scholarly journals A global to local genomics analysis ofClostridioides difficileST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

2019 ◽  
Author(s):  
Charles H.D. Williamson ◽  
Nathan E. Stone ◽  
Amalee E. Nunnally ◽  
Heidie M. Hornstra ◽  
David M. Wagner ◽  
...  
Keyword(s):  
Control Strategies ◽  
Sampling Period ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Infection Prevention And Control ◽  
Snp Analysis ◽  
Whole Genome ◽  
Surveillance Strategy ◽  
Northern Arizona ◽  
Healthcare Network

AbstractClostridioides difficileis a ubiquitous, diarrheagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion ofC. difficilecases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in theC. difficilemultilocus sequence typing (MLST) scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat un-related infections, which creates conditions ideal forC. difficilecolonization and proliferation. In this study, we analyzed 27 isolates from a healthcare network in northern Arizona, USA, and 1,352 public ST1 genomes to place locally-sampled isolates into a global context. Core genome, single nucleotide polymorphism (SNP) analysis demonstrated that at least 6 separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates following two of these introductions, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally, we compared all high-qualityC. difficilegenomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all otherC. difficilegenomes; analyses of other toxigenicC. difficilesequence types demonstrates that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type withC. difficileinfection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinicalC. difficileisolates provides a high-resolution surveillance strategy for monitoring persistence and transmission ofC. difficileand for assessing the performance of infection prevention and control strategies.

scholarly journals A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

2019 ◽  
Vol 5 (7) ◽  
Author(s):  
Charles H. D. Williamson ◽  
Nathan E. Stone ◽  
Amalee E. Nunnally ◽  
Heidie M. Hornstra ◽  
David M. Wagner ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Type ◽  
Infection Prevention And Control ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Content Type ◽  
Northern Arizona ◽  
Healthcare Network ◽  
Link Type ◽  
Clostridioides Difficile

Clostridioides difficile is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the C. difficile multilocus sequence typing scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat unrelated infections, which creates conditions ideal for C. difficile colonization and proliferation. In this study, we analysed 27 isolates from a healthcare network in northern Arizona, USA, and 1352 publicly available ST1 genomes to place locally sampled isolates into a global context. Whole genome, single nucleotide polymorphism analysis demonstrated that at least six separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally and in northern Arizona, we compared all high-quality C. difficile genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other C. difficile genomes; analyses of other toxigenic C. difficile sequence types demonstrate that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with C. difficile infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical C. difficile isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of C. difficile and for assessing the performance of infection prevention and control strategies.

scholarly journals Sequence Type 273 Carbapenem-Resistant Klebsiella pneumoniae Carrying bla NDM-1 and bla IMP-4

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Lu Liu ◽  
Yu Feng ◽  
Haiyan Long ◽  
Alan McNally ◽  
Zhiyong Zong
Keyword(s):  
Klebsiella Pneumoniae ◽  
Southeast Asia ◽  
Human Blood ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Transmissible Plasmid ◽  
Long Read

ABSTRACT A carbapenem-resistant Klebsiella pneumoniae isolate was recovered from human blood. Its whole-genome sequence was obtained using Illumina and long-read MinION sequencing. The strain belongs to sequence type 273 (ST273), which was found recently and caused an outbreak in Southeast Asia. It has two carbapenemase genes, bla NDM-1 (carried by an ST7 IncN self-transmissible plasmid) and bla IMP-4 (located on a self-transmissible IncHI5 plasmid). Non-KPC-producing ST237 may represent a lineage of carbapenem-resistant K. pneumoniae , which warrants further monitoring.

scholarly journals Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains

2019 ◽  
Vol 6 (2) ◽  
Author(s):  
Bradley T Endres ◽  
Khurshida Begum ◽  
Hua Sun ◽  
Seth T Walk ◽  
Ali Memariani ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
The United States ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Whole Genome ◽  
Ribotype 027 ◽  
Clostridioides Difficile

