Short communicationPreliminary analysis showed country-specific gut resistome based on 1267 feces samples
Introduction
The human gut is home to trillions of microbes (Qin et al., 2010, Li et al., 2014). Antibiotic abuse may lead to high abundance of various ARGs in human gut (Forslund et al., 2013), which could be transferred to microbial counterparts through MGEs (Davies & Davies, 2010) and delivered to new-born babies (Zhang et al., 2011). This will reduce the recovery rate of many infectious diseases and impact infants' health negatively, leading to a higher burden in public health. Since antibiotic are widely used in medicine (Goossens et al., 2005a) and food animal production (Davies & Davies, 2010), it will be significant to understand discrepancy of gut resistome at population-scale.
Kristoffer Forslund et al. demonstrated country-specific gut resistome based on 252 fecal samples from several countries (Forslund et al., 2013). In this report, ARGs were compared among these countries. And determinants for antibiotic resistance were also analyzed by various factors, including carriage by time in use, antibiotic policies of countries, possible origins and antibiotic use of corresponding hosts.
Previous findings did not cover enough samples, representing the main continents. Meanwhile, ARGs may be enriched in highly different microbes, suggestive of distinct microbial composition induced by diet, lifestyle and antibiotic regulation. Based on this, it will be important to collect data of more feces samples in different continents, and perform deep analysis on distribution pattern of ARGs in these continents to identify diversified ARG acquirement models. Based on this, we intended to integrate the newest reference catalogue of human gut microbiome (Li et al., 2014) and tried to disclose distribution of various antibiotic resistance determinants globally. Then, the evolution of these determinants could be traced and linked to veterinary and human medicine consumption, suggesting additional guidance to control antibiotic abuse.
Section snippets
Data collection and processing
The non-redundant gene catalog and gene profiles of 1267 human stool samples were collected from ICG website (http://meta.genomics.cn) (Li et al., 2014), including 139 American, 368 Chinese, 401 Danish and 359 Spanish samples from HMP, NCBI database, MetaHIT project, EBI and GEO database. All of the gene profiles were based on above public metagenomics sequencing, which were processed by the MOCAT pipeline (Kultima et al., 2012).
ARG annotation
To identify accumulation of ARGs in GM of different countries,
ARGs are spread in human guts
Totally 112 ARGs were distributed widely in guts of more than 90% humans living in different countries (Table 1). Antibiotic glycopeptides harbored the most diverse ARGs (41 types) in comparison to others, all of which was vancomycin resistance genes (Table 1). MLS resistance genes were the second most diverse, which contained 24 types of ARGs. Tetracyclines and beta-lactamases related ARGs (15 and 14 types, respectively) were also widely distributed in all four countries (Table 1). These
Discussion
Antibiotic abuse leads to highly abundant ARGs in gastrointestinal microbiota (Wright, 2007), which is a giant challenge for the health and food animal industry globally (WHO, 2014). However, distinct regulations on food and drug could lead to discrepant distribution of ARGs among countries. Therefore, analysis of ARGs in GM from different countries will promote interpretation about how these regulations or lifestyles impact human health, due to the important role of GM (Qin et al., 2010, Li et
Conclusions
This study reviewed the accumulation of gut ARGs for the most integrated gene catalogue of human gut microbiome. It suggests that Chinese holds most abundant gut ARGs, by comparison with European and American. Meanwhile, permission to antibiotic use in food animals and antibiotic delivery time is proportional to ARG enrichment globally. This will provide an important reference to understand antibiotic abuse and corresponding impact on antibiotic resistance.
Conflict of interest
All authors declare no competing interests.
Acknowledgements
This research was supported by the National High Technology Research and Development Program 863 (No: 2014AA022210-04).
References (39)
DANMAP: monitoring antimicrobial resistance in Denmark
Int. J. Antimicrob. Agents
(2000)- et al.
Outpatient antibiotic use in Europe and association with resistance: a cross-national database study
Lancet
(2005) - et al.
Outpatient antibiotic use in Europe and association with resistance: a cross-national database study
Lancet
(2005) Antibiotic in animal feed and their role in resistance development
Curr. Opin. Microbiol.
(2003)- et al.
Antimicrobial susceptibility patterns of thermophilic Campylobacter spp. from humans, pigs, cattle, and broilers in Denmark
Antimicrob. Agents Chemother.
(1997) A European study on the relationship between antimicrobial use and antimicrobial resistance
Emerg. Infect. Dis.
(2002)- et al.
The European ban on growth-promoting antibiotic and emerging consequences for human and animal health
J. Antimicrob. Chemother.
(2003) A public health action plan to combat antimicrobial resistance centers for disease control and prevention
European surveillance of antimicrobial consumption (ESAC): outpatient antibiotic use in Europe (1997–2009)
J. Antimicrob. Chemother.
(2011)- et al.
Restricting antimicrobial use in food animals: lessons from Europe
Microbe
(2011)
Long-term effects of an antimicrobial stewardship programme at a tertiary-care teaching hospital
Int. J. Antimicrob. Agents
Origins and evolution of antibiotic resistance
Microbiol. Mol. Biol. Rev.
Infectious diseases society of America and the society for healthcare epidemiology of America guidelines for developing an institutional program to enhance antimicrobial stewardship
Clin. Infect. Dis.
Regulation of antibiotic used in animal feeds
Guidance for industry #209
Guidance for industry #213
Country specific antibiotic use practices impact the human gut resistome
Genome Res.
ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
Antimicrob. Agents Chemother.
Pneumococcal resistance to antibiotic
Clin. Microbiol. Rev.
Cited by (0)
- 1
Authors contribute equally to this research.