scholarly journals Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

2016 ◽  
Author(s):  
Sebastien Breurec ◽  
Alexis Criscuolo ◽  
Laure Diancourt ◽  
Olaya Rendueles-Garcia ◽  
Mathias Vandenbogaert ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Population Biology ◽  
Capsular Polysaccharide ◽  
Bacterial Pathogen ◽  
Genomic Analysis ◽  
Gene Families ◽  
Neonatal Meningitis ◽  
Genomic Epidemiology ◽  
Niche Adaptation ◽  
Antimicrobial Resistance Genes

Elizabethkingia anophelis is an emerging pathogen. Genomic analysis of strains from clinical, environmental or mosquito sources is needed to understand the epidemiological emergence of E. anophelis and to uncover genetic elements implicated in antimicrobial resistance, pathogenesis, or niche adaptation. Here, the genomic sequences of two nosocomial isolates that caused neonatal meningitis in Bangui, Central African Republic, were determined and compared with Elizabethkingia isolates from other world regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent distinct genomic species and led to re-identification of several strains. Phylogenetic analysis of E. anophelis strains revealed several sublineages and demonstrated a single evolutionary origin of African clinical isolates, which carry unique antimicrobial resistance genes acquired by horizontal transfer. The Elizabethkingia genus and the species E. anophelis had pan-genomes comprising respectively 7,801 and 6,880 gene families, underlining their genomic heterogeneity. African isolates were capsulated and carried a distinctive capsular polysaccharide synthesis cluster. A core-genome multilocus sequence typing scheme applicable to all Elizabethkingia isolates was developed, made publicly available (http://bigsdb.web.pasteur.fr/elizabethkingia), and shown to provide useful insights into E. anophelis epidemiology. Furthermore, a clustered regularly interspaced short palindromic repeats (CRISPR) locus was uncovered in E. meningoseptica, E. miricola and in a few E. anophelis strains. CRISPR spacer variation was observed between the African isolates, illustrating the value of CRISPR for strain subtyping. This work demonstrates the dynamic evolution of E. anophelis genomes and provides innovative tools for Elizabethkingia identification, population biology and epidemiology.

Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China

2021 ◽  
Author(s):  
Zhenghui Liu ◽  
Yitong Zhao ◽  
Frederick Leo Sossah ◽  
Benjamin Azu Okorley ◽  
Daniel G. Amoako ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genomic Analysis ◽  
Gene Families ◽  
Effective Control ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Pseudomonas Tolaasii ◽  
Antimicrobial Resistance Genes

Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen’s ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.

scholarly journals Sequencing and Comparative Genomic Analysis of pK29, a 269-Kilobase Conjugative Plasmid Encoding CMY-8 and CTX-M-3 β-Lactamases in Klebsiella pneumoniae

2007 ◽  
Vol 51 (8) ◽  
pp. 3004-3007 ◽  
Author(s):  
Ying-Tsong Chen ◽  
Tsai-Ling Lauderdale ◽  
Tsai-Lien Liao ◽  
Yih-Ru Shiau ◽  
Hung-Yu Shu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Conjugative Plasmid ◽  
Comparative Genomic ◽  
Antimicrobial Resistance Genes ◽  
Genomic Analyses ◽  
The Common

ABSTRACT A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced. The plasmid harbors multiple antimicrobial resistance genes, including those encoding CMY-8 AmpC-type and CTX-M-3 extended-spectrum β-lactamases in the common backbone of IncHI2 plasmids. Mechanisms for dissemination of the resistance genes are highlighted in comparative genomic analyses.

scholarly journals Whole-genome sequence analysis of Vibrio cholerae from three outbreaks in Uganda, 2014 - 2016

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1340
Author(s):  
Dickson Aruhomukama ◽  
Ivan Sserwadda ◽  
Gerald Mboowa
Keyword(s):  
Antimicrobial Resistance ◽  
Vibrio Cholerae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Public Health Problem ◽  
Enrichment Analysis ◽  
Whole Genome Sequence ◽  
Pathogenicity Islands ◽  
Type Vi Secretion System ◽  
Antimicrobial Resistance Genes

