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
Microbiology
Rodrigo E. Mendes, Cory Hubler, J. H. Kimbrough, Valerie Kantro, Ian Critchley, Nicole Cotroneo, Mariana Castanheira
Summary: This study investigated the activity of oral carbapenem tebipenem against various subsets of Escherichia coli, and found that it showed good efficacy in screening for β-lactamases.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Infectious Diseases
Xuan Liu, Xin Li, A-wen Yang, Bin Tang, Zi-juan Jian, Yi-ming Zhong, Hong-ling Li, Yan-ming Li, Qun Yan, Xiang-hui Liang, Wen-en Liu
Summary: This study found a high carriage rate of ESBL-EC among healthy children, with CTX-M-14 being the dominant ESBL type. Additionally, high-risk clones were also detected.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Public, Environmental & Occupational Health
Veronica Weterings, Wouter van den Bijllaardt, Martin Bootsma, Yvonne Hendriks, Linda Kilsdonk, Ans Mulders, Jan Kluytmans
Summary: This study assessed the duration of rectal ESBL-producing E. coli colonization and found a prolonged colonization with ESBL-ST131. Subgroup analysis showed that the prolonged duration was mainly found in residents who were ESBL-EC positive at the beginning of the study. The previous study's results may have been biased by factors that occurred during the outbreak.
ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL
(2022)
Article
Infectious Diseases
Mario Galindo-Mendez, Humberto Navarrete-Salazar, Francisco Baltazar-Jimenez, Eduardo Munoz-de La Paz, Maria Fernanda Sanchez-Mawcinitt, Alexis Gomez-Pardo, Elvira Garza-Gonzalez, Luis Alfredo Ponce-de-Leon-Garduno, Rafael Franco-Cendejas, Rayo Morfin-Otero, Fabian Rojas-Larios, Juan Pablo Mena-Ramirez, Cecilia Teresita Morales-de-la-Pena, Lourdes Garcia-Mendoza, Elena Victoria Choy-Chang, Laura Karina Aviles-Benitez, Eduardo Lopez-Gutierrez, Jorge Luis Canizales-Oviedo, Nicolas Eric Barlandas-Rendon, Joyarib Yanelli Maldonado-Anicacio, Alina Aracely Rosales-Garcia, Heidy Leticia Ostos-Cantu
Summary: This study investigated the resistance mechanisms of ESBL-producing E. coli strains against fosfomycin. The results showed that fosA3 and fosA1 genes played important roles in fosfomycin resistance, and there was a strong association between fos and bla(CTX-M) genes and ST131 clones in uropathogenic E. coli.
Article
Infectious Diseases
Ahlem Jouini, Amira Klibi, Imen Elarbi, Meriem Ben Chaabene, Safa Hamrouni, Oussema Souiai, Mariem Hanachi, Abdeljelil Ghram, Abderrazak Maaroufi
Summary: The study found ESBL and AmpC beta-lactamase producing multi-resistant E. coli isolates in poultry with diarrhea in Tunisia. These strains carried various beta-lactamase genes, including the high-risk ST131-CTX-M-15-O25-B2 clone.
Article
Public, Environmental & Occupational Health
Melanie T. Mahoney, Hunter Brigman, Brian D. Johnston, James R. Johnson, Elizabeth B. Hirsch
Summary: This study characterized and compared Escherichia coli urine isolates from medical centers in Minneapolis and Boston, and found that ESBL production and virulence gene scores were higher in Boston isolates. The C1-M27 subclone and blaCTX-M-27 were unique to Boston isolates. More surveillance is needed to determine the prevalence of the globally successful C1-M27 subclone of ST131 in the United States.
