Article
Microbiology
Jie Sheng, Rory Cave, Mary M. Ter-Stepanyan, Nune Kotsinyan, Jiazhen Chen, Li Zhang, Taijiao Jiang, Hermine V. Mkrtchyan
Summary: This study reports the first whole-genome sequencing of a multidrug-resistant Klebsiella pneumoniae isolate from Armenia. The isolate exhibited resistance to multiple antibiotics and carried several antibiotic resistance genes. The study emphasizes the importance of genomic surveillance and implementation of infection prevention and control measures for emerging pathogens.
MICROBIOLOGY SPECTRUM
(2023)
Article
Public, Environmental & Occupational Health
Yuanyuan Bai, Chunhong Shao, Yingying Hao, Yueling Wang, Yan Jin
Summary: This study used WGS to track a hospital infection of IMP-4-producing K. pneumoniae ST2253 among neonates, revealing clonal relationships and potential transmission pathways.
FRONTIERS IN PUBLIC HEALTH
(2021)
Article
Infectious Diseases
Elsa de la Cadena, Maria Fernanda Mojica, Juan Carlos Garcia-Betancur, Tobias Manuel Appel, Jessica Porras, Christian Jose Pallares, Juan Sebastian Solano-Gutierrez, Laura J. Rojas, Maria Virginia Villegas
Summary: A study in Colombia identified clonal dissemination of polymyxin and carbapenem-resistant K. pneumoniae isolates, mainly associated with CG258 and bla(KPC-3), highlighting limited therapeutic options for carbapenem-resistant strains.
Article
Immunology
Celia C. Carlos, Melissa Ana L. Masim, Marietta L. Lagrada, June M. Gayeta, Polle Krystle Macaranas, Sonia B. Sia, Maria Adelina M. Facun, Janziel Fiel C. Palarca, Agnettah M. Olorosa, Gicell Anne C. Cueno, Monica Abrudan, Khalil Abudahab, Silvia Argimon, Mihir Kekre, Anthony Underwood, John Stelling, David M. Aanensen
Summary: A survey on Klebsiella pneumoniae isolates in the Philippines found prevalent antibiotic resistance mechanisms including bla(CTX-M-15) and bla(NDM-1). Whole-genome sequencing identified an epidemic plasmid carrying bla(NDM-1) and uncovered three previously unrecognized outbreaks, highlighting the utility of WGS in outbreak detection and public health.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Andrey Shelenkov, Lyudmila Petrova, Anna Mironova, Mikhail Zamyatin, Vasiliy Akimkin, Yulia Mikhaylova
Summary: Klebsiella pneumoniae is a major cause of healthcare-associated infections globally, and its antibiotic resistance has increased in recent years, especially during the COVID-19 pandemic. Whole genome sequencing is a promising approach to understanding the mechanisms of resistance, particularly in relation to mobile genetic elements like plasmids. This study sequenced three carbapenem-resistant K. pneumoniae isolates from COVID-19 patients, identifying a small plasmid carrying a resistance gene. These findings contribute to our understanding of antibiotic resistance mechanisms in this important pathogen and highlight the importance of ongoing genomic epidemiology surveillance of clinical isolates.
Article
Genetics & Heredity
Elvira R. Shaidullina, Michael Schwabe, Thomas Rohde, Valeria V. Shapovalova, Marina S. Dyachkova, Alina D. Matsvay, Yuliya A. Savochkina, Andrey A. Shelenkov, Yulia V. Mikhaylova, Katharina Sydow, Francois Lebreton, Evgeny A. Idelevich, Stefan E. Heiden, Karsten Becker, Roman S. Kozlov, German A. Shipulin, Vasiliy G. Akimkin, Michael Lalk, Sebastian Guenther, Andreas E. Zautner, Juergen A. Bohnert, Ayslu M. Mardanova, Ruth Bouganim, Dror Marchaim, Katharina J. Hoff, Katharina Schaufler, Mikhail V. Edelstein
Summary: This study is the first to investigate a large international collection of K. pneumoniae ST395 genomes, revealing the phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.
