Genomic Characterization of Listeria monocytogenes and Other Listeria Species Isolated from Sea Turtles

Listeria monocytogenes is a ubiquitous pathogen found both in the environment and food. It can cause listeriosis in a wide range of animals as well as in humans. Investigations on presence, spread and virulence are still limited to terrestrial and human environments. Embracing the One Health Approach, investigating the presence and spread of L. monocytogenes in marine ecosystems and among wildlife, would provide us with useful information for human health. This study investigated the presence of L. monocytogenes and Listeria spp. in two species of sea turtles common in the Mediterranean Sea (Caretta caretta and Chelonia mydas). A total of one hundred and sixty-four carcasses of sea turtles (C. caretta n = 161 and C. mydas n = 3) stranded along the Abruzzo, Molise, Campania, and Calabria coasts, were collected. Brain and fecal samples were taken, enriched, and cultured for the detection of Listeria spp. From the specimens collected, strains of L. monocytogenes (brain n = 1, brain and feces n = 1, multiorgan n = 1 and feces n = 1), L. innocua (feces n = 1 and brain n = 1), and L. ivanovii (brain n = 1) were isolated. Typical colonies were isolated for Whole Genome Sequencing (WGS). Virulence genes, disinfectants/metal resistance, and antimicrobial resistance were also investigated. L. monocytogenes, L. innocua, and L. ivanovii were detected in C. caretta, whilst only L. monocytogenes and L. innocua in C. mydas. Notable among the results is the lack of significant differences in gene distribution between human and sea turtle strains. Furthermore, potentially pathogenic strains of L. monocytogenes were found in sea turtles.

Listeria monocytogenes in ready-to-eat (RTE) delicatessen foods: Prevalence, genomic characterization of isolates and growth potential

This study investigated Listeria monocytogenes prevalence and count in 132 ready-to-eat (RTE) delicatessen samples belonging to different categories (starters with/without mayonnaise pasta/rice-based courses, meat/fish-based main courses) produced by an Italian industry. Whole Genome Sequencing characterized the isolates to map the pathogen circulation. Moreover, the growth potential of L. monocytogenes in the most contaminated product was investigated by a challenge test. L. monocytogenes was detected in 23 samples, giving an estimated prevalence of 17.4 %. Starters with mayonnaise showed a very high prevalence (56.7 %), showing the role of the sauce in the diffusion of the pathogen within the plant. A total of 49 isolates were obtained; they belonged to two different serogroups, IIb and IIa, and were related to two clonal complexes (CCs) and sequence types (STs) (CC288-ST330 and CC121-ST717), suggesting the possible persistence and circulation of the pathogen within the plant. The results of the challenge test showed a limited ability to grow in the selected product thanks to the presence of lactic microflora.

A comprehensive investigation of protein expression profiles in L. monocytogenes exposed to thermal abuse, mild acid, and salt stress conditions

Preventing L. monocytogenes infection is crucial for food safety, considering its widespread presence in the environment and its association with contaminated RTE foods. The pathogen's ability to persist under adverse conditions, for example, in food processing facilities, is linked to virulence and resistance mechanisms, including biofilm formation. In this study, the protein expression patterns of two L. monocytogenes 1/2a strains, grown under environmental stressors (mild acidic pH, thermal abuse, and high concentration of NaCl), were investigated. Protein identification and prediction were performed by nLC-ESI-MS/MS and nine different bioinformatic software programs, respectively. Gene enrichment analysis was carried out by STRING v11.05. A total of 1,215 proteins were identified, of which 335 were non-cytosolic proteins and 265 were immunogenic proteins. Proteomic analysis revealed differences in protein expression between L. monocytogenes strains in stressful conditions. The two strains exhibited unique protein expression profiles linked to stress response, virulence, and pathogenesis. Studying the proteomic profiles of such microorganisms provides information about adaptation and potential treatments, highlighting their genetic diversity and demonstrating the utility of bioinformatics and proteomics for a broader analysis of pathogens.

Predictive factors of selective transarterial embolization failure in acute renal bleeding: a single-center experience

PURPOSE

Transarterial embolization of renal artery branches (RTE) is a minimally invasive procedure commonly performed in life-threatening renal bleeding of different etiologies. Despite the widespread use of RTE, no consensus guidelines are currently available. Our aim was to investigate clinical and technical efficacy and to identify potential predictors for clinical failure of this procedure.

METHODS

All the RTE procedures performed in our Interventional Radiology unit in last 10 years were retrospectively collected and analyzed. All selected patients underwent both pre-procedural computed tomography angiography (CTA) and post-procedural CTA within 30 days. Clinical success was considered as primary endpoint. Demographic, laboratory, and diagnostic findings predictive of clinical failure of RTE were identified.

RESULTS

Over a total of 51 patients enrolled, 27 (53%) were females and 33 (64.7%) had a renal bleeding of iatrogenic origin. Technical and clinical success was 100% and 80.4%, respectively. Hematoma volumes > 258.5 cm3 measured at CTA, higher pre- and post-procedural serum creatinine (Scr) levels, an increase in Scr value > 0.135 mg/dl after the procedure, a worse post-procedural estimated glomerular filtration rate (eGFR), a post-procedural reduction of eGFR < 3.350 ml/min, and a post-procedural reduction of platelet count (PLT) > 46.50 × 103/mmc showed a significantly higher rate of clinical failure.

CONCLUSION

RTE is a safe and effective procedure in the management of acute renal bleeding of various origins. Hematoma volume, Scr, PLT, and eGFR values were found to be predictive factors of poor clinical outcome and should be closely monitored.

