För att utreda anledningen till bland annat otit och sinuit tas prov från nasofarynx, som enligt nuvarande metod utodlas på två separata plattor med blod- och hematinagar för att identifiera patogena luftvägsbakterier. Diagnostiska antibiotikadiskar används för att förenkla differentiering mellan olika bakterier. Odling på blodagar med optochin-disk är en tillförlitlig metod för identifiering av Streptococcus pneumoniae. Metoden är tidskrävande och agglutinationstest är ett alternativ för mer tidseffektiv artidentifiering. Syftet med arbetet var dels att validera en ny provsättningsmetod för nasofarynx-prov samt att utvärdera ett nytt agglutinationstest för artidentifiering av S. pneumoniae. För att validera provsättningsmetoden jämfördes den tidigare metoden med en ny där analyserna kombineras på samma platta (biplate) (N=165). För validering av nytt agglutinationstest inokulerades hästblod och bakterieisolat i blododlingsflaskor. Agglutinationstest utfördes därefter med två kommersiella kit, Dryspot, som idag används på laboratoriet, och Immulex. Fynden från nasofarynx efter odling på nya kombinerade plattor bestod av S. pneumoniae, Haemophilus influenzae och Moraxella catarrhalis. Överensstämmelsen mellan odlingsmetoderna var god för nasofarynxodlingar. Vid mätning av bakteriefri zon kring optochin-disk erhölls 18 – 31 mm för biplates respektive 16 – 24 mm för originalmetoden med odling på två separata plattor. För två prov var den bakteriefria zonen på biplates ej mätbar. Vid agglutinationstest för identifiering av S. pneumoniae erhölls agglutination inom respektive tidsgräns för samtliga referensisolat. Ett α-streptokock- och ett enterokock-isolat agglutinerade vid test med Immulex. Slutsatsen av studien är att biplates bör fungera som rutinmetod för odling av nasofarynxprov. Däremot verkar agglutinationstest med Immulex vara mindre pålitligt än Dryspot som används idag. / To investigate the cause of otitis and sinusitis, samples are taken from nasopharynx. To find airway pathogens samples are cultivated on blood agar and hematin agar, for further differentiation diagnostic antibiotic disks are used. Cultivation on blood agar with optochin disks is a reliable method to identify Streptococcus pneumoniae, although it is time-consuming. Agglutination test is a rapid method for identification of Streptococcus pneumoniae. The aim of this study was to validate a new method for cultivation of nasopharynx-samples. Moreover a new agglutination test for identification of S. pneumoniae was evaluated. To validate the new method of cultivation, the original method was compared with the new where blood and hematin agar are combined on the same plate (biplate) (N=165). To validate the new agglutination test, blood culture bottles were inoculated with blood and suspensions of relevant bacterial species. Agglutination tests were performed using Dryspot and Immulex commercial kits. Bacterial findings from nasopharynx after cultivation on the new combined plates included S. pneumoniae, Haemophilus influenzae and Moraxella catarrhalis. The correlation between the methods was good for nasopharynx-cultivations. The inhibitory zones around the optochin disk were 18 – 31 mm for biplates and 16 – 24 mm for the original method. All S. pneumoniae agglutinated within the time limits when agglutination test were performed. One α-Streptococcus and one Enterococcus agglutinated when tests were performed with Immulex, hence giving false positive results. In conclusion, the new cultivation method of nasopharynx samples proved functional.  Agglutination test with the kit presently used, Dryspot, performed better than Immulex.

