add TB culture HSI (#1453)

* modification to scenarios to get it running fast

* define mode1 baseline properly

* define mode1 baseline properly

* add culture test for tb dx
this occurs during program scale-up, only if person has had a negative prior test but has all symptoms indicative of tb

* remove unneeded todo statement

* remove ref to life expectancy in script

* remove unused imports

* update priority policies

* add scenario version with consumables always available

* update plots

* add outputs to test plot file

* revert analysis scripts

* remove suppress_footprint from HSI_Tb_Culture

* remove unused statement ACTUAL_APPT_FOOTPRINT = self.EXPECTED_APPT_FOOTPRINT

* roll back other files

---------

Co-authored-by: Tim Hallett <39991060+tbhallett@users.noreply.github.com>

src/tlo/methods/tb.py

@@ -782,6 +782,21 @@ def get_consumables_for_dx_and_tx(self):
             )
         )
 
+        # TB Culture
+        self.item_codes_for_consumables_required['culture_test'] = \
+            hs.get_item_code_from_item_name("MGIT960 Culture and DST")
+
+        # sensitivity/specificity set for smear status of cases
+        self.sim.modules["HealthSystem"].dx_manager.register_dx_test(
+            tb_culture_test=DxTest(
+                property="tb_inf",
+                target_categories=["active"],
+                sensitivity=1.0,
+                specificity=1.0,
+                item_codes=self.item_codes_for_consumables_required['culture_test']
+            )
+        )
+
         # 4) -------- Define the treatment options --------
         # treatment supplied as full kits for duration of treatment
         # adult treatment - primary
@@ -1458,6 +1473,7 @@ def __init__(self, module):
     def apply(self, population):
 
         self.module.update_parameters_for_program_scaleup()
+        # note also culture test used in target/max scale-up in place of clinical dx
 
 
 class TbActiveEvent(RegularEvent, PopulationScopeEventMixin):
@@ -1729,6 +1745,8 @@ def apply(self, person_id, squeeze_factor):
         # check if patient has: cough, fever, night sweat, weight loss
         # if none of the above conditions are present, no further action
         persons_symptoms = self.sim.modules["SymptomManager"].has_what(person_id=person_id)
+        person_has_tb_symptoms = all(symptom in persons_symptoms for symptom in self.module.symptom_list)
+
         if not any(x in self.module.symptom_list for x in persons_symptoms):
             return self.make_appt_footprint({})
 
@@ -1944,6 +1962,27 @@ def apply(self, person_id, squeeze_factor):
                             tclose=None,
                         )
 
+        # ------------------------- Culture testing if program scale-up ------------------------- #
+        # under program scale-up, if a person tests negative but still has symptoms
+        # indicative of TB, they are referred for culture test which has perfect sensitivity
+        # this has the effect to reduce false negatives
+        if not test_result and person_has_tb_symptoms:
+            if p['type_of_scaleup'] != 'none' and self.sim.date.year >= p['scaleup_start_year']:
+                logger.debug(
+                    key="message",
+                    data=f"HSI_Tb_ScreeningAndRefer: scheduling culture for person {person_id}",
+                )
+
+                culture_event = HSI_Tb_Culture(
+                    self.module, person_id=person_id
+                )
+                self.sim.modules["HealthSystem"].schedule_hsi_event(
+                    culture_event,
+                    priority=0,
+                    topen=now,
+                    tclose=None,
+                )
+
         # Return the footprint. If it should be suppressed, return a blank footprint.
         if self.suppress_footprint:
             return self.make_appt_footprint({})
@@ -1979,6 +2018,7 @@ def apply(self, person_id, squeeze_factor):
         df = self.sim.population.props
         now = self.sim.date
         person = df.loc[person_id]
+        p = self.module.parameters
         test_result = None
 
         # If the person is dead or already diagnosed, do nothing do not occupy any resources
@@ -2021,6 +2061,79 @@ def apply(self, person_id, squeeze_factor):
                     tclose=None,
                     priority=0,
                 )
+        # ------------------------- Culture testing if program scale-up ------------------------- #
+        # under program scale-up, if a person tests negative but still has all symptoms
+        # indicative of TB, they are referred for culture test which has perfect sensitivity
+        # this has the effect to reduce false negatives
+        person_has_tb_symptoms = all(symptom in persons_symptoms for symptom in self.module.symptom_list)
+
+        if not test_result and person_has_tb_symptoms:
+            if p['type_of_scaleup'] != 'none' and self.sim.date.year >= p['scaleup_start_year']:
+
+                logger.debug(
+                    key="message",
+                    data=f"HSI_Tb_ClinicalDiagnosis: scheduling culture for person {person_id}",
+                )
+
+                culture_event = HSI_Tb_Culture(
+                    self.module, person_id=person_id
+                )
+                self.sim.modules["HealthSystem"].schedule_hsi_event(
+                    culture_event,
+                    priority=0,
+                    topen=now,
+                    tclose=None,
+                )
+
+
+class HSI_Tb_Culture(HSI_Event, IndividualScopeEventMixin):
+    """
+    This the TB culture HSI used for microbiological diagnosis of TB
+    results (MGIT) are available after 2-6 weeks
+    will return drug-susceptibility
+    100% sensitivity in smear-positive
+    80-90% sensitivity in smear-negative
+    if this test is not available, not further action as this is
+    already preceded by a sequence of tests
+    """
+
+    def __init__(self, module, person_id):
+        super().__init__(module, person_id=person_id)
+        assert isinstance(module, Tb)
+
+        self.TREATMENT_ID = "Tb_Test_Culture"
+        self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({"LabTBMicro": 1})
+        self.ACCEPTED_FACILITY_LEVEL = '1b'
+
+    def apply(self, person_id, squeeze_factor):
+
+        df = self.sim.population.props
+
+        if not df.at[person_id, "is_alive"] or df.at[person_id, "tb_diagnosed"]:
+            return self.sim.modules["HealthSystem"].get_blank_appt_footprint()
+
+        test_result = self.sim.modules["HealthSystem"].dx_manager.run_dx_test(
+                dx_tests_to_run="tb_culture_test", hsi_event=self)
+
+        # todo equipment required: MGIT instrument, MGIT tube, reagent kit included in consumables
+        if test_result is not None:
+            self.add_equipment({'Autoclave', 'Blood culture incubator', 'Vortex mixer',
+                                'Dispensing pumps for culture media preparation', 'Biosafety Cabinet (Class II)',
+                                'Centrifuge'})
+
+        # if test returns positive result, refer for appropriate treatment
+        if test_result:
+            df.at[person_id, "tb_diagnosed"] = True
+            df.at[person_id, "tb_date_diagnosed"] = self.sim.date
+
+            self.sim.modules["HealthSystem"].schedule_hsi_event(
+                HSI_Tb_StartTreatment(
+                    person_id=person_id, module=self.module, facility_level="1a"
+                ),
+                topen=self.sim.date,
+                tclose=None,
+                priority=0,
+            )
 
 
 class HSI_Tb_Xray_level1b(HSI_Event, IndividualScopeEventMixin):