La résistance aux antibiotiques représente un problème de santé publique majeur. La pression de sélection liée à la surutilisation des antibiotiques en médecines humaine et vétérinaire est responsable de cette augmentation, mais l’environnement joue également son rôle dans la diffusion de ces résistances.En Guadeloupe, très peu d’études ont été réalisées sur l’état de la résistance aux antibiotiques, mais l’utilisation vétérinaire et humaine des antibiotiques est intensive. Les amendements issus de déchets humains et animaux sont également largement utilisés en production végétale.Cependant, les analyses moléculaires ont pu mettre évidence la persistance des gènes de résistance aux antibiotiques et des gènes de mobilité dans les composts et les sols amendés. L’abondance et la persistance des gènes de résistance de mobilité aux antibiotiques dans les cultures maraichères (concombres et patates douces) sont liées à leur concentration dans les amendements. Un épandage réalisé jusqu’à trois fois consécutivement ne modifie pas la structure génétique des communautés bactériennes dans les sols quel que soit l’amendement utilisé. Les phylums bactériens majoritairement retrouvés dans les composts et les sols sont les Proteobacteria, les Firmicutes et les Bacteroidetes qui sont susceptibles de porter les gènes de résistance aux antibiotiques. L’apport d’amendements organiques dans les sols ne semble pas constituer un risque majeur d’acquisition de résistances par l’homme via les légumes consommés. En revanche, dans les élevages de grande taille où les animaux confinés sont pourvoyeurs de BRAs et de GRAs, les éleveurs pourraient être exposés via les aérosols en cas d’exposition prolongée. En Guadeloupe, la valorisation des déchets organiques, quelle que soit leur origine, pour leur utilisation en production végétale ne semble pas favoriser la diffusion d’E. coli résistants de l’environnement à l’homme. Cependant, la qualité du compostage, les caractéristiques physico-chimiques des sols et les conditions climatiques sont à prendre en compte pour la planification des apports d’amendements afin de réduire le risque d’exposition, de diffusion et de persistance de isolats d’E. coli résistants.Quinze souches d’E. coli productrices de Bêtalactamase à spectre étendu (BLSE) ont été isolées des fèces des chevaux durant leur traitement antibiotique, trois pour le premier cheval et 12 pour le second. Les profils de résistance aux antibiotiques étaient congruents avec l'analyse des plasmides, les gènes de résistance détectés au moyen de WGS, et avec l'analyse phylogénétique basée sur le génome du noyau. On peut distinguer trois clones et quatre singletons indiquant qu'une grande diversité génétique existe parmi les souches d’E. coli producteurs de BLSE.Cette étude a permis de mettre en évidence la persistance des E. coli productrices de BLSE (E. coli BLSE) dans le microbiote des chevaux traités par des antibiotiques. Cette étude a pu démontrer qu’il y a résurgence d’E. coli BLSE dès les premiers jours de traitement avec une persistance de ces souches plus d’un mois après le traitement. En effet, deux mois après la fin du traitement, les E. coli BLSE n’étaient plus détectables. Cette surprenante diversité clonales et l’apparition d’E. coli BLSE avant tout traitement antibiotique laisse supposer que le portage d’E. coli BLSE est fréquent chez les chevaux de cet élevage et probablement à plus grande échelle. / The pressure of selection related to the overuse of antibiotics in human and veterinary medicines is responsible for this increase, but the environment also plays a role in the diffusion of these resistances.In Guadeloupe, very few things are known on the state of resistance to antibiotics, but both veterinary and human uses are intense and amendments resulting from human and animal wastes are widely used.In Guadeloupe, the use of waste from animal, plant and human activities in crop production does not appear to favor E. coli resistant strains spreading from the environment to humans. However, composting quality, soil physicochemical characteristics and climatic conditions should be taken into account when planning amendments to reduce the exposure risk, spread and persistence of E. coli resistant strains.Fifteen strains of E. coli were isolated from horses feces were isolated during their antibiotic treatment, three in the first horse and 12 in the second. Profiles of antibiotic resistance were congruent with the plasmid analysis, genotypes for resistance genes detected using WGS, and with the phylogenetic analysis based on the core genome. Three clones and four singletons could be distinguished indicating that a high genetic diversity exists among E. coli producing ESBL. This study evidenced the persistence of E. coli producing ESBL in the microbiota of horses treated with antibiotics. This study was able to demonstrate the resurgence of resistant phenotypes even before the first day of treatment with persistence of these strains more than one month after treatment. The absence of detection of E. coli producing ESBL was evedenced a few months after treatment. Thus, the diversity of antibiotic-resistant pathogenic microorganisms has probably higher than that described in previous studies.

