Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina.

The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.

Evaluation of the MALDI-TOF mass spectrometry technique for the identification of dermatophytes: Use of an extended database.

BACKGROUND: Identification of dermatophytes is usually performed through morphological analyses. However, it may be hindered due to the discovery of new species and complexes and, with some isolates, by the absence of fructification. Matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) seems to be an option for improving identification. AIMS: To develop a database (DB) for the identification of dermatophytes with MALDI-TOF MS, including 32 isolates from the Red de Micología de la Ciudad Autónoma de Buenos Aires [Mycology Network of the Autonomous City of Buenos Aires] (RMCABA) and one reference isolate (RMCABA DB), and evaluate its performance when added to the DB from the supplier, Bruker (Bruker DB). METHODS: All the isolates in the RMCABA DB were identified based on morphology and sequencing. To evaluate the performance of the extended DB (Bruker DB plus RMCABA DB), 136 clinical isolates were included. RESULTS: The percentages of identification at the species level increased from 45% to 88%, but the identification at the genus level decreased from 23% to 7%. CONCLUSIONS: MALDI-TOF MS yielded better performance in the identification of dermatophytes after including the RMCABA DB, which encompassed local isolates.

Evaluation of the MALDI-TOF mass spectrometry technique for the identification of dermatophytes: Use of an extended database / Evaluación de la técnica de espectrometría de masas MALDI-TOF para la identificación de dermatofitos: utilización de una base de datos ampliada

Background: Identification of dermatophytes is usually performed through morphological analyses. However, it may be hindered due to the discovery of new species and complexes and, with some isolates, by the absence of fructification. Matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) seems to be an option for improving identification. Aims: To develop a database (DB) for the identification of dermatophytes with MALDI-TOF MS, including 32 isolates from the Red de Micología de la Ciudad Autónoma de Buenos Aires [Mycology Network of the Autonomous City of Buenos Aires] (RMCABA) and one reference isolate (RMCABA DB), and evaluate its performance when added to the DB from the supplier, Bruker (Bruker DB). Methods: All the isolates in the RMCABA DB were identified based on morphology and sequencing. To evaluate the performance of the extended DB (Bruker DB plus RMCABA DB), 136 clinical isolates were included. Results: The percentages of identification at the species level increased from 45% to 88%, but the identification at the genus level decreased from 23% to 7%.Conclusions: MALDI-TOF MS yielded better performance in the identification of dermatophytes after including the RMCABA DB, which encompassed local isolates.(AU)

Antecedentes: La identificación de dermatofitos se realiza, usualmente, a través del análisis morfológico, pero puede verse dificultada por la aparición de nuevas especies y complejos de especies y, en algunos aislamientos, por la falta de elementos de fructificación. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) aparece como una alternativa para mejorar la identificación. Objetivos: Construir una base de datos (BaDa) para la identificación de dermatofitos mediante MALDI-TOF MS, con 32 aislamientos de la Red de Micología de la Ciudad Autónoma de Buenos Aires (RMCABA) y una cepa de referencia (BaDa RMCABA), y evaluar su desempeño al incorporarla a la BaDa del proveedor Bruker (BaDa Bruker). Métodos: Todos los aislamientos incorporados a la BaDa RMCABA se identificaron por morfología y secuenciación. Para la evaluación de la BaDa ampliada (BaDa Bruker más BaDa RMCABA) se incluyeron 136 aislamientos clínicos. Resultados: El porcentaje de identificación a nivel de especie se incrementó del 45 al 88%, mientras que la identificación a nivel de género disminuyó del 23 al 7%. Conclusiones: Con la incorporación de la BaDa RMCABA, que contó con aislamientos regionales, se observó un mejor desempeño en la identificación de dermatofitos por MALDI-TOF MS.(AU)

Actividad in vitro de delafloxacina frente a microorganismos aislados de infecciones osteoarticulares y de piel y partes blandas en Buenos Aires, Argentina