AMERICAN JOURNAL OF INFECTION CONTROL
(2023)
Article
Microbiology
Rory Cave, Mary M. Ter-Stepanyan, Hermine V. Mkrtchyan
Summary: Whole-genome sequencing analysis combining short and long reads provided important genetic information for understanding the transmission and evolution of ESBL-producing uropathogenic E. coli (UPEC) ST131 isolates recovered in Armenia. Hybrid genome assembly in countries without genomic surveillance studies can reveal new lineages with high virulence and antibiotic resistance genes on mobile genetic elements. This study analyzed four ESBL-producing E. coli ST131 isolates from patients in Armenia using both Illumina short-read and Oxford Nanopore Technologies long-read sequencing, identifying their genotypes and phylogeny. The isolates were closely related to those from the European Nucleotide Archive (ENA) database and carried important virulence genes and rare genetic elements.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
Faustinos Tatenda Takawira, Johann Dd Pitout, Gaetan Thilliez, Tapfumanei Mashe, Ana Victoria Gutierrez, Robert A. Kingsley, Gisele Peirano, Jorge Matheu, Stanley M. Midzi, Lusubilo W. Mwamakamba, David L. Gally, Andrew Tarupiwa, Leckson Mukavhi, Marthie M. Ehlers, Sekesai Mtapuri-Zinyowera, Marleen M. Kock
Summary: This study investigated ESBL-producing extraintestinal pathogenic Escherichia coli associated with urinary tract infections in different regions of Zimbabwe from 2017 to 2019. The results showed ST131 and ST410 as the predominant resistant clones, with an increasing trend in ESBL-producing E. coli strains over time. The establishment and evolution of ESBL clones in Zimbabwe pose a significant public health threat, highlighting the importance of continuous monitoring and targeted control programs for specific STs, such as ST131 and ST410, to reduce the spread of ESBLs among ExPEC.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
Article
Genetics & Heredity
Shiwen Xu, Yunfei Wu, Yingqi Liu, Ping Zhao, Zhuo Chen, Fan Song, Hu Li, Wanzhi Cai
Summary: This study focused on the comparative mitogenomic analysis of 55 species from eight common families of Pentatomoidea, revealing heterogeneity in base composition and contrasting evolutionary rates, especially in Urostylididae. Phylogenetic analyses under site-homogenous models showed more stable tree topologies with exclusion of Urostylididae or removal of third codon positions of protein coding genes, while analyses under the site-heterogeneous mixture model consistently recovered the relationships between families within Pentatomoidea.
Article
Virology
Reimar Johne, Simon H. Tausch, Rainer G. Ulrich, Katja Schilling-Loeffler
Summary: Rotaviruses are responsible for diarrhea in humans and animals. A new strain, RVK, was identified in common shrews in Germany and was found to be a separate species with low sequence identity to other rotavirus reference strains. Phylogenetic analysis showed that RVK and RVC formed a common branch within the RVA-like phylogenetic clade. Comparison of nucleotide sequences of other RVK strains from common shrews in Germany indicated high sequence variability within the putative species. RVK represents a novel rotavirus species closely related to RVC.
Article
Biochemistry & Molecular Biology
Gulraiz Ahmad, Aqsa Khalid, Muhammad Usman Qamar, Nasir Rasool, Malik Saadullah, Muhammad Bilal, Majed A. Bajaber, Ahmad J. Obaidullah, Hadil Faris Alotaibi, Jawaher M. Alotaibi
Summary: This study investigated the antibacterial activity of synthesized N-(4-methylpyridin-2-yl) thiophene-2-carboxamides (4a-h) against ESBL-producing E. coli ST131 strains. The isolates were identified as ESBL producers carrying the blaCTX-M gene, which provided resistance against cephalosporins and beta-lactam inhibitors but sensitivity to carbapenems. Compounds 4a and 4c exhibited high activity and showed the best fit and interactions with the binding pocket of the beta-lactamase enzyme.
Article
Virology
Reimar Johne, Katja Schilling-Loeffler, Rainer G. Ulrich, Simon H. Tausch
Summary: Rotaviruses, known for causing diarrhea in humans and animals, have been classified into species A to J, with potential new species K and L recently identified. Through genome analysis, strain KS14/0241 has been classified as a prototype strain of the novel rotavirus species L, showing only 47% identity to reference strains. Phylogenetic analyses show that species L clusters separately from known rotavirus species, with a close relationship to RVH and RVJ.
Article
Forestry
Xue-Jiao Zhang, Kang-Jia Liu, Ya-Chao Wang, Jian He, Yuan-Mi Wu, Zhi-Xiang Zhang
Summary: High genetic diversity and low differentiation in Salix present challenges in taxonomy and systematics. The chloroplast genomes of three shrubby willows were sequenced and analyzed, revealing high similarity among them. Phylogenetic analysis placed these willows in specific clades, providing insights into the evolutionary history of Salicaceae.
Article
Forestry
Huijuan Zhou, Xiaoxiao Gao, Keith Woeste, Peng Zhao, Shuoxin Zhang
Summary: Chloroplast (cp) DNA genomes of Castanea species show similar genomic structures with differences in gene loss and pseudogenization in certain genes. These findings contribute to a better understanding of the evolutionary history and phylogenetic relationships of chestnut species.
Article
Veterinary Sciences
Sara Frosth, Ellen Ruth A. Morris, Hayley Wilson, Lars Frykberg, Karin Jacobsson, Julian Parkhill, Jan-Ingmar Flock, Tim Wood, Bengt Guss, David M. Aanensen, Ashley G. Boyle, Miia Riihimaki, Noah D. Cohen, Andrew S. Waller
Summary: This study analysed the antigen sequences of 759 isolates of Streptococcus equi from around the world and found that the antigen sequences in the Strangvac vaccine are highly conserved.
