Biocontrol activity of Meyerozyma guilliermondii against mould growth and a study of local post-harvest systems for maize in Cameroon

Post-harvest loss is a major problem for farmers in sub-Saharan Africa. Substantial amounts of cereal grain are lost each year due to factors such as exposure to rain, extreme drought, physical damage and invasion of microorganisms. This decreases the availability of food/feed which in turn increases prices and the consumption of unsafe food. Therefore storage systems need to be developed to ensure a safe food supply with low losses. The project aimed to evaluate the inhibiting effects of Meyerozyma guilliermondii against mould growth on maize under local conditions in Cameroon. This was in order to determine if M. guilliermondii could be used for biocontrol storage of moist maize under airtight conditions. Previous studies have shown this system, together with the yeast Wickerhamomyces anomalus as biocontrol, to be very effective for grain preservation. Mini silos were inoculated with different moulds and yeasts. W. anomalus was used as a control since it has previously been shown to have an inhibiting effect on mould growth. Furthermore the project aimed to study local post-harvest systems for maize in two different areas of Cameroon. This was done by means of visiting farms and interviewing farmers. The new biocontrol system of moist grain was also explained to the farmers in order to introduce the idea to them and see if they were willing to try a new storage system. A hygiene study of the storages was also done by microbial quantification and calculation of colony forming units (CFU). No inhibition of mould growth was detected for either M. guilliermondii or W. anomalus. Several factors such as low moisture content, too much mould and the size and the material of the mini silos made the results questionable. More studies need to be made regarding the biocontrol activity of M. guilliermondii. The storage method and hygiene varied between different farms in the Nforya-Bamenda area. However none of the local storage systems seemed to have better hygienic status for yeasts and moulds. The biocontrol system seemed suitable for introduction in Nforya-Bamenda for several practical and socio-economic reasons. With current storage technology it would be no use increasing yield per hectare for maize in this region since farmers already produce more than they can store. Moreover, the change in maize storage technology could prove essential to improving women and children’s health in Cameroon, since many farmers smoke their maize indoors using fire-wood

Epidemiology of extended-spectrum β-lactamase-producing Escherichia coli

Extended-Spectrum β-Lactamase and plasmid mediated AmpC (ESBL/pAmpC)-producing Escherichia coli (E. coli) has during the last decades emerged worldwide and is now an increasing problem in both human and animal health. In order to slow down the spread it is important to study success factors and transmission routes so that preventive measures can be efficient. In paper I we studied what sectors that contribute to human carriage and human clinical infections by investigating the molecular epidemiology of ESBL/pAmpC-producing E. coli in leafy greens, meats, farm animals, human community carriers and human blood stream infections. We found that different ESBL/pAmpC-genes, plasmids and E. coli MLST lineages dominated in isolates from humans compared to isolates in farm animals, foods and meats, but some traits overlapped. All in all, we concluded that a very small proportion of human bloodstream infections with ESBL/pAmpC-producing E. coli could have originated from the foods we consume. To better understand the prevalence of ESBL/pAmpC-producing E. coli in the community we performed two carrier studies described in papers II and III. In paper II we found that 4.7% of the Swedish population carried ESBL/pAmpC-producing E. coli in their intestine. Risk factors associated with carriage was travel to countries in Asia and Africa and a diet that did not include pork. In paper II we also explored which E. coli populations that accumulated in clinical infections compared to carriers and found that the ESBL-gene blaCTX-M-15 and E. coli ST131 and its subclone H30-Rx/C2 were overrepresented in bloodstream infections. In paper III we joined forces with our neighbouring countries around the Baltic Sea, Finland, Latvia, Russia, Poland and Germany to investigate the prevalence of ESBL-producing E. coli and K. pneumoniae in specific populations in all participating countries. We found large differences in prevalence between countries with the highest in Russia (23.4%) and the lowest in Latvia (1.6%). No carbapenemase producing isolates were identified in any of the investigated countries. In paper II E. coli ST131 was identified as the most common ST to cause bloodstream infections in Swedish patients. This lineage is internationally wide-spread and commonly cause severe infections. In paper IV we explored the Swedish epidemiology of this highly pathogenic ESBL-producing E. coli lineage by conducting a phylogenetic comparison between Swedish and international isolates. We found, in accordance with our hypothesis, that several introductions from the international lineage have shaped the Swedish ST131 population. Tight genetic relationships between isolates in clonal clusters makes it difficult to perform outbreak investigations with ST131. In addition, we identified highly conserved plasmids in all clusters with Swedish isolates even though they had been separated for several years indicating a strong co-evolution of plasmids in some ST131 lineages. Taken together our studies show that although there is a high prevalence of ESBL/pAmpC-producing E. coli, particularly in poultry and chicken meat products, the major source for ESBL/pAmpC producing E. coli causing human infections is humans to human transmission. Although we do not see a great contribution from the animal and food sector in Sweden it could change in the future if an epidemiological shift to more human pathogenic strains take place in e.g. poultry. This is why a multi-sectorial approach to reduce the levels of ESBL/pAmpC-producing E. coli in all sectors is needed. Of particular interest is the highly pathogenic E. coli lineage ST131 that is responsible for a large proportion of infection with ESBL/pAmpC-producing E. coli. Carriers of ST131 could therefore be at greater risk of getting an infection and there might be incentive for considering them as high risk carriers. The high clinical relevance of ESBL-producing E. coli ST131 prompts further monitoring since this lineage has large potential to accumulate resistance to last resort drugs such as carbapenems and colistin

