Acinetobacter baumannii is an opportunistic pathogen prevalent in nosocomial infections, most commonly infecting humans with compromised immune systems during their hospital stays. The organism's success in such circumstances has to do with its ability to survive on dry, abiotic surfaces (e.g. catheters, bed railings, and other medical equipment) and its increasingly apparent antibiotic resistance. These factors make A. baumannii a serious problem for healthcare professionals and in public health generally. A. baumannii is paradigmatic and representative of the issues confronting healthcare in the ongoing antibiotic crisis, and many strains are showing multidrug resistant (MDR) phenotypes. Given that the patients infected by A. baumannii tend to be very vulnerable and traditional antibiotic treatment seems to be getting less and less effective, it is imperative to explore alternative treatment options that may lead to better outcomes, especially if their mechanisms are not the same as the traditional antibiotics that exert the selective pressures that have led to the current antibiotic crisis. A small molecule called M64 is known to inhibit a LysR-type transcription regulator (LTTR) important for virulence, but not cell growth or viability, in another opportunistic pathogen, Pseudomonas aeruginosa. The experiments presented here show that M64 was able to rescue mice infected with A. baumannii and to downregulate the expression of important metabolic genes downstream from A. baumannii LTTRs BenM and CatM in vitro while having no effect on bacterial growth. BenM and CatM regulate genes involved in the metabolism of benzoate and catechol respectively, both of which are parts of tryptophan metabolism and are eventually broken down to form acetyl-CoA and succinyl-CoA for energy production in the citric acid cycle. Such a pharmacodynamic profile offers a starting point in the design of alternative treatments of MDR bacterial infections, as successful outcomes are observed without the direct killing of cells in vitro seen in traditional antibiotics. In this case, as catechol metabolism is important for siderophore biosynthesis and thus bacterial virulence, inhibition of the transcription of genes involved in catechol metabolism may be playing a role in the observed rescue of infected mice. Further studies are required to ascertain the nature of the inhibitor's effect, however.

Acinetobacter baumannii é considerado um dos patógenos de maior importância clínica atualmente, sendo responsável por uma variedade de infeções nosocomiais como, bacteremias, infecções no trato urinário, pneumonias associadas a ventilação mecânica, meningites secundárias e infecções em feridas. Desde a última década o tratamento de infecções por Acinetobacter spp. vem sendo dificultado pela emergência de cepas multirresistentes. Nesse contexto, o objetivo deste trabalho foi determinar a dinâmica populacional e as características moleculares envolvidas na resistência de Acinetobacter spp. Foram avaliados isolados de Acinetobacter spp. provenientes de seis hospitais da cidade de Porto Alegre coletados entre janeiro de 2013 e março de 2014. A espécie Acinetobacter baumannii foi identificada pela presença do gene blaOXA-51, além de PCR multiplex para o gene gyrB. Carbapenemases (blaNDM, blaOXA-23-like, blaOXA-24/40-like, blaOXA-58-like e blaOXA-143-like), além dos integrons de classe 1 e 2 foram pesquisados por PCR. Um total de 524 isolados de Acinetobacter spp. foram coletados, e a maioria (487/92,9%) foram identificados como A. baumannii, seguidos pelas espécies A. nosocomialis (9/1,7%), A. pittii (3/0,6%), A. calcoaceticus (3/0,6%) e por fim, 22 (4,2%) isolados não pertenciam ao complexo A. baumannii-calcoaceticus. Quanto ao perfil de sensibilidade, 83% dos isolados demonstraram não ser sensíveis aos carbapenêmicos (imipenem e meropenem). Dos isolados de A. baumannii, 429 (88,1%) continham o gene blaOXA-23, além disso, foram observados dois isolados de A. nosocomialis contendo o gene blaOXA-23. Foi possível identificar dois isolados de A. baumannii produtores de blaOXA24/40 (0,8%) pela primeira vez na região Sul do país. A análise do gene por sequenciamento caracterizou como sendo a variante blaOXA-72, e a tipagem por MLST caracterizou os isolados como pertencentes a ST730 (CC79). Também foram analisados por MLST, isolados produtores de OXA-72 do estado de São Paulo e do Paraná. A análise dos dados demonstrou que estes isolados estão associados aos complexos clonais epidêmicos CC15 e CC79. A pesquisa para o gene blaNDM foi positiva para um isolado de A. pittii, sendo o primeiro isolado de Acinetobacter não baumannii produtor de NDM-1 no Brasil. A análise do contexto genético de blaNDM-1 demonstrou a presença de ISAba125 upstream ao gene, além disso, o gene demonstrou estar localizado no cromossomo da bactéria. Foi observada uma maior prevalência de integrons de classe 2 nos isolados avaliados (134/25,5%), quando comparada aos integrons de classe 1 (72/13,7%). Raros (2/0,4%) isolados apresentaram ambas as classes de integrons. Um total 244 