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Article ; Online: Skin microbiota interact with microbes on office surfaces

Hu Li / Shu-Yi-Dan Zhou / Roy Neilson / Xin-Li An / Jian-Qiang Su

Environment International, Vol 168, Iss , Pp 107493- (2022)

2022

Abstract: The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized ... ...

Abstract	The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized the bacterial and fungal communities from various sources typical of a working office environment including dust, fingers, and computer keyboards and mice. The composition of the dust bacterial community was significantly different from the other tested surfaces (P < 0.05), whereas the dust fungal community was only significantly different from fingers (P < 0.05). Bacterial and fungal communities were both shaped by deterministic processes, and bacterial communities had a higher migration rate. Results of a network analysis showed that the microbial community interactions of keyboards and mice were mainly competitive. Fast expectation–maximization microbial source tracking (FEAST) identified the sources of > 70 % of the keyboard and mouse microbial communities. Biomarkers for each sample types were identified by LDA Effect Size (LEfSE) analysis, some of which were soil-derived and potential anthropogenic pathogens, indicating the potential for exchange of microbes among outdoor, human and indoor surfaces. The current study shows that the source of microorganisms at the office interface is highly traceable and that their migration is linked to human activity. The migration of potentially pathogenic microbes were identified, emphasising the importance of personal hygiene.
Keywords	Skin microbiome ; Indoor environment ; Source tracking ; Indoor microbiome ; Pathogen ; Environmental sciences ; GE1-350
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables

Cai-Xia Zhao / Xiao-Xuan Su / Mei-Rong Xu / Xin-Li An / Jian-Qiang Su

Ecotoxicology and Environmental Safety, Vol 247, Iss , Pp 114282- (2022)

2022

Abstract: Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables ... ...

Abstract	Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1–2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.
Keywords	Endophytes ; Antibiotic resistance ; Horizontal gene transfer ; Integrons ; Human health ; Environmental pollution ; TD172-193.5 ; Environmental sciences ; GE1-350
Subject code	572
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: VFG-Chip

Shu-Ting Xie / Long-Jun Ding / Fu-Yi Huang / Yi Zhao / Xin-Li An / Jian-Qiang Su / Guo-Xin Sun / Ya-Qiong Song / Yong-Guan Zhu

Environment International, Vol 172, Iss , Pp 107761- (2023)

A high-throughput qPCR microarray for profiling virulence factor genes from the environment

2023

Abstract: As zoonotic pathogens are threatening public health globally, the virulence factor genes (VFGs) they carry underlie latent risk in the environment. However, profiling VFGs in the environment is still in its infancy due to lack of efficient and reliable ... ...

Abstract	As zoonotic pathogens are threatening public health globally, the virulence factor genes (VFGs) they carry underlie latent risk in the environment. However, profiling VFGs in the environment is still in its infancy due to lack of efficient and reliable quantification tools. Here, we developed a novel high-throughput qPCR (HT-qPCR) chip, termed as VFG-Chip, to comprehensively quantify the abundances of targeted VFGs in the environment. A total of 96 VFGs from four bacterial pathogens including Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli, and Salmonella enterica were targeted by 120 primer pairs, which were involved in encoding five types of virulence factors (VFs) like toxin, adherence, secretion system, immune evasion/invasion, and iron uptake. The specificity of VFG-Chip was both verified computationally and experimentally, with high identity of amplicon sequencing and melting curves analysis proving its robust capability. The VFG-Chip also displayed high sensitivity (by plasmid serial dilution test) and amplification efficiency averaging 97.7%. We successfully applied the VFG-Chip to profile the distribution of VFGs along a wastewater treatment system with 69 VFGs detected in total. Overall, the VFG-Chip provides a robust tool for comprehensively quantifying VFGs in the environment, and thus provides novel information in assessing the health risks of zoonotic pathogens in the environment.
Keywords	Virulence factor genes ; High-throughput qPCR ; VFG-Chip ; Zoonotic pathogenic bacteria ; Wastewater treatment system ; Environmental sciences ; GE1-350
Subject code	600
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Corrigendum to “Co-effect of cadmium and iron oxide nanoparticles on plasmid-mediated conjugative transfer of antibiotic resistance genes” [Environ. Int. 152 (2021) 106453]

Qiang Pu / Xiao-Ting Fan / An-Qi Sun / Ting Pan / Hu Li / Simon Bo Lassen / XinLi An / Jian-Qiang Su

Environment International, Vol 172, Iss , Pp 107790- (2023)

