Review
Immunology
Alicia G. Beukers, Frances Jenkins, Sebastiaan J. van Hal
Summary: Whole genome sequencing (WGS) is widely used in managing microbial outbreaks, but the current model of sending isolates to a central lab for sequencing has limitations. The slow rollout of WGS in clinical labs is due to the need for trained personnel and regulatory requirements. Onsite sequencing has benefits over centralized sequencing, allowing for collaboration with local infection control staff and rapid data analysis to understand transmission chains.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Kun Yin, Shanqing Huang, Weidong Ruan, Haopai Wei, He Dong, Dianyi Liang, Meijuan Zhao, Wei Qi, Chaoyong Yang, Zhi Zhu
Summary: Iso-seq is a rapid and uniform single-cell whole-genome sequencing method that uses a specially designed dual-well structure and a capillary-based centrifugal-driven droplet generator to isolate single cells and compartmentalize their genomes in droplets within 3 minutes. Iso-seq achieves high mapping ratio, broad coverage of the genome, and low coefficient of variation, making it promising for a wide variety of biological applications.
Article
Health Care Sciences & Services
Katie Dale, Maria Globan, Kristy Horan, Norelle Sherry, Susan Ballard, Ee Laine Tay, Simone Bittmann, Niamh Meagher, David J. Price, Benjamin P. Howden, Deborah A. Williamson, Justin Denholm
Summary: This study used whole genome sequencing to characterize the molecular epidemiology of tuberculosis and Mycobacterium tuberculosis transmission in a low-incidence setting in Victoria, Australia. The results suggest that Mtb transmission commonly occurs outside the household, particularly in social/religious settings. Further research is needed to optimize the use of whole genome sequencing in the public health management of tuberculosis.
LANCET REGIONAL HEALTH-WESTERN PACIFIC
(2022)
Article
Health Care Sciences & Services
Makenzie Beaman, Kimberley Fisher, Marie McDonald, Queenie K. G. Tan, David Jackson, Benjamin T. Cocanougher, Andrew P. Landstrom, Charlotte A. Hobbs, Michael Cotten, Jennifer L. Cohen
Summary: Rapid genome sequencing is crucial for providing targeted care to critically ill infants. A pilot study involving eight neonates showed a diagnostic rate of 37.5% using rapid whole genome sequencing alone, and 50% for the cohort overall. The diagnoses led to changes in management and identification of affected relatives. Challenges with sample collection were also discussed. The study also established a research protocol pipeline for cases where a diagnosis was not reached by rapid genome sequencing or other clinical testing. The benefits, limitations, challenges, and potential for incorporating rapid whole genome sequencing into routine clinical evaluation in the neonatal period were described.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Yuanhao Li, Bo Jiang, Weijun Dai
Summary: Essential genes are crucial for bacterial viability and new drug discovery, but some false positives generated by Tn-seq may result from gene deletions by bacteria themselves. Deleting genes should be considered when evaluating essentiality, as it has been underestimated in previous studies.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jayanthi Gangiredla, Hugh Rand, Daniel Benisatto, Justin Payne, Charles Strittmatter, Jimmy Sanders, William J. Wolfgang, Kevin Libuit, James B. Herrick, Melanie Prarat, Magaly Toro, Thomas Farrell, Errol Strain
Summary: GalaxyTrakr is a customized instance of the Galaxy platform designed for laboratory scientists conducting food safety regulatory research. It provides tools for quality assessment, linking clinical isolates with food/environmental samples, and exploring new methodologies like metagenomics. With over 600 registered users and 450,000 analytical jobs processed, it promotes collaboration across public health laboratories and supports consistent interpretation of results.
Book Review
Multidisciplinary Sciences
Heidi Ledford
Summary: Government responsibility for public health has influenced the nation's concept of freedom.
Article
Pathology
Katherine A. Lau, Anders Goncalves da Silva, Torsten Theis, Joanna Gray, Susan A. Ballard, William D. Rawlinson
Summary: The widespread adoption of whole genome sequencing (WGS) data for pathogen surveillance and infectious disease decision-making requires ensuring data quality standards are met for accurate identification and monitoring of pathogens. The development of a pilot proficiency testing program helps establish baseline guidelines for standardization of WGS data and facilitates accreditation of test processes through ongoing performance benchmarking.