isolados de A. baumannii resistentes aos carbapenêmicos foram submetidos à tipagem por REP-PCR, que demonstrou a presença de 20 grupos clonais entre os isolados analisados. Isolados de diferentes grupos clonais foram selecionados para a tipagem por MLST. Com o objetivo de realizarmos uma análise longitudinal dos clones circulantes desde o primeiro surto de Acinetobacter baumannii resistente aos carbapenêmicos (CRAB) na cidade de Porto Alegre, também foram selecionados para análise por MLST isolados de A. baumannii pertencentes ao nosso banco de dados com diferentes perfis clonais, coletados entre 2007 e 2008. Através da análise dos dados gerados pelo MLST no banco de dados do Instituto Pasteur, foram descritas 13 novas STs: ST883 (CC32), ST884 (CC221), ST885 (CC79), ST886, ST887, ST888, ST889 (CC464), ST892 (CC15), ST899, ST902 (CC1), ST903 (CC79), ST904 (CC15) e ST905 (CC32). A avaliação da dinâmica populacional de A. baumannii nos dois períodos avaliados demonstrou a permanência de isolados pertencentes aos complexos clonais CC15 e CC79 desde o período do primeiro surto de CRAB da cidade de Porto Alegre até o ano de 2014, demonstrando a capacidade desses clones de se manter por longos períodos no ambiente hospitalar. Além disso, estes CCs apresentaram uma elevada prevalência durante o primeiro período avaliado (2007-2008). Este dado que nos permite inferir que o primeiro surto de CRAB produtor de OXA-23 da cidade de Porto Alegre foi relacionado a disseminação de CC15 e CC79. / Acinetobacter baumannii is considered one of the main pathogens of clinical importance currently, being responsible for a wide range of nosocomial infections such as, bacteremias, urinary tract infections, ventilator-associated pneumonia, secondary meningitis and wound infections. Since the last decade the treatment of these infections has been impaired by the emergence of multiresistant strains. In this context, the aim of this study was to determine the population dynamic and the molecular characteristics involved in Acinetobacter spp. resistance. A total of 524 Acinetobacter spp. isolates were collected from six Porto Alegre hospitals from January 2013 to March 2014. A. baumannii species were identified by the presence of blaOXA-51 gene and by the gyrB multiplex PCR. Carbapenemase genes (blaNDM, blaOXA-23-like, blaOXA-24/40-like, blaOXA-58-like and blaOXA-143-like) as well as class 1 and 2 integrons were investigated by PCR. As expected, the majority (487/92.9%) of isolates were identified as A. baumannii, followed by A. nosocomialis (9/1.7%), A. pittii (3/0.6%), and A. calcoaceticus (3/0.6%). A total of 22 (4.2%) isolates were not identified as A. baumannii-calcoaceticus complex. Analysis of the susceptibility profile demonstrated that 83% of the isolates were not susceptible to carbapenems (imipenem e meropenem). Among the A. baumannii isolates, 429/487 (88.1%) presented blaOXA-23 gene. Two A. nosocomialis isolates also presented the blaOXA-23 gene. We also found, for the first time in Southern Brazil, two A. baumannii isolates containing blaOXA24/40 (0.8%). The sequencing of blaOXA24/40 identified the variant blaOXA-72, and MLST analysis characterized both isolates as ST730 (CC79). In addition, OXA-72-producing A. baumannii isolates from the states of São Paulo and Paraná were analyzed by MLST. Data analysis demonstrated that the isolates were associated to the clonal complexes CC15 and CC79. The screening of blaNDM gene was positive for an A. pittii isolate. Therewith, in the present study we described for the first time a Acinetobacter non-baumannii producing NDM-1 in Brazil. Analysis of the genetic environment of blaNDM-1 gene demonstrated the presence of ISAba125 upstream of the gene and that the gene was chromosome-located in A. pittii. It was observed an increased prevalence of class 2 integrons (134/25.5%) compared to class 1 integrons (72/13.7%). Only a few isolates presented both classes (2/0.4%). A total of 244 carbapenem-resistant A. baumannii isolates were typed by REP-PCR, which demonstrated the presence of 20 clonal groups. Isolates belonging to different clonal groups were selected for MLST typing. In order to conduct a longitudinal analysis of circulating clones from the first CRAB outbreak in the city of Porto Alegre, we also selected A. baumannii isolates with different clonal profiles collected between 2007 and 2008. According to MLST database from Pasteur Institute, we identified 13 new STs: ST883 (CC32), ST884 (CC221), ST885 (CC79), ST886, ST887, ST888, ST889 (CC464), ST892 (CC15), ST899, ST902 (CC1), ST903 (CC79), ST904 (CC15) and ST905 (CC32). The analysis of A. baumannii population dynamics in the two periods of the study demonstrated the persistence of the clonal complexes CC15 and CC79 from the first CRAB outbreak in Porto Alegre city, up to the year of 2014. Besides, these CCs presented a high prevalence during the first period (2007-2008) evaluated. These data allow us to infer that the first CRAB OXA-23-producing outbreak in Porto Alegre city was related to the dissemination of CC15 and CC79.