Resumen Se estudió la actividad in vitro de delafloxacina, ciprofloxacina y levofloxacina por los métodos epsilométrico y de difusión por discos frente a 181 aislamientos clínicos de infecciones de piel y osteoarticulares. Se incluyeron 40 Staphylococcus aureus resistentes a meticilina (SARM), 44 S. aureus sensibles a meticilina (SASM), 46 estafilococos coagulasa negativos (ECN), 23 Klebsiella pneumoniae y 28 Pseudomonas aeruginosa. Las CIM50/CIM90 (mg/l) de delafloxacina, ciprofloxacina y levofloxacina respectivamente fueron 0,004/0,064, 0,25/16 y 0,125/4 frente a SARM; 0,002/0,004, 0,125/0,25 y 0,125/0,25 frente a SASM; 0,008/0,25, 0,125/>32 y 0,25/>32 frente a ECN; 4/>32,>32/>32 y 16/>32 frente a K. pneumoniae y 1/>32, 0,5/>32 y 4/>32 frente a P. aeruginosa. La proporción de aislamientos sensibles a delafloxacina, ciprofloxacina y levofloxacina fue la siguiente: SARM, 97,5%; 82,5% y 82,5%; SASM, 97,7%; 95,5% y 95,5%; ECN, 93,5%; 63,0% y 60,9%; K. pneumoniae, 21,7%; 26,1% y 43,5%; P. aeruginosa, 35,7%; 53,6% y 42,8%. La concordancia categórica del método de difusión por discos y el método epsilométrico para evaluar la actividad in vitro de la delafloxacina fue del 98,8% en S. aureus y del 91,3% en ECN.

Abstract In vitro activities of delafloxacin, ciprofloxacin and levofloxacin were evaluated by epsilometric and disk diffusion methods against 181 bacterial isolates recovered from bone and skin infections. Isolates included were 84 Staphylococcus aureus (40 MRSA and 44 MSSA), 46 coagulase-negative staphylococci (CNS), 23 Klebsiella pneumoniae and 28 Pseudomonas aeruginosa. The MIC50/MIC90 (mg/l) for delafloxacin, ciprofloxacin and levofloxacin, respectively, were: MRSA, 0.004/0.064, 0.25/16 and 0.125/4; MSSA, 0.002/0.004, 0.125/0.25 and 0.125/0.25; CNS, 0.008/0.25, 0.125/>32 and 0.25/>32; K. pneumoniae, 4/>32,>32/>32 and 16/>32; P. aeruginosa, 1/>32, 0,5/>32 and 4/>32. Susceptibilities for delafloxacin, ciprofloxacin and levofloxacin, respectively, were: MRSA, 97.5%, 82.5% and 82.5%; MSSA, 97.7%, 95.5% and 95.5%; CNS, 93.5%, 63.0% and 60.9%; K. pneumoniae, 21.7%, 26.1% and 43.5%; P aeruginosa, 35.7%, 53.6% and 42.8%. The disk diffusion and epsilometric methods were concordant for evaluating in vitro susceptibility in staphylococci (categorical concordance of 98.8% for S. aureus and 91.3% for CNS).

Identificación directa de microorganismos a partir de hemocultivos positivos utilizando espectrometría de masas (MALDI-TOF MS) / Direct identification of microorganisms in positive blood culture bottles by mass spectrometry (MALDI-TOF MS)

Resumen La espectrometría de masas (MALDI-TOF MS) permite la identificación de microorganismos directamente de las colonias en pocos minutos. En este estudio se ha desarrollado y evaluado un protocolo reducido para identificar microorganismos directamente de las botellas de hemocultivos positivos en 30 minutos con una alta sensibilidad y especificidad, utilizando MALDITOF. Un total de 2535 hemocultivos positivos fueron estudiados por el método directo de MALDI-TOF MS, a partir de una alícuota de sangre de las botellas y el método de colonia, utilizando los cultivos desarrollados en medios sólidos. Del total de hemocultivos positivos incluidos en este estudio, 2381 (93,9%) fueron monomicrobianos y 146 (5,8%) polimicrobianos. Mil trescientos treinta (55,9%) de los aislamientos correspondieron a cocos gram positivos, 922 (38,7%) a bacilos gram negativos, 60 (2,5%) a anaerobios, 36 (1,5%) a bacilos gram positivos y 13 a levaduras. La concordancia global entre ambos métodos fue del 81,7% a nivel de especie (90,0% para bacilos gram negativos, 76,7% para cocos gram positivos y 33,3% para bacilos gram positivos). Se identificó al menos un germen en el 88% de las botellas positivas con desarrollo polimicrobiano. Los resultados del presente estudio demostraron que el protocolo basado en MALDI-TOF MS permite la identificación microbiana directamente de hemocultivos positivos en un tiempo corto, con una alta precisión, con excepción de los bacilos gram positivos.