Abstract Background The epidemic Clostridioides difficile ribotype 027 strain resulted from the dissemination of 2 separate fluoroquinolone-resistant lineages: FQR1 and FQR2. Both lineages were reported to originate in North America; however, confirmatory large-scale investigations of C difficile ribotype 027 epidemiology using whole genome sequencing has not been undertaken in the United States. Methods Whole genome sequencing and single-nucleotide polymorphism (SNP) analysis was performed on 76 clinical ribotype 027 isolates obtained from hospitalized patients in Texas with C difficile infection and compared with 32 previously sequenced worldwide strains. Maximum-likelihood phylogeny based on a set of core genome SNPs was used to construct phylogenetic trees investigating strain macro- and microevolution. Bayesian phylogenetic and phylogeographic analyses were used to incorporate temporal and geographic variables with the SNP strain analysis. Results Whole genome sequence analysis identified 2841 SNPs including 900 nonsynonymous mutations, 1404 synonymous substitutions, and 537 intergenic changes. Phylogenetic analysis separated the strains into 2 prominent groups, which grossly differed by 28 SNPs: the FQR1 and FQR2 lineages. Five isolates were identified as pre-epidemic strains. Phylogeny demonstrated unique clustering and resistance genes in Texas strains indicating that spatiotemporal bias has defined the microevolution of ribotype 027 genetics. Conclusions Clostridioides difficile ribotype 027 lineages emerged earlier than previously reported, coinciding with increased use of fluoroquinolones. Both FQR1 and FQR2 ribotype 027 epidemic lineages are present in Texas, but they have evolved geographically to represent region-specific public health threats.

scholarly journals Draft Whole-Genome Sequence of a Catalase-Negative Staphylococcus aureus subsp. aureus (Sequence Type 25) Strain Isolated from a Patient with Endocarditis and Septic Arthritis

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Byron Berenger ◽  
Justin Chen ◽  
Anne-Marie Bernier ◽  
Kathryn Bernard
Keyword(s):  
Staphylococcus Aureus ◽  
Septic Arthritis ◽  
Genome Sequence ◽  
Catalase Activity ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Invasive Infection ◽  
Whole Genome ◽  
Missense Mutations ◽  
Biochemical Methods

Staphylococcus aureus strains without catalase activity are rare, challenging to identify with conventional biochemical methods, and, despite a supposed decreased pathogenicity, can still cause disease. The first whole-genome sequence of a catalase-negative S. aureus isolate causing severe recurrent invasive infection with two novel missense mutations in the katA gene is reported here.

scholarly journals Whole Genome Sequence Analysis of Brucella abortus Isolates from Various Regions of South Africa

2021 ◽  
Vol 9 (3) ◽  
pp. 570
Author(s):  
Maphuti Betty Ledwaba ◽  
Barbara Akorfa Glover ◽  
Itumeleng Matle ◽  
Giuseppe Profiti ◽  
Pier Luigi Martelli ◽  
...  
Keyword(s):  
South Africa ◽  
Single Nucleotide Polymorphisms ◽  
South African ◽  
Genome Sequence ◽  
Brucella Abortus ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

The availability of whole genome sequences in public databases permits genome-wide comparative studies of various bacterial species. Whole genome sequence-single nucleotide polymorphisms (WGS-SNP) analysis has been used in recent studies and allows the discrimination of various Brucella species and strains. In the present study, 13 Brucella spp. strains from cattle of various locations in provinces of South Africa were typed and discriminated. WGS-SNP analysis indicated a maximum pairwise distance ranging from 4 to 77 single nucleotide polymorphisms (SNPs) between the South African Brucella abortus virulent field strains. Moreover, it was shown that the South African B. abortus strains grouped closely to B. abortus strains from Mozambique and Zimbabwe, as well as other Eurasian countries, such as Portugal and India. WGS-SNP analysis of South African B. abortus strains demonstrated that the same genotype circulated in one farm (Farm 1), whereas another farm (Farm 2) in the same province had two different genotypes. This indicated that brucellosis in South Africa spreads within the herd on some farms, whereas the introduction of infected animals is the mode of transmission on other farms. Three B. abortus vaccine S19 strains isolated from tissue and aborted material were identical, even though they originated from different herds and regions of South Africa. This might be due to the incorrect vaccination of animals older than the recommended age of 4–8 months or might be a problem associated with vaccine production.