Listeria monocytogenes in ready to eat meat products from Zambia: phenotypical and genomic characterization of isolates

The contamination of ready to eat foods (RTE) products due to Listeria monocytogenes could compromise the products safety becoming a great risk for the consumers. The high presence of L. monocytogenes in RTE products has been described worldwide, but few data are available about these products from African countries. The aims of this study were to report the presence of L. monocytogenes in Zambian RTE products, providing genomic characterization and data on similarity with African circulating strains using whole genome sequencing (WGS). A total of 304 RTE products, produced by different Zambian manufacturers, were purchased at retail, from major supermarkets located in Lusaka, Zambia, comprising 130 dairy and 174 meat products. L. monocytogenes was detected only in 18 (10.3%) RTE meat products of the 174 samples tested. The MLST analysis grouped the 18 L. monocytogenes isolates in 7 clonal complexes (CCs): CC1 (n = 5), CC2 (n = 4), CC9 (n = 4), CC5 (n = 2), CC121 (n = 1), CC155 (n = 1), and CC3 (n = 1). According to the cgMLST results, several clusters were detected, in particular belonging to hyper-virulent clones CC1 and CC2. Regarding the virulence factors, a complete L. monocytogenes Pathogenicity Island 3 (LIPI-3) was present both in the CC1 and CC3, in addition to LIPI-1. Several resistance genes and mobile genetic elements were detected, including Stress Islands, the bcrABC cassette and Tn6188_qac transposon, plasmids and intact prophages. Despite being a first preliminary work with a limited number of samples and isolates, this study helped to increase existing knowledge on contaminated RTE products in Zambia, confirming the presence of hyper-virulent L. monocytogenes CCs, which could play an important role in human diseases, posing a public health concern for consumers.

Identification by High-Throughput Real-Time PCR of 30 Major Circulating Listeria monocytogenes Clonal Complexes in Europe

Listeria monocytogenes is a ubiquitous bacterium that causes a foodborne illness, listeriosis. Most strains can be classified into major clonal complexes (CCs) that account for the majority of outbreaks and sporadic cases in Europe. In addition to the 20 CCs known to account for the majority of human and animal clinical cases, 10 CCs are frequently reported in food production, thereby posing a serious challenge for the agrifood industry. Therefore, there is a need for a rapid and reliable method to identify these 30 major CCs. The high-throughput real-time PCR assay presented here provides accurate identification of these 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations, along with the molecular serogroup of a strain. Based on the BioMark high-throughput real-time PCR system, our assay analyzes 46 strains against 40 real-time PCR arrays in a single experiment. This European study (i) designed the assay from a broad panel of 3,342 L. monocytogenes genomes, (ii) tested its sensitivity and specificity on 597 sequenced strains collected from 24 European countries, and (iii) evaluated its performance in the typing of 526 strains collected during surveillance activities. The assay was then optimized for conventional multiplex real-time PCR for easy implementation in food laboratories. It has already been used for outbreak investigations. It represents a key tool for assisting food laboratories to establish strain relatedness with human clinical strains during outbreak investigations and for helping food business operators by improving their microbiological management plans. IMPORTANCE Multilocus sequence typing (MLST) is the reference method for Listeria monocytogenes typing but is expensive and takes time to perform, from 3 to 5 days for laboratories that outsource sequencing. Thirty major MLST clonal complexes (CCs) are circulating in the food chain and are currently identifiable only by sequencing. Therefore, there is a need for a rapid and reliable method to identify these CCs. The method presented here enables the rapid identification, by real-time PCR, of 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations. The assay was then optimized on different conventional multiplex real-time PCR systems for easy implementation in food laboratories. The two assays will be used for frontline identification of L. monocytogenes isolates prior to whole-genome sequencing. Such assays are of great interest for all food industry stakeholders and public agencies for tracking L. monocytogenes food contamination.

The Slaughterhouse as Hotspot of CC1 and CC6 Listeria monocytogenes Strains with Hypervirulent Profiles in an Integrated Poultry Chain of Italy

In Europe, very few studies are available regarding the diversity of Listeria monocytogenes (L. monocytogenes) clonal complexes (CCs) and sequence types (ST) in poultry and on the related typing of isolates using whole genome sequencing (WGS). In this study, we used a WGS approach to type 122 L. monocytogenes strains isolated from chicken neck skin samples collected in two different slaughterhouses of an integrated Italian poultry company. The studied strains were classified into five CCs: CC1-ST1 (21.3%), CC6-ST6 (22.9%), CC9-ST9 (44.2%), CC121-ST121 (10.6%) and CC193-ST193 (0.8%). CC1 and CC6 strains presented a virulence gene profile composed of 60 virulence genes and including the Listeria Pathogenicity Island 3, aut_IVb, gltA and gltB. According to cgMLST and SNPs analysis, long-term persistent clusters belonging to CC1 and CC6 were found in one of the two slaughterhouses. The reasons mediating the persistence of these CCs (up to 20 months) remain to be elucidated, and may involve the presence and the expression of stress response and environmental adaptation genes including heavy metals resistance genes (cadAC, arsBC, CsoR-copA-copZ), multidrug efflux pumps (mrpABCEF, EmrB, mepA, bmrA, bmr3, norm), cold-shock tolerance (cspD) and biofilm-formation determinants (lmo0673, lmo2504, luxS, recO). These findings indicated a serious risk of poultry finished products contamination with hypervirulent L. monocytogenes clones and raised concern for the consumer health. In addition to the AMR genes norB, mprF, lin and fosX, ubiquitous in L. monocytogenes strains, we also identified parC for quinolones, msrA for macrolides and tetA for tetracyclines. Although the phenotypical expression of these AMR genes was not tested, none of them is known to confer resistance to the primary antibiotics used to treat listeriosis The obtained results increase the data on the L. monocytogenes clones circulating in Italy and in particular in the poultry chain.