<p>Tuberkulos (tbc) är en luftburen droppsmitta orsakad av mykobakterium tuberkulosis. Tbc är den sjukdom som efter AIDS orsakar flest dödsfall, trots att botande behandling finns. Behandlingen är krävande för den tbc-smittade att genomgå och bygger på en kombination av en rad antibiotika som måste intas under minst sex månader. Ett avvikande i behandlingen kan resultera i att mykobakterium tuberkulosis blir resistent mot de ordinerade antibiotika. Följsamhet av långtidsbehandlingar som tbc-behandling graderas till 50 %. Syftet med litteraturstudien var att ur ett globalt perspektiv beskriva hur sjuksköterskan kan påverka följsamhet vid tbc-behandling i syfte att minska resistensutvecklingen av mykobakterium tuberkulosis. Studien genomfördes som en litteraturstudie där 12 vetenskapliga artiklar granskades och analyserades. Resultatet visar tydligt att specifika faktorer påverkar följsamhet och därigenom resistensutvecklingen. Faktorerna innefattar patientundervisning, behandlingsstrategier, omgivningens påverkan och stöd.  Undervisningen resulterar i att patienten får ökad förståelse för behandlingen. För att minska stigmatiseringen och det lidande den innebär för den tbc-smittade är även omgivningen i behov av ökad kunskap och information om tbc. Ett flertal studier visar att DOTS-strategin är betydelsefull för ökad följsamhet vid antituberkulos behandling. Litteraturstudien medför ett förslag om att sjuksköterskeprogrammet ska öka fokuseringen på följsamhet vid läkemedelsanvändning. Sjuksköterskan är i behov av att redan under grundutbildningen få kunskap om ansvarsfull antibiotikahantering som leder till en följsamhetsomtanke.</p> / <p>Tuberculosis (TB) is an airborne droplet infection caused by mycobacterium tuberculosis. TB is the disease after AIDS that is most deadly, even though curative treatment exists. The treatment is demanding for the TB-infected to undergo and consists of a combination of a number of antibiotics that must be administered for at least six months. A dissenting in anti-tuberculosis treatment might result in mycobacterium tuberculosis strains that are resistant to antibiotics. As adherence to long-term treatment is graded at a low percentage (50 %) the aim of the literature study was from a global perspective to develop a working-strategy for nurses that promote compliance in TB-treatment in order to reduce resistance development of mycobacterium tuberculosis. The study was conducted as a literature study where 12 research articles were reviewed and analyzed. The results describe specific factors that are essential to compliance. These factors comprise patient education, treatment strategies, social influences and support. As knowledge gives the patient a better understanding for the treatment it provokes compliance. The social environment of the TB-infected patient demands increased knowledge in order to reduce stigma. Several studies show that the DOTS strategy is important for increasing compliance in anti-tuberculosis treatment. The literature study results in a proposal for the nursing program to focus more on compliance in taking medication. The nursing program’s attendants need to gain knowledge about prudent antibiotic treatment that leads to a compliance concern.</p>

<p>Streptococcus agalactiae, also designated group B streptococcus (GBS), is a Gram-positive coccus, and it is an important pathogen that causes invasive disease in neonates, pregnant adults, and non-pregnant adults with predisposing conditions. The group II intron GBSi1 is one of the major mobile genetic elements identified in S. agalactiae. The aim of this thesis was to characterize the GBSi1 distribution pattern, the population structure, and the influence of serotype- and clone-specific properties on the invasive capacity among clinical invasive and non-invasive isolates of S. agalactiae.</p><p>Two additional copies of GBSi1 were identified at sites different from the primarily identified scpB-lmb locus. The distribution of GBSi1 was uneven among different serotypes. Three intron copies were only found in isolates of serotype III, and these targeted all the three identified gene loci. In contrast, a single copy of GBSi1 was found in isolates of serotype II and V and only located at the scpB-lmb locus. Furthermore, at the 5′ flanking region of the scpB-lmb gene locus, a novel 2.1 kb DNA fragment with plasmid features was identified only in intron carrying isolates. This may suggest that GBSi1 once was brought into the S. agalactiae genome by an integrated plasmid.</p><p>Multilocus sequence typing was used to characterize totally 314 invasive and non-invasive S. agalactiae isolates collected in Northern and Western Sweden from the years 1988 to 2004. Five major genetic lineages (clonal complexes) were identified among both invasive and non-invasive isolates, including serotype Ia, Ib, and II to V, indicating a clonal population structure of S. agalactiae isolates. A number of genetically highly related isolates were found to express different capsular types, suggesting that capsule switching occurs rather frequently between isolates. Furthermore, non-invasive isolates belonging to the same clonal complexes displayed more heterogeneity in capsule expression as well as in the distribution patterns of mobile genetic elements than invasive isolates. This indicates that less variability is allowed in a highly selective environment such as the blood. All major clonal complexes and serotypes caused invasive disease, although their ability to do so varied greatly. CC17 was significantly associated with neonatal invasive disease; whereas CC19 was equally common among isolates from adult and neonatal disease, despite that both CC17 and CC19 expressed capsular type III. This striking difference seen between CC17 and CC19 suggests that clonal complex associated properties, in addition to capsular type, play important roles in the virulence of S. agalactiae. CC1, a new emerging clone since early 1990s, has caused substantial amount of disease among adults. In addition, mutually exclusive distribution of mobile elements GBSi1 and IS1548 was seen, and they were shown to constitute genetic markers for serotype III CC17 and CC19 isolates, respectively.</p>

