Article
Microbiology
Live L. Nesse, Solveig S. Mo, Silje N. Ramstad, Ingun L. Witso, Camilla Sekse, Anna Eline E. Bruvoll, Anne Margrete Urdahl, Lene K. Vestby
Summary: Norwegian monitoring program detected Extended-spectrum cephalosporin-resistant Escherichia coli (ESCR E. coli) with plasmids carrying the bla(CMY-2) resistance gene in the Norwegian broiler production chain, which displayed relatively low biofilm forming abilities. The study found that these plasmids may cause the observed reduction in biofilm formation through changes in flagellar expression or function.
Article
Public, Environmental & Occupational Health
Xiaofan Zhang, Lingxia Chen, Xia Zhang, Qian Wang, Jingjing Quan, Jintao He, Hongying Pan, Xi Li
Summary: This study identified the co-existence of an IncHI2 plasmid carrying mcr-1.1 and an IncI1-I plasmid carrying blaNDM-5 in a clinical E. coli isolate for the first time. The research expands the known diversity of plasmids in NDM-5-producing Enterobacterales strains.
JOURNAL OF INFECTION AND PUBLIC HEALTH
(2022)
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
Microbiology
Amanda Brumwell, Granger Sutton, Paul M. M. Lantos, Kate Hoffman, Felicia Ruffin, Lauren Brinkac, Thomas H. H. Clarke, Mark D. D. Adams, Vance G. G. Fowler Jr, Derrick E. E. Fouts, Joshua T. T. Thaden
Summary: This study aims to further understand the risk factors, clinical outcomes, and bacterial genetics associated with ST131 bloodstream infections. A cohort study was conducted in which 88 out of 227 patients with E. coli bloodstream infection were infected with ST131. There was no significant difference in in-hospital mortality between patients with ST131 and non-ST131 infections overall, but ST131 was associated with higher mortality in patients with urinary tract infections.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Melek Ben Aissa, Sana Ferjani, Mohamed Salah Abassi, Nada Al-Suwailem, Ilhem Boutiba
Summary: In this study, an antibiotic resistance mechanism was identified in the eastern region of Saudi Arabia. The clonal relatedness within Gram-negative bacteria was also investigated. The presence of various resistance genes, including bla genes and plasmid-mediated quinolone resistance genes, was detected. The study also revealed the occurrence of previously unreported genes and the prevalence of certain clones in the region.
APPLIED SCIENCES-BASEL
(2022)
Article
Food Science & Technology
Xiaobo Liu, Ruichao Li, Edward Wai-Chi Chan, Xiaodong Xia, Sheng Chen
Summary: Multiple plasmids carrying resistance genes were found in a multidrug resistant E. coli strain. One plasmid had a resistance region of 17.3kb and a transfer region of 56.7kb. Another plasmid resembled the backbone of other IncI2 plasmids and contained multiple functional genes.
Article
Infectious Diseases
Mackenzie Dorr, Aryeh Silver, Dylan Smurlick, Ananta Arukha, Subhashinie Kariyawasam, Adelumola Oladeinde, Kimberly Cook, Thomas Denagamage
Summary: This study sequenced and annotated three plasmids carrying the bla(CTX-M-1) gene, and confirmed their transferability between different serovars and species of bacteria. The transfer of plasmids was successful, with varying frequencies depending on the donor strain.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2022)
Article
Microbiology
Gaelle Gruel, David Couvin, Stephanie Guyomard-Rabenirina, Guillaume Arlet, Jean-Christophe Bambou, Matthieu Pot, Xavier Roy, Antoine Talarmin, Benoit Tressieres, Severine Ferdinand, Sebastien Breurec
Summary: This study determines the prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in feces of household and shelter pets in Guadeloupe. The study finds that the only risk factor associated with a higher prevalence of ESBL-E rectal carriage is a stay in a shelter. The study also identifies ESBL-E as mainly Escherichia coli, with certain plasmids carrying antimicrobial resistance genes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jeannete Zurita, Gabriela Sevillano, Ariane Paz y Mino, Nathali Haro, Marco Larrea-Alvarez, Iliana Alcocer, David Ortega-Paredes
Summary: This study found an increase in ESBL-producing E. coli in bloodstream infections over the past 10 years, with a certain level of correlation between the isolates found during this period. The majority of these isolates were resistant to ceftriaxone, cefepime, ceftazidime, ampicillin/sulbactam, piperacillin/tazobactam, and ciprofloxacin, but not carbapenems. Over 80% of the isolates were classified as extraintestinal pathogenic E. coli, and the combination of virulence traits:papA-papC-kpsMII-uitA was the most common. Phylogroup B2 was the most prevalent, and the bacteria predominantly belonged to ST131.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Microbiology
Solveig Solverod Mo, Madelaine Norstrom, Jannice Schau Slettemeas, Anne Margrete Urdahl, Amar Anandrao Telke, Marianne Sunde
Summary: This study characterized extended-spectrum cephalosporin-resistant Escherichia coli isolates from broiler farms and found various sequence types and resistance gene/plasmid combinations. The research indicated the potential coexistence of different STs and resistance gene/plasmid combinations on the same farm, as well as the persistence of strains and plasmids on farms. Further investigation is needed to understand the dynamics of strains, plasmids, and resistance genes within specific broiler flocks.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Max Laurence Cummins, Cameron J. Reid, Steven Philip Djordjevic
Summary: Escherichia coli sequence type 95 (ST95) is a pathogenic bacteria known for causing illness in humans and poultry. A study analyzed the genome of 668 ST95 isolates and identified different clades based on the presence of specific plasmids. It was found that certain plasmids were predominantly present in isolates from humans, while others were found in isolates from both humans and poultry. Additionally, the study observed similar patterns in a diverse collection of 34,176 E. coli genomes. This research highlights the importance of plasmids in influencing the host range and zoonotic potential of E. coli.
