Barramundi (Lates calcarifer) aquaculture is expanding throughout Australia and the Asia-Pacific region. The Department of Primary Industries, Queensland have estimated that the production from this industry could reach $30 million per annum in Australia by 2010. However, current production is severely impeded by outbreaks of Streptococcus iniae, which causes a fatal septicaemia in barramundi. S. iniae is a Gram positive bacterium which infects both humans and fish and was first reported in Australia in the 1980s in Queensland, but has rapidly disseminated to other states in Australia (Western Australia, Northern Territory, South Australia). Globally, there appears to be little geographical restriction to the distribution of S. iniae and infection occurs in temperate, sub-tropical and tropical, marine and fresh water fish with no evidence of species specificity. Outbreaks have been reported in North America, Middle East, Europe and Asia-Pacific, including Australia, Indonesia, Malaysia, Korea, China, Taiwan and Japan. Understanding distribution and spread of S. iniae is confounded by a number of factors. Firstly, identification of S. iniae is not straightforward, thus isolates often remain ‘unidentified’, as this bacterium is not included in commercial databases. In other cases it is misidentified as other bacteria such as S.uberis, S. dysgalactiae subsp. equisimilis and S. anginosus. Furthermore, variability in phenotypic traits has led to difficulty in identifying isolates using standard commercial diagnostic kits. Additionally, there is tangible evidence of geographic diversity and endemism with strain variability having been reported from fish isolates in Japan, USA and Israel, and in human isolates from Canada, USA and SE Asia. Understanding strain diversity amongst S. iniae is critically important in terms of managing the disease. Ability to track routes of distribution of the pathogen in imported fish, including ornamentals and food fish has implications for better biosecurity. Perhaps most importantly, strain diversity has been reported as a cause of vaccine failure in trout in Israel and in barramundi in Northern Territory, Australia. To date, very little information exists on strain diversity in S. iniae and no research has been conducted on the diversity amongst Australian isolates within the barramundi industry. The aim of this thesis is to develop reliable methods for identification of differing strains of S. iniae and to investigate antigenic diversity in order to better inform both vaccine design and biosecurity procedures with which to manage this important disease in Australia and globally. To achieve this, a collection of more than 100 isolates from Australia and throughout the world has been created and stored at the University of Queensland. In the first chapter of my thesis, routine confirmatory diagnosis using amplification of the lactate oxidase gene was performed to support biochemical and physiological identification provided by the supplying laboratories and veterinarians. During this initial screen, two important discoveries were made. Firstly, S. iniae isolates can be divided into two groups based on the different sizes of PCR product obtained, 869 bp (now named Type 1) and 921 bp (now named Type 2). This difference was only found in isolates from Northern Territory, Australia. In light of this, identity was further confirmed by the results of partial sequencing of the 16S rRNA gene with the 530F primer and submission to the BLAST server (http://www.ncbi.nlm.nih.gov/BLAST), which returned identities of 100% to S. iniae ATCC 29178. Sequence analysis of the lctO gene in isolates representing both the normal (lctO type 1) and higher molecular weight (lctO type 2) revealed that there is an insertion of 51 bp of repeat sequence in lctO type 2. Apart from the insertion sequence found in the 3' end of the gene in some isolates, three nucleotides in positions 211-213, not previously detected when the gene was described previously, resulted in an inserted valine residue in the translated product from all isolates. I also note an apparent error in the primary sequence and translation of the GenBank sequence (Y07622). This is likely to be due to an inserted C nucleotide at position 1148 at the far 3’ end of the gene sequence (inside the LOX-1, LOX-2 priming region) that has altered the reading frame. This means that the expected PCR product size of 870 bp is incorrect and is actually 869 bp. To determine the phenotypic relevance of the variation in lox gene product size, the lactate oxidase enzyme was extracted from cell lysates and assayed for activity. The two variant genes were each cloned and expressed in E. coli. Lactate oxidase enzyme activity also showed that there were differences in enzyme activity between the two gene products with strains expressing the higher molecular weight enzyme variant exhibiting higher enzyme activity. This suggests that positive selection may apply in favour of the larger gene in situations where lactate is the most readily available carbon source. However, no variation was detected in the lactate permease gene lctP, for any of the strains analysed. Whilst there was no difference in the Minimum Inhibitory Concentration Test (MIC) using different concentration of lactate there were differences detected in the growth rate of QMA0165 and QMA0177. Significant inhibition on growth rate of QMA0165 was detected with a 0.3% and 0.5% of lactate while there was no significant inhibition in QMA0177 with the same concentration. Prediction on three dimensional protein structure using PyMol based on Aerococcus viridans 3-D protein structure showed that there was an additional loop in lctO type 2 which suggested that it might play a role in enhancing enzyme activity of the binding site. The environment in barramundi farms in Northern Territory where the lctO type 2 isolates were isolated has 9 metre tides resulting in water flows in excess of 3km/h. It is likely that the resulting enforced swimming of the fish host has led to selection and maintenance of a gene encoding the