EQUINE VETERINARY JOURNAL
(2023)
Article
Immunology
Refath Farzana, Lim S. Jones, Md Anisur Rahman, Kirsty Sands, Andries J. van Tonder, Edward Portal, Jose Munoz Criollo, Julian Parkhill, Martyn F. Guest, W. John Watkins, Monira Pervin, Ian Boostrom, Brekhna Hassan, Jordan Mathias, Md Abul Kalam, Timothy R. Walsh
Summary: This study is the largest study from a South Asian public hospital combining clinical outcomes, microbiology, and genomics. The findings demonstrate the urgent need for targeted diagnostics, appropriate antibiotic use, and infection-control interventions in South Asian public institutions.
CLINICAL INFECTIOUS DISEASES
(2023)
Review
Gastroenterology & Hepatology
L. R. Caley, H. White, M. C. de Goffau, R. A. Floto, J. Parkhill, B. Marsland, D. G. Peckham
Summary: Gut dysbiosis is evident in individuals with cystic fibrosis (CF), characterized by reduced diversity and taxonomic changes. The relationship between gut dysbiosis and systemic and lung inflammation is limited. The causes of gut dysbiosis are multifactorial and the impact of CFTR modulators on the gut microbiota is still unclear.
DIGESTIVE DISEASES AND SCIENCES
(2023)
Article
Infectious Diseases
Katja Kero, Niina Hieta, Teemu Kallonen, Anne Ahtikoski, Hanna K. Laine, Jaana Rautava, Eveliina Munukka
Summary: Next-generation sequencing-based microbiological analysis is a complex method that can profile vaginal microbiome samples, with each step affecting the obtained results. Comparison between Puritan DNA/RNA swab (PS) and Copan FLOQ swab (CS) showed consistent and reliable microbiome profiles. Alpha and beta diversities were evaluated and compared between the two sampling methods, with no significant statistical differences found. Lactobacillus-dominated vaginal microbiome profiles were observed in 43% of women, regardless of the collection method.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2023)
Article
Multidisciplinary Sciences
Jody Phelan, Paula Josefina Gomez-Gonzalez, Nuria Andreu, Yosuke Omae, Licht Toyo-Oka, Hideki Yanai, Reiko Miyahara, Supalert Nedsuwan, Paola Florez de Sessions, Susana Campino, Neneh Sallah, Julian Parkhill, Nat Smittipat, Prasit Palittapongarnpim, Taisei Mushiroda, Michiaki Kubo, Katsushi Tokunaga, Surakameth Mahasirimongkol, Martin L. Hibberd, Taane G. Clark
Summary: This study identified eight genetic interaction points associated with susceptibility to tuberculosis, including human loci DAP and RIMS3, as well as FSTL5. The analysis supports the co-evolution and adaptation between host and pathogen in tuberculosis.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Sara E. Croxford, Veronique Martin, Sebastian B. Lucas, Robert F. Miller, Frank A. Post, Jane Anderson, Vanessa J. Apea, David Asboe, Garry Brough, David R. Chadwick, Simon Collins, Helen Corkin, Gillian Dean, Valerie C. Delpech, Maka Gogia, Deborah Gold, Anna Kafkalias, Marilena Korkodilos, Justyna D. Kowalska, Jacqueline Lindo, Jens D. Lundgren, Lucy Lynch, Esteban Martinez, Niall McDougall, Sarah North, Juergen K. Rockstroh, Caroline Sabin, Maria Vidal-Read, Laura J. Waters, Ann K. Sullivan
Summary: This paper presents consensus recommendations on defining preventable HIV-related mortality for public health monitoring using national HIV surveillance data. The study found that in the UK, 30% of deaths among people with HIV were HIV-related or possibly HIV-related, and at least 63% of these deaths were preventable or potentially preventable. The application of these recommendations by health authorities will ensure consistent monitoring of HIV elimination targets and identification of inequalities and areas for intervention.
