CHRO 2019

Transcript

1. Genomic variation among isolates from persistent Campylobacter infections in a pediatric cohort Keith Arora-Williams PhD(c)1, Francesca Schiaffino DVM PhD(c)2, Hannah Gray PhD(c)1, Ruthly Francois MSPH2, Craig T. Parker PhD3, Maribel Paredes Olortegui4, Sarah Preheim PhD1, Pablo Penataro-Yori RN5, Margaret N. Kosek MD5 1. Department of Environmental Health & Engineering, Johns Hopkins University, Baltimore, MD, USA 2. Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA 3. Agricultural Research Service, United States Department of Agriculture, Albany, California, USA 4. Project Manager, Asociacion Benefica PRISMA, Loreto, Peru 5. Professor, School of Medicine, University of Virginia
2. Campylobacter Epidemiology in Iquitos Population Attributable Fraction of Diarrhea (Platts-Mills et al. 2015) Incidence (Oberhelman et al. 2003) Colonization associated w/anthropometric outcomes (Lee et al. 2013) Persistent Infections (Rouhani et al. 2019 in press) 2
3. Campylobacter Epidemiology in Iquitos Population Attributable Fraction of Diarrhea (Platts-Mills et al. 2015) • 5.6% of cases in children <11mo, 10% in 12-24mo Incidence (Oberhelman et al. 2003) Colonization associated w/anthropometric outcomes (Lee et al. 2013) Persistent Infections (Rouhani et al. 2019 in press) 2
4. Campylobacter Epidemiology in Iquitos Population Attributable Fraction of Diarrhea (Platts-Mills et al. 2015) • 5.6% of cases in children <11mo, 10% in 12-24mo Incidence (Oberhelman et al. 2003) • 0.89 episodes / year, 1.4 positive samples / year. Colonization associated w/anthropometric outcomes (Lee et al. 2013) Persistent Infections (Rouhani et al. 2019 in press) 2
5. Campylobacter Epidemiology in Iquitos Population Attributable Fraction of Diarrhea (Platts-Mills et al. 2015) • 5.6% of cases in children <11mo, 10% in 12-24mo Incidence (Oberhelman et al. 2003) • 0.89 episodes / year, 1.4 positive samples / year. Colonization associated w/anthropometric outcomes (Lee et al. 2013) • Reduced weight gain over a 3 month period • 65.5 / 43.9 g (asymptomatic/ symptomatic) Persistent Infections (Rouhani et al. 2019 in press) 2
6. Campylobacter Epidemiology in Iquitos Population Attributable Fraction of Diarrhea (Platts-Mills et al. 2015) • 5.6% of cases in children <11mo, 10% in 12-24mo Incidence (Oberhelman et al. 2003) • 0.89 episodes / year, 1.4 positive samples / year. Colonization associated w/anthropometric outcomes (Lee et al. 2013) • Reduced weight gain over a 3 month period • 65.5 / 43.9 g (asymptomatic/ symptomatic) • Reduced linear growth over a 9 month period • 0.169 cm (severe cases) Persistent Infections (Rouhani et al. 2019 in press) 2
7. Campylobacter Epidemiology in Iquitos Population Attributable Fraction of Diarrhea (Platts-Mills et al. 2015) • 5.6% of cases in children <11mo, 10% in 12-24mo Incidence (Oberhelman et al. 2003) • 0.89 episodes / year, 1.4 positive samples / year. Colonization associated w/anthropometric outcomes (Lee et al. 2013) • Reduced weight gain over a 3 month period • 65.5 / 43.9 g (asymptomatic/ symptomatic) • Reduced linear growth over a 9 month period • 0.169 cm (severe cases) Persistent Infections (Rouhani et al. 2019 in press) • 55 children (20.3%) experienced persistent infections from 0-12m of age 2
8. Study Context: Etiology, Risk Factors and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development Multi-centric pediatric community-based cohort study. 3 Colston et al. 2018a
9. Research site IQTLAB Peruvian Amazon, peri-urban community 15 km southeast of Iquitos Santa Clara de Nanay and Santo Tomas (pop ~3,900) (Yori et al. 2014)
11. Outcome Definitions & Sampling Methods Sampling methodology Persisters Controls
12. Outcome Definitions & Sampling Methods Sampling methodology • Enrollment within first 17 days of life • Bi-weekly illness surveillance • Detection by PCR, ELISA & Culture Persisters Controls
