Case report: whole genome sequencing based investigation of maternal-neonatal listeriosis in Sichuan, China

Clinical and Genomic Characteristics of a Clinical Listeria Monocytogenes ST120 Isolate Recovered from a Pregnant Woman

Background

Maternal-fetal listeriosis, caused by Listeria monocytogenes, is a rare but serious infection. Herein, we report the clinical and genomic characteristics of a clinical L. monocytogenes ST120 isolate recovered from a pregnant woman.

Methods

The clinical symptoms and treatment in pregnant woman were described in detail. Whole genome sequencing (WGS) was performed on the L. monocytogenes isolate SJZ_LM001, and the genomic characterization of the isolate was deeply analyzed.

Results

The clinical symptoms in pregnant women were mainly fever, and the placenta experienced severe inflammation. The pregnant woman was treated with ampicillin for effective anti-infective therapy. Genomic analysis showed that isolate SJZ_LM001 is sequence type (ST) 120, belong to clonal complex (CC)8 and lineage II of L. monocytogenes. Additionally, the isolates SJZ_LM001 harbored a novel plasmid pSJZ_LM001, which carried arsenical resistance genes (arsACD and acr3), and cadmium resistance genes (cadAC). Drug susceptibility testing showed that the isolate SJZ-LM001 was susceptible to ampicillin, meropenem, penicillin, and cotrimoxazole.

Conclusion

This is the first to identify a clinical case of infection in a pregnant woman caused by ST120 L. monocytogenes in China. These findings could benefit our understanding of the genomic characteristics of L. monocytogenes, and the pregnancy-related listeriosis and providing early diagnosis and effective targeted treatment.

Listeriosis During Pregnancy: Maternal and Neonatal Consequences-A Case Report

Listeriosis is a rare but extremely dangerous infection for both mother and fetus. This pathogen can spread in humans' bodies by consumption of contaminated food. The main high-risk groups of people for being infected are immunosuppressed and especially pregnant women. We present a case of materno-neonatal listeriosis illustrating that empiric antimicrobial therapy of chorioamnionitis during labor and neonate postpartum can also cover listeriosis which was not diagnosed prior to obtaining cultures.

Genomic Characterization of a Clinical Listeria monocytogenes ST1 Isolate Recovered from the Blood Sample of a Woman with Third Trimester Stillbirth

Background

Listeria monocytogenes is a foodborne gram-positive bacterium which causes adverse pregnancy outcomes. Here, the genomic and phylogenetic characteristics of a L. monocytogenes isolate obtained from blood sample of a third trimester pregnant woman with stillbirth are investigated.

Methods

Whole genome DNA of L. monocytogenes ST1 was sequenced with HiSeq X Ten platform. The NCBI Prokaryotic Genome Annotation Pipeline was used to annotate the genome sequence. The sequence type (ST) and antimicrobial resistance genes were then identified. The core genome multilocus sequence typing (cgMLST) analysis with other closely related L. monocytogenes stored in the NCBI GenBank database was performed using BacWGSTdb 2.0.

Results

The complete genome sequence of L. monocytogenes ST1 is made up of 20 contigs totaling 2,914,725 bp, with 2886 protein-coding sequences and a GC content of 37.9%. Fosfomycin [fosX], Lincosamide antibiotic [lin] and peptide antibiotic [mprF] were discovered as antimicrobial resistance genes. In silico serogroup typing prediction revealed that L. monocytogenes ST1 belonged to serotype IVb. The closest relative of L. monocytogenes ST1, obtained from Poland in 2015, differs by only 15 cgMLST alleles.

Conclusion

We identified a L. monocytogenes ST1 strain from blood sample of a woman with third trimester stillbirth in China. These discoveries would aid in our understanding of the genomic characteristics, mechanisms of antimicrobial resistance, and epidemiological features of this pathogen.

Phenotypic, chemical component and molecular assessment of genetic diversity and population structure of Morinda officinalis germplasm

Background

Morinda officinalis How (MO) is a perennial herb distributed in tropical and subtropical regions, which known as one of the “Four Southern Herbal Medicines”. The extent of genetic variability and the population structure of MO are presently little understood. Here, nine morphological traits, six chemical components and Single nucleotide polymorphism (SNP) markers were used in integrative research of MO germplasm variation among 88 individuals collected from ten populations across four geographical provinces of China.

