ADSA Foundation Scholar Award--An integrated science-based approach to dairy food safety: Listeria monocytogenes as a model system

Wholegenome sequencing as the gold standard approach for control of Listeria monocytogenes in the food chain

Listeria monocytogenes has been implicated in numerous outbreaks and related deaths of listeriosis. In food production, L. monocytogenes occurs in raw food material and above all, through postprocessing contamination. The use of next-generation sequencing technologies such as whole-genome sequencing (WGS) facilitates foodborne outbreak investigations, pathogen source tracking and tracing geographic distributions of different clonal complexes, routine microbiological/epidemiological surveillance of listeriosis, and quantitative microbial risk assessment. WGS can also be used to predict various genetic traits related to virulence, stress, or antimicrobial resistance, which can be of great benefit for improving food safety management as well as public health.

Listeria monocytogenes Infection of Bat Pipistrellus nathusii Epithelial cells Depends on the Invasion Factors InlA and InlB

L. monocytogenes is a widespread facultative intracellular pathogen. The range of natural hosts that supporting L. monocytogenes persistence in the environment has not been fully established yet. In this study, we were interested in the potential of L. monocytogenes to infect cells of bats, which are being increasingly recognized as a reservoir for microorganisms that are pathogenic to humans and domestic animals. A stable epithelial cell line was developed from the kidneys of Pipistrellus nathusii, a small bat widely distributed across Europe. The wild-type L. monocytogenes strain EGDe infected this cell line with an invasion efficiency of 0.0078 ± 0.0009%. Once it entered bat cells, L. monocytogenes doubled within about 70 min. When L. monocytogenes lacked either of the major invasion factors, InlA and InlB, invasion efficiency decreased by a factor of 10 and 25 respectively (p < 0.000001). The obtained results suggest that bat epithelial cells are susceptible to L. monocytogenes infection and that L. monocytogenes invasion of bat cells depends on the major invasion factors InlA and InlB. These results constitute the first report on in vitro studies of L. monocytogenes infection in bats.

Survival of a native toxigenic isolate of Listeria monocytogenes CFR 1302 during storage of milk-based foods can be a potential cause of health risk

The ability of a native toxigenic culture of Listeria monocytogenes CFR 1302 to survive and elaborate associated toxigenic trait in ice cream and mango pulp-based lactic fermented milk was studied. The culture of L. monocytogenes inoculated at two initial levels of 4.6 and 5.6 log₁₀ CFU/ml almost remained unaltered during storage of the food products. However, in both the milk-based products, a marginal increase in viable population was observed during 2-4 d of storage as against the initial inoculum levels. The toxigenic trait, listeriolysin "O" was detected by PCR based on species-specific hlyA primers in the two products without any step of enrichment. The positive amplification in PCR was evidenced with initial population levels of 6.3, 7.3, and 8.3 log₁₀ CFU/ml of the respective products. In culture broth, PCR detection was positive with the lowest level of 2.3 log₁₀ CFU/ml. The established pathogenic strain of L. monocytogenes Scott A used as a reference culture revealed almost the same behavior to that of native culture in the food products. The findings of present study bring into focus that, irrespective of low storage temperatures, there exists the potential health hazard associated with foods initially contaminated with risk population levels of L. monocytogenes.

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Background

Describing the microbial populations present in small grain silage and understanding their changes during ensiling is of interest for improving the nutrient value of these important forage crops. Barley, oat and triticale forages as well as an intercropped mixture of the 3 crops were harvested and ensiled in mini silos for a period of 90 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages and bacterial and fungal communities during ensiling and aerobic exposure were described using 16S and 18S rDNA sequencing, respectively.

Results

All small grain silages exhibited chemical traits that were associated with well ensiled forages, such as low pH value (4.09 ± 0.28) and high levels of lactic acid (59.8 ± 14.59 mg/g DM). The number of microbial core genome operational taxonomic units (OTUs) decreased with time of ensiling. Taxonomic bacterial community profiles were dominated by the Lactobacillales after fermentation, with a notable increase in Bacillales as a result of aerobic exposure. Diversity of the fungal core microbiome was shown to also be reduced during ensiling. Operational taxonomic units assigned to filamentous fungi were found in the core microbiome at ensiling and after aerobic exposure, whereas the Saccharomycetales were the dominate yeast population after 90 days of ensiling and aerobic exposure. Bacterial and fungal orders typically associated with silage spoilage were identified in the core microbiome after aerobic exposure.