Article
Infectious Diseases
Azza S. Zakaria, Eva A. Edward, Nelly M. Mohamed
Summary: This study characterizes the pathogenicity islands (PAIs) in the chromosome of a Uropathogenic Escherichia coli (UPEC) strain from Egypt. The strain belongs to the globally disseminated O25:H4-ST131 pandemic lineage. It carries multiple virulence-associated genes and shows a multidrug-resistant phenotype.
Article
Infectious Diseases
Mustafa Sadek, Alaaeldin Mohamed Saad, Patrice Nordmann, Laurent Poirel
Summary: This article describes the phenotypic and genomic characteristics of an extensively drug-resistant E. coli strain isolated from the urine of a hospitalized patient in Switzerland. The strain is resistant to almost all beta-lactam antibiotics and carries multiple resistance genes. It is susceptible to tigecycline, colistin, and fosfomycin.
Article
Microbiology
Hyeon Jin Choi, Seok Hoon Jeong, Kyeong Seob Shin, Young Ah Kim, Young Ree Kim, Hyun Soo Kim, Jong Hee Shin, Jeong Hwan Shin, Young Uh, Songmee Bae, Eun-Jeong Yoon, Jung Sik Yoo
Summary: This study assessed 636 cases of E. coli urinary tract infections in South Korea, identifying risk factors for bloodstream infections and characterizing the genetic diversity of E. coli isolates. The findings provide insights for treatment options and the prevalence of antimicrobial-resistant organisms.
MICROBIOLOGY SPECTRUM
(2022)
Article
Infectious Diseases
Amel Mhaya, Rahma Trabelsi, Sabine Aillerie, Fatima M'Zali, Dominique Begu, Slim Tounsi, Radhouane Gdoura, Corinne Arpin
Summary: Multiple ESBL-producing strains were identified in Tunisian patients, including two emerging virulent clones, ST131-C2 and ST131-C1-M27, which were found to be prevalent in both community and hospital settings.
Article
Geriatrics & Gerontology
Corinna Ernst, Yolanda Pires-Afonso, Dritan Bejko, Conny Huberty, Thomas G. Dentzer, Anke Wienecke-Baldacchino, Eric Hugoson, Daniel Alvarez, Murielle Weydert, Anne Vergison, Joel Mossong
Summary: In spring 2021, a long-term care facility in Luxembourg experienced a severe outbreak of SARS-CoV-2, with 154 residents affected. The outbreak occurred a few days after a vaccination campaign. The investigation revealed that 55% of residents and 26% of staff tested positive, with a high case-fatality rate of 27%. Whole genome sequencing identified a specific variant, B.1.1.420, responsible for the outbreak. Vaccinated and convalescent residents had higher antibody responses than vaccinated residents without infection. A single vaccine dose was insufficient to control the outbreak.
