Bacterial causative agents of neonatal sepsis and their antibiotic susceptibility in neonatal intensive care units (Nicus) and neonatal wards in Iran: A systematic review

Context: Sepsis is one of the most common causes of neonatal mortality, especially in developing countries. The purpose of this study was to systematically review the bacterial causative agents of neonatal sepsis and their antibiotic susceptibility in Iran. Material and Methods: We searched all previously published papers to gather related information on Iranian neonatal sepsis in international and national databases (in both Persian and English) from 2006 to 2018. The standard STROBE checklist was used for quality assessment. The data were analyzed by statistical methods with a random-effects model using Stata 14 software. Results: A total of 89,472 neonates with sepsis (presented in 17 studies) were included in this systematic review. The mortality rate of neonates was 28.0. The proportions of neonatal sepsis caused by Gram-negative and Gram-positive bacteria were 66.0 and 33.0, respectively. The most common bacteria causing neonatal sepsis were Klebsiella pneumoniae and Pseudomonas aeruginosa (Gram-negative) and coagulase-negative staphylococci and Staphylococcus aureus (Gram-positive). Conclusions: Gram-negative bacteria are the most common causes of neonatal sepsis in Iran. Imipenem is the most effective antibiotic against Gram-negative bacilli and vancomycin against Gram-positive cocci causing neonatal sepsis in Iran. © 2020, Author(s)

B Cell Epitopes of Four Fimbriae Antigens of Klebsiella pneumoniae: A Comprehensive In Silico Study for Vaccine Development

Klebsiella pneumoniae is one of the major causes of nosocomial infections worldwide which can cause several diseases in children and adults. The globally dissemination of hyper-virulent strains of K. pneumoniae and the emergence of antibiotics-resistant isolates of this pathogen narrows down the treatment options and has renewed interest in its vaccines. Vaccine candidates of Klebsiella pneumoniae have not been adequately protective, safe and globally available yet. In K. pneumoniae infection, it is well known that B cells that induce robust humoral immunity are necessary for the host complete protection. Identifying the B cell epitopes of antigens is valuable to design novel vaccine candidates. In the present study using immunoinformatics approaches we found B cell epitopes of four K. pneumoniae type 1 fimbriae antigens namely FimA, FimF, FimG, and FimH. Linear and conformational B cell epitopes of each antigen were predicted using different programs. Subsequently, many bioinformatics assays were applied to choose the best epitopes including prediction antigenicity, toxicity, human similarity and investigation on experimental records. These assays resulted in final four epitopes (each for one Fim protein). These final epitopes were modeled and their physiochemical properties were estimated to be used as potential vaccine candidates. Altogether, we found four B cell epitopes of K. pneumoniae Fim antigens that are immunogen, antigenic, not similar to human peptides, not allergen and not toxic. Also, they have suitable physiochemical properties to administrate as vaccine, although their complete efficacy should be also shown in vitro and in vivo. © 2020, Springer Nature B.V

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

<p>Abstract</p> <p>Background</p> <p>The bacterial genus <it>Listeria </it>contains pathogenic and non-pathogenic species, including the pathogens <it>L. monocytogenes </it>and <it>L. ivanovii</it>, both of which carry homologous virulence gene clusters such as the <it>prfA </it>cluster and clusters of internalin genes. Initial evidence for multiple deletions of the <it>prfA </it>cluster during the evolution of <it>Listeria </it>indicates that this genus provides an interesting model for studying the evolution of virulence and also presents practical challenges with regard to definition of pathogenic strains.</p> <p>Results</p> <p>To better understand genome evolution and evolution of virulence characteristics in <it>Listeria</it>, we used a next generation sequencing approach to generate draft genomes for seven strains representing <it>Listeria </it>species or clades for which genome sequences were not available. Comparative analyses of these draft genomes and six publicly available genomes, which together represent the main <it>Listeria </it>species, showed evidence for (i) a pangenome with 2,032 core and 2,918 accessory genes identified to date, (ii) a critical role of gene loss events in transition of <it>Listeria </it>species from facultative pathogen to saprotroph, even though a consistent pattern of gene loss seemed to be absent, and a number of isolates representing non-pathogenic species still carried some virulence associated genes, and (iii) divergence of modern pathogenic and non-pathogenic <it>Listeria </it>species and strains, most likely circa 47 million years ago, from a pathogenic common ancestor that contained key virulence genes.</p> <p>Conclusions</p> <p>Genome evolution in <it>Listeria </it>involved limited gene loss and acquisition as supported by (i) a relatively high coverage of the predicted pan-genome by the observed pan-genome, (ii) conserved genome size (between 2.8 and 3.2 Mb), and (iii) a highly syntenic genome. Limited gene loss in <it>Listeria </it>did include loss of virulence associated genes, likely associated with multiple transitions to a saprotrophic lifestyle. The genus <it>Listeria </it>thus provides an example of a group of bacteria that appears to evolve through a loss of virulence rather than acquisition of virulence characteristics. While <it>Listeria </it>includes a number of species-like clades, many of these putative species include clades or strains with atypical virulence associated characteristics. This information will allow for the development of genetic and genomic criteria for pathogenic strains, including development of assays that specifically detect pathogenic <it>Listeria </it>strains.</p