13. Outcome Definitions & Sampling Methods Sampling methodology • Enrollment within first 17 days of life • Bi-weekly illness surveillance • Detection by PCR, ELISA & Culture • Surveillance samples: monthly collection • Diarrhea samples: Collection within 48 hours of an episode (maternal self- report) Persisters Controls
14. Outcome Definitions & Sampling Methods Sampling methodology • Enrollment within first 17 days of life • Bi-weekly illness surveillance • Detection by PCR, ELISA & Culture • Surveillance samples: monthly collection • Diarrhea samples: Collection within 48 hours of an episode (maternal self- report) Birth 1 year 2 years Adapted from Colston et al. 2018 Persisters Controls
15. Outcome Definitions & Sampling Methods Sampling methodology • Enrollment within first 17 days of life • Bi-weekly illness surveillance • Detection by PCR, ELISA & Culture • Surveillance samples: monthly collection • Diarrhea samples: Collection within 48 hours of an episode (maternal self- report) Birth 1 year 2 years Adapted from Colston et al. 2018 Persisters • Culture positive fecal sample for ≥2 consecutive months Controls
16. Outcome Definitions & Sampling Methods Sampling methodology • Enrollment within first 17 days of life • Bi-weekly illness surveillance • Detection by PCR, ELISA & Culture • Surveillance samples: monthly collection • Diarrhea samples: Collection within 48 hours of an episode (maternal self- report) Birth 1 year 2 years Adapted from Colston et al. 2018 Persisters • Culture positive fecal sample for ≥2 consecutive months • 22/30 individuals ≥ 3 consecutive months Controls
17. Outcome Definitions & Sampling Methods Sampling methodology • Enrollment within first 17 days of life • Bi-weekly illness surveillance • Detection by PCR, ELISA & Culture • Surveillance samples: monthly collection • Diarrhea samples: Collection within 48 hours of an episode (maternal self- report) Birth 1 year 2 years Adapted from Colston et al. 2018 Persisters • Culture positive fecal sample for ≥2 consecutive months • 22/30 individuals ≥ 3 consecutive months Controls • Culture positive sample with >93 days AFTER and >93 days BEFORE another culture positive sample
18. Persistence tied to Genome Variation
19. Persistence tied to Genome Variation • Relapse in immune-competent adults (Baqar et al. 2010) • Innate > acquired immune response
20. Persistence tied to Genome Variation • Relapse in immune-competent adults (Baqar et al. 2010) • Innate > acquired immune response • “No studies of community acquired exposures” • (Rimmer et al. 2018)
21. Persistence tied to Genome Variation • Relapse in immune-competent adults (Baqar et al. 2010) • Innate > acquired immune response • “No studies of community acquired exposures” • (Rimmer et al. 2018) • Campylobacter jejuni CG8421 – (Crofts et al. 2018)
22. Persistence tied to Genome Variation • Relapse in immune-competent adults (Baqar et al. 2010) • Innate > acquired immune response • “No studies of community acquired exposures” • (Rimmer et al. 2018) • Campylobacter jejuni CG8421 – (Crofts et al. 2018) • Sequenced 6 relapse strains, among 49 isolates
23. Persistence tied to Genome Variation • Relapse in immune-competent adults (Baqar et al. 2010) • Innate > acquired immune response • “No studies of community acquired exposures” • (Rimmer et al. 2018) • Campylobacter jejuni CG8421 – (Crofts et al. 2018) • Sequenced 6 relapse strains, among 49 isolates
24. Persistence tied to Genome Variation • Relapse in immune-competent adults (Baqar et al. 2010) • Innate > acquired immune response • “No studies of community acquired exposures” • (Rimmer et al. 2018) • Campylobacter jejuni CG8421 – (Crofts et al. 2018) • Sequenced 6 relapse strains, among 49 isolates • Variant accumulation in relapse strains • 2x as many variants as primary infection isolates • cmeR mutations à cmeABC constitutive expression • phase variation in cipA à increased mobility (?)