Streptococcus agalactiae, also designated group B streptococcus (GBS), is a Gram-positive coccus, and it is an important pathogen that causes invasive disease in neonates, pregnant adults, and non-pregnant adults with predisposing conditions. The group II intron GBSi1 is one of the major mobile genetic elements identified in S. agalactiae. The aim of this thesis was to characterize the GBSi1 distribution pattern, the population structure, and the influence of serotype- and clone-specific properties on the invasive capacity among clinical invasive and non-invasive isolates of S. agalactiae. Two additional copies of GBSi1 were identified at sites different from the primarily identified scpB-lmb locus. The distribution of GBSi1 was uneven among different serotypes. Three intron copies were only found in isolates of serotype III, and these targeted all the three identified gene loci. In contrast, a single copy of GBSi1 was found in isolates of serotype II and V and only located at the scpB-lmb locus. Furthermore, at the 5′ flanking region of the scpB-lmb gene locus, a novel 2.1 kb DNA fragment with plasmid features was identified only in intron carrying isolates. This may suggest that GBSi1 once was brought into the S. agalactiae genome by an integrated plasmid. Multilocus sequence typing was used to characterize totally 314 invasive and non-invasive S. agalactiae isolates collected in Northern and Western Sweden from the years 1988 to 2004. Five major genetic lineages (clonal complexes) were identified among both invasive and non-invasive isolates, including serotype Ia, Ib, and II to V, indicating a clonal population structure of S. agalactiae isolates. A number of genetically highly related isolates were found to express different capsular types, suggesting that capsule switching occurs rather frequently between isolates. Furthermore, non-invasive isolates belonging to the same clonal complexes displayed more heterogeneity in capsule expression as well as in the distribution patterns of mobile genetic elements than invasive isolates. This indicates that less variability is allowed in a highly selective environment such as the blood. All major clonal complexes and serotypes caused invasive disease, although their ability to do so varied greatly. CC17 was significantly associated with neonatal invasive disease; whereas CC19 was equally common among isolates from adult and neonatal disease, despite that both CC17 and CC19 expressed capsular type III. This striking difference seen between CC17 and CC19 suggests that clonal complex associated properties, in addition to capsular type, play important roles in the virulence of S. agalactiae. CC1, a new emerging clone since early 1990s, has caused substantial amount of disease among adults. In addition, mutually exclusive distribution of mobile elements GBSi1 and IS1548 was seen, and they were shown to constitute genetic markers for serotype III CC17 and CC19 isolates, respectively.

Bacterial chromosomes are highly dynamic, continuously changing with respect to gene content and size via a number of processes, including deletions that result in gene loss. How deletions form and at what rates has been the focus of this thesis. In paper II we investigated how chromosomal location affects chromosomal deletion rates in S. typhimurium. Deletion rates varied more than 100-fold between different chromosomal locations and some large deletions significantly increased the exponential growth rate of the cells. Our results suggest that the chromosome is heterogeneous with respect to deletion rates and that deletions may be genetically fixed as a consequence of natural selection rather than by drift or mutational biases. In paper I we examined in a laboratory setting how rapidly reductive evolution, i.e. gene loss, could occur. Using a serial passage approach, we showed that extensive genome reduction potentially could occur on a very short evolutionary time scale. For most deletions we observed little or no homology at the deletion endpoints, indicating that spontaneous deletions often form through a RecA independent process. In paper III we examined further how large spontaneous deletions form and, unexpectedly, showed that 90% of all spontaneous chromosomal deletions required error-prone translesion DNA polymerases for their formation. We propose that the translesion polymerases stimulate deletion formation by allowing extension of misaligned single-strand DNA ends. In paper IV we investigated how the translesion DNA polymerase Pol IV, RpoS and different types of stresses affect mutation rates in bacteria. Derepression of the LexA regulon caused a small to moderate increase in mutation rates that was fully dependent on functional endonucleases but only partly dependent on translesion DNA polymerases. RpoS levels and growth stresses had only minor effects on mutation rates. Thus, mutation rates appear very robust and are only weakly affected by growth conditions and induction of translesion polymerases and RpoS.