Results

Both phenotype and chemical composition have significant genetic variation, and there is a certain correlation between them such as root diameter and the nystose content, as well as geographical distribution. The principal component analysis (PCA) showed the leaf length, leaf width, nystose, 1^F-furanosaccharide nystose, and the section color were the major contributors to diversity. The cluster analysis based on phenotypic and oligosaccharide data distinguished three significant groups, which was consistent with the result of a corresponding analysis with 228,615 SNP markers, and importantly, they all showed a significant correlation with geographical origin. However, there was little similarity between two cluster results. The Shannon’s information index (I) varied from 0.17 to 0.53 with a mean of 0.37, suggesting a high level of genetic diversity in MO populations, which mainly existed among individuals within populations, accounting for 99.66% of the total according to the analysis of molecular variance (AMOVA) results. Each population also maintains the connection because of certain gene communication, so that the genetic differentiation between populations was not very significant. The STRUCTURE software was used to analyse the population structure and the result showed that 88 accessions were clustered into three groups, and 67% of them were pure type, which was also confirmed through PCA.

Conclusions

The comprehensive study of phenotypic, chemical and molecular markers will provide valuable information for future breeding plans and understanding the phylogenetic relationship of MO population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08817-w.

Dissecting Listeria monocytogenes Persistent Contamination in a Retail Market Using Whole-Genome Sequencing

Listeria monocytogenes is a foodborne pathogen that can cause invasive disease with high mortality in immunocompromised individuals and can survive in a variety of food-associated environments for a long time. L. monocytogenes clonal complex (CC) 87 is composed of ST87 and three other STs and has been identified as the most common subgroup associated with both foods and human clinical infections in China. Therefore, the persistence of CC87 L. monocytogenes in food-associated environments poses a significant concern for food safety. In this study, 83 draft genomes of CC87 L. monocytogenes, including 60 newly sequenced genomes, were analyzed with all isolates from our previous surveillance in Zigong, Sichuang, China. Sixty-eight of the studied isolates were isolated from one retail market (M1 market), while the others were from seven other markets (M2–M8 markets) in the same city. Whole-genome multilocus sequence typing (wg-MLST) and the whole-genome single nucleotide polymorphism (wg-SNP) analysis were performed. Three persistent contamination routes were identified in the M1 market, caused by 2 clusters (A and B) and a wgST31 type. Cluster A isolates were associated with the persistent contamination in a raw meat stall (M1-S77), while Cluster B isolates caused a persistent contamination in aquatic foods stalls. Five wgST31 isolates caused persistent contamination in a single aquatic stall (M1-S65). A pLM1686-like plasmid was found in all Cluster A isolates. A novel plasmid, pLM1692, a truncated pLM1686 plasmid without the cadmium, and other heavy metal resistance genes were conserved in all wgST31 isolates. By comparing persistent and putative non-persistent isolates, four genes that were all located in the prophage comK might be associated with persistence. These findings enhanced our understanding of the underlying mechanisms of contamination and assist in formulating targeted strategies for the prevention and control of L. monocytogenes transmission from the food processing chain to humans.

IMPORTANCE Contamination of food by Listeria monocytogenes at retail level leads to potential consumption of contaminated food with high risk of human infection. Our previous study found persistent contamination of CC87 L. monocytogenes from a retail market in China through pulsed-field gel electrophoresis and multilocus sequence typing. In this study, whole-genome sequencing was used to obtain the highest resolution inference of the source and reasons for persistent contamination; meat grinders and minced meat were the major reservoir of persistent contamination in meat stalls, whereas fishponds were the major reservoir in seafood stalls, with different L. monocytogenes isolates involved. These isolates carried different properties such as plasmids and prophages, which may have contributed to their ability to survive or adapt to the different environments. Our findings suggest that whole-genome sequencing will be an effective surveillance tool to detect persistent L. monocytogenes contamination in retail food markets and to design new control strategies to improve food safety.

A Whole Genome Sequencing-Based Epidemiological Investigation of a Pregnancy-Related Invasive Listeriosis Case in Central Italy

Listeriosis is currently the fifth most common foodborne disease in Europe. Most cases are sporadic; however, outbreaks have also been reported. Compared to other foodborne infections, listeriosis has a modest incidence but can cause life-threatening complications, especially in elderly or immunocompromised people and pregnant women. In the latter case, the pathology can be the cause of premature birth or spontaneous abortion, especially if the fetus is affected during the first months of gestation. The causative agent of listeriosis, Listeria monocytogenes, is characterized by the innate ability to survive in the environment and in food, even in adverse conditions and for long periods. Ready-to-eat food represents the category most at risk for contracting listeriosis. This study presents the result of an investigation carried out on a case of maternal-fetal transmission of listeriosis which occurred in 2020 in central Italy and which was linked, with a retrospective approach, to other cases residing in the same city of the pregnant woman. Thanks to the use of next-generation sequencing methodologies, it was possible to identify an outbreak of infection, linked to the consumption of ready-to-eat sliced products sold in a supermarket in the investigated city.

Clinical and Laboratory Characteristics of Patients infected by Listeria monocytogenes at a Tertiary Hospital in Hefei City, China

Background

Human listeriosis is a severe foodborne infection caused by Listeria monocytogenes and the data of patients with this infection are largely limited for the Hefei population.

