Prevalence and transmission characteristics of Listeria species from ruminants in farm and slaughtering environments in China

Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest

Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.

IMPORTANCE

As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.

Listeriosis: Characteristics, Occurrence in Domestic Animals, Public Health Significance, Surveillance and Control

Listeriosis is a dangerous zoonosis caused by bacteria of the genus Listeria, with Listeria monocytogenes (LM) being the most pathogenic species. Listeria monocytogenes has been detected in various animal species and in humans, and its ability to evolve from an environmental saprophyte to a powerful intracellular pathogen is driven by the invasion mechanisms and virulence factors that enable cell invasion, replication and cell-to-cell spread. Key regulatory systems, including positive regulatory factor A (PrfA) and the stress-responsive sigma factor σB, control the expression of virulence genes and facilitate invasion of host cells. Listeriosis poses a significant threat to cattle, sheep and goat herds, leading to abortions, septicemia and meningoencephalitis, and ruminants are important reservoirs for Listeria, facilitating transmission to humans. Other Listeria species such as Listeria ivanovii and Listeria innocua can also cause disease in ruminants. Resilience of LM in food processing environments makes it an important foodborne pathogen that is frequently transmitted through contaminated meat and dairy products, with contamination often occurring along the food production chain. In humans, listeriosis primarily affects immunocompromised individuals, pregnant women and the elderly and leads to severe conditions, such as meningitis, septicemia and spontaneous abortion. Possible treatment requires antibiotics that penetrate the blood-brain barrier. Despite the relatively low antimicrobial resistance, multidrug-resistant LM strains have been detected in animals, food and the environment. Controlling and monitoring the disease at the herd level, along with adopting a One Health approach, are crucial to protect human and animal health and to minimize the potential negative impacts on the environment.

The Development and Application of Lyophilized LAMP Detection Reagent for Listeria monocytogenes

Listeria monocytogenes, a zoonotic foodborne pathogen, presents a significant threat to global public health. Therefore, rapid and sensitive detection methods are crucial in mitigating the spread of L. monocytogenes induced diseases. This study introduced a loop-mediated isothermal amplification (LAMP) lyophilized powder detection reagent specifically designed for identifying Listeria monocytogenes. The reagent is user-friendly, quick, and can be easily transported and stored at room temperature. It exhibits no cross-reactivity with eight other types of bacteria and boasts a sensitivity of 101 CFU/mL. In a comparative study of 30 samples, the LAMP lyophilized powder detection reagent demonstrated higher sensitivity than the commercial Listeria monocytogenes qPCR detection kit. Additionally, the experimental time was reduced by approximately 30 min, making it highly suitable for rapid diagnosis. Preparation of lyophilized LAMP reagents may facilitate large-scale deployment, particularly in endemic areas or regions facing rapid outbreaks. This could greatly aid in controlling the transmission of pathogens, especially those transmitted through food.

Surveillance and genetic characterization of Listeria monocytogenes in the food chain in Montenegro during the period 2014-2022

Introduction

Listeria monocytogenes is an ubiquitous foodborne pathogen that represents a serious threat to public health and the food industry.

Methods

In this study Whole Genome Sequencing (WGS) was used to characterize 160 L. monocytogenes isolates obtained from 22,593 different food sources in Montenegro during the years 2014-2022.

Results

Isolates belonged to 21 different clonal complexes (CCs), 22 sequence types (STs) and 73 core genome multilocus sequence types (cgMLST) revealing a high diversity. The most prevalent STs were ST8 (n = 29), ST9 (n = 31), ST121 (n = 19) and ST155 (n = 20). All isolates carried virulence genes (VGs), 111 isolates carried mobile genetic elements (MGEs) (ranging from 1 to 7 MGEs) and 101 isolates carried plasmids (ranging from 1 to 3 plasmids). All isolates carried the intrinsic resistance genes fosX and lin. None of the isolates carried acquired antimicrobial resistance genes (ARGs).

Discussion/conclusion

Continuous monitoring and surveillance of L. monocytogenes is needed for improving and ameliorating the public health.