higher efficiency enzyme in S. iniae. As diversity has led to reported vaccine failure in Israel, and antigenic diversity has been recorded in Japan and in isolates from the USA, the second data chapter of this thesis explores surface antigenic diversity of Australian S. iniae isolates from barramundi using a whole cell ELISA using a suite of antibodies raised in barramundi against four S. inaie isolates from differing habitats (freshwater and marine) and states (Western Australia and Queensland) in Australia. Forty-one isolates predominantly from farmed fish throughout Australia between 1995 and 2006 were serotyped and compared with reference isolates from the USA and Canada. Multiple serotypes were identified using polyclonal sera raised in barramundi against four different Australian S. iniae isolates i.e. anti QMA0072 (Queensland), anti QMA0074 (Queensland), anti QMA0083 (Western Australia) and anti QMA0087 (Western Australia). Different serotypes were often isolated from the same sites either simultaneously or within short time periods, indicating potential coexistence of multiple isolates in a particular geographic location or habitat. Electrophoretic profiles of whole cell proteins and integral membrane proteins were similar amongst isolates when analysed by SDS- PAGE, regardless of serotype. The results presented here suggest that surface serotypic variability of S. iniae is complex and multifactorial involving capsular carbohydrate and some surface proteins. As raising consistent antiserum in barramundi is almost impossible, and rabbit antisera invariably recognise more epitopes than teleost fish, a more consistent molecular method of typing was investigated in the third data chapter. In this chapter, the whole genome of S. iniae was digested using SmaI and separated using Pulsed Field Gel Electrophoresis (PFGE). Twenty four isolates representing different geographical origin and host were analysed using this method. Reference isolates from dolphins, fish and humans were obtained from the Centers for Disease Control for comparison. PFGE profiles indicated at least 4 distinct groups amongst the Australian isolates, but these did not correlate with surface serotype. Interestingly, whilst there have been no reports of human cases of S. iniae infection in Australia, many of the isolates examined had closely related PFGE profile with reference human isolates from USA and Canada, but were markedly different from the type isolates isolated from dolphins. One of the major difficulties associated with PFGE is between lab variability, hence the requirement for inclusion of large numbers of reference isolates on each gel. Recently, multilocus sequence typing (MLST) has been developed for epidemiological studies in a variety of human pathogens. MLST is based on sequencing of 8 ubiquitous housekeeping genes, genes which evolve slowly, allowing clustering of isolates. As sequencing is consistent between laboratories, results can be posted on a website and compared internationally without requiring transfer of strains overseas. The fourth data chapter in my thesis develops for the first time an MLST scheme for S. iniae. Primers for eight housekeeping genes were designed and annealing temperature for amplification were optimized. The selected housekeeping genes were: adhP (Alcohol dehydrogenase), pheS (Phenylalanyl tRNA syhthetase), atr (Amino acid transporter), glnA (Glutamine synthetase), sdhA (Serine dehydrogenase), glcK (Glucose kinase) and tkt (Transketolase). However, glnA was dropped from the analysis because of the inconsistent PCR product. Thirty seven isolates were selected representing the Australian isolates and other international isolates from United States, Canada, Israel, Thailand, Reunion Island with different hosts i.e. Amazon freshwater dolphin, human, flying fox and different species of fish (Channa striata, Oncorhynchus mykiss and Lates calcarifer). As there is no database available for S. iniae in the MLST database yet, only limited isolates from the global collection that can be analysed with the Australian isolates. The present study found that MLST results are less discriminative when compared to PFGE, but were very useful in pinpointing origin to a particular country, perhaps indicating little transfer of isolates between nations. MLST grouped together Australian, Thailand (QMA0187 and QMA0190), human isolates from Canada and USA regardless the geographic origin (QMA0130, QMA0133 and QMA0137) and also fish isolate from Canada (QMA0139). The similarity of the human isolates with the Australian isolates supporting PFGE results, which had a similar SmaI PFGE profiles to many of the fish isolates from Australia. However, MLST managed to distinguish isolates QMA0140 (dolphin/ USA), QMA0141 (dolphin/ USA), QMA0136 (human/ USA) and other international isolates from Israel (QMA0186 and QMA0188), Reunion Island (QMA0189). Despite the degree of heterogeneity in other methods used (serotyping, PFGE), MLST method showed a high homogeneity amongst S. iniae from Australia, perhaps reflecting the slow evolution of these genes and no accidental import of isolates. During the 12 years of isolates covered by our strain collection, there would appear to have been no evolution of these highly conserved genes within Australia. The variation in serotype within a single Sequence Type showed that there may be frequent horizontal gene transfer, or more rapid evolution of genes involved in synthesis and transport of capsular polysaccharide or other surface features. Moreover, the PFGE results indicate that there is more genetic plasticity in amongst the genome of S. iniae than indicated by then MLST. In order to gain a more discriminative epidemiological perspective of S. iniae, the results presented in this thesis suggest combination of different typing methods such as PFGE and MLST, with the latter providing an accurate means of determining nation of origin of strains (and therefore of great potential for biosecurity purposes) whilst PFGE may provide better discrimination of movement of local isolates within Australia.

