A decade of clinical microbiology: top 10 advances in 10 years: what every infection preventionist and antimicrobial steward should know

Jhaveri, Tulip A.; Weiss, Zoe Freeman; Winkler, Marisa L.; Pyden, Alexander D.; Basu, Sankha S.; Pecora, Nicole D.

doi:10.1017/ash.2024.10

Cited by 6 publications

(1 citation statement)

References 92 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Next Generation Sequencing (NGS) offers huge promise for advancing surveillance of hospital pathogens, but it is still predominantly performed in larger reference or research laboratories [1]. However, this is a rapidly changing field and Oxford Nanopore Technologies (ONT) sequencing offers practical advantages as an accessible sequencing option for frontline diagnostic microbiology laboratories, including minimal footprint, low up-front capital expenses, and rapid sequence data generation [2].…”

Section: Introductionmentioning

confidence: 99%

Resolving a neonatal intensive care unit outbreak of methicillin-resistantStaphylococcus aureusto the SNV level using Oxford Nanopore simplex reads and HERRO error correction

Bloomfield,

Bakker,

Burton

et al. 2024

Preprint

View full text Add to dashboard Cite

ObjectivesOur laboratory began prospective genomic surveillance for healthcare-associated organisms in 2022 using Oxford Nanopore Technologies (ONT) sequencing as a standalone platform. This has permitted the early detection of outbreaks but has been insufficient for single-nucleotide variant (SNV)-level analysis due to lower read accuracy than Illumina sequencing. This study aimed to determine whether Haplotype-aware ERRor cOrrection (HERRO) of ONT data could permit high-resolution comparison of outbreak isolates.MethodsWe used ONT simplex reads from isolates involved in a recent outbreak of methicillin-resistantStaphylococcus aureus(MRSA) in our neonatal unit. The raw sequence data were re-basecalled and adapter-trimmed using Dorado v0.7.0. The simplex reads then underwent HERRO correction. The resulting genome assemblies and phylogenies were compared with previous analyses (using Dorado v0.3.4, no HERRO correction and data generated by Illumina sequencing).ResultsFive of nine outbreak isolates were included in the analysis. The remaining four isolates had insufficient read lengths (N50 values <10,000 bp) and did not provide complete chromosome coverage after HERRO correction. The average chromosome sequencing depth for nanopore data was 147× (range: 44–220×) with an average read N50 of 12,215 bp (interquartile range (IQR): 11,439–12,711 bp). The median pairwise SNV distance between outbreak isolates from the original investigation was 51 SNVs (range: 40–68), which decreased to 3 SNVs (range: 1–15) with HERRO correction. Illumina sequencing generated a median SNV distance of 2 (range: 0–13). The resulting standalone ONT HERRO-corrected phylogeny was almost indistinguishable from the standalone Illumina-generated phylogeny.ConclusionsThe addition of HERRO correction meant isolates from this MRSA outbreak could be resolved to a level on par with Illumina sequencing. ONT data following HERRO correction represents a viable standalone option for high-resolution genomic analysis of hospital outbreaks, provided sufficient read lengths can be generated.

show abstract

Section: Introductionmentioning

confidence: 99%

Resolving a neonatal intensive care unit outbreak of methicillin-resistantStaphylococcus aureusto the SNV level using Oxford Nanopore simplex reads and HERRO error correction

Bloomfield,

Bakker,

Burton

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Use of Multiplex Molecular Panels to Diagnose Urinary Tract Infection in Older Adults

Hatfield,

Kabbani,

See

et al. 2024

JAMA Netw Open

View full text Add to dashboard Cite

ImportanceMultiplex molecular syndromic panels for diagnosis of urinary tract infection (UTI) lack clinical data supporting their use in routine clinical care. They also have the potential to exacerbate inappropriate antibiotic prescribing.ObjectiveTo describe the frequency of unspecified multiplex testing in administrative claims with a primary diagnosis of UTI in the Medicare population over time, to assess costs, and to characterize the health care professionals (eg, clinicians, laboratories, physician assistants, and nurse practitioners) and patient populations using these tests.Design, Setting, and ParticipantsThis cohort study used Centers for Medicare &amp; Medicaid Services (CMS) claims data for Medicare beneficiaries. The study included older community-dwelling adults and nursing home residents with fee-for-service Medicare Part A and Part B benefits from January 1, 2016, to December 31, 2023.Main Outcomes and MeasuresMultiplex syndromic panels were identified using carrier claims (ie, claims for clinician office or laboratory services). The annual rate of claims was measured for multiplex syndromic panels with a primary diagnosis of UTI per 10 000 eligible Medicare beneficiaries. The performing and referring specialties of health care professionals listed on claims of interest and the proportion of claims that occurred among beneficiaries residing in a nursing home were described.ResultsBetween 31 110 656 and 36 175 559 Medicare beneficiaries with fee-for-service coverage annually (2016-2023) were included in this study. In this period, 1 679 328 claims for UTI multiplex testing were identified. The median age of beneficiaries was 77 (IQR, 70-84) years; 34% of claims were from male beneficiaries and 66% were from female beneficiaries. From 2016 to 2023, the observed rate of UTI multiplex testing increased from 2.4 to 148.1 claims per 10 000 fee-for-service beneficiaries annually, and the proportion of claims that occurred among beneficiaries residing in a nursing home ranged from 1% in 2016 to 12% in 2020. In addition to laboratories or pathologists, urology was the most common clinician specialty conducting this testing. The CMS-assigned referring clinician specialty was most frequently urology or advanced practice clinician for claims among community-dwelling beneficiaries compared with internal medicine or family medicine for claims among nursing home residents. In 2023, the median cost of a multiplex test in the US was $585 (IQR, $516-$695 for Q1-Q3), which was more than 70 times higher than the median cost of $8 for a urine culture (IQR, $8-$16 for Q1-Q3).Conclusions and RelevanceThis cohort study of Medicare beneficiaries with fee-for-service coverage from 2016 to 2023 found increasing use of emerging multiplex testing for UTI coupled with high costs to the Medicare program. Monitoring and research are needed to determine the effects of multiplex testing on antimicrobial use and whether there are clinical situations in which this testing may benefit patients.

show abstract

Molecular Diagnostics for Invasive Molds: From Lab to Bedside

Hannaford,

Hernandez-Acosta,

Little

et al. 2024

Clinics in Laboratory Medicine

View full text Add to dashboard Cite

A decade of clinical microbiology: top 10 advances in 10 years: what every infection preventionist and antimicrobial steward should know

Cited by 6 publications

References 92 publications

Resolving a neonatal intensive care unit outbreak of methicillin-resistantStaphylococcus aureusto the SNV level using Oxford Nanopore simplex reads and HERRO error correction

Resolving a neonatal intensive care unit outbreak of methicillin-resistantStaphylococcus aureusto the SNV level using Oxford Nanopore simplex reads and HERRO error correction

Use of Multiplex Molecular Panels to Diagnose Urinary Tract Infection in Older Adults

Molecular Diagnostics for Invasive Molds: From Lab to Bedside

Contact Info

Product

Resources

About