Citations
Since its launch in 2019, Bactopia has seen significant academic usage, being cited in at least 217 scholarly publications. We are excited to see Bactopia being used by the community and hope that it continues to be a valuable tool for researchers.
The citations below were retrieved from OpenAlex and are updated regularly, but not daily.
217: Robert A. Petit, Chayse M. Rowley, Taylor R. Fearing, Stefaan Verwimp, Rob G. Christensen, Jim A. Mildenberger, Joseph M. Reed, Timothy D. Read. camlhmp: a simple framework for building reproducible microbial genome-based typing tools Microbiology Resource Announcements (2026).
216: Noémie Vingadassalon, Jacques-Antoine Hennekinne, Yacine Nia, Sven Maurischat, Maria Borowiak, Brian Byrne, Lionel Kenneth Dygico, L. M. Ciupescu, Hugo Guedes, Gonçalo Almeida, et al. Impact of wet- and dry-lab workflows on genome assembly, typing and enterotoxin gene detection in whole-genome sequencing of foodborne Staphylococcus aureus International Journal of Food Microbiology (2026).
215: Laura Mondéjar, Victoria Ballén, Yaiza Gabasa, Laura Castellsagués, Anna Pinar-Méndez, Carles Vilaró, Belén Galofré, Aida González-Díaz, Sara Martí, Sergi Canyelles i Sanz, et al. Characterizing Aeromonas spp. as a Potential Sentinel Organism for Antimicrobial Resistance Dissemination in Wastewater and Drinking Water Treatment Systems: A Case Study in the Barcelona Metropolitan Area, Spain Antibiotics (2026).
214: Carla López-Causapé, Matias Bonet, Biel Taltavull, Paola Medina-Retiga, Miquel Àngel Sastre-Femenía, Sara Cortés-Lara, María A. Gomis-Font, Fernando Gómez-Romano, Antonio Oliver. Pa REx: an open-source pipeline for the automated analysis of Pseudomonas aeruginosa resistomes from whole-genome sequences Antimicrobial Agents and Chemotherapy (2026).
213: Gian Carlo González-Carballo, Christopher Mairena-Acuña, Cristian Pérez-Corrales, Javier Alfaro-Camacho, Cristina García-Marín, César Rodríguez. Novel ST557 Streptococcus equi subsp. zooepidemicus lineage associated with a human case of septic arthritis IJID One Health (2026).
212: Guillem López de Egea, Aida González-Díaz, Virginia Aragón, Óscar Cabezón, Gérard Guédon, D. Ortiz Berbel, Irene Cadenas-Jiménez, Johan Espunyes, Marta Planellas, M. Ángeles Domínguez, et al. Macrolide resistance determinants and their associations in streptococci from selected livestock and wildlife species from Catalonia, Northeast Spain Microbiology Spectrum (2026).
211: Víctor Fernández-Juárez, Francisco Salvà-Serra, G. Seguí, Alberto J. Martín-Rodríguez. Life in sediments fosters ‘sexual’ speciation in Shewanella baltica bioRxiv (Cold Spring Harbor Laboratory) (2026).
210: mohamed eltorki, Oluwatimilehin O. Ajayi, Jina Seok, Jianling Xie, Francesco A. Rizzuti, Byron M. Berenger, Phillip I. Tarr, Andrew T. Pavia, K. Snedeker, Silviu Grisaru, et al. Shiga Toxin–Producing Escherichia coli Outbreak in Canadian Daycare Centers JAMA Network Open (2026).
209: Covadonga Pérez-García, Joaquin Llorente, Maria Elena Aguirre Alustuey, Mirella Llamosí, Ruth Gil, Gabriel Laghlali, Farah El-Ayache, Vivian Yan, Michael Schotsaert, Jorge del Diego, et al. Outburst of serotype 4 IPD after COVID-19 is driven by ST15063/GPSC162 lineage associated with high-risk behaviors and greater virulence linked to influenza H3N2 virus coinfection and cigarette smoke medRxiv (2026).
