Genome Sequences of Listeria monocytogenes Serotype 4b Variant Strains Isolated from Clinical and Environmental Sources

Phenotypic and Genotypic Characteristics of Non-Hemolytic L. monocytogenes Isolated from Food and Processing Environments

Increasingly, Listeria monocytogenes (LM) with atypical phenotypic and genotypic characteristics are being isolated from food, causing problems with their classification and testing. From 2495 soil, food, and swab samples from the food industry, 262 LM isolates were found. A total of 30 isolates were isolated, mainly from soil and plant food, and were classified as atypical LM (aLM) because they lacked the ability to move (30/11.4%) and perform hemolysis (25/9.5%). The isolation environment affected aLM incidence, cell size, sugar fermentation capacity, antibiotic sensitivity, and the number of virulence genes. Therefore, despite several characteristics differentiating all aLMs/non-hemolytic isolates from reference LMs, the remaining phenotypic characteristics were specific to each aLM isolate (like a fingerprint). The aLM/non-hemolytic isolates, particularly those from the soil and meat industries, showed more variability in their sugar fermentation capacity and were less sensitive to antibiotics than LMs. As many as 11 (36.7%) aLM isolates had resistance to four different antibiotics or simultaneously to two antibiotics. The aLM isolates possessed 3-7 of the 12 virulence genes: prfA and hly in all aLMs, while iap was not present. Only five (16.7%) isolates were classified into serogroups 1/2c-3c or 4a-4c. The aLM/non-hemolytic isolates differed by many traits from L. immobilis and atypical L. innocua. The reference method of reviving and isolating LM required optimization of aLM. Statistical analyses of clustering, correlation, and PCA showed similarities and differences between LM and aLM/non-hemolytic isolates due to individual phenotypic traits and genes. Correlations were found between biochemical traits, antibiotic resistance, and virulence genes. The increase in the incidence of atypical non-hemolytic LM may pose a risk to humans, as they may not be detected by ISO methods and have greater antibiotic resistance than LM. aLM from LM can be distinguished based on lack of hemolysis, motility, growth at 4 °C, ability to ferment D-arabitol, and lack of six specific genes.

Distribution and phenotypic and genotypic characterization of Listeria monocytogenes isolated from food, Colombia, 2010-2018

Introduction: Listeria monocytogenes is a food-borne pathogen that may cause infections in humans such as meningitis, meningoencephalitis, and septicemia, as well as abortions. By serological typing 13 serotypes have been identified of which 4b is responsible for most of the outbreaks in the world. Objective: To determine the frequency and distribution of serotypes and molecular subtypes of L. monocytogenes isolated in Colombia from food from 2010 to 2018. Materials and methods: We conducted a retrospective and descriptive study based on the analysis of 2,420 isolates confirmed as L. monocytogenes and other species using biochemical and serological tests, and pulsed-field gel electrophoresis (PFGE) for molecular subtyping. Results: Of the 2,420 isolates received, 2,326 were confirmed as L. monocytogenes. The serotypes found were 4b (52%), 4d-4e (14.5%), 1/2a (11%), 1/2c (9.4%), 1/2b (9%), and 3a, 3b, 3c, 4c, 4d, 4e and 7 (less than 2%). The isolates came from Bogotá (43%), Antioquia (25%), Valle (10%), Nariño (9%), and other departments (7%). The genotypic characterization grouped the isolates in 167 PFGE patterns. The most frequent patterns were identified in various dairy and meat products, and in prepared foods. Conclusion: A 96.1% of the isolates corresponded to L. monocytogenes showing good agreement between isolates and identification. Serotype 4b, highly virulent, was the most frequent. The molecular analysis showed the possible dissemination and permanence over time of several serotypes, which highlights the importance of including this pathogen in epidemiological food surveillance programs.

