| Access to testing | Difficulties in transporting patients and/or their specimens to laboratories Lack of a supply chain for diagnostic resources needed for conventional testing Absence of phlebotomy Pathogen is too fastidious to culture in a minimally equipped bacteriology lab (eg, Mycobacterium, Neisseria, Campylobacter and Helicobacter) Existing surveillance systems not set up to accept point-of-care results that may be relevant to resistance
| Alternative or autonomous transportation systems Point of care/near patient technologies that is, GeneXpert, BioFire, loop-mediated isothermal amplification-based technologies, nanopore-based sequencing and point-of-care single nucleotide polymorphisms detection systems in development
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| Invasive sampling and associated biohazards | Absence of skilled healthcare workers that can retrieve specimens from normally sterile sites (Blood and CSF culture) High body fluid volumes required for some tests (eg, blood culture) Poor access to adequate biosafety resources and safe waste disposal
| Automated devices that can safely and aseptically retrieve blood, and possibly other specimens Tests that allow interrogation of smaller or non-invasive samples Point-of-care technologies
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| Data-entry and handling | Paper records that cannot be queried or viewed from more than one location | |
| Extensive, non-integrated quality assurance requirements | | Integrated quality assurance such as read quality analyses for WGS |
| In-lab processing time | Long incubation time makes direct benefits for testing patients requiring urgent care, or who cannot return to the laboratory for test results doubtful | Rapid nucleic acid-based testing Systems that accelerate pathogen growth or allow for its early detection Provision of intelligent data visualisation to guide empiric Rx/decision support/risk management
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| Subtyping | Subtyping is the most specialised part of testing needed for surveillance and therefore the least likely to be performed accurately. It is also typically the most expensive Many subtyping techniques are difficult or irreproducible and may not give the same results each time even when properly performed Subtyping methods differ from one species to another, so laboratories can often not house expertise and resources for typing a broad range of organisms Subtyping is essential for delineating some pathogens and for identifying outbreaks
| Rapid WGS with microfluidic DNA preparation, which can provide fine subtyping information along with identification and susceptibility information at no extra cost. To reduce costs, other methods are often batched at the species level, leading to longer turn-around times. WGS is as effective without species batching |
| Quality assurance | Access to external quality assurance is difficult in many resource settings | |
| The cold-chain | Current testing requires a large number of different reagents requiring cold storage to be shipped to testing laboratories | Stable reagents that can be transported at ambient temperatures and humidity Unified testing methods such as WGS that allow the same reagents to be used for different organism types Lab-on-chip technology that circumvents these issues
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| Human resources | There is a shortage of qualified laboratory technicians and a wide range of skills is needed for broad surveillance | Tests that have broad range so that the same suite of skills can be applied to different pathogens Automated or kit-based testing requiring lower skill levels Tele-training and other training formats that permit on-the-job training for existing technicians
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| Infrastructure | Electricity, running water and internet access are often unavailable or only intermittently available at remote testing sites | Equipment that can run off-line for example, portable sequencers, foldoscopes and paperfuges Leapfrog energy and water solutions
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| Data sharing and connectivity | Personal data needs to be protected and be compliant with General Data Protection Regulation and pseudonymised before sharing. Robust protocols are not always in place | Standards followed. Data gathering systems from all diagnostics. Context appropriate connectivity via local telecom systems Easy-to-use data visualisation
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