The new Ribopeaks (RPK-II): Updated and enlarged tool for bacterial classification based on r-protein m/z data.

Ribopeaks is a rapid, sensitive, and economic web tool for bacterial identification based on m/z data from MALDI-TOF MS. To provide greater accuracy and robustness in the Ribopeaks analyzes we present an updated bacterial identification tool version, called Ribopeaks II (RPK-II). RPK-II contains a larger database, with r-protein data from fully sequenced bacterial genomes and optimized algorithms. Furthermore, this new version provides additional information about the identified bacterium, regarding antibiotic resistance.

The impact of VITEK 2 implementation for identification and susceptibility testing of microbial isolates in a Brazilian public hospital.

Introduction. The use of automated systems in identification and susceptibility tests can improve antimicrobial therapy, and positively impact clinical outcomes with a decrease in antimicrobial resistance, hospitalization time, costs, and mortality.Aim. The aim of this study was to evaluate the clinical impact of an automated method for identification and susceptibility testing of microbial isolates.Methodology. This was a retrospective cross-sectional study aimed to analyse the results before and after the implementation period of a VITEK 2 system in a Brazilian university hospital. Based on data from medical records, patients with a positive culture of clinical samples from January to July 2017 (conventional method) and from August to December 2017 (automated method) were included in this study. Demographic data, hospitalization time, time interval between culture collection and results, culture results and site, susceptibility profile, minimum inhibitory concentration, and outcome data were evaluated. Chi-square and Fischer's tests were used in the analysis.Results. Of the total samples, 836 were considered valid by the inclusion criteria, with 219 patients before VITEK 2 system implementation group and 545 in the post-implementation group. The comparison between the two periods showed a reduction of 25 % of the time to culture reports, a decrease of 33.5 to 17.0 days of hospitalization, and a reduction in mortality from 44.3-31.0 %, respectively.Conclusion. The VITEK 2 system provided early access to appropriate antimicrobial therapy for patients and effected a positive clinical impact with a reduction in mortality and hospitalization time.

Identificación de especies de micobacterias mediante espectrometría de masas (MALDI-TOF) / Identification of mycobacteria species through mass spectrometry (MALDI-TOF)

Resumen Introducción: Las enfermedades producidas por micobacterias son de gran importancia clínica y epidemiológica presentando el complejo Mycobacterium tuberculosis (MTBc) una morbi-mortalidad mayor que la producida por micobacterias no tuberculosas (MNTB). La identificación tradicional está basada en sus características fenotípicas mediante procesos laboriosos e incapaces en algunos casos de distinguir entre especies. Actualmente, la mayoría de las técnicas utilizadas se basan en métodos moleculares que tienen alta veracidad, pero son complejas y de alto costo. La espectrometría de masas con desorción/ionización láser asistida por una matriz asociada a tiempo de vuelo (MALDI-TOF MS) se basa en la comparación del espectro proteico producido con respecto al de una base de datos de referencia. Objetivo: Evaluar el rendimiento de MALDI-TOF MS en la identificación de micobacterias comparado con métodos moleculares: Material y Métodos: Se analizaron 28 aislados de nueve especies distintas mediante MALDI-TOF MS. Resultados: Se identificó correctamente 78,5% de las aislados (22/28), concordante en 100% (9/9) de MNTB de crecimiento rápido, 60% (9/15) en las MNTB de crecimiento lento y 100% (4/4) de MTBc. Todas las especies no identificadas (6/6) pertenecen al complejo M. avium/intracellulare. Conclusión: MALDI-TOD MS es una metodología rápida, fácil y de bajo costo, con adecuada veracidad respecto a los métodos moleculares.

Abstract Background: Mycobacterial diseases are very important both clinically and epidemiologically. Mycobacterium tuberculosis complex (MTBc) infections confer higher morbidity and mortality rate than non-tuberculous mycobacteria (NTM) infections. Traditional species identification techniques are based on phenotypic characteristics which take a long time by laborious processes and in occasions are no conclusive. Currently, most used techniques are based on molecular methods, which are accurate but are expensive and complex. Matrix Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) is a simple, cheap and fast identification method based on comparing protein spectra with a reference database. Aim: To assess the performance of MALDI-TOF MS in the identification of MTBc and NTM, compared with molecular methods. Methods: For that purpose, 28 isolates of 9 different species were analyzed through MALDI-TOF MS. Results: 78.5% (22/28) of isolates were correctly identified, 100% (9/9) of rapidly growers NTM, 60% (9/15) of slow growing NTM and 100% (4/4) of MTBc. Every unidentified isolate (6/6) corresponded to M. avium/intracellulare complex. Conclusion: MALDI-TOF MS is fast, simple and cheaper than molecular methods and also has adequate accuracy.