The impact of the Listeria monocytogenes large plasmid on its interaction with HeLa cells and Acanthamoeba polyphaga trophozoites

Plasmids have been studied in Listeria monocytogenes, and plasmids with different sizes and functions have been reported. However, the role of large plasmids in the ecology of L. monocytogenes, in particular their impact on bacterial interactions with eukaryotes, has not been fully understood. In this study, the potential role of L. monocytogenes large plasmid DNA for invasion and intra-cellular growth in eukaryotic cells was determined by comparing the growth of the plasmid-cured versus wild type in HeLa cells and Acanthamoeba polyphaga trophozoites. Forty nine bacterial isolates were tested and 55% of environmental isolates contained plasmids. However, plasmid DNA was not found in clinical isolates. Both the plasmid-cured and the wild type bacteria showed similar behaviors in co-culture with HeLa cells and A. polyphaga trophozoites. After 10 successive passages through HeLa cells, the majority of bacteria recovered lost plasmid DNA. Our findings suggested that L. monocytogenes may lose large plasmids while growing in the enriched intra-cellular environment in eukaryotic cells. The result of this study indicated that plasmid-associated determinants have no significant impact on bacterial survival during co-culture with A. polyphaga and HeLa cells under conditions tested.Alisha Akya, Andrew Pointon and Connor Thoma

The Frequency of blaVIM, blaIMP, blaKPC and blaNDM Carbapenemase Genes in Clinical Isolates of Klebsiella Pneumoniae in Kermanshah Medical Centers

Background: Carbapenemase genes have been spread among strains of Klebsiella pneumoniae that make them resistant to carbapenems. Hence, the present study aimed to study the prevalence of carbapenmase genes within K. pneumoniae isolates in Kermanshah medical centers. Methods: Sixty isolates of K. pneumoniae were collected and identified using API kit. Then, antibiotic susceptibility of isolates was determined using a disk diffusion method. The carbapenems-resistant isolates were screened for carbapenemases production using the Modified Hodge Test (MHT). The carbapenemase genes of blaVIM, blaIMP, KPC and blaNDM were detected by PCR test . Results: Out of 60 isolates, 4 isolates were resistant to carbapenem antibiotics, but only one isolate was demonstrated to be positive for carbapenemases by MHT phenotypic testing. The gene of blaVIM was detected in three isolates by PCR, though other genes were not found in the isolates. Within the isolates, 6.67% and 100% were resistant to carbapenem and ampicillin, respectively. Conclusion: The study findings revealed that dissemination rate of carbapenemase genes was not reported to be high among isolates of K. pneumoniae in Kermanshah. Only blaVIM gene was probably more frequent than other tested genes. Since most isolates examined in this study were susceptible to carbapenem antibiotics, these antibiotics are still regarded as effective drugs against infections caused by K. pneumoniae

Surveys in Covid-19 and Post Covid-19 Days

The year 2020 has been an extraordinary year, with the emergence of a global pandemic caused by the highly infectious SARS-CoV-2 virus. The World Health Organization declared the pandemic on March 11, 2020, and since then, the virus has spread everywhere, causing deaths, health system capacity overloads, job loss, the introduction of non-pharmaceutical interventions such as social distancing, lockdowns, closing of schools, distance working, and many other developments and changes that came into life rapidly. These changes to the “normal” life we know introduced the necessity of data and research to answer all sorts of questions asked by researchers and policymakers. How much of the population was infected; what were the consequences of the pandemic on people in terms of their physical health, mental health, education, working status, financial situation, family arrangements, social interactions; how are people’s attitudes and behaviors regarding different dimensions of the pandemic, such as compliance with preventive measures, people’s concerns over the pandemic, their future evaluations, the evaluations of politicians and institutions in handling the situation, and so on. Survey research is among the top sources for finding answers to the questions stated above and has also been affected by the pandemic. With in-person contact being the main route of transmission of COVID-19, visiting households, for instance, has become very risky for both respondents and interviewers, and such household surveys have been suspended almost everywhere. As the case in many office jobs, telephone interviewing from CATI centers have also become risky for disease spread. With service sector interruptions, postal services for mail surveys, and even online support services for any web surveys became affected. However, the need for data was real and urgent, so there have been new surveys designed, mode switches have been employed for surveys already running or planned, and usage of other data sources has been more on the forefront. Survey researchers have been discussing these issues since early on in the pandemic. The European Survey Research Association’s journal, Survey Research Methods, published an extensive special issue in June, covering papers about design proposals, adaptions to ongoing surveys, and research initiatives. The World Population Association organized public webinars covering the challenges to surveys all around the world, with researchers attending from Asia, Africa, Latin America, Europe, and North America. In addition, the American Association for Public Opinion Research held workshops, and The Royal Statistics Society held two webinars on how the pandemic affected data collection from various aspects. The United Nations World Data Forum held a special session on the topic. International organizations have also been active in guiding survey organizations. A Task Force was founded under the UN Intersecretariat Working Group on Household Surveys. Pandemic related recommendations and briefs from UN agencies, such as the World Bank, UNICEF, UN Women, ILO, UNSD, and their regional offices. The World Health Organization and EUROSTAT have also provided documents for international use. In this project, we reviewed the developments in survey research based on similarsources listed above and survey organizations’ websites, with the aim of putting contemporary and future topics into perspective. Our desktop research covered the period from the pandemic’s beginning to midDecember 2020. We should underline that we do not cover all developments, and our review is limited to relatively more visible sources such as those above and those in English and Turkish. 2 To help with our understanding of issues, we decided to conduct expert interviews. We prepared separate interview guidelines for each expert, covering a wide range of topics overall while directing questions on each researcher’s area of expertise. We conducted a total of six interviews between September 25 and November 20. We asked Prof. James M. Lepkowski, Emeritus Professor at the Survey Methodology Program, University of Michigan Institute for Social Research, general questions about the effects of the pandemic on various modes and their implications for survey errors. Dr. Attila Hancıoğlu, the chief of the Data Collection Unit, Data & Analytic Section at the UNICEF Headquarters in New York, talked about the UNICEF Multiple Indicator Cluster Surveys program in the context of the pandemic. In our interview with Dr. Raphael Nishimura, the Director of Sampling in Survey Research Operations at the University of Michigan, he told us about his experience with household surveys from Brazil and the Institute for Social Research at the University of Michigan. We asked Prof. Frauke Kreuter, the Director of the Joint Program in Survey Methodology at the University of Maryland and Founder of the International Program for Survey and Data Science at the University of Mannheim, about more contemporary topics in survey research, such as web surveys and the use of big data. We also aimed to have a country-highlight, both in our desktop research and interviews. Enver Taştı, a senior expert and former-Deputy Director of TURKSTAT, shed light on the practices of TURKSTAT during the pandemic. Finally, our interview with Oğuzhan Akyıldırım, CEO of Tandans research company, reflected on the experiences of the private research sector in Turkey. This publication is aimed at the general reader, anyone who has an interest in surveys. For this purpose, we start with a background section that provides a historical background for surveys. We then move on to types of surveys based on different classifications. We have separate subsections on survey modes since they lie at the heart of many discussions mentioned in this publication. We talk about some international survey programs to introduce the readers to well-known survey series, with a special focus on Turkey. Overall, we introduce the basic concepts and terminology for readers from outside the field to prepare the sections ahead. Chapter 3 presents our review of online resources about the pandemic and surveys in the following section. Here we summarized our review separately for cross-sectional and longitudinal surveys. We also mentioned surveys designed specifically to focus on the impacts of the pandemic on various aspects of people’s lives while classifying them based on the type of sampling frame they used. We briefly reviewed some innovations in data collection deemed important during the pandemic. We allocated a brief section on surveys to estimate the extent of the spread of COVID-19 is and another on survey research in Turkey. We concluded with a short section on several ethical issues discussed by the researchers in their studies during this extraordinary period. In Chapter 4, we present the transcriptions of the interviews conducted with the experts presented above. The video recordings of these interviews are available on our Institute’s YouTube channel for those interested. We conclude our research and interviews in Chapter 5. In that section, we summarize our general conclusions and support them with observations from Chapter 3 and quotations from our expert interviews

