Prevalence of <i>emm1 Streptococcus pyogenes</i> having a novel type of genomic composition

Tatsuno, Ichiro; Isaka, Masanori; Matsumoto, M.; Hasegawa, Tadao

doi:10.1111/1348-0421.12739

Cited by 4 publications

(4 citation statements)

References 18 publications

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“…Targeting the water supply as the source of L. pneumophila-ST1326 required sequence-based typing, not just organism identification, as did confirming K. variicola transmission (2). RMg applied to severe CA-LRTI cases identified virulence factors (luk f/S) and emerging virulent clones missed by culture (S. dysgalactiae STG62647A and S. pyogenes emm1-M1uk) (23). The latter is of particular public health significance given its link with severe paediatric infections and deaths, first announced by UKHSA 8 weeks after this case (24,25).…”

Section: Discussionmentioning

confidence: 89%

Routine respiratory metagenomics service for intensive care unit patients

Charalampous

Alcolea-Medina

Snell

et al. 2023

Preprint

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Background: Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into clinical practice. Methods: Feasibility, performance and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service for patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory intensive care units (ICU) at Guys & St Thomas NHS foundation Trust, London. Results: RMg was performed on 128 samples from 87 patients during the first 15-weeks providing same-day results for 110 samples (86%) with median turnaround time of 6.7hrs (IQR 6.1-7.5 hrs). RMg was 92% sensitive and 82% specific for clinically-relevant pathogens compared with routine testing. 48% of RMg results informed antimicrobial prescribing changes (22% escalation; 26% de-escalation) with escalation based on speciation in 20/24 cases and detection of acquired-resistance genes in 4/24 cases. Fastidious or unexpected organisms were reported in 21 samples including anaerobes (n=12), Mycobacterium tuberculosis, Tropheryma whipplei, cytomegalovirus and Legionella pneumophila ST1326, which was subsequently isolated from the bed-side water outlet. Application to consecutive severe community-acquired LRTI cases identified Staphylococcus aureus (two with SCCmec and three with luk F/S virulence determinants), Streptococcus pyogenes (emm1-M1uk clone), S. dysgalactiae subspecies equisimilis (STG62647A) and Aspergillus fumigatus with multiple treatments and public-health impacts. Conclusions: RMg provides frequent diverse benefits for treatment, infection control and public health. The combination of rapid comprehensive results, alongside revealing and characterising a hidden burden of infections makes the case for expediting routine service implementation

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Section: Discussionmentioning

confidence: 89%

Routine respiratory metagenomics service for intensive care unit patients

Charalampous

Alcolea-Medina

Snell

et al. 2023

Preprint

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“…Targeting the water supply as the source of L. pneumophila -ST1326 required sequence-based typing, not just organism identification, as did confirming K. variicola transmission ( 2 ). RMg applied to severe CA LRTI cases identified virulence factors ( luk f/S ) and emerging virulent clones missed by culture ( S. dysgalactiae STG62647A and S. pyogenes emm1- M1uk) ( 28 ). The latter is of particular public health significance, given its link with severe pediatric infections and deaths, first announced by UK Health Security Agency 8 weeks after this case ( 29 , 30 ).…”

Section: Discussionmentioning

confidence: 99%

Routine Metagenomics Service for ICU Patients with Respiratory Infection

Charalampous,

Alcolea-Medina,

Snell

et al. 2024

Am J Respir Crit Care Med

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Rationale Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into routine clinical practice. Objectives Feasibility, performance, and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service. Methods RMg was performed on 128 samples from 87 patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory ICUs at Guy’s and St Thomas’ NHS Foundation Trust, London. Measurements and Main Results During the first 15 weeks, RMg provided same-day results for 110 samples (86%), with a median turnaround time of 6.7 hours (interquartile range = 6.1–7.5 h). RMg was 93% sensitive and 81% specific for clinically relevant pathogens compared with routine testing. Forty-eight percent of RMg results informed antimicrobial prescribing changes (22% escalation; 26% deescalation) with escalation based on speciation in 20 out of 24 cases and detection of acquired-resistance genes in 4 out of 24 cases. Fastidious or unexpected organisms were reported in 21 samples, including anaerobes ( n = 12), Mycobacterium tuberculosis , Tropheryma whipplei , cytomegalovirus, and Legionella pneumophila ST1326, which was subsequently isolated from the bedside water outlet. Application to consecutive severe community-acquired LRTI cases identified Staphylococcus aureus (two with SCCmec and three with luk F/S virulence determinants), Streptococcus pyogenes ( emm1- M1uk clone), S. dysgalactiae subspecies equisimilis (STG62647A), and Aspergillus fumigatus with multiple treatments and public health impacts. Conclusions This pilot study illustrates the potential of RMg testing to provide benefits for antimicrobial treatment, infection control, and public health when provided in a real-world critical care setting. Multicenter studies are now required to inform future translation into routine service.

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“…Bacteria were cultured in brain heart infusion broth (Eiken Chemical, Tokyo, Japan) supplemented with 0.3% yeast extract (Becton Dickinson, Sparks, MD, USA) (BHI-YE) at 37°C without agitation, as described previously [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

“…Typing of the M protein-coding gene ( emm ) of streptococcal isolates was performed according to the methods by CDC Streptococcus Laboratory ( https://www.cdc.gov/streplab/protocol-emm-type.html ) as described previously [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

General Phenotype of NADase Induction by CLI Treatment in Streptococcus pyogenes

Tatsuno

Isaka

Hasegawa

2022

International Journal of Microbiology

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The administration of high-dose clindamycin (CLI) along with penicillin is recommended for the treatment of streptococcal toxic-shock syndrome (STSS). However, we previously reported that a “subinhibitory dose” of CLI induced the expression of the NAD-glycohydrolase (NADase) exotoxin in an emm1-type Streptococcus pyogenes 1529 strain isolated from an STSS patient. In this study, we examine NADase induction by CLI treatment using an extracellular NADase activity assay instead of the previous two-dimensional gel electrophoresis assay. The examination revealed that CLI administration can induce NADase expression in a dose-dependent manner. We analyzed 23 CLI-susceptible strains (5 emm1 strains, 6 emm3 strains, 3 emm4 strains, 1 emm6 strain, 3 emm12 strains, 1 emm28 strain, and 4 emm89 strains), and 19 of the 23 strains showed similar NADase induction phenotypes to that shown in strain 1529. These results indicate that NADase induction by CLI treatment is not restricted to specific strains and it could be a standard phenotype among CLI-susceptible S. pyogenes strains. We also analyzed four CLI-resistant strains. All four strains showed increased extracellular NADase activities at high concentrations of CLI that did not inhibit bacterial growth. These results indicated that the subinhibitory dose of CLI was not the critical factor for NADase induction.

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Prevalence of emm1 Streptococcus pyogenes having a novel type of genomic composition

Cited by 4 publications

References 18 publications

Routine respiratory metagenomics service for intensive care unit patients

Routine respiratory metagenomics service for intensive care unit patients

Routine Metagenomics Service for ICU Patients with Respiratory Infection

General Phenotype of NADase Induction by CLI Treatment in Streptococcus pyogenes

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