Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study

Abstract Background Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case of hospitals, the environmental microorganisms may influence patient recovery and outcome. An understanding of the bacterial community structure in the hospital environment is pivotal for the prevention of hospital-acquired infections and the dissemination of antibiotic resistance genes. In this study, we performed a longitudinal metagenetic approach in a newly opened ward at the Charité Hospital (Berlin) to characterize the dynamics of the bacterial colonization process in the hospital environment after first patient occupancy. Results The sequencing data showed a site-specific taxonomic succession, which led to stable community structures after only a few weeks. This data was further supported by network analysis and beta-diversity metrics. Furthermore, the fast colonization process was characterized by a significant increase of the bacterial biomass and its alpha-diversity. The compositional dynamics could be linked to the exchange with the patient microbiota. Over a time course of 30 weeks, we did not detect a rise of pathogenic bacteria in the hospital environment, but a significant increase of antibiotic resistance determinants on the hospital floor. Conclusions The results presented in this study provide new insights into different aspects of the environmental microbiome in the clinical setting, and will help to adopt infection control strategies in hospitals and health care-related buildings.

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Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema

10.21203/rs.2.18486/v2 ◽

2020 ◽

Author(s):

Evelyn Loo ◽

Amanda Zain ◽

Gaik Chin Yap ◽

Rikky W Purbojati ◽

Daniela I Drautz-Moses ◽

...

Keyword(s):

Antibiotic Resistance ◽

Cohort Study ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

First Year ◽

Beta Lactam ◽

First Year Of Life

Abstract Background While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)- producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing .E coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. Methods We analysed ARGs in the first year of life among 75 infants who had stool samples collected at multiple timepoints using metagenomics. Results The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. Conclusion In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that the majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.

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Safety Evaluation of Oral Care Probiotics Weissella cibaria CMU and CMS1 by Phenotypic and Genotypic Analysis

International Journal of Molecular Sciences ◽

10.3390/ijms20112693 ◽

2019 ◽

Vol 20 (11) ◽

pp. 2693 ◽

Cited By ~ 6

Author(s):

Mi-Sun Kang ◽

Ji-Eun Yeu ◽

Sang-Phil Hong

Keyword(s):

Antibiotic Resistance ◽

Platelet Aggregation ◽

Pathogenic Bacteria ◽

Dna Analysis ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Toxic Metabolite ◽

Metabolite Production ◽

Weissella Cibaria ◽

Genotypic Analysis

Weissella cibaria CMU and CMS1 are known to exert beneficial effects on the oral cavity but have not yet been determined to be generally recognized as safe (GRAS), although they are used as commercial strains in Korea. We aimed to verify the safety of W. cibaria CMU and CMS1 strains through phenotypic and genotypic analyses. Their safety was evaluated by a minimum inhibitory concentration assay for 14 antibiotics, DNA analysis for 28 antibiotic resistance genes (ARGs) and one conjugative element, antibiotic resistance gene transferability, virulence gene analysis, hemolysis, mucin degradation, toxic metabolite production, and platelet aggregation reaction. W. cibaria CMU showed higher kanamycin resistance than the European Food Safety Authority (EFSA) cut-off, but this resistance was not transferred to the recipient strain. W. cibaria CMU and CMS1 lacked ARGs in chromosomes and plasmids, and genetic analysis confirmed that antibiotic resistance of kanamycin was an intrinsic characteristic of W. cibaria. Additionally, these strains did not harbor virulence genes associated with pathogenic bacteria and lacked toxic metabolite production, β-hemolysis, mucin degradation, bile salt deconjugation, β-glucuronidase, nitroreductase activity, gelatin liquefaction, phenylalanine degradation, and platelet aggregation. Our findings demonstrate that W. cibaria CMU and CMS1 can achieve the GRAS status in future.

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Prevalence of Antibiotic Resistance Genes in Air-Conditioning Systems in Hospitals, Farms, and Residences

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16050683 ◽

2019 ◽

Vol 16 (5) ◽

pp. 683 ◽

Cited By ~ 5

Author(s):

Yaying Li ◽

Hongkai Liao ◽

Huaiying Yao

Keyword(s):