Article
Infectious Diseases
Jasmina Al Janabi, Staffan Tevell, Raphael Niklaus Sieber, Marc Stegger, Bo Soderquist
Summary: This study investigated the susceptibility of Staphylococcus epidermidis strains from prosthetic joint infections to dalbavancin and the genomic variation in strains with reduced susceptibility. The results suggest that exposure to dalbavancin may lead to reduced susceptibility through selection of pre-existing subpopulations, epigenetic changes, or spontaneous mutations during antibiotic exposure. Therefore, source control and adequate antibiotic concentrations are important to prevent emerging reduced susceptibility during dalbavancin treatment.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Environmental Sciences
Andre Becker Simoes Saidenberg, Leticia Soares Franco, Jessica Nacarato Reple, Yaovi Mahuton Gildas Hounmanou, Monique Ribeiro Tiba Casas, Brenda Cardoso, Fernanda Esposito, Nilton Lincopan, Anders Dalsgaard, Marc Stegger, Terezinha Knobl
Summary: Salmonella serovars Heidelberg and Minnesota with resistance to third-generation cephalosporins and fluoroquinolones are frequently found in Brazilian poultry. Genomic analysis revealed the presence of virulent and multidrug-resistant characteristics in these isolates, with AmpC beta-lactamase (bla(CMY-2)) predominance in Salmonella Minnesota (SM) and some Salmonella Heidelberg (SH) on IncC plasmid replicons. The study also identified close genetic similarity between the Brazilian isolates and poultry/food isolates from Europe, as well as human isolates from European countries importing Brazilian poultry meat. Overall, this research highlights the ongoing acquisition and dissemination of antimicrobial resistance in SH and Minnesota, raising concerns for importing countries and emphasizing the need to control AMR in major poultry-exporting countries like Brazil.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Microbiology
Sofie Kromann, Sharmin Baig, Rikke Heidemann Olsen, Sofie Marie Edslev, Ida Thofner, Anders Miki Bojesen, Henrik Elvang Jensen, Marc Stegger
Summary: In 2019-2020, a significant outbreak of colibacillosis occurred among Danish broilers, leading to increased mortality and condemnation rates. The causative E. coli strains were characterized using pathology and genetic analysis, revealing the severe impact of certain strains. This study provides important insights for future interventions and treatments.
VETERINARY MICROBIOLOGY
(2023)
Article
Microbiology
Shewli Mukerji, Shafi Sahibzada, Rebecca Abraham, Marc Stegger, David Jordan, David J. Hampson, Mark O'Dea, Terence Lee, Sam Abraham
Summary: Human population and activities contribute significantly to the spread of antimicrobial resistant bacteria. This study focused on the carriage rates of critically important antimicrobial-resistant (CIA-R) Escherichia coli and Klebsiella pneumoniae by Silver Gulls and their proximity to human populations. The results showed a high prevalence of CIA-R E. coli and K. pneumoniae in Silver Gulls in urban areas compared to remote locations, indicating a strong association between anthropogenic activities and the acquisition of resistant bacteria by gulls.
VETERINARY MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Maliha Aziz, Amber Palmer, Soren Iversen, Juan E. Salazar, Tony Pham, Kelsey Roach, Karsten Becker, Ursula Kaspar, Lance B. Price, Sharmin Baig, Marc Stegger, Paal Skytt Andersen, Cindy M. M. Liu
Summary: This study developed and validated a PCR assay for detecting D. pigrum with high sensitivity and specificity. The assay targeted the murJ gene, a single-copy core species gene identified through whole genome sequence analysis. It achieved 100% sensitivity and specificity against D. pigrum and diverse bacterial isolates, and 91.1% sensitivity using nasal swabs. This assay provides a valuable tool for investigating the role of generalist and specialist bacteria in the nasal environment.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Idris Nasir Abdullahi, Carmen Lozano, Myriam Zarazaga, Andre Becker Simoes Saidenberg, Marc Stegger, Carmen Torres
Summary: This study determined the nasal carriage rate of coagulase-positive staphylococci (CoPS) in healthy dogs and in-contact people and investigated their genotypic characteristics and phylogenetic relatedness. The results showed clonally related CoPS in humans and dogs within some households, highlighting the importance of continuous surveillance from a One Health perspective.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Pediatrics
C. Ooms, J. Mossong, A. Vergison, A. Biver, K. Wagner, O. Niel, A. Parrish, T. T. Abdelrahman, I. de la Fuente Garcia
Summary: This observational retrospective cohort study estimated the incidence of multisystem inflammatory syndrome (MIS-C) in children (0-15 years) and the role of SARS-CoV-2 variants during the first two years of the COVID-19 pandemic in Luxembourg. It also described the demographic, biological, and clinical characteristics of the patients. The study found that MIS-C incidence and risk per infection changed significantly over time, with a higher incidence observed during the circulation of the Delta variant and the lowest rate observed during the Omicron variant. These findings highlight the importance of monitoring MIS-C incidence in future waves and guiding public health interventions and vaccination policies for children.