Yes / Background: Group B Streptococcus (GBS) is a leading cause of morbidity and mortality in infants in both developed and developing countries. To our knowledge, only a few studies have been reported the clinical features, treatment and outcomes of the GBS disease in China. The severity of neonatal GBS disease in China remains unclear. Population-based surveillance in China is therefore required. Methods: We retrospectively collected data of <3 months old infants with culture-positive GBS in sterile samples from three large urban tertiary hospitals in South China from Jan 2011 to Dec 2014. The GBS isolates and their antibiotic susceptibility were routinely identified in clinical laboratories in participating hospitals. Serotyping and multi-locus sequence typing (MLST) were also conducted for further analysis of the neonatal GBS disease. Results: Total 70 cases of culture-confirmed invasive GBS infection were identified from 127,206 live births born in studying hospitals, giving an overall incidence of 0.55 per 1000 live births (95% confidence interval [CI] 0.44–0.69). They consisted of 49 with early-onset disease (EOD, 0.39 per 1000 live births (95% CI 0.29–0.51)) and 21 with late-onset disease (LOD, 0.17 per 1000 live births (95% CI 0.11–0.25)). The incidence of EOD increased significantly over the studying period. Five infants (4 EOD and 1 LOD) died before discharge giving a mortality rate of 7.1% and five infants (7.1%, 2 EOD and 3 LOD) had neurological sequelae. Within 68 GBS isolates from GBS cases who born in the studying hospitals or elsewhere, serotype III accounted for 77.9%, followed by Ib (14.7%), V (4.4%), and Ia (2.9%). MLST analysis revealed the presence of 13 different sequence types among the 68 GBS isolates and ST-17 was the most frequent sequence type (63.2%). All isolates were susceptible to penicillin, ceftriaxone, vancomycin and linezolid, while 57.4% and 51.5% were resistant to erythromycin and clindamycin, respectively. Conclusions: This study gains the insight into the spectrum of GBS infection in south China which will facilitate the development of the guidance for reasonable antibiotics usage and will provide evidence for the implementation of potential GBS vaccines in the future. / Supported by medical and health science and technology projects of Health and Family Planning Commission of Guangzhou Municipality (grant number 20151A010034) and Guangdong provincial science and technology planning projects (grant number 2014A020212520).

Avian pathogenic Escherichia coli (APEC) causes a wide range of diseases in chickens called colibacillosis, resulting a substantial economic loss to the poultry industry. This dissertation aims at addressing this disease by exploring key virulence-associated genes (VAGs), swarming motility (SM), and multi-locus sequence types (MLST) of E. coli isolates obtained from colibacillosis-infected or asymptomatic commercial hens. Secondly, by classifying the E. coli isolates into different virulence categories based on the presence of five key VAGs [iroN, ompT, hlyF, iutA, and iss]. Finally, by performing embryo lethality assays and experimental infection studies to establish the effect of these VAGs. Our findings showed a significantly higher proportion of E. coli isolates obtained from colibacillosis lesions possessed the ompT gene compared to the isolates of asymptomatic commercial hens. A trend of a higher occurrence of the iutA gene was also observed in the isolates of colibacillosis cases. Based on the presence of all five VAGs, we categorized 87.5% of the isolates obtained from colibacillosis lesions into the virulent category and 64.71% of the isolates obtained from asymptomatic commercial hens into the avirulent category. During the embryo lethality assay, we found an interaction effect of virulence categories and SM on embryo mortality. Motile and hyper-motile isolates of virulent and moderately virulent categories caused significantly higher embryo mortality than the non-motile isolates of the same categories. Isolates of the avirulent category significantly reduced the relative embryo weight of the remaining live embryos. The MLST of the isolates did not have any influence on embryo lethality, or relative embryo weight. Yolk sac retention of the remaining live embryo was unaffected by virulence category, MLST, and SM of the isolates. During the experimental infection studies, we observed higher mortality and lesion scores in layer chicks inoculated intratracheally by virulent isolates compared to avirulent isolates. These two classes of isolates also had a different colonization pattern in the extra-intestinal tissues. The avirulent isolates preferably colonized deeper respiratory tracts such as airsacs whereas, the virulent isolates colonized systemic organs such as the liver. Overall, we expect this dissertation will establish the contribution of five key VAGs on embryo and chick mortality, lesion development, and colonization pattern of E. coli isolates. These findings will facilitate the selection of VAGs for field diagnosis of APEC.