Abstract Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) enables the identification of microorganisms directly from colonies within minutes. In this study this technology was adapted and tested for use with blood culture bottles, thus allowing identification in 30 minutes once the blood culture is detected as positive by the automate. A total of 2535 blood culture bottles reported as positive were tested by MALDI-TOF MS directly from positive blood culture bottles and colonies. A total of 2381 (93.9%) and 146 (5.8%) of the positive blood cultures were monomicrobial and polymicrobial, respectively. And 1330 (55.9%), 922 (38.7%), 60 (2.5%), 36 (1.5%) and 13 of the isolates were gram-positive cocci (GPC), gram-negative bacilli (GNB), anaerobic bacteria, gram-positive bacilli (GPB) and yeast respectively. Concordance between both methods was 81.7% (76.7% of GPC, 90% of GNB, 74.2% of anaerobic bacteria and 33.3% of GPB) in monomicrobial cultures. Eighty eight per cent of the polymicrobial cultures were identified correctly in at least one of the two bacteria. The results of the present study show that this fast, MALDI-TOF MS based method allows microbial identification directly from positive blood culture in a short time, with a high accuracy, with the exception of gram-positive bacilli.

Resumo A espectrometria de massa (MALDI-TOF MS) permite a identificação de microorganismos diretamente das colônias em minutos. Nesse estudo, foi desenvolvido um protocolo reduzido para identificar microrganismos diretamente das garrafas de hemoculturas positivas em 30 minutos com alta sensibilidade e especificidade, utilizando MALDI-TOF. Um total de 2535 hemoculturas positivas foram relatadas -o método direto de MALDI-TOF MS, a partir de uma alíquota de sangue dos vidros e o método de colônia, a partir das culturas desenvolvidas em meios sólidos. Do total de hemoculturas positivas incluídas neste estudo, 2.381 (93,9%) eram monomicrobianas e 146 (5,8%) eram polimicrobianas. Mil trezentos e trinta (55,9%) dos isolados corresponderam a cocos gram-positivos, 922 (38,7%) bacilos gram-negativos, 60 (2,5%) anaeróbios, 36 (1,5%) bacilos gram-positivos e 13 leveduras. A concordância geral entre os dois métodos foi de 81,7% em nivel de especie (90,0% para bacilos gram-negativos, 76,7% para cocos gram-positivos e 33,3% para bacilos gram-positivos). Pelo menos um germe foi identificado em 88% dos vidros positivos com desenvolvimento polimicrobiano. Os resultados do presente estudo demonstraram que o protocolo baseado em MALDI-TOF MS permite a identificação microbiana diretamente de hemoculturas positivas em um curto espaço de tempo, com alta precisão, com exceção de bacilos gram-positivos.

The dilemma of identifying Peptoniphilus species by using two MALDI-TOF MS systems.

Two commercial MALDI-TOF MS systems were used to identify 18 isolates, belonging to the Peptoniphilus genus; also the 16S rRNA sequencing identity was compared against the MALDI-TOF MS system results. Bruker Biotyper system provided higher accuracy than Vitek MS system, however, adding spectra could allow a more reliable species level identification.

[In vitro activity of delafloxacin against bacterial isolates from osteoarticular and skin infections in Buenos Aires, Argentina]. / Actividad in vitro de delafloxacina frente a microorganismos aislados de infecciones osteoarticulares y de piel y partes blandas en Buenos Aires, Argentina.

In vitro activities of delafloxacin, ciprofloxacin and levofloxacin were evaluated by epsilometric and disk diffusion methods against 181 bacterial isolates recovered from bone and skin infections. Isolates included were 84 Staphylococcus aureus (40 MRSA and 44 MSSA), 46 coagulase-negative staphylococci (CNS), 23 Klebsiella pneumoniae and 28 Pseudomonas aeruginosa. The MIC50/MIC90 (mg/l) for delafloxacin, ciprofloxacin and levofloxacin, respectively, were: MRSA, 0.004/0.064, 0.25/16 and 0.125/4; MSSA, 0.002/0.004, 0.125/0.25 and 0.125/0.25; CNS, 0.008/0.25, 0.125/>32 and 0.25/>32; K. pneumoniae, 4/>32,>32/>32 and 16/>32; P. aeruginosa, 1/>32, 0,5/>32 and 4/>32. Susceptibilities for delafloxacin, ciprofloxacin and levofloxacin, respectively, were: MRSA, 97.5%, 82.5% and 82.5%; MSSA, 97.7%, 95.5% and 95.5%; CNS, 93.5%, 63.0% and 60.9%; K. pneumoniae, 21.7%, 26.1% and 43.5%; P aeruginosa, 35.7%, 53.6% and 42.8%. The disk diffusion and epsilometric methods were concordant for evaluating in vitro susceptibility in staphylococci (categorical concordance of 98.8% for S. aureus and 91.3% for CNS).

