Whole-genome sequencing reveals genomic characterization of Listeria monocytogenes from food in China

IntroductionListeria monocytogenes is a foodborne bacterium that could persist in food and food processing environments for a long time. Understanding the population structure and genomic characterization of foodborne L. monocytogenes is essential for the prevention and control of listeriosis.MethodsA total of 322 foodborne L. monocytogenes isolates from 13 geographical locations and four food sources in China between 2000 and 2018 were selected for whole-genome sequencing.ResultsIn silico subtyping divided the 322 isolates into five serogroups, 35 sequence types (STs), 26 clonal complexes (CCs) and four lineages. Serogroup IIa was the most prevalent serogroup and ST9 was the most prevalent ST of foodborne L. monocytogenes strains isolated in China. The in-depth phylogenetic analysis on CC9 revealed that ST122 clone might be original from ST9 clone. Furthermore, 23 potentially relevant clusters were identified by pair-wised whole-genome single nucleotide polymorphism analysis, indicating that persistent- and/or cross-contamination had occurred in markets in China. ST8 and ST121 were the second and third top STs of L. monocytogenes in China, which had heterogeneity with that of L. monocytogenes isolates from other countries. The antibiotic resistance genes aacA4, tetM, tetS, dfrG carried by different mobile elements were found in L. monocytogenes strains. One lineage II strain carrying Listeria Pathogenicity Island 3 was first reported. In addition, a novel type of premature stop codon in inlA gene was identified in this study.DiscussionThese findings revealed the genomic characteristics and evolutionary relationship of foodborne L. monocytogenes in China on a scale larger than previous studies, which further confirmed that whole-genome sequencing analysis would be a helpful tool for routine surveillance and source-tracing investigation

The Isolation, Genetic Analysis and Biofilm Characteristics of <i>Listeria</i> spp. from the Marine Environment in China

Listeria monocytogenes is an important pathogen that can cause listeriosis. Despite the growing recognition of Listeria spp. as a foodborne and environmental pathogen, the understanding of its prevalence and characteristics of Listeria spp. in the marine environment remains unknown. In this study, we first investigated the genetic and phenotypic characteristics of Listeria species isolated in a coastal city in China. The findings revealed that the sequence type 87 (ST87) L. monocytogenes, a prevalent clinical and seafood strain in China, dominates in recreational beach sands and possesses a notable biofilm-forming capacity in seawater. The presence of ST87 L. monocytogenes in coastal environments indicates the potential health risks for both recreational activities and seafood consumption. Moreover, the ST121 isolates from sand had a versatile plasmid encoding multifunctional genes, including uvrX for UV resistance, gbuC for salt resistance, and npx for oxidative resistance and multiple transposases, which potentially aid in survival under natural environments. Black-headed gulls potentially facilitate the spread of L. monocytogenes, with similar ST35 strains found in gulls and beach sand. As a reservoir of microbes from marine environments and human/animal excrement, coastal sand would play an important role in the spread of L. monocytogenes and is an environmental risk for human listeriosis

Table_1_The population structure and genetic diversity of Listeria monocytogenes ST9 strains based on genomic analysis.XLSX

Listeria monocytogenes is a ubiquitous foodborne pathogen causing both invasive and non-invasive listeriosis. Sequence type (ST) 9 strains is common in food and food processing environments. In this study, the whole-genome sequences (WGS) of 207 ST9 isolates from different sources, geographical locations (14 countries), and isolated years were analyzed. The ST9 isolates were divided into three clusters after phylogenetic analysis; 67.63% of ST9 isolates contained putative plasmids with different sizes and genomic structure, the putative prophages inserted in the chromosome at ten hotspots, and seven types of premature stop codon (PMSC) mutations in inlA were found in 81.86% of the ST9 isolates. In addition, 78.26% of ST9 isolates harbored Tn554-like elements carrying arsenic resistance genes. All the ST9 isolates conservatively contained environment-resistance genes on the chromosome. This analysis of population structures and features of ST9 isolates was aimed to help develop effective strategies to control this prevalent pathogen in the food chain.</p

Data_Sheet_2_The population structure and genetic diversity of Listeria monocytogenes ST9 strains based on genomic analysis.PDF

Listeria monocytogenes is a ubiquitous foodborne pathogen causing both invasive and non-invasive listeriosis. Sequence type (ST) 9 strains is common in food and food processing environments. In this study, the whole-genome sequences (WGS) of 207 ST9 isolates from different sources, geographical locations (14 countries), and isolated years were analyzed. The ST9 isolates were divided into three clusters after phylogenetic analysis; 67.63% of ST9 isolates contained putative plasmids with different sizes and genomic structure, the putative prophages inserted in the chromosome at ten hotspots, and seven types of premature stop codon (PMSC) mutations in inlA were found in 81.86% of the ST9 isolates. In addition, 78.26% of ST9 isolates harbored Tn554-like elements carrying arsenic resistance genes. All the ST9 isolates conservatively contained environment-resistance genes on the chromosome. This analysis of population structures and features of ST9 isolates was aimed to help develop effective strategies to control this prevalent pathogen in the food chain.</p

Data_Sheet_1_The population structure and genetic diversity of Listeria monocytogenes ST9 strains based on genomic analysis.PDF

Listeria monocytogenes is a ubiquitous foodborne pathogen causing both invasive and non-invasive listeriosis. Sequence type (ST) 9 strains is common in food and food processing environments. In this study, the whole-genome sequences (WGS) of 207 ST9 isolates from different sources, geographical locations (14 countries), and isolated years were analyzed. The ST9 isolates were divided into three clusters after phylogenetic analysis; 67.63% of ST9 isolates contained putative plasmids with different sizes and genomic structure, the putative prophages inserted in the chromosome at ten hotspots, and seven types of premature stop codon (PMSC) mutations in inlA were found in 81.86% of the ST9 isolates. In addition, 78.26% of ST9 isolates harbored Tn554-like elements carrying arsenic resistance genes. All the ST9 isolates conservatively contained environment-resistance genes on the chromosome. This analysis of population structures and features of ST9 isolates was aimed to help develop effective strategies to control this prevalent pathogen in the food chain.</p

