, M. B., & Austin, C. M. (2015). MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Molecular Phylogenetics and Evolution, 85, 180-188. doi:10.1016/j.ympev.2015.02.009Wiens, J. J., & Morrill, M. C. (2011). Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data. Systematic Biology, 60(5), 719-731. doi:10.1093/sysbio/syr025Williams, C. E., & Clair, D. A. S. (1993). Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon esculentum. Genome, 36(3), 619-630. doi:10.1139/g93-083Zheng, X., Levine, D., Shen, J., Gogarten, S. M., Laurie, C., & Weir, B. S. (2012). A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics, 28(24), 3326-3328. doi:10.1093/bioinformatics/bts60

Cross-sectional study of hepatitis E virus (HEV) circulation in Italian pig farms

OHEJP Project: BIOPIGEE Foodborne transmission is considered the main way of spreading zoonotic hepatitis E virus (HEV) infection in Europe. In recent years, the human cases of hepatitis E in subjects without history of travel in endemic areas have raised, suggesting that domestic HEV transmission is increasing. Pork products with or without liver, are often indicated as the source of many human foodborne HEV cases as well as small outbreaks. Pigs are recognized as the main reservoir of the zoonotic HEV-3 genotype, the most frequently detected in human cases in the EU. In the absence of a harmonized surveillance of HEV circulation, data on prevalence are heterogeneous but confirm a widespread circulation of HEV-3 in pig herds across EU. HEV-3 can pass through the food chain from farm to fork when infected animals are slaughtered. In Italy, several studies reported the circulation of HEV-3 in pig farms, but results are heterogeneous due to dierent methodologies applied. In the present study, we performed a survey over 51 pig herds belonging to three main types of farms: breeding, fattening and farrow-to- finish. HEV-RNA was analyzed by broad range Real-time RT-PCR on 20 samples for each farm, obtained by pooling together feces from 10 individuals. Overall, HEV RNA was confirmed on 150 fecal pooled samples out of 1,032 (14.5%). At least one positive pooled sample was detected from 18 farms out of 51 tested (35.3%). By lowering the number of infected pigs at primary production, the risk of HEV-3 entering into the food chain can be reduced. Hence, information on HEV circulation in herds is highly relevant for choosing preventive measures and deserves development of a monitoring program and further investigations

Bacteriophage therapy to reduce colonization of campylobacter jejuni in broiler chickens before slaughter

Campylobacteriosis is the most commonly reported gastrointestinal disease in humans. Campybacter jejuni is the main cause of the infection, and bacterial colonization in broiler chickens is widespread and difficult to prevent, leading to high risk of occurrence in broiler meat. Phage therapy represents an alternative strategy to control Campylobacter in poultry. The aim of this work was to assess the efficacy of two field-isolated bacteriophages against experimental infections with an anti-microbial resistant (AMR) Campylobacter jejuni strain. A two-step phage application was tested according to a specific combination between chickens’ rearing time and specific multiplicities of infections (MOIs), in order to reduce the Campylobacter load in the animals at slaughtering and to limit the development of phage-resistant mutants. In particular, 75 broilers were divided into three groups (A, B and C), and phages were administered to animals of groups B and C at day 38 (Φ 16-izsam) and 39 (Φ 7-izsam) at MOI 0.1 (group B) and 1 (group C). All broilers were euthanized at day 40, and Campylobacter jejuni was enumerated in cecal contents. Reductions in Campylobacter counts were statistically significant in both group B (1 log10 colony forming units (cfu)/gram (gr)) and group C (2 log10 cfu/gr), compared to the control group. Our findings provide evidence about the ability of phage therapy to reduce the Campylobacter load in poultry before slaughtering, also associated with anti-microbial resistance pattern