Purpose

This is a retrospective study that evaluated the clinical and laboratory data of patients with listeriosis at a tertiary hospital in Hefei City.

Patients and Methods

A total of 24 listeriosis patients were admitted to the First Affiliated Hospital of Anhui Medical University from January 2003 to July 2021. Data from all patients were collected from the hospital’s electronic medical records.

Results

The most common symptom of all patients was fever (91.7%), followed by altered consciousness (50.0%), rashes (45.8%), respiratory distress symptoms (37.5%), nuchal rigidity (29.2%), and headaches (20.8%). Laboratory results also indicated elevated C-reactive protein (CRP) (79.1%), hypoproteinemia (75.0%), anemia (62.5%), leukocytosis (45.8%), and neutrophilia (45.8%). The mean value of 5.1 μg/mL (SD, 3.8) for D‐dimer (D‐D) was significantly higher than the normal value ((0.00–0.50) μg/mL), while both altered consciousness (6 vs 4, P = 0.034) and headaches (4 vs 1, P = 0.036) occurred more frequently in the neurolisteriosis group compared with the bacteremia one. Additionally, the mean maximal body temperature (°C) (40.5 ± 0.7) as well as white blood cell (WBC) (15.3 vs 7.5 ×10⁹/L, P = 0.014) and neutrophil (NEUT#) (13.2 vs 6.1 ×10⁹/L, P = 0.026) counts of neurolisteriosis patients were higher than those of bacteremia (39.4 ± 0.4) (P = 0.001). Of all patients, four (50%) from the maternal-neonatal group remained uncured.

Conclusion

Listeriosis is a rare disease with extremely variable clinical characteristics in Hefei City. Our data indicated that unexplained fever, altered consciousness, hypoproteinemia, anemia, elevated CRP and DD should be considered to assist diagnosis of listeriosis for early treatment interventions.

Plasmidome of Listeria spp.-The repA-Family Business

Bacteria of the genus Listeria (phylum Firmicutes) include both human and animal pathogens, as well as saprophytic strains. A common component of Listeria spp. genomes are plasmids, i.e., extrachromosomal replicons that contribute to gene flux in bacteria. This study provides an in-depth insight into the structure, diversity and evolution of plasmids occurring in Listeria strains inhabiting various environments under different anthropogenic pressures. Apart from the components of the conserved plasmid backbone (providing replication, stable maintenance and conjugational transfer functions), these replicons contain numerous adaptive genes possibly involved in: (i) resistance to antibiotics, heavy metals, metalloids and sanitizers, and (ii) responses to heat, oxidative, acid and high salinity stressors. Their genomes are also enriched by numerous transposable elements, which have influenced the plasmid architecture. The plasmidome of Listeria is dominated by a group of related replicons encoding the RepA replication initiation protein. Detailed comparative analyses provide valuable data on the level of conservation of these replicons and their role in shaping the structure of the Listeria pangenome, as well as their relationship to plasmids of other genera of Firmicutes, which demonstrates the range and direction of flow of genetic information in this important group of bacteria.

Function and distribution of the conjugative plasmid pLM1686 in foodborne Listeria monocytogenes in China

Listeria monocytogenes, a fatal foodborne pathogen has the extraordinary capacity to survive in harsh conditions and is a potential threat to public health. A novel 91 kb plasmid pLM1686 was found in the prevalent L. monocytogenes sequence type (ST) 87 strain in China. In this study, the function and distribution of pLM1686 were firstly investigated in L. monocytogenes. The results showed plasmid pLM1686 had self-transmissible ability and existed in various types of L. monocytogenes isolates belonging to two lineages (lineage I and II), four serotypes (1/2b, 3b, 1/2c and 1/2a) and four STs (ST87, ST59, ST9 and ST120). The wild strain LM1686 and transconjugant strain 10403S_P1686 exhibited significantly higher growth rate and biofilm formation in Modification of Welshimer's medium (MWB), greater salinity tolerance, stronger cell invasion and higher cytotoxicity than plasmid-cured strain and reference strain 10403S. Moreover, plasmid curing caused the loss of cadmium resistance of strain, and the recipient strain acquired cadmium resistance after conjugation. Thus, pLM1686 would provide L. monocytogenes advantages of surviving in adverse environments.