Background: Cholera remains a serious public health problem in Uganda and Africa. The aim of this study was to provide the complete array of antimicrobial resistance genes, integrative and conjugative elements, virulence genes, pathogenicity islands, plasmids, and insertion sequences in the strains. In addition, this study also aimed to provide a single nucleotide polymorphism (SNP) based phylogenetic analysis of the strains. Methods: In the analysis, both Linux and web-based bioinformatics approaches were used to analyze the study sequences. Databases used included; FastQC, MultiQC, Snippy, PANTHER, PATRIC, Unicycler, ISFinder, Center for Genomic Epidemiology pipelines (i.e. MLST, PlasmidFinder, MyDbFinder, and ResFinder), MashTree and IcyTree.  Results: The 10 sequenced strains of Vibrio cholerae were found to carry virulence-associated genes including MakA, ctxA, ctxB, carA, carB, trpB, clpB, ace, toxR, zot, rtxA, ompW, ompR, gmhA, fur, hlyA, and rstR. Also identified were: genes of the Type VI secretion system including vasA-L, vgrG-2, vgrG-3, vipA/mglA, and vipB/mglB; alsD (VC1589), involved in the synthesis of 2,3-butanediol; alsR, involved in the acetate-responsive LysR-type regulation; makA, the flagella-mediated cytotoxin gene; Type VI pilus genes including tcpA-F, tcpH-J, tcpN, tcpP-T, and icmF/vasK; adherence genes acfA-D and IlpA; and quorum sensing system genes luxS and cqsA. Pathogenicity islands identified comprised of VSP-1 and VSP-2, as well as VPI-1 and VPI-2. In addition, strA and B, APH(3'')-I, APH(3'')-Ib, APH(6)-Id, APH(6)-Ic, murA, pare, dfrA1, floR, catB, and catB9 were among the antimicrobial resistance genes found in the sequences. Analysis for SNPs shared among the sequences showed that the sequenced strains shared 218 SNPs and of these, 98 SNPs were missense. Gene enrichment analysis of these SNPs showed enrichment in genes that mediate transmembrane-signaling receptor activity, peptidyl-prolyl cis-trans isomerase activity, and phosphor-relay response regulator activity. Conclusions: This study applied bioinformatics approaches to provide comprehensive genomic analysis of V. cholerae genomes obtained from Uganda.

scholarly journals Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M Integrated in the Chromosome

2017 ◽  
Vol 61 (7) ◽  
Author(s):  
Weihua Huang ◽  
Guiqing Wang ◽  
Robert Sebra ◽  
Jian Zhuge ◽  
Changhong Yin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
De Novo ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Type I ◽  
Content Type ◽  
Antimicrobial Resistance Genes

ABSTRACT The extended-spectrum-β-lactamase (ESBL)- and Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae represent serious and urgent threats to public health. In a retrospective study of multidrug-resistant K. pneumoniae, we identified three clinical isolates, CN1, CR14, and NY9, carrying both bla CTX-M and bla KPC genes. The complete genomes of these three K. pneumoniae isolates were de novo assembled by using both short- and long-read whole-genome sequencing. In CR14 and NY9, bla CTX-M and bla KPC were carried on two different plasmids. In contrast, CN1 had one copy of bla KPC-2 and three copies of bla CTX-M-15 integrated in the chromosome, for which the bla CTX-M-15 genes were linked to an insertion sequence, ISEcp1, whereas the bla KPC-2 gene was in the context of a Tn4401a transposition unit conjugated with a PsP3-like prophage. Intriguingly, downstream of the Tn4401a-bla KPC-2-prophage genomic island, CN1 also carried a clustered regularly interspaced short palindromic repeat (CRISPR)-cas array with four spacers targeting a variety of K. pneumoniae plasmids harboring antimicrobial resistance genes. Comparative genomic analysis revealed that there were two subtypes of type I-E CRISPR-cas in K. pneumoniae strains and suggested that the evolving CRISPR-cas, with its acquired novel spacer, induced the mobilization of antimicrobial resistance genes from plasmids into the chromosome. The integration and dissemination of multiple copies of bla CTX-M and bla KPC from plasmids to chromosome depicts the complex pandemic scenario of multidrug-resistant K. pneumoniae. Additionally, the implications from this study also raise concerns for the application of a CRISPR-cas strategy against antimicrobial resistance.

scholarly journals Extensive Comparative Genomic Analysis of Enterococcus faecalis and Enterococcus faecium Reveals a Direct Association between the Absence of CRISPR–Cas Systems, the Presence of Anti-Endonuclease (ardA) and the Acquisition of Vancomycin Resistance in E. faecium