Chau Sze-lok. / Thesis submitted in: December 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 221-245). / Abstracts in English and Chinese. / ABSTRACT (English) --- p.i / ABSTRACT (Chinese) --- p.iii / ACKNOWLEDGMENT --- p.v / LIST OF CONTENTS --- p.vii / LIST OF TABLES --- p.xiv / LIST OF FIGURES --- p.xvii / ABBREVIATIONS --- p.xx / TERMS --- p.xxi / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / (PART A) / Chapter 1.1 --- Acinetobacter spp --- p.1 / Chapter 1.2 --- Clinical importance of Acinetobacter --- p.4 / Chapter 1.3 --- Resistance mechanisms / Chapter 1.3.1 --- Intrinsic resistance --- p.7 / Chapter 1.3.2 --- Acquired resistance --- p.15 / Chapter 1.4 --- Resistance in Acinetobacter --- p.21 / Chapter 1.4.1 --- The efflux system in Acinetobacter --- p.22 / Chapter 1.4.2 --- Other antibiotic resistance mechanisms in Acinetobacter --- p.23 / (PART B) / Chapter 1.5 --- Methods used in this study --- p.29 / Chapter 1.6 --- Rationale of this study --- p.35 / Chapter 1.7 --- Objectives --- p.37 / Chapter CHAPTER 2 --- MATERIALS AND METHODS --- p.39 / Chapter 2.1 --- Bacterial strains and isolates / Chapter 2.1.1 --- Isolates for studying blaIMP-4 --- p.39 / Chapter 2.1.2 --- Isolates for studying adeB --- p.39 / Chapter 2.1.3 --- Isolates for investigation of other efflux pump(s)in Acinetobacter GDG3 --- p.40 / Chapter 2.1.4 --- Isolates for studying the distribution of efflux pumps --- p.40 / Chapter 2.1.5 --- Reference strains --- p.41 / Chapter 2.2 --- Materials / Chapter 2.2.1 --- Sources of materials --- p.42 / Chapter 2.2.2 --- Buffers and solutions --- p.45 / Chapter 2.3 --- Instruments and software --- p.46 / Chapter 2.4 --- General bacteriological techniques / Chapter 2.4.1 --- Bacteriological dientification --- p.47 / Chapter 2.4.2 --- Stock isolates --- p.48 / Chapter 2.4.3 --- Retrieval of isolates --- p.48 / Chapter 2.5 --- General molecular biology techniques / Chapter 2.5.1 --- Agarose gel electrophoresis --- p.49 / Chapter 2.5.2 --- Polymerase chain reaction (PCR) --- p.50 / Chapter 2.5.3 --- Amplified Ribosomal Restriction DNA Analysis (ARDRA) --- p.51 / Chapter 2.5.4 --- Pulsed field gel electrophoresis (PFGE) --- p.53 / Chapter 2.5.5 --- Minimal inhibitory concentration (MIC) --- p.55 / Chapter 2.5.6 --- Antibiotic sensitivity test - disc diffusion test --- p.56 / Chapter 2.5.7 --- Detection of the presence of the common resistance mechanisms --- p.57 / Chapter 2.5.8 --- TA Cloning --- p.60 / Chapter 2.5.9 --- DNA Sequencing --- p.62 / Chapter 2.5.10 --- Sequence analysis --- p.64 / Chapter 2.5.11 --- CYBR Green Assay --- p.65 / Chapter 2.5.12 --- Complementary DNA (cDNA) preparation --- p.66 / Chapter 2.5.13 --- Real time RT-PCR --- p.67 / Chapter 2.5.14 --- Construction of Genome Walker Libraries --- p.69 / Chapter 2.6 --- "Selection of acinetobacters from ICU, blood culture and other clinical isolates" / Chapter 2.6.1 --- Isolates from existing stock cultures --- p.71 / Chapter 2.6.2 --- New isolates obtained for this study --- p.71 / Chapter 2.7 --- Study of expression level of the blaIMP-4 gene / Chapter 2.7.1a --- Verification of the specificity of primers for blaIMP-4 --- p.72 / Chapter 2.7.1b --- Verfication of the specificity of primers for 16S rRNA gene --- p.73 / Chapter 2.7.1c --- Construction of standard curve --- p.76 / Chapter 2.7.2 --- Expression levels of blaIMP-4 and meropenem MICin blaIMP-4+ blood culture isolates --- p.77 / Chapter 2.7.3 --- Intra-assay reproducibility --- p.11 / Chapter 2.7.4 --- Detection of the production of metallo-β-lactamase --- p.77 / Chapter 2.8 --- Study of adeABC expression / Chapter 2.8.1 --- Determination of the presence of the adeB gene --- p.78 / Chapter 2.8.2 --- Entirety of the adeABC operon --- p.79 / Chapter 2.8.3 --- Expression level of the adeB gene --- p.82 / Chapter 2.8.4 --- Expression levels of adeB in sets of serial isolates --- p.84 / Chapter 2.8.5 --- Intra-assay reproducibility --- p.84 / Chapter 2.8.6 --- Inter-assay reproducibility --- p.84 / Chapter 2.9 --- Investigation of other efflux pumps in acinetobacter genomic DNA group3 / Chapter 2.9.1 --- Detection of adeB homologue in a genomic DNA group 3isolate --- p.85 / Chapter 2.9.2 --- Chromosome walking of the adeB-like genes --- p.87 / Chapter 2.9.3 --- Sequences of AdeE and AdeY and their comparison --- p.105 / Chapter 2.9.4 --- Topology prediction of AdeE and AdeY --- p.105 / Chapter 2.9.5 --- The role of the putative pump AdeE --- p.106 / Chapter 2.10 --- Distribution of AdeB and the putative efflux pumps AdeE and AdeY in acinetobacters from different bacterial collections / Chapter 2.10.1 --- Distribution of adeB and the putative pumps (adeE and adeY) in blood cultures (1997-2000) --- p.113 / Chapter 2.10.2 --- Confirmation of the identity of the amplification products of adeE and ade Y in blood culture isolate (1997-2000) --- p.115 / Chapter 2.10.3 --- The presence of