Antibiotic Resistance ◽

Network Analysis ◽

16S Rrna ◽

Resistance Gene ◽

Resistance Genes ◽

Air Conditioning ◽

Antibiotic Resistance Gene ◽

Indoor Environments ◽

Beta Lactam ◽

Significant Difference

High-throughput quantitative PCR combined with Illumina sequencing and network analysis were used to characterize the antibiotic resistance gene (ARG) profiles in air-conditioning filters from different environments. In total, 177 ARGs comprising 10 ARG types were determined. The detectable numbers and the relative abundance of ARGs in hospitals and farms were significantly higher than those in city and village residences. Compared to hospitals, farms had a higher level of tetracycline, multidrug, integrase, and macrolide–lincosamide–streptogramin (MLS) B resistance genes but a lower level of beta-lactam resistance genes. The bl3_cpha gene was the most abundant resistance gene subtype in hospital samples with an abundance of 2.01 × 10−4 copies/16S rRNA, while a level of only 5.08 × 10−12 copies/16S rRNA was observed in farm samples. There was no significant difference in bacterial diversity among the hospitals, farms, and residences, and Proteobacteria was the most abundant phylum. Network analysis revealed that Proteobacteria and Actinobacteria were possible hosts of the beta-lactam, MLSB, aminoglycoside, multidrug, sulfonamide, and tetracycline resistance genes. The results demonstrate that ARGs exist in indoor environments and that farms and hospitals are important sources. This study provides a useful reference for understanding the distribution patterns and risk management of ARGs in indoor environments.

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Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments

10.1101/341487 ◽

2018 ◽

Cited By ~ 3

Author(s):

Karkman Antti ◽

Pärnänen Katariina ◽

Larsson D.G. Joakim

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Selection Pressure ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Gene ◽

Fecal Pollution ◽

Metagenomic Data ◽

Resistant Bacteria ◽

Environmental Selection

AbstractDischarge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. Such pollution can directly contribute to increased morbidity caused by the transmission of resistant fecal pathogens. Residual antibiotics in wastewaters have been speculated to select for resistant bacteria and thereby promote the evolution and emergence of new resistance factors. Increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments may, however, simply be a result of fecal contamination with resistant bacteria rather than caused by an on-site selection pressure. In this study we have disentangled these two alternative scenarios by relating the relative resistance gene abundance to the accompanying extent of fecal pollution in publicly available metagenomic data. This was possible by analyzing the abundance of a newly discovered phage which is exceptionally abundant in, and specific to, human feces. The presence of resistance genes could largely be explained by fecal pollution, with no clear signs of selection in the environment, the only exception being environments polluted by very high levels of antibiotics from manufacturing where selection is evident. Our results demonstrate the necessity to take in to account the fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance. The presence or absence of selection pressure has major implications for what the risk scenarios are (transmission versus evolution) and for what mitigations (reducing pathogenic bacteria or selective agents) should be prioritized to reduce health risks related to antibiotic resistance in the environment.

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Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema

10.21203/rs.2.18486/v3 ◽

2020 ◽

Author(s):

Evelyn Loo(Former Corresponding Author) ◽

Amanda Zain ◽

Gaik Chin Yap ◽

Rikky W Purbojati ◽

Daniela I Drautz-Moses ◽

...

Keyword(s):

Antibiotic Resistance ◽

Cohort Study ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

First Year ◽

Beta Lactam ◽

First Year Of Life

Abstract Background While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)- producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants. Methods: We analysed ARGs in the first year of life among 75 infants at risk of eczema who had stool samples collected at multiple timepoints using metagenomics. Results: The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively. Conclusion: In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.

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Early Bacterial Colonization and Antibiotic Resistance Gene Acquisition in Newborns

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2020.00332 ◽

2020 ◽

Vol 10 ◽

Author(s):

Tilman E. Klassert ◽

Cristina Zubiria-Barrera ◽

Stefanie Kankel ◽

Magdalena Stock ◽

Robert Neubert ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Bacterial Colonization ◽

Antibiotic Resistance Gene ◽

Gene Acquisition

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The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies

10.1101/2021.11.15.468399 ◽

2021 ◽

Author(s):

Jana Sanne Huisman ◽

Timothy G Vaughan ◽

Adrian Egli ◽

Sarah Tschudin-Sutter ◽

Tanja Stadler ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Resistance Gene ◽

Antibiotic Resistance Gene ◽

Sequencing Data ◽

Short Read ◽

Assembly Method ◽

Long Reads ◽

The Impact

The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples is rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty to extract plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum beta-lactamase producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long-reads during assembly graph generation (Canu). In contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method.

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Aerosol antibiotic resistance gene dissemination among hospital departments by culture-facilitated comparative metagenomics

10.21203/rs.2.20350/v1 ◽

2020 ◽

Author(s):

Xiang Li ◽

Ziqi Wu ◽

Chenyuan Dang ◽

Miao Zhang ◽

Bixi Zhao ◽

...