Bacterial identification, somatic cell count, antimicrobial profile and toxigenic Staphylococcus strains search from mastitic cow milk samples on small farms properties / Identificação bacteriana, contagem de células somáticas, perfil antimicrobiano e pesquisa de linhagens toxigênicas de Staphylococcus em amostras de leite bovino de pequenas propriedades rurais

Bovine mastitis has a negative impact on milk production and can pose risks to public health. The present study aimed to evaluate the quality of bovine milk from small farms in the Botucatu/SP region. Somatic cell counts (SCC), identification of pathogens involved in mastitis, and sensitivity antimicrobial profile of staphylococci isolated were performed. The presence of enterotoxin encoding genes in isolates of staphylococci obtained from milk was investigated. Milk samples from individual mammary quarters of cows were submitted to the California mastitis test (CMT) and SCC. Of the 239 dairy cows from 21 dairy herds evaluated (mean = 11.4 animals/property), two cows (0.8%) presented clinical mastitis and 86 (35.9%) subclinical mastitis. Bacterial culture was performed in 177 quarter milk samples. Staphylococci were identified in 55 (31.1%), corynebacteria in 45 (25.4%), streptococci in 25 (14.1%) and coliforms in four (2.3%) milk samples. Average SCC from culture-positive samples was 1598x103 cells/mL, in case of staphylococci was 1362x103 cells/ml, streptococci was 2857x103 cells/mL, corynebacteria was 976x103 cells/mL and in the cases of coliforms 1161x103 cells/mL were obtained. Staphylococci showed a high sensitivity (>95%) to cephalothin, cotrimoxazole, enrofloxacin, and gentamicin, with a 41.2% resistance to penicillin and 11.8% to oxacillin. Both coagulase positive (CPS) and negative staphylococci (CNS) carried genes encoding enterotoxins in 21.6% of the first group and 41.9% in the second. The sea gene was the most detected 45.8% (n=24) between them, followed by seb with 29.2% and sec with 25.0%. The sed gene was not identified. We highlight the potential risk to public health in the possibility of strains of Staphylococcus spp. enterotoxin-producing genes that can cause staphylococcal food poisoning.(AU)

A mastite bovina impacta negativamente a produção leiteira e pode acarretar riscos à saúde pública. O presente estudo teve como objetivo a avaliação da qualidade do leite bovino proveniente de pequenas propriedades na região de Botucatu/SP. Foi realizada a contagem de células somáticas (CCS), identificação dos patógenos envolvidos nas mastites, e realizado o perfil de sensibilidade aos antimicrobianos dos estafilococos isolados. Pesquisou-se a presença de genes codificadores de enterotoxinas em isolados de estafilococos obtidos a partir do leite mastítico. Amostras de leite de quartos mamários individuais de vacas foram submetidas ao "California mastitis test" (CMT) e à CCS. Das 239 vacas em lactação provenientes de 21 rebanhos leiteiros avaliados (média = 11,4 animais/propriedade), dois (0,8%) animais apresentaram mastite clínica e, 86 (35,9%) mastite subclínica. 177 amostras de leite foram cultivadas em ágar sangue bovino 5% e ágar MacConckey e obteve-se 55 (31,1%) Staphylococcus spp., 25 (14,1%) Streptococcus spp., 45 (25,4%) Corynebacterium spp. e quatro (2,3%) coliformes. A média da CCS das amostras procedentes de todos os quartos mamários infectados avaliados foi de 1598x103 células/mL, enquanto que nos casos que foram isolados Staphylococcus spp. foi de 1362x103 células/mL, Streptococcus spp. 2857x103 células/mL, Corynebacterium spp. de 976x103 células/mL e nos casos de coliformes 1161x103 células/mL. Os estafilococos revelaram grande sensibilidade (>95%) à cefalotina, cotrimoxazol, enrofloxacina e gentamicina, com resistência de 41,2% à penicilina e 11,8% à oxacilina. Tanto estafilococos coagulase positivos (ECP) como negativos (ECN) revelaram genes codificadores de enterotoxinas em 21,6% do primeiro grupo e 41,9% no segundo. O gene sea foi o mais detectado 45,8% (n=24), seguido pelo seb com 29,2% e sec com 25,0%. O gene codificador da sed não foi identificado. Frente aos resultados, destaca-se o risco potencial à saúde pública pela possibilidade de veiculação de linhagens de Staphylococcus spp. carreadores de genes produtores de enterotoxinas, podendo ocasionar toxi-infecções alimentares.(AU)

Bacterial identification, somatic cell count, antimicrobial profile and toxigenic Staphylococcus strains search from mastitic cow milk samples on small farms properties / Identificação bacteriana, contagem de células somáticas, perfil antimicrobiano e pesquisa de linhagens toxigênicas de Staphylococcus em amostras de leite bovino de pequenas propriedades rurais

