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Extra-intestinal pathogenic Escherichia coli (ExPEC) are a significant cause of urinary tract infections and bacteraemia in the UK and around the world. These E. coli primarily belong to phylogenetic groups B2 and D, with the clones ST131, ST127, ST95, ST73 and ST69 responsible for the majority of these infections. In the UK, studies of ExPEC have focused on isolates from the North of England, ST131 strains and ExPEC that possess extended-spectrum beta-lactamase (ESBL) enzymes. Therefore, very little is understood about the UK ExPEC population as a whole, the breadth of virulence factors contributing to these infections and the differences between urinary and bloodstream-derived ExPEC. In this study ST131 was more frequently detected in bloodstream isolates and ST95 was most prevalent in urinary isolates. Comparative virulence of the major clones in the Galleria mellonella infection model revealed ST131 isolates to effect the highest mortality, although serogroup O6, which is linked with ST73, was also associated with high mortality, potentially explaining the success of ST73-O6 in bacteraemia. Analysis of virulence factors identified pap, afa/dra and kpsMTII as important determinants in isolates causing urosepsis and those of ST131, while fyuA and fimH were distinctly lacking, demonstrating their role as colonisation factors rather than virulence factors. Although these findings are important, with appropriate treatment of urinary tract infections they can become redundant, as ExPEC would be eradicated before causing a severe infection such as bacteraemia or urosepsis. In urinary isolates, resistance to trimethoprim approached 50% and ampicillin resistance was >70%, while ST131 isolates as a whole demonstrated ciprofloxacin and trimethoprim resistance >50%. Together these indicate that empirical UTI guidelines need to be revisited, to prevent recurrence of infection and ascension to the kidneys and bloodstream. In addition, data from this study can be used to develop a point-of-care test to detect ST131, to guide appropriate treatment, without the delay associated with referring a urine specimen for microbiological investigation.

Staphylococcus aureus (S. aureus) is a bacterium that commonly colonises the skin and nares of around one third of otherwise healthy individuals. While colonisation is benign, S. aureus can cross skin and mucosal barriers to cause infections that manifest as clinical disease. Clinical outcomes are diverse and range from mild, non-complicated and often self-limiting skin and soft tissue infections (including boils, abscesses and cellulitis) to more severe and life-threatening conditions including pneumonia, toxic shock syndrome and bacteraemia. Medication isn’t always needed for mild S. aureus infections as often they resolve with time but, for severe or persistent cases, antimicrobial treatment is generally required. Following decades of widespread and intensive usage of topical, enteral and parenteral antimicrobials to treat S. aureus infections; AMR has become an established and ubiquitous problem in the treatment of infections caused by this microorganism, especially when in the methicillin resistant form (i.e. MRSA). The aim of this thesis was to examine aspects of S. aureus epidemiology (including MRSA and methicillin-sensitive S. aureus (MSSA)) in Scotland using statistical methods and data from several large public health databases. More specifically this involved: descriptions of spatial and temporal trends of morbidity and mortality; comparisons of epidemiological and molecular attributes (including antimicrobial resistance) of (1) MSSA and MRSA, and (2) the dominant clones of MRSA (i.e. EMRSA-15 and EMRSA-16); descriptions of spatial and temporal trends of antimicrobial prescribing in primary and secondary care and any associations between prescribing rates and MRSA antimicrobial resistance; and carrying out a hospital-level risk factor analysis of MRSA, testing hypotheses that hospital size, hospital connectivity (through shared transfer patients) and hospital category have an