news and views
Biodiversity and hypervirulence of Listeria monocytogenes Yonatan H Grad & Sarah M Fortune
Last year, after reports in the United States of L. monocytogenes contaminating two brands of ice cream, we fielded calls from pregnant friends who were worried about the threat to their health (Fig. 1). The concern was underscored by the ten cases of listeriosis and three deaths attributed to consumption of one of the ice cream brands, although presumably many people ate this ice cream without ill effect. Surveillance and rapid action were undoubtedly important in limiting the extent of disease. With multiple outbreaks a year and uncertainties about risk and the possible severe consequences of infection, a cautious publichealth response is warranted; but this response also highlights that there are opportunities to improve understanding of when, where and to whom potentially pathogenic organisms pose a risk—an issue investigated in a new report by Marc Lecuit and colleagues in this issue1. Why is there uncertainty as to the risk posed by L. monocytogenes in your ice cream? Clinically, L. monocytogenes causes foodborne infections, diagnosed in 1,600 individuals in the United States annually, of whom over 200 die2. Associated with the ingestion of contaminated meats and cheeses, L. monocytogenes causes a spectrum of clinical manifestations from an acute febrile gastroenteritis and bacteremia to meningitis to a range of complications in pregnant women, including fetal demise, preterm delivery and neonatal sepsis3. However, these cases clearly represent the tip of the iceberg in terms of the interactions of Listeria with people. Surveillance studies suggest that L. monocytogenes can be isolated in the stool cultures of ~2–4% of healthy, asymptomatic adults4, with these rates likely driven by widespread agricultural carriage of Listeria5. Heterogeneity in virulence These numbers raise a fundamental question Yonatan H. Grad and Sarah M. Fortune are in the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. e-mail: [email protected] or [email protected]
in considering the risk associated with L. monocytogenes exposure: why do some people get sick yet the vast majority does not? In clinical teaching, the risk of disease is attributed to host susceptibility, with pregnant women, neonates and immunocompromised individuals at highest risk. However, recent studies have suggested that there are important bacterial determinants of risk. L. monocytogenes is a Gram-positive bacterium that can be divided, on the basis of conventional typing methods, into four evolutionary lineages and further subdivided into 13 serotypes. Serotypes 4b, 1/2a, 1/2b and 1/2c are associated with human infection, but the genetic basis of the virulence in these strains—underlying their ability to cause invasive disease and the specific clinical syndromes that result—has remained unclear. Forward genetic studies to elucidate virulence determinants have pinpointed some determinants of invasion6 but are limited by the constraints of the model systems and the reference strains in which they are performed. In Maury et al., the authors take a population genetics–based approach to identify novel virulence factors mediating the central nervous system (CNS) and placental tropisms of L. monocytogenes1. Briefly, the authors leverage access to the French national surveillance system for Listeria, through which 6,633 isolates were collected, including 2,584 clinical and 4,049 food isolates. Metadata were available for each of these isolates, allowing the authors to assess the associations between strain and clinical syndrome (bacteremia and CNS and maternal infections). Having identified putatively hypervirulent strains and demonstrated their virulence in a mouse model, the authors then used targeted whole-genome sequencing to identify genetic elements in both the core and accessory genomes that are associated with virulence. In addition to known virulence determinants (InlA, LIPI-3 and teichoic acid biosynthesis genes), the authors identified a suite of novel putative virulence determinants, including a previously uncharacterized cellobiose family PTS system associated with CNS disease. The authors go on to show that this PTS system is required for CNS invasion in a mouse model.