Bovine mastitis has a negative impact on milk production and can pose risks to public health. The present study aimed to evaluate the quality of bovine milk from small farms in the Botucatu/SP region. Somatic cell counts (SCC), identification of pathogens involved in mastitis, and sensitivity antimicrobial profile of staphylococci isolated were performed. The presence of enterotoxin encoding genes in isolates of staphylococci obtained from milk was investigated. Milk samples from individual mammary quarters of cows were submitted to the California mastitis test (CMT) and SCC. Of the 239 dairy cows from 21 dairy herds evaluated (mean = 11.4 animals/property), two cows (0.8%) presented clinical mastitis and 86 (35.9%) subclinical mastitis. Bacterial culture was performed in 177 quarter milk samples. Staphylococci were identified in 55 (31.1%), corynebacteria in 45 (25.4%), streptococci in 25 (14.1%) and coliforms in four (2.3%) milk samples. Average SCC from culture-positive samples was 1598x103 cells/mL, in case of staphylococci was 1362x103 cells/ml, streptococci was 2857x103 cells/mL, corynebacteria was 976x103 cells/mL and in the cases of coliforms 1161x103 cells/mL were obtained. Staphylococci showed a high sensitivity (>95%) to cephalothin, cotrimoxazole, enrofloxacin, and gentamicin, with a 41.2% resistance to penicillin and 11.8% to oxacillin. Both coagulase positive (CPS) and negative staphylococci (CNS) carried genes encoding enterotoxins in 21.6% of the first group and 41.9% in the second. The sea gene was the most detected 45.8% (n=24) between them, followed by seb with 29.2% and sec with 25.0%. The sed gene was not identified. We highlight the potential risk to public health in the possibility of strains of Staphylococcus spp. enterotoxin-producing genes that can cause staphylococcal food poisoning.(AU)

A mastite bovina impacta negativamente a produção leiteira e pode acarretar riscos à saúde pública. O presente estudo teve como objetivo a avaliação da qualidade do leite bovino proveniente de pequenas propriedades na região de Botucatu/SP. Foi realizada a contagem de células somáticas (CCS), identificação dos patógenos envolvidos nas mastites, e realizado o perfil de sensibilidade aos antimicrobianos dos estafilococos isolados. Pesquisou-se a presença de genes codificadores de enterotoxinas em isolados de estafilococos obtidos a partir do leite mastítico. Amostras de leite de quartos mamários individuais de vacas foram submetidas ao "California mastitis test" (CMT) e à CCS. Das 239 vacas em lactação provenientes de 21 rebanhos leiteiros avaliados (média = 11,4 animais/propriedade), dois (0,8%) animais apresentaram mastite clínica e, 86 (35,9%) mastite subclínica. 177 amostras de leite foram cultivadas em ágar sangue bovino 5% e ágar MacConckey e obteve-se 55 (31,1%) Staphylococcus spp., 25 (14,1%) Streptococcus spp., 45 (25,4%) Corynebacterium spp. e quatro (2,3%) coliformes. A média da CCS das amostras procedentes de todos os quartos mamários infectados avaliados foi de 1598x103 células/mL, enquanto que nos casos que foram isolados Staphylococcus spp. foi de 1362x103 células/mL, Streptococcus spp. 2857x103 células/mL, Corynebacterium spp. de 976x103 células/mL e nos casos de coliformes 1161x103 células/mL. Os estafilococos revelaram grande sensibilidade (>95%) à cefalotina, cotrimoxazol, enrofloxacina e gentamicina, com resistência de 41,2% à penicilina e 11,8% à oxacilina. Tanto estafilococos coagulase positivos (ECP) como negativos (ECN) revelaram genes codificadores de enterotoxinas em 21,6% do primeiro grupo e 41,9% no segundo. O gene sea foi o mais detectado 45,8% (n=24), seguido pelo seb com 29,2% e sec com 25,0%. O gene codificador da sed não foi identificado. Frente aos resultados, destaca-se o risco potencial à saúde pública pela possibilidade de veiculação de linhagens de Staphylococcus spp. carreadores de genes produtores de enterotoxinas, podendo ocasionar toxi-infecções alimentares.(AU)

Bacterial identification, somatic cell count, antimicrobial profile and toxigenic Staphylococcus strains search from mastitic cow milk samples on small farms properties

ABSTRACT: Bovine mastitis has a negative impact on milk production and can pose risks to public health. The present study aimed to evaluate the quality of bovine milk from small farms in the Botucatu/SP region. Somatic cell counts (SCC), identification of pathogens involved in mastitis, and sensitivity antimicrobial profile of staphylococci isolated were performed. The presence of enterotoxin encoding genes in isolates of staphylococci obtained from milk was investigated. Milk samples from individual mammary quarters of cows were submitted to the California mastitis test (CMT) and SCC. Of the 239 dairy cows from 21 dairy herds evaluated (mean = 11.4 animals/property), two cows (0.8%) presented clinical mastitis and 86 (35.9%) subclinical mastitis. Bacterial culture was performed in 177 quarter milk samples. Staphylococci were identified in 55 (31.1%), corynebacteria in 45 (25.4%), streptococci in 25 (14.1%) and coliforms in four (2.3%) milk samples. Average SCC from culture-positive samples was 1598x103 cells/mL, in case of staphylococci was 1362x103 cells/ml, streptococci was 2857x103 cells/mL, corynebacteria was 976x103 cells/mL and in the cases of coliforms 1161x103 cells/mL were obtained. Staphylococci showed a high sensitivity (>95%) to cephalothin, cotrimoxazole, enrofloxacin, and gentamicin, with a 41.2% resistance to penicillin and 11.8% to oxacillin. Both coagulase positive (CPS) and negative staphylococci (CNS) carried genes encoding enterotoxins in 21.6% of the first group and 41.9% in the second. The sea gene was the most detected 45.8% (n=24) between them, followed by seb with 29.2% and sec with 25.0%. The sed gene was not identified. We highlight the potential risk to public health in the possibility of strains of Staphylococcus spp. enterotoxin-producing genes that can cause staphylococcal food poisoning.

