Suitability of the MinION long read sequencer for semi-targeted detection of foodborne pathogens

Foodborne pathogens are still a significant source of morbidity and mortality worldwide. In addition to this the current methodologies to track these microorganisms cannot cope with the current intensive production systems, thus novel methods are of outmost importance. DNA-based methods have already demonstrated suitable to address this issue, but most of them are targeted methods such as real-time PCR (qPCR), meaning that one will only find what is looking for, thus taking the risk of missing relevant pathogens in a given sample. To overcome this limitation we have developed an easy-to-implement methodology which enables the detection of several pathogens simultaneously by using long-read Next Generation Sequencing (NGS) with MinION. The method was named "semi-targeted" due to the combination of a non-targeted detection method, NGS, with the usage of selective media in order to partially eliminate non-pathogenic interfering bacteria. To this end, we included an enrichment step for the recovery of different pathogens, namely Salmonella Enteritidis and Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7, after DNA extraction and library preparation, the samples were analyzed with MinION implementing the low-cost Flongle Flow Cells. The methodology was successfully evaluated in spiked milk samples with an excellent agreement with the results obtained by qPCR and culture-based methods. The method can provide accurate results after only 2 h of sequencing. Sample multiplexing, along with the lower cost of the Flongle Flow Cells and the reduced price of the MinION platform, make the assay cost-effective that is of importance for the food industry. Starting the method with a classical microbiological approach, the enrichment, the method is easy to implement in testing laboratories, it provides flexibility in terms of potential pathogens to be detected, and the positive results can be easily confirmed following culture-based, or other type, of confirmation procedures.

Biofilm Formation by Listeria monocytogenes 15G01, a Persistent Isolate from a Seafood-Processing Plant, Is Influenced by Inactivation of Multiple Genes Belonging to Different Functional Groups

Listeria monocytogenes is a ubiquitous foodborne pathogen that results in a high rate of mortality in sensitive and immunocompromised people. Contamination of food with L. monocytogenes is thought to occur during food processing, most often as a result of the pathogen producing a biofilm that persists in the environment and acting as the source for subsequent dispersal of cells onto food. A survey of seafood-processing plants in New Zealand identified the persistent strain 15G01, which has a high capacity to form biofilms. In this study, a transposon library of L. monocytogenes 15G01 was screened for mutants with altered biofilm formation, assessed by a crystal violet assay, to identify genes involved in biofilm formation. This screen identified 36 transposants that showed a significant change in biofilm formation compared to the wild type. The insertion sites were in 27 genes, 20 of which led to decreased biofilm formation and seven to an increase. Two insertions were in intergenic regions. Annotation of the genes suggested that they are involved in diverse cellular processes, including stress response, autolysis, transporter systems, and cell wall/membrane synthesis. Analysis of the biofilms produced by the transposants using scanning electron microscopy and fluorescence microscopy showed notable differences in the structure of the biofilms compared to the wild type. In particular, inactivation of uvrB and mltD produced coccoid-shaped cells and elongated cells in long chains, respectively, and the mgtB mutant produced a unique biofilm with a sandwich structure which was reversed to the wild-type level upon magnesium addition. The mltD transposant was successfully complemented with the wild-type gene, whereas the phenotypes were not or only partially restored for the remaining mutants.IMPORTANCE The major source of contamination of food with Listeria monocytogenes is thought to be due to biofilm formation and/or persistence in food-processing plants. By establishing as a biofilm, L. monocytogenes cells become harder to eradicate due to their increased resistance to environmental threats. Understanding the genes involved in biofilm formation and their influence on biofilm structure will help identify new ways to eliminate harmful biofilms in food processing environments. To date, multiple genes have been identified as being involved in biofilm formation by L. monocytogenes; however, the exact mechanism remains unclear. This study identified four genes associated with biofilm formation by a persistent strain. Extensive microscopic analysis illustrated the effect of the disruption of mgtB, clsA, uvrB, and mltD and the influence of magnesium on the biofilm structure. The results strongly suggest an involvement in biofilm formation for the four genes and provide a basis for further studies to analyze gene regulation to assess the specific role of these biofilm-associated genes.

