Assessment of VITEK® MS IVD database V3.0 for identification of Nocardia spp. using two culture media and comparing direct smear and protein extraction procedures

Durand, Thibaut; Vautrin, Florian; Bergeron, Emmanuelle; Girard, Victoria; Polsinelli, Sophie; Monnin, Valérie; Durand, G.; Dauwalder, Olivier; Dumitrescu, Oana; Laurent, Frédéric; Rodríguez-Nava, Verónica

doi:10.1007/s10096-019-03758-x

Cited by 17 publications

(13 citation statements)

References 28 publications

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“…Due to the large number of Nocardia species, biochemical methods are insufficient to identify the clinically relevant species [ 4 ]. MALDI-TOF MS can rapidly identify the frequently encountered Nocardia species, but it is limited by the database and distinguishing closely related species [ 10 ]. The 16S rRNA gene sequencing is robust for accurate identification of Nocardia species, but it is also limited by discriminating closely related species due to high conservation [ 12 ].…”

Section: Discussionmentioning

confidence: 99%

“…With the development of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), the common clinical Nocardia species (e.g., N. cyriacigeorgica and N. farcinica ) can be identified rapidly. However, the available database of MALDI-TOF MS is limited for Nocardia strains leading to some uncommon isolates with no or false identification [ 10 , 11 ]. The 16S rRNA gene sequencing is generally considered as the primary means for accurate identification of the clinically encountered Nocardia isolates [ 12 ], but it cannot discriminate closely related species due to high conservation, unless it combines with a housekeeping gene, such as gyrB or rpoB [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

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MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

Wei

Yang

et al. 2021

BMC Microbiol

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Background With the increase of detection rate and long treatment period, nocardiosis has become a noticeable problem in China. However, there are limited large-scale studies on the epidemiology and antimicrobial susceptibility profiles of clinical Nocardia spp. in China. The present study aimed to explore the species distribution and drug susceptibility pattern of 82 clinical Nocardia isolates from three tertiary hospitals in China by multilocus sequence analysis (MLSA) and broth microdilution (BMD) method. Results Pulmonary nocardiosis (90.2%) was the most common clinical presentation of infection. N. cyriacigeorgica (n = 33; 40.2%) and N. farcinica (n = 20; 24.4%) were the most frequently encountered Nocardia species, followed by N. otitidiscaviarum (n = 7; 8.5%), N. abscessus (n = 5; 6.1%), N. asiatica (n = 4; 4.9%), and N. wallacei (n = 4; 4.9%). Trimethoprim/sulfamethoxazole (SXT) remained high activity against all Nocardia isolates (susceptibility rate: 98.8%). Linezolid and amikacin were also highly active; 100 and 95.1% of all isolates demonstrated susceptibility, respectively. Except for N. otitidiscaviarum, all the Nocardia isolates exhibited high susceptibility rates to imipenem. The resistance rates of all isolates to clarithromycin and ciprofloxacin were 92.7 and 73.2%, respectively, but the resistance rate of N. farcinica to ciprofloxacin was only 25%. Conclusions The clinically isolated Nocardia spp. had diverse antimicrobial susceptibility patterns, which were similar to the reports by other groups elsewhere, but some differences were also observed, mainly including imipenem and ciprofloxacin. According to this study, SXT still can be the first choice for empirical therapy due to the low resistance rate. Linezolid can be chosen when a patient is allergic to SXT, and amikacin and imipenem can be the choice in a combination regimen.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

Wei

Yang

et al. 2021

BMC Microbiol

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“…[40][41][42] A preliminary step of protein extraction (with glass beads and ethanol, followed by formic acid) and repeated spotting of different extracts is frequently required to increase the likelihood of identification. 43,44 complexes. When identified by MALDI-TOF MS, these species should therefore be referred to as "N. nova complex" or "N. abscessus complex" and/or should be analyzed using molecular biology (see earlier).…”

Section: Figurementioning

confidence: 99%

Invasive Nocardiosis: Disease Presentation, Diagnosis and Treatment – Old Questions, New Answers?

Lafont¹,

Conan²,

Rodríguez-Nava³

et al. 2020

IDR

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Nocardia spp. is an environmental filamentous Gram-positive bacterium that may cause infections in humans and, despite recent progress, many challenges remain regarding the management of nocardiosis. This review aims at describing most recently published data regarding the diagnosis, treatment and follow-up of patients with invasive nocardiosis. As nocardiosis mainly affects patients with cell-mediated immunity defects, a comprehensive workup is mandatory in case of invasive nocardiosis occurring in ”apparently healthy patients”. Indeed, invasive nocardiosis might reveal an unknown primary immunodeficiency or the presence of anti-GM-CSF autoantibodies. Even if the diagnosis of nocardiosis mostly relies on direct examination and bacterial culture, a genus-specific PCR may be used for the detection of Nocardia , when directly performed on a clinical sample. Brain imaging should always be performed, even in the absence of neurological symptoms. Cotrimoxazole (trimethoprim/sulfamethoxazole), linezolid, parenteral cephalosporins, carbapenems and amikacin may be used as initial antibiotics to treat nocardiosis. Cotrimoxazole or linezolid can be used as monotherapy in selected patients without brain involvement. Although treatment duration has historically been set to at least 6 months in the absence of central nervous system involvement, shorter durations (<120 days) seem to be associated with a favourable outcome.

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“…Durand et al evaluated the performance of VITEK ® MS (V3.0) for the identification of Nocardia spp. The identification rates at the species level can be improved by using repeat or new extracts [ 9 ].…”

Section: Accuracy For Microbial Identification and Other Applicationmentioning

confidence: 99%

“…MALDI-TOF MS is not limited to identifying strains cultured on solid media but can also directly identify them from the blood culture, cerebrospinal fluid, and urine [ 1 , 2 , 3 , 4 , 5 ]. MALDI-TOF MS identification has been used to identify gram-negative and gram-positive bacteria, aerobes, anaerobes, mycobacteria, Nocardia , yeasts, filamentous fungi and viruses [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

et al. 2021

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Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.

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Assessment of VITEK® MS IVD database V3.0 for identification of Nocardia spp. using two culture media and comparing direct smear and protein extraction procedures

Cited by 17 publications

References 28 publications

MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

MLSA phylogeny and antimicrobial susceptibility of clinical Nocardia isolates: a multicenter retrospective study in China

Invasive Nocardiosis: Disease Presentation, Diagnosis and Treatment – Old Questions, New Answers?

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

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