Article
Immunology
Claire C. Bristow, Tatum D. Mortimer, Sheldon Morris, Yonatan H. Grad, Olusegun O. Soge, Erika Wakatake, Rushlenne Pascual, Sara McCurdy Murphy, Kyra E. Fryling, Paul C. Adamson, Jo-Anne Dillon, Nidhi R. Parmar, Hai Ha Long Le, Hung Van Le, Reyna Margarita Ovalles Urena, Nireshni Mitchev, Koleka Mlisana, Teodora Wi, Samuel P. Dickson, Jeffrey D. Klausner
Summary: By analyzing the genome sequencing and phenotypic antimicrobial susceptibility data of global N. gonorrhoeae isolates, it was found that a single genetic marker, gyrA codon 91, can accurately predict susceptibility to ciprofloxacin. However, multiple genetic markers are needed to accurately predict susceptibility to other antimicrobials.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Virology
Gloria Ramirez-Nieto, Daiana Mir, Diego Almansa-Villa, Geovanna Cordoba-Argotti, Magda Beltran-Leon, Nelida Rodriguez-Osorio, Jone Garai, Jovanny Zabaleta, Arlen P. P. Gomez
Summary: This study reports the complete genome sequence of Infectious Bronchitis virus (IBV) from Colombia for the first time. By analyzing the phylogenetic evolution and genomic characteristics, the study provides a deeper understanding of the evolution and recombination of different lineages of the virus in the region.
Editorial Material
Microbiology
Kartika Afrida Fauzia, Ricky Indra Alfaray, Yoshio Yamaoka
Summary: Helicobacter pylori antimicrobial resistance is a significant public health issue. Whole genome sequencing can provide a comprehensive understanding of resistance mechanisms and improve treatment efficacy to prevent gastric cancer.
Article
Microbiology
Thomas Weinmaier, Rick Conzemius, Yehudit Bergman, Shawna Lewis, Emily B. Jacobs, Pranita D. Tamma, Arne Materna, Johannes Weinberger, Stephan Beisken, Patricia J. Simner
Summary: Next-generation sequencing using Oxford Nanopore Technologies (ONT) is increasingly being used in clinical settings for detection and characterization of antimicrobial-resistant pathogens. ONT sequencing offers several advantages such as real-time basecalling, long sequencing reads, short turnaround times, and uncomplicated sample preparation. However, ONT sequencing has lower per-read accuracy compared to short-read sequencing. This study aimed to identify best practices in ONT sequencing protocols and found that different DNA extraction kits showed comparable performance, with the DNeasy PowerSoil Pro kit having the highest sequencing yield. The application of ONT sequencing for whole-genome sequencing antimicrobial susceptibility testing (WGS-AST) showed promising results with high categorical agreement for different antibiotics.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Oncology
Kris G. Samsom, Luuk J. Schipper, Paul Roepman, Linda J. W. Bosch, Ferry Lalezari, Elisabeth G. Klompenhouwer, Adrianus J. de Langen, Tineke E. Buffart, Immy Riethorst, Lieke Schoenmaker, Daoin Schout, Vincent van der Noort, Jose G. van den Berg, Ewart de Bruijn, Jacobus J. M. van der Hoeven, Hans van Snellenberg, Lizet E. van der Kolk, Edwin Cuppen, Emile E. Voest, Gerrit A. Meijer, Kim Monkhorst
Summary: This study aimed to evaluate the feasibility and efficacy of whole-genome sequencing (WGS) in routine clinical practice. The results showed that WGS can be successfully applied to patients with metastatic cancer, providing comprehensive genomic profiling for the majority of patients and identifying actionable biomarkers and treatment options.
JOURNAL OF PATHOLOGY
(2022)
Review
Microbiology
Matus Dohal, Igor Porvaznik, Ivan Solovic, Juraj Mokry
Summary: Infections caused by non-tuberculous mycobacteria (NTM) are a growing public health concern. Traditional diagnostic tests lack sufficient specificity, but whole genome sequencing (WGS) has emerged as a crucial tool for identifying new species and gene mutations in clinical practice.
Article
Veterinary Sciences
William B. Crosby, Brandi B. Karisch, Lari M. Hiott, Lee J. Pinnell, Alexandra Pittman, Jonathan G. Frye, Charlene R. Jackson, John Dustin Loy, William B. Epperson, John Blanton, Sarah F. Capik, Paul S. Morley, Amelia R. Woolums
Summary: This study aimed to evaluate the impact of tulathromycin metaphylaxis on antimicrobial resistance in MH isolated from stocker calves, and found that metaphylaxis increased the risk of isolation of multidrug resistant MH. However, the antimicrobial resistance genes identified in the isolated MH were primarily associated with integrative conjugative elements (ICE).