2021 ◽  
Vol 9 (6) ◽  
pp. 1118
Author(s):  
Kodjovi D. Mlaga ◽  
Vincent Garcia ◽  
Philippe Colson ◽  
Ruimy Raymond ◽  
Jean-Marc Rolain ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Vancomycin Resistance ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
P Value ◽  
Antimicrobial Resistance Genes ◽  
Significant Difference ◽  
Direct Association

Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 1591) and E. faecium (n = 1981) and investigated the association between the presence or absence of CRISPR-Cas systems, endonuclease/anti-endonuclease systems and the acquisition of antimicrobial resistance, especially vancomycin resistance genes. Most of the analysed Enterococci were isolated from humans and less than 14% of them were from foods and animals. We analysed and detected CRISPR–Cas systems in 75.36% of E. faecalis genomes and only 4.89% of E. faecium genomes with a significant difference (p-value < 10−5). We found a negative correlation between the number of CRISPR–Cas systems and genome size (r = −0.397, p-value < 10−5) and a positive correlation between the genome %GC content and the number of CRISPR–Cas systems (r = 0.215, p-value < 10−5). Our findings showed that the presence of the anti-endonuclease ardA gene may explain the decrease in the number of CRISPR–Cas systems in E. faecium, known to deactivate the endonucleases’ protective activities and enable the E. faecium genome to be versatile in acquiring mobile genetic elements, including carriers of antimicrobial resistance genes, especially vanB. Most importantly, we observed that there was a direct association between the absence of CRISPR–Cas, the presence of the anti-CRISPR ardA gene and the acquisition of vancomycin resistance genes.

scholarly journals Complete Genome Sequence of a Canadian Strain of Raoultella planticola with Metal and Antimicrobial Resistance Genes

2021 ◽  
Vol 10 (25) ◽  
Author(s):  
Mingsong Kang ◽  
John Chmara ◽  
Sohail Naushad ◽  
Hongsheng Huang
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacterial Pathogen ◽  
Gene Clusters ◽  
Metal Resistance ◽  
Raoultella Planticola ◽  
Content Type ◽  
Antimicrobial Resistance Genes

Raoultella planticola is a Gram-negative opportunistic bacterial pathogen associated with hospital-acquired infections in humans. Here, we report the complete genome sequence of one Raoultella planticola strain isolated from Canadian wastewater treatment facilities containing one chromosome and four plasmids with four antimicrobial resistance (AMR) genes and four metal resistance gene clusters.

scholarly journals Comparison of Antimicrobial Resistance and Pan-Genome of Clinical and Non-Clinical Enterococcus cecorum from Poultry Using Whole-Genome Sequencing

Foods ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 686
Author(s):  
Poonam Sharma ◽  
Sushim K. Gupta ◽  
John B. Barrett ◽  
Lari M. Hiott ◽  
Tiffanie A. Woodley ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Gene Families ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Pan Genome ◽  
Antimicrobial Resistance Genes ◽  
Enterococcus Cecorum

Enterococcus cecorum is an emerging avian pathogen, particularly in chickens, but can be found in both diseased (clinical) and healthy (non-clinical) poultry. To better define differences between E. cecorum from the two groups, whole-genome sequencing (WGS) was used to identify and compare antimicrobial resistance genes as well as the pan-genome among the isolates. Eighteen strains selected from our previous study were subjected to WGS using Illumina MiSeq and comparatively analyzed. Assembled contigs were analyzed for resistance genes using ARG-ANNOT. Resistance to erythromycin was mediated by ermB, ermG, and mefA, in clinical isolates and ermB and mefA, in non-clinical isolates. Lincomycin resistance genes were identified as linB, lnuB, lnuC, and lnuD with lnuD found only in non-clinical E. cecorum; however, lnuB and linB were found in only one clinical isolate. For both groups of isolates, kanamycin resistance was mediated by aph3-III, while tetracycline resistance was conferred by tetM, tetO, and tetL. No mutations or known resistance genes were found for isolates resistant to either linezolid or chloramphenicol, suggesting possible new mechanisms of resistance to these drugs. A comparison of WGS results confirmed that non-clinical isolates contained more resistance genes than clinical isolates. The pan-genome of clinical and non-clinical isolates resulted in 3651 and 4950 gene families, respectively, whereas the core gene sets were comprised of 1559 and 1534 gene families in clinical and non-clinical isolates, respectively. Unique genes were found more frequently in non-clinical isolates than clinical. Phylogenetic analysis of the isolates and all the available complete and draft genomes showed no correlation between healthy and diseased poultry. Additional genomic comparison is required to elucidate genetic factors in E. cecorum that contribute to disease in poultry.