Article
Infectious Diseases
May Sherif, Mattia Palmieri, Caroline Mirande, Hadir El-Mahallawy, Hebatallah G. Rashed, Fadwa Abd-El-Reheem, Arwa Ramadan El-Manakhly, Radwa Ahmad Rabea Abdel-latif, Aliaa Gamaleldin Aboulela, Laila Yosef Saeed, Soheir Abdel-Rahman, Eman Elsayed, Alex van Belkum, Amani El-Kholy
Summary: The study conducted whole-genome sequencing of 39 multidrug-resistant Klebsiella pneumoniae strains from nine Egyptian hospitals, identifying 18 sequence types with ST101 and ST147 being the most common. Phylogenetic analyses revealed closely related isolates in some centers, mostly acquired independently or imported. The most commonly detected acquired resistance gene was bla(CTX-M-15), with several carbapenemase genes also identified.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Li Li, Renying Wang, Dan Qiao, Min Zhou, Peipei Jin
Summary: This study aimed to identify the origin and transmission route of a carbapenem-resistant Klebsiella pneumoniae (CRKP) outbreak in an emergency intensive care unit (EICU) and provide prevention and control strategies. The integration of genomic and epidemiological data yielded a clear transmission map of the CRKP outbreak. Early monitoring of the rapid evolution of CRKP, monitoring of CRKP after patient discharge, environmental hygiene, and effective antibiotic treatment are key to preventing and controlling CRKP outbreaks.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Microbiology
Angela W. Muraya, Cecilia Kyany'a, Shahiid Kiyaga, Hunter J. Smith, Caleb Kibet, Melissa J. Martin, Josephine Kimani, Lillian Musila
Summary: This study analyzed the epidemiology, resistance, and virulence genes of Klebsiella pneumoniae strains in Kenya. The results revealed diverse resistance and virulence genes in both clinical and hospital environmental isolates, highlighting the potential for unmanageable infection outbreaks.
Article
Microbiology
Qingqing Du, Qi Xu, Fen Pan, Yingying Shi, Fangyuan Yu, Tiandong Zhang, Jie Jiang, Wenxin Liu, Xiaozhou Pan, Dingding Han, Hong Zhang
Summary: This study demonstrates a strong association between CRKP intestinal colonization and extraintestinal infection, based on whole-genome sequencing data and phenotypic assays of antimicrobial resistance and virulence.
MICROBIOLOGY SPECTRUM
(2023)
Article
Immunology
David Villinger, Tilman G. Schultze, Victor M. Musyoki, Irene Inwani, Jalemba Aluvaala, Lydia Okutoyi, Anna-Henriette Ziegler, Imke Wieters, Christoph Stephan, Beatrice Museve, Volkhard A. J. Kempf, Moses Masika
Summary: This study investigates the colonization prevalence of multidrug-resistant organisms (MDRO) and carbapenem-resistant organisms (CRO) in a newborn unit at a Kenyan tertiary hospital. The results show a high detection rate of MDRO and CRO in newborns, mothers, and the hospital environment, with several independent transmission events identified. The most common CRO identified in this study were K. pneumoniae harboring bla(NDM-1) or bla(NDM-5).
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Jennifer Cornick, Patrick Musicha, Chikondi Peno, Ezgi Seager, Pui-Ying Iroh Tam, Sithembile Bilima, Aisleen Bennett, Neil Kennedy, Nicholas Feasey, Eva Heinz, Amy K. Cain
Summary: A study conducted in a large public hospital in Malawi identified a multi-drug resistant Klebsiella pneumoniae outbreak in the neonatal unit, which was difficult to treat; genomic characterisation revealed a specific strain implicated in the outbreak, providing valuable molecular information for tracking and characterizing this important hospital pathogen in sub-Saharan Africa.