[Incidence, clinical characteristic and evolution of Clostridioides difficile infection]. / Incidencia, características clínicas y evolución de la infección por Clostridioides difficile.

Clostridioides difficile infection (CDi) is one of the foremost hospital-acquired infections. We present an observational study aimed to describe the incidence, epidemiology, and clinical outcome of CDi in a tertiary university hospital in Buenos Aires. The episodes, diagnosed in 117 consecutive adult patients in the period 01/01/2017 to 01/04/2020, were distributed in three groups: 63 (53.9%) were classified as hospital-acquired infections (HA), 25 (21.4%) as community onset-health care-associated infections (CO-HCA) and 29 (24.8%) as community-associated infections (CA). The incidence of HA CDi infections was 3.1, 5. 2 and 2.8 every 10 000 patient days in 2017, 2018 and 2019, respectively. The microbiological diagnosis was made by immunochromatography with antigen GDH and C. difficile toxin positive in 51 episodes (43.6%) and by GDH positive, toxin negative and PCR positive in 66 episodes (56.4%). Older age (p = 0.018), chronic kidney disease (p = 0.013), immunosuppression (p = 0.021), and higher comorbidity Charlson score (p = 0.001) were observed in patients with IH and CA-HCA infections. No significant differences in clinical features were found among groups. During the hospital st ay, 13 patients (11.1%) required admission to the intensive care unit. Ten recurrences occurred, representing 8.5% of CDI episodes. The 90-day mortality was 19.8%, being significantly higher in HA and CO-HCA infections (p = 0.014). Our findings highlight both the local burden of CDi morbidity and mortality and the need for the implementation of preventive strategies.

La infección por Clostridioides difficile (ICD) es una de las más importantes infecciones intrahospitalarias. Se realizó un estudio observacional que describe la incidencia, las características epidemiológicas y la evolución clínica de la ICD en un hospital universitario de la Ciudad de Buenos Aires. Los episodios, diagnosticados en 117 pacientes adultos consecutivos entre el 01/01/2017 y el 01/04/2020, fueron clasificados en ICD intrahospitalaria (IH) en 63 (53.9%), de inicio comunitario y asociada al ámbito de la salud (ICAAS) en 25 (21.4%) y comunitaria (CO) en 29 (24.8%) pacientes. La incidencia de ICD IH fue 3.1, 5.2 y 2.8 cada 10 000 días paciente en 2017, 2018 y 2019, respectivamente. El diagnóstico microbiológico se realizó mediante inmunocromatografía con glutamato deshidrogenasa y toxina positivas en 51 (43.6%) y mediante glutamato deshidrogenasa positiva, toxina negativa y PCR positiva en 66 (56.4%). Los pacientes con ICD IH e ICAAS presentaron mayor edad (p = 0.018), mayor frecuencia de insuficiencia renal crónica (p = 0.013) e inmunosupresión (p = 0.021) y mayor puntaje en índice Charlson de comorbilidad (p = 0.001). No hubo diferencia significativa en la forma de presentación clínica entre los tres grupos. Durante la evolución de la ICD, 13 (11.1%) pacientes requirieron internación en terapia intensiva. Se registraron 10 recurrencias, que correspondieron al 8.5% de los episodios de ICD. La mortalidad a los 90 días fue 19.8%, significativamente mayor en los pacientes con ICD IH e ICAAS (p = 0.014). Estos hallazgos destacan la considerable carga de morbilidad de la ICD y la necesidad de implementar estrategias preventivas.

