Whole-genome analysis of the potentially zoonotic Elizabethkingia miricola FL160902 with two new chromosomal MBL gene variants

2019 ◽  
Vol 75 (3) ◽  
pp. 526-530 ◽  
Author(s):  
Ruixue Hu ◽  
Qi Zhang ◽  
Zemao Gu
Keyword(s):  
Phylogenetic Analysis ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genome Analysis ◽  
Snp Analysis ◽  
Gene Variants ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Circular Chromosome ◽  
Antimicrobial Resistance Genes

Abstract Objectives Elizabethkingia is an emerging life-threatening pathogen in both humans and animals. We describe the whole-genome analysis of an Elizabethkingia miricola strain isolated from a diseased frog in China and investigate the molecular mechanism of carbapenem resistance in this pathogen. Methods WGS of E. miricola FL160902 was performed using single-molecule, real-time technology. A phylogenetic tree was generated by SNP analysis, comparing the genome of our strain with other E. miricola isolates of amphibian and human origins. Antimicrobial resistance genes and virulence-related genes were identified using the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB). Two putative carbapenemase genes were expressed in Escherichia coli to evaluate their contribution to antimicrobial resistance. Results The genome of E. miricola FL160902 consists of a 4 249 586 bp circular chromosome with 27 putative resistance genes and 38 predicted virulence-associated genes. Comparative genomic analysis demonstrated that the E. miricola strains of human and amphibian origins have similar virulence-associated gene profiles. In addition, all the amphibian isolates clustered together with one of the human isolates in the phylogenetic analysis. WGS revealed the presence of two novel MBL genes, designated blaBlaB-16 and blaGOB-19. Cloning of blaBlaB-16 and blaGOB-19 into E. coli DH5α resulted in increased MICs of most β-lactams, including imipenem, meropenem and ampicillin. Conclusions We identified two chromosomal MBL gene variants, named blaBlaB-16 and blaGOB-19 in an amphibian E. miricola isolate, which was considered potentially zoonotic based on phylogenetic analysis and virulence-associated gene comparison. This study highlights the importance of E. miricola as a potential zoonotic pathogen and a reservoir of MDR genes.

scholarly journals Zoonotic Transfer ofClostridium difficileHarboring Antimicrobial Resistance between Farm Animals and Humans

2017 ◽  
Vol 56 (3) ◽  
Author(s):  
C. W. Knetsch ◽  
N. Kumar ◽  
S. C. Forster ◽  
T. R. Connor ◽  
H. P. Browne ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Farm Animals ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Health Concept ◽  
The One ◽  
Animal Strains

ABSTRACTThe emergence ofClostridium difficileas a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associatedC. difficileRT027 lineage, the community-associatedC. difficileRT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248C. difficileRT078 strains from 22 countries. Our results demonstrate limited geographical clustering forC. difficileRT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome ofC. difficileRT078. Thus, bidirectional spread ofC. difficileRT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the “One Health” concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.

scholarly journals Genomic Signature of Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates Related to a Massive Outbreak in Zambia between 2010 and 2012

2014 ◽  
Vol 53 (1) ◽  
pp. 262-272 ◽  
Author(s):  
Rene S. Hendriksen ◽  
Pimlapas Leekitcharoenphon ◽  
Oksana Lukjancenko ◽  
Chileshe Lukwesa-Musyani ◽  
Bushimbwa Tambatamba ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Plasmid Replicon ◽  
New Variant ◽  
Antimicrobial Resistance Genes

Retrospectively, we investigated the epidemiology of a massiveSalmonella entericaserovar Typhi outbreak in Zambia during 2010 to 2012. Ninety-four isolates were susceptibility tested by MIC determinations. Whole-genome sequence typing (WGST) of 33 isolates and bioinformatic analysis identified the multilocus sequence type (MLST), haplotype, plasmid replicon, antimicrobial resistance genes, and genetic relatedness by single nucleotide polymorphism (SNP) analysis and genomic deletions. The outbreak affected 2,040 patients, with a fatality rate of 0.5%. Most (83.0%) isolates were multidrug resistant (MDR). The isolates belonged to MLST ST1 and a new variant of the haplotype, H58B. Most isolates contained a chromosomally translocated region containing seven antimicrobial resistance genes,catA1,blaTEM-1,dfrA7,sul1,sul2,strA, andstrB, and fragments of the incompatibility group Q1 (IncQ1) plasmid replicon, the class 1 integron, and themeroperon. The genomic analysis revealed 415 SNP differences overall and 35 deletions among 33 of the isolates subjected to whole-genome sequencing. In comparison with other genomes of H58, the Zambian isolates separated from genomes from Central Africa and India by 34 and 52 SNPs, respectively. The phylogenetic analysis indicates that 32 of the 33 isolates sequenced belonged to a tight clonal group distinct from other H58 genomes included in the study. The small numbers of SNPs identified within this group are consistent with the short-term transmission that can be expected over a period of 2 years. The phylogenetic analysis and deletions suggest that a single MDR clone was responsible for the outbreak, during which occasional otherS. Typhi lineages, including sensitive ones, continued to cocirculate. The common view is that the emerging globalS. Typhi haplotype, H58B, containing the MDR IncHI1 plasmid is responsible for the majority of typhoid infections in Asia and sub-Saharan Africa; we found that a new variant of the haplotype harboring a chromosomally translocated region containing the MDR islands of IncHI1 plasmid has emerged in Zambia. This could change the perception of the term “classical MDR typhoid” currently being solely associated with the IncHI1 plasmid. It might be more common than presently thought thatS. Typhi haplotype H58B harbors the IncHI1 plasmid or a chromosomally translocated MDR region or both.