Polyclonal spread of blaCTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia

Objectives: The burden of antimicrobial resistance and spread of epidemic clones are rarely reported from low-income countries. We aimed to investigate the genome-based epidemiology of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) at a tertiary hospital in Jimma, Ethiopia. Methods: Bacteria were isolated from clinical specimens at Jimma Medical Center and subjected to species identification (MALDI-TOF), antimicrobial susceptibility testing (disk diffusion) and whole-genome sequencing (Illumina, HiSeq2500). Genomic data analysis was performed using EnteroBase and Center for Genomic Epidemiology bioinformatics pipelines. A maximum likelihood tree was generated using FastTree/2.1.8 based on single nucleotide polymorphisms (SNPs) in shared genomic regions to identify transmission clusters. Results: Escherichia coli isolates (n = 261) were collected from 1087 single non-duplicate clinical specimens over a 5-month period in 2016. The prevalence of ESBL-EC was 54.8% (143/261), 96% of which were resistant to multiple antibiotic classes. The blaCTX-M-15 ESBL gene was present in 88.4.% of isolates (122/138). Genes conferring resistance to aminoglycosides and ciprofloxacin [aac(6′)-Ib-cr, 62.3% (86/138)], phenicols [catB3, 56.5% (78/138)], sulfonamides [sul1, 68.1% (94/138), trimethoprim [dfrA17, 58.0% (80/138)] and macrolides [mph(A), 67.4% (93/138) were detected. The most prevalent sequence types were ST410 (23%), ST648 (17%), ST131 (10%) and ST167 (7%). Isolates of the same sequence type collected from different units of the hospital were highly similar in the SNP analysis. Conclusion: A high prevalence of ESBLs and dissemination of blaCTX-M-15 through multiple high-risk E. coli clones was detected. Nosocomial spread of multidrug-resistant ESBL-EC within the hospital puts vulnerable patients at risk of difficult-to-treat infections

High prevalence of bla(CTX-M-15) and nosocomial transmission of hypervirulent epidemic clones of Klebsiella pneumoniae at a tertiary hospital in Ethiopia

Background: Genomic epidemiology of antibiotic resistance is not sufficiently studied in low-income countries. Objectives: To determine prevalence of ESBL production, and resistome and virulome profiles, of Klebsiella pneumoniae isolated at Jimma Medical Center, Ethiopia. Methods: Strains isolated from patients with suspected infections between June and November 2016 were characterized by MALDI-TOF for species identification and disc diffusion for antimicrobial susceptibility testing. All K. pneumoniae isolates were characterized by double disc diffusion for ESBL production and all ESBL-producing strains (ESBL-KP) were subjected to WGS on the Illumina (HiSeq 2500) platform. DNA was extracted by automated systems (MagNA Pure 96). Genome assembly was performed using SPAdes (v. 3.9) and draft genomes were used for analysing molecular features of the strains. Maximum likelihood trees were generated using FastTree/2.1.8 based on SNPs in shared genomic regions to identify transmission clusters. Results: Of the 146 K. pneumoniae strains isolated, 76% were ESBL-KP; 93% of the ESBL-KP strains showed resistance to multiple antimicrobial classes. bla(CTX-M-15) (84.4%) was the most prevalent ESBL gene. Resistance genes for aminoglycosides and/or fluoroquinolones [aac(6)-Ib-cr (65.1%)], phenicols [catB3 (28.4%)], sulphonamides [sul1 (61.2%) and sul2 (60.5%)], trimethoprim [dfrA27 (32.1%)], macrolides [mph(A) (12.8%)] and rifampicin [arr2/arr3 (39.4%)] were prevalent. Plasmids of the IncF and IncR families were prevalent among ST218, ST147, ST15 and ST39. KL64 and KL57 capsular types and O1 and O2 LPSs were prevalent. A high-risk clone, ST218-KL57 encoding rmpA1/rmpA2 and iutA, was detected. Phylogenetic analysis showed a cluster of clonally related strains from different units of the hospital. Conclusions: Prevalence of ESBL-KP was high and bla(CTX-M-15) was the predominant ESBL gene. ESBL genes had spread through both clonal and polyclonal expansion of high-risk and hypervirulent clones. Nosocomial transmission of MDR strains between different units of the hospital was observed

