Cost-effective implementation of a custom MALDI-TOF library for the identification of South Australian Nocardia isolates

Morales, Manuel Pastor Forero; Hopprich, Ryan; Wise, Rolf; Shephard, Lisa; Weldhagen, Gerhard F.

doi:10.1016/j.pathol.2018.08.006

Cited by 6 publications

(5 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our literature review identified five publications describing the species distribution of Nocardia within Australian states and territories. 5,7,[13][14][15] This, along with our Western Australian data are provided in Table 1. For the majority of studies, N. nova, N. brasiliensis, N. cyriacigeorgica, and N. farcinica were the most frequently isolated Nocardia species.…”

Section: Resultsmentioning

confidence: 99%

“…Twenty‐one different Nocardia species were identified within our WA data set. Our literature review identified five publications describing the species distribution of Nocardia within Australian states and territories 5,7,13–15 . This, along with our Western Australian data are provided in Table 1.…”

Section: Resultsmentioning

confidence: 99%

“…13 Within Australia, such data is currently limited to small, single-centre or single-state studies. 5,7,8,[13][14][15][16] Western Australia (WA) is the nation's geographically largest state (area 2.65 million km 2 ) and is characterised by significant variations in climate, geography and population distribution. We aimed to: (i) compare Nocardia incidence in WA, (ii) formally review the published literature on species distribution within Australian states and territories and (iii) analyse summary Nocardia AST data from a nationwide passive antimicrobial resistance surveillance program.…”

Section: Introductionmentioning

confidence: 99%

“…This laboratory advancement facilitates the use of species‐specific antibiograms to more accurately predict AST results, enabling earlier, more appropriate empiric decision‐making 13 . Within Australia, such data is currently limited to small, single‐centre or single‐state studies 5,7,8,13‐16 …”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Nocardia species distribution and antimicrobial susceptibility within Australia

O'Brien,

Hart,

Higgins

et al. 2023

Internal Medicine Journal

View full text Add to dashboard Cite

BackgroundNocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation.AimsTo examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program.MethodsRetrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21‐year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022.ResultsNine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim‐sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third‐generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation.ConclusionsWe demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim‐sulphamethoxazole and linezolid, justifying their ongoing role as part of first‐line empiric therapy.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Nocardia species distribution and antimicrobial susceptibility within Australia

O'Brien,

Hart,

Higgins

et al. 2023

Internal Medicine Journal

View full text Add to dashboard Cite

show abstract

“…The development of custom-made databases to identify bacteria using MALDI-TOF MS as an alternative to commercially available databases proved successful for multiple species before [9-11]. Most notably, an earlier study developed a custom-made database to identify and distinguish Shigella spp .…”

Section: Introductionmentioning

confidence: 99%

Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass spectrometry using a custom-made database, biomarker assignment, or mathematical classifiers does not differentiate Shigella spp. and Escherichia coli

Beld

Rossen

Evers

et al. 2019

Preprint

View full text Add to dashboard Cite

PurposeShigella spp. and E. coli are closely related, and cannot be distinguished using Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) with commercially available databases. Here, three alternative approaches using MALDI-TOF for identification and distinction of Shigella spp., E. coli and its pathotype EIEC were explored.MethodsA custom-made database was developed, biomarkers were assigned and classification models using machine learning were designed and evaluated using spectra of 456 Shigella spp., 42 E. coli and 61 EIEC isolates, obtained by the direct smear method and the ethanol-formic acid extraction method.ResultsIdentification with a custom-made database resulted in >94% Shigella identified at the genus level, and >91% S. sonnei and S. flexneri at the species level, but distinction of S. dysenteriae, S. boydii and E. coli was poor. Moreover, 10-15% of duplicates rendered discrepant results. With biomarker assignment, 98% S. sonnei isolates were correctly identified, although the S. sonnei biomarkers were not specific as other species were also identified as S. sonnei. Discriminating markers for S. dysenteriae, S. boydii, and E. coli were not assigned at all. Classifiers identified Shigella in 96% of isolates correctly, but most E. coli isolates were also assigned to Shigella.ConclusionNone of the proposed alternative approaches is suitable for use in clinical diagnostics for the identification of Shigella spp., E. coli and EIEC because of their poor distinctive properties. We suggest the use of MALDI-TOF MS for identification of the Shigella spp./E. coli complex, but other tests should be used for distinction.

show abstract

Update on Nocardia infections in solid-organ transplantation

Saullo

Miller

2020

Current Opinion in Organ Transplantation

View full text Add to dashboard Cite

Purpose of review Nocardia is a ubiquitous pathogen associated with life-threatening opportunistic infections. Organ transplant recipients are uniquely predisposed to Nocardia infections due to their iatrogenic cell-mediated immune deficit necessary to maintain allograft function. This review aims to address recent updates in the epidemiology, clinical presentation, diagnostics, treatment, and outcomes of Nocardia infections in solid-organ transplant recipients. Recent findings The incidence of Nocardia infection depends on multiple patient and environmental factors. Among transplant recipients, lung recipients are most commonly affected. Species identification and antimicrobial susceptibility testing are critical for optimizing therapy as substantial variation occurs among and within Nocardia spp. This has been increasingly accomplished through advances in molecular methods leading to improved accuracy and wider accessibility to testing. There are emerging data applying novel therapeutics and short course therapy that may offer alternative management approaches for transplant associated nocardiosis to minimize drug toxicity and intolerance. Summary Further prospective, multicenter studies are needed to better characterize the epidemiology of Nocardia in transplant recipients, as well as evaluate the impact of diagnostic advancements and new treatment strategies.

show abstract

Cost-effective implementation of a custom MALDI-TOF library for the identification of South Australian Nocardia isolates

Cited by 6 publications

References 27 publications

Nocardia species distribution and antimicrobial susceptibility within Australia

Nocardia species distribution and antimicrobial susceptibility within Australia

Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass spectrometry using a custom-made database, biomarker assignment, or mathematical classifiers does not differentiate Shigella spp. and Escherichia coli

Update on Nocardia infections in solid-organ transplantation

Contact Info

Product

Resources

About