RESUMO: A mastite bovina impacta negativamente a produção leiteira e pode acarretar riscos à saúde pública. O presente estudo teve como objetivo a avaliação da qualidade do leite bovino proveniente de pequenas propriedades na região de Botucatu/SP. Foi realizada a contagem de células somáticas (CCS), identificação dos patógenos envolvidos nas mastites, e realizado o perfil de sensibilidade aos antimicrobianos dos estafilococos isolados. Pesquisou-se a presença de genes codificadores de enterotoxinas em isolados de estafilococos obtidos a partir do leite mastítico. Amostras de leite de quartos mamários individuais de vacas foram submetidas ao California mastitis test (CMT) e à CCS. Das 239 vacas em lactação provenientes de 21 rebanhos leiteiros avaliados (média = 11,4 animais/propriedade), dois (0,8%) animais apresentaram mastite clínica e, 86 (35,9%) mastite subclínica. 177 amostras de leite foram cultivadas em ágar sangue bovino 5% e ágar MacConckey e obteve-se 55 (31,1%) Staphylococcus spp., 25 (14,1%) Streptococcus spp., 45 (25,4%) Corynebacterium spp. e quatro (2,3%) coliformes. A média da CCS das amostras procedentes de todos os quartos mamários infectados avaliados foi de 1598x103 células/mL, enquanto que nos casos que foram isolados Staphylococcus spp. foi de 1362x103 células/mL, Streptococcus spp. 2857x103 células/mL, Corynebacterium spp. de 976x103 células/mL e nos casos de coliformes 1161x103 células/mL. Os estafilococos revelaram grande sensibilidade (>95%) à cefalotina, cotrimoxazol, enrofloxacina e gentamicina, com resistência de 41,2% à penicilina e 11,8% à oxacilina. Tanto estafilococos coagulase positivos (ECP) como negativos (ECN) revelaram genes codificadores de enterotoxinas em 21,6% do primeiro grupo e 41,9% no segundo. O gene sea foi o mais detectado 45,8% (n=24), seguido pelo seb com 29,2% e sec com 25,0%. O gene codificador da sed não foi identificado. Frente aos resultados, destaca-se o risco potencial à saúde pública pela possibilidade de veiculação de linhagens de Staphylococcus spp. carreadores de genes produtores de enterotoxinas, podendo ocasionar toxi-infecções alimentares.

Análise bacteriológica e físico-química de leite cru resfriado, proveniente de posto de refrigeração, sob inspeção federal, em Rio Bonito, RJ

Com o objetivo de avaliar a qualidade microbiológica e fisico-química do leite cru de propriedades rurais do município de Rio Bonito-RJ e arredores, foram analisadas 20 amostras de leite provenientes de Posto de Refrigeração, subsidiado à Indústria Nestlé, coletadas de latões e de tanque de refrigeração. Realizaram-se análises microbiológicas como Contagem Total de Bactérias Heterotróficas Aeróbias Mesófilas (B.H.A.M), Contagem total de Bactérias Heterotróficas Aeróbias Psicotrófilas (B.H.A.P) seguindo as análises fisico-químicas, tais como: temperatura, acidez titulável, prova alizarol, lactofermentação, prova da redução e contagem de células somáticas. Para as variáveis da prova do alizarol houve reprovação em 20% das amostras, já para acidez 95% estavam dentro dos padrões normais. A temperatura das amostras, no ato da coleta, apresentou grandes variações em decorrência da distância e transporte inadequados. No teste da redutase apenas 15% foram consideradas boas ou ótimas e na lactofermentação 100% das amostras formaram algum tipo de coágulo. Em relação à contagem de bactérias, as B.H.A.M foram encontradas fora dos padrões em 65% das amostras e nas B.H.A.P em 80% dos resultados encontrados. Quanto à contagem de células somáticas apenas uma amostra apresentou-se fora do padrão. Conclui-se que a qualidade do leite pode ser melhorada por meio de assistência técnica e instrucional aos produtores, considerando os aspectos da legislação vigente associados à higienização adequada dos latões e utensílios de ordenha. O leite deve ser resfriado na fazenda e transportado sem delongas até a cooperativa.(AU)

