Metagenomic characterization of bacterial community and antibiotic resistance genes found in the mass transit system in Seoul, South Korea

Guevarra, Robin B.; Hwang, Juchan; Lee, Hyunjung; Kim, Hyung Jun; Lee, Yun-Mi; Danko, David; Ryon, K; Young, Benjamin Grady; Mason, Christopher E.; Jang, Soojin

doi:10.1016/j.ecoenv.2022.114176

Cited by 6 publications

(5 citation statements)

References 45 publications

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“…The abundance of bacterial genus commonly present in indoor surfaces of built environments or transportation facilities with human presence has been documented. 23 , 24 , 37 The top taxa associated with indoor environments were recognisable as microbes associated with humans ( e.g. , Corynebacterium , Streptococcus , Enterobacteriaceae , Staphylococcus , Propionibacterium , Lactococcus ) 23 and are also comparable with our results, corroborating the findings of our study for pooled samples of the middle of the expedition, when passengers were confined.…”

Section: Discussionsupporting

confidence: 90%

“…The main results demonstrated that the most abundant bacterial phyla corresponding to the total fraction of microbiome were Proteobacteria , followed by Firmicutes , Actinobacteria , and Bacteroidetes and according to other studies conducted to evaluate the microbiome in indoor surfaces of built environments or transportation facilities. 24 , 36 , 37 However, it was possible to observe variations in the relative abundance of microbial families and genera during different expedition stages. At the beginning and end of the expedition, with a limited number of passengers on the ship, it was possible to observe the prevalence of bacterial genera commonly present in the environment, such as Pseudomonas spp.…”

Section: Discussionmentioning

confidence: 99%

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Microbiome and virome on indoor surfaces of an Antarctic research ship

Prado,

Magalhães,

Moreira

et al. 2023

Mem. Inst. Oswaldo Cruz

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BACKGROUND Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. OBJECTIVES AND METHODS We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship’s interior to track the microbial diversity. FINDINGS Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes , Actinobacteria , and Bacteroidetes . Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae , Chrysoviridae , Genomoviridae , Herelleviridae , Myoviridae , Partitiviridae , Podoviridae , Potyviridae , Siphoviridae , and Virgaviridae . MAIN CONCLUSIONS This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Microbiome and virome on indoor surfaces of an Antarctic research ship

Prado,

Magalhães,

Moreira

et al. 2023

Mem. Inst. Oswaldo Cruz

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“…For example, these studies describe how the diversity, composition, and functional potential of communities change over time and how occupants and building operations influence these interactions. Many built environments have been explored in this way, including workplaces [ 43-45 ], homes [ 46-49 ], and public transportation [ 50 , 51 ]. Of critical importance to understanding the interaction between surface-associated microbial ecology and pathogenic activity, hospital environments have been well characterized [ 25 , 26 , 52 ], providing some of the most compelling results to justify further intervention studies.…”

Section: Techniques For Investigating the Microbiome Of The Built Env...mentioning

confidence: 99%

Biocontrol in built environments to reduce pathogen exposure and infection risk

Gottel,

Hill,

Neal

et al. 2024

The ISME Journal

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The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonise and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.

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“…Such locations are considered hubs for microbes due to high human traffic, enclosed spaces, shared surfaces, air circulation, interconnected routes, and diverse passenger demographics. 1 The constant flow of people and close interactions in transit vehicles and stations create favorable conditions for the transmission and exchange of microorganisms. These environments can serve as reservoirs for various microbes, posing potential public health implications.…”

Section: Introductionmentioning

confidence: 99%

“…Urban mass transit systems, crucial conduits in modern cities, provide a habitat for a diverse range of microorganisms, forming complex urban microbiomes that intermingle with the lives of millions. Such locations are considered hubs for microbes due to high human traffic, enclosed spaces, shared surfaces, air circulation, interconnected routes, and diverse passenger demographics 1 . The constant flow of people and close interactions in transit vehicles and stations create favorable conditions for the transmission and exchange of microorganisms.…”

Section: Introductionmentioning

confidence: 99%

Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors

Sarkar,

Anyaso‐Samuel,

Qiu

et al. 2024

Statistics in Medicine

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Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or “phages”–viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage‐resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.

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Metagenomic characterization of bacterial community and antibiotic resistance genes found in the mass transit system in Seoul, South Korea

Cited by 6 publications

References 45 publications

Microbiome and virome on indoor surfaces of an Antarctic research ship

Microbiome and virome on indoor surfaces of an Antarctic research ship

Biocontrol in built environments to reduce pathogen exposure and infection risk

Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors

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