An Update Review on Listeria Infection in Pregnancy

Listeria monocytogenes (LM) is an intracellular, aerobic and facultative anaerobic, Gram-positive bacterium, which is primarily transmitted to humans orally via food. LM could occur in asymptomatic pregnant women; however, fetal infection is a serious condition, entailing premature birth, abortion, sepsis, central nervous system (CNS) involvement, or even death. If a pregnant woman exhibits symptoms, the performance is almost like influenza, such as fever, headache, diarrhea, myalgia, or other digestive-related symptoms. This review collected clinical and empirical results regarding the mechanism, clinical manifestations, obstetrical outcome, diagnosis, treatment, vertical transmission, neonatal infection, and prevention of listeriosi according to articles published in PubMed from January 1, 1980, to March 20, 2021. The early detection and diagnosis of pregnancy-associated listeriosis are significant since sensitive antibiotics are effective at enhancing the prognosis of newborns. Listeriosis can be diagnosed using positive cultures from maternal or neonatal blood, neonatal cerebrospinal fluid (CSF), amniotic fluid, intrauterine mucosa, or the placenta. Two weeks of high-dose intravenous amoxicillin (more than 6 g/day) is recommended for LM pregnant women without allergy. Terminating the pregnancy to save the mother’s life should be considered if maternal and fetal conditions aggravate. Neonatal Listeria infection is primarily transmitted through the placenta, which is a critical illness associated with a high mortality rate. The necessary dietary guidance for pregnant women can reduce the incidence rate of pregnancy-related listeriosis.

Maternal-neonatal listeriosis

Listeriosis is a rare and severe foodborne infection caused by Listeria monocytogenes. It manifests as septicemia, neurolisteriosis, and maternal-fetal infection. In pregnancy, it may cause maternal fever, premature delivery, fetal loss, neonatal systemic and central nervous system infections. Maternal listeriosis is mostly reported during the 2nd and 3rd trimester of pregnancy, as sporadic cases or in the context of outbreaks. Strains belonging to clonal complexes 1, 4 and 6, referred to as hypervirulent, are the most associated to maternal-neonatal infections. Here we review the clinical, pathophysiological, and microbiological features of maternal-neonatal listeriosis.

10-Year Molecular Surveillance of Listeria monocytogenes Using Whole-Genome Sequencing in Shanghai, China, 2009-2019

Listeria monocytogenes is an etiologic agent of listeriosis, and has emerged as an important foodborne pathogen worldwide. In this study, the molecular characteristics of 155 L. monocytogenes isolates from seven food groups in Shanghai, the biggest city in China, were identified using whole-genome sequencing (WGS). Most L. monocytogenes isolates (79.3%) were obtained between May and October from 2009 to 2019. The serogroups and clonal complexes (CCs) of L. monocytogenes were found useful for identifying potential health risks linked to foods. Differences in distributions of serogroups and CCs among different food groups were analyzed using t-test. The results showed that the IIa and IVb serogroups were identified among most of food groups. However, the prevalence of serogroup IIb was significantly higher in ready-to-eat (RTE) food and raw seafood than in other food groups, similar to group IIc in raw meat and raw poultry than others. Meanwhile, the prevalence of CC9 in raw meat and raw poultry, CC8 in raw poultry, and CC87 in raw seafood significantly exceeded that of in other food groups. Specially, CC87 was the predominant CC in foodborne and clinical isolates in China, indicating that raw seafood may induce a high-risk to food safety. Also, hypervirulence pathogenicity islands LIPI-3 and LIPI-4 were found in CC3, CC1, and CC87, respectively. The clonal group CC619 carried LIPI-3 and LIPI-4, as previously reported in China. Core genome multilocus sequence typing (cgMLST) analysis suggested that CC87 isolates from the same food groups in different years had no allelic differences, indicating that L. monocytogenes could persist over years. These 10-year results in Shanghai underscore the significance of molecular epidemiological surveillance of L. monocytogenes in foodborne products in assessing the potential risk of this pathogen, and further address food safety issues in China.

Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China

Background

Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food products, food associated environments and sporadic listeriosis in China. Here, we performed a comparative genomic analysis of the L. monocytogenes ST87 clone by sequencing 71 strains representing a diverse range of sources, different geographical locations and isolation years.

Results

The core genome and pan genome of ST87 contained 2667 genes and 3687 genes respectively. Phylogenetic analysis based on core genome SNPs divided the 71 strains into 10 clades. The clinical strains were distributed among multiple clades. Four clades contained strains from multiple geographic regions and showed high genetic diversity. The major gene content variation of ST87 genomes was due to putative prophages, with eleven hotspots of the genome that harbor prophages. All strains carry an intact CRISRP/Cas system. Two major CRISPR spacer profiles were found which were not clustered phylogenetically. A large plasmid of about 90 Kb, which carried heavy metal resistance genes, was found in 32.4% (23/71) of the strains. All ST87 strains harbored the Listeria pathogenicity island (LIPI)-4 and a unique 10-open read frame (ORF) genomic island containing a novel restriction-modification system.

Conclusion

Whole genome sequence analysis of L. monocytogenes ST87 enabled a clearer understanding of the population structure and the evolutionary history of ST87 L. monocytogenes in China. The novel genetic elements identified may contribute to its virulence and adaptation to different environmental niches. Our findings will be useful for the development of effective strategies for the prevention and treatment of listeriosis caused by this prevalent clone.