effect on hospital-level incidences of MRSA in mainland Scottish hospitals. Results showed that total S .aureus bacteraemia and MRSA bacteraemia in Scotland statistically declined over time (p < 0.0001), but MSSA bacteraemia did not (p > 0.05). While combined mortality rates (i.e. all MSSA deaths (both primary and secondary cause), or all MRSA deaths (both primary and secondary cause)) mirror these findings; case-fatality ratios (CFR) show no declines over time for either MRSA or MSSA. Results also show that several epidemiological factors point towards a predominant community source for MSSA isolates (i.e. outside healthcare) and hospital source for MRSA. Evidence for this included: (1) the lack of resistance genes in the MSSA population, (2) MRSA was more associated with long-term care and high-risk patients in the specialties care of the elderly, high dependency units/intensive care units (HDU/ICU), and surgery and conversely MSSA with specialties that commonly served outpatients, and (3) the abundance of non-EMRSA-15/non- EMRSA-16 ‘other’ clones in the MSSA population as compared with the hospital-associated CC22 (EMRSA-15) and CC30 (EMRSA-16) clones. EMRSA-15 was by far the most dominant MRSA clone in Scotland with EMRSA-16 declining significantly and non-EMRSA-15/non-EMRSA-16 clones causing an increasing number of infections (over the time period 2003-2013). EMRSA-16 was resistant to a larger number of antimicrobials than EMRSA-15, typically 9 versus 5, and while resistance varied for EMRSA-16 over the study period, resistance remained stable for EMRSA-15. There was little difference between clinical and screening MRSA isolates. Analyses of antimicrobial prescribing showed that prescribing rates of several drugs increased over time (2003-2013). Prescribing was far higher in primary care settings than in secondary care, although this differed between antimicrobials. Significant positive associations between prescribing and resistance rates were found for gentamicin (pr - p<0.0001, se - p<0.0001) and trimethoprim (pr - p<0.01, se - p<0.0001) in both primary (pr) and secondary (se) care, and clindamycin (p<0.0001) in primary care only. Finally, in Scotland there is a threshold of connectivity above which the majority of hospitals, regardless of size, are positive for MRSA. Higher levels of MRSA are associated with the large, highly connected teaching hospitals with high ratios of patients to domestic staff. While there were a number of data limitations, this body of work provides a better understanding of the epidemiology of S. aureus including MRSA in Scotland.

Thesis (MScMedSc (Pathology. Medical Microbiology))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: S. aureus causes serious infections in the hospital and community settings. The rate of MRSA infections are rapidly increasing worldwide. Currently, at Tygerberg hospital, approximately a third of S. aureus isolates are MRSA. This was the first epidemiological study of S. aureus conducted at Tygerberg Hospital that included prospective clinical data on patients with S. aureus bacteraemia together with spa typing of strains and the detection of the mecA and pvl genes in a multiplex PCR. Clonal cluster groups of S. aureus isolates were obtained by BURP analysis and compared to international important clones. The molecular epidemiology of hospital acquired (HA), health-care associated (HCA) and community acquired (CA) S. aureus bacteraemic strains at this hospital was examined. Lastly, repeat isolates of patients were collected to analyse any possible organism-related factors associated with persistent and recurrent bacteraemia. We investigated a total number of 113 S. aureus strains from 104 patients (70% MSSA, 30% MRSA). Repeat strains consisted of nine isolates (from 5 patients). All isolates were obtained from blood cultures collected during the period March 2008 to May 2009. Phenotypic and genotypic detection of methicillin resistance correlated well. According to the literature, most CA-MRSA strains are distinguishable from HA-MRSA strains based upon the presence of the PVL toxin. However, no CA-MRSA