25. Objectives
26. Objectives 1. Report population dynamics of community-acquired persistent Campylobacter infections
27. Objectives 1. Report population dynamics of community-acquired persistent Campylobacter infections 2. Detect systematic variation in the genomes of Campylobacter spp. isolated from:
28. Objectives 1. Report population dynamics of community-acquired persistent Campylobacter infections 2. Detect systematic variation in the genomes of Campylobacter spp. isolated from: • persistent versus typical infections in Iquitos cohort
29. Objectives 1. Report population dynamics of community-acquired persistent Campylobacter infections 2. Detect systematic variation in the genomes of Campylobacter spp. isolated from: • persistent versus typical infections in Iquitos cohort • relapse v. parental strains isolated in Crofts et al. study
30. Objectives 1. Report population dynamics of community-acquired persistent Campylobacter infections 2. Detect systematic variation in the genomes of Campylobacter spp. isolated from: • persistent versus typical infections in Iquitos cohort • relapse v. parental strains isolated in Crofts et al. study • All Iquitos isolates versus paired Genbank references
31. Sample Size & Population Changes in Persistent Cases 0 5 10 15 20 25 30 C. coli C. jejuni Species Stable Cases Jejuni to Coli Coli to Jejuni M LST-type m atched M LST type changes W ithin-library co-infctions Cases/ Patients Jejuni Coli Mix Controls Persisters
32. Sample Size & Population Changes in Persistent Cases Persisters Controls Num. patients 21 33 Average age (mo.) 15.6 22.0 # Multi-Locus Sequence Typed 66 33 # WGS (>16x) 34 31 0 5 10 15 20 25 30 C. coli C. jejuni Species Stable Cases Jejuni to Coli Coli to Jejuni M LST-type m atched M LST type changes W ithin-library co-infctions Cases/ Patients Jejuni Coli Mix Controls Persisters
33. Sample Size & Population Changes in Persistent Cases Persisters Controls Num. patients 21 33 Average age (mo.) 15.6 22.0 # Multi-Locus Sequence Typed 66 33 # WGS (>16x) 34 31 0 5 10 15 20 25 30 C. coli C. jejuni Species Stable Cases Jejuni to Coli Coli to Jejuni M LST-type m atched M LST type changes W ithin-library co-infctions Cases/ Patients Jejuni Coli Mix Controls Persisters
34. Sample Size & Population Changes in Persistent Cases Persisters Controls Num. patients 21 33 Average age (mo.) 15.6 22.0 # Multi-Locus Sequence Typed 66 33 # WGS (>16x) 34 31 0 5 10 15 20 25 30 C. coli C. jejuni Species Stable Cases Jejuni to Coli Coli to Jejuni M LST-type m atched M LST type changes W ithin-library co-infctions Cases/ Patients Jejuni Coli Mix Controls Persisters
35. Sample Size & Population Changes in Persistent Cases Persisters Controls Num. patients 21 33 Average age (mo.) 15.6 22.0 # Multi-Locus Sequence Typed 66 33 # WGS (>16x) 34 31 0 5 10 15 20 25 30 C. coli C. jejuni Species Stable Cases Jejuni to Coli Coli to Jejuni M LST-type m atched M LST type changes W ithin-library co-infctions Cases/ Patients Jejuni Coli Mix Controls Persisters
36. Phylogenetic Signal of Phenotype C. coli C. jejuni
37. Phylogenetic Signal of Phenotype C. coli C. jejuni
38. Phylogenetic Signal of Phenotype C. coli C. jejuni
39. Phylogenetic Signal of Phenotype C. coli C. jejuni
40. Phylogenetic Signal of Phenotype C. coli C. jejuni
41. Phylogenetic Signal of Phenotype C. coli C. jejuni