A comparative study on the occurrence, genetic characteristics, and factors associated with the distribution of Listeria species on cattle farms and beef abattoirs in Gauteng Province, South Africa

These cross-sectional studies reported the occurrence, genetic characteristics, and factors associated with the distribution of Listeria species on cattle farms and beef abattoirs in Gauteng Province, South Africa. A total of 328 samples (faeces, feeds, silage, and drinking water) were collected from 23 cattle farms (communal, cow-calf, and feedlot), and 262 samples (faeces, carcass swabs, and effluents) from 8 beef abattoirs (low throughput and high throughput) were processed using standard bacteriological and molecular methods to detect Listeria species. The factors associated with the prevalence of Listeria species were investigated, and multiplex polymerase chain reaction (mPCR) was used to determine Listeria species, the pathogenic serogroups, and the carriage of eight virulence-associated genes by Listeria monocytogenes. The overall prevalence of Listeria species in cattle farms was 14.6%, comprising Listeria innocua (11.3%), Listeria monocytogenes (3.4%), Listeria welshimeri (0.0%) compared with 11.1%, comprising Listeria innocua (5.7%), Listeria monocytogenes (4.6%), Listeria welshimeri (0.8%) for beef abattoirs. Of the three variables (area, type of farm/abattoir, and sample type) investigated, only the sample types at abattoirs had a significant (P < 0.001) effect on the prevalence of L. innocua and L. welshimeri. The frequency of distribution of the serogroups based on 11 L. monocytogenes isolated from farms was 72.7% and 27.3% for the serogroup 1/2a-3a and 4b-4d-4e, respectively, while for the 12 L. monocytogenes isolates recovered from abattoirs, it was 25%, 8.3%, 50% and 16.7% for the serogroup 1/2a-3a, 1/2b-3b, 1/2c-3c, and 4b-4d-4e respectively (P < 0.05). All (100%) isolates of L. monocytogenes from the farms and abattoirs were positive for seven virulence genes (hlyA, inlB, plcA, iap, inlA, inlC, and inlJ). The clinical and food safety significance of the findings cannot be ignored.

Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals

Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.

A rapid and inexpensive nucleic acid detection platform for Listeria monocytogenes based on the CRISPR/Cas12a system

Listeria monocytogenes (LM) is an important foodborne pathogen that is associated with a high mortality rate. Currently, there is an urgent need for an inexpensive and rapid assay for the large-scale diagnosis and monitoring of LM. To meet these requirements, we designed a one-step, low-cost platform for the simultaneous amplification and detection of LM based on the CRISPR/Cas12a system with a micro-amplification (named Cas12a-MA). This method utilizes a combination of CRISPR/Cas12a and recombinase polymerase amplification (RPA) in the same vessel to provide a contamination-free platform for rapid nucleic acid detection with high specificity and ultra-sensitivity. In this study, we screened for three specific genes and selected the hly gene in LM as the final target. Our data showed that the number of amplification products plays a crucial role in the function of the CRISPR/Cas12a system. Our method was then further optimized for the specific detection of target DNA on 4.4 CFU/g in 25min. These assays successfully detected LM in spiked pork samples and natural meat samples (pork, beef, and mutton). All results indicate that Cas12a-MA shows great promise for foodborne pathogen detection.

The Importance of the Slaughterhouse in Surveilling Animal and Public Health: A Systematic Review

From the point of public health, the objective of the slaughterhouse is to guarantee the safety of meat in which meat inspection represent an essential tool to control animal diseases and guarantee the public health. The slaughterhouse can be used as surveillance center for livestock diseases. However, other aspects related with animal and human health, such as epidemiology and disease control in primary production, control of animal welfare on the farm, surveillance of zoonotic agents responsible for food poisoning, as well as surveillance and control of antimicrobial resistance, can be monitored. These controls should not be seen as a last defensive barrier but rather as a complement to the controls carried out on the farm. Regarding the control of diseases in livestock, scientific research is scarce and outdated, not taking advantage of the potential for disease control. Animal welfare in primary production and during transport can be monitored throughout ante-mortem and post-mortem inspection at the slaughterhouse, providing valuable individual data on animal welfare. Surveillance and research regarding antimicrobial resistance (AMR) at slaughterhouses is scarce, mainly in cattle, sheep, and goats. However, most of the zoonotic pathogens are sensitive to the antibiotics studied. Moreover, the prevalence at the slaughterhouse of zoonotic and foodborne agents seems to be low, but a lack of harmonization in terms of control and communication may lead to underestimate its real prevalence.