adeE in GDG 3 acinetobacters from different sources --- p.116 / Chapter 2.10.4 --- "The presence of adeB, adeE and adeY in antibiotic susceptibility" --- p.116 / Chapter 2.10.5 --- "adeB, adeE and adeY and the clonally and epidemiologically related sets of isolates" --- p.116 / Chapter 2.10.6 --- "adeB, adeE and adeY and the blaIMP-4+ isolates" --- p.116 / Chapter CHAPTER 3 --- "SELECTION OF ACINETOBACTERS FROM ICU, BLOOD CULTURE AND OTHER CLINICAL ISOLATES" --- p.119 / Chapter 3.1 --- Results / Chapter 3.1.1 --- Isolates from existing stock cultures --- p.119 / Chapter 3.1.2 --- New isolates obtained for this study --- p.127 / Chapter 3.2 --- Discussion / Chapter 3.2.1 --- Identification of clonally related isolates by PFGE --- p.129 / Chapter 3.2.2 --- Correlation between the presence of common resistance mechanisms and the changes in antimicrobial susceptibility --- p.129 / Chapter 3.2.3 --- Development of resistance in serial isolates --- p.131 / Chapter CHAPTER 4 --- STUDY OF blaIMP-4 EXPRESSION --- p.133 / Chapter 4.1 --- Results / Chapter 4.1.1 --- Study of expression level of the blaIMP-4 gene --- p.134 / Chapter 4.1.2 --- Expression levels of blaIMP-4 and meropenem MIC in blaIMP-4+ blood culture isolates --- p.136 / Chapter 4.1.3 --- Intra-assay reproducibility \ --- p.37 / Chapter 4.1.4 --- Detection of the production of metallo-β-lactamase --- p.140 / Chapter 4.2 --- Discussion / Chapter 4.2.1 --- Dissociation curve --- p.140 / Chapter 4.2.2 --- Reproducibility of real time RT-PCR --- p.140 / Chapter 4.2.3 --- Relationship between mRNA level of blaIMP-4 and the meropenem MIC --- p.142 / Chapter CHAPTER 5 --- STUDY OF adeABC EXPRESSION --- p.145 / Chapter 5.1 --- Results / Chapter 5.1.1 --- Determination of the presence of the adeB gene --- p.145 / Chapter 5.1.2 --- Entirety of the adeABC operon --- p.146 / Chapter 5.1.3 --- Expression level of the adeB gene --- p.148 / Chapter 5.1.4 --- Expression levels of adeB in sets of serial isolates --- p.151 / Chapter 5.1.5 --- Intra-assay reproducibility --- p.154 / Chapter 5.1.6 --- Inter-assay reproducibility --- p.154 / Chapter 5.2 --- Discussion / Chapter 5.2.1 --- Detection of adeB --- p.156 / Chapter 5.2.2 --- Entirety of the adeABC operon --- p.156 / Chapter 5.2.3 --- Reproducibility of real time RT-PCR --- p.157 / Chapter 5.2.4 --- Relationship between adeB-mRNA level and antimicrobial susceptibility --- p.157 / Chapter CHAPTER 6 --- INVESTIGATION OF OTHER EFFLUX PUMPS IN ACINETOBACTER GENOMIC DNA GROUP3 --- p.159 / Chapter 6.1 --- Results / Chapter 6.1.1 --- Detection of adeB homologue in a genomic DNA group3 isolate --- p.159 / Chapter 6.1.2 --- Chromosome walking of the adeB-like genes --- p.162 / Chapter 6.1.3 --- Sequences of AdeE and AdeY and their comparison --- p.173 / Chapter 6.1.4 --- Topology prediction of AdeE and AdeY --- p.175 / Chapter 6.1.5 --- The role of the putative pump AdeE --- p.177 / Chapter 6.2 --- Discussion / Chapter 6.2.1 --- The AdeE RND transporter --- p.181 / Chapter 6.2.2 --- The theoretical AdeY protein --- p.183 / Chapter CHAPTER 7 --- DISTRIBUTION OF AdeB AND THE PUTATIVE EFFLUX PUMPS AdeE and AdeY IN ACINETOBACTERS FROM DIFFERENT BACTERIAL COLLECTIONS --- p.184 / Chapter 7.1 --- Results / Chapter 7.1.1 --- Distribution of adeB and the putative pumps (adeE and ade Y) in blood cultures (1997-2000) --- p.184 / Chapter 7.1.2 --- Confirmation of the identity of the amplification products of adeE and adeY in blood culture isolates (1997-2000) --- p.187 / Chapter 7.1.3 --- The presence of adeE in GDG 3 acinetobacters from different sources --- p.195 / Chapter 7.1.4 --- "The presence of adeB, adeE and ade Y in antibiotic susceptibility" --- p.196 / Chapter 7.1.5 --- "adeB, adeE and adeY and the clonally and epidemiologically related sets of isolates" --- p.202 / Chapter 7.1.6 --- "adeB, adeE and adeY and the blaIMP-4+ isolates" --- p.202 / Chapter 7.2 --- Discussion / Chapter 7.2.1 --- PCR-RFLP typing --- p.205 / Chapter 7.2.2 --- Distribution of adeB --- p.205 / Chapter 7.2.3 --- Distribution of adeE --- p.206 / Chapter 7.2.4 --- Distribution of adeY --- p.207 / Chapter 7.2.5 --- Distribution of adeE and adeY in GDG 3 isolates --- p.207 / Chapter CHAPTER 8 --- GENERAL DISCUSSION --- p.209 / Chapter 8.1 --- Significance of adeB and the putative pumps (adeE and adeY) --- p.211 / Chapter CHAPTER 9 --- CONCLUSION --- p.218 / Chapter 9.1 --- Conclusion --- p.218 / Chapter 9.2 --- Future Plan --- p.219 / REFERENCES --- p.221 / APPENDIX --- p.246 / Appendix1 --- p.246 / Appendix2 --- p.247 / Appendix3 --- p.252 / Appendix4 --- p.253 / Appendix5 --- p.259

