51
In US, the Department of Agriculture National Animal Health Laboratory
Network (NAHLN) and the FDA Veterinary Laboratory Investigation and Response
Network (Vet-LIRN) are initiating on gathering information on resistance and
whole genome sequencing data of pathogens from different sources. The US
Environmental Protection Agency conducts water surveys repeatedly for detection
of resistance genes. Initial stages comprises expansion of national public health
surveillance programs based on DNA sequencing information and licensing new
associations from resistome analyses of the data (Hendriksen et al. 2019a).
2.10.2 Metagenomics
Only a very few pathogens are targeted by current surveillance systems, primarily
based on passive reporting of phenotypic results as in the DANMAP (Danish monitoring system), resulting in a narrow range of pathogen, which does not cover all
relevant resistant genes. Majority of the antimicrobial resistance genes could be
present in the flora of commensal bacteria of animals, healthy humans or the environment. Metagenomics techniques benefit the ability to quantify thousands of
resistance conferring genes in a single sample using short read NGS (Next
Generation Sequencing) data with no prior selection of target genes. Metagenomics
can sequence all DNA of the sample including host DNA and food, which may lead
to low sensitivity. qPCR (Quantitative Polymerase Chain Reaction) procedures and
large scale capture PCR methodologies have already been developed, which provides higher sensitivity (Aarestrup et al. 1998; Lanza et al. 2018).
It was recently reported that metagenomics has got more merits over conventional methods for surveillance of antimicrobial resistance in pig herds (Munk et al.
2017), which is quite beneficial for comparing antimicrobial resistance across livestock (Munk et al. 2018), as well as epidemiological data related investigations (Van
Gompel et al. 2019). The usage for global surveillance of antimicrobial resistance
gene dissemination by international flights (Nordahl Petersen et al. 2015) and investigating the urban sewage to determine the domestic and global resistome has also
been proven (Hendriksen et al. 2019b; Pehrsson et al. 2016).
2.11 Present and Future of AMR Surveillance
There is big international consensus that surveillance of the levels of antimicrobial
resistance occurring in various systems emphasizes strategies to address the issue.
The main reasons for resistance surveillance are to determine (i) the magnitude of
the problem, (ii) whether resistance is escalating, (iii) whether a specific type of
resistance is spreading (Barlam et al. 2016) and whether previously reported
unknown types of resistance are rising, (v) whether a specific type of resistance is
associated with any outbreak (Simjee et al. 2018). The inference of acquiring and
2 Global Surveillance Programs on Antimicrobial Resistance
In US, the Department of Agriculture National Animal Health Laboratory
Network (NAHLN) and the FDA Veterinary Laboratory Investigation and Response
Network (Vet-LIRN) are initiating on gathering information on resistance and
whole genome sequencing data of pathogens from different sources. The US
Environmental Protection Agency conducts water surveys repeatedly for detection
of resistance genes. Initial stages comprises expansion of national public health
surveillance programs based on DNA sequencing information and licensing new
associations from resistome analyses of the data (Hendriksen et al. 2019a).
2.10.2 Metagenomics
Only a very few pathogens are targeted by current surveillance systems, primarily
based on passive reporting of phenotypic results as in the DANMAP (Danish monitoring system), resulting in a narrow range of pathogen, which does not cover all
relevant resistant genes. Majority of the antimicrobial resistance genes could be
present in the flora of commensal bacteria of animals, healthy humans or the environment. Metagenomics techniques benefit the ability to quantify thousands of
resistance conferring genes in a single sample using short read NGS (Next
Generation Sequencing) data with no prior selection of target genes. Metagenomics
can sequence all DNA of the sample including host DNA and food, which may lead
to low sensitivity. qPCR (Quantitative Polymerase Chain Reaction) procedures and
large scale capture PCR methodologies have already been developed, which provides higher sensitivity (Aarestrup et al. 1998; Lanza et al. 2018).
It was recently reported that metagenomics has got more merits over conventional methods for surveillance of antimicrobial resistance in pig herds (Munk et al.
2017), which is quite beneficial for comparing antimicrobial resistance across livestock (Munk et al. 2018), as well as epidemiological data related investigations (Van
Gompel et al. 2019). The usage for global surveillance of antimicrobial resistance
gene dissemination by international flights (Nordahl Petersen et al. 2015) and investigating the urban sewage to determine the domestic and global resistome has also
been proven (Hendriksen et al. 2019b; Pehrsson et al. 2016).
2.11 Present and Future of AMR Surveillance
There is big international consensus that surveillance of the levels of antimicrobial
resistance occurring in various systems emphasizes strategies to address the issue.
The main reasons for resistance surveillance are to determine (i) the magnitude of
the problem, (ii) whether resistance is escalating, (iii) whether a specific type of
resistance is spreading (Barlam et al. 2016) and whether previously reported
unknown types of resistance are rising, (v) whether a specific type of resistance is
associated with any outbreak (Simjee et al. 2018). The inference of acquiring and
2 Global Surveillance Programs on Antimicrobial Resistance