Data_Sheet_4_The population structure and genetic diversity of Listeria monocytogenes ST9 strains based on genomic analysis.PDF

Listeria monocytogenes is a ubiquitous foodborne pathogen causing both invasive and non-invasive listeriosis. Sequence type (ST) 9 strains is common in food and food processing environments. In this study, the whole-genome sequences (WGS) of 207 ST9 isolates from different sources, geographical locations (14 countries), and isolated years were analyzed. The ST9 isolates were divided into three clusters after phylogenetic analysis; 67.63% of ST9 isolates contained putative plasmids with different sizes and genomic structure, the putative prophages inserted in the chromosome at ten hotspots, and seven types of premature stop codon (PMSC) mutations in inlA were found in 81.86% of the ST9 isolates. In addition, 78.26% of ST9 isolates harbored Tn554-like elements carrying arsenic resistance genes. All the ST9 isolates conservatively contained environment-resistance genes on the chromosome. This analysis of population structures and features of ST9 isolates was aimed to help develop effective strategies to control this prevalent pathogen in the food chain.</p

Data_Sheet_3_The population structure and genetic diversity of Listeria monocytogenes ST9 strains based on genomic analysis.PDF

Listeria monocytogenes is a ubiquitous foodborne pathogen causing both invasive and non-invasive listeriosis. Sequence type (ST) 9 strains is common in food and food processing environments. In this study, the whole-genome sequences (WGS) of 207 ST9 isolates from different sources, geographical locations (14 countries), and isolated years were analyzed. The ST9 isolates were divided into three clusters after phylogenetic analysis; 67.63% of ST9 isolates contained putative plasmids with different sizes and genomic structure, the putative prophages inserted in the chromosome at ten hotspots, and seven types of premature stop codon (PMSC) mutations in inlA were found in 81.86% of the ST9 isolates. In addition, 78.26% of ST9 isolates harbored Tn554-like elements carrying arsenic resistance genes. All the ST9 isolates conservatively contained environment-resistance genes on the chromosome. This analysis of population structures and features of ST9 isolates was aimed to help develop effective strategies to control this prevalent pathogen in the food chain.</p

Risk Factors and Level of Listeria monocytogenes Contamination of Raw Pork in Retail Markets in China

Listeria monocytogenes can contaminate various foods via food processing environments and contamination of raw materials. There is a limited understanding of L. monocytogenes transmission in retail market and the role of insects in L. monocytogenes transmission in the retail environments. To better understand the risk factors of raw pork contamination, the prevalence of L. monocytogenes was examined in raw pork, retail environments and insects in a retail market over a 6-month period from March to August in 2016 in Beijing, China. A total of 2,789 samples were collected, including 356 raw pork samples, 1,392 meat contact surface swabs (MCS), 712 non-meat contact surface swabs (NMCS) and 329 insect samples. Overall, 424 (15.20%) of the samples were found to be contaminated by L. monocytogenes. Analyzed by serotyping, multilocus sequence typing and pulsed-field gel electrophoresis, the 424 L. monocytogenes isolates were divided into three serotypes (1/2c, 1/2a and 3a), 15 pulsotypes (PTs) and nine sequence types (STs), 1/2c/PT4/ST9 (244/424, 58%) was the most prevalent type of L. monocytogenes strains. The raw pork, MCS of the environments and insects were contaminated with higher levels of L. monocytogenes than NMCS of the environments, which suggested that cross contamination of L. monocytogenes between raw pork and the environment existed in the retail market, and long-term contaminated surfaces and vector insects would act as high risk factors to transmit L. monocytogenes to raw pork. Thus more effective strategies are needed to reduce the risk of retail pork meat contamination by L. monocytogenes and prevent foodborne human listeriosis

Image_1_Risk Factors and Level of Listeria monocytogenes Contamination of Raw Pork in Retail Markets in China.tif

<p>Listeria monocytogenes can contaminate various foods via food processing environments and contamination of raw materials. There is a limited understanding of L. monocytogenes transmission in retail market and the role of insects in L. monocytogenes transmission in the retail environments. To better understand the risk factors of raw pork contamination, the prevalence of L. monocytogenes was examined in raw pork, retail environments and insects in a retail market over a 6-month period from March to August in 2016 in Beijing, China. A total of 2,789 samples were collected, including 356 raw pork samples, 1,392 meat contact surface swabs (MCS), 712 non-meat contact surface swabs (NMCS) and 329 insect samples. Overall, 424 (15.20%) of the samples were found to be contaminated by L. monocytogenes. Analyzed by serotyping, multilocus sequence typing and pulsed-field gel electrophoresis, the 424 L. monocytogenes isolates were divided into three serotypes (1/2c, 1/2a and 3a), 15 pulsotypes (PTs) and nine sequence types (STs), 1/2c/PT4/ST9 (244/424, 58%) was the most prevalent type of L. monocytogenes strains. The raw pork, MCS of the environments and insects were contaminated with higher levels of L. monocytogenes than NMCS of the environments, which suggested that cross contamination of L. monocytogenes between raw pork and the environment existed in the retail market, and long-term contaminated surfaces and vector insects would act as high risk factors to transmit L. monocytogenes to raw pork. Thus more effective strategies are needed to reduce the risk of retail pork meat contamination by L. monocytogenes and prevent foodborne human listeriosis.</p