MICROBIAL GENOMICS
(2021)
Article
Microbiology
Qi Cheng, Zheng Ma, Zijun Gong, Yuelang Liang, Jiajia Guo, Xiaohua Ye, Zhigang Han, Zhenjiang Yao
Summary: In this study, nasal swab specimens were collected from an HIV Voluntary Counseling Testing outpatient department in Guangzhou, China. It was found that Klebsiella aerogenes isolates showed high resistance, especially to antibiotics used for respiratory infections. CC4 strains were identified to have a wide spread among men who have sex with men (MSM), highlighting the need for enhanced monitoring and control.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Karolina Stojowska-Swedrzynska, Adrianna Lupkowska, Dorota Kuczynska-Wisnik, Ewa Laskowska
Summary: Klebsiella pneumoniae is a common pathogen responsible for various infections, and its multidrug resistance has been recognized as a significant public health threat. Heteroresistance, a frequent phenotype in pathogens, may be associated with an increased risk of recurrent infections and treatment failure in K. pneumoniae.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Alexandra Chiaverini, Alessandra Cornacchia, Gabriella Centorotola, Elga Ersilia Tieri, Nadia Sulli, Ilaria Del Matto, Giorgio Iannitto, Domenico Petrone, Antonio Petrini, Francesco Pomilio
Summary: This study investigates the occurrence of Klebsiella pneumoniae in wildlife and its antimicrobial resistance. The results show the presence of resistant strains in wild animals, indicating a link between humans, domestic animals, and wildlife. This highlights the lack of knowledge about this ecological context and underestimation of potential health risks.
Article
Infectious Diseases
Aislinn Cook, Mike Sharland, Yasmine Yau, Julia Bielicki
Summary: A WISCA is a practical tool for evaluating empiric antibiotic regimens for pediatric sepsis based on local microbiology data. The coverage estimates for third-generation cephalosporins and meropenem ranged widely across pediatric hospitals globally, demonstrating the need for individualized prescribing guidelines to address antibiotic resistance.
EXPERT REVIEW OF ANTI-INFECTIVE THERAPY
(2022)
Article
Medicine, General & Internal
Christopher J. L. Murray, Kevin Shunji Ikuta, Fablina Sharara, Lucien Swetschinski, Gisela Robles Aguilar, Authia Gray, Chieh Han, Catherine Bisignano, Puja Rao, Eve Wool, Sarah C. Johnson, Annie J. Browne, Michael Give Chipeta, Frederick Fell, Sean Hackett, Georgina Haines-Woodhouse, Bahar H. Kashef Hamadani, Emmanuelle A. P. Kumaran, Barney McManigal, Ramesh Agarwal, Samuel Akech, Samuel Albertson, John Amuasi, Jason Andrews, Aleskandr Aravkin, Elizabeth Ashley, Freddie Bailey, Stephen Baker, Buddha Basnyat, Adrie Bekker, Rose Bender, Adhisivam Bethou, Julia Bielicki, Suppawat Boonkasidecha, James Bukosia, Cristina Carvalheiro, Carlos Castaneda-Orjuela, Vilada Chansamouth, Suman Chaurasia, Sara Chiurchiu, Fazle Chowdhury, Aislinn J. Cook, Ben Cooper, Tim R. Cressey, Elia Criollo-Mora, Matthew Cunningham, Saffiatou Darboe, Nicholas P. J. Day, Maia De Luca, Klara Dokova, Angela Dramowski, Susanna J. Dunachie, Tim Eckmanns, Daniel Eibach, Amir Emami, Nicholas Feasey, Natasha Fisher-Pearson, Karen Forrest, Denise Garrett, Petra Gastmeier, Ababi Zergaw Giref, Rachel Claire Greer, Vikas Gupta, Sebastian Haller, Andrea Haselbeck, Simon Hay, Marianne Holm, Susan Hopkins, Kenneth C. Iregbu, Jan Jacobs, Daniel Jarovsky, Fatemeh Javanmardi, Meera