208: Leslie M. Huggins, Rachel B. Sidebottom, William W. Johnson, Kurt Schwalm, Karissa Culbreath, Jesse Young, Meghan Brett, Darrell L. Dinwiddie, Daryl Domman. Genomic analysis of Klebsiella aerogenes circulating in New Mexico Microbial Genomics (2026).
207: Megan A Phillips, Robert A. Petit, Daniel B. Weissman, Timothy Read. Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years eLife (2026).
206: Sebastian Bruno Ulrich Jordi, Isabel Baertschi, Jiaqi Li, Nadia Fasel, Benjamin Misselwitz, Bahtiyar Yilmaz. StrainCascade: An automated, modular workflow for high-throughput long-read bacterial genome reconstruction and characterization bioRxiv (Cold Spring Harbor Laboratory) (2026).
205: Aida González-Díaz, M. Bessa Pinto, Irene Cadenas-Jiménez, Sara Lia Duarte, Carmen Ardanuy, M. Manuela Ribeiro, Sara Martí, Paula Bajanca-Lavado. First identification and molecular characterization of CTX-M-15 extended-spectrum β-lactamase and OXA-9 β-lactamase in Haemophilus influenzae in the Iberian Peninsula Antimicrobial Agents and Chemotherapy (2026).
204: H.A. Alshammari, Ahmed Albarrag, Ihab M. Moussa, Jaffar A. Al-Tawfiq, Sumayh A. Aldakeel, Ali M. Somily. Molecular analysis of carbapenemase-producing Pseudomonas aeruginosa strains in a tertiary care hospital in Riyadh Journal of Infection and Public Health (2026).
203: Belson Kutambe, Priyanka D. Patel, Kenneth Chizani, Niza Silungwe, Christopher Kukacha, Megan E. Carey, James Meiring, Matthew B. Laurens, Melita A. Gordon, Philip Ashton. Genomic Analysis of Salmonella Typhi from a Typhoid Conjugate Vaccine Trial medRxiv (2026).
202: Dalal M. Alkuraythi, Manal Muhammed Alkhulaifi, Dina A. Altwiley, Mohammed Alarwi, Mohammed I. Mujallad, Mohammad Alshomrani, Takashi Gojobori, Sulaiman M. Alajel. Genomic and epidemiological insights into the emergence and dominance of MRSA clones in Riyadh’s healthcare facilities Scientific Reports (2026).
201: Ismam Ahmed Protic, Md. Nasir Uddin, Andrew Gorzalski, Rashidul Islam, David Alvarez-Ponce. Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh BMC Genomics (2026).
200: Gerald Mboowa, Ivan Sserwadda, Stephen Kanyerezi. rMAP 2.0: a modular, reproducible, and scalable WDL–Cromwell–Docker workflow for genomic analysis of ESKAPEE pathogens Bioinformatics Advances (2026).
199: Virudhagiri Elamurugan, Subbiah Thamotharan, Vigneshwar Ramakrishnan. Pa VarDB: a database and web platform for missense variant analysis in Pseudomonas aeruginosa using an end-to-end BVbase pipeline Database (2026).
198: Shuo Jiang, Peng Gao, Ping Shen, Suying Hou, Chenlu Xiao, Richard Yi Tsun Kao, Ho Pak-Leung, Yonghong xiao, Huiluo Cao. Global emergence and evolution of Staphylococcus aureus clonal complex 59 mSystems (2025).
197: Chantisa Keeratipusana, Weerawat Phuklia, Vanheuang Phommadeechack, Janjira Thaipadungpanit, Vilada Chansamouth, Koukeo Phommasone, Sayaphet Rattanavong, Catrin E. Moore, Matthew T. Robinson, Allen L. Richards, et al. Complete genomes of Rickettsia typhi reveal a clonal population PLoS neglected tropical diseases (2025).
196: Nicholas J. Hathaway, Kathryn Murie, Maxwell Murphy, Alfred Simkin, Jorge Amaya-Romero, Alfred Hubbard, Jessica Briggs, Andrés Aranda-Díaz, Angela M. Early, Amy Wesolowski, et al. The Portable Microhaplotype Object and Tools bioRxiv (Cold Spring Harbor Laboratory) (2025).