was detected in our study, therefore the association between HA-MRSA versus CA-MRSA strains could not be analysed. In this study, CA-MSSA was identified in 22% of all MSSA isolates versus 0% CA-MRSA. PVL positive strains were found in 22.7% of all MSSA isolates with no detection in MRSA isolates. It was noted that MRSA strains clustered in spa CC-701 and CC-012, whereas CC-002 only contained MSSA strains. Likewise HA-strains representing the majority of MRSA strains also clustered in spa CC-701 and CC-012. Forty nine spa types were identified in 89.3% of all isolates, whereas 9.7% of these strains were non-typeable. Five novel spa types were revealed. We detected a diverse number of spa-types that correlated to international clones. The most predominant spa type found in our setting was t037 (only in MRSA), followed by t891. According to the literature, t037 is associated to the Brazilian/Hungarian clone (SCCmec type III; ST 239). Our findings, as well as other South African studies, indicate that t037 has been identified in clinical strains from numerous provinces in South Africa. Interestingly, all isolates from spa type t891 were PVL positive MSSA. Bacteraemia cases were predominantly related to catheter sepsis, followed by skin and soft tissue infections (SSTI). Only one persistent bacteraemia case was identified related to a HA-SSTI. Recurrent bacteraemia cases were found in patients on dialysis for chronic renal failure and in burns patients related to intravascular catheter infections. The local epidemiology of S. aureus and the prevalence rate of different strains are important to investigate. The information provided contributes to the epidemiology of staphylococcal strains causing bacteraemia in our setting. These insights are useful for optimal diagnostic and therapeutic measures. The techniques developed can be used to identify outbreaks and recurrent infections. / AFRIKAANSE OPSOMMING: S. aureus veroorsaak ernstige infeksies in die hospitaalomgewing en in die gemeenskap. Wêreldwyd, neem metisillien-weerstandige S. aureus (MRSA) infeksies vinnig toe. Huidiglik by Tygerberg hospitaal is ongeveer ‘n derde van S. aureus isolate MRSA. Hierdie is die eerste epidemiologiese studie by Tygerberg hospitaal wat prospektiewe kliniese data van pasiënte met S. aureus bakteremie saam met spa tipering en aantoning van die mecA en pvl gene in ‘n multipleks PKR insluit. Klonale groepe (spa-CC) van MRSA en MSSA isolate is deur BURP analise verkry, en vergelyk met internasionaal belangrike klone. Die molekulêre epidemiologie van hospitaalverworwe (HA), gesondheidsorgverworwe (HCA) en gemeenskapsverworwe (CA) S. aureus bakteremie by hierdie hospitaal is ondersoek. Laastens, oorspronklike en daaropvolgende herhaal isolate is gekollekteer om moontlike organisme- faktore geassosieerd met persisterende en herhalende bakteremiese episodes te analiseer. Ons het in totaal 113 S. aureus isolate van 104 pasiënte ondersoek (70% MSSA, 30% MRSA). Nege isolate (van 5 pasiënte) was herhaal isolate. Alle isolate was afkomstig vanaf bloedkulture wat gedurende die periode Maart 2008 tot Mei 2009 gekollekteer is. Fenotipiese en genotipiese aantoning van metisillien weerstandigheid het goed gekorreleer. Volgens die literatuur kan die meeste CA-MRSA isolate van HA-MRSA isolate onderskei word op grond van die teenwoordigheid van die PVL toksien. Geen CA-MRSA is egter in ons studie gevind nie, dus kon die assosiasie tussen HA-MRSA en CA-MRSA isolate nie ondersoek word nie. CA-MSSA was in 22% van alle MSSA geidentifiseer teenoor 0% CA-MRSA. PVL is in MSSA isolate gevind (22.7% van alle MSSA) maar glad nie in MRSA nie. Dit is opgemerk dat MRSA isolate hoofsaaklik in spa CC 701 en CC-012 kloongroepe voorkom, teenoor kloongroep CC-002 wat slegs MSSA isolate bevat het. Soortgelyk het HA-isolate wat die meerderheid van MRSA isolate verteenwoordig het ook in kloongroepe 1 & 2 gegroepeer. Nege-en-veertig spa tipes is geïdentifiseer in 89.3% of alle isolate en 9.7% was nie-tipeerbaar. Vyf nuwe spa tipes is getoon. Ons het ‘n diverse aantal spa-tipes geïdentifiseer wat met internasionale klone gekorreleer