Article
Microbiology
Romney M. Humphries, Eugene Bragin, Julian Parkhill, Grace Morales, Jonathan E. Schmitz, Paul A. Rhodes
Summary: The declining cost of bacterial whole-genome sequencing and the availability of sequence data have allowed the development of machine-learning models for predicting drug susceptibility in Escherichia coli. In this study, a ML-based model was tested for predicting the susceptibility of cefepime, a commonly used drug, in E. coli isolates. The results showed that the ML model had a high level of agreement with the reference method, indicating its potential use in clinical practice.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ram P. Maharjan, Geraldine J. Sullivan, Felise G. Adams, Bhumika S. Shah, Jane Hawkey, Natasha Delgado, Lucie Semenec, Hue Dinh, Liping Li, Francesca L. Short, Julian Parkhill, Ian T. Paulsen, Lars Barquist, Bart A. Eijkelkamp, Amy K. Cain
Summary: Using functional genomics, we have identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in Acinetobacter baumannii. DksA controls various aspects such as ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization. This study lays the groundwork for understanding the role of DksA as a major regulator in stress response and virulence in this important pathogen.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Dorota Jamrozy, Guduru Gopal Rao, Theresa Feltwell, Theresa Lamagni, Priya Khanna, Androulla Efstratiou, Julian Parkhill, Stephen D. D. Bentley
Summary: This study characterized the population structure of GBS isolates from pregnant women in London and found that the majority of isolates belonged to five main lineages. The study also identified nine serotypes, with III, V, II, and Ia being the most common. Moreover, it revealed associations between maternal ethnicity and GBS population structure.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Christopher Ruis, Thomas P. Peacock, Luis M. Polo, Diego Masone, Maria Soledad Alvarez, Angie S. Hinrichs, Yatish Turakhia, Ye Cheng, Jakob McBroome, Russell Corbett-Detig, Julian Parkhill, R. Andres Floto
Summary: Through mutational spectrum analysis, we found distinct mutational patterns in SARS-CoV-2 variants, with the Omicron variant showing reduced G>T mutations compared to other lineages. The mutational analysis also revealed a strong association of high G>T mutations with replication in the lower respiratory tract. Monitoring mutation rates over time showed early divergence of Omicron from Beta, Gamma, and Delta, while the mutational patterns in Alpha varied with changes in transmission source.
MICROBIAL GENOMICS
(2023)
Review
Genetics & Heredity
Gerry Tonkin-Hill, Jukka Corander, Julian Parkhill
Summary: Horizontal gene transfer (HGT) and patterns of gene gain and loss are essential in bacterial evolution. Understanding these patterns can shed light on selection's role in the evolution of bacterial pangenomes and bacterial adaptation to new niches. However, predicting gene presence or absence can be prone to errors, which can complicate the study of HGT dynamics. This review discusses the challenges of constructing accurate pangenomes and the potential consequences of errors on downstream analyses, with the goal of improving bacterial pangenome analyses.
MICROBIAL GENOMICS
(2023)
Article
Genetics & Heredity
Jo Dicks, Mohammed-Abbas Fazal, Karen Oliver, Nicholas E. Grayson, Jake D. Turnbull, Evangeline Bane, Edward Burnett, Ana Deheer-Graham, Nancy Holroyd, Dorota Kaushal, Jacqueline Keane, Gemma Langridge, Jane Lomax, Hannah McGregor, Steve Picton, Michael Quail, Deepak Singh, Alan Tracey, Jonas Korlach, Julie E. Russell, Sarah Alexander, Julian Parkhill
Summary: The National Collection of Type Cultures (NCTC) was established in 1920 in the UK to centralize bacterial and fungal strains. It is one of the oldest collections of this kind worldwide, holding about 6000 strains with medical and scientific importance, available for global academic and veterinary institutions. The NCTC3000 project, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute, aims to sequence and assemble the genomes of up to 3000 NCTC strains.
MICROBIAL GENOMICS
(2023)
Article
Infectious Diseases
My H. Pham, Le Thi Hoi, Mathew A. Beale, Fahad A. Khokhar, Nguyen Thi Hoa, Patrick Musicha, Grace A. Blackwell, Hoang Bao Long, Dang Thi Huong, Nguyen Gia Binh, Dao Xuan Co, Tran Giang, Cuong Bui, Hai Ninh Tran, James Bryan, Archie Herrick, Theresa Feltwell, Behzad Nadjm, Julian Parkhill, Hindrik Rogier van Doorn, Nguyen Vu Trung, Nguyen Van Kinh, Mili Estee Torok, Nicholas R. Thomson
Summary: A study in Hanoi, Vietnam, highlights the high prevalence of ESBL-positive carbapenem-resistant K pneumoniae in intensive care units. The study also reveals that the important resistance genes are carried broadly by patients entering the two hospitals directly or through referral.
Article
Microbiology
Juan M. Belardinelli, Divya Arora, Charlotte Avanzi, William H. Wheat, Josephine M. Bryant, John S. Spencer, Tom L. Blundell, Julian Parkhill, R. Andres Floto, Mary Jackson
Summary: Functional genomics analysis of Mycobacterium abscessus clinical isolates revealed phoR as one of the genes under strong evolutionary pressure during lung adaptation. This study demonstrated that acidic pH upregulates phoP in M. abscessus and that clinically relevant non-synonymous mutations in PhoR exacerbate this response. PhoR modulates the autoregulation of its cognate response regulator, PhoP, by controlling its dephosphorylation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Susannah J. Salter, Robyn L. Marsh, Julian Parkhill
Summary: This study reports the complete genome sequence of the Ornithobacterium hominis type strain MSHR-COH1 (ATCC TSD-185/NCTC 14317), a bacterial species isolated from the human nasopharynx. Long-read sequencing reveals that the genome is 2,036,909 bp in length, with a GC content of 35.72%.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
