Integrated epidemiologic investigation and genomic confirmation of a Klebsiella pneumoniae neonatal sepsis outbreak in Botswana

Klebsiella pneumoniae (Kpn) is a major cause of infant mortality worldwide, with most transmission occurring among hospitalized neonates in low- and middle-income countries where infections caused by ...

doi.org

Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection | Keystone Symposia

Join us at the Keystone Symposia on Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection, May 2026, in Breckenridge, with field leaders!

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Frontiers | If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice

BackgroundThe microbiome-gut-brain axis is a mediator of stress-related disorders. The number of preclinical studies exploring the potential causal mechanism...

frontiersin.org

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

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Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection - Nature Communications

In this work, authors use whole genome tracking in a neonatal intensive care unit to reveal a strong link between Staphylococcus aureus colonization and invasive infection, pinpointing critical new ta...

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Children’s Hospital of Philadelphia, Penn Medicine Researchers Identify Strategies for Preventing the Most Infectious Strains of S. aureus in the NICU

A new study has identified which strains of Staphylococcus aureus – commonly known as staph – are commonly transmitted in neonatal intensive care units. A new study led by researchers at Children’s Hospital of Philadelphia (CHOP) and the Perelman School of Medicine at the University of Pennsylvania (Penn Medicine) has identified which strains of Staphylococcus aureus – commonly known as staph – are commonly transmitted in neonatal intensive care units and which specific strains are most likely to cause invasive and serious infections.The findings, published today in Nature Communications, offer a critical blueprint for precision surveillance of staph in the NICU and provide an important foundation for reducing infections in vulnerable newborns.Staphylococcus aureus is a bacterium often found on the skin and in the noses of healthy people. While usually harmless, certain strains can cause anything from mild skin infections to more serious bloodstream infections and pneumonia. A recent study found that one in four healthcare-acquired infections in very preterm U.S. infants were due to staph. Lakshmi Srinivasan, MD, FAAP As part of bi-monthly surveillance sampling at CHOP led by co-lead author Lakshmi Srinivasan, MD, an attending physician in the Division of Neonatology and the Pediatric Sepsis Program, nurses routinely swab the noses of babies in the neonatal intensive care unit (NICU) to test for the presence of these bacteria. However, there are currently no standard approaches for NICU surveillance of staph, and there is little evidence for when to begin or stop surveillance, how frequently to test, and which patients to closely monitor. Joseph P. Zackular, PhD “Staph is a critical human pathogen and a major cause of severe infection in our highest-risk infants,” said co-senior study author Joseph Zackular, PhD, a researcher in the Department of Pathology and Laboratory Medicine and Co-Director of the Center for Microbial Medicine at CHOP. “In this study, we brought together basic researchers, clinicians, and computational biologists in a highly collaborative effort to address a major challenge in pediatric health.”Utilizing expertise in CHOP’s NICU, the Center for Microbial Medicine, the Infectious Disease Diagnostics Laboratory, and the Microbiome Sequencing Center, researchers performed precision surveillance of invasive infections of staph in high-risk infants with the goal of identifying new strategies for prevention and control. Over three years, whole-genome sequencing showed that shared spaces and physical proximity were major drivers of staph transmission. Stable colonization by two types of staph, MSSA and MRSA, occurred across all areas within the NICU, and an analysis of more than 1,000 staph genomes revealed strain-specific persistence and colonization patterns, with MSSA causing more colonization and invasive disease than MRSA. Ahmed M. Moustafa, BPharm, PhD “Our study demonstrated that certain strains of staph pose significantly greater risk by being more transmissible and potentially more invasive, suggesting that a more effective prevention strategy might isolate and target the strains that cause the most infections,” said co-senior study author Ahmed M. Moustafa, BPharm, PhD, a researcher in the Division of Gastroenterology, Hepatology and Nutrition and Co-Director of the Center for Microbial Medicine at CHOP and the Sequencing Core Director of the CHOP Microbiome Center. Paul J. Planet, MD, PhD “This study provides a path forward for real-time interventions and improved surveillance that we hope can be implemented in NICUs around the country and improve the health and safety of preterm infants,” said co-senior study author Paul J. Planet, MD, PhD, an attending physician in the Division of Infectious Diseases at Children's Hospital of Philadelphia and Co-Director of the Center for Microbial Medicine at CHOP.This study was supported by the Center for Microbial Medicine at the Children’s Hospital of Philadelphia and National Institutes of Health grant 1R01AI185544.She et al, “Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection.” Nat Commun. Online February 9, 2026. DOI: 10.1038/s41467-026-69074-z

chop.edu

Enterococcus faecalis modulates phase variation in Clostridioides difficile | Journal of Bacteriology

Clostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; how...

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Constructing a “periodic table” of bacteria to map diversity in trait space

Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen

academic.oup.com

Research Technician III-Microbiome Center in Philadelphia, Pennsylvania, United States of America | Research at Children’s Hospital of Philadelphia

Apply for Research Technician III-Microbiome Center job with Children’s Hospital of Philadelphia in Philadelphia, Pennsylvania, United States of America. Research at Children’s Hospital of Philadelphi...

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Research Technician IV in Philadelphia, Pennsylvania, United States of America | Research at Children’s Hospital of Philadelphia

Apply for Research Technician IV job with Children’s Hospital of Philadelphia in Philadelphia, Pennsylvania, United States of America. Research at Children’s Hospital of Philadelphia

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Microbial bellwether: Community-scale metabolic modeling to predict infection

Microbial colonization is shaped by a complex network of interactions that influence both commensals and pathogens, including the public-health threat…

sciencedirect.com

Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut

Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key metabolic strategies ex...

cell.com

Transmission of Staphylococcus aureus in the neonatal intensive care unit predicts invasive infection

Background : Staphylococcus aureus is a leading cause of healthcare-associated infection and is one of the most common pathogens causing serious invasive infection in the neonatal intensive care unit ...

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