het. Die mees dominante spa tipe in ons omgewing was t037 (slegs in MRSA), gevolg deur t891. Volgens die literatuur word t037 met die Brasiliaanse/Hongaarse kloon geassosieer (SCCmec tipe III; ST 239). Ons bevindings, asook ander Suid Afrikaanse studies, dui aan dat t037 in kliniese isolate vanaf talle provinsies in Suid-Afrika aangetoon is. Van belang is dat al die isolate van spa tipe t891 MSSA en PVL positief was. Bakteremiese gevalle was hoofsaaklik geassosieer met kateter-sepsis, gevolg deur vel en sagteweefsel infeksies (SSTI). Slegs een persisterende bakteremiese geval was geïdentifiseer geassosieer met HA-SSTI. Herhalende bakteremiese episodes is in pasiënte op dialise vir kroniese nierversaking en in brandwonde pasiënte met intra-vaskulêre kateter infeksies aangetoon. Die lokale epidemiologie van S. aureus en die prevalensie koers van verskillende stamme is van belang. Hierdie inligting dra by tot kennis van die epidemiologie van stafilokokkale stamme wat in ons omgewing bakteremie veroorsaak. Hierdie insigte is nuttig vir optimale diagnostiese en terapeutiese riglyne. Die tegnieke wat ontwikkel is, kan gebruik word om uitbrake en herhalende infeksies te identifiseer.

ABSTRACT Introduction Invasive pneumococcal disease (IPD) is an important cause of morbidity and mortality in many parts of the world. It is estimated that pneumococcal disease causes more than one million-childhood deaths every year and the burden of disease is greater in developing countries. The main aim of this study was to analyze risk factors associated with mortality in invasive pneumococcal disease in all ages in South Africa. Materials and Methods We performed an analytical cross-sectional analysis of secondary data from national population-based surveillance for invasive Streptococcus pneumoniae infection in South Africa. The study period was 1 January 2003 to 31 December 2005, and the mortality analysis used a subset of laboratory-confirmed cases who had a completed case report form and available mortality data. Multiple logistic regression models were constructed to identify risk factors significantly associated with the increased risk of death in patients with invasive pneumococcal disease. Separate models were used to evaluate risk factors for death in patients with meningitis and those with other IPD. Results There were 1154 (24%) cases of Streptococcus pneumoniae meningitis and 3736 (76%) cases of other invasive disease. The overall case fatality rate was 1360/4890 (27.8%) of which 911 (67%) patients died within 2 days of admission and 449 (33%) died between 2 days and 30 days of admission. Variables associated with mortality in a logistic regression analysis of all IPD patients included meningitis (OR 2.8, CI 1.9 – 3.9, P=<0.001), HIV-infection (OR 2.8, CI 1.6 – 4.6, P=<0.001), acute severe illness measured by Pitt bacteraemia score >=4 (OR 4.7, CI 2.8 – 7.7, P=<0.001) and prior antibiotic use within 2 months before first positive culture (OR 2.1, CI 1.4 – 3.1, P=<0.001). In addition to this children less than 1 year and adults ≥45 years were more likely to die compared to other age groups. Patients from Western Cape Province were significantly less likely to die (OR 0.27, CI 0.15 – 0.50, P=<0.001) compared to other provinces. Amongst HIV-positive patients severe immunosuppression (low CD4+ count) was a risk factor for death. Risk factors for death were similar in patients with other IPD and meningitis except for HIV which was associated with death in the meningitis group but not in the other IPD group. Antibiotic resistance and vaccine-serotype disease were not associated with increased risk of death. Discussion and Conclusions IPD is associated with a high mortality in South Africa. Our findings of increased risk of death in HIV-positive patients especially those with low CD4+ count are of importance given the high prevalence of HIV amongst patients with IPD. Introduction of the pneumococcal conjugate vaccine as part of the national expanded program for immunization (EPI) and ensuring access to antiretroviral therapy for HIV-positive patients where indicated should be prioritized.