Data Science in the Food Industry

Food safety is one of the main challenges of the agri-food industry that is expected to be addressed in the current environment of tremendous technological progress, where consumers' lifestyles and preferences are in a constant state of flux. Food chain transparency and trust are drivers for food integrity control and for improvements in efficiency and economic growth. Similarly, the circular economy has great potential to reduce wastage and improve the efficiency of operations in multi-stakeholder ecosystems. Throughout the food chain cycle, all food commodities are exposed to multiple hazards, resulting in a high likelihood of contamination. Such biological or chemical hazards may be naturally present at any stage of food production, whether accidentally introduced or fraudulently imposed, risking consumers' health and their faith in the food industry. Nowadays, a massive amount of data is generated, not only from the next generation of food safety monitoring systems and along the entire food chain (primary production included) but also from the Internet of things, media, and other devices. These data should be used for the benefit of society, and the scientific field of data science should be a vital player in helping to make this possible.

Molecular Typing of Listeria monocytogenes IVb Serogroup Isolated from Food and Food Production Environments in Poland

Listeria monocytogenes is one of the most important foodborne pathogens that may be present in food and in food processing environments. In the present study, 91 L. monocytogenes isolates of serogroup IVb from raw meat, ready-to-eat food and food production environments in Poland were characterized by whole genome sequencing (WGS). The strains were also compared, using core genome multi-locus sequence typing (cgMLST) analysis, with 186 genomes of L. monocytogenes recovered worldwide from food, environments, and from humans with listeriosis. The L. monocytogenes examined belonged to three MLST clonal complexes: CC1 (10; 11.0% isolates), CC2 (70; 76.9%), and CC6 (11; 12.1%). CC1 comprised of two STs (ST1 and ST515) which could be divided into five cgMLST, CC2 covered two STs (ST2 and ST145) with a total of 20 cgMLST types, whereas CC6 consisted of only one ST (ST6) classified as one cgMLST. WGS sequences of the tested strains revealed that they had several pathogenic markers making them potentially hazardous for public health. Molecular comparison of L. monocytogenes strains tested in the present study with those isolated from food and human listeriosis showed a relationship between the isolates from Poland, but not from other countries.

Development and Validation of a Quantitative PCR Method for Species Verification and Serogroup Determination of Listeria monocytogenes Isolates

ABSTRACT

Listeria monocytogenes (Lm) is one of the leading causes of death because of foodborne illness, affecting the elderly, pregnant women, neonates, and people who are immunocompromised. Serologically, Lm can be classified into 13 serotypes, although only 4 are typically linked with food contamination and illness. Since 2000, a shift in serotypes involved in listeriosis outbreaks has been observed, suggesting that tracking of serotypes could help identify emerging trends. A PCR method developed in 2004 allowed detection of the four major serotypes as molecular serogroups, corresponding to broad phylogenetic groups. In this study, a novel quantitative PCR (qPCR) method was developed that uses two multiplex qPCRs, one to confirm the Listeria genus and Lm species and the second for Lm molecular serogrouping. This method was compared with the U.S. Food and Drug Administration Bacteriological Analytical Manual (BAM) method for Lm and the seroagglutination method, using a 208-strain panel. Comparison of the genus and species qPCR assay with the BAM methods found an equal or slightly higher accuracy for the qPCR method (>98%), compared with the BAM protocol (>96%), when evaluated against independent characterization data. Molecular serogrouping using the qPCR method (96.6%) was more accurate than the seroagglutination assay (75.6%). The qPCR method identified Lm 4bV strains, which could not be resolved using seroagglutination. The qPCR could not identify lineage III and IV serotype 4b strains but did correctly identify 16 of 18 lineage III and IV strains. The qPCR method performed genus identification for the Listeria species Lm, L. innocua, L. welshimeri, L. ivanovii, and L. seeligeri. In addition, the method performed species identification for Lm and classified Lm into six molecular serogroups: 2A, 2B, 2C, 4B, NT, and 4bV. This method provided a rapid and accurate confirmation of Lm and serogroup determinations; furthermore, it could help identify otherwise unlinked strains by enabling whole genome sequencing analysis based on broad phylogeny, independent of other information.