195: Massimiliano S. Tagliamonte, Abhinav Sharma, Alberto Riva, Monika Moir, Marco Salemi, Cheryl Baxter, Túlio de Oliveira, Carla Mavian, Eduan Wilkinson. CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation Bioinformatics (2025).
194: Kaitlin E. Creamer, Gabriel Castro‐Falcón, Ebru İnce, Victoria Vasilat, David Vereau Gorbitz, Alyssa M. Demko, Paul R. Jensen. Taxonomic and biosynthetic diversity of the marine actinomycete Salinispora across spatial scales Applied and Environmental Microbiology (2025).
193: Cheikh Tidiane Houmenou, Cheikh Sokhna, Florence Fenollar, Oleg Mediannikov. Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data Infection Genetics and Evolution (2025).
192: Casey Vieni, Tanner E. Rothstein, Stephen L. Johnson, Audrey N. Schuetz, Andrew P. Norgan, Robin Patel. Whole genome sequence analysis of Helicobacter pylori isolates reveals incomplete characterization of antimicrobial resistance mechanisms iScience (2025).
191: Ismam Ahmed Protic, Mohammed Nasir Uddin, Andrew Gorzalski, Md. Rashidul Islam, David Alvarez‐Ponce. Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh bioRxiv (Cold Spring Harbor Laboratory) (2025).
190: Alison Yee-Ting Lam, Chun-Hei Lau, Wing-Yin Tam, Chloe Toi-Mei Chan, Tsun-Ming Lok, Lorna Kwai Ping Suen, Lam-Kwong Lee, Elaine Yin-Ying Yeung, Tsz-Kei Lam, Wai-Kam Cheung, et al. Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms Environmental Microbiome (2025).
189: Jonathan Strysko, Tefelo Thela, Andries Feder, Janet Thubuka, Tichaona Machiya, Jack Mkubwa, Kagiso Mochankana, Celda Tiroyakgosi, Kgomotso Kgomanyane, Tlhalefo Dudu Ntereke, et al. Carbapenem-resistant Acinetobacter baumannii at a hospital in Botswana: detecting a protracted outbreak using whole genome sequencing Microbiology Spectrum (2025).
188: Clayton W. Hall, Nicholas Waglechner, E C Choi, Patryk Aftanas, Kevin Katz, Christie Vermeiren, Finlay Maguire, Robert Kozak, Xena X. Li. Evaluation of Phenotypic and Genotypic Susceptibility Testing Methods for Newer β-lactam/β-lactamase Inhibitor Combinations in Multidrug Resistant Pseudomonas aeruginosa The Journal of Infectious Diseases (2025).
187: Mohammed Alarawi, Musaad A. Altammami, Mohammed H. Abutarboush, Maxat Kulmanov, Dalal M. Alkuraithy, Şenay Kafkas, Robert Radley, Marwa Abdelhakim, Hind Aldakhil, Reema A. Bawazeer, et al. Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing Microbial Genomics (2025).
186: Mingkwan Yingkajorn, Thunchanok Yaikhan, Worawut Duangsi-Ngoen, Chollachai Klaysubun, Thitaporn Dechathai, Sarunyou Chusri, Kamonnut Singkhamanan, Rattanaruji Pomwised, Monwadee Wonglapsuwan, Komwit Surachat. Phylogenomics and Antimicrobial Resistance of Clinical Bacteroides Isolates from a Tertiary Hospital in Southern Thailand Antibiotics (2025).
185: Nattarika Chaichana, Jirasa Boonsan, Sirikan Suwannasin, Kamonnut Singkhamanan, Monwadee Wonglapsuwan, Rattanaruji Pomwised, Thunchanok Yaikhan, Chollachai Klaysubun, Siriwimon Konglue, Rusneeta Chema, et al. Genomic insights and functional characterization of Lactiplantibacillus pentosus CLP10 isolated from the traditional fermented Thai stinky beans Journal of Agriculture and Food Research (2025).
184: Idowu B. Olawoye, David Alexander, Jennifer L. Guthrie. Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution Microbial Genomics (2025).
