Reproduction and Productivity in Dairy Cattle after Abortions Both Related and Unrelated to Coxiella burnetii.

C. burnetii is a widespread pathogen, causing abortions and reproductive disorders in ruminants. The study aimed to evaluate animal reproductive capacity and productivity after abortion, related and unrelated to C. burnetii. We compared data about the abortion time, the outcome of the animals after an abortion, further reproduction, and productivity for C. burnetii-positive (n = 148) and C. burnetii-negative (n = 149) aborted dairy cows and heifers. C. burnetii-positive animals had a positive serological response or presence of C. burnetii DNA at the time of abortion. C. burnetii-positive animals had a significantly higher number of lactations at the time of abortion. However, in the other indicators, we observed no significant differences between the groups. Comparing indicators of all the aborted animals, we found that if animals started a new lactation after abortion, they had a significantly lower milk yield, lower fat, protein, and somatic cell counts (SCCs) in milk during the standard lactation for both primiparous and multiparous cows compared to herd averages in each group. Lower SCCs can be due to animals with a high SCC being culled earlier. We found an economic disadvantage to aborting, not only because of the loss of offspring, but also because of the high culling rate and lower productivity in both primiparous and multiparous cows.

Coxiella Burnetii DNA in Milk, Milk Products, and Fermented Dairy Products.

INTRODUCTION: Q fever in dairy cattle has been investigated in Latvia since 2012. In 2015, 10.7% of farms tested positive for the DNA of C. burnetii, its aetiological agent, in bulk tank milk. The presence of C. burnetii DNA and infectious bacteria in dairy products has been assessed in several countries, and because Latvian milk may contain them, parallel assessment in this country is recommended. Accordingly, the present study tested shop and farm retail dairy products from Latvia and included foreign products for comparison. MATERIAL AND METHODS: Investigation was carried out of 187 samples of a diverse range of dairy products from 41 Latvian milk producers. Twenty-six comparable samples pooled from Estonia, France, Germany, Greece, Italy, Lithuania, the Netherlands, Poland and Spain were also included. The all-countries total number of fermented milk products was 160. Special attention was paid to products that could be more attractive to children because of their added chocolate, cacao, berry and fruit content. DNA was extracted and amplification of C. burnetii IS1111 was performed using a commercial PCR kit. RESULTS: Overall positivity was 60.56%. Domestic products were positive more often (60.96%) than foreign ones (57.69%). Only 26.67% of unpasteurised Latvian cow's milk samples were positive whereas 76.47% of pasteurised equivalents and 63.13% of fermented milk products were. Sweetened and fruit-containing samples were 71.43% positive. CONCLUSION: The shedding of C. burnetii via milk should be monitored and only milk from healthy animals allowed for sale for direct human consumption without pasteurisation. Raw milk quality and the effectiveness of industrial heat treatment and pasteurisation methods in Latvia and other countries should be carefully assessed to ensure adequate consumer health protection.

Occurrence of Pathogenic and Potentially Pathogenic Bacteria in Microgreens, Sprouts, and Sprouted Seeds on Retail Market in Riga, Latvia.

Microgreens and sprouts have been used for raw consumption for a long time and are generally viewed as a healthy food. However, several serious outbreaks of foodborne illness have been recorded in European countries, Japan, and North America. Many companies in Latvia nowadays are producing this type of products. The aim of this study was to characterize the incidence of Shiga toxin-producing Escherichia coli (STEC), Salmonella spp., and Listeria spp. in microgreens, sprouts, and seeds intended for domestic production of microgreens on retail market in Riga, Latvia, from January to April 2019. The background microflora was identified as well. A total of 45 samples were purchased, including fresh and processed sprouts, microgreens, baby greens, as well as seeds intended for domestic production of microgreens and sprouts. The samples were processed according to the methods set by the International Organization for Standardization (ISO)-ISO/TS 13136:2012 for STEC, ISO 6579-1:2017 for Salmonella spp., and ISO 11290-1:2017 for Listeria spp. Molecular detection of Salmonella spp. was also performed using real-time polymerase chain reaction. The typical and atypical colonies isolated from selective plates were identified with matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. Listeria monocytogenes was not detected in any of the tested samples. However, the presence of Listeria innocua was detected in two (4.4%) of the samples. Three (6.7%) samples of dried sprouts were positive for the STEC virulence genes. Salmonella spp. was detected in one (2.2%) sample of common sunflower seeds. Altogether, 46 different background bacterial species were identified. The majority were environmental bacteria characteristic to soil, water, and plants, including coliform bacteria. The results provide evidence that microgreens and seeds available for Latvian consumers are generally safe, however, attention has to be paid to dried sprouts.

Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.