Conclusion

Next Generation Sequencing was successfully used to describe bacterial communities and the first record of fungal communities throughout the process of ensiling and utilization. Adequately describing the microbial ecology of silages could lead to improved ensiling practices and the selection of silage inoculants that act synergistically with the natural forage microbiome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0947-0) contains supplementary material, which is available to authorized users.

Metagenomic Analysis of Silage

Metagenomics is defined as the direct analysis of deoxyribonucleic acid (DNA) purified from environmental samples and enables taxonomic identification of the microbial communities present within them. Two main metagenomic approaches exist; sequencing the 16S rRNA gene coding region, which exhibits sufficient variation between taxa for identification, and shotgun sequencing, in which genomes of the organisms that are present in the sample are analyzed and ascribed to "operational taxonomic units"; species, genera or families depending on the extent of sequencing coverage. In this study, shotgun sequencing was used to analyze the microbial community present in cattle silage and, coupled with a range of bioinformatics tools to quality check and filter the DNA sequence reads, perform taxonomic classification of the microbial populations present within the sampled silage, and achieve functional annotation of the sequences. These methods were employed to identify potentially harmful bacteria that existed within the silage, an indication of silage spoilage. If spoiled silage is not remediated, then upon ingestion it could be potentially fatal to the livestock.

Evolution of the Microbiological Profile of Vacuum-Packed Ricotta Salata Cheese During Shelf-Life

Ricotta salata cheese is a salted variety of ricotta traditionally made in Sardinia (Italy) from the whey remaining after the production of Pecorino Romano protected designation of origin or other sheep milk cheeses. Ricotta salata cheese is very critical for the possible growth of pathogenic and spoilage microorganisms. Sporadic cases of listeriosis associated with ricotta salata cheese have been reported over recent years. The objective of the present study was to assess the evolution of spoilage and pathogen microorganism of vacuum-packed ricotta salata cheese during the entire product shelf-life. The durability study was conducted on 18 vacuum-packed ricotta salata cheese samples analysed at the beginning of the shelf-life and after 60 and 90 days of refrigerated storage. Pathogens as Listeria monocytogenes and Bacillus cereus were never detected. During shelf-life total bacterial counts ranged between 7.90±0.64 and 9.19±0.58 CFU g-1 on the rind and between 2.95±0.68 and 4.27±1.10 CFU g-1 in the inner paste, while Enterobacteriaceae ranged between 4.22±0.66 and 5.30±0.73 CFU g-1 on the rind and 3.13±1.80 and 2.80±0.88 CFU g-1 in the inner paste. By considering the technology used, the intrinsic properties and the almost total absence of competing microflora, ricotta salata cheese can support the growth of spoilage and pathogen microorganisms originating from the processing environment. The high level of total bacterial counts and Enterobacteriaceae observed both on the rind and in the inner paste suggests contamination of the product from the processing environment. Therefore, a strict implementation of hygiene during processing is essential in order to reduce the load of environmental contaminants that may grow during refrigerated storage.

Listeriosis during Pregnancy: A Public Health Concern

Listeria was first described in 1926 by Murray, Webb, and Swann, who discovered it while investigating an epidemic infection among laboratory rabbits and guinea pigs. The role of Listeria monocytogenes as a foodborne pathogen was definitively recognized during the 1980s. This recognition was the consequence of a number of epidemic human outbreaks due to the consumption of contaminated foods, in Canada, in the USA and in Europe. Listeriosis is especially severe in immunocompromised individuals such as pregnant women. The disease has a low incidence of infection, although this is undeniably increasing, with a high fatality rate amongst those infected. In pregnant women listeriosis may cause abortion, fetal death, or neonatal morbidity in the form of septicemia and meningitis. Improved education concerning the disease, its transmission, and prevention measures for immunocompromised individuals and pregnant women has been identified as a pressing need.