What is known and objective: Treatment of methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia is a long-standing challenge to health care, often complicated by metastatic infections, treatment failure and mortality. When MRSA bacteraemia persists despite adequate initial treatment, current Infectious Diseases Society of America guidelines recommend evaluation and removal of possible sources of infection. In addition, a change in therapy may be considered. The objective of this review was to explore the therapeutic options for the treatment of persistent MRSA bacteraemia. Methods: A literature search of PubMed, MEDLINE and Google Scholar was performed using the following search terms: [methicillin-resistant Staphylococcus aureus OR MRSA] AND [bacteraemia OR bloodstream infection] AND [persistent OR persistence OR refractory OR treatment failure OR salvage] AND treatment. We evaluated relevant, adult, English-language, peer-reviewed studies published between 1985 and May 2018. In vitro and animal studies were considered as supportive of in vivo data. Results and discussion: Randomized, controlled trials are lacking. However, case series and case reports support multiple treatment options including high-dose daptomycin in combination with an antistaphylococcal β-lactam, ceftaroline, trimethoprim-sulfamethoxazole (TMP-SMX) or fosfomycin; ceftaroline alone or in combination with vancomycin or TMP-SMX; linezolid alone or in combination with a carbapenem, or telavancin. What is new and conclusion: Given the heterogeneity of the data, a preferred regimen has not emerged. Prescribers must take into consideration recent exposure, source control, and available synergy and clinical data. Further comparative trials are needed to establish a preferred regimen and the creation of a universal treatment algorithm.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18888号 / 医博第3999号 / 新制||医||1009(附属図書館) / 31839 / 京都大学大学院医学研究科医学専攻 / (主査)教授 中川 一路, 教授 木原 正博, 教授 西渕 光昭 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Background: Neisseria meningitidis is a gram-negative bacterium with the potential to cause invasive disease. Invasive meningococcal disease (IMD) can be fatal if delay to antibiotic therapy. There are six serogroups, which are capable of causing invasive disease in humans; A, B, C, W, X and Y. Since 2015, serogroup W and serogroup Y account for the majority of IMD cases reported in Sweden. Aim: To investigate the clinical presentations of IMD caused by Neisseria meningitidis serogroup W and Y. Method: Two databases, PubMed and Cochrane, were used to find articles that described the clinical picture of IMD. Articles with description of clinical features of the studied serogroups and with eight cases or more in every study were included. In addition, only original articles were included. Results: A total of 633 articles were found and 11 fulfilled all the inclusion criteria. Five out of seven articles found meningococcemia as the predominating presentation of serogroup W IMD. Two out of the four articles that studied serogroup Y IMD found meningitis at a higher number. Conclusion: The results of this systematic review suggest meningococcemia as a relatively common presentation of serogroup W IMD while meningitis and pneumonia might occur more frequently in serogroup Y IMD. However, these results should be interpreted carefully because the included articles were mostly retrospective studies and future prospective studies are needed to better identify clinical presentations of serogroup W and Y IMD.