HIGHLIGHTS

Genomic and phenotypic diversity of Listeria monocytogenes clonal complexes associated with human listeriosis

Listeria monocytogenes is a pathogen of significant concern in many ready to eat foods due to its ability to survive and multiply even under significant environmental stresses. Listeriosis in humans is a concern, especially to high-risk populations such as those who are immunocompromised or pregnant, due to the high rates of morbidity and mortality. Whole genome sequencing has become a routine part of assessing L. monocytogenes isolated from patients, and the frequency of different genetic subtypes associated with listeriosis is now being reported. The recent abundance of genome sequences for L. monocytogenes has provided a wealth of information regarding the variation in core and accessory genomic elements. Newly described accessory genomic regions have been linked to greater virulence capabilities as well as greater resistance to environmental stressors such as sanitizers commonly used in food processing facilities. This review will provide a summary of our current understanding of stress response and virulence phenotypes of L. monocytogenes, within the context of the genetic diversity of the pathogen.

A Comprehensive Evaluation of the Genetic Relatedness of Listeria monocytogenes Serotype 4b Variant Strains

Recently, we have identified a link between four listeriosis incidents/outbreaks to a variant of Listeria monocytogenes (Lm) serotype 4b strains, 4bV. Although 4bV strains have been reported from clinical specimens as well as from foods, listeriosis outbreaks occurring in 2014–2016 were the first reported outbreaks involving 4bV in the USA. Since traditional typing methods do not detect members of this group, we undertook a systematic and retrospective analysis of all Lm in the NCBI WGS Sequence Read Archive database to investigate the burden of 4bV strains among all listeriosis cases. This analysis identified the presence of isolates causing sporadic cases as well as those associated with the aforementioned outbreaks, as determined by WGS and traditional epidemiology. In total, approximately 350 Lm 4bV strains were identified from multiple parts of the USA as well as from Australia and Chile, dating back to 2001. The genomic relatedness of these strains was compared using the CFSAN SNP Pipeline and multi-virulence-locus sequence typing (MVLST). Using the CFSAN Pipeline tool, the 4bV strains were found to group into seven clusters that were separate from 4b strains. All seven clades appeared to contain isolates from both clinical and non-clinical sources. Conversely, the MVLST analysis revealed that practically all of the strains belonged to a single clade, suggesting that 4bV strains from disparate geographic regions and sources are under varied selective pressure, restricting diversity across these six virulence loci while allowing more variability across the genome as a whole. Further evaluation of these 4bV strains identified genes potentially acquired from a lineage II source external to the lmo0733–lmo0739 region, as well as highly conserved SNPs unique to the 4bV strains when compared to those from other lineages. Taken together, these data suggest that 4bV strains have undergone adaptive responses to selective pressures that may enhance survival in the environment while maintaining the pathogenic potential of serotype 4b strains.

Genomic characterization of novel Listeria monocytogenes serotype 4b variant strains

Over 90% of the human listeriosis cases are caused by Listeria monocytogenes serotypes 1/2a, 1/2b and 4b strains. As an alternative to antigen-antibody based serotyping, a PCR-based method for serogrouping has been developed and validated. In this communication, we report an in-depth analysis of five 4b variant strains, four clinical isolates from Australia and one environmental isolate from USA. Although these five strains were serotype 4b by classical serotyping method, the serogrouping PCR profiles of these strains show the presence of a 1/2a-3a specific amplicon in addition to the standard 4b-4d-4e specific amplicons. These strains were further analyzed by pulsed field gel electrophoresis, binary gene typing, multi-locus variable-number-tandem-repeat analysis and a high density pan-genomic Listeria microarray. Using these sub-typing results, the clinical isolates were grouped into two distinct genomic groups- one of which could be part of an unidentified outbreak. The microarray results when compared with our database of other 4b outbreak isolates indicated that the serotype 4b variant strains represent very different genotypic profiles than the known reported 4b outbreak strains representing major epidemic clones. The acquisition of serotype 1/2a gene clusters by the 4b variant strains appears to be independent in origin, spanning large areas of geographical and temporal space and may indicate predisposition of some 4b strains towards accepting DNA from related organisms.