2023

Keywords	Environmental sciences ; GE1-350
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Local environment, surface characteristics and stochastic processes shape the dynamics of urban dustbin surface microbiome

Xin-Li An / Mei-Rong Xu / Xiao-Fang Pan / Guan-Jing Cai / Cai-Xia Zhao / Hu Li / Zhi-Long Ye / Yong-Guan Zhu / Jian-Qiang Su

Environment International, Vol 177, Iss , Pp 108004- (2023)

2023

Abstract: Dustbins function as critical infrastructures for urban sanitation, creating a distinct breeding ground for microbial assemblages. However, there is no information regarding the dynamics of microbial communities and the underlying mechanism for community ...

Abstract	Dustbins function as critical infrastructures for urban sanitation, creating a distinct breeding ground for microbial assemblages. However, there is no information regarding the dynamics of microbial communities and the underlying mechanism for community assembly on dustbin surfaces. Here, surface samples were collected from three sampling zones (business building, commercial street and residential community) with different types (kitchen waste, harmful waste, recyclables, and others) and materials (metallic and plastic); and distribution pattern and assembly of microbial communities were investigated by high-throughput sequencing. Bacterial and fungal communities showed the distinct community variations across sampling zones and waste sorting. Core community and biomarker species were significantly correlated with the spatial distribution of overall community. The detection of pathogens highlighted the potential risk of surface microbiome. Human skin, human feces and soil biomes were the potential source environments of the surface microbiomes. Neutral model prediction suggested that microbial community assembly was significantly driven by stochastic processes. Co-association patterns varied with sampling zones and waste types, and neutral amplicon sequence variants (ASVs) that fall within the 95 % confidence intervals of neutral model were largely involved in the stability of microbial networks. These findings improve our understanding of the distribution pattern and the underlying assembly of microbial community on the dustbin surface, thus enabling prospective prediction and assessment of urban microbiomes and their impacts on human health.
Keywords	Microbial assembly ; Dustbin microbiome ; Pathogens ; Network analysis ; Biomarker ; Environmental sciences ; GE1-350
Subject code	710
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Urban greenness and plant species are key factors in shaping air microbiomes and reducing airborne pathogens

Hu Li / Zhi-Feng Wu / Xiao-Ru Yang / Xin-Li An / Yin Ren / Jian-Qiang Su

Environment International, Vol 153, Iss , Pp 106539- (2021)

2021

Abstract: Urban green space has been implicated in shaping airborne microbes, but there is an only rudimentary understanding of the key factors of urban green space affecting the composition and structures of airborne microbes. Here, we selected 40 urban sites ... ...

Abstract	Urban green space has been implicated in shaping airborne microbes, but there is an only rudimentary understanding of the key factors of urban green space affecting the composition and structures of airborne microbes. Here, we selected 40 urban sites based on stratified random sampling design and investigated the effects of multiple factors including landscapes, plant, soil, and anthropogenic factors on airborne microbial communities, especially bacterial and fungal pathogens. Bacterial and fungal communities in the control area with lower greenness were significantly (P < 0.05) different from those in other areas with a gradient of green space. The relative abundance of bacterial and fungal pathogens significantly (P < 0.05) decreased with increasing greenness. Other than soil thickness, soil type, slope position, and population density, plant species considerably contributed to the shift in the composition and abundance of potential bacterial and fungal pathogens. A significantly (P < 0.05) reduced abundance of bacterial and fungal pathogens was observed in areas with >30% masson pine. Together, these results provide insights into the importance of green space for providing health benefits for city dwellers by reducing pathogens in air, as well as providing support for the inclusion of plant species in the management of urban green space to reduce exposure risk of airborne pathogens.
Keywords	Urban green space ; Bacteria ; Fungi ; Masson pine ; Human activity ; Environmental sciences ; GE1-350
Subject code	333
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Co-effect of cadmium and iron oxide nanoparticles on plasmid-mediated conjugative transfer of antibiotic resistance genes

Qiang Pu / Xiao-Ting Fan / An-Qi Sun / Ting Pan / Hu Li / Simon Bo Lassen / Xin-Li An / Jian-Qiang Su

Environment International, Vol 152, Iss , Pp 106453- (2021)

2021

Abstract: Conjunctive transfer of antibiotic resistance genes (ARGs) among bacteria driven by plasmids facilitated the evolution and spread of antibiotic resistance. Heavy metal exposure accelerated the plasmid-mediated conjunctive transfer of ARGs. Nanomaterials ... ...