Incidencia, características clínicas y evolución de la infección por Clostridioides difficile / Incidence, clinical characteristic and evolution of Clostridioides difficile infection

Resumen La infección por Clostridioides difficile (ICD) es una de las más importantes infecciones intrahospitalarias. Se realizó un estudio observacional que describe la incidencia, las características epi demiológicas y la evolución clínica de la ICD en un hospital universitario de la Ciudad de Buenos Aires. Los episodios, diagnosticados en 117 pacientes adultos consecutivos entre el 01/01/2017 y el 01/04/2020, fueron clasificados en ICD intrahospitalaria (IH) en 63 (53.9%), de inicio comunitario y asociada al ámbito de la salud (ICAAS) en 25 (21.4%) y comunitaria (CO) en 29 (24.8%) pacientes. La incidencia de ICD IH fue 3.1, 5.2 y 2.8 cada 10 000 días paciente en 2017, 2018 y 2019, respectivamente. El diagnóstico microbiológico se realizó mediante inmunocromatografía con glutamato deshidrogenasa y toxina positivas en 51 (43.6%) y mediante glutamato deshidrogenasa positiva, toxina negativa y PCR positiva en 66 (56.4%). Los pacientes con ICD IH e ICAAS presentaron mayor edad (p = 0.018), mayor frecuencia de insuficiencia renal crónica (p = 0.013) e inmu nosupresión (p = 0.021) y mayor puntaje en índice Charlson de comorbilidad (p = 0.001). No hubo diferencia significativa en la forma de presentación clínica entre los tres grupos. Durante la evolución de la ICD, 13 (11.1%) pacientes requirieron internación en terapia intensiva. Se registraron 10 recurrencias, que correspondieron al 8.5% de los episodios de ICD. La mortalidad a los 90 días fue 19.8%, significativamente mayor en los pacientes con ICD IH e ICAAS (p = 0.014). Estos hallazgos destacan la considerable carga de morbilidad de la ICD y la necesidad de implementar estrategias preventivas.

Abstract Clostridioides difficile infection (CDi) is one of the foremost hospital-acquired infections. We present an observa tional study aimed to describe the incidence, epidemiology, and clinical outcome of CDi in a tertiary university hospital in Buenos Aires. The episodes, diagnosed in 117 consecutive adult patients in the period 01/01/2017 to 01/04/2020, were distributed in three groups: 63 (53.9%) were classified as hospital-acquired infections (HA), 25 (21.4%) as community onset-health care-associated infections (CO-HCA) and 29 (24.8%) as community-associated infections (CA). The incidence of HA CDi infections was 3.1, 5. 2 and 2.8 every 10 000 patient days in 2017, 2018 and 2019, respectively. The microbiological diagnosis was made by immunochromatography with antigen GDH and C. difficile toxin positive in 51 episodes (43.6%) and by GDH positive, toxin negative and PCR positive in 66 episodes (56.4%). Older age (p = 0.018), chronic kidney disease (p = 0.013), immunosuppression (p = 0.021), and higher comorbidity Charlson score (p = 0.001) were observed in patients with IH and CA-HCA infections. No significant differences in clinical features were found among groups. During the hospital st ay, 13 patients (11.1%) required admission to the intensive care unit. Ten recurrences occurred, representing 8.5% of CDI episodes. The 90-day mortality was 19.8%, being significantly higher in HA and CO-HCA infections (p = 0.014). Our findings highlight both the local burden of CDi morbidity and mortality and the need for the implementation of preventive strategies.

Development and validation of an extended database for yeast identification by MALDI-TOF MS in Argentina.

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microorganisms in clinical laboratories because it is rapid, relatively simple to use, accurate, and can be used for a wide number of microorganisms. Several studies have demonstrated the utility of this technique in the identification of yeasts; however, its performance is usually improved by the extension of the database. Here we developed an in-house database of 143 strains belonging to 42 yeast species in the MALDI Biotyper platform, and we validated the extended database with 388 regional strains and 15 reference strains belonging to 55 yeast species. We also performed an intra- and interlaboratory study to assess reproducibility and analyzed the use of the cutoff values of 1.700 and 2.000 to correctly identify at species level. The creation of an in-house database that extended the manufacturer's database was successful in view of no incorrect identification was introduced. The best performance was observed by using the extended database and a cutoff value of 1.700 with a sensitivity of .94 and specificity of .96. A reproducibility study showed utility to detect deviations and could be used for external quality control. The extended database was able to differentiate closely related species and it has potential in distinguishing the molecular genotypes of Cryptococcus neoformans and Cryptococcus gattii.