Foodborne diseases (FBDs) are infections of the gastrointestinal tract caused by foodborne pathogens (FBPs) such as bacteria [Salmonella, Listeria monocytogenes and Shiga toxin-producing E. coli (STEC)] and several viruses, but also parasites and some fungi. Artificial intelligence (AI) and its sub-discipline machine learning (ML) are re-emerging and gaining an ever increasing popularity in the scientific community and industry, and could lead to actionable knowledge in diverse ranges of sectors including epidemiological investigations of FBD outbreaks and antimicrobial resistance (AMR). As genotyping using whole-genome sequencing (WGS) is becoming more accessible and affordable, it is increasingly used as a routine tool for the detection of pathogens, and has the potential to differentiate between outbreak strains that are closely related, identify virulence/resistance genes and provide improved understanding of transmission events within hours to days. In most cases, the computational pipeline of WGS data analysis can be divided into four (though, not necessarily consecutive) major steps: de novo genome assembly, genome characterization, comparative genomics, and inference of phylogeny or phylogenomics. In each step, ML could be used to increase the speed and potentially the accuracy (provided increasing amounts of high-quality input data) of identification of the source of ongoing outbreaks, leading to more efficient treatment and prevention of additional cases. In this review, we explore whether ML or any other form of AI algorithms have already been proposed for the respective tasks and compare those with mechanistic model-based approaches.

Campylobacter species prevalence, characterisation of antimicrobial resistance and analysis of whole-genome sequence of isolates from livestock and humans, Latvia, 2008 to 2016.

BackgroundCampylobacter is the main cause of bacterial gastroenteritis worldwide. The main transmission route is through consumption of food contaminated with Campylobacter species or contact with infected animals. In Latvia, the prevalence of campylobacteriosis is reported to be low (4.6 cases per 100,000 population in 2016).AimTo determine prevalence, species spectrum and antimicrobial resistance (AMR) of Campylobacter spp. in Latvia, using data from various livestock and human clinical samples.MethodsWe analysed data of Campylobacter microbiological monitoring and AMR (2008 and 2014-16) in Latvia. Data from broilers, poultry, pigs, calves and humans were used to determine prevalence of Campylobacter. Additionally, 45 different origin isolates (22 human) were sequenced on the Illumina MiSeq platform; for each isolate core genome multilocus sequence typing was used and relevant antimicrobial resistance mechanisms were identified.ResultsOverall, Campylobacter prevalence in was 83.3% in pigs, 50.2% in broilers, 16.1% in calves and 5.3% in humans; C. jejuni was the predominant species in all sources except pigs where C. coli was main species. High level of resistance in Campylobacter were observed against fluoroquinolones, tetracycline and streptomycin, in most of sequenced isolates genetic determinants of relevant AMR profiles were identified.ConclusionsIn Latvia, prevalence of Campylobacter in livestock is high, especially in pigs and broilers; prevalence in poultry and humans were lower than in other European countries. AMR analysis reveals increase of streptomycin and tetracycline resistant broiler origin C. jejuni strains. WGS demonstrates a high compliance between resistance phenotype and genotype for quinolones and tetracyclines.

Potential risk evaluation for unintended entry of genetically modified plant Propagating material in Europe through import of seeds and animal feed - the experience of Latvia.

Significant attention has been drawn to the adventitious and technically unavoidable presence of genetically modified (GM) organisms in the food and feed imported into the European Union (EU), while the potential presence of GM seeds in material for cultivation is less studied. Here we report a study from an EU member state, Latvia, during years 2017-2018 regarding monitoring for the presence of GM seeds in certified seed and animal feed material. Eighty-two and 28 samples of seeds intended for cultivation were analyzed in 2017 and 2018, respectively. One soybean sample contained MON40-3-2 soybean seeds (0.09 ± 0.01%) and one maize sample contained MON810 maize seeds (0.08 ± 0.01%). In addition, 102 samples of feed imported from outside of the EU or produced locally were also analyzed for the presence of genetically modified organisms (GMOs) and viability of grains. One oilseed rape cake sample contained GT73 (1.04 ± 0.01%) and one soybean cake sample contained MON40-3-2 (<0.045%). One sample of declared MON40-3-2 GM soybean cake was confirmed to be positive, with MON40-3-2 content of 94.78 ± 10.01%. One soybean sample submitted by feed producer and originating from Argentina contained 54.9 ± 1.1% of MON40-3-2 and one rapeseed sample originating from Ukraine contained 5.30 ± 3.95% of GT73. Although only two seed samples contained low levels of GMOs authorized in the EU for food and feed uses, this study reinforced the need to maintain regular monitoring programs that assist farmers in their efforts to comply with the current EU GMO legislation.

Genetically modified seeds and plant propagating material in Europe: potential routes of entrance and current status.

Genetically modified organisms (GMO), mainly crop plants, are increasingly grown worldwide leading to large trade volumes of living seeds and other plant material both for cultivation and for food and animal feed. Even though all the traded GMOs have been assessed for their safety with regards to human and animal health and the environment, there still are some concerns regarding the potential uncontrolled release in the environment of authorized or unauthorized GM plants. In this review, we identify the possible entrance routes of GM seeds and other propagating plant material in the EU which could be linked to unauthorized release of GMOs in the environment. In addition, we discuss the situation with GM plant cultivation in some non-EU countries in terms of potential risks for GM seed imports. The available body of information suggests that GM seeds and plant propagating material can enter the EU due to problems with labeling/traceability of GM seed lots, contamination of conventional seed lots and accidental release into the environment of grains imported for food and animal feed. Even though cases of uncontrolled release of authorized GMOs, as well as, release of unauthorized GMOs have been reported, they can be generally attributed to adventitious and technically unavoidable presence with little environmental impact. In conclusion, the probability of GM seeds and plant propagating material illegally entering the cultivation in EU is unlikely. However, specific monitoring programs need to be established and maintained to facilitate the compliance of European farmers with the current GMO legislation.