First Report of Septicaemic Listeriosis in a Loggerhead Sea Turtle (Caretta caretta) Stranded along the Adriatic Coast: Strain Detection and Sequencing

Although there are increasing reports on the prevalence of Listeria monocytogenes in wild species, this is the first case of listeriosis in sea turtle. An adult female Caretta caretta was rescued after being stranded alive along the coast of the Abruzzo region (Italy) in summer 2021. The turtle died in 6 days due to respiratory failure. The necropsy showed widespread organ lesions, such as yellow foci of necrosis in many organs, gastrointestinal erosions, pericarditis, and granulomatous pneumonia. Microbiological and histological analyses were performed on several organs. Listeria monocytogenes was isolated from multiple organs, indicating a case of septicaemic listeriosis, and the genome was sequenced and characterized. All the colonies analysed belonged to the same strain serogroup IVb, ST388, and CC388.

Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions

Listeria monocytogenes is one of the main foodborne pathogens worldwide. Although its response to stress conditions has been extensively studied, it is still present in the food processing environments and is a concern for consumers. To investigate how this microorganism adapts its proteome in mild stress conditions, a combined proteomics and bioinformatics approach was used to characterize the immunogenic protein profile of an ST7 strain that caused severe listeriosis outbreaks in central Italy. Extracted proteins were analyzed by immunoblotting using positive sera against L. monocytogenes and nLC-ESI-MS/MS, and all data were examined by five software to predict subcellular localization. Two hundred and twenty-six proteins were extracted from the bands of interest, 58 of which were classified as potential immunogenic antigens. Compared to control cells grown under optimal conditions, six proteins, some of which under-described, were expressed under mild acid and salt stress conditions and/or at 12°C. In particular, adaptation and shaping of the proteome mainly involved cell motility at 12°C without acid and salt stress, whereas the combination of the same temperature with mild acid and salt stress induced a response concerning carbohydrate metabolism, oxidative stress and DNA repair. Raw data are available via ProteomeXchange with identifier PXD033519. This article is protected by copyright. All rights reserved.

Atypical Serogroup IVb-v1 of Listeria monocytogenes Assigned to New ST2801, Widely Spread and Persistent in the Environment of a Pork-Meat Producing Plant of Central Italy

In this study, we characterized 84 Listeria monocytogenes (Lm) strains having an atypical IVb-v1 profile and isolated in a meat producing plant of Central Italy. They were assigned to the new MLST type ST2801 (CC218). The new ST was widespread in the food-producing environment where it was able to persist for over a year even after cleaning and sanitation. Cluster analysis identified three main clusters genetically close to each other (0–22 allelic differences and 0–28 SNPs) from two different cgMLST types, suggesting a common source. The coexistence of closely related clusters over time could be the result of a different evolution path starting from a common ancestor first introduced in the plant and/or the consequence of the repetitive reintroduction of closely related clones probably by raw materials. All the strains presented several determinants for heavy metals resistance, stress response, biofilm production, and multidrug efflux pumps with no significant differences among the clusters. A total of 53 strains carried pLI100 and the j1776 plasmids, while in one strain, the pLM33 was found in addition to pLI100. Only the strains carrying plasmids presented cadA and cadC for cadmium resistance and the mco gene encoding a multicopper oxidase and gerN for an additional Na+/H+-K+ antiporter. All the strains presented a virulence profile including a full-length inlA gene and the additional LIPI-3. The isolation of a new ST with a large pattern of stress-adaptation genes and able to persist is an important contribution to deepening the current knowledge on the uncommon IVb-v1 and in general on the genomic diversity of Lm.

In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes

Background

Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles.

Methods

We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision.

Results

The isolate’s genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences.

Conclusions

This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08437-4.

Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak

From May 2015 to March 2016, a severe outbreak due to Listeria monocytogenes ST7 strain occurred in Central Italy and caused 24 confirmed clinical cases. The epidemic strain was deeply investigated using whole-genome sequencing (WGS) analysis. In the interested area, the foodborne outbreak investigation identified a meat food-producing plant contaminated by the outbreak strain, carried by pork-ready-to-eat products. In the same region, in March 2018, the epidemic strain reemerged causing one listeriosis case in a 10-month-old child. The aim of this study was to investigate the phylogeny of the epidemic and reemergent strains over time and to compare them with a closer ST7 clone, detected during the outbreak and with different pulsed-field gel electrophoresis (PFGE) profiles, in order to identify genomic features linked to the persistence and the reemergence of the outbreak. An approach combining phylogenetic analysis and genome-wide association study (GWAS) revealed that the epidemic and reemergent clones were genetically closer to the ST7 clone with different PFGE profiles and strictly associated with the pork production chain. The repeated detection of both clones was probably correlated with (i) the presence of truly persistent clones and the repeated introduction of new ones and (ii) the contribution of prophage genes in promoting the persistence of the epidemic clones. Despite that no significant genomic differences were detected between the outbreak and the reemergent strain, the two related clones detected during the outbreak can be differentiated by transcriptional factor and phage genes associated with the phage LP-114.

A proteomic approach of the different environmental conditions of Listeria monocytogenes

 