scholarly journals Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

2020 ◽  
Vol 11 ◽  
Author(s):  
Grazielle Lima Rodrigues ◽  
Pedro Panzenhagen ◽  
Rafaela Gomes Ferrari ◽  
Anamaria dos Santos ◽  
Vania Margaret Flosi Paschoalin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
In Silico ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Antimicrobial Resistance Genes

scholarly journals Presence and Characterization of a Novel cfr-Carrying Tn558 Transposon Derivative in Staphylococcus delphini Isolated From Retail Food

2021 ◽  
Vol 11 ◽  
Author(s):  
Feng Zhang ◽  
Shi Wu ◽  
Jiahui Huang ◽  
Runshi Yang ◽  
Jumei Zhang ◽  
...  
Keyword(s):  
Public Health ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Poultry Meat ◽  
Whole Genome ◽  
Chloramphenicol Resistance ◽  
Antimicrobial Resistance Genes ◽  
Retail Food

Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S. delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.

scholarly journals Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles

2021 ◽  
Vol 12 ◽  
Author(s):  
Jessica Esther Agius ◽  
David Norton Phalen ◽  
Karrie Rose ◽  
John-Sebastian Eden
Keyword(s):  
Antimicrobial Resistance ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Immune Recognition ◽  
Snp Analysis ◽  
Whole Genome Analysis ◽  
Circular Chromosome ◽  
Christmas Island ◽  
Clinically Significant

Whole genome analysis of a novel species of enterococci, Enterococcus lacertideformus, causing multi-systemic and invariably fatal disease in critically endangered Christmas Island reptiles was undertaken to determine the genetic elements and potential mechanisms conferring its pathogenic nature, biofilm-forming capabilities, immune recognition avoidance, and inability to grow in vitro. Comparative genomic analyses with related and clinically significant enterococci were further undertaken to infer the evolutionary history of the bacterium and identify genes both novel and absent. The genome had a G + C content of 35.1%, consisted of a circular chromosome, no plasmids, and was 2,419,934 bp in length (2,321 genes, 47 tRNAs, and 13 rRNAs). Multi-locus sequence typing (MLST), and single nucleotide polymorphism (SNP) analysis of multiple E. lacertideformus samples revealed they were effectively indistinguishable from one another and highly clonal. E. lacertideformus was found to be located within the Enterococcus faecium species clade and was closely related to Enterococcus villorum F1129D based on 16S rDNA and MLST house-keeping gene analysis. Antimicrobial resistance (DfreE, EfrB, tetM, bcrRABD, and sat4) and virulence genes (Fss3 and ClpP), and genes conferring tolerance to metals and biocides (n = 9) were identified. The detection of relatively few genes encoding antimicrobial resistance and virulence indicates that this bacterium may have had no exposure to recently developed and clinically significant antibiotics. Genes potentially imparting beneficial functional properties were identified, including prophages, insertion elements, integrative conjugative elements, and genomic islands. Functional CRISPR-Cas arrays, and a defective prophage region were identified in the genome. The study also revealed many genomic loci unique to E. lacertideformus which contained genes enriched in cell wall/membrane/envelop biogenesis, and carbohydrate metabolism and transport functionality. This finding and the detection of putative enterococcal biofilm determinants (EfaAfs, srtC, and scm) may underpin the novel biofilm phenotype observed for this bacterium. Comparative analysis of E. lacertideformus with phylogenetically related and clinically significant enterococci (E. villorum F1129D, Enterococcus hirae R17, E. faecium AUS0085, and Enterococcus faecalis OG1RF) revealed an absence of genes (n = 54) in E. lacertideformus, that encode metabolic functionality, which potentially hinders nutrient acquisition and/or utilization by the bacterium and precludes growth in vitro. These data provide genetic insights into the previously determined phenotype and pathogenic nature of the bacterium.

