CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Campylobacter jejuni e Campylobacter coli sÃo importantes agentes etiolÃgicos de doenÃa diarrÃica na populaÃÃo mundial. A infecÃÃo por Campylobacter sp. à usualmente identificada por cultivo microbiolÃgico que leva aproximadamente 72 horas para identificaÃÃo do gÃnero. Nosso objetivo principal foi pesquisar a prevalÃncia de C. jejuni e C. coli em populaÃÃo infantil, com idade entre 2-36 meses, da Ãrea urbana de Fortaleza/CE, Brasil, em estudo do tipo epidemiolÃgico observacional caso-controle, utilizando, como ferramenta de detecÃÃo, a reaÃÃo em cadeia da polimerase (PCR). Outros objetivos consistiram em: investigar o impacto nutricional da infecÃÃo (casos) ou da colonizaÃÃo (controles) por Campylobacter sp.; determinar a presenÃa de trÃs genes de virulÃncia para a toxina citoletal distensora (CDT) de C. jejuni e avaliar a ocorrÃncia de inflamaÃÃo intestinal nas infecÃÃes causadas por Campylobacter sp. A populaÃÃo estudada consistiu de 83 casos e 83 controles, sendo os casos, crianÃas com histÃrico de diarrÃia nos 14 dias pregressos à seleÃÃo para o estudo. Foram avaliados parÃmetros sÃcio-econÃmicos atravÃs de questionÃrio epidemiolÃgico. Medidas antropomÃtricas foram coletadas para determinaÃÃo de escores-z no intuito de avaliar o perfil nutricional das crianÃas. A detecÃÃo de Campylobacter nas amostras congeladas foi realizada por ensaio imuno-enzimÃtico (ELISA) e PCR. Pela PCR tambÃm investigamos a presenÃa dos genes cdtA, cdtB e cdtC da CDT de C. jejuni. A avaliaÃÃo da inflamaÃÃo intestinal foi realizada pela pesquisa de lactoferrina fecal (LFF), atravÃs de ELISA semiquantitativa. Foi detectado, por PCR, C. jejuni em 9,6% dos casos (8/83) e 7,2% dos controles (6/83). C. coli foi detectado em 6,0% dos casos (5/83) e 1,2% dos controles (1/83). Os genes cdtA, cdtB e cdtC foram encontrados em 50% das amostras hipO+ (7/14). Houve diferenÃa significativa (p<0,05) dos escores WAZ e WHZ entre casos e controles portadores de C. jejuni, sendo que casos portadores apresentaram mÃdia inferior de WAZ e WHZ, quando comparados com os controles portadores. No grupo Casos, os portadores de C. jejuni apresentavam valor mÃdio de WHZ inferior ao valor mÃdio apresentado pelos casos nÃo-portadores. Mais de 80,0% das crianÃas estudadas apresentaram inflamaÃÃo intestinal caracterizada por elevados nÃveis de LFF, independente da presenÃa de diarrÃia e Campylobacter sp. Em conclusÃo, nossos achados corroboram dados da literatura cientÃfica relacionados à prevalÃncia de C. jejuni e C. coli na populaÃÃo infantil, existÃncia de portadores assintomÃticos e associaÃÃo entre a detecÃÃo do microorganismo e desnutriÃÃo. AlÃm disso, nossos dados apontam para ocorrÃncia de variabilidade genÃtica dentre as cepas de C. jejuni detectadas na populaÃÃo estudada em relaÃÃo à presenÃa ou ausÃncia dos genes de CDT. / Campylobacter jejuni and Campylobacter coli are important etiologic agents of worldwide diarrheal disease. Campylobacter sp. infection is usually identified by a 72 hour microbiological culture that identifies the genus of the responsible organism. Our main goal was to investigate the prevalence of C. jejuni and C. coli in children, aged 2-36 months, from urban Fortaleza, CE, Brazil, in an observational epidemiological case-control study using, as a tool of detection, the polymerase chain reaction (PCR). Our other goals were to investigate the nutritional impact of infection (cases) or colonization (controls) for Campylobacter sp., to determine the presence of three virulence genes of C. jejuni cytolethal distending toxin (CDT), and to evaluate the occurrence of inflammation in intestinal infections caused by Campylobacter sp. The study population consisted of 83 cases and 83 controls, where the cases consisted of children with a history of diarrhea in the 14 days prior to selection for the study. We assessed socioeconomic parameters through an epidemiological questionnaire. Anthropometric measurements were collected to determine z-score parameters for assessing the nutritional status of the children. Detection of Campylobacter from frozen samples was performed by enzyme-linked immunosorbent assay (ELISA) and PCR. Also, using PCR technology, we investigated the presence of C. jejuni genes cdtA, cdtB and cdtC. Intestinal inflammation was assessed by semi-quantitative ELISA detection of fecal lactoferrin (LFF). PCR technology detected C. jejuni in 9.6% of the cases (8/83) and 7.2% of the controls (6/83), while C. coli was detected in 6.0% of the cases (5/83) and 1.2% of the controls (1/83). CDT genes were found in 50% of hipO+ samples (7/14). There was a significant difference (p <0.05) in the weight for age z-scores (WAZ) and the weight for height z-scores (WHZ) between case and control carriers of C. jejuni, where case carriers showed lower average WAZ and WHZ than control carriers. Moreover, in the case group, carriers of C. jejuni showed a lower WHZ average than that of non-carrier cases of C. jejuni. More than 80.0% of the children studied had intestinal inflammation characterized by high levels of LFF regardless of the presence of diarrhea and Campylobacter sp. In conclusion, our findings corroborate data in the scientific literature related to the prevalence of C. jejuni and C. coli in pediatric populations, the existence of asymptomatic carriers and an association between the detection of the microorganism and malnutrition. In addition, our data suggest a genetic variability among the strains of C. jejuni detected in the study population, related to presence o absence of CDT genes.