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Microbiology
David C. Gaston, Heather B. Miller, John A. Fissel, Emily Jacobs, Ethan Gough, Jiajun Wu, Eili Y. Klein, Karen C. Carroll, Patricia J. Simner
Summary: This study evaluated the performance of NGS workflows in detecting respiratory pathogens in BAL fluid specimens, with targeted RPIP workflow and untargeted metagenomic workflow showing similar performances, each with its own strengths and weaknesses.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Infectious Diseases
Alemitu Beyene Gebre, Tsegaye Alemayehu Begashaw, Moges Desta Ormago
Summary: This study investigated the bacterial profile and antimicrobial susceptibility pattern of lower respiratory tract infections among adult patients in Southern Ethiopia. Results showed a high prevalence of community acquired lower respiratory tract infections, with isolates demonstrating resistance to common antibiotics such as ampicillin and tetracycline. Culture and susceptibility testing are important for appropriate management of lower respiratory tract infections in this area.
BMC INFECTIOUS DISEASES
(2021)
Article
Biotechnology & Applied Microbiology
Yustinus Maladan, Hana Krismawati, Tri Wahyuni, Ratna Tanjung, Kamla Awaludin, Kholis Abdurachim Audah, Arli Aditya Parikesit
Summary: The study utilized whole-genome sequencing of TB clinical samples from Papua, Indonesia to detect mutations associated with TB-drug resistance, revealing multiple mutations in genes linked to resistance against various TB drugs. The results contribute to the surveillance of TB-drug resistance, identifying MDR samples but no XDR samples, with resistance mainly observed against the second-line drug Amikacin.
Article
Biotechnology & Applied Microbiology
Ahmer Bin Hafeez, Karolina Pelka, Kamila Buzun, Randy Worobo, Piotr Szweda
Summary: This study aimed to analyze the whole genome and assess the antimicrobial potential of bacterial isolates from honey in northern Poland. A total of 132 strains were obtained from three honey samples, and the antimicrobial activity of CFAM was used to select strains for detailed genomic investigation. Two isolates were classified as Bacillus paralicheniformis and one isolate as Bacillus subtilis, and all three isolates showed potential as producers of antimicrobial compounds.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Respiratory System
Robert Chapman, Luke Jones, Alberto D'Angelo, Ahmed Suliman, Muhammad Anwar, Stefan Bagby
Summary: Respiratory tract infection (RTI) is a significant global cause of morbidity and mortality. Traditional culture-based methods for identifying pathogens in respiratory samples are slow and prolong the use of broad-spectrum antimicrobial therapy. Nanopore sequencing (NPS) offers faster and more efficient pathogen identification and antimicrobial resistance profiling. However, there are questions regarding the clinical utility and implementation of NPS in RTI diagnostics.
Article
Microbiology
Zun Wu, Yating Wu, Haofeng Gao, Xuexin He, Qiang Yao, Zhanglei Yang, Jinyi Zhou, Linting Ji, Jinwei Gao, Xuying Jia, Yong Dou, Xiaoyu Wang, Peng Shao
Summary: V. vulnificus EPL 0201 biotype 2 is a multi-drug resistant strain with high pathogenicity in pearl gentian grouper. The strain possesses key virulence factor genes and exhibits resistance against multiple antibiotics.
Article
Microbiology
Xiaocui Wu, Guangkun Tan, Wei Sha, Haican Liu, Jinghui Yang, Yinjuan Guo, Xin Shen, Zheyuan Wu, Hongbo Shen, Fangyou Yu
Summary: In this study, whole-genome sequencing (WGS) was used to predict drug resistance of Mycobacterium tuberculosis complex (MTBC) from early positive liquid cultures. The results show that WGS could be a promising method for predicting MTBC resistance.