Multiple-locus variable number of tandem repeat analysis (MLVA) of Listeria monocytogenes directly in food samples

Listeria monocytogenes is the etiologic agent of listeriosis responsible for severe and fatal infections in humans. Listeria contamination occurs quite often in a wide range of foods due to its ubiquitous nature. Isolates need to be characterized to a strain level for accurate diagnosis of Listeria infection, epidemiological studies, investigation of outbreaks and effective prevention and control of food-borne listeriosis. The purpose of this research was to evaluate the multiple-locus variable number of tandem repeat analysis (MLVA) for sub-typing L. monocytogenes isolates in pure cultures and in food matrices. Two multiplex PCR assays were formulated to amplify six specific loci using fluorescently-labeled primers; and the amplicons were analyzed by capillary electrophoresis. The MLVA method resulted in 34 unique DNA fingerprint patterns from 46 L. monocytogenes isolates of 10 serotypes which had 29 or 30 PFGE patterns with a single restriction enzyme and 34 AFLP patterns. The MLVA patterns of the 46 isolates remained unchanged in the presence of pre-enriched food matrices including sausage, ham, chicken, milk and lettuce. The MLVA method successfully typed L. monocytogenes strains spiked in cheese, roast beef, egg salad and vegetable samples after 48 h enrichment at the initial inoculation levels of 1-5 CFU per 25 g of food or higher. The limits of detection (typing) of the MLVA method were 10(3)-10(4)CFU/mL of pre-enriched food broth when evaluated using post-spiked sausage, ham, chicken, milk and lettuce samples. The MLVA method was simple, highly discriminatory, and easy to perform with portable (numerical) results. To our knowledge, this is the first report that describes the application of the MLVA method directly to food samples and demonstrates the possibility to obtain rapid and accurate subtyping results before an isolate is obtained.

Species-specific detection of Listeria monocytogenes using polymerase chain reaction assays targeting the prfA virulence gene cluster

Sequence comparison of individual genes in the prfA virulence gene cluster (pVGC), a central virulence gene cluster, from different Listeria species indicated that priming sites within the genes appeared to be specific for Listeria monocytogenes exclusively. Therefore, the pVGC was targeted for polymerase chain reaction (PCR) assays to detect and specifically identify L. monocytogenes. Each gene of the pVGC was specifically amplified in L. monocytogenes but not in other Listeria species.

Characterization of Listeria monocytogenes isolates from 50 small-scale Austrian cheese factories

One hundred eighty-one small-scale cheese factories (annual production < 100,000 kg) were tested for the presence of Listeria monocytogenes in cheese and smear samples from 1997 to 2000. In total, 2615 samples were drawn. Fifty (27.6%) of 181 enterprises yielded L. monocytogenes. From 14 of the cheese-making facilities, we obtained more than four L. monocytogenes isolates. A total of 182 mostly cheese- and smear-borne L. monocytogenes strains were characterized by serotyping and pulsed-field gel electrophoresis. In 12 of 14 cheese factories, over half of the L. monocytogenes isolates were genetically indistinguishable by pulsetype. On average, genetically indistinguishable isolates were recovered for 11.9 months. Regarding serotypes, 27.3% of the isolates were of serovar 4b. Inadequate personal hygiene could explain the high prevalence of serovar 4b isolates in small-scale cheesemaking facilities. Forty-two percent of the serovar 4b isolates recovered from epidemiologically unlinked facilities (in comparison to 40 and 29% of the 1/2a and 1/2b isolates, respectively) were genetically indistinguishable from at least one other isolate. Indistinguishable serovar 1/2a and 1/2b isolates belonged to five and six different pulsetypes, respectively, whereas serovar 4b isolates belonged to only two pulsetypes. This finding suggested a wide distribution of genetically homologous serovar 4b isolates among the facilities tested in our study.