Listeria monocytogenes is the ubiquitous food-borne pathogen which causes listeriosis, a disease with a high mortality rate, mostly transmitted through contaminated ready-to-eat foods. To better understand the systemic response of L. monocytogenes exposed at 3 environmental factors (T, pH and NaCl), the proteome of L. monocytogenes strain NRG 1749-2016, isolated from a meat product, was investigated to identify differences in the protein patterns of such pathogen. Four different conditions were carried out as follows: A) T 37 °C, pH 7.0, NaCl 0.5%; B) T 37 °C, pH 5.5, NaCl 7%; C) T 12° pH 7, NaCl 0.5%; D) T 12 °C, pH 5.5, NaCl 7%. The proteins belonging to cytosol (C1) and vesicles (C2) were isolated and purified by CelLytic B Cell Lysis Reagent and CelLytic IB Inclusion Body Solubilization Reagent according manufacturer's instructions. The analysis were conducted by SDS PAGE and Immunoblotting techniques. The protein concentrations were evaluated by Pierce BCA Protein Assay Kit. From preliminary results, the protein banding patterns generated by 1D SDS PAGE were found to be different at visual observation for C1 and C2, in A, B, C and D conditions. The presence of specific antigen-antibody immunocomplexes (Ag-Ab ICs) was identified by Immunoblotting, in C1 at 100, 60, 55, 35 and 25 kDa for all incubated conditions with a positive serum to L. monocytogenes. As regards C2, Ag-Ab ICs at 110 kDa were observed in A and B, Ag-Ab ICs at 80 kDa in C and D, Ag-Ab ICs at 60 kDa in A and D, while Ag-Ab ICs at 40 and 30 kDa in all conditions. The analysis of the proteome profiles shows an intra-strain variation in the protein patterns produced by L. monocytogenes during the adaptation at different environmental conditions. Further analysis will be carried out to better understand the systemic response of L. monocytogenes, in particular in order to characterize the immunogenic proteins highlighted by Immunoblotting and their role in the virulence expression of such pathogen.

Key messages

Understand how L. monocytogenes adapts physiologically to different environmental factors. Development of new detection method of L. monocytogenes and prevention strategies for listeriosis outbreaks.

Fast WGS source attribution of Listeria monocytogenes outbreak in a sheep flock in Abruzzo region

Background

Listeriosis is a life-threatening disease in human as well as animals, cows and sheep are the most sensible to the disease. Correlation to feed is well documented (silage). Some clonal complexes (CCs) are more virulent than others and frequently involved in animal and human listeriosis. Whole genome sequencing (WGS) and in silico CCs identification and core genome multilocus sequence typing (cgMLST) determination are the best way to characterize isolates and confirm connection between clinical strains and source of contamination. This work aimed to demonstrate the advantages of using WGS to find the source of Listeria monocytogenes (Lm), causing an outbreak in an ovine farm in Abruzzo region.

Methods

Lm was detected according to ISO 11290-1:2017. Serogroup was determined by multiplex PCR. WGS data were obtained using Illumina platform. Sequences were used to assess CCs and cgMLST according to BIGSdb Pasteur platform. Two brain samples and 1 lymph node from 2 sheep, one sample of silage (15 analytical portion), and 1 sample of hay were tested.

Results

Lm was detected in all animal specimens and in 2 analytical portions of feed (silage) tested. Out of 35 colonies detected 28 were identified as Lm (27 serogoup IVb and 1 sample of silage serogroup IIa). Five colonies were selected for WGS (one from each animal brain, one from the lymph node and one from each positive analytical portion of silage), among them only one colony from the silage showed the same CC of the strains isolated from sheep (CC1). cgMLST revealed no allelic distances between these strains.

Conclusions

CC1 is the main virulent clone among Lm isolates often involved in human and animal outbreak. Feed may be a vehicle for Lm and could be the outbreak source. Cases ceased after removing the silage. Use of WGS is a definitive help in source attribution when feed is available and the sampling is done in a correct manner.

Key messages

Silage can be cause of listeriosis in livestock. WGS can improve source attribution of outbreaks detecting the relatedness of the strains and improving the epidemiological investigation in case of outbreak.

Shiga-toxin producing Escherichia coli detection in samples from Abruzzo and Molise regions, Italy

Background

Top five serogroups (O157, O111, O26, O103 and O145) of Shiga-toxin producing Escherichia coli (STEC) represent the third most important increasing zoonosis reported in European Union. The ISO methods of analysis, used in foods and environmental samples, quite often does not confirm the molecular detection of STEC genes (stx1 and stx2) in enrichment broth. The aim of this study was to summarize the results of the tests carried out at Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise in the last six years (2016-2021), comparing genes detection in enrichment broth and in colonies grown on agar plates.

Methods

Along the 2016-2021, a total of 1716 foods and environmental samples from Abruzzo and Molise regions were tested, according to ISO/TS 13136:2012.

Results

Out of 1716 samples, 16 (0.9%) shown presumptive positive presence of STEC (stx1 and/or stx2) in broth. In spite of that, the presence of STEC (positive colonies for stx1 and/or stx2) was confirmed only in 4 out of 16 samples (one sample of cheese and 3 of minced meat). Then, eae gene was found in 54 samples in broth and only in 3 samples from colonies, during a foodborne outbreak investigation. Serogroup specific targets were detected in 6 broth samples (O26, O145 and O157) and confirmed in colonies only in 2 minced meat samples (O157).

Conclusions

STEC are a heavy hazard for the consumers and the number of cases is slightly increasing since 2015. Our results highlight a low number of presumptive positive samples and even lower number of STEC detection obtained with the ISO classical method. Furthermore, detection of the target genes in broth was rarely confirmed after plating, highlighting a weak point of the analytical method that needs to be investigated. Efforts are necessary to improve the method and the STEC confirmation from colonies. Immunomagnetic beads targeting the top five serogroups and digital PCR could help in increasing the recovery rate of cultivable STEC.

Key messages

The presumptive positive samples for STEC genes in foodstuffs from the Abruzzo and Molise regions are quite rare, even lower is the number of confirmed colonies by agar plate isolation. Specific immunomagnetic beads for the top five STEC serogroups could improve the method and the STEC colonies detection, increasing the recovery rate of cultivable strains.

Genomic persistence of Listeria monocytogenes strains in dairy and meat processing plants in Italy

Background

Persistence of Listeria monocytogenes (Lm) in food processing plants (FPP) is still considered the major source of food contamination during processing. Correlations among different Lm strains and evaluation of the isolates persistence in FPP environments is an essential tool to improve food safety. The aim of this study was to investigate the genomic characteristics of persistent Lm strains (e.g. Metal and Detergent Resistance, SSIs and genomic island).

