A Protracted Outbreak of Invasive Group A Streptococcal Infection at a UK Long-Term Facility Investigated Using Whole Genome Sequencing

Abstract Whole-genome analysis was applied to investigate atypical point-source transmission of 2 invasive group A streptococcal (GAS) infections. Isolates were serotype M4, ST39, and genetically indistinguishable. Comparison with MGAS10750 revealed nonsynonymous polymorphisms in ropB and increased speB transcription. This study demonstrates the usefulness of whole-genome analyses for GAS outbreaks.

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Increase in Invasive Group A Streptococcal Disease and Emergence of Mucoid Strains in a Pediatric Population: February–June 2017

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz275 ◽

2019 ◽

Vol 6 (7) ◽

Cited By ~ 1

Author(s):

Lorne W Walker ◽

Lindsay Montoya ◽

Sopio Chochua ◽

Bernard Beall ◽

Michael Green

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Hospital Admissions ◽

Disease Incidence ◽

Tertiary Care ◽

Incidence Rates ◽

Screening Tests ◽

Whole Genome ◽

Invasive Group ◽

Group A

Abstract Background Infection with group A Streptococcus (GAS) can cause severe systemic and locally invasive disease. Invasive group A streptococcal (iGAS) disease incidence varies both seasonally and year-to-year, and it may exhibit clustered outbreaks. We observed an upswing in iGAS cases at a tertiary care Children’s Hospital, prompting further characterization of local iGAS disease. Methods Cases of iGAS disease were abstracted from the medical record by manual chart review of all positive screening tests and cultures for GAS over a 4-year span. Incidence rates per 1000 hospital admissions and per 100 positive GAS tests were calculated and compared. Selected isolates were further characterized by whole-genome sequencing. Results Significant year-to-year differences in per-admission iGAS incidence rate were observed in February and June, although per-positive test incidence rates were not significantly different. Whole-genome sequencing revealed 2 dominant serotypes—emm3 and emm6—with high rates of mucoid phenotype and systemic bacteremia. Conclusions We document a significant but transient increase in iGAS disease incidence in 2 months of 2017. Genome sequencing revealed 2 dominant serotypes associated with mucoid phenotypes and severe disease, highlighting the dynamic nature of iGAS disease pattern.

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Severe emm89 Group A Streptococcal Disease Characterized by Toxic Shock and Endocarditis

Case Reports in Infectious Diseases ◽

10.1155/2019/6568732 ◽

2019 ◽

Vol 2019 ◽

pp. 1-4

Author(s):

Morouge Alramadhan ◽

Gloria P. Heresi ◽

Anthony R. Flores

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rare Case ◽

Whole Genome ◽

Toxic Shock ◽

Invasive Group ◽

Streptococcal Disease ◽

Group A ◽

Common Infections

Invasive group A Streptococcus infections are associated with diverse presentations. We report a severe, rare case of GAS infection with dissemination including endocarditis and STSS. While whole genome sequencing of blood and pharyngeal isolates did not reveal any unique features attributable to the severe presentation, our approach serves as a template for investigation of severe manifestations of common infections.

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Whole genome sequencing reveals extensive community-level transmission of group AStreptococcusin remote communities

Epidemiology and Infection ◽

10.1017/s095026881500326x ◽

2016 ◽

Vol 144 (9) ◽

pp. 1991-1998 ◽

Cited By ~ 11

Author(s):

A. C. BOWEN ◽

T. HARRIS ◽

D. C. HOLT ◽

P. M. GIFFARD ◽

J. R. CARAPETIS ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Remote Communities ◽

Single Nucleotide ◽

Indigenous Children ◽

Primary Driver ◽

Group A ◽

Sequence Types

SUMMARYImpetigo is common in remote Indigenous children of northern Australia, with the primary driver in this context beingStreptococcus pyogenes[or group AStreptococcus(GAS)]. To reduce the high burden of impetigo, the transmission dynamics of GAS must be more clearly elucidated. We performed whole genome sequencing on 31 GAS isolates collected in a single community from children in 11 households with ⩾2 GAS-infected children. We aimed to determine whether transmission was occurring principally within households or across the community. The 31 isolates were represented by nine multilocus sequence types and isolates within each sequence type differed from one another by only 0–3 single nucleotide polymorphisms. There was evidence of extensive transmission both within households and across the community. Our findings suggest that strategies to reduce the burden of impetigo in this setting will need to extend beyond individual households, and incorporate multi-faceted, community-wide approaches.

