Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

D’Souza, Alaric W.; Potter, Robert F.; Wallace, Meghan A.; Shupe, Angela; Patel, Sanket; Sun, Xiaoqing; Gul, Danish; Kwon, Jennie H.; Andleeb, Saadia; Burnham, Carey Ann D.; Dantas, Gautam

doi:10.1038/s41467-019-12563-1

Cited by 46 publications

(49 citation statements)

References 93 publications

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“…The most common external perturbations to the microbiome are diet, medications (especially antibiotics), and the environment [26][27][28][29][30][31]. In this review, we focus on antibiotic perturbation throughout life and associations with other factors including age and maturity of the microbiome, diet and the environment, and the co-morbidities of the individual (Fig.…”

Section: Introductionmentioning

confidence: 99%

Understanding the impact of antibiotic perturbation on the human microbiome

2020

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The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome’s ecological balance, commonly by antibiotics, can cause and exacerbate diseases. To predict and successfully rescue such perturbations, first, we must understand the underlying taxonomic and functional dynamics of the microbiome as it changes throughout infancy, childhood, and adulthood. We offer an overview of the healthy gut bacterial architecture over these life stages and comment on vulnerability to short and long courses of antibiotics. Second, the resilience of the microbiome after antibiotic perturbation depends on key characteristics, such as the nature, timing, duration, and spectrum of a course of antibiotics, as well as microbiome modulatory factors such as age, travel, underlying illness, antibiotic resistance pattern, and diet. In this review, we discuss acute and chronic antibiotic perturbations to the microbiome and resistome in the context of microbiome stability and dynamics. We specifically discuss key taxonomic and resistance gene changes that accompany antibiotic treatment of neonates, children, and adults. Restoration of a healthy gut microbial ecosystem after routine antibiotics will require rationally managed exposure to specific antibiotics and microbes. To that end, we review the use of fecal microbiota transplantation and probiotics to direct recolonization of the gut ecosystem. We conclude with our perspectives on how best to assess, predict, and aid recovery of the microbiome after antibiotic perturbation.

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Section: Introductionmentioning

confidence: 99%

Understanding the impact of antibiotic perturbation on the human microbiome

2020

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“…Through core genome phylogenetic analysis, we found that our CRAB isolates are dominated by single lineage. Previous report of A. baumannii and E. faecium isolates from Pakistan and the USA hospital system showed they were similarly dominated by single lineages (D'Souza et al, 2019). Contrastingly, these strains were composed of three clusters and eight clones.…”

Section: Discussionmentioning

confidence: 80%

Molecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms

Zhang

Awan

et al. 2021

Front. Cell. Infect. Microbiol.

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Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of nosocomial infections and hospital outbreaks worldwide, remaining a critical clinical concern. Here we characterized and investigated the phylogenetic relationships of 105 CRAB isolates from an intensive care unit from one hospital in China collected over six years. All strains carried blaOXA-23, blaOXA-66 genes for carbapenem resistance, also had high resistance gene, virulence factor, and insertion sequence burdens. Whole-genome sequencing revealed all strains belonged to ST2, the global clone CC2. The phylogenetic analysis based on the core genome showed all isolates were dominated by a single lineage of three clusters and eight different clones. Two clones were popular during the collection time. Using chi-square test to identify the epidemiologically meaningful groupings, we found the significant difference in community structure only existed in strains from separation time. The haplotype and median-joining network analysis revealed genetic differences appeared among clusters and changes occurred overtime in the dominating cluster. Our results highlighted substantial multidrug-resistant CRAB burden in the hospital ICU environment demonstrating potential clone outbreak in the hospital.

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“…Plates were incubated at 35°C under aerobic conditions (except in the case of anaerobic brucella blood agar) for 14 h. Individual bacterial colonies from the selective media were identified by MALDI-TOF MS (bioMérieux Vitek MS), and antimicrobial susceptibility testing (AST) was performed using Kirby-Bauer disk diffusion and interpreted using CLSI standards. DNA extraction was performed as previously described ( 28 ). C. difficile was cultured anaerobically and isolated (with ribotyping and toxin gene detection performed) as previously described ( 29 , 30 ).…”

Section: Methodsmentioning

confidence: 99%

“…Library preparation and sequencing of metagenomes and isolate genomes. Illumina libraries of fecal metagenomic DNA, C. difficile isolate DNA, and VRE isolate DNA were prepared as described previously (28,31). Reads for both metagenomes and isolate genomes were processed and filtered as described previously (Text S1) (28,32).…”

Section: Methodsmentioning

confidence: 99%

Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients

Fishbein

Hink

Reske

et al. 2021

mSphere

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Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin (n = 8) or placebo (n = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity (P = 0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes (P = 0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile, and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.) IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile, perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile/ARO-related outcomes and transmission.

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Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

Cited by 46 publications

References 93 publications

Understanding the impact of antibiotic perturbation on the human microbiome

Understanding the impact of antibiotic perturbation on the human microbiome

Molecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms

Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients

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