scholarly journals Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments

Pathogens ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 822
Author(s):  
Hee Jin Kwon ◽  
Zhao Chen ◽  
Peter Evans ◽  
Jianghong Meng ◽  
Yi Chen
Keyword(s):  
Listeria Monocytogenes ◽  
Food Processing ◽  
Genetic Relatedness ◽  
Mobile Genetic Elements ◽  
Recent Common Ancestor ◽  
Nucleotide Substitution Rate ◽  
Genetic Elements ◽  
Most Recent Common Ancestor ◽  
Long Read ◽  
The U.S

Recently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of Listeria monocytogenes (Lm) epidemic clone II (ECII) from seven ready-to-eat meat or poultry processing facilities, not known to be associated with outbreaks, were shotgun sequenced, and among them, five isolates were further subjected to long-read sequencing. Additionally, 26 genomes of Lm ECII isolates associated with three listeriosis outbreaks in the U.S. and South Africa were obtained from the National Center for Biotechnology Information (NCBI) database and analyzed to evaluate if MGEs may be used as a high-resolution genetic marker for identifying and sourcing the origin of Lm. The analyses identified four comK prophages in 11 non-outbreak isolates from four facilities and three comK prophages in 20 isolates associated with two outbreaks that occurred in the U.S. In addition, three different plasmids were identified among 10 non-outbreak isolates and 14 outbreak isolates. Each comK prophage and plasmid was conserved among the isolates sharing it. Different prophages from different facilities or outbreaks had significant genetic variations, possibly due to horizontal gene transfer. Phylogenetic analysis showed that isolates from the same facility or the same outbreak always closely clustered. The time of most recent common ancestor of the Lm ECII isolates was estimated to be in March 1816 with the average nucleotide substitution rate of 3.1 × 10−7 substitutions per site per year. This study showed that complete MGE sequences provide a good signal to determine the genetic relatedness of Lm isolates, to identify persistence or repeated contamination that occurred within food processing environment, and to study the evolutionary history among closely related isolates.

Whole-genome analysis-based phylogeographic investigation of Streptococcus pneumoniae serotype 19A sequence type 320 isolates in Japan.

2021 ◽  
Author(s):  
Satoshi Nakano ◽  
Takao Fujisawa ◽  
Bin Chang ◽  
Yutaka Ito ◽  
Hideki Akeda ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Sampling Bias ◽  
Health Concern ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Identification Rate ◽  
Most Recent Common Ancestor ◽  
The Common ◽  
The U.S

After the introduction of the seven-valent pneumococcal conjugate vaccine, the global spread of multidrug resistant serotype 19A-ST320 strains became a public health concern. In Japan, the main genotype of serotype 19A was ST3111, and the identification rate of ST320 was low. Although the isolates were sporadically detected in both adults and children, their origin remains unknown. Thus, by combining pneumococcal isolates collected in three nationwide pneumococcal surveillance studies conducted in Japan between 2008 and 2020, we analyzed 56 serotype 19A-ST320 isolates along with 931 global isolates, using whole-genome sequencing to uncover the transmission route of the globally distributed clone in Japan. The clone was frequently detected in Okinawa Prefecture, where the U.S. returned to Japan in 1972. Phylogenetic analysis demonstrated that the isolates from Japan were genetically related to those from the U.S.; therefore, the common ancestor may have originated in the U.S. In addition, Bayesian analysis suggested that the time to the most recent common ancestor of the isolates form Japan and the U.S. was approximately the 1990s to 2000, suggesting the possibility that the common ancestor could have already spread in the U.S. before the Taiwan 19F-14 isolate was first identified in a Taiwanese hospital in 1997. The phylogeographical analysis supported the transmission of the clone from the U.S. to Japan, but the analysis could be influenced by sampling bias. These results suggested the possibility that the serotype 19A-ST320 clone had already spread in the U.S. before being imported into Japan.

scholarly journals Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Federica Palma ◽  
Thomas Brauge ◽  
Nicolas Radomski ◽  
Ludovic Mallet ◽  
Arnaud Felten ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Processing Plants ◽  
Seafood Processing

scholarly journals Evidence of an epidemic spread of KPC-producing Enterobacterales in Czech hospitals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lucie Kraftova ◽  
Marc Finianos ◽  
Vendula Studentova ◽  
Katerina Chudejova ◽  
Vladislav Jakubu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Infection Control ◽  
Mobile Genetic Elements ◽  
Epidemic Spread ◽  
Sequencing Data ◽  
Genetic Elements ◽  
Long Read ◽  
Genetic Rearrangements