183: Michael B. Hall, Chenxi Zhou, Lachlan Coin. Genome size estimation from long read overlaps Bioinformatics (2025).
182: Zachary Foster, Martha A. Sudermann, Camilo H. Parada-Rojas, Logan Blair, Fernanda Iruegas Bocardo, Upasana Dhakal, Ricardo I. Alcalá-Briseño, Hung Phan, Tori R. Schummer, Alexandra J. Weisberg, et al. PathogenSurveillance : an automated pipeline for population genomic analyses and pathogen identification bioRxiv (Cold Spring Harbor Laboratory) (2025).
181: Camryn M. Bonn-Dunbar, Idowu B. Olawoye, Akanksha Thukral, Jennifer L. Guthrie, Martin J. McGavin. Widespread emergence of Staphylococcus aureus with variant FarR regulators and enhanced resistance to antimicrobial fatty acids within clonal complex CC5, CC8, and CC97 strains from human and bovine hosts Microbiology Spectrum (2025).
180: Gillian A.M. Tarr, William Finical, Joshua Rounds, Anna Panek, Kirk Smith. The conundrum of Shiga toxin-producing Escherichia coli O157:H7 persistence: Evidence for locally persistent lineages bioRxiv (Cold Spring Harbor Laboratory) (2025).
179: Emanuel Becerra Soto, Adam James Oliver, Marcos H. de Moraes. Pandoomain, a scalable pipeline for genomic and protein domain context analysis, reveals widespread PT-TG domain architectural diversity and novel polymorphic toxins bioRxiv (Cold Spring Harbor Laboratory) (2025).
178: Brittany N. Ross, Emma Evans, Frances L. Diggle, Paul Briaud, Marvin Whiteley. The role of colony morphotype in shaping gene essentiality in Mycobacteroides abscessus Proceedings of the National Academy of Sciences (2025).
177: Donovan H. Parks, Pierre-Alain Chaumeil, Aaron J. Mussig, Christian Rinke, Maria Chuvochina, Philip Hugenholtz. GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Nucleic Acids Research (2025).
176: Daniele Smedile, Elena Lavinia Diaconu, Matteo Grelloni, Barbara Middei, Virginia Carfora, Antonio Battisti, Patricia Alba, Alessia Franco. Enteroflow: Automated Pipeline for In Silico Characterization of Enterococcus faecium/faecalis Isolates from Short Reads International Journal of Molecular Sciences (2025).
175: Kara K. Tsang, Iana Amke, David M. Aanensen, Jabir Abdulahi, Alexander M. Aiken, Michael A. Bachman, Stephen Baker, Katherine Barry, Gherard Batisti Biffignandi, Emília Maria Medeiros de Andrade Belitardo, et al. Ciprofloxacin resistance in Klebsiella pneumoniae : phenotype prediction from genotype and global distribution of resistance determinants bioRxiv (Cold Spring Harbor Laboratory) (2025).
174: Harry C. H. Hung, Narender Kumar, Victoria Dyster, Corin Yeats, Benjamin J. Metcalf, Yuan Li, Paulina A. Hawkins, Lesley McGee, Stephen D. Bentley, Stephanie W. Lo. GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project Nature Communications (2025).
173: Megan Phillips, Robert A. Petit, Daniel B. Weissman, Timothy D. Read. Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years bioRxiv (Cold Spring Harbor Laboratory) (2025).
172: Michelle Su, Kim L. Hoang, McKenna J. Penley, Michelle H. Davis, Jennifer D. Gresham, Levi T. Morran, Timothy D. Read. Host and antibiotic jointly select for greater virulence in Staphylococcus aureus ** (2025).
171: Qiaoxin Zhang, Junle Ren, Siyao Wu, Yadi Tan, Wenliang Wang, Feng Cai, Liqian Zhao, Zhiwei Zhu. Plasmid‐Free CRISPR/Cpf1 Genome Editing With In Vivo T7 RNA Polymerase‐Transcribed CRISPR RNA From Short Double‐Stranded DNA Biotechnology and Bioengineering (2025).
