Mining of novel species-specific primers for PCR detection of Listeria monocytogenes based on genomic approach

Prevalence and antimicrobial resistance profile of Listeria spp. isolated from raw fish

BACKGROUND

Listeria spp. contamination in food, particularly antimicrobial-resistant strains, poses an escalating concern for public health. This study investigated the prevalence and antimicrobial resistance profiles of Listeria spp. isolated from raw fish collected from diverse sources in Northern Poland.

METHODS

A total of 750 raw fish samples were collected from standing freshwater tanks, flowing freshwater reservoirs, and a saltwater reservoir. Isolation was performed following the standard protocol, which describes the horizontal method for detecting Listeria spp., including Listeria monocytogenes. The antimicrobial resistance profiles of isolated strains were performed using the disk diffusion method. Antimicrobial resistance genes were identified using PCR, targeting 11 genes associated with resistance to β-lactams, macrolides, glycopeptides, and sulfonamides. Statistical analyses included Phi correlation coefficients, hierarchical clustering, and logistic regression to examine associations between phenotypic resistance patterns and antimicrobial resistance genes.

RESULTS

Listeria spp. was isolated from 13.9% of samples (104 positive samples), comprising L. seeligeri (34.6%), L. welshimeri (28.8%), L. monocytogenes (23.1%), and L. innocua (13.5%). Phenotypic antimicrobial susceptibility testing revealed universal resistance to oxacillin (100%) across all Listeria spp. isolates. High resistance levels were also observed for cefotaxime (97.1%), cefoxitin (92.3%), rifampicin (92.3%), clindamycin (96.2%), and trimethoprim-sulfamethoxazole (91.3%). Alarmingly, 98.1% of all Listeria spp. isolates exhibited multidrug resistance (MDR), reaching 100% MDR among L. monocytogenes isolates. Specifically, L. monocytogenes isolates exhibited complete resistance to meropenem, cefoxitin, cefotaxime, rifampicin, and trimethoprim-sulfamethoxazole, and significant resistance to ciprofloxacin (91.7%), clindamycin (83.3%), tetracycline (75.0%), erythromycin (75.0%), benzylpenicillin (70.8%), and nitrofurantoin (70.8%). Molecular analysis identified blaTEM (100%), ampC (37.5%), and ereB (37.5%) as the most prevalent antimicrobial resistance genes in L. monocytogenes.

CONCLUSIONS

The exceptionally high prevalence of multidrug-resistant Listeria spp., particularly L. monocytogenes, in raw fish underscores a critical public health risk, suggesting the urgent need for ongoing surveillance and robust risk mitigation strategies in aquaculture and seafood processing. The elevated antimicrobial resistance levels may also indicate aquatic environmental contamination, warranting further investigation into the sources and broader ecological implications of antimicrobial resistance in these ecosystems.

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.

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.

Rapid-Response Magnetic Enrichment Strategy for Significantly Improving Sensitivity of Multiplex PCR Analysis of Pathogenic Listeria Species

Listeria monocytogenes and Listeria ivanovii are important pathogenic Listeria spp. that cause infections in humans and animals. Establishing a rapid and sensitive method for the simultaneous screening of pathogenic Listeria spp. is of great significance for ensuring food safety. Multiplex polymerase chain reaction (mPCR) has been extensively reported to simultaneously detect several pathogens in food with high sensitivity, but a time-consuming pre-enrichment process is necessary. In this study, we report the usage of surface-modified polyethyleneimine-coated positively charged magnetic nanoparticles (PEI-MNPs) for rapid enrichment of pathogenic Listeria spp. through electrostatic interactions. The enrichment process takes only 10 min with high capture efficiency (more than 70%) at a wide pH range and ionic strength. Combined with mPCR analysis, the PEI-MNPs-mPCR strategy can simultaneously, rapidly, and sensitively detect pathogenic Listeria spp. without a time-consuming pre-concentration process. Under the optimal conditions, the detection limits of L. monocytogenes and L. ivanovii in lettuce were both as low as 101 CFU/mL, which was a hundred times lower than that without magnetic enrichment. In conclusion, the magnetic enrichment strategy based on charge interaction combined with mPCR analysis has great application potential in shortening the pre-concentration time of foodborne pathogens and improving the detection sensitivity.

Mining of novel target genes through pan-genome analysis for multiplex PCR differentiation of the major Listeria monocytogenes serotypes

The abundant information provided by the pan-genome analysis approach reveals the diversity among Listeria monocytogenes serotypes. The objective of this study was to mine novel target genes using pan-genome analysis for multiplex PCR detection and differentiation of the major L. monocytogenes serotypes present in food. Pan-genome analysis and PCR validation revealed a total of 10 specific targets: one for lineage I, two for serogroup I.1, one for serogroup I.2, two for lineage II, one for serogroup II.1, three for lineage III. Primers for the novel targets were highly specific in individual reactions. The detection limits were 10³-10⁴ colony-forming units (CFU)/mL in pure bacterial cultures, meeting the requirements of molecular detection. Based on these novel targets, two new "lineage" multiplex PCR assays were developed to simultaneously distinguish between three lineages (I, II, and III) and five major serotypes (1/2a, 1/2b, 1/2c, 4b, and 4c) of L. monocytogenes. The detection limits of lineage I and lineage II&III mPCRs were 0.771 pg/μL and 1.76 pg/μL genomic DNA, respectively. The specificity of the mPCRs was robustly verified using other L. monocytogenes and non-L. monocytogenes serotypes. These results suggest that the two "lineage" multiplex PCRs based on novel targets offer a promising approach for accurate, sensitive, and rapid identification of L. monocytogenes serotypes.