Antimicrobial resistance of Escherichia coli isolates from outpatient urinary tract infections in women in six European countries including Russia

Objectives In the Northern Dimension Antibiotic Resistance Study (NoDARS), Finland, Germany, Latvia, Poland, Russia and Sweden collected urine samples from outpatient women (aged 18–65 years) with symptoms of uncomplicated urinary tract infection (UTI) to investigate the levels of antimicrobial resistance (AMR) among Escherichia coli isolates. Methods A total of 775 E. coli isolates from 1280 clinical urine samples were collected from October 2015 to January 2017. Antimicrobial susceptibility testing was performed and the results were interpreted according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Results Overall AMR rates to the commonly used antibiotics nitrofurantoin, fosfomycin and mecillinam (except for Germany that was missing a result for mecillinam) were 1.2%, 1.3% and 4.1%, respectively. The highest overall resistance rates were determined for ampicillin (39.6%), trimethoprim (23.8%), trimethoprim/sulfamethoxazole (22.4%), amoxicillin/clavulanic acid (16.7%) and ciprofloxacin (15.1%), varying significantly between countries. The rate of extended-spectrum β-lactamase (ESBL) production was 8.7%. None of the isolates showed resistance to meropenem. Conclusions In most cases, low AMR rates were detected against the first-line antibiotics recommended in national UTI treatment guidelines, giving support to their future use. These results also support the European Association of Urology guidelines stating that nitrofurantoin, fosfomycin and mecillinam are viable treatment options for uncomplicated UTI.Peer Reviewe

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Psychometric Properties and Correlates of Precarious Manhood Beliefs in 62 Nations

Precarious manhood beliefs portray manhood, relative to womanhood, as a social status that is hard to earn, easy to lose, and proven via public action. Here, we present cross-cultural data on a brief measure of precarious manhood beliefs (the Precarious Manhood Beliefs scale [PMB]) that covaries meaningfully with other cross-culturally validated gender ideologies and with country-level indices of gender equality and human development. Using data from university samples in 62 countries across 13 world regions (N = 33,417), we demonstrate: (1) the psychometric isomorphism of the PMB (i.e., its comparability in meaning and statistical properties across the individual and country levels); (2) the PMB’s distinctness from, and associations with, ambivalent sexism and ambivalence toward men; and (3) associations of the PMB with nation-level gender equality and human development. Findings are discussed in terms of their statistical and theoretical implications for understanding widely-held beliefs about the precariousness of the male gender role