Khorana, Niranjan Kissoon, Elsa Kobeissi, Tomislav Kostyanev, Fiorella Krapp, Ralf Krumkamp, Ajay Kumar, Hmwe H. Kyu, Cherry Lim, Direk Limmathurotsakul, Michael James Loftus, Miles Lunn, Jianing Ma, Neema Mturi, Tatiana Munera-Huertas, Patrick Musicha, Marisa Marcia Mussi-Pinhata, Tomoka Nakamura, Ruchi Nanavati, Sushma Nangia, Paul Newton, Chanpheaktra Ngoun, Amanda Novotney, Davis Nwakanma, Christina W. Obiero, Antonio Olivas-Martinez, Piero Olliaro, Ednah Ooko, Edgar Ortiz-Brizuela, Anton Yariv Peleg, Carlo Perrone, Nishad Plakkal, Alfredo Ponce-de-Leon, Mathieu Raad, Tanusha Ramdin, Amy Riddell, Tamalee Roberts, Julie VictoriaRobotham, Anna Roca, Kristina E. Rudd, Neal Russell, Jesse Schnall, John Anthony Gerard Scott, Madhusudhan Shivamallappa, Jose Sifuentes-Osornio, Nicolas Steenkeste, Andrew James Stewardson, Temenuga Stoeva, Nidanuch Tasak, Areerat Thaiprakong, Guy Thwaites, Claudia Turner, Paul Turner, H. Rogier van Doorn, Sithembiso Velaphi, Avina Vongpradith, Huong Vu, Timothy Walsh, Seymour Waner, Tri Wangrangsimakul, Teresa Wozniak, Peng Zheng, Benn Sartorius, Alan D. Lopez, Andy Stergachis, Catrin Moore, Christiane Dolecek, Mohsen Naghavi
Summary: Antimicrobial resistance (AMR) poses a significant threat to global human health, and this study provides the most comprehensive estimates of AMR burden to date. By estimating deaths and disability-adjusted life-years (DALYs) associated with bacterial AMR in 204 countries and territories in 2019, the study highlights the impact of resistance and the leading pathogen-drug combinations contributing to it.
Article
Biochemistry & Molecular Biology
Siyuan Feng, Zhuoxing Wu, Wanfei Liang, Xin Zhang, Xiujuan Cai, Jiachen Li, Lujie Liang, Daixi Lin, Nicole Stoesser, Yohei Doi, Lan-Lan Zhong, Yan Liu, Yong Xia, Min Dai, Liyan Zhang, Xiaoshu Chen, Jian-Rong Yang, Guo-Bao Tian
Summary: The study predicts the evolutionary trajectories of antibiotic resistance genes using a combination of laboratory approaches and deep learning models, providing valuable insights for designing sustainable treatment strategies.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Kalisvar Marimuthu, Indumathi Venkatachalam, Vanessa Koh, Stephan Harbarth, Eli Perencevich, Benjamin Pei Zhi Cherng, Raymond Kok Choon Fong, Surinder Kaur Pada, Say Tat Ooi, Nares Smitasin, Koh Cheng Thoon, Paul Anantharajah Tambyah, Li Yang Hsu, Tse Hsien Koh, Partha Pratim De, Thean Yen Tan, Douglas Chan, Rama Narayana Deepak, Nancy Wen Sim Tee, Andrea Kwa, Yiying Cai, Yik-Ying Teo, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Weizhen Xu, Wei Xin Khong, David Henderson, Nicole Stoesser, David W. Eyre, Derrick Crook, Michelle Ang, Raymond Tzer Pin Lin, Angela Chow, Alex R. Cook, Jeanette Teo, Oon Tek Ng
Summary: Carbapenemase-producing Enterobacterales cause healthcare-associated infections, but modes of transmission are not well understood. This study finds evidence of transmission without direct patient contact, suggesting the presence of undetected environmental reservoirs, as well as plasmid-mediated transmission accounting for 50% of dissemination. The traditional infection control practices based on detecting carriers may not effectively address plasmid-mediated transmission at the population level.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Karina Doris Vihta, Koen B. Pouwels, Tim Ea Peto, Emma Pritchard, Thomas House, Ruth Studley, Emma Rourke, Duncan Cook, Ian Diamond, Derrick Crook, David A. Clifton, Philippa C. Matthews, Nicole Stoesser, David W. Eyre, Ann Sarah Walkerand