MICROBIOLOGY SPECTRUM
(2022)
Article
Immunology
Laura T. Phillips, Adam A. Witney, Martina Furegato, Ken G. Laing, Liqing Zhou, S. Tariq Sadiq
Summary: Early versions of nanopore technology show promise as a real-time surveillance tool, capable of accurately identifying closely related Neisseria gonorrhoeae strains and important antimicrobial resistance markers from cultured isolates, with very short sequencing times.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biotechnology & Applied Microbiology
Gretchen Tibbits, Abdelrhman Mohamed, Suzanne Gelston, Laure Flurin, Yash S. Raval, Kerryl E. Greenwood-Quaintance, Robin Patel, Haluk Beyenal
Summary: The activity of an electrochemical bandage producing hypochlorous acid (e-bandage) in preventing and removing biofilms formed by methicillin-resistant Staphylococcus aureus (MRSA) was assessed using a porcine explant biofilm model. The results showed that the e-bandage was effective in inhibiting MRSA infection and reducing the viable cell counts of MRSA biofilms.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Immunology
Robin Patel, Ephraim L. Tsalik, Scott Evans, Vance G. Fowler, Sarah B. Doernberg
Summary: The lack of a gold standard poses challenges in evaluating the accuracy of diagnostic tests for infectious diseases. Various approaches, such as multitest comparators and clinically adjudicated reference standards, can be used to overcome this challenge.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Microbiology
Thomas Weinmaier, Rick Conzemius, Yehudit Bergman, Shawna Lewis, Emily B. Jacobs, Pranita D. Tamma, Arne Materna, Johannes Weinberger, Stephan Beisken, Patricia J. Simner
Summary: Next-generation sequencing using Oxford Nanopore Technologies (ONT) is increasingly being used in clinical settings for detection and characterization of antimicrobial-resistant pathogens. ONT sequencing offers several advantages such as real-time basecalling, long sequencing reads, short turnaround times, and uncomplicated sample preparation. However, ONT sequencing has lower per-read accuracy compared to short-read sequencing. This study aimed to identify best practices in ONT sequencing protocols and found that different DNA extraction kits showed comparable performance, with the DNeasy PowerSoil Pro kit having the highest sequencing yield. The application of ONT sequencing for whole-genome sequencing antimicrobial susceptibility testing (WGS-AST) showed promising results with high categorical agreement for different antibiotics.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Microbiology
Nischal Ranganath, Joshua D. Shirley, Douglas W. Challener, Ryan W. Stevens, Dalton R. Kind, Isin Y. Comba, Robin Patel, Audrey N. Schuetz, Aditya S. Shah
Summary: Leptotrichia species are increasingly recognized as pathogens capable of causing invasive infections, especially among immunocompromised patients. However, there is limited data on the epidemiology, antimicrobial susceptibility, treatment, and clinical outcomes of Leptotrichia bacteremia. Evaluation of patient risk factors, treatment approaches, and outcomes, as well as examination of Leptotrichia isolates over the past decade, provided important insights. Evaluation of antimicrobial susceptibility testing is crucial due to evolving resistance patterns.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Microbiology
Scott A. Cunningham, Christophe Rodriguez, Paul-Louis Woerther, Christophe Menigaux, Thomas Bauer, Jean-Louis Herrmann, Martin Rottman, Anne-Laure Roux, Jean-Louis Gaillard, Robin Patel, Faten El Sayed
Summary: In this study, we report the first emergence of dual resistance to levofloxacin and rifampin in C. avidum in vivo, in a patient who received both antibiotics orally during salvage debridement and implant retention of an ODRI. This study highlights potential limitations of the combination of oral rifampin and levofloxacin in patients undergoing these surgical procedures and the potential need to evaluate specific optimal therapy for emerging ODRI pathogens.
MICROBIOLOGY SPECTRUM
(2023)
Article
Pharmacology & Pharmacy
Yash S. Raval, Derek Fleming, Abdelrhman Mohamed, Melissa J. Karau, Jayawant N. Mandrekar, Audrey N. Schuetz, Kerryl E. Greenwood-Quaintance, Haluk Beyenal, Robin Patel
Summary: A novel electrochemical bandage composed of carbon fabric and controlled by a wearable potentiostat is evaluated for its effectiveness against antibiotic-resistant bacterial biofilms in wound infections. The bandage, which continuously delivers low amounts of hydrogen peroxide, shows significant reductions in both monospecies and mixed-species wound infections without causing adverse reactions.