Methods

Totally 221 strains isolated from 10 FPP in the Abruzzo and Molise regions, Italy, were enrolled (4 of dairy products FPP - DP - and 6 of meat products FPP - MP). Sampling was performed in 6 sessions, from March 2017 to May 2018. Strains were sequenced using Illumina platform. The CCs, cgMLST analysis and Metal and Detergent Resistance, SSIs and genomic island (GI) detection was carried using the Pasteur scheme.

Results

Results returned 13 CCs and 2 singletons. cgMLST clustering showed two persistent clusters DP and 9 clusters in MP. In DP CC3 and CC9 were persistent. While in MP CC5, CC8, CC9, CC37, CC121 and CC155. The presence of SSI-1, was detected in 100% of the persistent strains from DP and 80% from MP, in particular in all strains of CC155, CC5, CC8 and CC9. In CC121 and CC37 it was absent. The presence of loci of Lm GI3, was in 100% of persistent strains of DP and in 52.3% of MP plant, in particular in 100% of CC121, CC8, CC5 and 16.3% of CC9. The 100% of CC121 in DP and MP plant harboured Tn6188 and SSI-2. The inlA PMSC mutations were detected in 100% of CC9 and CC121 strains.

Conclusions

The persistence of strains inside FPP was confirmed using NGS data, most of the strains were characterised by the presence of genes involved in resistance and adaptation. NGS is confirmed to be a powerful tool to study Lm persistence in FPP, looking also at strains' ecology.

Key messages

Most of persistent strains showed genes involved in resistance and adaptation in the food processing environment. NGS could help in facing Lm persistence in food producing plants giving new insights on the genomic characteristics of persistent strains.

Genotyping of Listeria monocytogenes strains in Italian food-processing environments

Background

In 2019, case fatality from Listeria monocytogenes (Lm) was higher than the previous years confirming Lm as a major public health problem. Food is the main source of Lm infection and cross-contamination from the food-processing environment (FPEs) is the most common route of contamination. The aim of this work was to characterize FPEs Lm strains collected from the National Reference Laboratory (NRL) for Lm in order to evaluate circulating clonal complexes (CCs) and their environmental adaptation.

Methods

NRL Lm database actually consists of 798 FPEs sequenced strains. In silico MLST was evaluated. Sequences related to prevalent CCs were further investigated using Pasteur's cgMLST scheme and detecting metal and detergent resistance genes and stress survival islet (SSI).

Results

MLST identified 25 CCs and 4 singleton. Nine isolates gave inexact match with existing alleles and were not classified. CC9 (17.4%) and CC121 (14.2%) were the prevalent clones. CC9 cgMLST analysis revealed a relatedness among strains isolated from the same establishment type (meat or dairy), even if sampled in different regions. Indeed, CC121 cgMLST clustering analysis was strictly associated to the point of sampling. Regarding stress adaptation genes, SSI1 and brcABC genes were detected in 100% and 2.9% of the CC9 strains, respectively. Meanwhile, SSI2 and transposon Tn6188 were detected, respectively, in 100% and 97.3% of CC121 strains.

Conclusions

Results confirmed, in Italian FPEs, prevalence of hypovirulent Lm strains, as previously observed in Italian food. Tested isolates highlighted adaptation to low pH and high salt concentration (SSI1 genes for CC9), to alkaline and oxidative stress (SSI2 genes for CC121) and benzalkonium chloride tolerance (Tn6188 in CC121) resulting in a best survival under stress conditions. Interestingly, CC9 clustering denoted allelic proximity among strains isolated in different Italian regions paying attention to clones spreading at national level.

Key messages

Listeria monocytogenes CC9 and CC121 prevalence in Italian establishment confirms environment is the main route of food contamination at production level. Prevalent food-processing environmental Italian Listeria monocytogenes strains denotes adaptation to environmental stress and clones spreading at national level.

Antimicrobial resistance of Listeria monocytogenes human strains and correlation to genomic data

Background

Studies checking antimicrobial resistance (AMR) of Listeria monocytogenes (Lm) are ongoing, coupled with disease surveillance. Lm resistant strains are reported and are increasing. The aim of the work was to investigate AMR of clinical strains of Lm collected from nine regions (mostly in Lombardy and Marche regions) from 2008 to 2020.

Methods

The dataset consisted of 233 Lm human strains collected from nine regions during the period 2008-2020. All the strains were tested using Sensititre™ Haemophilus Plate (Thermo Scientific, Milano, Italy). Results were expressed according to EUCAST breakpoints for Lm, S. pneumoniae and E. faecalis. Resistant strains were sequenced using Illumina platform, ABRicate was used to predict antimicrobial resistance genes and plasmids.

Results

Most of the strains were detected in Lombardy and Marche. The MIC results showed that 11 out of 233 strains were resistant, one to ampicillin, four to tetracycline and six to clarithromycin. Analysing the sequences, all the resistant strains showed to have a common antimicrobial resistant pattern (mprF, norB, FosX, (MLS)lin, lin and lmo0919). Genomic determinants for ampicillin and clarithromycin resistance were not detected. Indeed, only in 3 out of 4 resistant strains tetM was found. Meanwhile, plasmids were detected in 7 strains.

Conclusions

The distribution of the strains considered in this work did not reflect the real epidemiological situation in Italy, because their origin was mostly from two regions. The emergence of AMR also for Lm needs to be considered. Moreover, official breakpoints for Lm are not defined and to date limited to five antimicrobials excluding clarithromycin and tetracycline, where the pathogen showed resistance. Finally, the incongruence between phenotypic and genomic data suggests that the mechanisms involved in the resistance is not fully known especially for ampicillin. Further investigations are needed to improve the knowledge on Lm AMR.

