One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces

Abstract

Several studies have shown the ubiquitous presence of bacteria in the hospital environmental surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contributes to a major public health issue by increasing patient morbidity and mortality during or after hospital stay. Bacterial high-throughput amplicon gene sequencing along with AMR genes identification and whole genome sequencing (WGS) are new biotechnological tools that allow multiple-sample screening for a diversity of bacteria. In this paper, we used these methods to perform an one-year cross sectional profiling of bacteria and AMR genes in adult and neonatal intensive care units (ICU and NICU) in a Brazilian public hospital. Our results showed high abundances of HAI-related bacteria as S. epidermidis, S. aureus, K. pneumoniae, A. baumannii complex, E. coli, E. faecalis and P. aeruginosa in patients and hospital surfaces. Most abundant AMR genes detected throughout ICU and NICU were mecA, blaCTX-M-1 group, blaSHV-like and blaKPC-like. We found that NICU environment and patients were more widely contaminated with pathogenic bacteria than ICU. Patient samples, despite the higher bacterial load, have lower bacterial diversity than environmental samples in both units. Finally, we also identified contamination hotspots in the hospital environment showing constant frequencies of bacterial and AMR contamination throughout the year. WGS sequencing, 16S rRNA oligotypes and AMR identification allowed a high-resolution data analysis for bacterial characterization and its distributions along the hospital microbiome profile.

A novel bacteriocin produced by Bifidobacterium longum subsp. infantis has dual antimicrobial and immunomodulatory activity

“…Moreover, these infants are often exposed to multidrug resistant bacteria, and they harbour a high number of commensal bacteria that encode AMR genes (29,30), thus identification and development of novel anti-microbial strategies, like bacteriocins, are crucial. However, to date, our understanding and characterisation of bacteriocin producing microbiota members and bacteriocin function is somewhat limited.…”

“…This is particularly important in at-risk groups such as neonates (including preterm infants) who do not have a mature immune system and lack a robust early life gut microbiota, which limits their ability to mount effective anti-pathogen responses. Moreover, these infants are often exposed to multidrug resistant bacteria, and they harbour a high number of commensal bacteria that encode AMR genes ( 29, 30 ), thus identification and development of novel anti-microbial strategies, like bacteriocins, are crucial. However, to date, our understanding and characterisation of bacteriocin producing microbiota members and bacteriocin function is somewhat limited.…”

Prevalence of carbapenem resistance and its potential association with antimicrobial use in humans and animals in rural communities in Vietnam

“… 6 , 7 Data from Vietnamese hospitals have documented that this leads to increased mortality and associated health care costs. 8 , 9 Prevalence of infection with CRE among patients correlates with length of hospitalization (from 13% on admission to 89% at day 15). 9 Laboratory data indicate increased prevalence of carbapenem resistance between 2012 and 2016 among Escherichia coli (CREC) (from 6% to 8%) and Klebsiella pneumoniae (CRKP) (from 17% to 24%).…”

Clinically Relevant Pathogens on Surfaces Display Differences in Survival and Transcriptomic Response in Relation to Probiotic and Traditional Cleaning Strategies

“…Acinetobacter baumannii and Klebsiella pneumoniae have been recognized as a major source of healthcare-associated infections associated with high morbidity and mortality rates due to their resistance to many antibiotics including carbapenems 15, 16 . These organisms not only persist on surfaces for up to several months 17 but are commonly found in healthcare environments, especially in low- and middle-income countries.…”

“…These organisms not only persist on surfaces for up to several months 17 but are commonly found in healthcare environments, especially in low- and middle-income countries. K. pneumoniae have been found on surfaces in hospitals in Brazil 16, 15 , Tunisia 17 , Russia 18 , China 19 and Ghana 20 A. baumannii was found on surfaces in hospitals in Brazil 21 , Turkey 21 , Saudi Arabia 22 and on the surfaces of medical devices in Iran 23 . It was also found on surfaces in buildings surrounding hospitals in the US 24 .…”