Antibiotic resistance challenges the practice and development of modern medicine. The aim of this thesis was to test the hypothesis that antibiotic resistance is reversible once the selection pressure of an antibiotic is removed. A decisive reduction (85%) in trimethoprim and trimethoprim-sulfamethoxazole over 24 months in Kronoberg County, Sweden, is described. The resistance baseline prior to the intervention and the effects of the intervention on resistance levels, trimethoprim resistance genes (dfr-genes) and population structure in Escherichia coli were studied. The effects of different algorithms for excluding patient duplicate isolates were small but systematic. An identical algorithm was used throughout. The drastic decrease in the use of trimethoprim containing drugs did not result in a corresponding decrease in trimethoprim resistance. This was true both for total trimethoprim resistance and for trimethoprim mono-resistance. The distributions of E. coli phenotypes, dfr-genes and E. coli sequence types were stable. The marginal effect on resistance rates was explained by a low fitness cost of trimethoprim resistance observed in vitro and the high levels of associated resistance in trimethoprim resistant isolates. Trimethoprim resistance was, although widespread in the E. coli population, more common in certain E. coli sequence types. The distributions of dfr-genes were different in E. coli and K. pneumoniae and between different E. coli sequence types. These results indicate mechanisms related to the genetic back-bone of E coli to be important for the acquisition and persistence of antibiotic resistance. The findings of this thesis indicates that, at least for some classes of antibiotics, we may have overestimated the usefulness of a strategy for reversing antimicrobial resistance based on the fitness cost of resistance. We have equally underestimated the conserving effects of associated resistance. The stability of the dfr-genes and E. coli sequence types underlines the importance of associated resistance and successful lineages in the spread and maintenance of antibiotic resistance in E. coli.

Antibiotic resistance is a growing problem on a global scale. Increasing numbers of bacteria resistant toward one or multiple antibiotics could return us to the high mortality rates for infectious diseases of the pre-antibiotic era. The need for development of new classes of antibiotics is great as is increased understanding of the mechanisms underlying the development of antibiotic resistance. We have investigated the emergence of resistance to peptide deformylase inhibitors, a new class of antibiotics that target bacterial protein synthesis. The fitness of resistant mutants as well as their propensity to acquire secondary compensatory mutations was assessed in order to gain some insight into the potential clinical risk of resistance development. Most of this work was done in the bacterium Salmonella typhimurium, due to the availability of excellent genetic tools to study these phenomena. In addition, we have studied the bacterium Staphylococcus aureus as peptide deformylase inhibitors have been shown to have the greatest effect on Gram-positive organisms. In the course of this work we also examined the mechanistic aspects of translation initiation. Using a cell-free in vitro translation system we studied the effects of various components on translation initiation. These results have been combined with results obtained from resistant and compensated bacterial strains in vivo to gain new insights into the mechanisms of translation initiation.