Key messages

Monitoring AMR of Listeria monocytogenes is crucial, only effective drug in clinical cases should be used. Further investigations are needed to explore the mechanisms involved in antimicrobial resistance of Listeria monocytogenes.

Genetic relationships and biofilm formation of Listeria monocytogenes isolated from the smoked salmon industry

Among pathogens, L. monocytogenes has the capability to persist on Food Processing Environment (FPE), first of all posing safety issues, then economic impact on productivity. The aim of this work was to determine the influence of biofilm forming-ability and molecular features on the persistence of 19 Listeria monocytogenes isolates obtained from FPE, raw and processed products of a cold-smoked salmon processing plant. To verify the phenotypic and genomic correlations among the isolates, different analyses were employed: serotyping, Clonal Complex (CC), core genome Multi-Locus Sequence Typing (cgMLST) and Single Nucleotide Polymorphisms (SNPs) clustering, and evaluation of the presence of virulence- and persistence-associated genes. From our results, the biofilm formation was significantly higher (*P < 0.05) at 37 °C, compared to 30 and 12 °C, suggesting a temperature-dependent behaviour. Moreover, the biofilm-forming ability showed a strain-specific trend, not correlated with CC or with strains persistence. Instead, the presence of internalin (inL), Stress Survival Islet (SSI) and resistance to erythromycin (ermC) genes was correlated with the ability to produce biofilms. Our data demonstrate that the genetic profile influences the adhesion capacity and persistence of L. monocytogenes in food processing plants and could be the result of environmental adaptation in response to the external selective pressure.

Intensive Environmental Surveillance Plan for Listeria monocytogenes in Food Producing Plants and Retail Stores of Central Italy: Prevalence and Genetic Diversity

Listeria monocytogenes (Lm) can persist in food processing environments (FPEs), surviving environmental stresses and disinfectants. We described an intensive environmental monitoring plan performed in Central Italy and involving food producing plants (FPPs) and retail grocery stores (RSs). The aim of the study was to provide a snapshot of the Lm circulation in different FPEs during a severe listeriosis outbreak, using whole genome sequencing (WGS) to investigate the genetic diversity of the Lm isolated, evaluating their virulence and stress resistance profiles. A total of 1217 samples were collected in 86 FPEs with 12.0% of positive surfaces at FPPs level and 7.5% at RSs level; 133 Lm isolates were typed by multilocus sequencing typing (MLST) and core genome MLST (cgMLST). Clonal complex (CC) 121 (25.6%), CC9 (22.6%), CC1 (11.3%), CC3 (10.5%), CC191 (4.5%), CC7 (4.5%) and CC31 (3.8%) were the most frequent MLST clones. Among the 26 cgMLST clusters obtained, 5 of them persisted after sanitization and were re-isolated during the follow-up sampling. All the CC121 harboured the Tn6188_qac gene for tolerance to benzalkonium chloride and the stress survival islet SSI-2. The CC3, CC7, CC9, CC31 and CC191 carried the SSI-1. All the CC9 and CC121 strains presented a premature stop codon in the inlA gene. In addition to the Lm Pathogenicity Island 1 (LIPI-1), CC1, CC3 and CC191 harboured the LIPI-3. The application of intensive environmental sampling plans for the detection and WGS analysis of Lm isolates could improve surveillance and early detection of outbreaks.

Occurrence of Listeria spp. and Listeria monocytogenes Isolated from PDO Taleggio Production Plants

The present study evaluated the presence of Listeria spp. and L. monocytogenes in four plants producing PDO Taleggio cheese. A total of 360 environmental samples were collected from different areas during production. The sampling points were identified as Food Contact Surfaces (FCS), transfer-Non Food Contact Surfaces (tr-NFCS), and non-transfer-NFCS (non-tr-NFCS). Fifty-nine ingredients/products were also analyzed. Listeria spp. was found in all the plants with a mean prevalence of 23.1%; plants that included a ripening area showed significantly higher prevalence if compared to the other plants. The positivity rate detected on FCS was moderate (~12%), but significantly lower if compared to NFCS (about 1/4 of the samples, p < 0.01). Among the FCS, higher prevalence was revealed on ripening equipment. Listeria spp. was never detected in the ingredients or products. A total of 125 Listeria spp. isolates were identified, mostly as L. innocua (almost 80%). L. monocytogenes was detected only from two FCS samples, in an area dedicated to the cutting of ripened blue cheeses; strain characterization by whole genome sequencing (WGS) evidenced a low virulence of the isolates. The results of the present study stress the importance of Listeria spp. management in the dairy plants producing PDO Taleggio and similar cheeses, mainly by the application of strict hygienic practices.

Listeria monocytogenes clones in Italian food products: virulence and environmental adaptation

Background

Food is the main source of Listeria monocytogenes (Lm) infection. Lm is a highly heterogeneous species composed of hypervirulent and hypovirulent clones. Understanding the distribution of Lm clonal complexes (CCs) in different food categories has strong implications for risk assessment. The aim of this work was to analyse collection of Lm strains of National Reference Laboratory (NRL Lm) in order to assess link between genetic profile and matrices and the level of pathogenicity of circulating strains based on CCs.

Methods

NRL Lm database actually consists of 906 sequenced strains isolated in 10 years from 5 food compartments (meat, fish, dairy, vegetables and composite dishes). Epidata were analysed to remove redundant strains based on the same epidemiological description. After that, WGS data from 465 Lm strains were investigated. In silico MLST was defined and Roary 3.12.0 was used to obtain a pan-genome profile. Genes were later uploaded to Pasteur Institute platform for characterization.

Results

In silico MLST identified 36 CCs and 6 singleton. CC9 (23.0%), CC8 (15.3%) and CC121 (13.3%) were the prevalent CCs. In particular, CC9 was present in 35.2% of meat samples and CC8 in 25.8% of fish samples. Pan genome profile revealed high prevalence (&gt;98%) of genes related to biofilm formation and resistance to environmental stress in CC9 strains and genes involved in tolerance to quaternary ammonium compounds in CC121 strains.