Chronic intramammary infection by Listeria monocytogenes in a clinically healthy goat - a case report

BACKGROUND

Listeria monocytogenes is a ubiquitous Gram-positive bacterium responsible for a severe foodborne disease in humans, and contaminated dairy products can be an important source of infection. Typically, infected dairy ruminants show clinical manifestations including encephalitis, septicemia, abortion, and diarrhea, but may also become asymptomatic carriers and shed L. monocytogenes in the feces acting as an important source of viable bacteria. Isolation from individual goat milk has been documented very rarely, and chronic, asymptomatic intramammary infection by L. monocytogenes with continuous milk shedding of viable bacteria has never been described in this dairy species.

CASE PRESENTATION

At the routine controls, cheese and bulk milk were positive for L. monocytogenes in a herd of 200 lactating Alpine goats, but none showed clinical signs of listeriosis. Individual milk was subjected to bacterial culture and a clinically healthy goat was identified as affected by a chronic intramammary infection (IMI) by L. monocytogenes. The goat had never shown clinical signs of mastitis or other diseases. Her right half-udder milk was positive to L. monocytogenes in two consecutive samples collected one week apart, as demonstrated by bacterial culture and molecular analysis. Mammary tissues collected after culling were also positive to L. monocytogenes by culture. Histological examination highlighted a chronic interstitial mastitis with leukocyte infiltration, atrophy of the alveoli and presence of corpora amylacea. Immunohistochemistry (IHC) and immunofluorescence (IF) confirmed the presence of high numbers of bacteria in the lumen of mammary alveoli, with intracellular bacteria mainly located in macrophages, but also present in neutrophils and epithelial cells. After culling of the positive goat, bulk tank milk tested negative to L. monocytogenes at the following controls.

CONCLUSION

This study demonstrates that L. monocytogenes can establish a chronic, subclinical IMI in goats with high numbers of bacteria shed in milk, representing a source of contamination for the herd and its dairy products. This underscores the importance of frequently monitoring all dairy herds that sell directly milk and/or fresh cheese and indicates that a chronic L. monocytogenes IMI should also be considered as source of bacteria when bulk tank milk contamination is detected in a dairy goat farm.

Genomics-based Sensitive and Specific Novel Primers for Simultaneous Detection of Burkholderia glumae and Burkholderia gladioli in Rice Seeds

Panicle blight and seed rot disease caused mainly by Burkholderia glumae and Burkholderia gladioli is threatening rice cultivation worldwide. The bacteria have been reported as seed-borne pathogens from rice. Accurate detection of both pathogens on the seeds is very important for limiting the disease dissemination. Novel primer pairs targeting specific molecular markers were developed for the robust detection of B. glumae and B. gladioli. The designed primers were specific in detecting the target species with no apparent crossreactions with other related Burkholderia species at the expected product size. Both primer pairs displayed a high degree of sensitivity for detection of B. glumae and B. gladioli separately in monoplex PCR or simultaneously in duplex PCR from both extracted gDNA and directly preheated bacterial cell suspensions. Limit of detection was as low as 0.1 ng of gDNA of both species and 3.86 × 102 cells for B. glumae and 5.85 × 102 cells for B. gladioli. On inoculated rice seeds, the designed primers could separately or simultaneously detect B. glumae and B. gladioli with a detection limit as low as 1.86 × 103 cells per rice seed for B. glumae and 1.04 × 104 cells per rice seed of B. gladioli. The novel primers maybe valuable as a more sensitive, specific, and robust tool for the efficient simultaneous detection of B. glumae and B. gladioli on rice seeds, which is important in combating rice panicle blight and seed rot by early detection and confirmation of the dissemination of pathogen-free rice seeds.

Specific and Sensitive Primers Developed by Comparative Genomics to Detect Bacterial Pathogens in Grains

Accurate and rapid detection of bacterial plant pathogen is the first step toward disease management and prevention of pathogen spread. Bacterial plant pathogens Clavibacter michiganensis subsp. nebraskensis (Cmn), Pantoea stewartii subsp. stewartii (Pss), and Rathayibacter tritici (Rt) cause Goss's bacterial wilt and blight of maize, Stewart's wilt of maize and spike blight of wheat and barley, respectively. The bacterial diseases are not globally distributed and not present in Korea. This study adopted comparative genomics approach and aimed to develop specific primer pairs to detect these three bacterial pathogens. Genome comparison among target pathogens and their closely related bacterial species generated 15-20 candidate primer pairs per bacterial pathogen. The primer pairs were assessed by a conventional PCR for specificity against 33 species of Clavibacter, Pantoea, Rathayibacter, Pectobacterium, Curtobacterium. The investigation for specificity and sensitivity of the primer pairs allowed final selection of one or two primer pairs per bacterial pathogens. In our assay condition, a detection limit of Pss and Cmn was 2 pg/μl of genomic DNA per PCR reaction, while the detection limit for Rt primers was higher. The selected primers could also detect bacterial cells up to 8.8 × 10³ cfu to 7.84 × 10⁴ cfu per gram of grain seeds artificially infected with corresponding bacterial pathogens. The primer pairs and PCR assay developed in this study provide an accurate and rapid detection method for three bacterial pathogens of grains, which can be used to investigate bacteria contamination in grain seeds and to ultimately prevent pathogen dissemination over countries.