The possibility of identifying single nucleotide polymorphisms (SNPs) that would be useful for rapid bacterial typing was investigated. Neisseria meningitidis was the organism chosen for modelling the approach since informative SNPs could be found amongst the sequence data available for multi-locus sequence typing (MLST) at http://www.mlst.net. The hypothesis tested was that a small number of SNPs located within the seven gene fragments sequenced for MLST provide information equivalent to MLST. Preliminary investigations revealed that a small number of SNPs could be utilised to highly discriminate sequence types (STs) of clinical interest. Laboratory procedures demonstrated that SNP fingerprinting of N. meningitidis isolates is achievable. Further tests showed that laboratory identification of a defining SNP in the genome of isolates was to be a practical method of obtaining relevant typing information. Identification of the most discriminating SNPs amongst the ever-increasing amount of MLST sequence data summoned the need for computer-based assistance. Two methods of SNP selection devised by the author of this thesis were translated into computer-based algorithms by contributing team members. Software for two computer programs was produced. The algorithms facilitate the optimal selection of SNPs useful for (1) distinguishing specific STs and (2) differentiating non-specific STs. Current input information can be obtained from the MLST database and consequently the programs can be applied to any bacterial species for which MLST data have been entered. The two algorithms for the selection of SNPs were designed to serve contrasting purposes. The first of these was to determine the ST identity of isolates from an outbreak of disease. In this case, isolates would be tested for their membership to any of the STs known to be associated with disease. It was shown that one SNP per ST could distinguish each of four hyperinvasive STs of N. meningitidis from between 92.5% and 97.5% of all other STs. With two SNPs per ST, between 96.7% and 99.0% discrimination is achieved. The SNPs were selected from MLST loci with the assistance of the first algorithm which scores SNPs according to the number of base mismatches in a sequence alignment between an allele of an ST of interest and alleles belonging to all other STs at a specified locus. The second purpose was to determine whether or not isolates from different sources belong to the same ST, regardless of their actual ST identity. It was shown that with seven SNPs, four sample STs of N. meningitidis could, on average, be discriminated from 97.1% of all other STs. The SNPs were selected with the aid of the second algorithm which scores SNPs at MLST loci for the relative frequency of each nucleotide base in a sequence alignment as a measure of the extent of their polymorphism. A third algorithm for selecting SNPs has been discussed. By altering the method of scoring SNPs, it is possible to overcome the limitations inherent in the two algorithms that were utilised for finding SNPs. In addition, the third approach caters for finding SNPs that distinguish members of a complex from non-members.

Předmětem této diplomové práce je vytvoření databáze známých sekvenčních a melt typů patogenních bakterií a nástroje pro správu databáze. Metoda popisovaná v této práci je poměrně nová technika typizace patogenních bakterií založena na překladu sekvenčních typů na příslušející melt typ a využívá k tomu převodní klíč, který byl vytvořen ve spolupráci s Centrem molekulární biologie a genové terapie Interní hematologické a onkologické kliniky Fakultní nemocnice Brno. Obsahem práce je vytvoření prostoru na databázovém serveru, načtení potřebných dat, aplikace převodního klíče, vytvoření GUI, vytvoření dalších vhodných ošetření a rozšíření, testování a následná analýza výsledků. V první kapitole jsou diskutovány nejznámější metody bakteriální typizace, další kapitola je pak věnována server-client aplikacím a databázovým nástrojům. Třetí kapitola popisuje implementaci databáze na server a čtvrtá kapitola stručně shrnuje všechny funkce programu. V poslední kapitole je pak popsána analýza vylepšení převodního klíče, které získalo pracovní název půlené alely.

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