Analysis of virulence genes and molecular typing of Listeria monocytogenes isolates from human, food, and livestock from 2008 to 2016 in Iran

The frequency of Listeria monocytogenes isolates collected from a total of 1150 samples including food (n = 300), livestock (n = 50), and human clinical (n = 800) was evaluated during 2008-2016. Antimicrobial resistance patterns, virulence factors, and molecular characteristics of these isolates were analyzed using disk diffusion method, sequencing, serotyping, and pulsed-field gel electrophoresis (PFGE). The analysis of 44 L. monocytogenes isolates showed that 72.7% (32 of 44) of all the isolates belonged to Serotype 1/2c, and 15.9% (7 of 44) belonged to Serotype 3c. All 44 isolates were resistant to one or more antimicrobial agents with the most frequent resistance to penicillin (75%) and tetracycline (47.7%). Of the 44 L. monocytogenes strains, 100, 69.2, and 62.5% of livestock, human, and food strains were resistant to penicillin, respectively. Using pulsed-field gel electrophoresis (PFGE) technique, the isolates' genetic diversity was determined, and 28 PFGE patterns with 8 common (CT) and 20 single types (ST) were identified. This study highlights the high prevalence of Serotype 1/2c in clinical and livestock samples, while different serotypes were observed in food samples. The presence of rare serotypes such as 4c, belonging to the Lineage III, as well as 4e and 1/2c which are infrequent in Iran indicates that paying attention to uncommon serotypes, especially 1/2c, during the listeriosis outbreaks is necessary.

Characteristics of Listeria monocytogenes Strains Isolated from Milk and Humans and the Possibility of Milk-Borne Strains Transmission

Listeria monocytogenes is the etiological factor of listeriosis. The main source of these organisms is food, including dairy products. The aim was to determine the multiple correlations between the drug susceptibility, virulence genes (VGs), and biofilm formation on silicone teat cups of milk-borne and human L. monocytogenes strains. The spread of L. monocytogenes via contaminated teat rubbers was assessed. The L. monocytogenes strains recovered from milk (18), human blood (10), and the reference strain ATCC®19111™ were used in the study. Penicillin resistance was the most prevalent resistance in the milk isolates (n=8; 44.4%), whereas among clinical strains erythromycin resistance was predominating - (n=6; 60%). The most frequent VGs among strains isolated from milk were hlyA (100%) and plcB (100%) whereas in strains isolated from blood - hlyA (100%) and prfA (90%). All tested VGs were present in 50% of blood isolates and 11% of milk-borne strains. The strains isolated from milk formed a significantly stronger biofilm. The strains with more numerous virulence genes were resistant to more antibiotics and formed a stronger biofilm. It was shown that contaminated teat cups might contribute to the transmission of L. monocytogenes in the herd. It seems reasonable to monitor the occurrence of L. monocytogenes biofilm in a dairy processing environment.

Listeria monocytogenes is the etiological factor of listeriosis. The main source of these organisms is food, including dairy products. The aim was to determine the multiple correlations between the drug susceptibility, virulence genes (VGs), and biofilm formation on silicone teat cups of milk-borne and human L. monocytogenes strains. The spread of L. monocytogenes via contaminated teat rubbers was assessed. The L. monocytogenes strains recovered from milk (18), human blood (10), and the reference strain ATCC®19111™ were used in the study. Penicillin resistance was the most prevalent resistance in the milk isolates (n=8; 44.4%), whereas among clinical strains erythromycin resistance was predominating – (n=6; 60%). The most frequent VGs among strains isolated from milk were hlyA (100%) and plcB (100%) whereas in strains isolated from blood – hlyA (100%) and prfA (90%). All tested VGs were present in 50% of blood isolates and 11% of milk-borne strains. The strains isolated from milk formed a significantly stronger biofilm. The strains with more numerous virulence genes were resistant to more antibiotics and formed a stronger biofilm. It was shown that contaminated teat cups might contribute to the transmission of L. monocytogenes in the herd. It seems reasonable to monitor the occurrence of L. monocytogenes biofilm in a dairy processing environment.