Article
Environmental Sciences
Avram Levy, Jake Gazeley, Terence Lee, Andrew Jardine, Cameron Gordon, Natalie Cooper, Richard Theobald, Clare Huppatz, Sandra Sjollema, Meredith Hodge, David Speers
Summary: Western Australia was mostly free of COVID-19 from March 2020 to 2022, with limited community transmission. However, genomic analysis of wastewater samples showed that even a small number of positive individuals could be used to identify the source of active cases and rule out transmission between different catchments.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Immunology
Praveen Kumar, Alexander J. Sundermann, Elise M. Martin, Graham M. Snyder, Jane W. Marsh, Lee H. Harrison, Mark S. Roberts
Summary: A study developed an infection prevention program based on WGS surveillance, finding it to be more cost-effective and efficient in preventing hospital outbreaks compared to standard of care. The cost of performing WGS and the number of isolates sequenced per year under WGS surveillance were identified as key factors affecting the economic value.
CLINICAL INFECTIOUS DISEASES
(2021)
Review
Medicine, General & Internal
Arturo Ortega-Arroyo, Maria Delmans Flores-Chavez, Jesus Puente-Alcaraz
Summary: This systematic scoping review demonstrates that the simultaneous use of at least two immunochromatographic rapid tests is a valid option for the definitive diagnosis of chronic Chagas in endemic rural areas. Further studies in more countries are necessary to provide additional evidence and investigate cost-effectiveness.
Article
Multidisciplinary Sciences
Kathy E. Raven, Sophia T. Girgis, Asha Akram, Beth Blane, Danielle Leek, Nicholas Brown, Sharon J. Peacock
Summary: The study introduces a universal protocol for simultaneous DNA extraction and sequencing of multiple bacterial species, demonstrating high reproducibility and effectiveness. The addition of lysozyme and lysostaphin together proved to be essential for generating sufficient DNA across all 20 tested species, supporting low-volume and rapid turnaround time for local clinical microbiology laboratories.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Yee Mey Seah, Mary K. K. Stewart, Daniel Hoogestraat, Molly Ryder, Brad T. T. Cookson, Stephen J. J. Salipante, Noah G. G. Hoffman
Summary: The identification and analysis of clinically relevant bacteria strains increasingly rely on whole-genome sequencing. However, the accuracy of variant callers for short-read sequences has seldom been validated against haploid genomes. In this study, a computational workflow was developed to introduce mutations into bacterial reference genomes and generate synthetic sequencing reads. The method was applied to three different bacterial strains, and several variant callers were evaluated using the synthetic reads as a truth set. The results showed that variant callers with high-quality soft-clipped reads and base mismatches had the highest precision and recall for identifying insertions and deletions.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Microbiology
Arnon Chukamnerd, Kongpop Jeenkeawpiam, Sarunyou Chusri, Rattanaruji Pomwised, Kamonnut Singkhamanan, Komwit Surachat
Summary: This paper introduces BacSeq, an automated bioinformatics pipeline for analyzing bacterial genome sequencing data. BacSeq enables the assembly, annotation, and identification of key genes related to multidrug resistance, virulence factors, and plasmids in bacterial genomes. Additionally, the pipeline allows for comparative analysis among different isolates, including phylogenetic tree analysis and identification of single-nucleotide polymorphisms (SNPs). To facilitate easy analysis and support processing of multiple isolates, BacSeq provides a graphical user interface (GUI) based on the JAVA platform, specifically designed for users without extensive bioinformatics skills.
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
Respiratory System
Andries J. van Tonder, Huw C. Ellis, Colin P. Churchward, Kartik Kumar, Newara Ramadan, Susan Benson, Julian Parkhill, Miriam F. Moffatt, Michael R. Loebinger, William O. C. Cookson
Summary: This study investigates the transmission potential of Mycobacterium avium complex (MAC) among CF and non-CF patients. The results show possible transmission clusters for MAC species, but few epidemiological links were found. Global transmission clusters of Mycobacterium chimaera were associated with heater-cooler units, but the initial ancestor was already circulating among patients.