Seroprevalence of Brucella suis in eastern Latvian wild boars (Sus scrofa).

Brucellosis due to Brucella suis biovar 2 is one of the most important endemic diseases in wild boar (Sus scrofa) populations in Europe. The aim of the present study was to determine the seroprevalence of brucellosis in wild boars in the eastern part of Latvia. Wild boars killed by hunters in the period from January to April 2015 (n = 877) and from March to April in 2016 (n = 167) were examined for antibodies against B. suis by the Rose Bengal test (RBT), a complement fixation test (CFT), and by enzyme-linked immunosorbent assays. In 2015, 199 samples (22.7%) were positive by RBT and/or CFT while 36 samples (21.6%) were seropositive in 2016. Of the Brucella seropositive samples from 2015 and 2016 (n = 235), 162 (68.9%) were also seropositive to Yersinia enterocolitica. Considering cross-reactivity of serological tests, the seroprevalence of B. suis biovar 2 exposure in wild boars in the eastern part of Latvia was calculated to 14.0% in 2015 and 9.6% in 2016. From selected seropositive samples (42 in 2015 and 36 in 2016) total DNA was extracted and analyzed with an IS711-based nested polymerase chain reaction (PCR) assay. Species and biovar identification was conducted for bacteria isolated in monoculture from PCR positive samples by species specific primers and Bruce-ladder multiplex PCR. Brucella suis biovar 2 was isolated from 12/20 samples in 2015 and 9/9 samples in 2016. The average seroprevalence was relatively low compared to that found in certain other European countries. Males and females had an equal level of seropositivity, but a positive age-trend was observed for both males and females.

Microbiome symbionts and diet diversity incur costs on the immune system of insect larvae.

Communities of symbiotic microorganisms that colonize the gastrointestinal tract play an important role in food digestion and protection against opportunistic microbes. Diet diversity increases the number of symbionts in the intestines, a benefit that is considered to impose no cost for the host organism. However, less is known about the possible immunological investments that hosts have to make in order to control the infections caused by symbiont populations that increase because of diet diversity. Using taxonomical composition analysis of the 16S rRNA V3 region, we show that enterococci are the dominating group of bacteria in the midgut of the larvae of the greater wax moth (Galleria mellonella). We found that the number of colony-forming units of enterococci and expressions of certain immunity-related antimicrobial peptide (AMP) genes such as Gallerimycin, Gloverin, 6-tox, Cecropin-D and Galiomicin increased in response to a more diverse diet, which in turn decreased the encapsulation response of the larvae. Treatment with antibiotics significantly lowered the expression of all AMP genes. Diet and antibiotic treatment interaction did not affect the expression of Gloverin and Galiomicin AMP genes, but significantly influenced the expression of Gallerimycin, 6-tox and Cecropin-D Taken together, our results suggest that diet diversity influences microbiome diversity and AMP gene expression, ultimately affecting an organism's capacity to mount an immune response. Elevated basal levels of immunity-related genes (Gloverin and Galiomicin) might act as a prophylactic against opportunistic infections and as a mechanism that controls the gut symbionts. This would indicate that a diverse diet imposes higher immunity costs on organisms.

Critical tests for determination of microbiological quality and biological activity in commercial vermicompost samples of different origins.

The aim of the present paper was to show that differences in biological activity among commercially produced vermicompost samples can be found by using a relatively simple test system consisting of microorganism tests on six microbiological media and soilless seedling growth tests with four vegetable crop species. Significant differences in biological properties among analyzed samples were evident both at the level of microbial load as well as plant growth-affecting activity. These differences were mostly manufacturer- and feedstock-associated, but also resulted from storage conditions of vermicompost samples. A mature vermicompost sample that was produced from sewage sludge still contained considerable number of Escherichia coli. Samples from all producers contained several potentially pathogenic fungal species such as Aspergillus fumigatus, Pseudallescheria boidii, Pseudallescheria fimeti, Pseudallescheria minutispora, Scedosporium apiospermum, Scedosporium prolificans, Scopulariopsis brevicaulis, Stachybotrys chartarum, Geotrichum spp., Aphanoascus terreus, and Doratomyces columnaris. In addition, samples from all producers contained plant growth-promoting fungi from the genera Trichoderma and Mortierella. The described system can be useful both for functional studies aiming at understanding of factors affecting quality characteristics of vermicompost preparations and for routine testing of microbiological quality and biological activity of organic waste-derived composts and vermicomposts.