Introducción: Acinetobacter baummannii es el principal patógeno en la lista de la Organización Mundial de la Salud de resistencia antibiótica. Este ha surgido como patógeno a nivel mundial debido a la expansión de clonas epidémicas internacionales (CI) productoras de carbapenemasas de clase D (tipo OXA). Durante la última década, sin embargo, los reportes de la CI-I en Latinoamérica son escasos e inexistentes para las CI-II y CI-III. Objetivo: Este estudio evalúa la resistencia fenotípica, la presencia de mecanismos moleculares de resistencia a carbapenemos y la relación clonal de 80 muestras clínicas de A. baumannii recolectados desde Febrero de 2014 y Abril de 2016 en dos hospitales de tercer nivel en Lima. Materiales y métodos: La identificación de especies se realizó por espectrometría de masas (MALDI-TOF MS), la susceptibilidad antimicrobiana por difusión de discos y E-test, excepto para colistina, que fue determinado por microdilución en caldo de cultivo e interpretado según las guías del CLSI. Para tigeciclina se utilizó las guías EUCAST para Enterobacterias. Los genes de resistencia a carbapenémicos se detectaron por PCR y secuenciación. La relación clonal se estudió por electroforesis de campo pulsado (PFGE) y MLST con el esquema Pasteur. Resultados: La mayoría de las cepas eran resistentes a carbapenémicos (97.5%) y la susceptibilidad se encontraba elevada únicamente para colistina (95%). La electroforesis de campo pulsado identificó dos clonas principales en ambos hospitales: la clona D comprendiendo 51 aislamientos (61.3%) asociada con la secuencia-tipo 2 (ST2) portadora de OXA-72 y la clona F de 13 aislamientos (16.3%), asociada con ST79 y portadora de OXA-72. Estas eran endémicas en al menos un hospital. Se identificaron cepas ST1 y ST3 productoras de OXA-23, representando aislamientos esporádicos. Resulta resaltante la presencia de la nueva variante OXA-253 de la OXA-143 con una nueva secuencia de inserción (ISAba47). Conclusión: Mientras las líneas clonales predominantes de A. baummannii en Latinoamérica se relacionan con ST79, ST25, ST15 y ST1 productoras de OXA-23, en el estudio se reporta el surgimiento de ST2 altamente resistentes (CI-II) productoras de OXA-72 y la primera identificación de ST3 (CI-III) en Latinoamérica, ambas representando un serio riesgo para la salud pública a nivel mundial. / Background: Carbapenem-resistant Acinetobacter baumannii is the top-ranked pathogen in the World Health Organisation priority list of antibiotic-resistant bacteria. It emerged as a global pathogen due to the successful expansion of a few epidemic lineages, or international clones (IC), producing acquired class-D carbapenemases (OXA-type). During the last decade, however, reports regarding IC-I isolates in Latin America are scarce and non-existent for IC-II and IC-III isolates. Objective: This study evaluates the phenotypic resistance patterns, the presence of carbapenem-resistance mechanisms and the clonal relatedness of 80 non-duplicate clinical samples of A. baumannii collected from February 2014 through April 2016 at two tertiary care hospitals in Lima. Methods and materials: Species identification was performed by MALDI-TOF MS, antimicrobial susceptibility testing was analysed by disk diffusion and E-test for all antibiotics but colistin, which was determined by broth microdilution, and interpreted according to CLSI guidelines for Acinetobacter spp. Tigecycline results were interpreted following EUCAST guidelines for Enterobacteriaceae. Carbapenemase genes were detected by PCR and Sanger DNA sequencing. The clonal relatedness was examined by pulsed-field gel electrophoresis (PFGE) and MLST with the Pasteur scheme. Results: Almost all isolates were carbapenem-resistant (97.5%), and susceptibility only remained high for colistin (95%). PFGE showed two main clusters spread between both hospitals: cluster D containing 51 isolates (63.8%) associated with sequence type 2 (ST2) and carrying OXA-72, and cluster F containing 13 isolates (16.3%) associated with ST79 and also carrying OXA-72. ST2 and ST79 were endemic in at least one of the hospitals. International clone I (IC-I) ST1 and IC-III (ST3) OXA-23-producing isolates were also identified. They accounted for sporadic hospital isolates. Interestingly, two isolates carried the novel OXA-253 variant of OXA-143 together with an upstream novel insertion sequence (ISAba47). Conclusion: While the predominant A. baumannii lineages in Latin America are linked to ST79, ST25, ST15, and ST1 producing OXA-23 enzymes, we report the emergence of highly-resistant ST2 (IC-II) isolates in Peru producing OXA-72 and the first identification of ST3 isolates (IC-III) in Latin America, both considered a serious threat to public health worldwide. / Tesis

