Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils.

Bacteria from the Burkholderia cepacia complex (Bcc) are capable of causing severe infections in patients with cystic fibrosis (CF). These opportunistic pathogens are also widely distributed in natural and man-made environments. After a 12-year epidemiological surveillance involving Bcc bacteria from respiratory secretions of Argentinean patients with CF and from hospital settings, we found six isolates of the Bcc with a concatenated species-specific allele sequence that differed by more than 3 % from those of the Bcc with validly published names. According to the multilocus sequence analysis (MLSA), these isolates clustered with the agricultural soil strain, Burkholderia sp. PBP 78, which was already deposited in the PubMLST database. The isolates were examined using a polyphasic approach, which included 16S rRNA, recA, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), DNA base composition, average nucleotide identities (ANIs), fatty acid profiles, and biochemical characterizations. The results of the present study demonstrate that the seven isolates represent a single novel species within the Bcc, for which the name Burkholderia puraquae sp. nov. is proposed. Burkholderia puraquae sp. nov. CAMPA 1040T (=LMG 29660T=DSM 103137T) was designated the type strain of the novel species, which can be differentiated from other species of the Bcc mainly from recA gene sequence analysis, MLSA, ANIb, MALDI-TOF MS analysis, and some biochemical tests, including the ability to grow at 42 °C, aesculin hydrolysis, and lysine decarboxylase and ß-galactosidase activities.

[Cystic Fibrosis Cloud database: An information system for storage and management of clinical and microbiological data of cystic fibrosis patients]. / Cystic Fibrosis Cloud database: Un sistema informático para el almacenamiento y manejo de datos clínicos y microbiológicos del paciente con fibrosis quística.

The epidemiological and clinical management of cystic fibrosis (CF) patients suffering from acute pulmonary exacerbations or chronic lung infections demands continuous updating of medical and microbiological processes associated with the constant evolution of pathogens during host colonization. In order to monitor the dynamics of these processes, it is essential to have expert systems capable of storing and subsequently extracting the information generated from different studies of the patients and microorganisms isolated from them. In this work we have designed and developed an on-line database based on an information system that allows to store, manage and visualize data from clinical studies and microbiological analysis of bacteria obtained from the respiratory tract of patients suffering from cystic fibrosis. The information system, named Cystic Fibrosis Cloud database is available on the http://servoy.infocomsa.com/cfc_database site and is composed of a main database and a web-based interface, which uses Servoy's product architecture based on Java technology. Although the CFC database system can be implemented as a local program for private use in CF centers, it can also be used, updated and shared by different users who can access the stored information in a systematic, practical and safe manner. The implementation of the CFC database could have a significant impact on the monitoring of respiratory infections, the prevention of exacerbations, the detection of emerging organisms, and the adequacy of control strategies for lung infections in CF patients.

First Case of Fungemia Due to Pseudozyma aphidis in a Pediatric Patient with Osteosarcoma in Latin America.

We report the first case of blood infection due to Pseudozyma aphidis in Latin America. We contribute evidence showing this organism to be a potential human pathogen, and we provide new data about its identification, drug susceptibility, and treatment outcome.

Genetic diversity of Burkholderia contaminans isolates from cystic fibrosis patients in Argentina.

A total of 120 Burkholderia cepacia complex isolates collected during 2004-2010 from 66 patients in two cystic fibrosis reference centers in Argentina were analyzed. Burkholderia contaminans was the species most frequently recovered (57.6%), followed by Burkholderia cenocepacia (15%), a species distribution not reported so far. The recA-PCR-based techniques applied to the B. contaminans isolates revealed that 85% of the population carried the recA-ST-71 allele. Our results showed the utility of BOX-PCR genotyping in analyzing B. contaminans diversity. This approach allowed us to address clonal transmission during an outbreak and the genetic changes occurring in infecting bacteria over the course of chronic infection.

Fourier transform infrared spectroscopy for rapid identification of nonfermenting gram-negative bacteria isolated from sputum samples from cystic fibrosis patients.