nature genetics | volume 48 | number 3 |March 2016
In short, the authors close the circle and, in doing so, provide a road map for how to use bacterial population genetics to identify clinically important determinants of outcome. What distinguishes this study from many published efforts to exploit bacterial population genetics, fueled by the plummeting cost of wholegenome sequencing? First, the authors start with an exceptional isolate collection, notable for the available metadata and the fact that in addition to the strains of interest—here strains associated with clinical disease—attention was given to the food-associated strains that effectively acted as controls. Second, the authors were smart in their sequencing, taking into account population structure and phenotype. Thus, they avoided the trap of sequencing hundreds of isolates of the same transmitted clone—useful when trying to track outbreaks, but less so when trying to define the genetic basis of a phenotype. Finally, the authors tested their predictions experimentally, providing convincing evidence to support their genetic associations. Population genomics to phenotypes At a time when whole-genome sequencing is much cheaper and easier and can explore
Marina Corral Spence/Nature Publishing Group
npg
© 2016 Nature America, Inc. All rights reserved.
The integration of large, well-sampled collections of bacterial isolates with genomics and experimental methods provides opportunities for ‘top-down’ discovery of the genetic basis of phenotypes of interest. In a new report, the authors apply this approach to investigate the heterogeneity in manifestations of disease caused by Listeria monocytogenes and demonstrate that a previously uncharacterized cellobiose PTS system is involved in central nervous system infection.
Figure 1 A pregnant woman eating an ice cream cone contaminated with L. monocytogenes, which are depicted as brown flagellated bacteria in the zoom-in callout. Listeriosis in pregnant women can lead to severe health complications that can compromise gestation.
229
news and views the best experiments? As in the example of Maury et al., well-sampled collections can equip investigators to tackle enduring questions (among the most fascinating in infectious diseases) about the heterogeneity in the manifestations of infections and the extent to which this heterogeneity is attributable to pathogen factors. With greater incorporation of patient data—from HLA types to B and T cell repertoires—more opportunities will emerge to untangle the complex interactions between hosts and pathogens. We emphasize that this work critically depends on thoughtful sampling strategies, robust metadata, development of statistical tools to interrogate these large collections of data and experimental models to test the resulting hypotheses when possible. But one can be optimistic that we might soon see more nuanced clinical and public-health
risk stratifications that incorporate pathogen factors along with host susceptibilities. URLs. CDC report on the 2015 Listeria outbreaks in ice cream, http://www.cdc.gov/ listeria/outbreaks/ice-cream-03-15/index. html; CDC foodborne outbreaks, http:// wwwn.cdc.gov/foodborneoutbreaks/. COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. 1. Maury, M.M. et al. Nat. Genet. 48, 308–313 (2016). 2. Scallan, E. et al. Emerg. Infect. Dis. 17, 7–15 (2011). 3. Hohmann, E.L. & Portnoy, D.A. in Harrison’s Principles of Internal Medicine 18th edn (eds. Longo, D.L. et al.) Ch. 139, 1194–1196 (McGraw Hill Professional, 2011). 4. Gahan, C.G. & Hill, C. Front. Cell. Infect. Microbiol. 4, 9 (2014). 5. Esteban, J.I., Oporto, B., Aduriz, G., Juste, R.A. & Hurtado, A. BMC Vet. Res. 5, 2 (2009). 6. Vázquez-Boland, J.A. et al. Clin. Microbiol. Rev. 14, 584–640 (2001).
npg
© 2016 Nature America, Inc. All rights reserved.