scholarly journals Whole-Genome Sequences of 35 Incompatibility Group I1 Plasmid-Carrying Salmonella enterica Isolates from Food Animal and Clinical Sources

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
Nesreen H. Aljahdali ◽  
Pravin R. Kaldhone ◽  
Steven L. Foley ◽  
Bijay K. Khajanchi
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Whole Genome ◽  
Genome Sequences ◽  
Incompatibility Group ◽  
Content Type ◽  
Food Animal ◽  
Antimicrobial Resistance Genes ◽  
Genotypic Characteristics

We sequenced 35 Salmonella enterica isolates carrying incompatibility group I1 (IncI1) plasmids from different serotypes to study their genotypic characteristics. The isolates originated from food animals (n = 32) and human patients (n = 3). All isolates carried IncI1 plasmids, and many had additional plasmids detected along with virulence and antimicrobial resistance genes.

scholarly journals Prevalence and Characteristics of Ceftriaxone-Resistant Salmonella in Children’s Hospital in Hangzhou, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiucheng Shi ◽  
Yihua Ye ◽  
Peng Lan ◽  
Xinhong Han ◽  
Jingjing Quan ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Resistance Mechanism ◽  
Resistance Rate ◽  
High Rate ◽  
Whole Genome ◽  
Older Children ◽  
Whole Genome Analysis ◽  
Antimicrobial Resistance Genes ◽  
Resistance Rates ◽  
M 14

The non-Typhi Salmonella (NTS) infection is critical to children’s health, and the ceftriaxone is the important empirical treatment choice. With the increase resistance rate of ceftriaxone in Salmonella, the molecular epidemiology and resistance mechanism of ceftriaxone-resistant Salmonella needs to be studied. From July 2019 to July 2020, a total of 205 NTS isolates were collected, 195 of which (95.1%) were cultured from stool, but 10 isolates were isolated from an extraintestinal site. Serogroup B accounted for the vast majority (137/205) among the isolates. Fifty-three isolates were resistant to ceftriaxone, and 50 were isolated from children younger than 4years of age. The resistance rates for ceftriaxone, ciprofloxacin, and levofloxacin were significantly higher in younger children than the older children. The resistance genes in the ceftriaxone-susceptible isolates were detected by PCR, and ceftriaxone-resistant Salmonella were selected for further whole-genome sequencing. Whole-genome analysis showed that serotype Typhimurium and its monophasic variant was the most prevalent in ceftriaxone-resistant isolates (37/53), which comprised ST34 (33/53), ST19 (2/53), and ST99 (2/53), and they were close related in the phylogenetic tree. However, the other isolates were diverse, which included one Enteritidis (ST11), one Indiana (ST17), one Derby (ST40), four Kentucky (ST198), two Goldcoast (ST2529, ST358), one Muenster (ST321), one Virchow (ST359), one Rissen (ST469), one Kedougou (ST1543), two Uganda (ST684), and one Kottbus (ST8839). Moreover, CTX-M-55 ESBLs production (33/53) was found to be mainly responsible for ceftriaxone resistance, followed by blaCTX-M-65 (12/53), blaCTX-M-14 (4/53), blaCTX-M-9 (2/53), blaCTX-M-64 (1/53), blaCTX-M-130 (1/53), and blaCMY-2 (1/53). ISEcp1, IS903B, IS Kpn26, IS1F, and IS26 were connected to antimicrobial resistance genes transfer. In conclusion, the dissemination of ESBL-producing Salmonella isolates resulted in an increased prevalence of ceftriaxone resistance in young children. The high rate of multidrug resistance should be given additional attention.

scholarly journals Conjugal Transfer, Whole-Genome Sequencing, and Plasmid Analysis of Four mcr-1-Bearing Isolates from U.S. Patients

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Wenming Zhu ◽  
Adrian Lawsin ◽  
Rebecca L. Lindsey ◽  
Dhwani Batra ◽  
Kristen Knipe ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Whole Genome ◽  
Colistin Resistance ◽  
Content Type ◽  
Plasmid Analysis ◽  
Antimicrobial Resistance Genes

ABSTRACT Four Enterobacteriaceae clinical isolates bearing mcr-1 gene-harboring plasmids were characterized. All isolates demonstrated the ability to transfer colistin resistance to Escherichia coli; plasmids were stable in conjugants after multiple passages on nonselective media. mcr-1 was located on an IncX4 (n = 3) or IncN (n = 1) plasmid. The IncN plasmid harbored 13 additional antimicrobial resistance genes. Results indicate that the mcr-1-bearing plasmids in this study were highly transferable in vitro and stable in the recipients.

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