With the objective of evaluating the microbiology and physicochemical quality of raw milk from rural properties in the city of Rio Bonito-RJ and surrounding areas, were analyzed 20 samples of raw milk from Refrigeration Station, subsidized by Nestlé, collected from bulk milk collectors and cooling tank. Microbiological analyzes were performed as Total Counting of Mesophilic Aerobic Heterotrophic Bacteria (MA.H.B), Total Counting of Heterotrophic Aerobic Psychophotrophic Bacteria (H.A.P.B) and physicochemical analyzes: temperature, titratable acidity, alizarol test, lactofermentation, reduction test and cell count somatic cells. For the variables of the alizarol test there was reprobation in 20% of the samples, already for acidity 95% were within normal standards. The temperature of the samples, at the time of collection, presented great variations due to inadequate distance and transport. In the reductase test only 15% were considered good or optimal and in the lactofermentation 100% of the samples formed some type of clot. Regarding bacterial counts, M.A.H.B. were found out of standards in 65% of samples and in H.A.P.B in 80% of the results found. As for somatic cell count, only one sample was out of standard. It is concluded that the quality of milk can be improved by providing technical and instructional assistance to producers and by appropriate hygiene of brass and milking utensils. The milk should be cooled on the farm and transported without delay to the Milk Collection Centers.(AU)

Análise bacteriológica e físico-química de leite cru resfriado, proveniente de posto de refrigeração, sob inspeção federal, em Rio Bonito, RJ

Com o objetivo de avaliar a qualidade microbiológica e físico-química do leite cru de propriedades rurais do município de Rio Bonito-RJ e arredores, foram analisadas 20 amostras de leite provenientes de Posto de Refrigeração, subsidiado à Indústria Nestlé, coletadas de latões e de tanque de refrigeração. Realizaram-se análises microbiológicas como Contagem Total de Bactérias Heterotróficas Aeróbias Mesófilas (B.H.A.M), Contagem total de Bactérias Heterotróficas Aeróbias Psicotrófilas (B.H.A.P) seguindo as análises físico-químicas, tais como: temperatura, acidez titulável, prova alizarol, lactofermentação, prova da redução e contagem de células somáticas. Para as variáveis da prova do alizarol houve reprovação em 20% das amostras, já para acidez 95% estavam dentro dos padrões normais. A temperatura das amostras, no ato da coleta, apresentou grandes variações em decorrência da distância e transporte inadequados. No teste da redutase apenas 15% foram consideradas boas ou ótimas e na lactofermentação 100% das amostras formaram algum tipo de coágulo. Em relação à contagem de bactérias, as B.H.A.M foram encontradas fora dos padrões em 65% das amostras e nas B.H.A.P em 80% dos resultados encontrados. Quanto à contagem de células somáticas apenas uma amostra apresentou-se fora do padrão. Conclui-se que a qualidade do leite pode ser melhorada por meio de assistência técnica e instrucional aos produtores, considerando os aspectos da legislação vigente associados à higienização adequada dos latões e utensílios de ordenha. O leite deve ser resfriado na fazenda e transportado sem delongas até a cooperativa.

With the objective of evaluating the microbiology and physicochemical quality of raw milk from rural properties in the city of Rio Bonito-RJ and surrounding areas, were analyzed 20 samples of raw milk from Refrigeration Station, subsidized by Nestlé, collected from bulk milk collectors and cooling tank. Microbiological analyzes were performed as Total Counting of Mesophilic Aerobic Heterotrophic Bacteria (M.A.H.B), Total Counting of Heterotrophic Aerobic Psychophotrophic Bacteria (H.A.P.B) and physicochemical analyzes: temperature, titratable acidity, alizarol test, lactofermentation, reduction test and cell count somatic cells. For the variables of the alizarol test there was reprobation in 20% of the samples, already for acidity 95% were within normal standards. The temperature of the samples, at the time of collection, presented great variations due to inadequate distance and transport. In the reductase test only 15% were considered good or optimal and in the lactofermentation 100% of the samples formed some type of clot. Regarding bacterial counts, M.A.H.B were found out of standards in 65% of samples and in H.A.P.B in 80% of the results found. As for somatic cell count, only one sample was out of standard. It is concluded that the quality of milk can be improved by providing technical and instructional assistance to producers and by appropriate hygiene of brass and milking utensils. The milk should be cooled on the farm and transported without delay to the Milk Collection Centers.

Análise bacteriológica e físico-química de leite cru resfriado, proveniente de posto de refrigeração, sob inspeção federal, em Rio Bonito, RJ

Com o objetivo de avaliar a qualidade microbiológica e fisico-química do leite cru de propriedades rurais do município de Rio Bonito-RJ e arredores, foram analisadas 20 amostras de leite provenientes de Posto de Refrigeração, subsidiado à Indústria Nestlé, coletadas de latões e de tanque de refrigeração. Realizaram-se análises microbiológicas como Contagem Total de Bactérias Heterotróficas Aeróbias Mesófilas (B.H.A.M), Contagem total de Bactérias Heterotróficas Aeróbias Psicotrófilas (B.H.A.P) seguindo as análises fisico-químicas, tais como: temperatura, acidez titulável, prova alizarol, lactofermentação, prova da redução e contagem de células somáticas. Para as variáveis da prova do alizarol houve reprovação em 20% das amostras, já para acidez 95% estavam dentro dos padrões normais. A temperatura das amostras, no ato da coleta, apresentou grandes variações em decorrência da distância e transporte inadequados. No teste da redutase apenas 15% foram consideradas boas ou ótimas e na lactofermentação 100% das amostras formaram algum tipo de coágulo. Em relação à contagem de bactérias, as B.H.A.M foram encontradas fora dos padrões em 65% das amostras e nas B.H.A.P em 80% dos resultados encontrados. Quanto à contagem de células somáticas apenas uma amostra apresentou-se fora do padrão. Conclui-se que a qualidade do leite pode ser melhorada por meio de assistência técnica e instrucional aos produtores, considerando os aspectos da legislação vigente associados à higienização adequada dos latões e utensílios de ordenha. O leite deve ser resfriado na fazenda e transportado sem delongas até a cooperativa.

