Bacterial identification in the diagnostic laboratory: How much is enough.

The major impetus for bacterial identification came after the advent of solid culture media. Morphological appearance of bacterial colonies was often sufficient for their identification in the laboratory. Even in modern times, preliminary identification of most cultivable bacteria is based on such morphological characters. Advances have been made media for the presumptive identifi cation of common organisms encountered in clinical samples. Phenotypic characterisation of bacteria with, physiological tests with a battery of biochemical tests differentiate related bacterial genera as well as confirm their identity. . Each laboratory can select its own method(s) of identification, provided they are based on scientific / epidemiological evidence; clinical laboratory and standards institute (CLSI) is a widely accepted organization and laboratories in many parts of the world follow its recommendations for bacterial identification. Some of the latest advances in identification include Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectroscopy (MALDI-TOF) is a state of art facility used for fast and reliable species-specific identification of bacteria including Mycobacteria and fungi including yeasts. However the single most important factor that decides the method of bacterial identification in any laboratory is the cost involved. In the final analysis, selection of tests for bacterial identification should be based on their standardization with proper scientific basis. Considering the cost and lack of easy availability of commercial kits, we have put forward a simplified and rapid method of identification for most commonly encountered bacterial pathogens causing human infection in India

Cord factor detection and macroscopic evaluation of mycobacterial colonies: an efficient combined screening test for the presumptive identification of Mycobacterium tuberculosis complex on solid media / Detecção do fator corda e avaliação do aspecto macroscópico das colônias de micobactérias: um eficiente teste de triagem combinado para a identificação presuntiva do complexo Mycobacterium tuberculosis em meios só

OBJECTIVE: The rapid differentiation between Mycobacterium tuberculosis and nontuberculous mycobacteria is fundamental for patients co-infected with tuberculosis and HIV. To that end, we use two methods in our laboratory: detection of cord factor and PCR-restriction enzyme analysis (PRA). The objective of this study was to evaluate the accuracy of a screening test on solid medium as a rapid method for the presumptive identification of M. tuberculosis complex, considering costs and turnover time. METHODS: A total of 152 strains were submitted to a combined screening test, consisting of the detection of cord factor under microscopy (Ziehl-Neelsen staining) and evaluation of the macroscopic aspect of colonies, as well as to PRA, which was used as the gold standard. Costs were estimated by calculating the price of all of the materials needed for each test. RESULTS: The overall accuracy of cord factor detection alone was 95.4 percent (95 percent CI: 90.7-98.1 percent), and that of the combined screening test was 99.3 percent (95 percent CI: 96.4-100 percent). Cord factor detection costs US$ 0.25, whereas the PRA costs US$ 7.00. Results from cord factor detection are ready in 2 days, whereas PRA requires 4 days to yield results. CONCLUSIONS: The presumptive identification of M. tuberculosis using the macroscopic evaluation of colonies combined with cord factor detection under microscopy is a simple, rapid and inexpensive test. We recommend the combined screening test to rapidly identify M. tuberculosis in resource-poor settings and in less well-equipped laboratories while awaiting a definite identification by molecular or biochemical methods.

OBJETIVO: A diferenciação rápida entre Mycobacterium tuberculosis e micobactérias não-tuberculosas é fundamental para os pacientes coinfectados com tuberculose e HIV. Para tanto, utilizamos duas metodologias em nosso laboratório: detecção do fator corda e PCR-restriction enzyme analysis (PRA). O objetivo do estudo foi avaliar a acurácia desse teste de triagem em meio sólido como um método rápido para a identificação presuntiva do complexo M. tuberculosis, considerando custos e tempo de resultado. MÉTODOS: Foram processadas 152 cepas pelo teste de triagem combinado, que consistiu da detecção do fator corda por microscopia (esfregaço corado por Ziehl-Neelsen) e avaliação do aspecto macroscópico das colônias, e PRA (padrão ouro). Os custos foram estimados através da obtenção dos preços dos insumos necessários para a realização de cada teste. RESULTADOS: A acurácia da detecção do fator corda foi de 95,4 por cento (IC95 por cento: 90,7-98,1 por cento) e a do teste de triagem combinado foi de 99,3 por cento (IC95 por cento: 96,4-100 por cento). O custo da detecção do fator corda foi de R$ 0,60 e do PRA de R$ 16,00. Os resultados da detecção do fator corda estão prontos em 2 dias, ao passo que os de PRA necessitam de 4 dias. CONCLUSÕES: A identificação presuntiva de M. tuberculosis usando o aspecto macroscópico das colônias em conjunto com a detecção de fator corda por microscopia é um teste simples, rápido e de baixo custo. Recomendamos o teste de triagem combinado para rapidamente identificar M. tuberculosis em sítios com poucos recursos financeiros e em laboratórios menos equipados, enquanto se aguarda a identificação definitiva por métodos moleculares ou bioquímicos.