170: Adesola Olalekan, Sébastien Boutin, Christopher M. Watson, Luiza H. Galarion, Solayide A. Adesida, Bamidele Iwalokun, Olayiwola Popoola, Seraphine Nkie Esemu, Richard A. Adegbola, Dennis Nurjadi. Molecular landscape of methicillin-resistant Staphylococcus aureus strains in clinical infections from hospitals in Lagos, Nigeria JAC-Antimicrobial Resistance (2025).
169: Victoria Ballén, Laura Mondéjar, Yaiza Gabasa, Laura Castellsagués, Manuel Alcalde‐Rico, Anna Pinar-Méndez, Carles Vilaró, Belén Galofré, Sara M. Soto. Integrated metagenomic, culture-based, and whole genome sequencing analyses of antimicrobial resistance in wastewater and drinking water treatment plants in Barcelona, Spain International Journal of Hygiene and Environmental Health (2025).
168: Francesca Sivori, Massimo Francalancia, Mauro Truglio, Ilaria Cavallo, Carmelina Pronesti, Giorgia Fabrizio, Ilaria Celesti, Andrea Cazzani, Lorenzo Furzi, Fulvia Pimpinelli, et al. Meropenem/vaborbactam activity against carbapenem-resistant Klebsiella pneumoniae from catheter-related bloodstream infections Frontiers in Cellular and Infection Microbiology (2025).
167: Margaret Free, Nicole Soper, James C. Slaughter, Andries Feder, Colleen Bianco, Ahmed M. Moustafa, Paul J. Planet, C. Buddy Creech, Isaac Thomsen. Evolution of strain diversity and virulence factor repertoire in pediatric Staphylococcus aureus isolates PLoS ONE (2025).
166: Emily A. Felton, Mary-Elizabeth Jobson, Nathanial Torres, Rachel M Washburn, Ariana M. Virgillio, Joshua Alvior, Eleonora Cella, Amorce Lima, Deanna Becker, Suzane Silbert, et al. Emergence of ST3390: A Novel Apigmented MRSA Clone From the CC5 Lineage The Journal of Infectious Diseases (2025).
165: Karyn Havas, Roy Edler, Laura Ruesch, Marlee Braun, Peter Ferm, Noelle Noyes, Laura B. Goodman, H.M. Scott, Joel Nerem, Taylor Spronk, et al. Assessment of a program for monitoring antimicrobial purchase and resistance in Escherichia coli and Salmonella enterica on pig farms in the Midwestern United States from May 2020 through October 2023 Frontiers in Veterinary Science (2025).
164: Ana Rafaela Kruemmel, Jessica L. Halpin, Victoria Foltz, Janet K. Dykes, Carolina Lúquez. Detection of a streptogramin A O-acetyltransferase gene ( vatD ) in the chromosome of Clostridium botulinum isolated from infants in the United States Applied and Environmental Microbiology (2025).
163: Brooke M. Talbot, Natasia F Jacko, Katrina S. Hofstetter, Tara Alahakoon, Kévin Bouiller, Timothy D. Read, Michael David. Methicillin-Resistant Staphylococcus aureus Bacteremia Relapses Show Diverse Genomic Profiles but Convergence in Bacteremia-Associated Genes The Journal of Infectious Diseases (2025).
162: Thunchanok Yaikhan, Mingkwan Yingkajorn, Worawut Duangsi-Ngoen, Ei Phway Thant, Nattarika Chaichana, Sirikan Suwannasin, Kamonnut Singkhamanan, Saranyou Churi, Komwit Surachat. Genomic characterization of a clinical Enterocloster aldenensis strain: First report in Thailand Infection Genetics and Evolution (2025).
161: Thomas D. Stanton, Marit Andrea Klokkhammer Hetland, Iren H. Löhr, Kathryn E. Holt, Kelly L. Wyres. Fast and accurate in silico antigen typing with Kaptive 3 Microbial Genomics (2025).
160: Martin Larralde, Georg Zeller, Laura M. Carroll. PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity NAR Genomics and Bioinformatics (2025).