42. Abouheif’s Proximity Test Sample Group Iquitos C. coli Crofts et al Isolates Iquitos C. jejuni MLST loci* <0.08 NA <0.04 Persistence status 0.01 0.02 0.35 Multi-drug resistance 0.76 NA 0.01 * aspA, tkt, uncA Phylogenetic Signal of Phenotype C. coli C. jejuni
43. Campylobacter Pangenome
44. Campylobacter Pangenome
45. Campylobacter Pangenome Crofts et al. isolates (C. jejuni) Iquitos C. jejuni Isolates Iquitos C. coli Isolates Note: darker bands are Genbank references*
46. Campylobacter Pangenome Crofts et al. isolates (C. jejuni) Iquitos C. jejuni Isolates Iquitos C. coli Isolates Note: darker bands are Genbank references* Presence/Absence of Gene Clusters
47. Campylobacter Pangenome Crofts et al. isolates (C. jejuni) Iquitos C. jejuni Isolates Iquitos C. coli Isolates Note: darker bands are Genbank references* Presence/Absence of Gene Clusters
48. Campylobacter Pangenome Crofts et al. isolates (C. jejuni) Iquitos C. jejuni Isolates Iquitos C. coli Isolates Note: darker bands are Genbank references* Presence/Absence of Gene Clusters
49. C. coli References (n=5) Iquitos Persisters (n=6) Iquitos Controls (n=8) C rofts et al Persisters (n=6) C rofts et al C ontrols (n=6) Iquitos Persisters (n=28) Iquitos C ontrols (n=23) C . Jejuni R eferences (n=28) C. coli-specific: Multiple variants associated with surface polysaccharides and loss of beta-lactamase Persistence- associated variants Crofts et al. isolates Chemotaxis gene variant changed and glycosyl transferase lost Multi-group comparisons Methylases lost and gained. Type IV Secretion Systems depleted in C. coli and Crofts et al. persisters while Type VI enriched in C. jejuni
50. Summary • Persistent Campylobacter detections in infants may be caused by true persistence, serial reinfection, or polyclonal infection • Significant of phylogenetic clustering of phenotype correlates with recovery of enrichment of gene clusters • Iquitos isolates are genomically distinct from closest complete references • Variability in surface structures may be associated with persistence phenotype in C. coli
51. Acknowledgments • PhD Advisor: Sarah Preheim • Lab PI: Margaret Kosek • Addl. co-authors: Francesca Schiaffino, Hannah Gray, Ruthly Francois, Craig T. Parker, Maribel Paredes Olortegui, Pablo Penataro-Yori • PRISMA field team: Dixner Renfigo, Mery Siguas, Marvin Yalta, Victoria Lopez • Johns Hopkins Whiting School of Engineering Questions?
52. References • Colston et al., (2018) Evaluating meteorological data from weather stations, and from satellites and global models for a multi-site… Environmental Research. 165, pp. 91-109 • Crofts et al., (2018) Campylobacter jejuni transcriptional and genetic adaptation during human infection. Nature Microbiology 3, pp. 494–502 • Yori et al., (2014) Santa Clara de Nanay: The MAL-ED Cohort in Peru. Clinical Infectious Diseases, 59(4), pp. S310-S316 • Lee et al. (2013) Symptomatic and Asymptomatic Campylobacter Infections Associated with Reduced Growth in Peruvian Children. PLOS Neglected Tropical Diseases. e2036 pp. 1935-2735 • Oberhelman et al. (2003) Campylobacter Transmission in a Peruvian Shantytown: A Longitudinal Study Using Strain Typing… Journal of Infectious Diseases, 187(2), pp. 260-269 • Rimmer et al. (2018) Rifaximin Fails to Prevent Campylobacteriosis in the Human Challenge Model: A Randomized, Double-Blind, Placebo-Controlled Trial. Clinical Infectious Diseases. 66(9), pp. 1435-1441 • Delmont T.O and Eren, A. M. (2018) Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ:e4320