scholarly journals Porcine commensalEscherichia coli: A reservoir for class 1 integrons associated with IS26

2017 ◽  
Author(s):  
Cameron J. Reid ◽  
Ethan R. Wyrsch ◽  
Piklu Roy Chowdhury ◽  
Tiziana Zingali ◽  
Michael Liu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Metal Resistance ◽  
Whole Genome Sequence ◽  
Class 1 Integron ◽  
E Coli ◽  
Class 1 Integrons ◽  
Antimicrobial Resistance Genes ◽  
Class 1

AbstractPorcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial resistance and virulence-associated genes (VAGs) and the zoonotic potential of commensalEscherichia colifrom swine is largely unknown. Furthermore, little is known about the role of commensalE. colias contributors to the mobilisation of antimicrobial resistance genes between food animals and the environment. Here, we report whole genome sequence analysis of 141E. colifrom the faeces of healthy pigs. Most strains belonged to phylogroups A and B1 and carried i) a class 1 integron; ii) VAGs linked with extraintestinal infection in humans; iii) antimicrobial resistance genesblaTEM, aphAl, cmlA, strAB, tet(A)A,dfrA12, dfrA5, sul1, sul2, sul3; iv)IS26;and v) heavy metal resistance genes (merA, cusA, terA). Carriage of the sulphonamide resistance genesul3was notable in this study. The 141 strains belonged to 42 multilocus sequence types, but clonal complex 10 featured prominently. Structurally diverse class 1 integrons that were frequently associated with IS26 carried unique genetic features that were also identified in extraintestinal pathogenicE. coli(ExPEC) from humans. This study provides the first detailed genomic analysis and point of reference for commensalE. coliof porcine origin, facilitating tracking of specific lineages and the mobile resistance genes they carry.Conflict of Interest StatementNone to declare.

scholarly journals Salmonella Derby: A Comparative Genomic Analysis of Strains From Germany

2021 ◽  
Vol 12 ◽  
Author(s):  
Belén González-Santamarina ◽  
Silvia García-Soto ◽  
Helmut Hotzel ◽  
Diana Meemken ◽  
Reinhard Fries ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Animal Species ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Antimicrobial Treatment ◽  
Comparative Genomic ◽  
The Public ◽  
Antimicrobial Resistance Genes

Salmonella enterica subspecies enterica serovar Derby (S. Derby) is one of the most frequent causes for salmonellosis in humans and animals. Understanding the genetic diversity of S. Derby, as well as the nature and origin of its resistance to antimicrobial treatment are thus the key to epidemiological control and surveillance. Here, we report an analysis of 15 S. Derby strains isolated from pig and cattle in slaughterhouses across Germany (2000–2015), which belonged to multilocus sequence types (ST) ST39, ST40 and ST682. Strains were compared to publicly available S. Derby sequence data of these three STs from Germany, comprising 65 isolates collected between 2004 and 2018 from different sources (i.e., pigs, humans, cattle, wild boar, and poultry). A total of 80 sequences (ST39 = 34, ST40 = 21, and ST682 = 25) were analyzed to assess genetic diversity, to identify virulence-associated and antimicrobial resistance genes (ARGs), and to characterize plasmid content. Strains belonging to all three STs were identified in each source examined. Strains with the same ST were closely related regardless of origin. Altogether, 72.5% of the isolates carried at least one resistance gene, furthermore ST40 carried most of the ARGs and the plasmid replicons. The IncI1 replicon was detected in eleven isolates, four of them carried IncI1 plasmid ST26 with clonal complex 2. The comparison of these four isolates with an IncI1 ST26 plasmid reported in 2010 from a German pig (JX566770), showed only variations in a region carrying different ARGs and mobile genetic elements. The strains of our collection had similar genetic diversity as the strains taken from the public database. Moreover, we found that strains harboring multidrug resistant IncI plasmid were found in different animal species, indicating that S. Derby may be implicated in the spread of antimicrobial resistance among animal species. Results may contribute to the knowledge about the diversity in S. Derby in Germany, which may be useful for the future surveillance and antimicrobial resistance of this serovar.

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