159: Nattarika Chaichana, Sirikan Suwannasin, Jirasa Boonsan, Thunchanok Yaikhan, Chollachai Klaysubun, Kamonnut Singkhamanan, Monwadee Wonglapsuwan, Rattanaruji Pomwised, Siriwimon Konglue, Rusneeta Chema, et al. Genomic Characterization and Safety Evaluation of Enterococcus lactis RB10 Isolated from Goat Feces Antibiotics (2025).
158: Ahmed Yousef Alhejaili, Ge Zhou, Heba Halawa, Jiayi Huang, Omniya Fallatah, Raneem Hirayban, Sara Iftikhar, Abrar AlAsmari, Mathew Milner, Manuel Banzhaf, et al. Methicillin-resistant Staphylococcus aureus in Saudi Arabia: genomic evidence of recent clonal expansion and plasmid-driven resistance dissemination Frontiers in Microbiology (2025).
157: Josiah Bennett, Sarah Lohsen, Elizabeth Y. Kim, Pranavi Ravichandran, William K. Blake, Kimberly Workowski, Sarah W. Satola, Matthew H. Collins, Danielle Barrios Steed. A Haemophilus influenzae -associated mycotic aneurysm months after treated bacteremia ASM Case Reports (2025).
156: Chantisa Keeratipusana, Weerawat Phuklia, Vanheuang Phommadeechack, Janjira Thaipadungpanit, Vilada Chansamouth, Koukeo Phommasone, Sayaphet Rattanavong, Catrin E. Moore, Matthew T. Robinson, Allen L. Richards, et al. Complete genomes of Rickettsia typhi reveal a clonal population bioRxiv (Cold Spring Harbor Laboratory) (2025).
155: Sarah Shrum Davis, Paris S. Hamm, Karen Edge, Tim Hanosh, Jessica P. Houston, Anastacia Griego-Fisher, F. Lugo, Nicholas Wenzel, D’Eldra Malone, Carol Bradford, et al. Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA Nature Communications (2025).
154: Helena M. B. Seth-Smith, Ashley M. Rooney, Adrian Egli. Strain Typing (Bacterial, Viral, Fungal, and Mycobacterial) ** (2025).
153: Agnetor Mutheo, Carren Bosire, Victor Tunje Jeza, George Githinji, Sammy Wambua. Metagenomic exploration of antimicrobial resistance genes in marine bacteria ecosystem Wellcome Open Research (2025).
152: Xiaobao Xie, Rong Li, Qiang Yu, Qiang Yu, Xue Zhang, Dongbo Chen, Yuchen Li, Feng Xue, Qinghua Yu, Qinghua Yu. The high utilization of human milk oligosaccharides with glycoside hydrolase family exsH gene in Akkermansia species Carbohydrate Polymer Technologies and Applications (2025).
151: Silvia García-Cobos, Natalia Seco Alberca, Blanca Bravo, Verónica Casquero-García, Eva Ramírez de Arellano, Cristina Calvo, Guillermo Ruíz-Carrascoso, Iker Falces‐Romero, Nieves Larrosa, Belen Viñado-Pérez, et al. Genomic analysis of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) causing infections in children—a Spanish multicenter study Frontiers in Microbiology (2025).
150: Simon Goldie, Laurie C. Lau, Huw Jones, Philip G. Harries, Andrew F. Walls, Rami J. Salib. Identification of Novel Staphylococcus aureus Core and Accessory Virulence Patterns in Chronic Rhinosinusitis International Journal of Molecular Sciences (2025).
149: João Vitor Wagner Ordine, E Silva, Lívia S. Zaramela. Global cross-genome comparison of carbohydrate transporters in Staphylococcus aureus with distinct antimicrobial susceptibility profiles Next research. (2025).
148: Aaron Asmus, K. M. Heimer, Kristin Davis, Peter Ferm, K. E. Belk, Randall S. Singer, Timothy J. Johnson, Noelle Noyes. Temporality and Genetic Relatedness of Salmonella in a Pork Processing Facility Journal of Food Protection (2025).