ADVANCED THERAPEUTICS
(2023)
Article
Immunology
Minggui Wang, Lizhao Ge, Liang Chen, Lauren Komarow, Blake Hanson, Jinnethe Reyes, Eric Cober, Thamer Alenazi, Zhiyong Zong, Qing Xie, Zhengyin Liu, Lanjuan Li, Yunsong Yu, Hainv Gao, Souha S. Kanj, Jairo Figueroa, Erica Herc, Ezequiel Cordova, Gregory Weston, Paul Ananth Tambyah, Julia Garcia-Diaz, Keith S. Kaye, Sorabh Dhar, Jose M. Munita, Robert A. Salata, Samuel Vilchez, Martin E. Stryjewski, Maria Virginia Villegas Botero, Alina Iovleva, Scott R. Evans, Keri Baum, Carol Hill, Barry N. Kreiswirth, Robin Patel, David L. Paterson, Cesar A. Arias, Robert A. Bonomo, Henry F. Chambers, Vance G. Fowler, Michael J. Satlin, David van Duin, Yohei Doi
Summary: In this international, prospective observational cohort of 842 hospitalized patients with carbapenem-resistant Acinetobacter baumannii, infection types and clinical outcomes differed significantly across regions. Although clonal group 2 (CG2) strains were predominant, non-CG2 strains were associated with higher mortality.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Heather R. Cross, Kerryl E. Greenwood-Quaintance, Maria Souli, Lauren Komarow, Holly S. Geres, Toshimitsu Hamasaki, Henry F. Chambers, Vance G. Fowler Jr, Scott R. Evans, Robin Patel
Summary: This article describes the key components involved in realizing the scientific agenda of the ARLG, including the roles and activities of the Scientific Leadership Center, Clinical Operations Center, Statistical and Data Management Center, and Laboratory Center.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Kimberly E. Hanson, Ritu Banerjee, Sarah B. Doernberg, Scott R. Evans, Lauren Komarow, Michael J. Satlin, Nyssa Schwager, Patricia J. Simner, L. Gayani Tillekeratne, Robin Patel
Summary: The Antibacterial Resistance Leadership Group prioritizes the advancement of diagnostics for infectious diseases and addresses the unmet needs in this field. Accurate diagnostics are critical in the fight against antibiotic-resistant bacterial infections.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Michael J. Satlin, David van Duin, Pranita D. Tamma, Thomas P. Lodise, Daria Van Tyne, Keith A. Rodvold, Nadine Rouphael, Scott R. Evans, Vance G. Fowler, Toshimitsu Hamasaki, Robin Patel, Lauren Komarow, Keri Baum, Maria Souli, Nyssa Schwager, Robert A. Bonomo, Yohei Doi
Summary: Addressing antibacterial-resistant gram-negative infections is a priority of the Antibacterial Resistance Leadership Group. The focus of investigation has evolved from elucidating the epidemiology of these infections to improving patient care through clinical trials of optimizing pharmacokinetics and of novel therapies.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Henry F. Chambers, Heather R. Cross, Maria Souli, Scott R. Evans, Robin Patel, Vance G. Fowler Jr
Summary: The Antibacterial Resistance Leadership Group (ARLG) has made important contributions to patient care, clinical trials design, and mentorship. Their research focuses on gram-positive and gram-negative infections as well as diagnostics. They have developed innovative approaches to clinical trials design, such as DOOR, and the MASTERMIND protocol for evaluating multiple infection diagnostics. They have also conducted research on bacteriophage therapy and have a mentorship program to attract and retain investigators in the field.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Scott R. Evans, Robin Patel, Toshimitsu Hamasaki, Jessica Howard-Anderson, Tori Kinamon, Heather A. King, Deborah Collyar, Heather R. Cross, Henry F. Chambers, Vance G. Fowler Jr, Helen W. Boucher
Summary: Clinical research networks conduct important studies and contribute to scientific advancements by developing new methodologies and tools, addressing common issues, and anticipating future research needs.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Critical Care Medicine
Naomi P. O'Grady, Earnest Alexander, Waleed Alhazzani, Fayez Alshamsi, Jennifer Cuellar-Rodriguez, Brian K. Jefferson, Andre C. Kalil, Stephen M. Pastores, Robin Patel, David van Duin, David J. Weber, Stanley Deresinski
CRITICAL CARE MEDICINE
(2023)
Article
Infectious Diseases
Luz Cuello, Judith Alvarez Otero, Kerryl E. Greenwood-Quaintance, Liang Chen, Blake Hanson, Jinnethe Reyes, Lauren Komarow, Lizhao Ge, Zane D. Lancaster, Garrett G. Gordy, Audrey N. Schuetz, Robin Patel
Summary: The MALDI Biotyper MBT Subtyping Module can detect Klebsiella pneumoniae carbapenemase (KPC) and p019 gene in Klebsiella species with high specificity, but has poor sensitivity in detecting bla(KPC)-positive isolates.
Article
Biology
Melissa J. Karau, Jay Mandrekar, Dario Lehoux, Raymond Schuch, Cara Cassino, Robin Patel
Summary: Orthopedic foreign body-associated infection is challenging to treat due to the formation of biofilms. A study found that exebacase, an antistaphylococcal lysin, showed significant reduction and bactericidal activity against MRSA biofilms. This supports further evaluation of exebacase as a potential treatment for orthopedic implant infections.
BMC RESEARCH NOTES
(2023)