Abstract	Conjunctive transfer of antibiotic resistance genes (ARGs) among bacteria driven by plasmids facilitated the evolution and spread of antibiotic resistance. Heavy metal exposure accelerated the plasmid-mediated conjunctive transfer of ARGs. Nanomaterials are well-known adsorbents for heavy metals removal, with the capability of combatting resistant bacteria/facilitating conjunctive transfer of ARGs. However, co-effect of heavy metals and nanomaterials on plasmid-mediated conjunctive transfer of ARGs was still unknown. In this study, we investigated the effect of the simultaneous exposure of Cd2+ and nano Fe2O3 on conjugative transfer of plasmid RP4 from Pseudomonas putida KT2442 to water microbial community. The permeability of bacterial cell membranes, antioxidant enzyme activities and conjugation gene expression were also investigated. The results suggested that the combination of Cd2+ and high concentration nano Fe2O3 (10 mg/L and 100 mg/L) significantly increased conjugative transfer frequencies of RP4 plasmid (p < 0.05). The most transconjugants were detected in the treatment of co-exposure to Cd2+ and nano Fe2O3, the majority of which were identified to be human pathogens. The mechanisms of the exacerbated conjugative transfer of ARGs were involved in the enhancement of cell membrane permeability, antioxidant enzyme activities, and mRNA expression levels of the conjugation genes by the co-effect of Cd2+ and nano Fe2O3. This study confirmed that the simultaneous exposure to Cd2+and nano Fe2O3 exerted a synergetic co-effect on plasmid-mediated conjunctive transfer of ARGs, emphasizing that the co-effect of nanomaterials and heavy metals should be prudently evaluated when combating antibiotic resistance.
Keywords	Nanomaterials ; Conjugative transfer ; Horizontal gene transfer ; Microbial community ; Plasmid ; Environmental sciences ; GE1-350
Subject code	660
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Does nano silver promote the selection of antibiotic resistance genes in soil and plant?

Qing-Lin Chen / Dong Zhu / Xin-Li An / Jing Ding / Yong-Guan Zhu / Li Cui

Environment International, Vol 128, Iss , Pp 399-

2019 Volume 406

Abstract: Growing evidences have demonstrated that heavy metal contamination can promote the proliferation of antibiotic resistance genes (ARGs) via co-selection. However, effects of nano-metal-materials on the occurrence and level of ARGs in the soil and plant, ... ...

Abstract	Growing evidences have demonstrated that heavy metal contamination can promote the proliferation of antibiotic resistance genes (ARGs) via co-selection. However, effects of nano-metal-materials on the occurrence and level of ARGs in the soil and plant, have not been fully explored. To gain insights into this impact, we conducted a pot experiment by adding nano‑silver particles (AgNPs) as a stimuli and Ag ion (AgNO3) and tetracycline as a comparison. By using high throughput quantitative PCR, our results indicated that application of AgNPs (~20 nm and ~50 nm) at a concentration of 100 ppm resulted in no significant changes in the abundance of ARGs in either soil or phyllosphere (P > 0.05). Nevertheless, the overall pattern of resistome, especially in soil, was shifted following AgNPs application, with a significance increase in the relative abundance of efflux pumps genes, which is an important mechanism for co-selection of ARGs by heavy metals. By comparison, Ag ion at an equivalent Ag mass of AgNPs markedly increased ARGs abundance and shifted ARGs profile in soil, indicating that free Ag ion had a stronger impact on ARGs than AgNPs. These findings provide new insights in assessing the risks of manufactured nanomaterials accumulated in the environment. Keywords: Nano-materials, Silver nanoparticles, Antibiotic resistance, Co-selection, Plant microbiome
Keywords	Environmental sciences ; GE1-350
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Effect of biochar amendment on the alleviation of antibiotic resistance in soil and phyllosphere of Brassica chinensis L

Chen, Qing-Lin / Xiao-Ting Fan / Dong Zhu / Xin-Li An / Jian-Qiang Su / Li Cui

Soil biology & biochemistry. 2018 Apr., v. 119

2018

Abstract: The increasing prevalence of antibiotic resistance is a global threat to public health. Antibiotic resistance genes (ARGs) in soil have been demonstrated to be able to enter food chain. Strategies to mitigate the spread of antibiotic resistance from soil ...