Nas últimas três décadas, o A. baumannii passou de um germe de patogenicidade questionável para um importante agente causador de infecções no mundo, principalmente por sua capacidade de se tornar resistente aos antimicrobianos. Surtos de A. baumannii resistente aos carbapenêmicos (ABRC) têm sido descritos em vários países. O objetivo deste estudo foi avaliar a mortalidade, em 30 dias, de pacientes colonizados e/ou infectados por ABRC, bem como os fatores preditores desse desfecho. Uma coorte história foi conduzida durante o período de março de 2006 a dezembro de 2008, e os pacientes internados em uma Unidade de Terapia Intensiva (UTI) de hospital terciário de Porto Alegre com cultura positiva para ABRC foram incluídos. Os potenciais preditores de mortalidade foram avaliados. Foram incluídos 66 pacientes, e a taxa de mortalidade em 30 dias foi de 47%. Na análise de regressão multivariada, a presença de choque séptico e o escore de gravidade APACHE II no momento da identificação do ABRC foram os fatores de risco estatisticamente significativos associados à mortalidade. Terapia antimicrobiana apropriada foi um fator protetor, embora sem significância estatística, fato que pode ser em razão do uso de doses subótimas de polimixina B. O mecanismo de resistência identificado nas amostras testadas foi a produção de OXA-23, e foram identificados quatro clones envolvidos no surto. Apesar de não atingir significância estatística no modelo de análise multivariada, pacientes que receberam terapia adequada para infecções por ABRC apresentaram forte tendência a menor mortalidade em 30 dias. Terapêutica adequada pode ser a única variável modificável capaz de influir beneficamente no desfecho clínico de pacientes com infecções por ABRC.

Acinetobacter baumannii é um patógeno nosocomial que está envolvido em um amplo espectro de infeções hospitalares. A maior preocupação atual é devido a sua alta capacidade de adquirir mecanismos de resistência, principalmente aos carbapenêmicos, fármacos utilizados normalmente para o tratamento dessas infecções. Desta forma, as opções terapêuticas tornam-se restritas e por isso, as polimixinas (polimixina B e colistina) voltaram a serem utilizadas na prática clínica. A heterorresistência a colistina já foi descrita em estudos recentes com isolados de A. baumannii e outros estudos detectaram a presença de resistência adaptativa as polimixinas. O objetivo deste estudo foi investigar a presença do fenômeno de heterorresistência e resistência adaptativa a polimixina B, e avaliar sua estabilidade. A pesquisa foi feita em isolados pertencentes a 15 clones diferentes de A. baumannii resistentes aos carbapenênicos e sensíveis a polimixina B. A avaliação da heterorresistência foi feita através da análise do perfil da população (PAP) para 29 isolados, selecionados aleatoriamente (pelo menos um de cada clone). A indução da resistência foi avaliada para 22 isolados, selecionados aleatoriamente (pelo menos um de cada clone), submetendo os isolados ao cultivo em concentrações crescentes de polimixina B. A determinação da estabilidade das subpopulações e da indução da resistência foi feita através de passagens, em dias consecutivos, em meio livre de antibiótico. Foram consideradas subpopulações heterogêneas aquele isolado que possuía colônias com uma CIM maior do que a população original para polimixina B. A CIM foi reavaliada após 75 e 60 dias de estocagem em -80ºC para os isolados que apresentaram subpopulação heterogênea ou indução da resistência para a polimixina B, respectivamente. Dos 29 isolados, submetidos a avaliação da heterorresistência, 26 (90%) apresentaram subpopulações heterogêneas para polimixina B. Nenhum isolado apresentou subpopulação superior a 2 μg/mL para polimixina B, ou seja, não foi encontrado neste estudo subpopulações heterorresistentes. As CIMs das subpopulações heterogêneas permaneceram iguais após os subcultivos em meio livre de antibiótico, mas quando a CIM foi reavaliada depois da estocagem, os valores obtidos foram os mesmos da população original. Dos 22 isolados submetidos a indução de resistência, 12 (55%) apresentaram algum crescimento até a concentração de 64 μg/mL de polimixina B. Após as passagens em meio livre de antibiótico a CIM diminuiu, voltando a CIM original na reavaliação após a estocagem a -80ºC. Este estudo mostra pela primeira vez a avaliação da heterorresistência e indução da resistência para polimixina B em isolados de A. baumannii resistentes aos carbapenêmicos. O fenômeno de heterorresistência não foi encontrado neste estudo, no entanto, subpopulações com uma CIM maior do que a original foram identificadas em 90% dos isolados. As CIMs das subpopulações permaneceram estáveis após 4 dias de passagens em meio livre de antibiótico, mas retornaram a CIM original após estocagem, o que sugere o envolvimento de mecanismos moleculares neste fenômeno. A presença da resistência induzida a polimixina B foi detectada em 55% dos isolados, sugerindo que este fenômeno pode ser comum entre os isolados de A. baumannii resistentes aos carbapenêmicos, frente a polimixina B. Embora a presença de subpopulações heterogêneas e a indução da resistência a polimixina B tenha sido comum neste estudo, mais estudos são necessários para um melhor entendimento do significado clínico e das implicações terapêuticas destes dois fenômenos.