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Insights into the long-term persistence of Legionella in facilities from whole-genome sequencing

Infection Genetics and Evolution ◽

10.1016/j.meegid.2018.07.040 ◽

2018 ◽

Vol 65 ◽

pp. 200-209 ◽

Cited By ~ 2

Author(s):

Megan Wells ◽

Erica Lasek-Nesselquist ◽

Dianna Schoonmaker-Bopp ◽

Deborah Baker ◽

Lisa Thompson ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks

Microbial Genomics ◽

10.1099/mgen.0.000672 ◽

2021 ◽

Vol 7 (11) ◽

Author(s):

Isabelle Bernaquez ◽

Christiane Gaudreau ◽

Pierre A. Pilon ◽

Sadjia Bekal

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Type Species ◽

Core Genome ◽

Outbreak Detection ◽

Whole Genome ◽

Content Type ◽

Link Type ◽

Interpretation Criteria

Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus sequence typing (MLST)-based allele differences and/or core genome single-nucleotide variants (SNVs). In addition to being a food- and travel-associated outbreak pathogen, most Shigella spp. cases occur through continuous person-to-person transmission, predominantly involving men who have sex with men (MSM), leading to long-term and recurrent outbreaks. Continuous transmission patterns coupled to genetic evolution under antibiotic treatment pressure require an assessment of existing WGS-based subtyping methods and interpretation criteria for cluster inclusion/exclusion. An evaluation of 4 WGS-based subtyping methods [SNVPhyl, coreMLST, core genome MLST (cgMLST) and whole-genome MLST (wgMLST)] was performed on 9 foodborne-, travel- and MSM-related retrospective outbreaks from a collection of 91 Shigella flexneri and 232 Shigella sonnei isolates to determine the methods’ epidemiological concordance, discriminatory power, robustness and ability to generate stable interpretation criteria. The discriminatory powers were ranked as follows: coreMLST<SNVPhyl<cgMLST<wgMLST (range: 0.970–1.000). The genetic differences observed for non-MSM-related Shigella spp. outbreaks respect the standard 0–10 allele/SNV guideline; however, mobile genetic element (MGE)-encoded loci caused inflated genetic variation and discrepant phylogenies for prolonged MSM-related S. sonnei outbreaks via wgMLST. The S. sonnei correlation coefficients of wgMLST were also the lowest at 0.680, 0.703 and 0.712 for SNVPhyl, coreMLST and cgMLST, respectively. Plasmid maintenance, mobilization and conjugation-associated genes were found to be the main source of genetic distance inflation in addition to prophage-related genes. Duplicated alleles arising from the repeated nature of IS elements were also responsible for many false cg/wgMLST differences. The coreMLST approach was shown to be the most robust, followed by SNVPhyl and wgMLST for inter-laboratory comparability. Our results highlight the need for validating species-specific subtyping methods based on microbial genome plasticity and outbreak dynamics in addition to the importance of filtering confounding MGEs for cluster detection.

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Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region

Microorganisms ◽

10.3390/microorganisms9091985 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1985

Author(s):

Alessandra Piccirilli ◽

Sabrina Cherubini ◽

Anna Azzini ◽

Evelina Tacconelli ◽

Giuliana Lo Cascio ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Long Term Care ◽

Whole Genome ◽

Italian Region ◽

Term Care ◽

Sequencing Platform ◽

Carbapenem Resistant ◽

Care Facilities

K. pneumoniae (KPN) is one of the widest spread bacteria in which combined resistance to several antimicrobial groups is frequent. The most common β-lactamases found in K. pneumoniae are class A carbapenemases, both chromosomal-encoded (i.e., NMCA, IMI-1) and plasmid-encoded (i.e., GES-enzymes, IMI-2), VIM, IMP, NDM, OXA-48, and extended-spectrum β-lactamases (ESBLs) such as CTX-M enzymes. In the present study, a total of 68 carbapenem-resistant KPN were collected from twelve long-term care facilities (LTCFs) in the Northern Italian region. The whole-genome sequencing (WGS) of each KPN strain was determined using a MiSeq Illumina sequencing platform and analysed by a bacterial analysis pipeline (BAP) tool. The WGS analysis showed the prevalence of ST307, ST512, and ST37 as major lineages diffused among the twelve LTCFs. The other lineages found were: ST11, ST16, ST35, ST253, ST273, ST321, ST416, ST1519, ST2623, and ST3227. The blaKPC-2, blaKPC-3, blaKPC-9, blaSHV-11, blaSHV-28, blaCTX-M-15, blaOXA-1, blaOXA-9, blaOXA-23, qnrS1, qnrB19, qnrB66, aac(6′)-Ib-cr, and fosA were the resistance genes widespread in most LTCFs. In this study, we demonstrated the spreading of thirteen KPN lineages among the LTCFs. Additionally, KPC carbapenemases are the most widespread β-lactamase.