Abstract	The increasing prevalence of antibiotic resistance is a global threat to public health. Antibiotic resistance genes (ARGs) in soil have been demonstrated to be able to enter food chain. Strategies to mitigate the spread of antibiotic resistance from soil to crops are of great importance for food safety and human health. Soil amendment with biochar is a widely used approach to improve soil fertility. However, the impact of biochar on mitigating antibiotic resistance of soil and organically produced vegetables that are eaten raw is largely unknown. To gain insights into this impact, pot experiments planting Brassica chinensis L. in soil amended with biochar were conducted and antibiotic resistance genes (ARGs) were characterized by HT-qPCR targeting almost all major classes of ARGs and 10 mobile genetic elements (MGEs) marker genes. A total of 131 ARGs and 9 MGEs in soil and phyllosphere samples were identified. After biochar amendment, the abundance of ARGs was significantly decreased in non-planted soil. By comparison, no significant decrease of ARGs was found in rhizosphere and phyllosphere, indicating that vegetable planting affected antibiotic resistome in biochar-amended soil. To understand this effect, bacterial phylogeny structures within soil and phyllosphere were analyzed and found to correlate with their respective resistome, indicating that planting can influence the effect of biochar on soil antibiotic resistome by altering microbial community compositions. Structure equation models further revealed that a higher bacterial diversity corresponded to a decreased ARGs content. These results suggested that biochar amendment alone was not sufficient enough to alleviate ARGs level in planted soil and crops, instead, maintaining or increasing soil microbial diversity is potentially more useful in mitigating ARG spread and accumulation.
Keywords	Brassica rapa subsp. chinensis ; antibiotic resistance ; antibiotic resistance genes ; antibiotics ; biochar ; crops ; equations ; food chain ; food safety ; genetic markers ; interspersed repetitive sequences ; microbial communities ; models ; phyllosphere ; phylogeny ; planting ; public health ; rhizosphere ; soil ; soil amendments ; soil fertility ; vegetables
Language	English
Dates of publication	2018-04
Size	p. 74-82.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2018.01.015
Database	NAL-Catalogue (AGRICOLA)

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Article: Do manure-borne or indigenous soil microorganisms influence the spread of antibiotic resistance genes in manured soil?

Chen, Qing-Lin / Hu Li / Jian-Qiang Su / Li Cui / Xin-Li An / Yong-Guan Zhu

Soil biology & biochemistry. 2017 Nov., v. 114

2017

Abstract: Manure application is a common practice that not only adds nutrients and organic matter to arable soils for crop growth, but also introduces antibiotic resistance genes (ARGs), posing a potential risk to human health. To investigate the mechanisms ... ...

Abstract	Manure application is a common practice that not only adds nutrients and organic matter to arable soils for crop growth, but also introduces antibiotic resistance genes (ARGs), posing a potential risk to human health. To investigate the mechanisms underlying the spread of ARGs in manured soil, especially the impact of manure-borne and indigenous soil microorganisms, a microcosm experiment with four specially designed treatments over a period of two months was conducted, including soil, soil with irradiated pig manure, irradiated soil with pig manure, and soil with pig manure. A total of 240 unique ARGs were detected via a high-throughput quantitative PCR (HT-qPCR) targeting almost all major classes of ARGs. Manure application significantly increased the diversity and abundance of ARGs in soil (P < 0.01), and also markedly shifted the bacterial composition that was significantly correlated with ARGs profiles. Manure-borne microorganisms contributed largely to the elevation of ARGs due to both the addition of manure-borne antibiotic resistant bacteria (ARB) in soil and potential horizontal gene transfer (HGT) via mobile genetic elements (MGEs) from manure-borne ARB to indigenous soil microorganisms. In contrast, indigenous soil microorganisms were demonstrated to prevent the dissemination of ARGs from manure to soil. The reason could be due to that indigenous soil microorganisms prevented the invasion and establishment of manure-borne ARB in soil. The abundance of ARG in manured soil decreased over time, but was still higher than that in control soil, indicating the persistence of ARGs in manured soil. These findings may shed light on the mechanisms underlying the spread and fate of ARGs in manured soil and also clues for ARGs mitigation.
Keywords	antibiotic resistance ; arable soils ; bacteria ; genetic resistance ; horizontal gene transfer ; human health ; interspersed repetitive sequences ; irradiation ; manure spreading ; nutrients ; organic matter ; pig manure ; quantitative polymerase chain reaction ; risk ; soil microorganisms
Language	English
Dates of publication	2017-11
Size	p. 229-237.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2017.07.022
Database	NAL-Catalogue (AGRICOLA)

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