Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements

IntroductionExtended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producingEscherichia coliwas increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control.Methods and analysisThis protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment.Ethics and disseminationThis study has been approved by the local ethics committee (Ethikkommission Nordwest-und Zentralschweiz) as a quality control project (Project-ID 2017–00100). The results of this study will be published in peer-reviewed medical journals, communicated to participants, the general public and all relevant stakeholders.

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Microevolution and Gain or Loss of Mobile Genetic Elements of Outbreak-Related Listeria monocytogenes in Food Processing Environments Identified by Whole Genome Sequencing Analysis

Frontiers in Microbiology ◽

10.3389/fmicb.2020.00866 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 1

Author(s):

Helen Yang ◽

Maria Hoffmann ◽

Marc W. Allard ◽

Eric W. Brown ◽

Yi Chen

Keyword(s):

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Food Processing ◽

Mobile Genetic Elements ◽

Whole Genome ◽

Sequencing Analysis ◽

Genetic Elements

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Independent Microevolution Mediated by Mobile Genetic Elements of IndividualClostridium difficileIsolates from Clade 4 Revealed by Whole-Genome Sequencing

mSystems ◽

10.1128/msystems.00252-18 ◽

2019 ◽

Vol 4 (2) ◽

Cited By ~ 4

Author(s):

Yuan Wu ◽

Chen Liu ◽

Wen-Ge Li ◽

Jun-Li Xu ◽

Wen-Zhu Zhang ◽

...

Keyword(s):

Drug Resistance ◽

Clostridium Difficile ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mobile Genetic Elements ◽

High Rate ◽

Whole Genome ◽

Content Type ◽

Genetic Elements ◽

Sequence Types

ABSTRACTHorizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome ofClostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37C. difficileisolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly,catD, known to be harbored by Tn4453a/b, was replaced byaac(6′) aph(2′′)in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges betweenC. difficileand other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified inC. difficileisolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number ofC. difficileisolates resistant to all antibiotics tested here suggests the ease with which resistance is acquiredin vivo. This study gives insights into the genetic mechanism of microevolution within clade 4.IMPORTANCEMobile genetic elements play a key role in the continuing evolution ofClostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4C. difficileisolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/bwithaac(6′) aph(2′′)instead ofcatD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

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Methicillin-Resistant and Methicillin-Susceptible Staphylococcus from Vervet Monkeys (Chlorocebus sabaeus) in Saint Kitts

Antibiotics ◽

10.3390/antibiotics10030290 ◽

2021 ◽

Vol 10 (3) ◽

pp. 290

Author(s):

Andreas Hoefer ◽

Filip Boyen ◽

Amy Beierschmitt ◽

Arshnee Moodley ◽

Marilyn C. Roberts ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mobile Genetic Elements ◽

Pcr Analysis ◽

Whole Genome ◽

Vervet Monkeys ◽

Methicillin Resistant ◽

Genetic Elements ◽

Maldi Tof ◽

Staphylococcus Spp

Antimicrobial resistance has been described in all ecosystems, including wildlife. Here we investigated the presence of methicillin-resistant and susceptible staphylococci in both colony-born and wild vervet monkeys (Chlorocebus sabaeus). Through selective isolation, PCR, MALDI-TOF, and whole-genome sequencing, methicillin-resistant and susceptible Staphylococcus spp. isolated from vervet monkeys were characterized. We obtained putatively methicillin-resistant staphylococci from 29 of the 34 nasal samples collected. Strains were identified by MALDI-TOF analysis. Staphylococcus cohnii (n = 15) was the most commonly isolated species, while nine other species were isolated one or two times. PCR analysis indicated that eight [28%] strains were mecA positive. The whole-genome sequencing [WGS] included eight methicillin-resistant strains (S. epidermidis (n = 2), S. cohnii (n = 3), S. arlettae (n = 2) and S. hominis (n = 1)), nine additional S. cohnii strains and two strains that could not be identified by MALDI-TOF, but genetically characterized as one S. cohnii and one S. warneri. Different resistance genes carried by different mobile genetic elements, mainly blaZ (n = 10) and tet(K) (n = 5) were found, while msr(A), cat, fosB, dfrG, erm(C), mph(C) and str were identified in one to three strains. Phylogenetic analysis of the S. cohnii strains based on SNPs indicated four clusters associated with colony born or wild. In addition, one singleton S. cohnii isolated did not form a separate group and clustered within other S. cohnii strains submitted to the NCBI. In this study, we demonstrated the presence of AMR and mobile genetic elements to both colony-born and wild vervet monkeys. We also identified a previously undescribed prevalence of S. cohnii in the nasal flora of these monkeys, which merits further investigation.