AbstractThe aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018–2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the presence of several types of blaKPC-carrying plasmids; 19 out of 25 blaKPC-carrying plasmids could be assigned to R (n = 12), N (n = 5), C (n = 1) and P6 (n = 1) incompatibility (Inc) groups. Five of the remaining blaKPC-carrying plasmids were multireplicon, while one plasmid couldn’t be typed. Additionally, phylogenetic analysis confirmed the spread of blaKPC-carrying plasmids among different clones of diverse Enterobacterales species. Our findings demonstrated that the increased prevalence of KPC-producing isolates was due to plasmids spreading among different species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC-carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC-producing strains.

scholarly journals The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

2020 ◽  
Vol 10 (5) ◽  
pp. 1457-1467 ◽  
Author(s):  
Corrinne E. Grover ◽  
Mengqiao Pan ◽  
Daojun Yuan ◽  
Mark A. Arick ◽  
Guanjing Hu ◽  
...  
Keyword(s):  
De Novo ◽  
Diploid Species ◽  
Recent Common Ancestor ◽  
Linkage Drag ◽  
Cotton Production ◽  
Reniform Nematode ◽  
Most Recent Common Ancestor ◽  
A Genome ◽  
Long Read ◽  
Gossypium Longicalyx

Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx. This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed.

scholarly journals Diverse mobile genetic elements support the persistence of Listeria monocytogenes on dairy farms

2021 ◽  
Author(s):  
Hanna Castro ◽  
Francois Douillard ◽  
Hannu Korkeala ◽  
Miia Lindström
Keyword(s):  
Listeria Monocytogenes ◽  
Resistance Genes ◽  
Dairy Farms ◽  
Mobile Genetic Elements ◽  
Mobile Elements ◽  
Modification System ◽  
Genetic Elements ◽  
Restriction Modification System ◽  
Biocide Resistance ◽  
Potential Reservoir

Listeria monocytogenes is a food-borne pathogen and a resilient environmental saprophyte. Dairy farms are a reservoir of L. monocytogenes and strains can persist on farms for years. Here, we sequenced the genomes of 250 L. monocytogenes isolates to investigate the persistence and mobile genetic elements of Listeria inhabiting dairy farms. We found that prophages and other mobile elements were significantly more numerous among persistent than sporadically occurring strains. We identified a remarkable diversity of mobile elements among farm isolates, including a novel group of plasmids infecting hypervirulent subtypes of L. monocytogenes and occasionally carrying biocide resistance determinants bcrABC or qacH. Resistance genes against bacitracin, arsenic and cadmium were significantly more prevalent among persistent than sporadic strains. Several of the mobile elements in Listeria were identical to the mobile elements of Enterococci, indicative of recent transfer between these genera. Finally, we demonstrated that the CRISPR-cas IIa system and a type II restriction-modification system were negatively associated with persistence on farms. Our findings suggest that mobile elements support the persistence of L. monocytogenes on dairy farms and that L. monocytogenes inhabiting the agroecosystem is a potential reservoir of mobile elements harbouring resistance genes against antimicrobials, biocides, and heavy metals.

scholarly journals New kinship and FST estimates reveal higher levels of differentiation in the global human population

2019 ◽  
Author(s):  
Alejandro Ochoa ◽  
John D. Storey
Keyword(s):  
Population Structure ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Recent Common Ancestor ◽  
Human Populations ◽  
Population Genetic Analysis ◽  
Most Recent Common Ancestor ◽  
Complex Population ◽  
Population Structures ◽  
Modern Population

Kinship coefficients and FST, which measure genetic relatedness and the overall population structure, respectively, have important biomedical applications. However, existing estimators are only accurate under restrictive conditions that most natural population structures do not satisfy. We recently derived new kinship and FST estimators for arbitrary population structures [1, 2]. Our estimates on human datasets reveal a complex population structure driven by founder effects due to dispersal from Africa and admixture. Notably, our new approach estimates larger FST values of 26% for native worldwide human populations and 23% for admixed Hispanic individuals, whereas the existing approach estimates 9.8% and 2.6%, respectively. While previous work correctly measured FST between subpopulation pairs, our generalized FST measures genetic distances among all individuals and their most recent common ancestor (MRCA) population, revealing that genetic differentiation is greater than previously appreciated. This analysis demonstrates that estimating kinship and FST under more realistic assumptions is important for modern population genetic analysis.

scholarly journals Novel canine high-quality metagenome-assembled genomes, prophages, and host-associated plasmids by long-read metagenomics together with Hi-C proximity ligation