Conclusions

Results, in particular for meat products, confirmed in Italy, the prevalence of hypovirulent Lm strains previously observed at European Union level. The high presence of stress resistance and disinfectant tolerance genes in these strains could make them able to persist in food-production environment and should be taken into account evaluating the health hazards. In fish product is also relevant the prevalence of CC8 strains which are potentially highly pathogenic and have been responsible of recent European multi country outbreak.

Key messages

Pangenome of Listeria monocytogenes isolated from Italian food revealed high presence of disinfectant tolerance and stress resistance genes in meat products and virulence genes in fish products. Listeria monocytogenes CC9 and CC121 prevalence in Italian meat product confirms occurrence of hypovirulent strains detected at European Union level.

Listeria monocytogenes in poultry: Detection and strain characterization along an integrated production chain in Italy

In this study, thirteen batches of broiler chicken from an integrated Italian poultry company were investigated for the detection of Listeria monocytogenes. The prevalence was evaluated in faeces samples at farm level and after transport, caecal contents and carcass neck skin from 2 slaughterhouses (M1 and M2), for a total of 2080 samples, throughout a 27-month period. No positive results were recorded in faeces, while the overall prevalence of contamination in carcass neck skin was 26.7%. Then, 123 isolates out of 139 positive skin samples, with the prevalent serotypes 4b (76%) and 1/2b (94%) from slaughterhouses M1 and M2 respectively, were PFGE characterized, showing the presence of 18 different pulsotypes and 8 genetic clusters. The same pulsotypes were found in carcasses from different farms, but slaughtered in the same abattoir, highlighting the environmental origin of contamination. The persistence of the pathogen over long time seemed to be very likely, considering that undistinguishable pulsotypes were found in carcasses slaughtered in the same slaughterhouse after periods up to 18 months long. The implementation of cleaning and sanitation at slaughterhouse level could represent the main factor for the control of such pathogen in the poultry meat processing line.

A Real-Time PCR Screening Assay for Rapid Detection of Listeria Monocytogenes Outbreak Strains

From January 2015 to March 2016, an outbreak of 23 human cases of listeriosis in the Marche region and one human case in the Umbria region of Italy was caused by Listeria monocytogenes strains showing a new pulsotype never described before in Italy. A total of 37 clinical strains isolated from patients exhibiting listeriosis symptoms and 1374 strains correlated to the outbreak were received by the Italian National Reference Laboratory for L. monocytogenes (It NRL Lm) of Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM) for outbreak investigation. A real-time PCR assay was purposely designed for a rapid screening of the strains related to the outbreak. PCR-positive strains were successively typed through molecular serogrouping, pulsed field gel electrophoresis (PFGE), and Next Generation Sequencing (NGS). Applying the described strategy, based on real-time PCR screening, we were able to considerably reduce time and costs during the outbreak investigation activities.

A severe outbreak of listeriosis in central Italy with a rare pulsotype associated with processed pork products

PURPOSE

From May 2015 to March 2016, an outbreak due to Listeria monocytogenes serotype 1/2a and clinical pulsotype never previously isolated in Europe occurred in central Italy, involving 24 confirmed clinical cases. The article provides a description of the outbreak and the investigation carried out by a multidisciplinary network.

METHODOLOGY

Epidemiological and microbiological surveillance was conducted to confirm the outbreak and to detect the food vehicle of infection. The origin and destination of the implicated food and its ingredients were investigated by tracing-back and -forward investigation.

RESULTS

Next-generation sequencing confirmed the unique outbreak strain. On 4 January 2016, a L. monocytogenes strain with pulsotype indistinguishable from that isolated from clinical cases in the outbreak was detected in a sample of hog head cheese purchased from a retail supermarket by one of the patients. The hog head cheese was produced by a small meat processing plant in the Marche region, where microbiological investigation confirmed environmental and food contamination by the outbreak strain. Plant production was suspended and all contaminated batches of the hog head cheese were withdrawn from the market by 19 February by local health authority. We subsequently observed a sharp decline in clinical cases, the last being reported on 11 March 2016.

CONCLUSION

The key factor in the timely conclusion of this investigation was intersectoral collaboration among epidemiologists, microbiologists, veterinarians, statisticians and health and food safety authorities at national, regional and local levels.

Detection and characterisation of potentially pathogenic species of Vibrio in the Vibrata river, Abruzzo Region, Italy

This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evaluate the seasonal distribution of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus strains isolated from the Vibrata river (Abruzzo Region, Italy) during a monitoring period of one year. Detection was performed according to ISO/TS 21872-1-2:2007. Species identification and characterisation were achieved using molecular methods. Vibrio spp. were detected in 50% (23) of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 18 (39.1%), 4 (8.7%), and 2 (4.3%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 75% were positive for trh gene. In 30 V. cholerae isolates, the polymerase chain reaction (PCR) assay for detecting virulence and regulatory genes (ctxA, toxR, tcpA, ompU, hlyA, tcpI, zot, and stn/sto) revealed 6 genotypes associated to different levels of pathogenicity. Pulsed-field gel electrophoresis (PFGE) characterisation of the V. cholerae strains identified 13 different pulsotypes. A greater degree of similarity was shown for strains isolated in the same period of the year. Results of our study reveal a potential health risk associated with the waters of the Vibrata river, which are used for irrigation and next to the swimming areas of Abruzzo coastline.