EUROPEAN RESPIRATORY JOURNAL
(2023)
Article
Microbiology
Shukrani Phillip, Martha F. Mushi, Arun Gonzales Decano, Jeremiah Seni, Blandina T. Mmbaga, Happiness Kumburu, Eveline T. Konje, Joseph R. Mwanga, Benson R. Kidenya, Betrand Msemwa, Stephen Gillespie, Antonio Maldonado-Barragan, Alison Sandeman, Wilber Sabiti, Mathew T. G. Holden, Stephen E. Mshana
Summary: This study aimed to determine the virulence potential, antimicrobial resistance genes, and sequence types of coagulase-negative Staphylococci (CoNS) isolated from patients with urinary tract infection (UTI) symptoms and pyuria in Tanzania. Out of 65 CoNS isolates, Staphylococcus haemolyticus and Staphylococcus epidermidis were the predominant species, and they harbored virulence genes and antimicrobial resistance genes associated with UTI. Follow-up studies are needed to document the outcome of treated patients and provide more evidence that CoNS are UTI pathogens.
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
Public, Environmental & Occupational Health
Emmanuel Olamijuwon, Eveline Konje, Catherine E. Kansiime, Mike F. Kesby, Katherine Keenan, Stella Neema, Benon Asiimwe, Stephen J. Mshana, Martha Mushi, Olga R. Loza, Benjamin Sunday, Alison Sandeman, Derek Sloan, Fernando Benitez-Paez, Joseph Mwanga, Wilber Sabiiti, Matthew T. G. Holden
Summary: This study explores the drug seller-client interaction and antibiotic dispensing patterns for simulated COVID-19 symptoms in Tanzania and Uganda. The findings indicate low adherence to COVID-19 preventive measures, dispensing of prescription-only antibiotics without prescription, and providing incomplete doses of antibiotics by drug sellers.
ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL
(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
Multidisciplinary Sciences
Barbra Tuhamize, Benon B. Asiimwe, Kennedy Kasaza, Wilber Sabiiti, Mathew Holden, Joel Bazira
Summary: This study found that a high percentage of Escherichia coli strains isolated from humans and livestock in rural south western Uganda carry the blaKPC gene, with a significant proportion of strains not actively expressing the gene. The results suggest that besides the KPC gene, other mechanisms may be involved in carbapenem resistance.
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
Rachida Namoune, Abla Djebbar, Rebecca Mekler, Martin Mchugh, Mohammed El Amine Bekara, Arun Decano, Matthew T. G. Holden, Mohammed Sebaihia
Summary: This study used whole genome sequencing to analyze the genotypes and genetic determinants of antimicrobial resistance in clinical isolates of Staphylococcus aureus from two hospitals in Algeria. The isolates showed high rates of multidrug resistance, with the ST80 type being predominant. The results emphasize the importance of continuous surveillance to monitor the spread of S. aureus in healthcare settings.
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)
Letter
Immunology
Nick K. Jones, Juliana Coelho, Julie M. J. Logan, Karen Broughton, Katie L. Hopkins, Bruno Pichon, Isabelle Potterill, Yu Wan, Alex W. N. Reid, Theodore Gouliouris
EMERGING INFECTIOUS DISEASES
(2023)
Article
Public, Environmental & Occupational Health
Dominique L. Green, Katherine Keenan, Kathryn J. Fredricks, Sarah Huque, Martha F. Mushi, Catherine Kansiime, Benon Asiimwe, John Kiiru, Stephen E. Mshana, Stella Neema, Joseph R. Mwanga, Mike Kesby, Andy G. Lynch, Hannah Worthington, Emmanuel Olamijuwon, Mary Abed Al Ahad, Annette Aduda, John Mwaniki Njeru, Blandina T. Mmbaga, Joel Bazira, Alison Sandeman, John Stelling, Stephen H. Gillespie, Gibson Kibiki, Wilber Sabiiti, Derek J. Sloan, Matthew T. G. Holden, the H. A. T. U. A. Consortium HATUA Consortium
Summary: This study investigated the relationship between multidimensional poverty and antibiotic use in patient populations in Kenya, Tanzania, and Uganda. The results showed that regardless of poverty status, structural barriers such as inefficiencies in public health care, financial constraints, and unregulated antibiotic access contribute to antibiotic misuse and treatment non-adherence. When designing interventions to reduce antibiotic misuse and address antimicrobial resistance, greater attention should be paid to these structural barriers.
LANCET GLOBAL HEALTH
(2023)