The accurate and rapid identification of bacteria isolated from the respiratory tract of patients with cystic fibrosis (CF) is critical in epidemiological studies, during intrahospital outbreaks, for patient treatment, and for determination of therapeutic options. While the most common organisms isolated from sputum samples are Pseudomonas aeruginosa, Staphylococcus aureus, and Haemophilus influenzae, in recent decades an increasing fraction of CF patients has been colonized by other nonfermenting (NF) gram-negative rods, such as Burkholderia cepacia complex (BCC) bacteria, Stenotrophomonas maltophilia, Ralstonia pickettii, Acinetobacter spp., and Achromobacter spp. In the present study, we developed a novel strategy for the rapid identification of NF rods based on Fourier transform infrared spectroscopy (FTIR) in combination with artificial neural networks (ANNs). A total of 15 reference strains and 169 clinical isolates of NF gram-negative bacteria recovered from sputum samples from 150 CF patients were used in this study. The clinical isolates were identified according to the guidelines for clinical microbiology practices for respiratory tract specimens from CF patients; and particularly, BCC bacteria were further identified by recA-based PCR followed by restriction fragment length polymorphism analysis with HaeIII, and their identities were confirmed by recA species-specific PCR. In addition, some strains belonging to genera different from BCC were identified by 16S rRNA gene sequencing. A standardized experimental protocol was established, and an FTIR spectral database containing more than 2,000 infrared spectra was created. The ANN identification system consisted of two hierarchical levels. The top-level network allowed the identification of P. aeruginosa, S. maltophilia, Achromobacter xylosoxidans, Acinetobacter spp., R. pickettii, and BCC bacteria with an identification success rate of 98.1%. The second-level network was developed to differentiate the four most clinically relevant species of BCC, B. cepacia, B. multivorans, B. cenocepacia, and B. stabilis (genomovars I to IV, respectively), with a correct identification rate of 93.8%. Our results demonstrate the high degree of reliability and strong potential of ANN-based FTIR spectrum analysis for the rapid identification of NF rods suitable for use in routine clinical microbiology laboratories.

Draft Genome Sequence of Burkholderia puraquae Type Strain CAMPA 1040, Isolated from Hospital Settings in Córdoba, Argentina.

We report here the draft genome sequence of Burkholderia puraquae type strain CAMPA 1040, a member of the Burkholderia cepacia complex. This strain, isolated from a hemodialysis water reservoir, harbors several stress tolerance genes, such as the systems for low oxygen survival, for copper tolerance, and for osmotic stress resistance.

[Pertussis predictors in hospitalized infants with acute lower respiratory tract infection]. / Predictores de coqueluche al ingreso en lactantes hospitalizados con infección respiratoria aguda baja.

BACKGROUND: Pertussis, or whooping cough, caused by Bordetella pertussis (BP) is a re-emerging problem in our environment. Although generally considered that the disease is relatively easy to identify infections respiratory syncytial virus (RSV) can present with similar symptoms in infants remains difficult discrimination. OBJECTIVE: Compare clinical symptoms at admission and complementary studies in infants hospitalized with acute respiratory infection (ARI) and RSV by BP to establish markers that enable their early clinical prediction. MATERIALS AND METHODS: Observational, analytical, case-crossover cross comparing younger than 6 months hospitalized with suspected IRA and pertussis (2007-2012) in which BP identified (PCR and culture) and / or VRS (immunofluorescence in nasal secretions). Coinfections were excluded. Bivariate analysis was performed by calculating OR with 95% CI. Were considered significant at p <0.05. The variables studied were age, sex, hits cough, cyanosis, vomiting, apnea, wheezing and CBC with differential RESULTS: We included 174 infants, 72 (41%) BP and 102 (59%) VRS. Age 2 ± 1 months (range :1-6). In both groups was documented cough and wheeze (OR: 1.2 (0.9 to 1.5) p: 0.1 and OR = 0.9 (0.8 to 1.06) p: 0.2, respectively ). Cyanosis (87% vs. 6%, OR: 14.8 p <0.01), apnea (38% vs. 3%, OR: 13.4 p <0.01) and vomiting (26% vs. 5% , OR: 3.4 p <0.01) were more frequent in infants with BP. The absolute lymphocyte count was significantly higher in children with BP (9387 ± 6317 vs. 5127 ± 2766, p <0.01). By ROC curve was identified at 9000 cells / ml as the best point to differentiate VSR BP (AUC = 0.73, 95% CI :0,64-0, 81). CONCLUSIONS: In infants under 6 months with IRA income presence of apnea, cyanosis and lymphocytosis allowing predict significantly differentiate between pertussis those with RSV infections.