FRONTIERS IN PEDIATRICS
(2023)
Article
Infectious Diseases
Tommy Nyberg, Peter Bager, Ingrid Bech Svalgaard, Dritan Bejko, Nick Bundle, Josie Evans, Tyra Grove Krause, Jim McMenamin, Joel Mossong, Heather Mutch, Ajibola Omokanye, Andre Peralta-Santos, Pedro Pinto-Leite, Jostein Starrfelt, Simon Thelwall, Lamprini Veneti, Robert Whittaker, John Wood, Richard Pebody, Anne M. Presanis
Summary: Several SARS-CoV-2 variants show differences in severity, and international collaborative studies are crucial for timely assessment. A study conducted by WHO Regional Office for Europe and ECDC demonstrated lower hospital admission, ICU admission, and death rates for Omicron BA.1 compared to Delta cases.
Article
Infectious Diseases
Pimlapas Leekitcharoenphon, Hakan Vigre, Rolf Sommer Kaas, Frank M. Aarestrup
Summary: This study analyzed 421 Salmonella Dublin genomes from cattle and food in Denmark to determine the trend of the bacterial population and the impact of intervention. The results showed a decrease in the population size of Salmonella Dublin in both cattle and humans, indicating the effectiveness of surveillance programs. Whole genome sequencing combined with phylogenetic analysis is an important tool for assessing the impact of control measures on bacterial population and human infection risk.
INFECTION GENETICS AND EVOLUTION
(2023)
Article
Medicine, General & Internal
Armita Armina Abedi, Claus Varnum, Alma Becic Pedersen, Kirill Gromov, Jesper Hallas, Pernille Iversen, Thomas Jakobsen, Espen Jimenez-Solem, Kristian Kidholm, Anne Kjerulf, Jeppe Lange, Anders Odgaard, Flemming S. Rosenvinge, Soren Solgaard, Kim Sperling, Marc Stegger, Robin Christensen, Soren Overgaard
Summary: Prosthetic joint infection (PJI) is a feared complication after total hip arthroplasty (THA) and is associated with high morbidity and mortality. Prophylactic antibiotics can reduce the risk of PJI, but there is no consensus on the dosages. This study aims to compare the effect of a single versus multiple doses of prophylactic antibiotics on PJI.
Article
Medicine, General & Internal
Man-Hung Eric Tang, Kim Lee Ng, Sofie Marie Edslev, Kirsten Ellegaard, Marc Stegger, Soren Alexandersen, Danish COVID Genom Consortium DCGC
Summary: A study found no significant statistical relationship between the levels of subgenomic RNAs in SARS-CoV-2 and host-related factors, suggesting that differences in target cell tropism, viral replication/transcription kinetics, or gene sequence features may contribute to the observed differences between lineages.
Article
Genetics & Heredity
Valeria Michelacci, Adrien Assere, Simone Caccio, Marina Cavaiuolo, Kirsten Mooijman, Stefano Morabito, Susanne Karlsmose Pedersen, Maroua Sayeb, Bo Segerman, Magnus Simonsson, Hanna Skarin, Rosangela Tozzoli, Angela van Hoek, Rene Sjogren Hendriksen
Summary: The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) has been working since 2017 to promote the adoption of NGS by the National Reference Laboratories (NRLs) in the European Union. By releasing guidance documents and working together, the EURLs have aimed to improve preparedness in the use of NGS for characterizing microbial hazards and tracing infection sources.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Gordan Kompes, Sanja Duvnjak, Irena Reil, Rene S. Hendriksen, Lauge Holm Sorensen, Maja Zdelar-Tuk, Boris Habrun, Luka Cvetnic, Antonela Bagaric, Silvio Spicic
Summary: In 2021, a multi-drug resistant E. coli strain with the mcr-1 gene was isolated from pig in Croatia. The isolate showed resistance to multiple antimicrobial classes and harbored various resistance genes and virulence genes. The mcr-1 gene was located within a conjugative plasmid, highlighting the importance of identifying mcr-1-carrying E. coli isolates in Croatia, especially in food-producing animals.
Article
Cell Biology
Omid Pajand, Hamzeh Rahimi, Farzad Badmasti, Faeze Gholami, Tahereh Alipour, Narges Darabi, Frank M. Aarestrup, Pimlapas Leekitcharoenphon
Summary: In this study, the transmission of bla(NDM-1) in K. pneumoniae in Iran was found to occur both clonally and horizontally via various combinations of mobile genetic elements (MGEs), with ST147 being the major clone associated with bla(NDM-1) dissemination. This is the first analysis of the Iranian ST147/NDM+ clone in the global context.
JOURNAL OF BIOMEDICAL SCIENCE
(2023)