Introdução: O gênero Acinetobacter sp apresenta considerável heterogeneidade possuindo inúmeras espécies. Atualmente, 23 espécies já foram nomeadas e nove outras espécies já foram descritas. Quatro destas espécies possuem contextos clínicos e epidemiológicos diferentes, no entanto são agrupadas em um complexo denominado Acinetobacter calcoaceticus-Acinetobacter baumannii (ABC) devido à sua similaridade genética e fenotípica. Diversos testes para diferenciação do complexo já foram descritos, porém a maioria não pode ser realizado na rotina laboratorial, pois são caros e laboriosos. Objetivos: Avaliar um método rápido e viável na rotina laboratorial, capaz de diferenciar as espécies do complexo ABC; Determinar a prevalência das diferentes espécies do complexo ABC; Avaliar o perfil de suscetibilidade aos antimicrobianos nas diferentes espécies. Métodos: Foram analisadas 118 amostras de dois hospitais de Porto Alegre-RS através do método Multiplex PCR para o gene gyrB e posteriormente confirmadas pelo padrão-ouro: sequenciamento do 16S-23S ITS. O perfil de suscetibilidade foi realizado através de microdiluição em caldo. Resultados: Das 118 amostras identificadas inicialmente como Acinetobacter sp., a grande maioria dos isolados (106 -89.9%) foram identificados como A. baumannii; mas doze isolados foram identificados como sendo das demais espécies do complexo ABC: 6 (5.1%) A. nosocomialis, 5 (4.2%) A. pittii, e 1 (0.8%) A. genoespécie 10, através da técnica de Multiplex PCR. Todos os resultados foram confirmados por sequenciamento. A. baumannii apresentou um elevado nível (72,6%) de resistência ao imipenem em comparação com as outras espécies seguido da espécie A. nosocomialis que apresentou metade de seus isolados resistentes. Todas as espécies apresentaram baixos índices (inferior a 7,5%) de resistência à Polimixina B e Tigeciclina. Conclusão: O Multiplex PCR para o gene gyrB apresentou resultados fidedignos quando comparados ao padrão-ouro, demonstrando, assim, ser um método confiável para a identificação das espécies do complexo ABC. Outras espécies, além de A. baumannii, ABC podem apresentar percentuais significativos de resistência ao imipenem. / Background: Introduction: The genus Acinetobacter sp presents considerable heterogeneity possessing numerous species. Currently, 23 species have been named and nine other species have been described. Four of these species have different clinical and epidemiological contexts, but are grouped in a complex called Acinetobacter calcoaceticus-Acinetobacter baumannii (ABC) due to their genetic and phenotypic similarity. Several tests for differentiation of the complex have been described, but most can not be performed routinely in the laboratory, they are expensive and laborious. Objectives: To evaluate a fast and feasible in routine laboratory able to differentiate the species of the complex ABC; determine the prevalence of different species of the complex ABC; evaluate the antimicrobial susceptibility profile of the different species. Methods: We analyzed 118 samples from two hospitals in Porto Alegre-RS by the method of Multiplex PCR for gene gyrB and subsequently confirmed by the gold standard: sequencing the 16S-23S ITS. The susceptibility profile was performed by microdilution. Results: Of the 118 samples initially identified as Acinetobacter sp. The great majority of isolates (106 -89.9%) were identified as A. baumannii, but twelve isolates were identified as being from other species of the complex ABC: 6 (5.1%) A. nosocomialis, 5 (4.2%) A. pittii, and 1 (0.8%) A. genospécie 10 by Multiplex PCR technique. All results were confirmed by sequencing. A. baumannii showed a high level (72.6%) of imipenem resistance in comparison with the other species followed by the species A. nosocomialis showed that half of his resistant isolates. All species showed low levels (less than 7.5%) of resistance to Polymyxin B and Tigecycline. Conclusion: Multiplex PCR for gene gyrB results presented totally reliable when compared to the gold standard, demonstrating thus be a safe method for the laboratory. Other species besides A. baumannii, ABC may have significant percentages of resistance to imipenem.

The purpose of this study is to isolate and identify the crude oil-degrading bacteria from oil polluted soil. Their physiological characteristics and oil-degrading capability were also studied. Eight polluted soil samples were taken from the Kaohsiung Refingery Factory of the Chinese Petroleum Corporation (CPC). The microbiota of the Kaohsiung refinery soil sample P37-2 (#6) could degrade crude oil from 2000 ppm to 572 ppm in 10 days. Bacteria in polluted soil samples were selected and isolated by minimal medium with 2000 ppm crude oil as the sole carbon source. Biochemical test, PCR-DGGE, and 16S DNA sequencing were used to identify and characterize the bacteria isolates. Three strains were identified as Pseudomonas aeruginosa (NSYSU-1-1), Acinetobacter sp. (NSYSU-4-1), and Pseudomonas sp. (NSYSU-7-1). These three strains and microbiota #6 were tested for their capability of degrading the total petroleum hydrocarbons (TPH). We found that microbiota #6 performed better than the other three bacterial strains in degrading the crude oil. In this study, we also found temperature was not the major factor of influcing the biodegradation; however, high oxygen concentration and providing nitrogen soure couled improve the biodegradation rate. Although both NSYSU-1-1 and NSYSU-7-1 are Pseudomonas strains, they performed different on degrading the oil. All strains tested could degrade the crude oil to a concentration below 1000 ppm to meet the government emission standard. The bacterial strains and techniques developed in this study provide a choice for future bioremediation of crude oil pollution.