Background: Antimicrobial resistance (AMR) is a global public health challenge since infection with resistant organisms may cause death, can spread across the community, and increase health care costs at individual, community and government level as more expensive antimicrobials will have to be made available for the treatment of infections caused by resistant bacteria. This calls for urgent and consolidated efforts in order to effectively curb this growing crisis, to prevent the world from slipping back to the pre-antibiotic era. The World Health Organization made a call in 2011 advocating for strengthening of surveillance and laboratory capacity as one-way of detecting and monitoring trends and patterns of emerging AMR. Knowledge of AMR guides clinical decisions regarding choice of antimicrobial therapy, during an episode of bacteraemia and forms the basis of key strategies in containing the spread of resistant bacteria. The current study focused on Staphylococcus aureus (SA), Klebsiella pneumoniae (KP), and Pseudomonas aeruginosa (PA), as they are common hospital acquired infections which are prone to developing resistance to multiple antibiotics. Aim: The aim of this project was to assess and utilize the laboratory information system (LIS) at the National Health Laboratory Services (NHLS), as a tool for reporting AMR and monitoring resistance patterns and trends over time of clinical isolates of SA, KP and PA, cultured from the blood of patients admitted to seven tertiary public hospitals in three provinces in South Africa. Methods: A retrospective and prospective analysis was done on isolates of SA, KP, PA from blood specimens collected from patients with bacteraemia and submitted to diagnostic microbiology laboratories of the NHLS at seven tertiary public hospitals in three provinces in South Africa. These hospitals comprised the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH), Chris Hani Baragwanath Hospital (CBH), Helen Joseph Hospital (HJH), Steve Biko Pretoria Academic Hospital (SBPAH), Groote Schuur Hospital (GSH), Tygerberg Hospital (TH) and the Universitas Hospital of the Free State (UH). For retrospective analysis, data submitted during the period July 2005 to December 2009 were used and for prospective analysis, data relating to AMR in SA, KP, PA, collected by the Group for Enteric, Respiratory and Meningeal disease Surveillance in South Africa, (GERMS-SA) from July 2010 to June 2011 were used. AMR in these three pathogens to commonly used antimicrobial drugs was systematically investigated. Multivariate logistic regressions models were used to assess factors associated with AMR. In addition, a systematic review of research done to date on AMR in bacterial pathogens commonly associated with hospital-acquired infections was conducted in order to understand the existing antimicrobial surveillance systems and baseline resistance patterns in South Africa. Results: A total of 9969 isolates were reported from the retrospective dataset. These were 3942 (39.5%) SA, 4466 (44.8%) KP and 1561 (15.7%) PA. From the prospective dataset, a total of 3026 isolates were reported, 1494 (49.4%) SA and 1532 (50.6%) KP isolates respectively. The proportion of invasive bacteraemia was higher in the <5 year old children. Nearly all strains of SA in South Africa were resistant to penicillin, and >30% up to as high as 80% were resistant to methicillin-related drugs among~560 invasive SA isolates over the two year period. Methicillin resistant Staphylococcus aureus (MRSA) rates significantly differed between hospitals (p=<0.001). The proportion of MRSA isolates in relation to methicillin-susceptible strains showed a declining trend from 22.2% in 2005 to 10.5% in 2009 (p=0.042). Emerging resistance was observed for vancomycin: 1 isolate was identified in 2006 and 9 isolates between July 2010-June 2011, and all except 1 were from Gauteng hospitals. The study found increasing rates of carbapenem-resisant KP of 0.4% in 2005 to 4.0% in 2011 for imipenem. The mean rate of extended spectrum beta lactamase (ESBL-KP) producing KP was 74.2%, with the lowest rate of 62.4% in SBPAH and the highest rate of 81.3% in UH, showing a significant geographical variation in rates of resistance (p=0.021). PA showed a tendency for multi-drug resistance with resistance rates of >20% to extended spectrum cephalosporins, fluoroquinolones and aminoglycosides respectively. Emerging resistance in PA isolates was observed to colistin, showing a resistance rate of 1.9% over the 5 years period. In the multivariate model, age <5 years, male gender, and hospital location were factors significantly associated with MRSA, while ESBL-KP was significantly associated with age <5 years and hospital location. Concluding remarks: The study has clearly demonstrated that AMR is relatively common in South Africa among children <5 years. Enhancement of continued surveillance of nosocomial infections through use of routine laboratory data should be reinforced as this will facilitate effective interpretation and mapping of trends and patterns of AMR. Therefore, the LIS as a tool for gathering such data should be strengthened to provide reliable AMR data for improved understanding of the extent of the AMR, and present evidence on which future policies and practices aimed at containing AMR could be based. Key words: Laboratory information system, Trends, Patterns, Antimicrobial resistance, Bacterial pathogens, Nosocomial infections, Surveillance, Bacteraemia, Blood culture.