Keyword(s):

Antibiotic Resistance ◽

16S Rrna ◽

Resistance Gene ◽

Antibiotic Resistance Gene ◽

Distribution Patterns ◽

Hospital Environment ◽

Rrna Gene ◽

Similar Distribution ◽

Gaseous State ◽

Comparative Metagenomics

Abstract Background: Genes make microorganisms resistant to antibiotics are overwhelmingly present in environments, and those in the air seem to consistently worsen human health, especially in built-in hospitals. In this study, we sampled two distinct seasonal solid-, liquid- and gaseous-state samples in a large occupied hospital, and mainly aim to study the temporal and spatial micro-ecology and antibiotic resistance gene (ARG) distribution patterns within hospital settings using culture-facilitated comparative metagenomics in combinations with other widely applied methods. Results: Hospital aerosol resistome showed concentration of 0.00042 copies per 16S rRNA gene which was comparable to that of drinking water (0.00024 copies/16S rRNA). Winter aerosols showed higher resistome concentration and exhibited similar distribution patterns among different departments; while evident microbial accumulation and stronger level of inter-species ARG exchange was observed in summer aerosol samples. Network analysis and cultural isolate whole genome sequencing results confirmed some of these exchanges were mediated via plasmids. Additionally, ARGs and microbial community source tracking results illustrated Outpatient hall could serve as a major resistome pollution source all year long. Conclusions: The state-of-art metagenomics analyses and culture facilitated sequencing with strict cutoff guarantee the result accuracy of resistome pattern observed in built-in hospital environment, and our novel genotype sharing network confirmed the plasmid-mediated transferring mechanism in hospital air for the first time. Overall, this study illustrated valuable and quality hospital aerosol dissemination patterns and our effort will encourage more metagenomics applications in hospital studies.

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Early bacterial colonization and antibiotic resistance gene acquisition in newborns

10.26226/morressier.5aeaf2d35800a00019097f58 ◽

2018 ◽

Author(s):

Hortense Slevogt

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Bacterial Colonization ◽

Antibiotic Resistance Gene ◽

Gene Acquisition

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Identification and characterization of colistin-resistant E. coli and K. pneumoniae isolated from Lower Himalayan Region of India

SN Applied Sciences ◽

10.1007/s42452-021-04596-3 ◽

2021 ◽

Vol 3 (6) ◽

Author(s):

Avinash Singh ◽

Anand Kumar Keshri ◽

Suraj Singh Rawat ◽

Deepak Swami ◽

Kala Venkata Uday ◽

...

Keyword(s):

Antibiotic Resistance ◽

Pathogenic Bacteria ◽

Health Workers ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Phenotypic Characterization ◽

Lag Phase ◽

Bacterial Strains ◽

E Coli

AbstractMultidrug resistance is one of the worldwide public health concerns. Water represents the most suitable environment, for the exchange of antibiotic resistance genes among pathogenic to non-pathogenic bacteria. Therefore, we aimed to screen the presence of blaNDM-1, blaTEM, blaSHV, blaCTX-M and mcr1–5 genes among water samples from different locations of Lower Himachal Pradesh. We examined the genotypic incidences of blaNDM-1, blaTEM, blaSHV, blaCTXM and mcr1–5 by polymerase chain reaction. Survivability assay, fitness cost assay and biofilm assay were performed for phenotypic characterization. The presence of blaNDM-1 and its related variants were analysed and confirmed by sequencing-based approaches. A total of 73 bacterial strains were identified on M-lauryl sulphate agar medium. Out of 73 colistin-resistant isolates, 34 were E. coli and 39 were K. pneumoniae. Out of 34 samples, 2 (5.8%), 2 (5.8%), 5 (14.7%), 5 (14.7%) and 4 (11.76%) E. coli were blaTEM, blaSHV,blaCTXM-1, blaCTXM-2 and blaCTXM-15 positive, respectively. Among 39 K. pneumoniae, 15 (38.4%), 6 (15.3%), 10 (25.6%), 9 (23.07%) and 10 (25.6%) were blaTEM, blaSHV, blaCTXM-1, blaCTXM-2 and blaCTXM-15 positive, respectively. Interestingly, we observed one E. coli (HG4) isolate with both blaNDM-1 and mcr-1 gene. Further analysis showed HG4 isolate has lesser survivability on the cotton swab, long lag phase and less biofilm production compared to colistin-sensitive isolates. Detection of E. coli with blaNDM-1 and mcr-1 in this geographical region is an alarming signal for tourists, community, health workers and policymakers. Hence, it is utmost important to take appropriate measures to control the dissemination of antibiotic resistance gene in such pristine locations.

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