2021 ◽  
Author(s):  
Anna Cusco ◽  
Daniel Perez ◽  
Joaquim Vines ◽  
Norma Fabregas ◽  
Olga Francino
Keyword(s):  
Mobile Genetic Elements ◽  
Bacterial Host ◽  
High Quality ◽  
Short Read ◽  
Genetic Elements ◽  
Proximity Ligation ◽  
Long Read ◽  
Ribosomal Operons ◽  
Species Specific ◽  
Public Datasets

Long-read metagenomics facilitates the assembly of high-quality metagenome-assembled genomes (HQ MAGs) out of complex microbiomes. It provides highly contiguous assemblies by spanning repetitive regions, complete ribosomal genes, and mobile genetic elements. Hi-C proximity ligation data bins the long contigs and their associated extra-chromosomal elements to their bacterial host. Here, we characterized a canine fecal sample combining a long-read metagenomics assembly with Hi-C data, and further correcting frameshift errors. We retrieved 27 HQ MAGs and seven medium-quality (MQ) MAGs considering MIMAG criteria. All the long-read canine MAGs improved previous short-read MAGs from public datasets regarding contiguity of the assembly, presence, and completeness of the ribosomal operons, and presence of canonical tRNAs. This trend was also observed when comparing to representative genomes from a pure culture (short-read assemblies). Moreover, Hi-C data linked six potential plasmids to their bacterial hosts. Finally, we identified 51 bacteriophages integrated into their bacterial host, providing novel host information for eight viral clusters that included Gut Phage Database viral genomes. Even though three viral clusters were species-specific, most of them presented a broader host range. In conclusion, long-read metagenomics retrieved long contigs harboring complete assembled ribosomal operons, prophages, and other mobile genetic elements. Hi-C binned together the long contigs into HQ and MQ MAGs, some of them representing closely related species. Long-read metagenomics and Hi-C proximity ligation are likely to become a comprehensive approach to HQ MAGs discovery and assignment of extra-chromosomal elements to their bacterial host.

Characterization of Listeria monocytogenes Recovered from Imported Cheese Contributed to the National PulseNet Database by the U.S. Food and Drug Administration from 2001 to 2008

2010 ◽  
Vol 73 (8) ◽  
pp. 1511-1514 ◽  
Author(s):  
BABGALEH B. TIMBO ◽  
CHRISTINE KEYS ◽  
KARL KLONTZ
Keyword(s):  
Listeria Monocytogenes ◽  
Drug Administration ◽  
Genetic Relatedness ◽  
Tracking System ◽  
Food And Drug Administration ◽  
The United States ◽  
Surveillance Network ◽  
Imported Foods ◽  
The U.S

Imported foods must meet the same U.S. Food and Drug Administration (FDA) standards as domestic foods. The FDA determines whether an imported food is in compliance with the Federal Food, Drug, and Cosmetic Act. Pursuant to its regulatory activities, the FDA conducts compliance surveillance on imported foods offered for entry into the U.S. commerce. The National PulseNet Database is the molecular surveillance network for foodborne infections and is widely used to provide real-time subtyping support to epidemiologic investigations of foodborne diseases. FDA laboratories use pulsed-field gel electrophoresis to subtype foodborne pathogens recovered from imported foods and submit the molecular patterns to the National PulseNet Database at the Centers for Disease Control and Prevention. There were 60 isolates of Listeria monocytogenes in the FDA Field Accomplishment and Compliance Tracking System from 2001 to 2008 due to cheese imported from the following countries: Mexico (n = 21 isolates), Italy (19), Israel (9), Portugal (5), Colombia (3), Greece (2), and Spain (1). We observed genetic diversity of L. monocytogenes isolates and genetic relatedness among strains recovered from imported cheese products coming to the United States from different countries. Consistent characterization of L. monocytogenes isolates recovered from imported cheeses, accompanied by epidemiologic investigations to ascertain human illness associated with these strains, could be helpful in the control of listeriosis acquired from imported cheeses.

scholarly journals Genome Sequence of Listeria monocytogenes Plasmid pLM-C-273 Carrying Genes Related to Stress Resistance

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Lindsay Liang ◽  
Saravanamuttu Gnaneshan ◽  
Rafael A. Garduño ◽  
Gustavo V. Mallo
Keyword(s):  
Antibiotic Resistance ◽  
Listeria Monocytogenes ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Stress Resistance ◽  
Clinical Sample ◽  
Mobile Genetic Elements ◽  
Metal Resistance ◽  
Genetic Elements

Mobile genetic elements in bacteria, such as plasmids, act as important vectors for the transfer of antibiotic resistance, virulence, and metal resistance genes. Here, we report the genome sequence of a new plasmid pLM-C-273, identified in a Listeria monocytogenes strain isolated from a clinical sample in Ontario, Canada.

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