Background There has been an increasing awareness of the role of the hospital environment as a reservoir of Acinetobacter baumannii. A. baumannii is an important nosocomial pathogen and is difficult to control due to the increasing cases of resistance to carbapenem. Objectives The objectives of this study areto examine carbapenem-resistant Acinetobacter baumannii (CRAB) positive patients according to their environmental sample to determine how frequently the environment surrounding the patient becomes contaminated and which environmental surfaces are most commonly contaminated. Methodology During June 2011 to December 2011, data regarding 30 hospitalized patients with at least one positive CRAB clinical sample were collected from hospital X in Kowloon of Hong Kong. For 30 case patients, one patient in the ICU ward had been isolated in a single room and the other 29 patients stayed in a multi-room. Fifteen surfaces in the patient cubicle and nine surfaces in health care worker stations were evaluated for the presence of CRAB. 29 control environmental samples were obtained from the surroundings of patients without CRAB in the same cubicle and one control environmental sample was obtained from the surroundings of patients without CRAB in the other room of ICU. Pulsed-field gel electrophoresis was performed on all environmental isolates and clinical samples. Results Of the 30casepatients, 26 patients (86.7%) were found to have CRAB contamination in their surrounding environment and 6negative control patients (20%) were found to have CRAB in their environmental samples. The percentage of positive CRAB cultures in the case environment, control and health care worker stations was 28.9% (117/405), 3.4% (14/406) and 1.9% (5/265)respectively. In the surrounding case patient area, pillows (60% 18/30) and bed sheets on which the patients sleep on (60% 18/30), bed sheets covering the patients (50% 15/30) and bedside table tops (40% 12/30) were the most commonly contaminated. For 26casepatientswere found to have CRAB contamination in their surrounding environment, 23 (88.5%) of these patients were found to have the clone of isolates in the case environment related to the patients. Conclusion For patients with CRAB, the surrounding environment is frequently contaminated. Surfaces often touched by the patients are commonly contaminated. CRAB was also found on surfaces that were not closely related to the patient which are frequently touched by healthcare workers during patient care. / published_or_final_version / Microbiology / Master / Master of Medical Sciences

Acinetobacter baumannii is an important nosocomial pathogen worldwide because of its remarkable ability to acquire antibiotic resistance. The global emergences of multidrug-resistant A. baumannii (MDR-AB) clones are predominated by a number of widely disseminated clones, namely clonal complex (CC) 1, CC2, and CC3. In early 2010, we reported two major clones of MDR-AB, designated HKU1 and HKU2 belong to sequence types (ST) 96 and ST92, widely disseminating in our hospitals. ST92 is a predominant clone that is prevalent in more than 30 countries, whereas ST96 has been identified recently and is geographically confined to certain parts of China. Our previous study only investigated the isolates collected in the year 2005-2006. We therefore extended our investigation over a six-year period (2005-2010) to generate a more complete picture of the molecular epidemiology and resistance mechanisms in A. baumannii. Firstly, we performed the susceptibility test on various antimicrobial agents and employed molecular methods to characterize the epidemiology of the target A. baumannii isolates. For the entire study period, increased resistance rates were noted for the seven antimicrobial agents, namely imipenem, piperacillin-tazobactam, cefoperazone, ticarcillin-clavulanate, ciprofloxacin, gentamicin and amikacin (P <0.01). Worryingly, an increased trend was also observed for the pandrug-resistant rate, from 0.2% in the year 2005-2006, to 1.9-2.9% in the year 2007-2008 and up to 6.0-8.1% in the year 2009-2010 (chi square for trend, P <0.001). Pulsed-field gel electrophoresis and multilocus sequence typing (PFGE/MLST) categorized 100 out of 108 (92.6%) isolates into four clones (PFGE/MLST), namely HKU2/ST92 (n = 14), HKU3/ST254 (n = 73), HKU4/ST137 (n = 5), and HKU5/ST362 (n = 8), respectively. PCR showed that 88.9% (96/108) of the amikacin-resistant isolates were armA positive and all isolates were found to harbour at least one of the OXA-type carbapenemases with frequencies as follows: OXA-51-like (98/108, 90.7%), OXA-23-like (85/108, 78.7%), OXA-58-like (9/108, 8.3%) and OXA-24-like (8/108, 7.4%). Secondly, we compared the biological fitness of the circulating clones by performing the doubling time and adhesion experiment. The results demonstrated that HKU3/ST254 has a higher capability for replication and adherence to human bronchial epithelial cells. Together with the higher antibiotic resistance rate, the selective advantages in terms of biological fitness may facilitate the clonal expansion and wide dissemination of this lineage. Finally, whole genome sequence data showed a high amount of resistance genes intermixed with various insertion sequence (IS) elements, integrons and transponsons clustering inside the resistance islands. The presence of a second genomic resistance island conferring aminoglycoside and sulphonamide resistance, additional loci outside the resistance islands harbouring resistance genes and the high amount of antibiotic efflux pumps in various A. baumannii genomes demonstrated that resistance islands contribute a significant part to the multidrug-resistant phenotype in A. baumannii but are not the only factor. The correlation analysis further demonstrated the significance of IS elements in the dissemination of antibiotic resistance genes in the A. baumannii genomes. As a whole, whole genome sequence data may provide an informative and efficient approach to generating a more comprehensive picture to study the resistance mechanism of the epidemic strains. / published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy