Article
Immunology
James R. Johnson, Connie Clabots, Stephen B. Porter, Tricia Bender, Brian D. Johnston, Paul Thuras
Summary: This study found that ST131-H30 subclone of Escherichia coli exhibits exceptional intestinal persistence, possibly due to a combination of fluoroquinolone resistance and virulence factors. These findings provide new insights for further study on the pandemic emergence of ST131-H30.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Infectious Diseases
Virginia Nunez-Samudio, Maydelin Pecchio, Gumercindo Pimentel-Peralta, Yohana Quintero, Mellissa Herrera, Ivan Landires
Summary: The study conducted in two hospitals in central Panama identified ESBL-producing E. coli strains as a significant public health concern in Central America, with the pandemic clone ST43/ST131 carrying CTX-M-15. This is the first report confirming the presence of this antimicrobial-resistant organism in inpatients and outpatients in the region, highlighting potential challenges in treating infections.
Article
Microbiology
Sabiha Shaik, Anuradha Singh, Arya Suresh, Niyaz Ahmed
Summary: This study provides a comprehensive understanding of the genomic features, ST-specific proteins, and resistance mechanisms in different lineages of E. coli. Machine learning approaches were used to identify important features and ST-specific signature proteins, which can be further studied to predict associations with phenotypic profiles and improve our understanding of virulence and resistance mechanisms among different clonal lineages of E. coli.
Article
Multidisciplinary Sciences
Joao A. A. Ascensao, Kelly M. M. Wetmore, Benjamin H. H. Good, Adam P. P. Arkin, Oskar Hallatschek
Summary: Ascensao et al. engineered knockout libraries of a nascent bacterial community and found that ecological and epistatic patterns combine to shape adaptive landscapes, despite idiosyncratic behavior of individual knockouts. The study also revealed that fitness effects are correlated with evolutionary outcomes for certain conditions, indicating shifting patterns of adaptation.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Amin Khoshbayan, Rezvan Golmoradi Zadeh, Majid Taati Moghadam, Shiva Mirkalantari, Atieh Darbandi
Summary: This study found the importance and high prevalence of E. coli O25b/ST131 among UTI isolates, with the ability to rapidly spread and disseminate antibiotic resistance genes.
ANNALS OF CLINICAL MICROBIOLOGY AND ANTIMICROBIALS
(2022)
Article
Infectious Diseases
Sada M. Boyd, Kristen L. Rhinehardt, Akamu J. Ewunkem, Scott H. Harrison, Misty D. Thomas, Joseph L. Graves
Summary: The rise in antimicrobial resistant bacteria has led to the search for antibiotic alternatives, with significant attention given to the use of antimicrobial copper. This study explores the evolution of copper resistance in Escherichia coli and its potential effects on resistance to other antibiotics. The results show that E. coli can rapidly evolve resistance to copper, but this selection may inhibit growth in other antimicrobials, suggesting an evolutionary trade-off.
Article
Genetics & Heredity
Sara Del Duca, Alberto Vassallo, Giulia Semenzato, Renato Fani
Summary: Gene elongation involves the duplication and divergence of a gene, resulting in a gene with two divergent paralogous modules. This process is poorly understood and has only been extensively studied in the histidine biosynthetic genes hisA and hisF. This study simulated the last step of gene elongation in the hisF gene and found that bacterial cells have the ability to modify their genome under selective conditions.
Article
Microbiology
Aamir Jamal Gondal, Nakhshab Choudhry, Hina Bukhari, Zainab Rizvi, Nighat Yasmin
Summary: The emergence of carbapenem-resistant Escherichia coli poses a significant threat to public health. This study characterized 184 clinical strains of carbapenem-resistant E. coli and found differences in resistance patterns, resistance genes, plasmids, and sequence types. Silver nanoparticles showed efficacy against carbapenemase-positive E. coli.
Article
Biochemistry & Molecular Biology
Emily M. Kibby, Amy N. Conte, A. Maxwell Burroughs, Toni A. Nagy, Jose A. Vargas, Lindsay A. Whalen, L. Aravind, Aaron T. Whiteley
Summary: Bacteria possess immune systems that can counter phage infection, and certain genes involved in these systems are similar to those found in eukaryotes, suggesting horizontal gene transfer. This study shows that bacteria also have proteins containing a NACHT module which defend against phages, and these proteins share similarities with human NLRs, indicating a shared signaling mechanism. The presence of NACHT module-containing proteins in bacteria establishes their ancient role as mediators of innate immunity.
Article
Multidisciplinary Sciences
Fatlum Hajredini, Ranajeet Ghose
Summary: By comparing the catalytic mechanisms of BY-kinases and NTPases, the study reveals the enzymatic activity differences between them, providing a theoretical basis for bacteria to reuse ancient domains to achieve tyrosine phosphorylation.
Editorial Material
Microbiology
Johann D. D. Pitout
Summary: Escherichia coli is a major cause of bloodstream infections worldwide. A longitudinal study in a Madrid hospital found that certain E. coli B2 phylogroups dominated the community E. coli population and were often introduced into hospital settings. Longitudinal surveys from England and Canada also showed that certain ST131 subclades were responsible for increased resistance to fluoroquinolones and cephalosporins in E. coli during the mid- to late 2000s.
Article
Infectious Diseases
Jeremiah Seni, Gisele Peirano, Stephen E. Mshana, Johann D. D. Pitout, Rebekah DeVinney
Summary: This study aimed to characterize antimicrobial resistance of ExPEC strains, sequence types, and ST131 clades from patients in Tanzania. ESBL production was more common among strains from children compared to pregnant women, with bla(CTX-M-15) being the predominant cause. The ST131 clades were associated with fluoroquinolone resistance and ESBL production. The molecular tools used in this study can be valuable for surveillance programs in resource-limited settings.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Akira Fukuda, Hiromi Nakamura, Kaoru Umeda, Kaori Yamamoto, Yuji Hirai, Masaru Usui, Jun Ogasawara
Summary: The study found that the antimicrobial resistance rates of E. coli isolated from healthy individuals in non-clinical settings were relatively low, but the rates of ciprofloxacin resistance and O25b-ST131 clone frequency increased during the study period.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2021)
Article
Infectious Diseases
Andre Birgy, Fouad Madhi, Camille Jung, Corinne Levy, Aurelie Cointe, Philippe Bidet, Claire Amaris Hobson, Stephane Bechet, Elsa Sobral, Hoang Vuthien, Agnes Ferroni, Said Aberrane, Gaelle Cuzon, Laetitia Beraud, Vincent Gajdos, Elise Launay, Didier Pinquier, Herve Haas, Marie Desmarest, Marie-Aliette Dommergues, Robert Cohen, Stephane Bonacorsi
Summary: The study investigated the impact of beta-lactamases and Enterobacterales' genotypes on the MICs of cefixime, cefpodoxime, mecillinam alone and combined with amoxicillin/clavulanate. The results showed that most isolates were resistant to cefixime and cefpodoxime, but susceptibility was restored with the addition of amoxicillin/clavulanate, indicating potential clinical efficacy. The in vivo efficacy of cefixime + amoxicillin/clavulanate combination therapy was satisfactory, even in cases of initial treatment failure, suggesting it as a viable option for FUTIs.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Microbiology
Razib Mazumder, Arif Hussain, Jody E. E. Phelan, Susana Campino, S. M. Arefeen Haider, Araf Mahmud, Dilruba Ahmed, Md Asadulghani, Taane G. G. Clark, Dinesh Mondal
Summary: The study reveals the presence of multi-resistant non-lactose fermenting E. coli strains responsible for intestinal and extraintestinal infections. Whole-genome sequencing and analysis identified high-risk clonal lineages and important genetic features. The findings suggest that non-lactose fermenting E. coli strains can cause infections and highlight the need for monitoring and prevention strategies.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Psychology, Developmental
Ulrike Ravens-Sieberer, Anne Kaman, Michael Erhart, Christiane Otto, Janine Devine, Constanze Loeffler, Klaus Hurrelmann, Monika Bullinger, Claus Barkmann, Nico A. Siegel, Anja M. Simon, Lothar H. Wieler, Robert Schlack, Heike Hoelling
Summary: The German COPSY study is a longitudinal study that examines the mental health impact of the COVID-19 pandemic on children and adolescents. The study found that during the pandemic, the health-related quality of life (HRQoL) of children and adolescents decreased, and there was an increase in emotional problems, peer-related mental health problems, anxiety, depressive symptoms, and psychosomatic complaints. Socially disadvantaged children and children of mentally burdened parents were more at risk of impaired mental health, while female gender and older age were associated with fewer mental health problems. A positive family climate and social support supported the mental health of children and adolescents during the pandemic.
EUROPEAN CHILD & ADOLESCENT PSYCHIATRY
(2023)
Article
Public, Environmental & Occupational Health
Andre Hajek, Freia De Bock, Christina Merkel, Sarah Eitze, Cornelia Betsch, Michael Bosnjak, Lothar H. Wieler, Hans-Helmut Koenig
Summary: This study aimed to shed light on attitudes towards influenza vaccination in Germany in 2021/2022 based on the COSMO survey. The results showed that about one-third of respondents and healthcare workers plan to get a flu shot this year. Among the at-risk group of people aged 60 and older, more than half plan to get vaccinated. Correlates, such as gender, were identified, with women having a lower likelihood of planning to get a flu shot. The study concludes that physicians should inform women, especially during the pandemic, about the advantages of influenza vaccination and communicate the proven protective effect convincingly.
Article
Biology
Sumeet K. Tiwari, Boas C. L. van der Putten, Thilo M. Fuchs, Trung N. Vinh, Martin Bootsma, Rik Oldenkamp, Roberto La Ragione, Sebastien Matamoros, Ngo T. Hoa, Christian Berens, Joy Leng, Julio Alvarez, Marta Ferrandis-Vila, Jenny M. Ritchie, Angelika Fruth, Stefan Schwarz, Lucas Dominguez, Maria Ugarte-Ruiz, Astrid Bethe, Charlotte Huber, Vanessa Johanns, Ivonne Stamm, Lothar H. Wieler, Christa Ewers, Amanda Fivian-Hughes, Herbert Schmidt, Christian Menge, Torsten Semmler, Constance Schultsz
Summary: This study analyzes the genetic determinants of host specificity in E. coli and identifies specific genes associated with different hosts. The nan-9 gene cluster shows a strong association with the human host, while previously known sialic acid regulon genes show no significant association with any host.
Article
Public, Environmental & Occupational Health
Simone Scheithauer, Alexander Dilthey, Anna Bludau, Sandra Ciesek, Victor Corman, Tjibbe Donker, Tim Eckmanns, Richard Egelkamp, Hajo Grundmann, Georg Haecker, Martin Kaase, Berit Lange, Alexander Mellmann, Martin Mielke, Mathias Pletz, Bernd Salzberger, Andrea Thuermer, Andreas Widmer, Lothar H. Wieler, Thorsten Wolff, Soeren Gatermann, Torsten Semmler
Summary: The deficit of genomic pathogen surveillance infrastructure in Germany has been revealed during the SARS-CoV-2 pandemic. Establishing an efficient and adaptable genomic pathogen surveillance network is urgently needed to prepare for future pandemics. This paper proposes measures based on global and country-specific best practices to achieve integrated genomic pathogen surveillance, which includes linking epidemiological data with pathogen genomic data, sharing and coordinating resources, making surveillance data available to decision-makers, public health service, and the scientific community, and engaging all stakeholders.
BUNDESGESUNDHEITSBLATT-GESUNDHEITSFORSCHUNG-GESUNDHEITSSCHUTZ
(2023)
Article
Public, Environmental & Occupational Health
Christopher Irrgang, Tim Eckmanns, Max von Kleist, Esther-Maria Antao, Katharina Ladewig, Lothar Wieler, Nils Koerber
Summary: Societal health is facing new challenges due to climate change, demographic ageing, and globalization. The One Health approach aims to understand health holistically by linking human, animal, and environmental sectors. Artificial intelligence techniques offer opportunities for cross-sectoral assessment of health threats. This article discusses the applications and challenges of AI techniques in the context of One Health, using antimicrobial resistance as an example.
BUNDESGESUNDHEITSBLATT-GESUNDHEITSFORSCHUNG-GESUNDHEITSSCHUTZ
(2023)
Article
Infectious Diseases
Bernd Salzberger, Alexander Mellmann, Anna Bludau, Sandra Ciesek, Victor Corman, Alexander Dilthey, Tjibbe Donker, Tim Eckmanns, Richard Egelkamp, Soeren G. Gatermann, Hajo Grundmann, Georg Haecker, Martin Kaase, Berit Lange, Martin Mielke, Mathias W. Pletz, Torsten Semmler, Andrea Thuermer, Lothar H. Wieler, Thorsten Wolff, Andreas F. Widmer, Simone Scheithauer
Summary: The COVID-19 pandemic has highlighted the importance of effective infection surveillance and infrastructure. Germany's genomic pathogen sequencing infrastructure was inadequate due to a lack of equipment, resources, data management, and coordination. The authors propose the establishment of comprehensive genomic pathogen surveillance in Germany, including sequencing, data collection, data linkage, and target pathogens, to better address future epidemics and pandemics and learn from the lessons of the COVID-19 pandemic.
Article
Genetics & Heredity
Claire K. A. Elek, Teagan L. Brown, Thanh Le Viet, Rhiannon Evans, David J. Baker, Andrea Telatin, Sumeet K. Tiwari, Haider Al-Khanaq, Gaetan Thilliez, Robert A. Kingsley, Lindsay J. Hall, Mark A. Webber, Evelien M. Adriaenssens
Summary: In this study, ten novel przondoviruses targeting Klebsiella spp. were successfully isolated and characterized. A hybrid and poly-polish phage assembly workflow named HYPPA was developed, which combined long-read and short-read sequencing to resolve the issue of phage chromosomal terminal repeats and correct errors, eliminating the need for laborious primer walking and Sanger sequencing validation. The study highlights the importance of careful curation of phage assemblies before publication and prior to using them for comparative genomics.
MICROBIAL GENOMICS
(2023)
Article
Medical Informatics
Anatol-Fiete Naeher, Carina N. Vorisek, Sophie A. Klopfenstein, Moritz Lehne, Sylvia Thun, Shada Alsalamah, Sameer Pujari, Dominik Heider, Wolfgang Ahrens, Iris Pigeot, Georg Marckmann, Mirjam A. Jenny, Bernhard Y. Renard, Max von Kleist, Lothar H. Wieler, Felix Balzer, Linus Grabenhenrich
Summary: Substantial opportunities for global health intelligence and research can be achieved through the combined and optimised use of secondary data within data ecosystems. This includes data from emerging sources such as the internet, wearables, mobile phone apps, electronic health records, and genome sequencing. Guidance on available sources and approaches for processing secondary data, as well as criteria for assessing reusability, can support policy decision making and improve early detection and prevention of emerging health threats.
LANCET DIGITAL HEALTH
(2023)
Article
Public, Environmental & Occupational Health
Benjamin F. Maier, Annika H. Rose, Angelique Burdinski, Pascal Klamser, Hannelore Neuhauser, Ole Wichmann, Lars Schaade, Lothar H. Wieler, Dirk Brockmann
Summary: After the winter of 2021/2022, a considerable number of people in Germany have been infected with or vaccinated against the SARS-CoV-2 variant. However, due to under-reporting and unknown overlap between the vaccinated and recovered populations, the exact extent is difficult to estimate. This study provides estimates of the share of immunologically naive individuals in each age group for the German population by integrating infectious-disease modeling and vaccine uptake data. The study shows that a significant proportion of the population in Germany remains immunologically naive, highlighting the impact of the Omicron waves.
EPIDEMIOLOGY AND INFECTION
(2023)
Article
Veterinary Sciences
Dordia Anindita Rotinsulu, Christa Ewers, Katharina Kerner, Amrozi Amrozi, Retno Damayanti Soejoedono, Torsten Semmler, Rolf Bauerfeind
Summary: This study aimed to characterize S. equi equi isolates obtained from suspected strangles cases in Indonesia in 2018. The results showed that all isolates belonged to ST179 and carried seM allele 166. The isolates differed from each other by only 2 to 14 cgSNPs and formed an exclusive sub-cluster within the BAPS-2 of S. equi equi cgMLST scheme. Furthermore, all isolates were susceptible to beta-lactam antibiotics penicillin G, ampicillin, and ceftiofur.
VETERINARY SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Katharine A. Seton, Marianne Defernez, Andrea Telatin, Sumeet K. Tiwari, George M. Savva, Antonietta Hayhoe, Alistair Noble, Ana L. S. de Carvalho-KoK, Steve A. James, Amolak Bansal, Thomas Wileman, Simon R. Carding
Summary: This study investigates the relationship between gut microbiome and immune function in patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). The results show immune dysfunction and reduced immune response to gut microbiota in these patients, providing a theoretical basis for further research on immune-microbiome interactions in ME/CFS patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)