species diversity more comprehensively than classic bacterial genetics, we are at the start of an explosion of genetic association studies linking bacterial genes to clinically relevant phenotypes such as antibiotic resistance and virulence. A critical need is the development and rigorous assessment of statistical methods for these association studies that consider the ecological and biological idiosyncrasies of microbial pathogens and data sets. For example, how should sampling vary by expected within-host diversity, and what are the potential solutions for developing association tools for organisms as different as Mycobacterium tuberculosis, which does not recombine, and Neisseria gonorrhoeae or Helicobacter pylori, which undergo extensive recombination? In the design of these studies, what strategies might enable researchers to perform informative power calculations a priori to help define
230
volume 48 | number 3 |March 2016 | nature genetics
Biodiversity and hypervirulence of Listeria monocytogenes Yonatan H Grad & Sarah M Fortune
Last year, after reports in the United States of L. monocytogenes contaminating two brands of ice cream, we fielded calls from pregnant friends who were worried about the threat to their health (Fig. 1). The concern was underscored by the ten cases of listeriosis and three deaths attributed to consumption of one of the ice cream brands, although presumably many people ate this ice cream without ill effect. Surveillance and rapid action were undoubtedly important in limiting the extent of disease. With multiple outbreaks a year and uncertainties about risk and the possible severe consequences of infection, a cautious publichealth response is warranted; but this response also highlights that there are opportunities to improve understanding of when, where and to whom potentially pathogenic organisms pose a risk—an issue investigated in a new report by Marc Lecuit and colleagues in this issue1. Why is there uncertainty as to the risk posed by L. monocytogenes in your ice cream? Clinically, L. monocytogenes causes foodborne infections, diagnosed in 1,600 individuals in the United States annually, of whom over 200 die2. Associated with the ingestion of contaminated meats and cheeses, L. monocytogenes causes a spectrum of clinical manifestations from an acute febrile gastroenteritis and bacteremia to meningitis to a range of complications in pregnant women, including fetal demise, preterm delivery and neonatal sepsis3. However, these cases clearly represent the tip of the iceberg in terms of the interactions of Listeria with people. Surveillance studies suggest that L. monocytogenes can be isolated in the stool cultures of ~2–4% of healthy, asymptomatic adults4, with these rates likely driven by widespread agricultural carriage of Listeria5. Heterogeneity in virulence These numbers raise a fundamental question Yonatan H. Grad and Sarah M. Fortune are in the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. e-mail: [email protected] or [email protected]
in considering the risk associated with L. monocytogenes exposure: why do some people get sick yet the vast majority does not? In clinical teaching, the risk of disease is attributed to host susceptibility, with pregnant women, neonates and immunocompromised individuals at highest risk. However, recent studies have suggested that there are important bacterial determinants of risk. L. monocytogenes is a Gram-positive bacterium that can be divided, on the basis of conventional typing methods, into four evolutionary lineages and further subdivided into 13 serotypes. Serotypes 4b, 1/2a, 1/2b and 1/2c are associated with human infection, but the genetic basis of the virulence in these strains—underlying their ability to cause invasive disease and the specific clinical syndromes that result—has remained unclear. Forward genetic studies to elucidate virulence determinants have pinpointed some determinants of invasion6 but are limited by the constraints of the model systems and the reference strains in which they are performed. In Maury et al., the authors take a population genetics–based approach to identify novel virulence factors mediating the central nervous system (CNS) and placental tropisms of L. monocytogenes1. Briefly, the authors leverage access to the French national surveillance system for Listeria, through which 6,633 isolates were collected, including 2,584 clinical and 4,049 food isolates. Metadata were available for each of these isolates, allowing the authors to assess the associations between strain and clinical syndrome (bacteremia and CNS and maternal infections). Having identified putatively hypervirulent strains and demonstrated their virulence in a mouse model, the authors then used targeted whole-genome sequencing to identify genetic elements in both the core and accessory genomes that are associated with virulence. In addition to known virulence determinants (InlA, LIPI-3 and teichoic acid biosynthesis genes), the authors identified a suite of novel putative virulence determinants, including a previously uncharacterized cellobiose family PTS system associated with CNS disease. The authors go on to show that this PTS system is required for CNS invasion in a mouse model.