Antecedentes. La tos ferina o coqueluche, producida por Bordetella pertussis (BP) representa un problema re-emergente en nuestro medio. Aunque suele considerarse que la enfermedad es relativamente fácil de identificar, las infecciones por Virus Respiratorio Sincicial (VRS) pueden presentarse con síntomas similares en los lactantes siendo difícil su discriminación. Objetivo. Comparar síntomas clínicos y estudios complementarios al ingreso en lactantes hospitalizados con infección respiratoria aguda (IRA) por BP y por VSR a fin de establecer marcadores que posibiliten su predicción clínica temprana. Material y método. Estudio observacional, analítico, transversal de casos cruzados, comparando menores de 6 meses internados por IRA y sospecha de coqueluche (2007-2012) en los que se identificó BP (PCR y cultivo) y/o VRS (inmunofluorescencia en secreciones nasales); se excluyeron los pacientes con coinfecciones. Se realizó un análisis bivariado mediante el cálculo de OR con IC95%. Se consideró significativo un valor de p<0,05. Las variables en estudio fueron: edad, sexo, tos en accesos, cianosis, vómitos, apneas, sibilancias y hemograma completo con fórmula leucocitaria Resultados. Se incluyeron 174 lactantes; 72 (41%) BP y 102 (59%) VRS. Edad 2±1 mes (Rango:1-6). En ambos grupos se documentó tos y sibilancias (OR:1,2 (0,9-1,5) p:0,1 y OR:0,9 (0,8-1,06) p:0,2, respectivamente). Cianosis (87% vs. 6%;OR:14,8 p<0,01), apnea (38% vs. 3%;OR:13,4 p<0,01) y vómitos (26% vs. 5%;OR:3,4 p<0,01) fueron más frecuentes en lactantes con BP. El recuento absoluto de linfocitos fue significativamente mayor en niños con BP (9387±6317 vs. 5127±2766;p<0,01). Por curva ROC se identificó a 9000 cel/ml como el mejor punto para diferenciar BP de VSR (abc= 0,73; IC95%:0,64-0,81). Conclusiones. En lactantes menores de 6 meses con IRA la presencia al ingreso de apnea, cianosis y linfocitosis predicen significativamente coqueluche permitiendo diferenciarlos de aquellos con infecciones por VRS.

Cystic Fibrosis Cloud database: Un sistema informático para el almacenamiento y manejo de datos clínicos y microbiológicos del paciente con fibrosis quística / Cystic Fibrosis Cloud database: An information system for storage and management of clinical and microbiological data of cystic fibrosis patients

El manejo clínico y epidemiológico de los pacientes con fibrosis quística (FQ) con exacerbaciones pulmonares agudas o infecciones pulmonares crónicas demanda una actualización permanente de procedimientos médicos y microbiológicos, estos se asocian con la constante evolución de los agentes patógenos durante la colonización de su hospedador. Para poder monitorear la dinámica de estos procesos es fundamental disponer de sistemas expertos que permitan almacenar, extraer y utilizar la información generada a partir de estudios realizados sobre el paciente y los microorganismos aislados de aquel. En este trabajo hemos diseñado y desarrollado una base de datos on-line basada en un sistema informático que permite el almacenamiento, el manejo y la visualización de la información proveniente de estudios clínicos y de análisis microbiológicos de bacterias obtenidas del tracto respiratorio del paciente con FQ. Este sistema informático fue designado como Cystic Fibrosis Cloud database (CFC database) y está disponible en el sitio http://servoy.infocomsa.com/cfc_database. Está compuesto por una base de datos principal y una interfaz on-line, la cual emplea la arquitectura de productos Servoy basada en tecnología Java. Si bien el sistema CFC database puede ser implementado como un programa local de uso privado en los centros de asistencia a pacientes con FQ, admite también la posibilidad de ser empleado, actualizado y compartido por diferentes usuarios, quienes pueden acceder a la información almacenada de manera ordenada, práctica y segura. La implementación del CFC database podría tener una gran impacto en la monitorización de las infecciones respiratorias, la prevención de exacerbaciones, la detección de organismos emergentes y la adecuación de las estrategias de control de infecciones pulmonares en pacientes con FQ

The epidemiological and clinical management of cystic fibrosis (CF) patients suffering from acute pulmonary exacerbations or chronic lung infections demands continuous updating of medical and microbiological processes associated with the constant evolution of pathogens during host colonization. In order to monitor the dynamics of these processes, it is essential to have expert systems capable of storing and subsequently extracting the information generated from different studies of the patients and microorganisms isolated from them. In this work we have designed and developed an on-line database based on an information system that allows to store, manage and visualize data from clinical studies and microbiological analysis of bacteria obtained from the respiratory tract of patients suffering from cystic fibrosis. The information system, named Cystic Fibrosis Cloud database is available on the http://servoy.infocomsa.com/cfc_database site and is composed of a main database and a web-based interface, which uses Servoy's product architecture based on Java technology. Although the CFC database system can be implemented as a local program for private use in CF centers, it can also be used, updated and shared by different users who can access the stored information in a systematic, practical and safe manner. The implementation of the CFC database could have a significant impact on the monitoring of respiratory infections, the prevention of exacerbations, the detection of emerging organisms, and the adequacy of control strategies for lung infections in CF patients

Mucoidy, quorum sensing, mismatch repair and antibiotic resistance in Pseudomonas aeruginosa from cystic fibrosis chronic airways infections.

Survival of Pseudomonas aeruginosa in cystic fibrosis (CF) chronic infections is based on a genetic adaptation process consisting of mutations in specific genes, which can produce advantageous phenotypic switches and ensure its persistence in the lung. Among these, mutations inactivating the regulators MucA (alginate biosynthesis), LasR (quorum sensing) and MexZ (multidrug-efflux pump MexXY) are the most frequently observed, with those inactivating the DNA mismatch repair system (MRS) being also highly prevalent in P. aeruginosa CF isolates, leading to hypermutator phenotypes that could contribute to this adaptive mutagenesis by virtue of an increased mutation rate. Here, we characterized the mutations found in the mucA, lasR, mexZ and MRS genes in P. aeruginosa isolates obtained from Argentinean CF patients, and analyzed the potential association of mucA, lasR and mexZ mutagenesis with MRS-deficiency and antibiotic resistance. Thus, 38 isolates from 26 chronically infected CF patients were characterized for their phenotypic traits, PFGE genotypic patterns, mutations in the mucA, lasR, mexZ, mutS and mutL gene coding sequences and antibiotic resistance profiles. The most frequently mutated gene was mexZ (79%), followed by mucA (63%) and lasR (39%) as well as a high prevalence (42%) of hypermutators being observed due to loss-of-function mutations in mutL (60%) followed by mutS (40%). Interestingly, mutational spectra were particular to each gene, suggesting that several mechanisms are responsible for mutations during chronic infection. However, no link could be established between hypermutability and mutagenesis in mucA, lasR and mexZ, indicating that MRS-deficiency was not involved in the acquisition of these mutations. Finally, although inactivation of mucA, lasR and mexZ has been previously shown to confer resistance/tolerance to antibiotics, only mutations in MRS genes could be related to an antibiotic resistance increase. These results help to unravel the mutational dynamics that lead to the adaptation of P. aeruginosa to the CF lung.

Predictores de coqueluche al ingreso en lactantes hospitalizados con infección respiratoria aguda baja / [Pertussis predictors in hospitalized infants with acute lower respiratory tract infection].

BACKGROUND: Pertussis, or whooping cough, caused by Bordetella pertussis (BP) is a re-emerging problem in our environment. Although generally considered that the disease is relatively easy to identify infections respiratory syncytial virus (RSV) can present with similar symptoms in infants remains difficult discrimination. OBJECTIVE: Compare clinical symptoms at admission and complementary studies in infants hospitalized with acute respiratory infection (ARI) and RSV by BP to establish markers that enable their early clinical prediction. MATERIALS AND METHODS: Observational, analytical, case-crossover cross comparing younger than 6 months hospitalized with suspected IRA and pertussis (2007-2012) in which BP identified (PCR and culture) and / or VRS (immunofluorescence in nasal secretions). Coinfections were excluded. Bivariate analysis was performed by calculating OR with 95

CI. Were considered significant at p <0.05. The variables studied were age, sex, hits cough, cyanosis, vomiting, apnea, wheezing and CBC with differential RESULTS: We included 174 infants, 72 (41

) BP and 102 (59

) VRS. Age 2 ± 1 months (range :1-6). In both groups was documented cough and wheeze (OR: 1.2 (0.9 to 1.5) p: 0.1 and OR = 0.9 (0.8 to 1.06) p: 0.2, respectively ). Cyanosis (87

, OR: 13.4 p <0.01) and vomiting (26

, OR: 3.4 p <0.01) were more frequent in infants with BP. The absolute lymphocyte count was significantly higher in children with BP (9387 ± 6317 vs. 5127 ± 2766, p <0.01). By ROC curve was identified at 9000 cells / ml as the best point to differentiate VSR BP (AUC = 0.73, 95

CI :0,64-0, 81). CONCLUSIONS: In infants under 6 months with IRA income presence of apnea, cyanosis and lymphocytosis allowing predict significantly differentiate between pertussis those with RSV infections.