scholarly journals Phylogeny of Yersinia pestis Strains Belonging to 0.ANT Branch, Isolated in Tien-Shan and Pamir-Alay in XX–XXI Centuries

2020 ◽  
pp. 76-84
Author(s):  
G. A. Eroshenko ◽  
A. K. Dzhaparova ◽  
E. G. Oglodin ◽  
Zh. V. Al’khova ◽  
L. M. Kukleva ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Tien Shan ◽  
Whole Genome Sequence ◽  
Clinical Strain ◽  
Snp Analysis ◽  
Whole Genome ◽  
Kyrgyz Republic ◽  
Natural Foci ◽  
First Time ◽  
Wide Dissemination

Objective of the study was to conduct phylogenetic analysis of Yersinia pestis strains of the main subspecies, belonging to antique biovar, phylogenetic branch 0.ANT, isolated in XX – early XXI centuries in the foci of Tien-Shan and Pamir-Alay to identify the regularities of spatial-temporal circulation of plague agent in the territory of the foci. Materials and methods. We have carried out whole genome SNP-analysis of Y. pestis strains of antique biovar, isolated in natural foci of Kyrgyz Republic in 1928–2016. Phylogenetic investigation is based on 1646 identified core SNPs in 51 included in the analysis strains of different phylogenetic lines. Phylogenetic tree was constructed using Maximum Likelihood algorithm, PHYML software package, and HKY85 model. Results and discussion. All 29 studied Y. pestis strains isolated between 1928 and 2016 in the foci of Tien-Shan and Pamir-Alay fall under the phylogenetic branches 0.ANT3 and 0.ANT5 of antique biovar of the main subspecies. Strains of 0.ANT3 branch were collected predominantly in Aksay and Alay foci, while strains of 0. ANT5 – in Upper-Naryn and Sarydzhas foci of Tien-Shan. Strains of phylogenetic lines 0.ANT1 and 0.ANT2 were not found in the foci of Kyrgyz Republic. According to the results of whole genome SNP-analysis, Y. pestis strains isolated in the XXI century belong to phylogenetic branch 0.ANT5. This branch also comprises a strain obtained from a patient (lethal case) in Sarydzhas plague focus in 2013. Genetic homogeneity of the modern strains of 0.ANT5 branch and their wide dissemination testify to the extension of the areal of this population and activation of Tien-Shan foci, caused by climate warming. For the first time ever, genomes of Y. pestis 0.ANT5 branch, isolated in XXI century, including clinical strain dated 2013, have been sequenced. We have obtained the whole-genome sequence of Y. pestis strain, 0.ANT3 branch, which caused pneumonic plague outbreak in Tien-Shan in 1928.

COMPARISON OF WHOLE GENOME SEQUENCE-BASED METHODS AND PCR RIBOTYPING FOR SUBTYPING OF Clostridioides difficile

2021 ◽  
Author(s):  
A Baktash ◽  
J Corver ◽  
C Harmanus ◽  
W. K. Smits ◽  
W Fawley ◽  
...  
Keyword(s):  
Epidemiological Data ◽  
Discriminatory Power ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Whole Genome ◽  
Gastrointestinal Infections ◽  
Single Nucleotide ◽  
Clostridioides Difficile ◽  
Pcr Ribotyping ◽  
Allele Difference

Clostridioides difficile is the most common cause of antibiotic-associated gastrointestinal infections. Capillary-electrophoresis (CE)-PCR ribotyping is currently the gold standard for C. difficile typing but lacks discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better and provide standardized and interlaboratory exchangeable data. Using a well-characterized collection of diverse strains (N=630; 100 unique ribotypes (RTs)), we compared the discriminatory power of core genome multilocus sequence typing (cgMLST) (SeqSphere & EnteroBase), whole genome MLST (wgMLST) (EnteroBase) and single nucleotide polymorphism (SNP) analysis. A unique cgMLST profile (>6 allele differences) was observed in 82/100 RTs, indicating that cgMLST could distinguish most, but not all, RTs. Application of cgMLST in two outbreak settings with RT078 and RT181 (known with a low intra-RT allele difference) showed no distinction between outbreak- and non-outbreak strains, in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize and offers higher discrimination. However, adjusted cut-off thresholds and epidemiological data are necessary to recognize outbreaks of some specific RTs. We propose to use an allelic threshold 3 alleles to identify outbreaks.