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Long-Term Clonal Dynamics upon Allogeneic Haematopoietic Stem Cell Transplantation Revealed Using Somatic Mutations As Clonal Tracking Marks in HSC Donor and Recipient Pairs

Blood ◽

10.1182/blood-2021-146151 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3813-3813

Author(s):

Michael Spencer Chapman ◽

C. Matthias Wilk ◽

Steffen Boettcher ◽

Larisa V. Kovtonyuk ◽

Emily Mitchell ◽

...

Keyword(s):

Stem Cell ◽

Stem Cell Transplantation ◽

Whole Genome Sequencing ◽

Cell Transplantation ◽

Genome Sequencing ◽

Haematopoietic Stem Cell Transplantation ◽

Somatic Mutations ◽

Haematopoietic Stem Cell ◽

Whole Genome

Abstract Allogeneic haematopoietic stem cell transplantation (HSCT) is a potentially curative treatment for over 40,000 patients/year in Europe and the US alone. However, substantial treatment-related mortality and morbidity, as well as risks of disease relapse give a survival rate of about 50% and leave considerable room for improvement. Despite being an established treatment for over 50 years, fundamental questions remain regarding its biology. For example, how many of the frequently >100 million transplanted CD34+ cells are true haematopoietic stem cells (HSCs), determined by long-term engraftment and contribution to multi-lineage hematopoiesis (long-term engrafting HSCs [LTE-HSCs])? What are the mutational consequences for transplanted HSCs given their proliferation and potential mutagenic insults in the post-transplant period? Most recently, the discovery of clonal haematopoiesis (CH) has raised interest in the interaction between this and HSCT. Do such clones further expand during HSCT? This may potentially lead to the devastating complication of donor-cell leukemia or other CH-related risks, e.g. cardiovascular disease. Recently, some studies have addressed this using targeted sequencing panels for myeloid cancer genes. However, many clonal expansions in normal blood are not driven by mutations in such genes, with evidence suggesting that the set of potential 'driver' genes is much larger than currently recognized (Poon et al, bioRXiv 2020). Advances in HSC tracking methodologies - using naturally-occurring somatic mutations as clonal markers (Lee-Six et al, Nature 2018) - provide a powerful tool to simultaneously address these questions. Whole-genome sequencing of hundreds of single-cell derived haematopoietic stem and progenitor cell (HSPC) colonies from a single individual is used to compile a complete set of somatic mutations in each colony founder cell, and the pattern of shared mutations amongst cells used to infer their phylogeny or 'family tree'. The constant rate of mutation acquisition during post-development life allows estimation of the timing of mutation acquisition. Using phylodynamic approaches borrowed from pathogen biology, patterns of branching points can be used to infer important parameters such as the size of population 'bottlenecks' (in this context the number of LTE-HSCs), and the growth dynamics of expanded clones. We selected 7 donor/ recipient (D/ R) pairs who had undergone HSCT 9-31 years previously. For each individual (D and R), peripheral blood CD34+ HSPC-derived colonies were grown on methylcellulose medium. Whole-genome sequencing (WGS) was performed on 100-300 colonies per individual - a total of 2,278 genomes. Mutations were called using established pipelines, then filtered to remove artefacts, germline variants, and in vitro mutations leaving only somatically-acquired mutations. Phylogenies for each D/R pair were inferred, using a maximum parsimony algorithm. Mutational signatures were extracted using a hierarchical dirichlet process. D/R phylogenies were compared using metrics of phylogenetic diversity. Clonal fractions of expanded clones in D/R were compared. Approximate Bayesian computation was used to estimate numbers of LTE-HSCs. Our results reveal that HSCT engraftment is remarkably polyclonal, with thousands of transplanted HSCs (in most cases >5,000) actively contributing to haematopoiesis decades after transplant. HSCs suffer little consequence in terms of their somatic mutation burden. Recipient haematopoiesis showed decreased clonal diversity compared to their donors with a mean 20% decrease of the Shannon's Diversity Index. This may partly result from increased selective pressures during HSCT. Intriguingly, several DNMT3A-driven expansions seen in donors had lower clonal fractions in recipients. Conversely, clones with >1 driver mutation (e.g. DNMT3A/CHEK2) showed larger expansions in recipients compared to donors, despite originating in the donor. DNMT3A mutations frequently originated in early development - in one case occurring in utero. We demonstrate the power of applying a novel clonal tracking approach to HSCT, for the first time giving a detailed picture of the clonal dynamics of engraftment. Overall, our findings are reassuring from a safety perspective, but the different clonal composition in recipients merits further investigation to better understand the factors involved. Disclosures Manz: University of Zurich: Patents & Royalties: CD117xCD3 TEA; CDR-Life Inc: Consultancy, Current holder of stock options in a privately-held company. Campbell: Mu Genomics: Current holder of individual stocks in a privately-held company, Membership on an entity's Board of Directors or advisory committees.

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