147: Brooke M. Talbot, Natasia F Jacko, Katrina S. Hofstetter, Tara Alahakoon, Kévin Bouiller, Timothy D. Read, Michael David. Genomic investigation of MRSA bacteremia relapse reveals diverse genomic profiles but convergence in bacteremia-associated genes medRxiv (2025).
146: Alba Frias‐De‐Diego, Manuel Jara, Cristina Lanzas. Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens Open Forum Infectious Diseases (2025).
145: Brianna J. Bixler, Charlotte J. Royer, Robert A. Petit, Abraham Moller, Samantha Sefton, Stepy Thomas, Amy Tunali, Lauren F. Collins, Monica M. Farley, Sarah W. Satola, et al. Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta PeerJ (2025).
144: Emily A. Felton, Mary-Elizabeth Jobson, Ariana M. Virgillio, Joshua Alvior, Eleonora Cella, Amorce Lima, Deanna Becker, Suzane Silbert, Taj Azarian, Kami Kim, et al. Emergence of ST3390: A non-pigmented HA-MRSA clone with enhanced virulence bioRxiv (Cold Spring Harbor Laboratory) (2025).
143: Carter N. Abbott, Aditi Dhillon, Sushma Timalsina, Elise Furr, Patrick Vélicitat, Adam Belley, Navaneeth Narayanan, Keith S. Kaye, David S. Weiss. The association between undetected heteroresistance and antibiotic treatment failure in complicated urinary tract infection medRxiv (2025).
142: Kat Steinke, Karina Gravgaard Thomsen, Silje Vermedal Hoegh, Sanne Løkkegaard Larsen, Karina Kubel Vilhelmsen, Thøger Gorm Jensen, Marianne Nielsine Skov, Thomas Vognbjerg Sydenham. RSYD-BASIC: a bioinformatic pipeline for routine sequence analysis and data processing of bacterial isolates for clinical microbiology Access Microbiology (2025).
141: Daichi Morita, Teruo Kuroda. Recent Antimicrobial Resistance Situation and Mechanisms of Resistance to Key Antimicrobials in Enterotoxigenic <i>Escherichia coli</i> Biological and Pharmaceutical Bulletin (2025).
140: Sirikan Suwannasin, Kamonnut Singkhamanan, Rattanaruji Pomwised, Nattarika Chaichana, Monwadee Wonglapsuwan, Thunchanok Yaikhan, Komwit Surachat. Phenotypic and genomic analysis of Enterococcus avium MC09 pathogenicity isolated from Scylla spp. (mud crab) in a Thai market Microbial Pathogenesis (2025).
139: Joseph J. Zeppa, Ellen G. Avery, Patryk Aftanas, Erin Choi, Simone Uleckas, Prachi Patel, Nicholas Waglechner, Hubert Jimenez, Christie Vermeiren, Kevin Katz, et al. Comparison of pharyngeal and invasive isolates of Streptococcus pyogenes by whole-genome sequencing in Toronto, Canada Microbiology Spectrum (2025).
138: Thomas D. Stanton, Marit Andrea Klokkhammer Hetland, Iren H. Löhr, Kathryn E. Holt, Kelly L. Wyres. Fast and Accurate in silico Antigen Typing with Kaptive 3 bioRxiv (Cold Spring Harbor Laboratory) (2025).
137: Ahmed Yousef Alhejaili, Ge Zhou, Heba Halawa, Jiayi Huang, Omniya Fallatah, Raneem Hirayban, Sara Iftikhar, Abrar AlAsmari, Mathew Milner, Manuel Banzhaf, et al. Methicillin-resistant Staphylococcus aureus in Saudi Arabia: genomic evidence of recent clonal expansion and plasmid-driven resistance dissemination medRxiv (2025).
136: Emanuele Nicitra, Morena Terrana, Dafne Bongiorno, Saveria Dodaro, Francesca Greco, Sonia Greco, Nadia Marascio, Maria Vittoria Mauro, Marta Pantanella, Grete Francesca Privitera, et al. Circulation of a Unique Klebsiella pneumoniae Clone, ST147 NDM-1/OXA-48, in Two Diverse Hospitals in Calabria (Italy) Antibiotics (2025).