scholarly journals Institutional outbreak involving multiple clades of IMP-producing Enterobacter cloacae complex sequence type 78 at a cancer center in Tokyo, Japan

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sohei Harada ◽  
Kotaro Aoki ◽  
Daisuke Ohkushi ◽  
Koh Okamoto ◽  
Kazumi Takehana ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Cancer Center ◽  
Snp Analysis ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Class 1 Integron ◽  
Clonal Relatedness

Abstract Background Information about the clinical and microbiological characteristics of IMP-producing Enterobacterales has been limited. Here, we describe an institutional outbreak of IMP-producing Enterobacter cloacae complex (ECC) involving multiple clades of ECC sequence type (ST) 78 strains. Methods Antimicrobial susceptibility testing, whole-genome sequencing, and conjugation experiments of 18 IMP-producing ECC strains isolated during four-year study period were performed. Species and subspecies were determined by average nucleotide identity analysis and clonal relatedness of the isolates was analyzed with multilocus sequence typing and core-genome single nucleotide polymorphism (SNP) analysis. Relevant clinical information was extracted from medical records. Results Fourteen of 18 IMP-producing ECC isolates were determined as Enterobacter hormaechei ST78. Sixteen isolates, including 13 isolates belonging to ST78, carried blaIMP-1 in In316-like class 1 integron and also carried IncHI2 plasmids. Conjugation experiments were successful for 12 isolates carrying blaIMP-1 on IncHI2 plasmids and for an isolate carrying blaIMP-11 on an IncL/M plasmid. Although isolation of ST78 strains was clustered in a 14-months period suggesting nosocomial transmission, these strains were subdivided into three clades by SNP analysis: clade A (n = 10), clade B (n = 1), clade C (n = 3). A part of clonal relatedness was unexpected by the epidemiological information at the time of isolation of the strains. Most of the IMP-producing ECC strains were susceptible to non-β-lactam antibiotics and had relatively low minimum inhibitory concentrations to carbapenems (≤4 μg/mL). Five of six infections caused by IMP-producing ECC were treated successfully. Conclusions Whole-genome sequencing analysis revealed the outbreak was caused by three different clades of ST78 strains, where patients had favorable treatment outcome of the infections compared with that caused by Enterobacterales producing other carbapenemases, possibly due to their non-multidrug-resistant phenotype.

scholarly journals Clostridium botulinum Group II Isolate Phylogenomic Profiling Using Whole-Genome Sequence Data

2015 ◽  
Vol 81 (17) ◽  
pp. 5938-5948 ◽  
Author(s):  
K. A. Weedmark ◽  
P. Mabon ◽  
K. L. Hayden ◽  
D. Lambert ◽  
G. Van Domselaar ◽  
...  
Keyword(s):  
Genome Sequence ◽  
In Silico ◽  
Clostridium Botulinum ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Whole Genome ◽  
Content Type ◽  
Genome Sequence Data ◽  
Group Ii

ABSTRACTClostridium botulinumgroup II isolates (n= 163) from different geographic regions, outbreaks, and neurotoxin types and subtypes were characterizedin silicousing whole-genome sequence data. Two clusters representing a variety of botulinum neurotoxin (BoNT) types and subtypes were identified by multilocus sequence typing (MLST) and core single nucleotide polymorphism (SNP) analysis. While one cluster included BoNT/B4/F6/E9 and nontoxigenic members, the other comprised a wide variety of different BoNT/E subtype isolates and a nontoxigenic strain.In silicoMLST and core SNP methods were consistent in terms of clade-level isolate classification; however, core SNP analysis showed higher resolution capability. Furthermore, core SNP analysis correctly distinguished isolates by outbreak and location. This study illustrated the utility of next-generation sequence-based typing approaches for isolate characterization and source attribution and identified discrete SNP loci and MLST alleles for isolate comparison.

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