Evaluation of methods and costs for detecting methicillin-resistant Staphylococcus aureus isolates from clinical specimens at regional hospitals in Trinidad and Tobago / Evaluación de métodos y costos para la detección de aislados de Staphylococcus aureus resistentes a la meticilina a partir de especímenes clínicos en los hospitales regionales de Trinidad y Tobago

OBJECTIVES: To evaluate and determine the most cost effective, rapid and specific method for detection of methicillin resistance in clinical isolates of S aureus in a setting with limited personnel and resources. METHODS: Standard laboratory methods were used to identify S aureus isolates. The conventional Methicillin Resistance Staphylococcus aureus (MRSA) detection methods used included, 1 µg oxacillin disk diffusion, oxacillin salt agar screen (CLSI), penicillin binding protein (PBP 2') latex agglutination test and E-tests oxacillin. Results of conventional tests were compared with a polymerase chain reaction (PCR) method for detecting MRSA isolates. Polymerase chain reaction detection of the mecA gene in S aureus was used as the " gold standard" for MRSA identification. RESULTS: All methods had 100% sensitivity except for oxacillin disk diffusion and oxacillin-salt agar screening with 98% and 99%, respectively. Specificity was also 100% for all methods except for oxacillin-disk diffusion (99%). Turn around time (TAT) for detection of MRSA was calculated to be within six hours for PCR. The fastest TAT of 1.25 hours was obtained for PBP 2' latex agglutination. Total cost for labour and materials to perform each method was highest for E-test, US$13.76/isolate. The cost for PCR when compared to that of latex agglutination was not statistically significant (US$3.74 vs US5.91, p = 0.4). CONCLUSIONS: All methods presented high sensitivity and specificity, but the latex agglutination test had the advantage of giving a reliable, rapid and most cost effective result that compares well to PCR in this environment.

OBJETIVOS: Evaluar y determinar el método más específico, rápido y costo-efectivo para la detección de la resistencia a la meticilina en aislados clínicos de S aureus en un lugar con personal y recursos limitados. MÉTODOS: A fin de identificar los aislados de S aureus, se utilizaron métodos estándar de laboratorio. Los métodos convencionales de detección de SARM usados incluyeron difusión por disco de oxacilina de 1 µg, prueba de tamizaje (" screening" ) de oxacilina en agar-sal (CLSI), test de aglutinación en látex para la detección de la proteína 2 fijadora de la penicilina (PBP 2'), y la prueba E-Test de oxacilina. Los resultados de las pruebas convencionales fueron comparados con un método de PCR para la detección de aislados SARM. La detección por PCR del gene mecA en S aureus fue usada como " estándar de oro" para la identificación de SARM. RESULTADOS: Todos los métodos tuvieron 100% de sensibilidad excepto la difusión por disco de oxacilina y el tamizaje de oxacilina en agar-sal, con 98% y 99% respectivamente. La especificad también fue de 100% para todos los métodos, con excepción de la difusión por disco de oxacilina (99%). El tiempo de respuesta (TAT, del inglés turn around time) para la detección de SARM se halla, según los cálculos, dentro de las seis horas para PCR. El TAT más rápido, 1.25 hrs, se obtuvo en la aglutinación en látex de PBP 2'. El costo total del trabajo y los materiales en la ejecución de cada método fue más alto en la prueba de E-Test, aislado/$13.76 USD. El costo de PCR en comparación con el de la aglutinación látex no fue estadísticamente significativo ($3.74 USD vs $5.91USD, p = 0.4). CONCLUSIONES: Todos los métodos presentaron alta sensibilidad y especificidad, pero el test de aglutinación en látex tuvo como ventaja el ofrecer un resultado confiable, rápido y altamente costo-efectivo, no muy diferente del PCR en este ambiente.