Significance and Characteristics of Listeria monocytogenes in Poultry Products

Listeria monocytogenes is one of the most common foodborne pathogens. Poultry meat and products are of the main vehicles of pathogenic strains of L. monocytogenes for human. Poultry products are part of the regular diet of people and, due to nutrient content, more content of protein, and less content of fat, gain more attention. In comparison with red meat, poultry meat is more economical. So, it had a greater rate of consumption especially in barbecue form in which the growth of bacterium is favored. Subtyping of L. monocytogenes isolates is essential for epidemiological investigation and for identification of the source of contamination. In the following review, the main facet of presence of L. monocytogenes in poultry will be discussed. Most pathogenic serotypes of L. monocytogenes were detected in different products of poultry meat. Unfortunately, these isolated pathogens had sometimes resistance to commonly used antibiotics which were used for treatment of human infection.

Increasing Incidence of Listeriosis and Infection-associated Clinical Outcomes

BACKGROUND

Listeriosis caused by Listeria monocytogenes has a high case-fatality rate (CFR) of approximately 20% to 30%. An increasing incidence of listeriosis has been reported in many countries recently. We investigated the annual incidence, clinical characteristics, and outcomes of listeriosis at three different hospitals in Korea and evaluated the effects of appropriate empiric antimicrobial treatments on patient outcomes.

METHODS

We retrospectively collected the data of all culture-positive cases of human listeriosis from three hospitals of different sizes in Korea during 2006-2016 and calculated the annual number of cases and incidence per 100,000 admissions.

RESULTS

A total of 58 patients with L. monocytogenes were included in this study. The incidence of listeriosis was significantly higher in 2013-2016 than in 2006-2012 (RR 3.1; 95% CI 1.79-5.36; P<0.001), mainly because of an increase in patients over 60 years of age (RR 3.69; 95% CI 1.70-8.02; P<0.001). Multivariate analysis showed that healthcare-associated infection (adjusted OR, 12.15; 95% CI, 2.56-86.01; P=0.004) and empirical treatment with first-line antimicrobial agents (adjusted OR, 0.08; 95% CI, 0.00-0.63; P=0.044) were associated with CFR.

CONCLUSIONS

Healthcare-associated infections caused by L. monocytogenes are associated with high CFR. Adequate initial empirical treatments could reduce CFR, suggesting that careful consideration of an empirical antimicrobial regimen is warranted for elderly or immunocompromised patients admitted to the hospital.

Occurrence of Listeria monocytogenes on the seafood contact surfaces of Tuticorin Coast of India

Listeria monocytogenes was screened from different seafood contact surfaces in five sampling sites of fishing harbour, fish landing centers, seafood processing plants, fish market, and fish curing yards of Tuticorin Coast of India. 115 swab samples were collected and tested for the occurrence of L. monocytogenes by conventional and molecular methods. Overall, 5.22% of swab samples collected were positive for L. monocytogenes. The fishing harbour had high incidence (10.3%) of L. monocytogenes followed by fish landing centers (5.9%), and seafood processing plants (4.1%). Boat deck, fish transport tricycle were the two seafood contact surfaces in fishing harbour, which had the occurrence of L. monocytogenes. The swab samples from fish market and fish curing yards were negative for L. monocytogenes. All the isolated colonies of L. monocytogenes were confirmed by PCR assay targeting virulent hlyA gene. The DNA of all the isolates yielded a product of 174 bp on PCR amplification in comparison with L. monocytogenes Type culture (MTCC 1143). The results clearly indicated the occurrence of L. monocytogenes in seafood contact surfaces along the Tuticorin Coast of India.