Summary: A UK community study found that loss of taste/smell was less common in Omicron BA.1/BA.2 infections compared to Delta severe acute respiratory syndrome coronavirus 2 infections. There were smaller declines in reported shortness of breath, myalgia, and fatigue/weakness, but increases in sore throat, challenging symptom-based testing algorithms.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Multidisciplinary Sciences
Jia Wei, Philippa C. Matthews, Nicole Stoesser, Ian Diamond, Ruth Studley, Emma Rourke, Duncan Cook, John Bell, John N. Newton, Jeremy Farrar, Alison Howarth, Brian D. Marsden, Sarah Hoosdally, E. Yvonne Jones, David Stuart, Derrick W. Crook, Tim E. A. Peto, A. Sarah Walker, David W. Eyre, Koen B. Pouwels
Summary: Individuals who have previously been infected with SARS-CoV-2 and receive a single dose of vaccine generate similar antibody responses to those who have not been infected and receive two doses of vaccine. Prior infection significantly enhances antibody responses, resulting in higher peak levels and/or longer half-lives after one dose of any of the three vaccines. In those with prior infection, the median time above the positivity threshold was over 1 year after the first vaccination. Single-dose vaccination targeted to those previously infected may provide at least equivalent protection to two-dose vaccination among those without previous infection.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, General & Internal
Yin Mo, Mathupanee Oonsivilai, Cherry Lim, Rene Niehus, Ben Cooper
Summary: This study used mathematical modeling and meta-analysis to demonstrate that reducing antibiotic treatment duration can reduce the carriage of antibiotic-resistant bacteria. The models showed that the effectiveness of shortening duration depends on the growth and decline rates of resistant bacteria under antibiotic selection pressure. The meta-analysis found that each additional day of antibiotic treatment is associated with a 7% increase in the risk of resistance carriage. These findings highlight the potential benefits and risks of shortening antibiotic treatment duration in reducing antimicrobial resistance.
Article
Microbiology
Chalita Chomkatekaew, Janjira Thaipadungpanit, Pasco Hearn, Sona Soeng, Sreymom Pol, Leakhena Neou, Jill Hopkins, Paul Turner, Elizabeth M. M. Batty
Summary: Infection with ESBL-E is common in infants and leads to increased ICU admission and mortality. This study investigated the role of maternal transmission in colonization of infants using paired isolates from mothers and neonates. The results showed that vertical transmission outside hospitals is a common cause of ESBL-E colonization in neonates.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Infectious Diseases
Shweta R. Singh, Cheng Yee Tang, Bunsoth Mao, Sona Soeng, Clare L. Ling, Jocelyn Qi-Min Teo, Saphonn Vonthanak, Paul Turner, Li Yang Hsu, Rick Twee-Hee Ong
Summary: This study explored the association between recent hospitalization and asymptomatic carriage of multidrug-resistant Enterobacterales (MDRE) in Siem Reap, Cambodia using whole-genome sequencing (WGS). The results showed that MDRE is likely endemic within the Siem Reap community, and ESBL genes can be found in almost all commensal Escherichia coli.