nature genetics | volume 48 | number 3 |March 2016
In short, the authors close the circle and, in doing so, provide a road map for how to use bacterial population genetics to identify clinically important determinants of outcome. What distinguishes this study from many published efforts to exploit bacterial population genetics, fueled by the plummeting cost of wholegenome sequencing? First, the authors start with an exceptional isolate collection, notable for the available metadata and the fact that in addition to the strains of interest—here strains associated with clinical disease—attention was given to the food-associated strains that effectively acted as controls. Second, the authors were smart in their sequencing, taking into account population structure and phenotype. Thus, they avoided the trap of sequencing hundreds of isolates of the same transmitted clone—useful when trying to track outbreaks, but less so when trying to define the genetic basis of a phenotype. Finally, the authors tested their predictions experimentally, providing convincing evidence to support their genetic associations. Population genomics to phenotypes At a time when whole-genome sequencing is much cheaper and easier and can explore
Marina Corral Spence/Nature Publishing Group
npg
© 2016 Nature America, Inc. All rights reserved.
The integration of large, well-sampled collections of bacterial isolates with genomics and experimental methods provides opportunities for ‘top-down’ discovery of the genetic basis of phenotypes of interest. In a new report, the authors apply this approach to investigate the heterogeneity in manifestations of disease caused by Listeria monocytogenes and demonstrate that a previously uncharacterized cellobiose PTS system is involved in central nervous system infection.
Figure 1 A pregnant woman eating an ice cream cone contaminated with L. monocytogenes, which are depicted as brown flagellated bacteria in the zoom-in callout. Listeriosis in pregnant women can lead to severe health complications that can compromise gestation.
229
news and views the best experiments? As in the example of Maury et al., well-sampled collections can equip investigators to tackle enduring questions (among the most fascinating in infectious diseases) about the heterogeneity in the manifestations of infections and the extent to which this heterogeneity is attributable to pathogen factors. With greater incorporation of patient data—from HLA types to B and T cell repertoires—more opportunities will emerge to untangle the complex interactions between hosts and pathogens. We emphasize that this work critically depends on thoughtful sampling strategies, robust metadata, development of statistical tools to interrogate these large collections of data and experimental models to test the resulting hypotheses when possible. But one can be optimistic that we might soon see more nuanced clinical and public-health
risk stratifications that incorporate pathogen factors along with host susceptibilities. URLs. CDC report on the 2015 Listeria outbreaks in ice cream, http://www.cdc.gov/ listeria/outbreaks/ice-cream-03-15/index. html; CDC foodborne outbreaks, http:// wwwn.cdc.gov/foodborneoutbreaks/. COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. 1. Maury, M.M. et al. Nat. Genet. 48, 308–313 (2016). 2. Scallan, E. et al. Emerg. Infect. Dis. 17, 7–15 (2011). 3. Hohmann, E.L. & Portnoy, D.A. in Harrison’s Principles of Internal Medicine 18th edn (eds. Longo, D.L. et al.) Ch. 139, 1194–1196 (McGraw Hill Professional, 2011). 4. Gahan, C.G. & Hill, C. Front. Cell. Infect. Microbiol. 4, 9 (2014). 5. Esteban, J.I., Oporto, B., Aduriz, G., Juste, R.A. & Hurtado, A. BMC Vet. Res. 5, 2 (2009). 6. Vázquez-Boland, J.A. et al. Clin. Microbiol. Rev. 14, 584–640 (2001).
npg
© 2016 Nature America, Inc. All rights reserved.
species diversity more comprehensively than classic bacterial genetics, we are at the start of an explosion of genetic association studies linking bacterial genes to clinically relevant phenotypes such as antibiotic resistance and virulence. A critical need is the development and rigorous assessment of statistical methods for these association studies that consider the ecological and biological idiosyncrasies of microbial pathogens and data sets. For example, how should sampling vary by expected within-host diversity, and what are the potential solutions for developing association tools for organisms as different as Mycobacterium tuberculosis, which does not recombine, and Neisseria gonorrhoeae or Helicobacter pylori, which undergo extensive recombination? In the design of these studies, what strategies might enable researchers to perform informative power calculations a priori to help define
230
volume 48 | number 3 |March 2016 | nature genetics
