Chlamydia

Chlamydia (Chlamydia trachomatis) follows the SEIS (susceptible-exposed-infectious-susceptible) pattern with sex-stratified symptom probabilities and natural clearance.

Class: sti.Chlamydia | Alias: 'ct' | Base class: SEIS

States and transitions

     ┌─────────────┐
     │ Susceptible │◄──────────────────────────────────────┐
     └──────┬──────┘                                       │
            │ infection                                     │
            ▼                                               │
     ┌─────────────┐                                       │
     │   Exposed   │  Latent period                        │
     │   (~1 wk)   │  (not yet infectious)                 │
     └──────┬──────┘                                       │
            │                                               │
            ├────────────────────┐                          │
            ▼                    ▼                          │
     ┌─────────────┐     ┌──────────────┐                  │
     │Asymptomatic │     │ Symptomatic  │                  │
     │  F: 80%     │     │  F: 20%      │                  │
     │  M: 46%     │     │  M: 54%      │                  │
     └──────┬──────┘     └──────┬───────┘                  │
            │                   │                           │
            │                   ├───────────┐               │
            │                   ▼           ▼               │
            │            ┌───────────┐  ┌───────┐          │
            │            │ Seeks care│  │  PID  │ (F only) │
            │            └───────────┘  └───────┘          │
            │                                               │
            └───────── natural clearance ──────────────────┘
                    F: ~18 mo   M: ~12 mo

Parameters

Natural history

Parameter	Default	Description
dur_exp	1 wk	Duration of exposed (latent) period
p_symp	[0.20, 0.54]	Probability of symptoms [F, M]
dur_presymp	F: [1 wk, 10 wk]; M: [0.25 wk, 1 wk]	Time to symptom onset [mean, std]
dur_asymp2clear	F: [18 mo, 1 mo]; M: [12 mo, 1 mo]	Duration of asymptomatic infection [mean, std]
dur_symp2clear	F: [18 mo, 1 mo]; M: [12 mo, 1 mo]	Duration of symptomatic infection [mean, std]

Care seeking

Parameter	Default	Description
p_symp_care	[0.42, 0.83]	Probability of seeking care if symptomatic [F, M]
dur_symp2care	F: [2 mo, 1 mo]; M: [1 wk, 2 wk]	Time from symptoms to care seeking [mean, std]

Complications

Parameter	Default	Description
p_pid	0.0	Probability of pelvic inflammatory disease (females)
dur_prepid	lognorm(1.5 mo, 3 mo)	Time to PID onset

Transmission

Parameter	Default	Description
beta_m2f	0.06	Per-act male-to-female transmission probability
rel_beta_f2m	0.5	Female-to-male transmission relative to male-to-female
beta_m2c	None	Mother-to-child transmission probability
beta_m2m	None	Male-to-male transmission probability
eff_condom	0.0	Condom efficacy
init_prev	0.01	Initial prevalence