Enterobacteriaceae belong to the normal enteric flora in humans and may cause infections. Escherichia coli is the leading urinary tract pathogen with septicaemic potential, whereas Klebsiella pneumoniae causes opportunistic infections and often outbreaks in hospital settings. Beta-lactams are the first choice for treatment of infections caused by Enterobacteriaceae, and might be destroyed by extended-spectrum beta-lactamases, ESBLs. ESBLs hydrolyse all beta-lactams except cephamycin and carbapenems, and constitute a large heterogeneous group of enzymes with different origins. The phenotypic and molecular characteristics of a K. pneumoniae strain causing a major outbreak at Uppsala University Hospital between 2005 and 2008 were described. The strain was multiresistant and produced CTM-M-15, a common ESBL type in Europe. Due to the lack of obvious epidemiological links between patients, a case-control study was performed, which identified risk factors for the acquisition of the outbreak strain in urine cultures. The complex chain of transmission facilitated by patient overcrowding and the interventions applied to curb the outbreak, was revealed in the subsequent study. In the final study, the genetic background of the observed increase in ESBL-producing E. coli isolates during the K. pneumoniae outbreak was explored. The utility of six typing methods in epidemiological investigations of a local outbreak with ESBL-producing E. coli was compared. The increase of ESBL-producing E. coli isolates was not secondary to the K. pneumoniae outbreak. Twentytwo per cent belonged to the epidemic O25b-ST131 clone and only a limited number of infections were caused by nosocomial transmission. ESBL-producing Enterobacteriaceae are a challenge to clinical microbiology laboratories and infection control teams. To investigate their dissemination, typing methods need to be continuously adapted to the current situation. Proper hand disinfection and structural key problems such as over-crowding, under-staffing, lack of single rooms and bathrooms must be adressed to limit transmission.

The study of bacterial evolution is fundamental for addressing current problems of antibiotic resistance and emerging infectious diseases and lays a solid foundation for successful and rational design in biotechnology and synthetic biology. The main aim of this thesis is to test evolutionary hypotheses, largely based on theoretical considerations and sequence analysis, by designing scenarios in a laboratory setting to obtain experimental data. Paper I examines how genomic GC-content can be reduced following a change in mutation rate and spectrum. Transcription-related biases in mutation location were found, but no replicative bias was detected. Paper II explores the distribution of fitness effects of random substitutions in two ribosomal protein genes using a highly sensitive fitness assay. The substitutions had a weakly deleterious effect, with low frequencies of both neutral and inactivating mutations. The surprising finding that synonymous and non-synonymous substitutions have very similar distribution of fitness effects suggests that, at least for these genes, fitness constraints are present mainly on the level of mRNA instead of protein. Paper III examines selective barriers to inter-species gene transfer by constructing mutants with a native gene replaced by an orthologue from another species. Results suggest that the fitness costs of these gene replacements are large enough to provide a barrier to this kind of horizontal gene transfer in nature. The paper also examines possible compensatory mechanisms that can reduce the cost of the poorly functioning alien genes and found that gene amplification acts as a first step to improve the selective contribution after transfer. Paper IV investigates the fitness constraints on horizontal gene transfer by inserting DNA from other species into the Salmonella chromosome. Results suggest that insertion of foreign DNA often is neutral and the manuscript provides new experimental data for theoretical analysis of interspecies genome variation and horizontal gene transfer between species.

Chlamydia trachomatis is an obligate intracellular bacterium of major human health concern, causing urogential chlamydia infections, lymphogranuloma venereum (LGV) and trachoma. Chlamydia is one of the most common sexually transmitted infections worldwide and can cause infertility. In the first four papers described herein we used a high resolution multilocus sequence typing (MLST) system to investigate the epidemiology of C. trachomatis, and showed that MLST is superior to conventional ompA genotyping with respect to resolution. In the fifth paper we simplified the methodology by developing and validating a multilocus typing (MLT) DNA microarray based on the MLST system. In more detail, MLST analysis of consecutive specimens from 2006 in Örebro County in Sweden, and comparison to specimens from 1999-2000, showed that the new variant C. trachomatis (nvCT) is monoclonal and likely has appeared in recent years. MLST analysis of LGV specimens from men who have sex with men (MSM) showed that the increase of LGV in Europe in the last decade indeed was a clonal outbreak, contrary to the USA where LGV might have been present all along. In the third paper, clinical symptoms could not be correlated with the MLST genotypes, suggesting, together with the combined results of all previous studies, that bacterial factors, if important, need to be understood in the context of host factors. MLST analysis of specimens from a high incidence C. trachomatis area in North Norway revealed interesting epidemiological details concerning unusual genetic variants, the nvCT and MSM, but found no significant difference in genetic diversity compared to two other geographic areas in Norway. Lastly, we developed a MLT array that provides high resolution while being rapid and cost-effective, which makes it an interesting alternative for C. trachomatis genotyping. In conclusion, the MLST system and the MLT array have proven to be useful tools and should now be applied in further investigations to improve our understanding of C. trachomatis epidemiology.