The Prevalence and Antibiotic-Resistant of Listeria monocytogenes in Livestock and Poultry Meat in China and the EU from 2001 to 2022: A Systematic Review and Meta-Analysis

To compare the prevalence and antibiotic resistance rate of Listeria monocytogenes in livestock and poultry (beef, pork and chicken) meat between China and the European Union (EU), a meta-analysis was conducted. Ninety-one out of 2156 articles in Chinese and English published between January 2001 and February 2022 were selected from four databases. The prevalence of L. monocytogenes in livestock and poultry (beef, pork and chicken) meat in China and Europe was 7.1% (3152/56,511, 95% CI: 5.8-8.6%) and 8.3% (2264/889,309, 95% CI: 5.9-11.0%), respectively. Moreover, a decreasing trend was observed in both regions over time. Regarding antibiotic resistance, for the resistance to 15 antibiotics, the pooled prevalence was 5.8% (95% CI: 3.1-9.1%). In both regions, the highest prevalence was found in oxacillin, ceftriaxone and tetracycline, and a large difference was reported between China and the EU in ceftriaxone (52.6% vs. 17.3%) and cefotaxime (7.0% vs. 0.0%). Based on the above, it remains a significant challenge to enforce good control measures against the meat-sourced L. monocytogenes both in China and in the EU.

Transmission Scenarios of Listeria monocytogenes on Small Ruminant On-Farm Dairies

Listeria monocytogenes can cause severe foodborne infections in humans and invasive diseases in different animal species, especially in small ruminants. Infection of sheep and goats can occur via contaminated feed or through the teat canal. Both infection pathways result in direct (e.g., raw milk from an infected udder or fresh cheese produced from such milk) or indirect exposure of consumers. The majority of dairy farmers produces a high-risk product, namely fresh cheese made from raw ewe's and goat's milk. This, and the fact that L. monocytogenes has an extraordinary viability, poses a significant challenge to on-farm dairies. Yet, surprisingly, almost no scientific studies have been conducted dealing with the hygiene and food safety aspects of directly marketed dairy products. L. monocytogenes prevalence studies on small ruminant on-farm dairies are especially limited. Therefore, it was our aim to focus on three main transmission scenarios of this important major foodborne pathogen: (i) the impact of caprine and ovine listerial mastitis; (ii) the significance of clinical listeriosis and outbreak scenarios; and (iii) the impact of farm management and feeding practices.

Genetic diversity and known virulence genes in Listeria innocua strains isolated from cattle abortions and farm environment

Listeria innocua is considered as non-pathogenic bacteria living in an environment although several cases of immunocompromised humans and ruminant listeriosis infections have been reported. Previously, L. innocua was identified as a potential pathogen and virulence in association with L. monocytogenes PrfA dependent virulence (LIPI-1) gene cluster was demonstrated in hemolytic L. innocua. L. innocua usually considered non-pathogenic versus pathogenic L. monocytogenes and L. ivanovii because of the main virulence gene loss. There are limited studies and reports available about L. innocua-caused illness in cattle. A total of 18 STs were identified in cattle abortions while 17 STs in the farm environment with majority of STs were present in both abortions and environmental samples. Genome sequencing showed that in one farm identical L. innocua clones were represented in water, feed, soil, and faeces sample groups, suggesting that animals most likely through the faecal shedding may remain as the main source of L. innocua in a farm environment. Out of all L. innocua isolates PrfA-dependent virulence genes were not found in aborted foetuses isolates and environmental L. innocua isolate groups; however, in 20% of isolates a complete LIPI-3 pathogenicity island encoding listeriolysin S was identified. In this study, we demonstrated that genetically diverse L. innocua clones were widely distributed in cattle farm environment and certain isolates had a significant pathogenicity potential for cattle, thus causing adverse health effects, including abortions.

Modelling the Adhesion and Biofilm Formation Boundary of Listeria monocytogenes ST9

Listeria monocytogenes is a major foodborne pathogen that can adhere to or form a biofilm on food contact surfaces, depending on the environmental conditions. The purpose of this work is to determine the adhesion and biofilm formation boundaries for L. monocytogenes ST9 under the combination environments of temperature (5, 15, and 25 °C), NaCl concentration (0%, 3%, 6%, and 9% (w/v)) and pH (5.0, 6.0, 7.0, and 8.0). The probability models of adhesion and biofilm formation were built using the logistic regression. For adhesion, only the terms of linear T and NaCl are significant for L. monocytogenes ST9 (p < 0.05), whereas the terms of linear T, NaCl, and pH, and the interaction between T and pH were significant for biofilm formation (p < 0.05). By analyzing contour maps and their surface plots for two different states, we discovered that high temperature promoted adhesion and biofilm formation, whereas excessive NaCl concentration inhibited both of them. With a stringent threshold of 0.1667, the accuracy rate for identifying both adhesion/no-adhesion and biofilm formation/no-biofilm formation events were 0.929, indicating that the probability models are reasonably accurate in predicting the adhesion and biofilm formation boundary of L. monocytogenes ST9. The boundary model may provide a useful way for determining and further controlling L. monocytogenes adhesion and biofilm formation in various food processing environments.

Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-associated hypervirulent clones: a longitudinal study in 19 farms

Studies have shown that ruminants constitute reservoirs of Listeria monocytogenes, but little is known about the epidemiology and genetic diversity of this pathogen within farms. Here we conducted a large-scale longitudinal study to monitor Listeria spp. in 19 dairy farms during three consecutive seasons (N = 3251 samples). L. innocua was the most prevalent species, followed by L. monocytogenes. Listeria monocytogenes was detected in 52.6% of farms and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was most prevalent in environmental samples. Sixty-one different L. monocytogenes cgMLST types were found, 28% common to different animals and/or surfaces within the same farm and 21% previously reported elsewhere in the context of food and human surveillance. Listeria monocytogenes prevalence was not affected by farm hygiene but by season: higher prevalence was observed during winter in cattle, and during winter and spring in sheep farms. Cows in their second lactation had a higher probability of L. monocytogenes faecal shedding. This study highlights dairy farms as a reservoir for hypervirulent L. monocytogenes.

Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-associated hypervirulent clones: a longitudinal study in 19 farms

Studies have shown that ruminants constitute reservoirs of Listeria monocytogenes, but little is known about the epidemiology and genetic diversity of this pathogen within farms. Here we conducted a large-scale longitudinal study to monitor Listeria spp. in 19 dairy farms during three consecutive seasons (N = 3251 samples). L. innocua was the most prevalent species, followed by L. monocytogenes. Listeria monocytogenes was detected in 52.6% of farms and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was most prevalent in environmental samples. Sixty-one different L. monocytogenes cgMLST types were found, 28% common to different animals and/or surfaces within the same farm and 21% previously reported elsewhere in the context of food and human surveillance. Listeria monocytogenes prevalence was not affected by farm hygiene but by season: higher prevalence was observed during winter in cattle, and during winter and spring in sheep farms. Cows in their second lactation had a higher probability of L. monocytogenes faecal shedding. This study highlights dairy farms as a reservoir for hypervirulent L. monocytogenes.

Whole Genome Analysis of Three Multi-Drug Resistant Listeria innocua and Genomic Insights Into Their Relatedness With Resistant Listeria monocytogenes

Listeria innocua are Gram-positive rod-shaped bacteria, which are not generally infectious as opposed to Listeria monocytogenes. However, the comparatively high genomic similarity between both along with on occasion, their coexistence in similar ecological niches may present the opportunity for resistance or virulence gene transfer. In this study, three multi-drug resistant L. innocua originally cultured from food were put forward for long-read genome sequencing. Chromosome and plasmid genomes were assembled and annotated. Analysis demonstrated that the resistant phenotypes correlated well with genotypes. Three plasmids pLI42, pLI203, and pLI47-1 were identified which harbor resistance islands. Sequence alignments suggested that plasmids pLI42 and pLI203 were highly similar to a previously sequenced L. monocytogenes plasmid pLR1. Similarly, another three types of resistance gene islands were observed on chromosome, including tet(M) gene islands (transposon Tn916 orthologs), dfrG gene islands and optrA-erm(A) gene islands. All three L. innocua isolates possessed listeria pathogenicity island-4 (LIPI-4) which is linked to cases of mengitis. Further genome environment and phylogenic analysis of regions flanking LIPI-4 of L. innocua and L. monocytogenes showed that these may have common origins and with the potential to transmit from the former. Our findings raise the possible need to include both L. monocytogenes and L. innocua in food surveillance programs so as to further understand of the origins of antimicrobial resistance and virulence markers of public health importance in L. monocytogenes.