Campylobacter jejuni is the commonest cause of bacterial foodborne gastroenteritis in industrialised countries. Despite its significance, it remains unclear how C. jejuni is disseminated in the environment, whether particular strains are more pathogenic than others, and by what routes this bacterium is transmitted to humans. One major factor hampering this knowledge is the lack of a standardised method for fingerprinting C. jejuni. Therefore, the overall aim of this project was to develop systematic and novel genotyping methods for C. jejuni. Chapter Three describes the use of single nucleotide polymorphisms (SNPs) derived from the multilocus sequence typing (MLST) database of C. jejuni and the closely related Campylobacter coli for genotyping these pathogens. The MLST database contains DNA sequence data for over 4000 strains, making it the largest comparative database available for these organisms. Using the in-house software package "Minimum SNPs", seven SNPs were identified from the C. jejuni/C. coli MLST database that gave a Simpson's Index of Diversity (D), or resolving power, of 0.98. An allele-specific real-time PCR method was developed and tested on 154 Australian C. jejuni and C. coli isolates. The major advantage of the seven SNPs over MLST is that they are cheaper, faster and simpler to interrogate than the sequence-based MLST method. When the SNP profiles were combined with sequencing of the rapidly evolving flaA short variable region (flaA SVR) locus, the genotype distributions were comparable to those obtained by MLST-flaA SVR. Recent technological advances have facilitated the characterisation of entire bacterial genomes using comparative genome hybridisation (CGH) microarrays. Chapter Four of this thesis explores the large volume of CGH data generated for C. jejuni and eight binary genes (genes present in some strains but absent in others) were identified that provided complete discrimination of 20 epidemiologically unrelated strains of C. jejuni. Real-time PCR assays were developed for the eight binary genes and tested on the Australian isolates. The results from this study showed that the SNP-binary assay provided a sufficient replacement for the more laborious MLST-flaA SVR sequencing method. The clustered regularly interspaced short palindromic repeat (CRISPR) region is comprised of tandem repeats, with one half of the repeat region highly conserved and the other half highly diverse in sequence. Recent advances in real-time PCR enabled the interrogation of these repeat regions in C. jejuni using high-resolution melt differentiation of PCR products. It was found that the CRISPR loci discriminated epidemiologically distinct isolates that were indistinguishable by the other typing methods (Chapter Five). Importantly, the combinatorial SNP-binary-CRISPR assay provided resolution comparable to the current 'gold standard' genotyping methodology, pulsed-field gel electrophoresis. Chapter Six describes a novel third module of "Minimum SNPs", 'Not-N', to identify genetic targets diagnostic for strain populations of interest from the remaining population. The applicability of Not-N was tested using bacterial and viral sequence databases. Due to the weakly clonal population structure of C. jejuni and C. coli, Not-N was inefficient at identifying small numbers of SNPs for the major MLST clonal complexes. In contrast, Not-N completely discriminated the 13 major subtypes of hepatitis C virus using 15 SNPs, and identified binary gene targets superior to those previously found for phylogenetic clades of C. jejuni, Yersinia enterocolitica and Clostridium difficile, demonstrating the utility of this additional module of "Minimum SNPs". Taken together, the presented work demonstrates the potentially far-reaching applications of novel and systematic genotyping assays to characterise bacterial pathogens with high accuracy and discriminatory power. This project has exploited known genetic diversity of C. jejuni to develop highly targeted assays that are akin to the resolution of the current 'gold standard' typing methods. By targeting differentially evolving genetic markers, an epidemiologically relevant, high-resolution fingerprint of the isolate in question can be determined at a fraction of the time, effort and cost of current genotyping procedures. The outcomes from this study will pave the way for improved diagnostics for many clinically significant pathogens as the concept of hierarchal combinatorial genotyping gains momentum amongst infectious disease specialists and public health-related agencies.