Gonorrhea, caused by the human pathogen Neisseria gonorrhoeae, is a severe public health problem worldwide with more than 82 million new infections each year. N. gonorrhoeae is transmitted by sexual contact and primarily causes urogenital mucosal infections in men and women. Left untreated, this infection may cause severe complications, especially in females. Eye infections of the newborn can occur. Gonorrhea infections enhance HIV transmission. The highly prevalent antibiotic resistance and the emergence of new drug resistances render treatment of the infections increasingly difficult. Close monitoring of antimicrobial susceptibility of this pathogen is crucial, and enhanced knowledge of molecular mechanisms of gonococcal antimicrobial resistance is urgently needed. There are no vaccines available against N. gonorrhoeae. Control of gonorrhea relies on comprehensive strategies which can be better formulated by understanding, at molecular levels, how N. gonorrhoeae is transmitted in communities. My research aimed to illustrate the severe burden of antimicrobial resistance in N. gonorrhoeae temporally and geographically in China and to reveal the molecular mechanisms of antibiotic resistance particularly the development of reduced susceptibility to ceftriaxone in N. gonorrhoeae isolates. To determine specific strain distributions, N. gonorrhoeae isolates were characterized using molecular typing methods such as a modified porB-based typing scheme and the N. gonorrhoeae Multi-Antigen Typing (NG-MAST) method, compared to traditional epidemiological approaches. The ultimate goal was to provide information for better formulating disease control strategies for gonorrhea. In this research, male patients with gonorrhea and their sex partners were recruited in Shanghai (2005 and 2008) and in Urumchi (2007-2008), China. Epidemiological information pertaining to sexual contacts was collected. N. gonorrhoeae isolates were investigated for their antimicrobial susceptibility. Molecular mechanisms of antimicrobial resistance were explored by analysis of potential resistant determinants (gyrA, parC, porB, mtrR, ponA and penA). The molecular data were combined with bioinformatic analysis and traditional epidemiological data. High percentages of N. gonorrhoeae isolates (11% - 19% in Shanghai, 4.5% in Urumchi) exhibited reduced susceptibility to ceftriaxone (MICs = 0.125-0.25 mg/L), the first line drug recommended for the treatment of gonorrhea in China. The majority of isolates (>98%) were susceptible to spectinomycin, an alternative regimen for gonorrhea treatment; however, the proportion of isolates having intermediate levels of susceptibility increased from 1.9% in 2005 to 9.9% in 2008. The majority of isolates tested were resistant to penicillin (80% - 93%), tetracycline (56% - 65%) and ciprofloxacin (98% - 100%). Plasmid-mediated resistance in N. gonorrhoeae isolates were highly prevalent (51% - 79%) in Shanghai and Urumchi. Analysis of 60 clinical isolates revealed that reduced susceptibility to ceftriaxone is mediated by porB1b allele and is associated with specific mutations in penicillin binding protein 2 and in the DNA binding and dimerization domains of MtrR. Penicillin binding protein 1 is not involved in reduced susceptibility to ceftriaxone. Although mutation patterns in quinolone resistant determinant regions (QRDRs) varied, the majority of ciprofloxacin resistant isolates had double mutations in GyrA (S91F and D95G/A/N) and most isolates also carried a S87R/N mutation in ParC. The presence of mutations in the QRDR of ParC is correlated with elevated ciprofloxacin MICs. A modified porB-based molecular typing scheme was developed and involved ~82% of the DNA sequence of gonococcal porB. This typing method proved to have high discriminatory ability (index of discrimination = 0.93 0.96), and was cost effective and easy to perform as compared to the NG-MAST analysis. Using the modified porB-based typing method, N. gonorrhoeae isolates were reliably differentiated, and transmission clusters were identified. Molecular epidemiology using the porB-based method confirmed direct sexual connections and identified sexual networks otherwise unrevealed by the patient self-reporting or traditional case-tracing methods.

The purpose of this dissertation is threefold: to determine the differences in apparent prevalence and the antimicrobial susceptibility of Campylobacter spp. between antimicrobial-free and conventional swine farms; secondly, to introduce an appropriate statistical model to compare the minimum inhibitory concentration distributions of Escherichia coli and Campylobacter spp. isolated from both farm types; and thirdly, to examine the potential herd level risk factors that may be associated with antimicrobial resistance of Campylobacter spp. and E. coli isolates from finishers on antimicrobial-free and conventional farming systems. In addition, a critical review of studies that have compared the levels and patterns of antimicrobial resistance among animals from antimicrobial-free and conventional farming practices was performed. Fecal samples from 15 pigs were collected from each of 35 antimicrobial-free and 60 conventional farms in the Midwestern U.S. Campylobacter spp. was isolated from 464 of 1,422 fecal samples, and each isolate was tested for susceptibility to 6 antimicrobials. The apparent prevalence of Campylobacter spp. isolates was approximately 33 percent on both conventional and antimicrobial-free farms. The proportion of antimicrobial resistance among Campylobacter was higher for three antimicrobials within conventional compared to antimicrobial-free farms. The susceptibilities of populations of bacteria to antimicrobial drugs were summarized as minimum inhibitory concentration (MIC) frequency distributions. The use of MIC values removed the subjectivity associated with the choice of breakpoints which define an isolate as susceptible or resistant. A discrete-time survival analysis model was introduced as the recommended statistical model when MICs are the outcome. A questionnaire was completed by each farm manager on biosecurity, preventive medication, vaccines, disease history, and production management. Multivariable population-averaged statistical models were used to determine the relationships among antimicrobial susceptibility patterns and potential herd-level risk factors. Controlling for herd type (antimicrobial-free versus conventional), each antimicrobial-bacterial species combination yielded unique combinations of risk factors; however, housing type, history of rhinitis, farm ventilation, and history of swine flu were significant in more than one model. A variety of herd-level practices were associated with the prevalence of antimicrobial resistance on swine farms. Further studies are encouraged when considering interventions for antimicrobial resistance on both antimicrobial-free and conventional farms.

Gonorrhea, caused by the human pathogen Neisseria gonorrhoeae, is a severe public health problem worldwide with more than 82 million new infections each year. N. gonorrhoeae is transmitted by sexual contact and primarily causes urogenital mucosal infections in men and women. Left untreated, this infection may cause severe complications, especially in females. Eye infections of the newborn can occur. Gonorrhea infections enhance HIV transmission. The highly prevalent antibiotic resistance and the emergence of new drug resistances render treatment of the infections increasingly difficult. Close monitoring of antimicrobial susceptibility of this pathogen is crucial, and enhanced knowledge of molecular mechanisms of gonococcal antimicrobial resistance is urgently needed. There are no vaccines available against N. gonorrhoeae. Control of gonorrhea relies on comprehensive strategies which can be better formulated by understanding, at molecular levels, how N. gonorrhoeae is transmitted in communities. My research aimed to illustrate the severe burden of antimicrobial resistance in N. gonorrhoeae temporally and geographically in China and to reveal the molecular mechanisms of antibiotic resistance particularly the development of reduced susceptibility to ceftriaxone in N. gonorrhoeae isolates. To determine specific strain distributions, N. gonorrhoeae isolates were characterized using molecular typing methods such as a modified porB-based typing scheme and the N. gonorrhoeae Multi-Antigen Typing (NG-MAST) method, compared to traditional epidemiological approaches. The ultimate goal was to provide information for better formulating disease control strategies for gonorrhea. In this research, male patients with gonorrhea and their sex partners were recruited in Shanghai (2005 and 2008) and in Urumchi (2007-2008), China. Epidemiological information pertaining to sexual contacts was collected. N. gonorrhoeae isolates were investigated for their antimicrobial susceptibility. Molecular mechanisms of antimicrobial resistance were explored by analysis of potential resistant determinants (gyrA, parC, porB, mtrR, ponA and penA). The molecular data were combined with bioinformatic analysis and traditional epidemiological data. High percentages of N. gonorrhoeae isolates (11% - 19% in Shanghai, 4.5% in Urumchi) exhibited reduced susceptibility to ceftriaxone (MICs = 0.125-0.25 mg/L), the first line drug recommended for the treatment of gonorrhea in China. The majority of isolates (>98%) were susceptible to spectinomycin, an alternative regimen for gonorrhea treatment; however, the proportion of isolates having intermediate levels of susceptibility increased from 1.9% in 2005 to 9.9% in 2008. The majority of isolates tested were resistant to penicillin (80% - 93%), tetracycline (56% - 65%) and ciprofloxacin (98% - 100%). Plasmid-mediated resistance in N. gonorrhoeae isolates were highly prevalent (51% - 79%) in Shanghai and Urumchi. Analysis of 60 clinical isolates revealed that reduced susceptibility to ceftriaxone is mediated by porB1b allele and is associated with specific mutations in penicillin binding protein 2 and in the DNA binding and dimerization domains of MtrR. Penicillin binding protein 1 is not involved in reduced susceptibility to ceftriaxone. Although mutation patterns in quinolone resistant determinant regions (QRDRs) varied, the majority of ciprofloxacin resistant isolates had double mutations in GyrA (S91F and D95G/A/N) and most isolates also carried a S87R/N mutation in ParC. The presence of mutations in the QRDR of ParC is correlated with elevated ciprofloxacin MICs. A modified porB-based molecular typing scheme was developed and involved ~82% of the DNA sequence of gonococcal porB. This typing method proved to have high discriminatory ability (index of discrimination = 0.93 0.96), and was cost effective and easy to perform as compared to the NG-MAST analysis. Using the modified porB-based typing method, N. gonorrhoeae isolates were reliably differentiated, and transmission clusters were identified. Molecular epidemiology using the porB-based method confirmed direct sexual connections and identified sexual networks otherwise unrevealed by the patient self-reporting or traditional case-tracing methods.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Além de micro-organismos causadores de Doenças Transmitidas por Alimentos, a presença de bactérias resistentes a antimicrobianos deve ser monitorada para garantir a inocuidade da carne suína. O objetivo deste estudo foi determinar a frequência de Salmonella enterica e Listeria monocytogenes em amostras de fezes e carcaças suínas, e avaliar a resistência a antimicrobianos entre isolados de Escherichia coli provenientes das mesmas origens. Dois ciclos de amostragem foram conduzidos em três matadouros-frigoríficos localizados no Estado de Santa Catarina. Em cada ciclo, fezes colhidas a partir do piso da pocilga de espera, e suabes de superfície de 14 carcaças no pré-resfriamento foram amostrados em três lotes abatidos. As amostras foram analisadas quanto à presença dos gêneros Salmonella e Listeria e foi determinada a média de coliformes totais nas carcaças em cada ciclo de amostragem. Isolados de E. coli foram avaliados quanto à frequência de resistência a antimicrobianos pelo método de difusão em ágar. Das fezes colhidas 83,33% (15/18) apresentaram Salmonella sp., e 5,5% (1/18) L. monocytogenes. Do total de 252 carcaças, 27,38% (69/252) foram positivas para Salmonella sp. e 19,84% (50/252) para L. monocytogenes. Em 3,17% (8/252) carcaças houve o isolamento concomitante dos dois patógenos. Os isolados de Salmonella foram classificados em dez sorovares distintos, predominando S. Typhimurium nas fezes e S. Derby nas carcaças. A média de coliformes totais nas carcaças variou de 5,27x101 a 9,73x103. Em relação ao teste de resistência frente a antimicrobianos realizado em isolados de E. coli, observou-se maior frequência de resistência em isolados de fezes do que nos originados de carcaças, com diferença significativa para tetraciclina (P<0,001), ampicilina (P<0,001) e sulfonamida (P=0,022). Entre os matadouros-frigoríficos, houve diferença na frequência de isolados resistentes para florfenicol e gentamicina (P<0,05) em isolados de fezes, e para ácido nalidíxico, sulfonamida e tetraciclina (P<0,05) em isolados de carcaça. A elevada frequência de resistência a princípios ativos utilizados na suinocultura indicam pressão de seleção exercida pelo uso indiscriminado de antimicrobianos e podem resultar na co-seleção de genes de resistência localizados em cassetes gênicos. Os isolados multi-resistentes foram mais presentes nas fezes quando comparados com carcaças (P<0,001), sugerindo que há diminuição da frequência de isolados resistentes ao longo do processo de abate. Com os resultados obtidos no presente estudo, conclui-se que maior atenção deve ser dispensada ao monitoramento das etapas do abate para identificar possíveis falhas que estão determinando a presença de carcaças contaminadas na fase de pré-resfriamento, além da necessidade do uso mais prudente dos antimicrobianos na suinocultura. / Besides the contamination of pig carcasses with food borne pathogens, the presence of bacteria resistant to antimicrobials represent a new hazard that should be monitored in order to ensure the safety of pork. This study aimed at determining the frequency of Salmonella enterica and Listeria monocytogenes in samples of swine feces and carcasses, and at evaluating antimicrobial resistance among isolates of Escherichia coli from the same origin. Two cycles of sampling were carried out in three slaughterhouses located in the State of Santa Catarina. For each cycle, feces collected from the floor of the pen, and surface swabs of 14 carcasses at the pre-chill were sampled in three slaughtered batches. The samples were analyzed for the presence of Salmonella and Listeria, and the average of total coliforms on carcasses in each sampling cycle was determined. Isolates of E. coli were evaluated for the frequency of antimicrobial resistance by the agar diffusion method. Out of the feces collected 83.33% (15/18) had Salmonella sp., and 5.5% (1/18) L. monocytogenes. Out of the total of 252 carcasses, 19.84% (50/252) were positive for Salmonella sp. and 27.38% (69/252) for L. monocytogenes. In 3.96% (10/252) carcasses both pathogens were isolated. Salmonella isolates were classified in ten serovars, predominantly S. Typhimurium in the feces and S. Derby on the carcasses. The average of total coliforms on carcasses varied between 5.27x101 to 9.73x103. Regarding the antimicrobial resistance tests carried out in isolates of E. coli, we observed a higher frequency of resistance in isolates from feces than from carcasses, with a significant difference for tetracycline (P<0.001), ampicillin (P<0.001) and sulfonamide (P=0.022). Among the slaughterhouses, there were differences in the frequency of resistance against florfenicol and gentamicin (P<0.05) in isolates from feces, and against nalidixic acid, sulfonamide and tetracycline (P<0.05) in isolated from carcasses. The high frequencies of resistance to drugs used in swine production indicate selection pressure exerted by the indiscriminate use of antibiotics and may result from co-selection of resistance genes located in gene cassettes. Multi-resistant isolates were more frequent in the feces compared to carcasses (P<0.001), suggesting that there is a decrease in the frequency of resistant isolates during the slaughter process. From the results obtained in this study, it is concluded that more attention should be paid to monitoring the stages of the slaughter in order to identify possible flaws that are causing the presence of contaminated carcasses at the pre-chill, as well as the need for more prudent use of antimicrobials in swine production.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2013-10-18T18:53:21Z No. of bitstreams: 1 Vivian Galvão. Caracterizaçao de cepas...2012.pdf: 1132531 bytes, checksum: c5a7374a74f6f74d8bd7cc7573c224f5 (MD5) / Made available in DSpace on 2013-10-18T18:53:21Z (GMT). No. of bitstreams: 1 Vivian Galvão. Caracterizaçao de cepas...2012.pdf: 1132531 bytes, checksum: c5a7374a74f6f74d8bd7cc7573c224f5 (MD5) Previous issue date: 2012 / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / A doença pneumocócica invasiva (DPI) continua sendo uma das principais causas de morbidade e mortalidade no mundo, mesmo com a disponibilidade atual de terapias antimicrobianas e vacinas conjugadas. O objetivo desse estudo foi caracterizar o perfil fenotípico e genotípico das cepas invasivas de Streptococcus pneumoniae isoladas de diferentes sítos de infecção que circulam em hospitais públicos e privados da cidade de Salvador-Brasil no período de janeiro de 2008 a julho de 2011. Os isolados de S. pneumoniae de doença invasiva foram identificados por métodos microbiológicos clássicos e submetidos à determinação capsular através da técnica de Multiplex-PCR. A sensibilidade aos antimicrobianos foi determinada pela técnica de microdiluição em caldo. A caracterização genotípica foi realizada por PFGE e MLST. No período do estudo foram identificados 75 casos de DPI com cultura positiva, sendo 82,7% provenientes de hemocultura, 9,3% de líquido pleural e 8,0% de líquor. As crianças representaram 37,9% e os idosos 24,0% da população em estudo. Os sorotipos mais prevalentes foram o 14 (14,7%), 19F (13,3%), 6B (10,7%), 23F (9,3%), 3 (9,3%) e 19A (6,7%). Um total de 57,3% dos sorotipos identificados estão representados na vacina PCV10. Não-susceptibilidade à penicilina (CIM ≥ 4μg/mL) foi observada em 5,3% dos isolados. Para o SMX-TMP, tetraciclina e eritromicina, os índices de não-susceptibilidade foram de 55%, 15% e 11%, respectivamente. A tipagem por PFGE classificou 61,3% dos isolados de DPI como não-clonais e 29 (38,7%) em 10 perfis clonais. Quando comparados aos isolados de meningite isolados no Hospital Couto Maia, 22,7% apresentaram perfis semelhantes, que foram distribuídos em seis grupos clonais (quatro grupos clonais com isolados não-susceptíveis à penicilina e dois sensíveis). Foram encontrados 22 STs diferentes entre as 26 amostras caracterizadas por MLST. Quando comparado aos clones já caracterizados pelo PMEN, verificou-se que na cidade de Salvador circulam clones já identificados em outros países, a exemplo dos clones: Colombia23F-26 (SLV 338), Portugal19F-21 (ST 177), Spain9V-3 (SLV 156) e Netherlands3-31 (ST 180). Os isolados de pneumococos deste estudo apresentam maior taxa de resistência, incluindo resistência a múltiplas drogas quando comparados aos dos casos de meningite identificados em casos de meningite, com exceção da penicilina. Embora os clones mais frequentemente associados aos casos de meningite pneumocócia em Salvador tenham sido identificados nesta casuistica, os isolados de pneumococos provenientes de outras formas de doença invasiva apresentaram uma maior diversidade fenotípica e genotípica, ressaltando a importância do monitoramento contínuo das cepas invasivas nas diferentes manifestações da doença pneumocócica no tempo das vacinas conjugadas. / Invasive pneumococcal disease (IPD) remains one of the major causes of morbidity and mortality worldwide, even with the current availability of antimicrobial therapies and conjugate vaccines. The objective of the present study was to characterize the phenotypic and genotypic profiles of invasive pneumococcal isolates obtained from patients admitted to public and private hospitals in Salvador, from the period of Jan/2008 to Jul/2011. The pneumococcal isolates from invasive disease were identified by classical microbiological methods and submitted to capsular deduction by multiplex-PCR. The antimicrobial susceptibility was performed by broth microdilution method. The genotypic profile was accessing by PFGE and MLST. During the study period, 75 consecutive culture-positive cases of IPD were characterized, being 82.7% from blood, 9.3% from pleural fluid and 8.0% from CSF. The study population comprised of 37.9% of children (under 5 years old) and 24.0% of elderly (upper 64 years old). The most prevalent serotypes were: 14 (14.7%), 19F (13.3%), 6B (10.7%), 23F (9.3%), 3 (9.3%) and 19A (6.7%). A total of 57.3% of the serotypes identified are represented in the vaccine PCV10. Non-susceptibility to penicillin (MIC ≥ 4μg/mL) was observed in 5.3% of the isolates. The non-susceptibility rate for SMX-TMP, tetracycline and erythromycin was found in 55%, 15% and 11% of the isolates, respectively. The PFGE pattern analysis classified 61.3% of IPD isolates as non-clonal and 29 (38.7%) isolates were clustered in ten PFGE profiles. When the clonal strains were compared with pneumococcal meningitis isolates from Hospital Couto Maia, 22.7% showed similar profiles by PFGE, being distributed into six clonal groups (four clonal groups of penicillin non-susceptible and two of penicillin susceptible). Twenty-two STs were observed among the 26 samples characterized by MLST. When compared to already characterized PMEN clones, it was found that some circulating clones in the city of Salvador have been identified in other countries, such as: Colombia23F-26 (SLV 338), Portugal19F-21 (ST 177), Spain9V-3 (SLV 156) and Netherlands3-31 (ST 180). The pneumococcal strains in the study have a higher rate of resistance, including multidrug resistance when compared to cases of meningitis identified in the HCM, except for penicillin. Although the clones most frequently associated with cases of meningitis in Salvador have been identified in this study, isolates of pneumococci from other forms of IPD had a higher phenotypic and genotypic diversity, highlighting the importance of continuous monitoring of invasive strains in different manifestations of pneumococcal infection in the time of conjugate vaccines.

Hospital infections are the most frequent complications occurring in hospitalized patients, especially in trauma hospitals, where the seriousness of the injury is predictive factor for the emergence of infections. This study evaluated the profile of infection in the Emergency Unit of Agreste (UEA) through data from CCIH and analysis of clinical samples. The antimicrobial resistance profile was determined too. Isolates have been subjected to 16S rRNA sequencing and analysis in GenBank and RDP. Among 271 patients analyzed, 154 (57%) exhibited positivity in culture (PC). Automobile accidents were the main causes of hospitalization (47,2%). The median of hospitalization was 26 days. PC patients were 10 days more than the median. The use of urinary catheter was 15±13 days, being more 9,5 days in patients PC, on average. Of the 252 PC, 43 were isolated over a microorganism, totaling 269 bacteria and 26 yeasts. Pseudomonas aeruginosa (16,9%) and Acinetobacter baumannii (12,9%) were more frequent. Antimicrobial empirical therapy was made by 76,6% of patients, being 58,1% by cephalosporins. Vancomycin (100%) and chloramphenicol (82,4%) were the most sensitive between the antimicrobial Gram positive cocci, and carbapenems (90,1%) among Gram negative bacilli. The results of UEA compared to international monitoring programmes exhibited greater resistance. However, there were similarities with the Brazilian program RM Network and even greater sensitivity of P. aeruginosa to cefepime and carbapenems. Two-hundred-two sequenced microorganisms were identified by BLASTn at GenBank and RDP banks. They provided identification, respectively: 88,1% and 88,6% in species; 7,9% and 6,4% on genus; 3,5% and 4% in family; and 0,5% and 1% in class. There was agreement among banks in 84,7% to species; 93,7% in genus and 99% in family. The microorganisms most frequently were P. aeruginosa (22,8%), A. baumannii (18,8%) and Klebsiella pneumoniae (11,9%). Among the rarest microorganisms are Brevibacillus agri, Acinetobacter radioresistens, Corynebacterium amycolatum, Corynebacterium striatum, Pseudomonas cedrina subsp. fulgida, Pseudomonas putida and Staphylococcus sciuri. In some cases there was a high similarity between different species not allowing assignment of identification. The differentiation was accomplished through the creation of consensus sequences with reference sequences for CLUSTALW alignment for each microorganism that has similarity. Among 10 cases identified only as Klebsiella, 7 were K. pneumoniae, 2 K. granulomatis and 1 without definition. Eleven Enterobacteriaceae were defined as: 3 Escherichia coli, 2 Enterobacter cancerogenus, 2 Enterobacter sp., 2 group E. coli / Shigella and 2 without definition in genus. The 2 sequences with the same score to Serratia marcescens, Pseudomonas fluorescens strains were identified as S. marcescens. Identification by sequencing is superior to phenotypic tests, especially for atypical biochemist profile, slow growth, rare species and microorganisms of difficult cultivation. Despite difficulties for service deployment and the need for caution in attributing identification, sequencing remains as a promising technique for use in routine laboratories, guiding proper medical team for a better management of the patient. / As infecções hospitalares são as mais frequentes complicações ocorridas em pacientes hospitalizados principalmente em hospitais de trauma, onde a gravidade da lesão é fator preditivo para o surgimento de infecções. O presente estudo avaliou o perfil das infecções na Unidade de Emergência do Agreste (UEA) através de dados da CCIH e análise de amostras clínicas. O perfil de resistência aos antimicrobianos também foi determinado. Os isolados foram submetidos ao sequenciamento do gene rRNA 16S e análise no bancos GenBank e RDP para identificação. Dos 271 pacientes analisados, 154 (57%) exibiram positividade em cultura (CP). Acidentes automobilísticos foram os principais motivos de internação (47,2%). A mediana de internação foi de 26 dias, sendo 10 dias a mais em pacientes CP. O uso de sonda vesical foi de 15±13 dias, sendo 9,5 dias a mais em pacientes CP, em média. Das 252 CP, em 43 foram isolados mais de um microrganismo, totalizando 269 bactérias e 26 leveduras. Pseudomonas aeruginosa (16,9%) e Acinetobacter baumannii (12,9%) foram os mais frequentes. Estavam em uso empírico de antimicrobianos, 76,6% dos pacientes, sendo 58,1% por cefalosporinas. A vancomicina (100%) e o cloranfenicol (82,4%) foram os antimicrobianos de melhor atividade frente aos Gram positivos, e os carbapenêmicos (90,1%), entre Gram negativos. Os resultados da UEA, comparados aos programas de vigilância internacionais, exibiram maior resistência. No entanto, houve semelhanças com o programa brasileiro Rede RM, e ainda maior sensibilidade de P.aeruginosa frente aos carbapenêmicos e cefepime. Dos 202 microrganismos sequenciados, a atribuição de identificação por BLASTn nos bancos genéticos GenBank e RDP forneceram identificação, respectivamente de 88,1% e 88,6% em espécie; 7,9% e 6,4% em gênero; 3,5% e 4% em família e 0,5% e 1% em classe. Houve concordância entre os bancos de 84,7% em espécie; 93,7% em gênero e 99% em família. Os microrganismos mais frequentes foram P. aeruginosa (22,8%), A. baumannii (18,8%) e Klebsiella pneumoniae (11,9%). Entre os mais raros estão Brevibacillus agri, Acinetobacter radioresistens, Corynebacterium amycolatum e Corynebacterium striatum, Pseudomonas cedrina subsp. fulgida, Pseudomonas putida e Staphylococcus sciuri. Em alguns casos, houve elevada similaridade entre diferentes espécies, não permitindo a atribuição de identificação. A diferenciação foi realizada através da criação de sequências consenso de referência por alinhamento no CLUSTALW para cada microrganismo que apresentou similaridade. Dos 10 casos determinados somente como Klebsiella, 7 eram K. pneumoniae, 2 K. granulomatis e 1 sem definição. Das 11 Enterobacteriaceae, 3 foram Escherichia coli, 2 Enterobacter cancerogenus, 2 Enterobacter sp., 2 E. coli / Shigella e 2 sem definição. As 2 sequências com mesma pontuação para Serratia marcescens e Pseudomonas fluorescens foram identificadas como S. marcescens. A identificação por sequenciamento é superior aos testes fenotípicos, sobretudo para isolados com perfil bioquímico atípico, crescimento lento, espécies raras e microrganismos de difícil cultivo. Apesar das dificuldades para implantação do serviço e a necessidade de cautela na atribuição de identificação, o sequenciamento permanece como uma técnica promissora para a utilização em laboratórios de rotina, orientando adequadamente a equipe médica para um melhor manejo do paciente.

Estafilococos têm sido relatados como os agentes mais prevalentes de mastite bovina. Este gru-po bacteriano pode transportar múltiplos elementos de resistência provenientes inclusive de outras populações bacterianas, tornando-se um grande problema de saúde pública, uma vez que também está envolvido em vários processos de doença em humanos, incluindo infecções da pele e dos tecidos moles, septicemia, osteomielite e pneumonia. A caracterização do perfil de resis-tência dos estafilococos aos antimicrobianos é importante para controlar a sua disseminação. O presente trabalho avaliou a distribuição de multirresistência entre mais de 3.500 isolados de um estudo transversal repetido, realizado entre 2010 e 2011 nas principais regiões produtoras de leite do Brasil. As bactérias foram classificadas de acordo com métodos fenotípicos e os padrões de resistência antimicrobiana foram determinados pelo teste de difusão em disco ao invés de testes moleculares e ensaios quantitativos. Para avaliar os principais fatores relacionados à vari-ável resposta – proporção de bactérias resistentes a três ou mais classes de antimicrobianos, ou multirresistência – diversas variáveis explicativas foram acessadas por meio de um questionário epidemiológico. Um modelo misto foi construído com um componente aleatório multinível, a saber, a variação de multirresistência entre as bacias leiteiras (segundo nível) e a variação dass propriedades em cada bacia (primeiro nível) durante os quatro momentos de amostragem, ou seja, a variação entre-sujeitos e intra-sujeitos, respectivamente. A avaliação dos perfis de resis-tência revelou que as penicilinas, seguidas por tetraciclina e sulfonamida, foram os antimicrobi-anos com menor eficácia em estafilococos (n = 3009). Estafilococos coagulase negativa pare-cem ter semelhanças com S. aureus e alguns outros estafilococos coagulase positiva testados, demonstrando um padrão de grupo com moderada resistência a múltiplas drogas. Ilustrativa-mente, alguns estreptococos (n = 480) também foram submetidos a testes de suscetibilidade a antimicrobianos, os quais mostraram moderada a alta resistência à tetraciclina, gentamicina e clindamicina. O modelo misto indicou que o tratamento de mastite feito de imediato, a aplicação de terapia antimicrobiana pelo próprio produtor ao invés de um veterinário, e a interação entre este último fator e o sistema de produção intensivo aumentou a probabilidade de resistência múltipla em nível de rebanho. O coeficiente de correlação intraclasse (ICC) foi baixo e mostrou que a maior parte da variação de resistência múltipla é explicada pelas características em nível de hospedeiro, seguido por fatores em nível de rebanho (ICC = 0,126). Esses fatores são exem-plos importantes de como o uso leigo de antimicrobianos em vacas leiteiras tem grande poten-cial para seleção, expansão e manutenção de populações de bactérias resistentes a múltiplas drogas em ambientes de produção animal, em especial nos mais intensivos. / Staphylococci have already been reported as the most prevalent mastitis agents. Such bacterial species can carry multidrug-resistant elements coming from other bacteria species, and so on are becoming a great public health concern, once it is also involved in several human disease. The characterization of their antimicrobial resistance profile is important to better control their dissemination. The present work evaluated the distribution of multidrug-resistance among more than 3500 isolates from a repeated cross-sectional study performed from 2010 to 2011 in the main dairy regions of Brazil. The bacteria were classified according to phenotypic methods and the antimicrobial resistance patterns were determined by disk diffusion. To evalu-ate the main factors related to the response variable – the proportion of bacteria resistant to three or more antimicrobial classes, or multidrug resistance – several explanatory variables were accessed by means of an epidemiological questionnaire. A multivariable mixed model was created to access the strength of association between several putative risk factors and re-sistance to multiple drugs. Resistance profiles evaluation revealed that penicillins, followed by tetracycline and sulfonamide, were the antimicrobials with lower effectiveness in staphylococci (n = 3009). Coagulase negative staphylococci seemed to have similarities with coagulase posi-tive tested, performing moderate resistance pattern to multiple drugs. Some streptococci (n = 480) were also submitted to antimicrobial susceptibility tests, and showed moderate to high resistance to tetracycline, gentamycin and clindamycin. The mixed model indicated that mastitis treatment made immediately rather than cautiously; applicaton of antimicrobial therapy by the producer itself rather than a veterinarian practitioner; and the interaction between the produc-er as applicator and the intensive, modern production system increased the likelihood of multi-ple-resistance at herd level. The low intraclass correlation coefficient at region level showed that resistance variance is most explained at herd level, and it characteristics, rather than re-gion level. Probably the host level factors not evaluated in this study explains more than the herd level factors, but, considering the coverage of our study, these factors give us insights of how cattle antimicrobial consumption can affect the maintenance and expansion of multidrug resistant bacteria populations in animal production environments.

Made available in DSpace on 2015-03-26T13:52:02Z (GMT). No. of bitstreams: 1 texto completo.pdf: 207338 bytes, checksum: e8ae32d5d73829fe54385cc857a2a2cd (MD5) Previous issue date: 2006-02-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The effects of heat shock, acid treatment, exposure to bile salts and the presence of H2O2 on antimicrobial resistance in Lactobacillus delbrueckii UFV H2b20 were determined. Agar diffusion assays results indicated that this bacterium is resistant to vancomycin, sulphamethoxazole, colistin, some [Beta]-lactams, aminoglycosides, nitrofurans and quinolones. It is moderately susceptible to choramphenicol, tetracycline, cephalothin, ampicillin and erythromycin. L. delbrueckii UFV H2b20 can grow on high concentrations of H2O2 and complete inhibition will be observed only at 70 µg mL-1. Diferent effects on the Minimal Inhibitory Concentration (MIC) of the antimicrobials were observed when the bacterial cells were exposed to several stress conditions. Heat shock affected resistance to different aminoglycosides and [Beta]-lactams in various ways; it diminished resistance to nitrofurans and to tetracycline; however, it had no effect over resistance to choramphenicol and espiramycin. The same results were observed for acid pre-treatment at pH 3,5 for 30 min, except that it resulted in enhancement of espiramycin resistance. Cell exposure to 0,5% bile salts resulted in diminuished MICs for almost all tested antibiotics, except, apparently, furazolidone, sulphametoxol and nalidix acid, which maintained resistance to the highest concentrations tested. The presence of H2O2, 20 µg mL-1, had various effects on aminoglycosides, diminuished resistance to nitrofurans, [Beta]-lactams, tetracycline and espiramycin; however, it enhanced resistance to choramphenicol. These results demonstrate an ample diversity of responses to heat shock, acid shock, presence of H2O2, and also a general response when cells of L. delbrueckii UFV H2b20 are exposed to bile salts. / A resistência a antimicrobianos e o efeito de peróxido de hidrogênio sobre o crescimento em Lactobacillus delbrueckii UFV H2b20 foram estudados. Os efeitos de choque térmico, choque ácido, exposição a sais biliares e presença de peróxido de hidrogênio sobre a resistência a antimicrobianos nesta bactéria também foram investigados. A determinação do modelo de resistência, pelo método de difusão em meio sólido, indicou que L. delbrueckii UFV H2b20 apresenta resistência a vancomicina, a alguns [Beta]-lactâmicos, a sulfametoxol, a aminoglicosídeos, a nitrofuranos, a quinolonas e a colistina e susceptibilidade moderada a cloranfenicol, a tetraciclina, a cefalotina, a ampicilina e a eritromicina. L. delbrueckii UFV H2b20 é capaz de crescer em altas concentrações de peróxido de hidrogênio e inibição completa do crescimento só foi observada com 70 µg mL-1. Os efeitos de condições de estresse sobre a resistência a antimicrobianos foram determinados pela comparação da Concentração Inibitória Mínima (CIM), realizada pelo método de microdiluição em meio líquido, de células submetidas e de não submetidas às condições de estresse citadas. O choque térmico provocou efeitos diversos sobre a resistência a aminoglicosídeos e a [Beta]-lactâmicos, diminuiu a resistência a nitrofuranos e a tetraciclina e não alterou a resistência a cloranfenicol e a espiramicina. O choque ácido também provocou efeitos diferentes sobre a resistência a aminoglicosídeos e a [Beta]-lactâmicos, diminuiu a resistência a nitrofuranos e a tetraciclina, não alterou a CIM de cloranfenicol e aumentou a resistência a espiramicina. A exposição das células de L. delbrueckii UFV H2b20 a sais biliares provocou diminuição da CIM de quase todos os antimicrobianos testados, exceto furazolidona, sulfametoxol e ácido nalidíxico, que não tiveram a resistência alterada até a concentração máxima testada. A presença de peróxido de hidrôgenio provocou efeitos diferentes sobre a resistência a aminoglicosídeos, diminuiu a resistência a nitrofuranos, a [Beta]-lactâmicos, a tetraciclina e a espiramicina e aumentou a resistência a cloranfenicol. Os resultados demonstram ampla diversidade nas respostas ao choque térmico, ao choque ácido e ao peróxido de hidrogênio e similaridade na resposta à exposição das células de L. delbrueckii UFV H2b20 a sais biliares.