Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment

Raplee, Isaac; Walker, Lacey; Xu, Lei; Surathu, Anil; Chockalingam, Ashok; Stewart, Sharron; Han, Xiaomei; Rouse, Rodney; Li, Zhihua

doi:10.1186/s13756-021-00903-0

Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment

Journal Article · Mon Feb 15 00:00:00 EST 2021 · Antimicrobial Resistance & Infection Control

DOI:https://doi.org/10.1186/s13756-021-00903-0· OSTI ID:1817036

Raplee, Isaac ^[1]; Walker, Lacey ^[2]; Xu, Lei ^[2]; Surathu, Anil ^[2]; Chockalingam, Ashok ^[2]; Stewart, Sharron ^[2]; Han, Xiaomei ^[2]; Rouse, Rodney ^[2]; ^[2]

U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States); OSTI
U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States)

Introduction: According to the Centers for Disease Control’s 2015 Hospital Acquired Infection Hospital Prevalence Survey, 1 in 31 hospital patients was infected with at least one nosocomial pathogen while being treated for unrelated issues. Many studies associate antibiotic administration with nosocomial infection occurrence. However, to our knowledge, there is little to no direct evidence of antibiotic administration selecting for nosocomial opportunistic pathogens. Aim: This study aims to confirm gut microbiota shifts in an animal model of antibiotic treatment to determine whether antibiotic use favors pathogenic bacteria. Methodology: We utilized next-generation sequencing and in-house metagenomic assembly and taxonomic assignment pipelines on the fecal microbiota of a urinary tract infection mouse model with and without antibiotic treatment. Results: Antibiotic therapy decreased the number of detectable species of bacteria by at least 20-fold. Furthermore, the gut microbiota of antibiotic treated mice had a significant increase of opportunistic pathogens that have been implicated in nosocomial infections, like Acinetobacter calcoaceticus/baumannii complex, Chlamydia abortus, Bacteroides fragilis, and Bacteroides thetaiotaomicron. Moreover, antibiotic treatment selected for antibiotic resistant gene enriched subpopulations for many of these opportunistic pathogens. Conclusions: Oral antibiotic therapy may select for common opportunistic pathogens responsible for nosocomial infections. In this study opportunistic pathogens present after antibiotic therapy harbored more antibiotic resistant genes than populations of opportunistic pathogens before treatment. Our results demonstrate the effects of antibiotic therapy on induced dysbiosis and expansion of opportunistic pathogen populations and antibiotic resistant subpopulations of those pathogens. Follow-up studies with larger samples sizes and potentially controlled clinical investigations should be performed to confirm our findings.

View Accepted Manuscript (DOE)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1817036

Journal Information:: Antimicrobial Resistance & Infection Control, Journal Name: Antimicrobial Resistance & Infection Control Journal Issue: 1 Vol. 10; ISSN 2047-2994

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Antibiotic resistance
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Nosocomial

Additional file 1 of Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment Raplee, Isaac; Walker, Lacey; Xu, Lei https://doi.org/10.6084/m9.figshare.14037889 The current record is supplemented by this dataset	dataset	January 2021
Additional file 1 of Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment Raplee, Isaac; Walker, Lacey; Xu, Lei https://doi.org/10.6084/m9.figshare.14037889.v1 The current record is supplemented by this dataset	dataset	January 2021
Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment Raplee, Isaac; Walker, Lacey; Xu, Lei https://doi.org/10.6084/m9.figshare.c.5306206 The current record is supplemented by this collection	collection	January 2021

Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment

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