Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria

Blake, Kevin S; Choi, Joo-Hee; Dantas, Gautam

doi:10.1007/s00018-020-03717-2

Cited by 32 publications

(32 citation statements)

References 230 publications

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“…Many reports support the view that plasmid transfer is a relevant mechanism how AMG spread within the hospital setting [ 19 , 20 , 21 , 22 ]. However, investigating plasmid transfer based on short-read sequencing data is challenging.…”

Section: Discussionmentioning

confidence: 99%

The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample

et al. 2022

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Plasmid transfer is one important mechanism how antimicrobial resistance can spread between different species, contributing to the rise of multidrug resistant bacteria (MDRB) worldwide. Here were present whole genome sequencing (WGS) data of two MDRB isolates, an Escherichia coli and a Klebsiella quasipneumoniae, which were isolated from a single patient. Detailed analysis of long-read sequencing data identified an identical F2:A-:B- lncFII plasmid containing blaCTX-M-27 in both isolates, suggesting horizontal plasmid exchange between the two species. As the plasmid of the E. coli strain carried multiple copies of the resistance cassette, the genomic data correlated with the increased antimicrobial resistance (AMR) detected for this isolate. Our case report demonstrates how long-read sequencing data of MDRB can be used to investigate the role of plasmid mediate resistance in the healthcare setting and explain resistance phenotypes.

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Section: Discussionmentioning

confidence: 99%

The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample

et al. 2022

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“…By far the main driver of sequencing of pathogen genomes is the interest in understanding epidemiological relationships and antimicrobial resistance in bacteria. Antimicrobial resistance patterns serve as an early indicator of potential clonality of strains; however, much richer information can be obtained from sequencing [ 8 ]. Sequencing DNA extracted from bacterial isolates is simple, fast, and relatively inexpensive compared with many other sequencing approaches.…”

Section: Bacterial Sequencing In Hospital Outbreaksmentioning

confidence: 99%

NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology

Greninger

Zerr

2021

Journal of the Pediatric Infectious Diseases Society

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Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.

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“…In addition, broad-spectrum antibiotic use can allow the proliferation of resistant bacteria of new-origin or already present in the gut [20]. Furthermore, there is an increased dissemination of these bacteria into the ICU environment via contact with healthcare workers, adjacent patients or contaminated objects [21]. Other operations typical of ICU patients, potentially responsible for gut dysbiosis, are proton pump inhibitors usage and enteral feeding or delayed enteral feeding [20].…”

Section: Gut Microbiota Composition In Health and Critically Ill Patientmentioning

confidence: 99%

Nutritional Status and the Critically Ill Patient: Gut Microbiota and Immuno-Nutrition in I.C.U. at the Time of SARS-COV 2 Pandemic

Scarpellini¹,

Scarcella

Romanelli³

et al. 2021

Gastroenterology Insights

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Background: Gut microbiota is a complex ecosystem of bacteria, viruses, archaea, protozoa and yeasts in our intestine. It has several functions, including maintaining human body equilibrium. Microbial “dysbiosis” can be responsible for outbreak of local and systemic infections, especially in critically ill patients. Methods: to build a narrative review, we performed a Pubmed, Medline and EMBASE search for English language papers, reviews, meta-analyses, case series and randomized controlled trials (RCTs) by keywords and their associations: critically ill patient; nutrition; gut microbiota; probiotics; gut virome; SARS-COV 2. Results: Over the antibiotic-based “selective decontamination”, potentially responsible for drug-resistant microorganisms development, there is growing interest of scientists and the pharmaceutical industry for pre-, probiotics and their associations as safe and reliable remedies restoring gut microbial “eubiosis”. Very first encouraging evidences link different gut microbiota profiles with SARS-COV 2 disease stage and gravity. Thus, there is frame for a probiotic therapeutic approach of COVID-19. Conclusions: gut microbiota remodulation seems to be a promising and safe therapeutic approach to prevent local and systemic multi-resistant bug infections in the intensive care unit (ICU) patients. This approach deserves more and more attention at the time of SARS-COV 2 pandemic.

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Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria

Cited by 32 publications

References 230 publications

The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample

The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample

NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology

Nutritional Status and the Critically Ill Patient: Gut Microbiota and Immuno-Nutrition in I.C.U. at the Time of SARS-COV 2 Pandemic

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