Evolution and molecular phylogeny of Listeria monocytogenes isolated from human and animal listeriosis cases and foods

To probe the evolution and phylogeny of Listeria monocytogenes from defined host species and environments, L. monocytogenes isolates from human (n = 60) and animal (n = 30) listeriosis cases and food samples (n = 30) were randomly selected from a larger collection of isolates (n = 354) obtained in New York State between 1999 and 2001. Partial sequencing of four housekeeping genes (gap, prs, purM, and ribC), one stress response gene (sigB), and two virulence genes (actA and inlA) revealed between 11 (gap) and 33 (inlA) allelic types as well as 52 sequence types (unique combination of allelic types). actA, ribC, and purM demonstrated the highest levels of nucleotide diversity (pi > 0.05). actA and inlA as well as prs and the hypervariable housekeeping genes ribC and purM showed evidence of horizontal gene transfer and recombination. actA and inlA also showed evidence of positive selection at specific amino acid sites. Maximum likelihood phylogenies for all seven genes confirmed that L. monocytogenes contains two deeply separated evolutionary lineages. Lineage I was found to be highly clonal, while lineage II showed greater diversity and evidence of horizontal gene transfer. Allelic types were exclusive to lineages, except for a single gap allele, and nucleotide distance within lineages was much lower than that between lineages, suggesting that genetic exchange between lineages is rare. Our data show that (i) L. monocytogenes is a highly diverse species with at least two distinct phylogenetic lineages differing in their evolutionary history and population structure and (ii) horizontal gene transfer as well as positive selection contributed to the evolution of L. monocytogenes.

Ecology and transmission of Listeria monocytogenes infecting ruminants and in the farm environment

A case-control study involving 24 case farms with at least one recent case of listeriosis and 28 matched control farms with no listeriosis cases was conducted to probe the transmission and ecology of Listeria monocytogenes on farms. A total of 528 fecal, 516 feed, and 1,012 environmental soil and water samples were cultured for L. monocytogenes. While the overall prevalence of L. monocytogenes in cattle case farms (24.4%) was similar to that in control farms (20.2%), small-ruminant (goat and sheep) farms showed a significantly (P < 0.0001) higher prevalence in case farms (32.9%) than in control farms (5.9%). EcoRI ribotyping of clinical (n = 17) and farm (n = 414) isolates differentiated 51 ribotypes. L. monocytogenes ribotypes isolated from clinical cases and fecal samples were more frequent in environmental than in feed samples, indicating that infected animals may contribute to L. monocytogenes dispersal into the farm environment. Ribotype DUP-1038B was significantly (P < 0.05) associated with fecal samples compared with farm environment and animal feedstuff samples. Ribotype DUP-1045A was significantly (P < 0.05) associated with soil compared to feces and with control farms compared to case farms. Our data indicate that (i) the epidemiology and transmission of L. monocytogenes differ between small-ruminant and cattle farms; (ii) cattle contribute to amplification and dispersal of L. monocytogenes into the farm environment, (iii) the bovine farm ecosystem maintains a high prevalence of L. monocytogenes, including subtypes linked to human listeriosis cases and outbreaks, and (iv) L. monocytogenes subtypes may differ in their abilities to infect animals and to survive in farm environments.

Intraspecific phylogeny and lineage group identification based on the prfA virulence gene cluster of Listeria monocytogenes

Listeria monocytogenes is a serious food-borne pathogen that can cause invasive disease in humans and other animals and has been the leading cause of food recalls due to microbiological concerns in recent years. In order to test hypotheses regarding L. monocytogenes lineage composition, evolution, ecology, and taxonomy, a robust intraspecific phylogeny was developed based on prfA virulence gene cluster sequences from 113 L. monocytogenes isolates. The results of the multigene phylogenetic analyses confirm that L. monocytogenes comprises at least three evolutionary lineages, demonstrate that lineages most frequently (lineage 1) and least frequently (lineage 3) associated with human listeriosis are sister-groups, and reveal for the first time that the human epidemic associated serotype 4b is prevalent among strains from lineage 1 and lineage 3. In addition, a PCR-based test for lineage identification was developed and used in a survey of food products demonstrating that the low frequency of association between lineage 3 isolates and human listeriosis cases likely reflects rarity of exposure and not reduced virulence for humans as has been previously suggested. However, prevalence data do suggest lineage 3 isolates may be better adapted to the animal production environment than the food-processing environment. Finally, analyses of haplotype diversity indicate that lineage 1 has experienced a purge of genetic variation that was not observed in the other lineages, suggesting that the three L. monocytogenes lineages may represent distinct species within the framework of the cohesion species concept.