Sleep disturbances are underappreciated in prostate cancer survivorship

The prevalence of sleep disturbances among prostate cancer (PCa) survivors, and extent of urologist involvement in sleep care are not well-studied. PCa survivors (n = 167) and urologists (n = 145) were surveyed about sleep disturbances and survivorship care practices. Most PCa survivors had sleep disturbances, including 50.9% with poor sleep quality, 18.0% with clinical/severe insomnia, and 36.5% at high-risk for sleep apnea. Few urologists routinely screened for sleep disturbances, as recommended in national cancer survivorship guidelines. Optimal PCa survivorship care should incorporate screening for sleep disturbances, addressing comorbid factors affecting sleep and referring to sleep medicine when appropriate

Child, Early and Forced Marriage in Turkey

Çocuk yaşta, erken ve zorla evlilikler (ÇEZE) küresel ölçekte önemli toplumsal sorunlardan biridir. Çocuk haklarının açık bir şekilde ihlali olan bu sorun, özellikle insan haklarına yönelik ihlaller arasında da yer almaktadır. Aynı zamanda, sonuçları itibarıyla kadınların yaşamlarında daha belirgin olmak üzere olumsuzluklara neden olmaktadır. ÇEZE’nin önlenmesine yönelik çalışmalara yön vermesi hedeflenen bu raporda, güncel duruma ilişkin bilgi 2018-TNSA verisinin detaylı analizlerinden elde edilmiştir. Ayrıca, 1993, 1998, 2003, 2008 ve 2013 yıllarında gerçekleştirilen TNSA verileri analiz edilerek, Türkiye’nin son 25 yılı için bir kesit sunulmuştur. ÇEZE, kadınların eğitim ve iş yaşamına katılım hakkı, cinsel sağlık ve üreme sağlığı hakları ve şiddetsiz yaşama hakkı gibi sahip oldukları birçok hakkı kullanmalarını engelleyen toplumsal cinsiyet eşitsizliklerini pekiştirir. Çok boyutlu bir konu olan ÇEZE, bir ayrımcılık biçimi ve halk sağlığı sorunu, uluslararası alanda kabul gören bir suç olmanın yanı sıra sürdürülebilir kalkınmanın engeli ve toplumsal cinsiyet temelli şiddet biçimlerinden biri olarak da tanımlanmaktadır. Bu çalışma, Türkiye’de ÇEZE’nin önlenmesine yönelik çaba ve çalışmalara, üreme sağlığı alanı öncelikli olacak biçimde veri temelli bir analiz ile katkıda bulunmayı amaçlamaktadır. Analizlerde, Türkiye Nüfus ve Sağlık Araştırmaları (TNSA) verisi kullanılmıştır. TNSA’lar, 15-49 yaş grubundaki kadınların üreme sağlığına, sosyo-ekonomik durumlarına, evliliklerine, çalışma yaşamları ve tutumlarına yönelik kapsamlı ve ayrıntılı bilgi toplayan önemli veri kaynaklarıdır