JAC-ANTIMICROBIAL RESISTANCE
(2023)
Article
Multidisciplinary Sciences
Ben S. Cooper, Stephanie Evans, Yalda Jafari, Thi Mui Pham, Yin Mo, Cherry Lim, Mark G. Pritchard, Diane Pople, Victoria Hall, James Stimson, David W. Eyre, Jonathan M. Read, Christl A. Donnelly, Peter Horby, Conall Watson, Sebastian Funk, Julie V. Robotham, Gwenan M. Knight
Summary: This study uses data from acute hospitals in England to quantify hospital-based transmission of SARS-CoV-2, evaluate the pathways of spread and factors associated with increased transmission risk, and explore the wider consequences. The study estimates that between June 2020 and March 2021, 95,000 to 167,000 inpatients acquired SARS-CoV-2 in hospitals, accounting for 1% to 2% of all hospital admissions during this period.
Article
Multidisciplinary Sciences
Arjun Chandna, Yoel Lubell, Lazaro Mwandigha, Phattaranit Tanunchai, Asama Vinitsorn, Melissa Richard-Greenblatt, Constantinos Koshiaris, Direk Limmathurotsakul, Francois Nosten, Mohammad Yazid Abdad, Rafael Perera-Salazar, Claudia Turner, Paul Turner
Summary: Reliable tools are needed for managing childhood pneumonia in resource-limited settings. This study investigated the value added by biomarkers of infection response for triage of children with pneumonia. The combination of Ang-2 and LqSOFA showed improved discrimination and greater net benefit, guiding referrals in community settings. Further development and integration into patient triage is required.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Sean Cavany, Stella Nanyonga, Cathrin Hauk, Cherry Lim, Joel Tarning, Benn Sartorius, Christiane Dolecek, Celine Caillet, Paul N. Newton, Ben S. Cooper
Summary: Approximately 10% of antimicrobials used in low- and middle-income countries are substandard or falsified, which can potentially impact antimicrobial resistance levels. Our understanding of this relationship is limited, and further research is needed to understand how different drug exposures affect resistance emergence and spread, as well as the distribution of active pharmaceutical ingredients in substandard and falsified medicines.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Arjun Chandna, Lazaro Mwandigha, Constantinos Koshiaris, Direk Limmathurotsakul, Francois Nosten, Yoel Lubell, Rafael Perera-Salazar, Claudia Turner, Paul Turner
Summary: This study validates the performance of three severity scores in children from resource-limited primary care settings, with LqSOFA score showing the best discrimination. Converting the scores into clinical prediction models improves performance, reducing unnecessary referrals and incorrect management.
SCIENTIFIC REPORTS
(2023)
Article
Health Care Sciences & Services
Vilada Chansamouth, Danoy Chommanam, Tamalee Roberts, Sommay Keomany, Viladeth Paphasiri, Chanthala Phamisith, Siho Sengsavang, Khamsay Detleuxay, Phisith Phoutsavath, Sengvong Bouthavong, Anousone Douangnouvong, Manivanh Vongsouvath, Sommana Rattana, Bounxou Keohavong, Nicholas P. J. Day, Paul Turner, H. Rogier van Doorn, Mayfong Mayxay, Elizabeth A. Ashley, Paul N. Newton
Summary: The prevalence of antimicrobial use among hospitalized patients in Laos is high, with frequent inappropriate use, especially for surgical prophylaxis. Continued monitoring and enhanced antimicrobial stewardship interventions are needed in Lao hospitals.
LANCET REGIONAL HEALTH-WESTERN PACIFIC
(2022)
Article
Genetics & Heredity
Sudaraka Mallawaarachchi, Gerry Tonkin-Hill, Nicholas J. Croucher, Paul Turner, Doug Speed, Jukka Corander, David Balding
Summary: This study proposes methods for analyzing bacterial traits using whole-genome sequencing and applies them to analyze several phenotypes of Streptococcus pneumoniae. The results show high heritability and prediction accuracy for minimum inhibitory concentrations (MIC), revealing genetic associations and surprising findings regarding resistance. The study also suggests the moderate heritability and polygenic nature of within-host carriage duration.
NAR GENOMICS AND BIOINFORMATICS
(2022)