Mycotoxins are secondary metabolites produced by fungi especially those belonging to the genus Aspergillus, Penicillum and Fusarium. Mycotoxin contamination can occur in all agricultural commodities in the field and/or during storage, if conditions are favourable to fungal growth. Regarding animal feed, five mycotoxins (aflatoxins, deoxynivalenol, zearalenone, fumonisins and ochratoxin A) are covered by EU legislation (regulation or recommendation). Transgressions of these limits are rarely observed in official monitoring programs. However, low level contamination by Fusarium toxins is very common (e.g., deoxynivalenol (DON) is typically found in more than 50% of the samples) and co-contamination is frequently observed. Multi-mycotoxin studies reported 75%–100% of the samples to contain more than one mycotoxin which could impact animal health at already low doses. Co-occurrence of mycotoxins is likely to arise for at least three different reasons (i) most fungi are able to simultaneously produce a number of mycotoxins, (ii) commodities can be contaminated by several fungi, and (iii) completed feed is made from various commodities. In the present paper, we reviewed the data published since 2004 concerning the contamination of animal feed with single or combinations of mycotoxins and highlighted the occurrence of these co-contaminations.

During an 8-year period, 17 316 samples of feed and feed raw materials from all over the world were analysed for contamination with aflatoxins, ochratoxin A, zearalenone, deoxynivalenol and fumonisins. Overall, 72% of the samples tested positive for at least one mycotoxin and 38% were found to be co-contaminated. Mycotoxin concentrations were generally low and the majority of the samples were compliant with the most stringent EU guidance values or maximum levels for mycotoxins in feed. However, in their present state these regulations do not address co-contamination and associated risks. Long-term trends are difficult to establish as strong yearly variations were observed regarding mycotoxin prevalence and contamination levels. In some cases unusual weather conditions can be linked with high observed mycotoxin loads. An exception to this rule is South-East Asia, where a steady increase of aflatoxin prevalence has been observed. The percentage of aflatoxin-positive samples in this region rose from 32% in 2005 to 71% in 2011.

The development of liquid chromatography-mass spectrometry (LC-MS)/mass spectrometry (MS) methods for the simultaneous detection and quantification of a broad spectrum of mycotoxins has facilitated the screening of a larger number of samples for contamination with a wide array of less well-known “emerging” mycotoxins and other metabolites. In this study, 83 samples of feed and feed raw materials were analysed. All of them were found to contain seven to 69 metabolites. The total number of detected metabolites amounts to 139. Fusarium mycotoxins were most common, but a number of Alternaria toxins also occurred very often. Furthermore, two so-called masked mycotoxins (i.e., mycotoxin conjugates), namely deoxynivalenol-3-glucoside (75% positives) and zearalenone-4-sulfate (49% positives), were frequently detected. Although the observed median concentrations of the individual analytes were generally in the low μg/kg range, evaluating the toxicological potential of a given sample is difficult. Toxicity data on less well-known mycotoxins and other detected metabolites are notoriously scarce, as an overview on the available information on the most commonly detected metabolites shows. Besides, the possible synergistic effects of co-occurring substances have to be considered.

Mycotoxins are ubiquitously present in agricultural commodities, such as cereals and oil seeds. If ingested in sufficiently high concentrations, they exert severe toxic effects in humans and animals. In 2004, a survey programme was launched to assess the extent of mycotoxin contamination in feed and feed raw materials. Since then, over 19,000 samples have been analysed and more than 70,000 individual analyses have been conducted. While it is difficult to infer any long-term trends on a global level, the data confirm that high mycotoxin contamination is often linked to unusual weather. Overall, 72% of the samples contained detectable amounts of aflatoxins, fumonisins, deoxynivalenol, zearalenone or ochratoxin A. Co-contamination with two or more mycotoxins was detected in 38% of the samples. In most cases the concentrations were low enough to ensure compliance with EU guidance values or maximum levels. However, co-contaminated samples with concentrations below guidance and maximum values might still exert adverse effects due to synergistic interactions of the mycotoxins. Emerging mycotoxins and masked mycotoxins may also contribute to the overall toxicity of the feed and their presence is frequently detected with multi-mycotoxin LC-MS/MS. Since by-product feeds, such as distillers dried grain with solubles, often concentrate the mycotoxins of the original substrate, they contribute excessively to the overall contamination of feed rations and therefore need special attention. Regarding food the situation is quite similar: low level contamination is frequently observed in official controls but maximum levels are rarely exceeded in developed countries. As it is very difficult to remove mycotoxins from contaminated commodities, preventing them from accumulation in agricultural commodities is the most effective strategy to combat the problem. Preventive measures range from crop rotation and resistance breeding to inoculation with microbial antagonists. Nevertheless, excessive mycotoxin levels may occur despite all preventive measures. Therefore, continuous monitoring is essential and efficient detoxification strategies are needed to deal with such outbreaks.

Multiple-locus variable-number tandem repeat analysis (MLVA) is useful to establish transmission routes and sources of infections for various microorganisms including Mycobacterium tuberculosis complex (MTC). The recently released SITVITWEB database contains 12-loci Mycobacterial Interspersed Repetitive Units – Variable Number of Tandem DNA Repeats (MIRU-VNTR) profiles and spoligotype patterns for thousands of MTC strains; it uses MIRU International Types (MIT) and Spoligotype International Types (SIT) to designate clustered patterns worldwide. Considering existing doubts on the ability of spoligotyping alone to reveal exact phylogenetic relationships between MTC strains, we developed a MLVA based classification for MTC genotypic lineages. We studied 6 different subsets of MTC isolates encompassing 7793 strains worldwide. Minimum spanning trees (MST) were constructed to identify major lineages, and the most common representative located as a central node was taken as the prototype defining different phylogenetic groups. A total of 7 major lineages with their respective prototypes were identified: Indo-Oceanic/MIT57, East Asian and African Indian/MIT17, Euro American/MIT116, West African-I/MIT934, West African-II/MIT664, M. bovis/MIT49, M.canettii/MIT60. Further MST subdivision identified an additional 34 sublineage MIT prototypes. The phylogenetic relationships among the 37 newly defined MIRU-VNTR lineages were inferred using a classification algorithm based on a bayesian approach. This information was used to construct an updated phylogenetic and phylogeographic snapshot of worldwide MTC diversity studied both at the regional, sub-regional, and country level according to the United Nations specifications. We also looked for IS6110 insertional events that are known to modify the results of the spoligotyping in specific circumstances, and showed that a fair portion of convergence leading to the currently observed bias in phylogenetic classification of strains may be traced back to the presence of IS6110. These results shed new light on the evolutionary history of the pathogen in relation to the history of peopling and human migration.