Being pregnant and giving birth in a new country : A qualitative meta-synthesis

Bakgrund: Migration är ett ständigt pågående fenomen, som kan leda till en förbättrad eller försämrad hälsa över tid. Att bli förälder innebär en omvälvande tid, och att samtidigt migrera kan medförahinder som skapar en svårare övergång till föräldraskapet. Barnmorskans vård och stöd kan underlätta för kvinnan under graviditet, förlossning och postpartum och underlätta övergången till moderskapet. Syfte: Syftet var att beskriva migrerande kvinnors upplevelser av att vara gravid och föda barn i ett nytt land. Metod: Kvalitativ metasyntes med metaetnografi som analysmetod. Databaser som användes var: CINAHL, PubMed och PsycInfo. Efter kvalitetsgranskning enligt Joanna Briggs granskningsmall och analys har metasyntesens resultat framställts från 18 vetenskapliga artiklar. Resultat: Fem huvudteman identifierades; hinder i kommunikationen, kulturella aspekter, kvinnosjukvården i det nya landet, diskriminering, och stöd. Elva underteman identifierades; språkförbistring, bristande information, kulturella skillnader, en kulturkrock, tillgänglig kvinnosjukvård bidrar till trygghet, barnmorskeledd, kvinnocentrerad vård i nya landet, ignorans och avsaknad av kulturell kompetens, dåligt bemötande bidrar till minskat förtroende för vården, bristande socialt stöd, förändring i traditionell rollfördelning, och barnmorskans professionella stöd. Slutsats: Kvinnor som migrerat och genomgår graviditet och förlossning i ett nytt land är sårbara i mötet med kvinnosjukvården. Språkförbistring och ett minskat socialt nätverk medför att behovet av barnmorskans professionella stöd ökar. Det finns utvecklingsmöjligheter inom vården, genom ökad kulturell kompetens hos personal, stödgrupper, förstärkt postpartumvård och barnmorskeledd vård genom hela vårdkedjan skulle vården för kvinnor i migration förbättras. Klinisk tillämpbarhet: Resultatet kan ses som en vägledning för barnmorskor och annan vårdpersonal genom ökad förståelse för migrerande kvinnors upplevelser. Förhoppningsvis medför detta en ökad medvetenhet om behovet av kulturell kompetens hos barnmorskor samt att sammanställningen i arbetet kan ge underlag för att bemöta kvinnorna utifrån deras behov.Background: Migration is a constant ongoing phenomenon, which can contribute to improved or deteriorated health over time. Becoming a parent is a turbulent time, and migrating at the same time can bring obstacles that make the transition to parenthood more difficult. The midwife's care and support can make it easier for the woman during pregnancy, childbirth and postpartum and facilitate the transition to motherhood. Aim: The aim is to describe migrant women's experiences of pregnancy and giving birth in a new country. Method: Qualitative meta-synthesis with meta-ethnography as analysis method. Databases used were: CINAHL, PubMed and PsycInfo. After quality assessment and data- analysis, the results of the meta-synthesis have been prepared from 18 scientific articles. Results: Five main themes were identified, language confusion, cultural differences, healthcare in the new country, discrimination, and the importance of support. Eight sub-themes were identified, lack of communication, a culture clash, available women's care, differences in women's care, poor treatment, lack of support, the support of one's own family friends and the partner and the midwife's professional support. Conclusion: Migrant women who undergo pregnancy and childbirth in a new country are vulnerable in the encounter with maternity care settings. Language confusion and a reduced social network means that the need for the midwife's professional support increases. There are opportunities for development in care, through increased cultural competence in midwifes, support groups, strengthened postpartum care and providing midwife-led care through the entire care chain, the care for migrant women would improve. Clinical implications: The result can be seen as a guide for midwives and other healthcare professionals through increased understanding of migrant women's experiences. Hopefully this leads to an increased awareness of the need of cultural competence in midwives but also the compilation may provide a basis for supporting migrant women according to their needs

Genome and plasmid diversity of Extended-Spectrum beta-Lactamase-producing Escherichia coli ST131-tracking phylogenetic trajectories with Bayesian inference

Clonal lineages of ESBL (Extended-Spectrum beta-Lactamase)-producing E. coli belonging to sequence type 131 (ST131) have disseminated globally during the last 30 years, leading to an increased prevalence of resistance to fluoroquinolones and extended-spectrum cephalosporins in clinical isolates of E. coli. We aimed to study if Swedish ESBL-producing ST131 isolates originated from single or multiple introductions to the population by assessing the amount of genetic variation, on chromosomal and plasmid level, between Swedish and international E. coli ST131. Bayesian inference of Swedish E. coli ST131 isolates (n = 29), sequenced using PacBio RSII, together with an international ST131 dataset showed that the Swedish isolates were part of the international ST131 A, C1 and C2 clades. Highly conserved plasmids were identified in three clusters although they were separated by several years, which indicates a strong co-evolution between some ST131 lineages and specific plasmids. In conclusion, the tight clonal relationship observed within the ST131 clades, together with highly conserved plasmids, challenges investigation of strain transmission events. A combination of few SNPs on a genome-wide scale and an epidemiological temporospatial link, are needed to track the spread of the ST131 subclones