Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

Abstract Background Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on “resistomes” (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.

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Soil types influence the fate of antibiotic-resistant bacteria and antibiotic resistance genes following the land application of sludge composts

Environment International ◽

10.1016/j.envint.2018.05.029 ◽

2018 ◽

Vol 118 ◽

pp. 34-43 ◽

Cited By ~ 41

Author(s):

Junya Zhang ◽

Qianwen Sui ◽

Juan Tong ◽

Hui Zhong ◽

Yawei Wang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Land Application ◽

Soil Types ◽

Resistant Bacteria ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant

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Diversity, abundances and distribution of antibiotic resistance genes and virulence factors in the South China Sea revealed by metagenomic sequencing

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.152803 ◽

2022 ◽

pp. 152803

Author(s):

Haochang Su ◽

Xiaojuan Hu ◽

Wujie Xu ◽

Yu Xu ◽

Guoliang Wen ◽

...

Keyword(s):

Antibiotic Resistance ◽

South China Sea ◽

Virulence Factors ◽

South China ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

The South China Sea ◽

Metagenomic Sequencing ◽

The South ◽

China Sea

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Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa172 ◽

2020 ◽

Vol 96 (10) ◽

Author(s):

Bo Li ◽

Zeng Chen ◽

Fan Zhang ◽

Yongqin Liu ◽

Tao Yan

Keyword(s):

Antibiotic Resistance ◽

Microbial Diversity ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Soil Samples ◽

16S Rrna Genes ◽

Rrna Genes ◽

Metagenomic Sequencing ◽

Clinical Issue ◽

Abundance And Diversity

ABSTRACT Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05–0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.

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Fate and Transport of Antibiotic Residues and Antibiotic Resistance Genes following Land Application of Manure Waste

Journal of Environmental Quality ◽

10.2134/jeq2008.0128 ◽

2009 ◽

Vol 38 (3) ◽

pp. 1086-1108 ◽

Cited By ~ 398

Author(s):

Joanne C. Chee-Sanford ◽

Roderick I. Mackie ◽

Satoshi Koike ◽

Ivan G. Krapac ◽

Yu-Feng Lin ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Fate And Transport ◽

Land Application ◽

Antibiotic Residues

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Antibiotic Resistance Genes in Lemur Gut and Soil Microbiota Along a Gradient of Anthropogenic Disturbance

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.704070 ◽

2021 ◽

Vol 9 ◽

Author(s):

Sally L. Bornbusch ◽

Christine M. Drea

Keyword(s):

Antibiotic Resistance ◽

Antibiotic Treatment ◽

Resistance Genes ◽

Anthropogenic Disturbance ◽

Antibiotic Resistance Genes ◽

Single Species ◽

The United States ◽

Metagenomic Sequencing ◽

Natural Habitats ◽

Human Contact

The overuse of man-made antibiotics has facilitated the global propagation of antibiotic resistance genes in animals, across natural and anthropogenically disturbed environments. Although antibiotic treatment is the most well-studied route by which resistance genes can develop and spread within host-associated microbiota, resistomes also can be acquired or enriched via more indirect routes, such as via transmission between hosts or via contact with antibiotic-contaminated matter within the environment. Relatively little is known about the impacts of anthropogenic disturbance on reservoirs of resistance genes in wildlife and their environments. We therefore tested for (a) antibiotic resistance genes in primate hosts experiencing different severities and types of anthropogenic disturbance (i.e., non-wildlife animal presence, human presence, direct human contact, and antibiotic treatment), and (b) covariation between host-associated and environmental resistomes. We used shotgun metagenomic sequencing of ring-tailed lemur (Lemur catta) gut resistomes and associated soil resistomes sampled from up to 10 sites: seven in the wilderness of Madagascar and three in captivity in Madagascar or the United States. We found that, compared to wild lemurs, captive lemurs harbored greater abundances of resistance genes, but not necessarily more diverse resistomes. Abundances of resistance genes were positively correlated with our assessments of anthropogenic disturbance, a pattern that was robust across all ten lemur populations. The composition of lemur resistomes was site-specific and the types of resistance genes reflected antibiotic usage in the country of origin, such as vancomycin use in Madagascar. We found support for multiple routes of ARG enrichment (e.g., via human contact, antibiotic treatment, and environmental acquisition) that differed across lemur populations, but could result in similar degrees of enrichment. Soil resistomes varied across natural habitats in Madagascar and, at sites with greater anthropogenic disturbance, lemurs and soil resistomes covaried. As one of the broadest, single-species investigations of wildlife resistomes to date, we show that the transmission and enrichment of antibiotic resistance genes varies across environments, thereby adding to the mounting evidence that the resistance crisis extends outside of traditional clinical settings.

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Antibiotic resistance potential of the healthy preterm infant gut microbiome

PeerJ ◽

10.7717/peerj.2928 ◽

2017 ◽

Vol 5 ◽

pp. e2928 ◽

Cited By ~ 23

Author(s):

Graham Rose ◽

Alexander G. Shaw ◽

Kathleen Sim ◽

David J. Wooldridge ◽

Ming-Shi Li ◽

...

Keyword(s):

Antibiotic Resistance ◽

Preterm Infant ◽

Resistance Genes ◽

Gut Microbiome ◽

Antibiotic Resistance Genes ◽

Taxonomic Diversity ◽

Metagenomic Sequencing ◽

Important Species ◽

Antimicrobial Resistance Genes ◽

Infant Gut Microbiome

Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.

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