Listeria monocytogenes in Smoked Salmon and Other Smoked Fish at Retail in Italy: Frequency of Contamination and Strain Characterization in Products from Different Manufacturers

Seven hundred seventy-eight samples of packaged smoked fish (774 smoked salmon and 4 smoked swordfish) on sale in Italy, from 50 different manufacturers located in 12 European Union countries, were purchased from the Italian market between May and December 2011. The surface temperatures of the samples on sale ranged from 0 to 13°C (3.4 ± 1.5°C, mean ± SD). Six hundred eighty (87.4%) of 778 samples were stored at ≤4°C. One hundred fifty-seven samples (20.2%, 95% confidence interval 17.5 to 23.1%) were contaminated by Listeria monocytogenes , with 26 samples (3.3%, 95% confidence interval 2.3 to 4.8%) at levels >100 CFU/g. The maximum level of contamination was 1.3 ×10⁶ CFU/g. The differences in the level of contamination of smoked fish between countries (χ² = 91.54, P < 0.05) and manufacturers (χ² = 193.22, P < 0.05) were significant. The frequency of detection for products from different manufacturing premises ranged from 0 to 76.9%. Serotyping by serological agglutination revealed that the main serotypes detected were 1/2a (65.3%) and 1/2b (22.4%). Pulsed-field gel electrophoresis typing with restriction enzymes AscI and ApaI yielded 36 pulsotypes from 144 isolates, clustering into 17 groups. Eight main pulsotypes accounted for 70.8% of the isolates. Three of the main pulsotypes were exclusively from products of a single manufacturer. In general, products from the same manufacturer showed genetic homogeneity, with one strongly prevalent pulsotype. Different manufacturers usually showed very different levels of contamination of the final product, confirming the importance of the management of process hygiene for controlling L. monocytogenes contamination.

Comparison of Multiple‑Locus Variable number tandem repeat Analysis and Pulsed Field Gel Electrophoresis in molecular subtyping of Listeria monocytogenes isolates from Italian cheese

Subtyping of Listeria monocytogenes strains is an essential epidemiological tool to trace contamination and determine evolutionary relationships among different strains. Pulsed field gel electrophoresis (PFGE) is the current gold standard method for Listeria characterization. Multiple-Locus Variable-number tandem repeat Analysis (MLVA) is a rapid subtyping method based on Polymerase Chain Reaction (PCR) amplification that has been successfully developed for subtyping bacterial genera. The purpose of this study was to evaluate MLVA for subtyping L. monocytogenes strains isolated from Italian cheese and to compare it with PFGE. The type ability and discriminatory power of MLVA was determined on a collection of 90 isolates corresponding to 5 serotypes and 29 pulsotypes with enzymes AscI and ApaI. A panel of 5 variable-number tandem repeat loci was used. MLVA and PFGE showed very similar discriminatory power (Simpson's Index of diversity 0.840 with 95% Confidence Interval [CI] 0.780/0.899 and 0.837 with 95% CI 0.768/0.906, respectively). MLVA is an easy test to perform. It is relatively fast, reproducible and could be implemented in any molecular laboratory but, according to the performed protocol, it is not sufficient for discriminating the L. monocytogenes strains isolated from cheese. This method could be combined with PFGE to increase the discrimination in molecular subtyping of these strains.

Detection of Vibrio splendidus and related species in Chamelea gallina sampled in the Adriatic along the Abruzzi coastline

Vibrio species are an important and widespread component of marine microbial communities. Some Vibrio strains are potentially pathogenic to marine vertebrates and invertebrates. The aim of this study was to identify vibrios, in particular Vibrio splendidus and related species, isolated from clams (Chamelea gallina) collected along the coasts of the Abruzzi region from May to October 2007. The isolates obtained were phenotyped and classified as belonging to the genus Vibrio. The strains underwent biochemical testing in accordance with Alsina's scheme for V. splendidus identification. Molecular analysis of the 16S-23S intergenic space region and recA gene was used to identify V. splendidus and related species. All the samples examined were found to contain halophylic Vibrio species, with V. alginolyticus, V. splendidus-related species and V. mediterranei most commonly found. A polymerase chain reaction of the 16S-23S intergenic space region and sequencing of the recA gene from isolates confirmed that phenotyping of Vibrio species is not sufficient to distinguish between different species. Differentiation of the highly related species among V. splendidus-related clusters remains an important issue. In this regard, our data suggests sequencing the recA genes was far more discriminatory than sequencing 16S rDNA for this purpose.

Characterisation of Listeria monocytogenes strains isolated from soft and semi-soft cheeses sampled in a region of Italy

A total of 47 Listeria monocytogenes strains isolated in a survey of cheeses sampled from retail outlets were characterised. Five cheeses (Gorgonzola, Taleggio, Asiago, Crescenza and Brie) were chosen from the most popular soft and semi-soft cheeses consumed in Italy and most commonly contaminated with L. monocytogenes. The serotype and antibiotic resistance pattern were determined for each strain and their macrorestriction profile was analysed with pulsed-field gel electrophoresis (PFGE). The main serotypes detected were 1/2a (76.6%) and 1/2c (21.3%). Serotype 1/2b was found in only one sample. A total of 97.9% of strains were resistant to oxacillin (OX), 80.9% to lincomycin (L) and 78.7% to clindamycin (CC). Of these strains, 17% were found to be resistant to two antibiotics (OX-CC or OX-L) while 70.2% were resistant to three antibiotics (OX-CC-L). No strains were susceptible to all the compounds tested. A combined analysis of the macrorestriction profiles AscI and ApaI identified eleven pulsotypes divided into three clusters. Two pulsotypes predominated, accounting for 57.4% and 21.3% of the isolated strains. Analysis of the PFGE profiles did not reveal any correlation between pulsotype and type of cheese, producer or retail outlet. A temporal analysis revealed that one pulsotype was persistent throughout the study period, with the exception of August and September, in which time a different pulsotype was detected. This variability suggests the influence of factors affecting the dynamics of the contamination of these products. Large-scale studies could help clarify this phenomenon.