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Whole-Genome Sequencing of Sphingobium sp. Strain RSMS, a Highly Efficient Tributyl Phosphate-Degrading Bacterium

Microbiology Resource Announcements ◽

10.1128/mra.00600-20 ◽

2020 ◽

Vol 9 (42) ◽

Author(s):

Shyam Sunder Rangu ◽

Ashish Beck ◽

Mohak Sharda ◽

Rita Mukhopadhyaya ◽

Aswin Sai Narain Seshasayee ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Tributyl Phosphate ◽

Organic Pollutant ◽

Whole Genome ◽

Future Studies ◽

Genetic Elements ◽

Highly Efficient ◽

Degrading Bacterium

ABSTRACT Sphingobium sp. strain RSMS was described earlier as an efficient degrader of tributyl phosphate, an organic pollutant. This report describes the generation and annotation of the genome sequence of Sphingobium sp. strain RSMS, which will facilitate future studies to identify genetic elements responsible for the degradation of tributyl phosphate.

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Salmonella entericaPhylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic Elements

mBio ◽

10.1128/mbio.02303-18 ◽

2018 ◽

Vol 9 (6) ◽

Cited By ~ 24

Author(s):

Jay Worley ◽

Jianghong Meng ◽

Marc W. Allard ◽

Eric W. Brown ◽

Ruth E. Timme

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Foodborne Pathogens ◽

Bacterial Species ◽

Whole Genome Sequence ◽

Nucleotide Sequencing ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Content Type ◽

Genetic Elements

ABSTRACTUsing whole-genome sequence (WGS) data from the GenomeTrakr network, a globally distributed network of laboratories sequencing foodborne pathogens, we present a new phylogeny ofSalmonella entericacomprising 445 isolates from 266 distinct serovars and originating from 52 countries. This phylogeny includes two previously unidentifiedS. entericasubsp.entericaclades. Serovar Typhi is shown to be nested within clade A. Our findings are supported by both phylogenetic support, based on a core genome alignment, and Bayesian approaches, based on single-nucleotide polymorphisms. Serovar assignments were refined byin silicoanalysis using SeqSero. More than 10% of serovars were either polyphyletic or paraphyletic. We found variable genetic content in these isolates relating to gene mobilization and virulence factors which have different distributions within clades. Gifsy-1- and Gifsy-2-like phages appear more prevalent in clade A; other viruses are more evenly distributed. Our analyses reveal IncFII is the predominant plasmid replicon inS. enterica. Few core or clade-defining virulence genes are observed, and their distributions appear probabilistic in nature. Together, these patterns demonstrate that genetic exchange withinS. entericais more extensive and frequent than previously realized, which significantly alters how we view the genetic structure of the bacterial species.IMPORTANCERapid improvements in nucleotide sequencing access and affordability have led to a drastic increase in availability of genetic information. This information will improve the accuracy of molecular descriptions, including serovars, withinS. enterica. Although the concept of serovars continues to be useful, it may have more significant limitations than previously understood. Furthermore, the discrete absence or presence of specific genes can be an unstable indicator of phylogenetic identity. Whole-genome sequencing provides more rigorous tools for assessing the distributions of these genes. Our phylogenetic and genetic content analyses reveal how active genetic elements are dynamically distributed within a species, allowing us to better understand genetic reservoirs and underlying bacterial evolution.

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Molecular Analysis of bla KPC-2 -Harboring Plasmids: Tn 4401a Interplasmid Transposition and Tn 4401a -Carrying ColRNAI Plasmid Mobilization from Klebsiella pneumoniae to Citrobacter europaeus and Morganella morganii in a Single Patient

mSphere ◽

10.1128/msphere.00850-21 ◽

2021 ◽

Author(s):

Kayoko Sugita ◽

Kotaro Aoki ◽

Kohji Komori ◽

Tatsuya Nagasawa ◽

Yoshikazu Ishii ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Molecular Analysis ◽

Mobile Genetic Elements ◽

Whole Genome ◽

Single Patient ◽

Morganella Morganii ◽

Content Type ◽

Plasmid Mobilization

Plasmid transfer plays an important role in the interspecies spread of carbapenemase genes, including the Klebsiella pneumoniae carbapenemase (KPC)-coding gene, bla KPC . We conducted whole-genome sequencing (WGS) analysis and transmission experiments to analyze bla KPC-2 -carrying mobile genetic elements (MGEs) between the bla KPC-2 -harboring K. pneumoniae , Citrobacter europaeus , and Morganella morganii strains isolated from a single patient. bla KPC-2 was contained within an MGE, Tn 4401a .

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