Pathogen hide-and-'seq'


This month's Genome Watch looks at how genome sequence analysis aids our understanding of pathogen survival within hosts.


Credit: NPG

Following exposure to pathogenic microorganisms, the host relies on the innate immune system for protection from infection. If this response is insufficient, the host will mount an adaptive immune response. However, some pathogens have evolved specific evasion strategies to escape immune clearance by the host and can cause persistent infections even in the presence of inflammation and specific antimicrobial mechanisms. One such strategy involves 'hiding' from the immune system of the host, which protects the invading microorganisms from detection and elimination as well as from exposure to drugs, thereby increasing the potential for relapse infections. Whole-genome sequencing (WGS) of isolates from various organs within the same host can help to elucidate the persistence strategies of viral1, bacterial2 and fungal3 pathogens within specific host niches.

Paradoxically, the secondary lymphoid organs of the host immune system, where priming of the immune system initially occurs, can become a hiding place for pathogens. HIV-1 establishes persistent viral reservoirs that harbour integrated provirus within host cellular DNA. Although antiretroviral therapy (ART) decreases the production and replication of HIV-1 to levels that are undetectable in the blood, the virus may continue to replicate and evolve in lymphoid tissue reservoirs. Lorenzo-Redondo et al. deep-sequenced HIV-1 DNA from the blood and lymph nodes of three patients who are undergoing ART and found that despite undetectable levels of virus in the blood there was continued production of the virus from infected cells in lymphoid tissue, where intracellular drug concentrations are much lower1. Furthermore, the authors observed substantial genetic variations of HIV-1 between the two compartments. Phylogenetic analyses revealed a strong relationship between viral genetic divergence and sampling time, which suggests that the virus had continued to replicate and mutate inside the lymph nodes despite ART. Finally, the authors identified higher migration rates of viral populations from lymphoid tissues to blood than vice versa, which further suggests that the lymph nodes are the source of new viral lineages that spread to the blood. Given these observations, the team concluded that lymph nodes might act as sanctuary sites that enable the virus to replicate and replenish the blood compartment. Therefore, drug treatment might not only be limited by the evolution of resistance but also by the failure of the drug to effectively reach these sites.

In addition to viruses, bacterial pathogens have been suggested to establish persistent reservoirs in the lymph nodes of the host. Paterson et al. deep sequenced 141 methicillin-resistant Staphylococcus aureus (MRSA) isolates from a dog that was being treated for infection with this pathogen2. The team constructed a phyloanatomic tree of isolates that were collected from an abdominal wound and the nares, axilla, legs, antebrachium and prescapular lymph node of the dog, noting that the majority of isolates were identical. However, isolates from the prescapular lymph node contained two unique non-synonymous mutations that were located in the virulence regulator, agr, which led to agr dysfunction. Interestingly, MRSA with agr dysfunction predominates in patients with persistent infection4. Inactivation of this gene might promote persistent colonization and enable MRSA to establish reservoirs in the lymph node of the dog.

Fungal pathogens are too large to hide inside the lymph node cells of the host, but they may instead remove or switch their surface antigens and become completely invisible to detection by the host immune system. Ma et al. sequenced the genomes of Pneumocystis species, a group of fungal pathogens that resides in the mammalian lung3. Genomic analyses and bioassays confirmed the loss of two important components of the cell wall in this genus — chitin and outer chain N-mannans — two known pathogen-associated molecular patterns that trigger the innate host defence. Interestingly, the team observed an expansion of a gene family that encodes the surface glycoprotein Msg, which contrasts to the extensive reduction observed in other gene families. Using an RNA-sequencing approach, the team also reported high levels of expression of the gene encoding Msg in infected mice, which led them to conclude that antigenic variation of Msg isoforms may benefit immune evasion during infection.

Together, these studies highlight how genomic analyses of within-host evolution can provide a detailed picture of this pathogen 'hide-and-seek' that may hand the advantage to the seekers.


  1. 1

    Lorenzo-Redondo, R. et al. Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature 530, 51–56 (2016).

    CAS  Article  Google Scholar 

  2. 2

    Paterson, G. K. et al. Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat. Commun. 6, 6560 (2015).

    CAS  Article  Google Scholar 

  3. 3

    Ma, L. et al. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat. Commun. 7, 10740 (2016).

    CAS  Article  Google Scholar 

  4. 4

    Fowler, V. G. et al. Persistent bacteremia due to methicillin-resistant Staphylococcus aureus infection is associated with agr dysfunction and low-level in vitro resistance to thrombin-induced platelet microbicidal protein. J. Infect. Dis. 190, 1140–1149 (2004)

    CAS  Article  Google Scholar 

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Correspondence to Claire Chewapreecha or Angèle Bénard or Sandra Reuter.

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Chewapreecha, C., Bénard, A. & Reuter, S. Pathogen hide-and-'seq'. Nat Rev Microbiol 14, 271 (2016).

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