135: Christine Marie George, Alves Namunesha, Kelly Endres, Willy Felicien, Presence Sanvura, Jean‐Claude Bisimwa, Jamie Perin, Justin Bengehya, Ghislain Maheshe, Cirhuza Cikomola, et al. Epidemiologic and Genomic Surveillance of Vibrio cholerae and Effectiveness of Single-Dose Oral Cholera Vaccine, Democratic Republic of the Congo Emerging infectious diseases (2025).
134: Gillian A.M. Tarr, Linda Chui, Kim Stanford, Emmanuel W. Bumunang, Rahat Zaheer, Vincent Li, Stephen B. Freedman, Chad Laing, Tim A. McAllister. Persistent cross-species transmission systems dominate Shiga toxin-producing Escherichia coli O157:H7 epidemiology in a high incidence region: A genomic epidemiology study eLife (2025).
133: Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega-Sanz, Jacob L. Steenwyk, Samuel Sihvonen. Solu: a cloud platform for real-time genomic pathogen surveillance BMC Bioinformatics (2025).
132: Guillem López de Egea, Aída González-Díaz, Randall J. Olsen, Gérard Guédon, Dàmaris Berbel, Inmaculada Grau, Jordi Cámara, Lucía Saiz-Escobedo, Sara Calvo-Silveria, Irene Cadenas-Jiménez, et al. Emergence of invasive Streptococcus dysgalactiae subsp. equisimilis in Spain (2012-2022): genomic insights and clinical correlations International Journal of Infectious Diseases (2025).
131: Olusola Olagoke, Ammar Aziz, Lucile H Zhu, Timothy D. Read, Deborah Dean. Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline NAR Genomics and Bioinformatics (2025).
130: Gaetano Maugeri, Maddalena Calvo, Dafne Bongiorno, Dalida Bivona, Giuseppe Migliorisi, Grete Francesca Privitera, Guido Scalia, Stefania Stefani. Sequencing Analysis of Invasive Carbapenem-Resistant Klebsiella pneumoniae Isolates Secondary to Gastrointestinal Colonization Microorganisms (2025).
129: Christian Zirbes, Andries Feder, Anthony J. Pamatmat, Alyssa R. Bartels, Nicholas J. Pitcher, Alexis L. Rozen, M. Teresi, J. Krogh, Margaret Regan, Erin A. Arnold, et al. Genetic Concordance of Staphylococcus aureus From Oropharyngeal and Sputum Cultures in People With Cystic Fibrosis Pediatric Pulmonology (2025).
128: Nattarika Chaichana, Jirasa Boonsan, Sirikan Suwannasin, Kamonnut Singkhamanan, Monwadee Wonglapsuwan, Rattanaruji Pomwised, Thunchanok Yaikhan, Chollachai Klaysubun, Siriwimon Konglue, Rusneeta Chema, et al. Integrative Genomic and Phenotypic Profiling of Lactiplantibacillus pentosus CLP10: A Probiotic Candidate from Traditional Fermented Thai Stinky Beans SSRN Electronic Journal (2025).
127: Derek Kong Lam, Sree Vadlamudi, Ria Poluru, Ashley Fang, Chujing Zheng, C.H. Lee, Anna Zhang, Yujie Men, Linda Shi. Automation and Comparative Evaluation of the Bactopia Pipeline for Environmental Tracking of Antibiotic Resistance Genes Using Genomic and Visualization Frameworks Journal of Biomedical Engineering and Biosciences (2025).
126: Liviu-Iulian Rotaru, Marius Surleac. PeGAS: a versatile bioinformatics pipeline for antimicrobial resistance, virulence and pangenome analysis Bioinformatics Advances (2024).
125: Grete Francesca Privitera, Adriana Antonella Cannata, Floriana Campanile, Salvatore Alaimo, Dafne Bongiorno, Alfredo Pulvirenti. BacExplorer: an integrated platform for de novo bacterial genome annotation Bioinformatics Advances (2024).
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