Detection of Brucella abortus Vaccine Strain RB51 in Water Buffalo (Bubalus bubalis) Milk

The isolation of B. abortus RB51 vaccine strain from a milk sample in a water buffalo farm in southern Italy emphasizes the risk to public health of consuming contaminated milk or milk products following illegal vaccination.

The Current Landscape of Antibiotic Resistance of Salmonella Infantis in Italy: The Expansion of Extended-Spectrum Beta-Lactamase Producers on a Local Scale

Salmonella enterica serovar Infantis is one of the five main causes of human salmonellosis in the European Union (EU) and in recent years, has been increasingly reported to carry multiple antimicrobial resistance determinants, including extended-spectrum beta-lactamase (ESBL) genes. In our study, we used WGS-based tools to characterize S. Infantis strains circulating in the Abruzzo and Molise regions of Italy between 2017 and 2020 and compared this local dataset to the S. Infantis population present in Italy over the last two decades. Phylogenetic analyses demonstrated that the majority of strains isolated from poultry and turkeys from Abruzzo and Molise were closely related and belonged to one of the two main genetic clusters present in Italy, which were grouped predominantly as ESBL-producing strains that harbored pESI-like plasmid. We showed that 60% of the local strains carried multiple antibiotic resistance genes, including ESBL gene bla_CTX–M–1 as well as aadA1, dfrA1, dfrA14, sul1, and tet(A) genes present on the pESI-like megaplasmid. The analysis of strains from Abruzzo and Molise and the publicly available Italian S. Infantis sequences revealed a dramatic increase in the number of identified AMR genes in the strains isolated after 2011. Moreover, the number of strains resistant to five or more antibiotic classes increased from 20–80% in the last decade likely due to the acquisition of the megaplasmid. The persistence of the ESBL-producing and the multidrug-resistant (MDR) clone of S. Infantis in poultry populations in Italy and in Europe requires rapid and efficient intervention strategies to prevent further expansion of the clone.

Collection, genotyping and virus elimination of cassava landraces from Tanzania and documentation of farmer knowledge

Cassava (Manihot esculenta Crantz.) has been a vital staple and food security crop in Tanzania for several centuries, and it is likely that its resilience will play a key role in mitigating livelihood insecurities arising from climate change. The sector is dominated by smallholder farmers growing traditional landrace varieties. A recent surge in virus diseases and awareness in the commercial potential of cassava has prompted a drive to disseminate improved varieties in the country. These factors however also threaten the existence of landraces and associated farmer knowledge. It is important that the landraces are conserved and utilized as the adaptive gene complexes they harbor can drive breeding for improved varieties that meet agro-ecological adaptation as well as farmer and consumer needs, thereby improving adoption rates. Here we report on cassava germplasm collection missions and documentation of farmer knowledge in seven zones of Tanzania. A total of 277 unique landraces are identified through high-density genotyping. The large number of landraces is attributable to a mixed clonal/sexual reproductive system in which the soil seed bank and incorporation of seedlings plays an important role. A striking divergence in genetic relationships between the coastal regions and western regions is evident and explained by (i) independent introductions of cassava into the country, (ii) adaptation to prevailing agro-ecological conditions and (iii) farmer selections according to the intended use or market demands. The main uses of cassava with different product profiles are evident, including fresh consumption, flour production, dual purpose incorporating both these uses and longer-term food security. Each of these products have different trait requirements. Individual landraces were not widely distributed across the country with limited farmer-to-farmer diffusion with implications for seed systems.

Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden

Human infections with Brucella melitensis are occasionally reported in Sweden, despite the fact that the national flocks of sheep and goats are officially free from brucellosis. The aim of our study was to analyze 103 isolates of B. melitensis collected from patients in Sweden between 1994 and 2016 and determine their putative geographic origin using whole genome sequencing (WGS)-based tools. The majority of the strains were assigned to East Mediterranean and African lineages. Both in silico Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) and core genome Multilocus Sequence Typing (cgMLST) analyses identified countries of the Middle East as the most probable source of origin of the majority of the strains. Isolates collected from patients with travel history to Iraq or Syria were often associated with genotypes from Turkey, as the cgMLST profiles from these countries clustered together. Sixty strains were located within a distance of 20 core genes to related genotypes from the publicly available database, and for eighteen isolates, the closest genotype was different by more than 50 loci. Our study showed that WGS based tools are effective in tracing back the geographic origin of infection of patients with unknown travel status, provided that public sequences from the location of the source are available.

Quantitation of multiple mycotoxins and cyanogenic glucosides in cassava samples from Tanzania and Rwanda by an LC-MS/MS-based multi-toxin method

A multi-mycotoxin method based on liquid chromatography/tandem mass spectrometry (LC-MS/MS) was used for a mycotoxin survey in 627 samples of processed cassava collected from different districts across Tanzania and Rwanda after the method performance for this matrix had been determined. Matrix effects as well as extraction efficiencies were found to be similar to most other previously investigated matrices with the exception of distinct matrix effects in the negative ionisation mode for early eluting compounds. Limits of detection were far below the regulatory limits set in the European Union for other types of commodities. Relative standard deviations were generally lower than 10% as determined by replicates spiked on two concentration levels. The sample-to-sample variation of the apparent recoveries was determined for 15 individually spiked samples during three different analytical sequences. The related standard deviation was found to be lower than 15% for most of the investigated compounds, thus confirming the applicability of the method for quantitative analysis. The occurrence of regulated mycotoxins was lower than 10% (with the exception of zearalenone) and the related limits were exceeded only in few samples, which suggests that cassava is a comparatively safe commodity as regards mycotoxins. The most prevalent fungal metabolites were emodin, kojic acid, beauvericin, tryptophol, 3-nitropropionic acid, equisetin, alternariol methylether, monocerin, brevianamide F, tenuazonic acid, zearalenone, chrysophanol, monilifomin, enniatins, apicidin and macrosporin. The related concentrations exceeded 1 mg kg(-1) only in few cases. However, extremely high levels of cyanogenic plant toxins, which had been previously added to the method, were observed in few samples, pointing out the need for improved post-harvest management to decrease the levels of these compounds.