With the objective of evaluating the microbiology and physicochemical quality of raw milk from rural properties in the city of Rio Bonito-RJ and surrounding areas, were analyzed 20 samples of raw milk from Refrigeration Station, subsidized by Nestlé, collected from bulk milk collectors and cooling tank. Microbiological analyzes were performed as Total Counting of Mesophilic Aerobic Heterotrophic Bacteria (MA.H.B), Total Counting of Heterotrophic Aerobic Psychophotrophic Bacteria (H.A.P.B) and physicochemical analyzes: temperature, titratable acidity, alizarol test, lactofermentation, reduction test and cell count somatic cells. For the variables of the alizarol test there was reprobation in 20% of the samples, already for acidity 95% were within normal standards. The temperature of the samples, at the time of collection, presented great variations due to inadequate distance and transport. In the reductase test only 15% were considered good or optimal and in the lactofermentation 100% of the samples formed some type of clot. Regarding bacterial counts, M.A.H.B. were found out of standards in 65% of samples and in H.A.P.B in 80% of the results found. As for somatic cell count, only one sample was out of standard. It is concluded that the quality of milk can be improved by providing technical and instructional assistance to producers and by appropriate hygiene of brass and milking utensils. The milk should be cooled on the farm and transported without delay to the Milk Collection Centers.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of bacteria isolated from pharmaceutical clean rooms.

INTRODUCTION: During the manufacturing of sterile drugs, it is of the utmost importance to meet the minimum requirements for asepsis recommended by the legislations on good manufacturing practices-based efficient environmental monitoring. AIMS AND METHODS: The availability of relatively simple to use matrix-assisted laser desorption ionization-time of flight mass spectromtomy (MALDI-TOF MS) devices in the last years has changed the laboratory workflows for the microbial identification, mainly in the clinical area. Thus, the objective of this work was to evaluate the suitability of the MALDI-TOF MS technique for the identification of bacteria isolated from the environment of clean rooms used in some stages of the production of a viral vaccine. Eighteen known bacterial species commonly isolated from clean rooms studied were identified by MALDI-TOF technique and by a biochemical technique (BBL Crystal® System). RESULTS: Performance of MALDI-TOF MS was better than biochemical technique for correct species identifications (88.89% and 38.89%, respectively) and produced less unreliable identification (5.55% and 22.22%). CONCLUSION: MALDI-TOF MS can be implemented for routine identification of bacteria in a pharmaceutical quality control laboratory, but as a database-dependent system, maybe some isolated not identified by this technique must be additionally studied and, if appropriate, added to an in-house database.

The classical Bordetella species and MALDI-TOF technology: a brief experience.

PURPOSE: The aim of this work was to evaluate and optimize the identification of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica (usually known as the classical Bordetella species) using Bruker Biotyper matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS). METHODOLOGY: A set of 106 previously characterized clinical isolates was used. The results were interpreted according to the manufacturer's recommendations and, in addition, a new score value cutoff was used for species identification. Further, the 10 % rule (previously adopted by other authors) and the new 5 % breaking point (proposed in this work) were evaluated in order to optimize identification rates.Results/Key findings. Our results suggest that it is possible to distinguish different species of the classical Bordetella species by following a simple algorithm without additional testing being required. CONCLUSION: MALDI-TOF might be a reliable tool for the identification of this group of bacteria when a combination of cutoff scores is used. This procedure allows us to increase the identification rates for the classical Bordetella species significantly; however, more studies will be required to determine the applicability of the method to other difficult-to-distinguish organisms.

Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil.

BACKGROUND: Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. METHODS: We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods. RESULTS: The first two bacterial species were confirmed while the third group of species could not be identified using standard identification protocols. These isolates were subsequently identified by Multi-Locus Sequence Analysis as Phytobacter diazotrophicus, a species related to strains from similar outbreaks in the United States in the 1970's. Within each species, TPN and blood isolates proved to be clonal, whereas the R. radiobacter isolates retrieved from CG were found to be unrelated. CONCLUSION: This is the first report of a three-species outbreak caused by TPN contaminated with A. baumannii, R. radiobacter and P. diazotrophicus. The concomitant presence of clonal A. baumannii and P. diazotrophicus isolates in several TPN and blood samples, as well as the case of one patient, where all three different species were isolated simultaneously, suggest that the outbreak may be ascribed to a discrete contamination of TPN. In addition, this study highlights the clinical relevance of P. diazotrophicus, which has been involved in outbreaks in the past, but was often misidentified as P. agglomerans.

Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species.

Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov Models (HMMs) to detect enzymes participating in the various pathways and performed ab initio protein structure modeling and molecular docking to confirm specific results. We found a differential distribution among the various strains of genes that code for some important enzymes, such as beta-phosphoglucomutase and fructokinase, and also for individual components of carbohydrate transport systems, including the fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) and the ribose-specific ATP-binging cassette (ABC) transporter. Horizontal gene transfer plays a role in the biochemical variability of the isolates, as some genes needed for sucrose fermentation were seen to be present in genomic islands. Noteworthy, using profile HMMs, we identified an enzyme with putative alpha-1,6-glycosidase activity only in some specific strains of C. diphtheriae and this may aid to understanding of the differential abilities to utilize glycogen and starch between the biovars.

Challenges in the identification of Chryseobacterium indologenes and Elizabethkingia meningoseptica in cases of nosocomial infections and patients with cystic fibrosis.

Rare nonfermenting Gram-negative bacilli, such as Chryseobacterium indologenes and Elizabethkingia meningoseptica, have clinical importance in nosocomial infections and cystic fibrosis (CF), and their identification is a challenge to microbiology laboratories. Thus, the objective of this study was to verify the performance of phenotypic and mass spectrometry (matrix-assisted desorption ionization-time of flight mass spectrometry, MALDI-TOF MS) methods to identify C. indologenes and E. meningoseptica. In this context, the results obtained with phenotypic methods-namely manual biochemical and automated VITEK 2 (bioMérieux, Marcy l'Etoile, France) and Phoenix tests (Becton Dickinson (BD), San Diego, CA, USA)-and by MALDI-TOF MS-namely MALDI-TOF VITEK MS (MALDI-MS; bioMérieux) and MALDI-TOF BioTyper (MALDI-BD; BD)-of 22 isolates (blood cultures of patients with nosocomial infection (n = 15) and from patients with CF (n = 7)), initially identified as C. indologenes and E. meningoseptica, were compared. As result, using the manual phenotypic method, it was possible to identify the species level in 18/22; no identification was found in 4/22. There was a low agreement level between manual and VITEK 2 automated phenotypic methods when considering the genus level. The greatest agreement for genus-level identification occurred in MALDI-TOF MS equipment (15/22). When comparing all methods to identify the 22 isolates, there was agreement of 4/22 at the genus level and of 4/22 at the species level. In conclusion, there is low agreement level among identification methods of C. indologenes and E. meningoseptica. Although MALDI-TOF MS equipment shows a higher agreement level among them, results present low levels of confidence.

Efficient differentiation of Corynebacterium striatum, Corynebacterium amycolatum and Corynebacterium xerosis clinical isolates by multiplex PCR using novel species-specific primers.

A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and by VITEK-MS.

Direct identification from positive blood broth culture by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS)

ABSTRACT Bloodstream infections (BSIs) are among the most concerning bacterial infections. They are one of the leading causes of morbidity and mortality, and occur in 30-70% of critical care patients. The prompt identification of the causative microorganism can help choosing the appropriate antimicrobial therapy that will lead to better clinical outcomes. Blood culture is one of the most relevant tests for microbiological diagnosis of bacterial infections. The introduction of the MALDI-TOF microbiological diagnosis significantly decreased the time of identifying microorganisms. However, it depends on the growth on solid culture medium. In this study, 538 bottles of positive blood cultures were evaluated to test the accuracy of an in house modified protocol. The study sample consisted of 198 Gram-negative and 350 Gram-positive bacteria. In all, 460 (83.94%) species were identified based on the direct plate findings. The protocol allowed the identification of 185/198 (93.43%) of the Gram-negative bacteria, including aerobes, anaerobes, and non-fermenters, and 275/350 (78.85%) of the Gram-positive bacteria. The proposed method has the potential to provide accurate results in comparison to the traditional method with the potential to reduce the turnaround time for the results and optimize antimicrobial therapy in BSI.

Direct identification from positive blood broth culture by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS).

Bloodstream infections (BSIs) are among the most concerning bacterial infections. They are one of the leading causes of morbidity and mortality, and occur in 30-70% of critical care patients. The prompt identification of the causative microorganism can help choosing the appropriate antimicrobial therapy that will lead to better clinical outcomes. Blood culture is one of the most relevant tests for microbiological diagnosis of bacterial infections. The introduction of the MALDI-TOF microbiological diagnosis significantly decreased the time of identifying microorganisms. However, it depends on the growth on solid culture medium. In this study, 538 bottles of positive blood cultures were evaluated to test the accuracy of an in house modified protocol. The study sample consisted of 198 Gram-negative and 350 Gram-positive bacteria. In all, 460 (83.94%) species were identified based on the direct plate findings. The protocol allowed the identification of 185/198 (93.43%) of the Gram-negative bacteria, including aerobes, anaerobes, and non-fermenters, and 275/350 (78.85%) of the Gram-positive bacteria. The proposed method has the potential to provide accurate results in comparison to the traditional method with the potential to reduce the turnaround time for the results and optimize antimicrobial therapy in BSI.

Variation in extragenic repetitive DNA sequences in Pseudomonas syringae and potential use of modified REP primers in the identification of closely related isolates.

In this study, Pseudomonas syringe pathovars isolated from olive, tomato and bean were identified by species-specific PCR and their genetic diversity was assessed by repetitive extragenic palindromic (REP)-PCR. Reverse universal primers for REP-PCR were designed by using the bases of A, T, G or C at the positions of 1, 4 and 11 to identify additional polymorphism in the banding patterns. Binding of the primers to different annealing sites in the genome revealed additional fingerprint patterns in eight isolates of P. savastanoi pv. savastanoi and two isolates of P. syringae pv. tomato. The use of four different bases in the primer sequences did not affect the PCR reproducibility and was very efficient in revealing intra-pathovar diversity, particularly in P. savastanoi pv. savastanoi. At the pathovar level, the primer BOX1AR yielded shared fragments, in addition to five bands that discriminated among the pathovars P. syringae pv. phaseolicola, P. savastanoi pv. savastanoi and P. syringae pv. tomato. REP-PCR with a modified primer containing C produced identical bands among the isolates in a pathovar but separated three pathovars more distinctly than four other primers. Although REP- and BOX-PCRs have been successfully used in the molecular identification of Pseudomonas isolates from Turkish flora, a PCR based on inter-enterobacterial repetitive intergenic concensus (ERIC) sequences failed to produce clear banding patterns in this study.

Identificación bacteriana basada en el espectro de masas de proteínas: Una nueva mirada a la microbiología del siglo XXI / Bacterial identification based on protein mass spectrometry: A new insight at the microbiology of the 21st century

Bacterial identification is important for the proper treatment of infected patients hospitalized with serious infections especially in critical care units. Identification by conventional methods used in microbiology laboratories takes at least 16 hours since a culture is positive. The introduction of mass spectrometry, specifically MALDI-TOF MS (matrix-assisted laser desorption/ ionization time-of-flight mass spectrometer) in the microbiology laboratory could mean a radical change in the identification accuracy, turn around time (6 minutes per bacteria) and cost (about 5 times cheaper than conventional identification). Since its introduction in clinical microbiology laboratories in 2008, many reports about its usefulness in identifying microorganisms from colonies, as well as directly from positive blood cultures and urine samples have been published. This review describes MALDI-TOF MS methodology, its identification performance for bacteria (aerobic and anaerobic), mycobacterium and yeasts, its future applications in microbiology and its main disadvantages.

La identificación bacteriana es muy importante en el manejo adecuado de los pacientes infectados, especialmente aquellos con infecciones graves hospitalizados en unidades de pacientes críticos. La identificación por los métodos convencionales utilizados en los laboratorios de microbiología clínica demora al menos 16 horas desde que un cultivo es positivo. La introducción de la espectrometría de masas, específicamente del espectrómetro de masas por tiempo de migración (tiempo de vuelo) con desorción/ionización laser asistida por una matriz (MALDI-TOF MS, por su sigla en inglés matrix-assisted laser desorption/ionization time-of-flight mass spectrometer), en el laboratorio de microbiología podría significar un cambio radical en la precisión de la identificación, el tiempo de detección (6 minutos por bacterias) y el costo (aproximadamente 5 veces más económico que la identificación convencional). Desde su introducción en los laboratorios de microbiología clínica en el año 2008, se han escrito numerosas publicaciones sobre su utilidad en la identificación de microorganismos desde colonias, así como directamente desde hemocultivos positivos y de muestras de orina. Esta revisión describe la metodología de MALDI-TOF MS, su rendimiento en la identificación de bacterias aerobias, anaerobias, micobacterias y levaduras, sus futuras aplicaciones en microbiología y sus principales desventajas.

BOX-PCR-based identification of bacterial species belonging to Pseudomonas syringae: P. viridiflava group

The phenotypic characteristics and genetic fingerprints of a collection of 120 bacterial strains, belonging to Pseudomonas syringae sensu lato group, P. viridiflava and reference bacteria were evaluated, with the aim of species identification. The numerical analysis of 119 nutritional characteristics did not show patterns that would help with identification. Regarding the genetic fingerprinting, the results of the present study supported the observation that BOX-PCR seems to be able to identify bacterial strains at species level. After numerical analyses of the bar-codes, all pathovars belonging to each one of the nine described genomospecies were clustered together at a distance of 0.72, and could be separated at genomic species level. Two P. syringae strains of unknown pathovars (CFBP 3650 and CFBP 3662) and the three P. syringae pv. actinidiae strains were grouped in two extra clusters and might eventually constitute two new species. This genomic species clustering was particularly evident for genomospecies 4, which gathered P. syringae pvs. atropurpurea, coronafaciens, garçae, oryzae, porri, striafaciens, and zizaniae at a noticeably low distance.