diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5..392ddef 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -35,6 +35,7 @@ jobs:
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
+        version: 25.10
 
       - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6a..42e519b 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/bin/parse_sequenceQC.py b/bin/parse_sequenceQC.py
index b98184c..0f6164c 100755
--- a/bin/parse_sequenceQC.py
+++ b/bin/parse_sequenceQC.py
@@ -48,9 +48,12 @@ def load_json(path):
     "n50_value",
     "nr_contigs",
     "length",
+    "wgmlst_loci_count",
 }
 
-CHECKM_TEST = "checkm_contamination"
+CHECKM_TEST = "checkm2_contamination"
+
+WGMLST_TEST = "wgmlst_loci_count"
 
 PNC_FAIL_MESSAGE = (
     "[SEQ_FAIL] Resequencing is recommended. QUALITY_METRICS did not meet PNC requirements."
@@ -96,6 +99,8 @@ def build_typingQC_message(sample_data, species, failed_tests):
         base_message = CHECKM_FAIL_MESSAGE
     elif failed_tests.intersection(ABSOLUTE_FAIL_TESTS):
         base_message = PNC_FAIL_MESSAGE
+    elif WGMLST_TEST in failed_tests:
+        base_message = PNC_FAIL_MESSAGE
     elif failed_tests.intersection(WARNING_TESTS):
         base_message = WARNING_MESSAGE
     else:
diff --git a/bin/parse_sistrQC.py b/bin/parse_sistrQC.py
index e216ddb..f5bd108 100755
--- a/bin/parse_sistrQC.py
+++ b/bin/parse_sistrQC.py
@@ -3,6 +3,7 @@
 import json
 import csv
 import argparse
+import re
 from pathlib import Path
 import gzip
 
@@ -56,6 +57,29 @@ def load_reportable_serovars(reportable_file):
 SEROVAR_KEY = f"{SISTR_PREFIX}serovar"
 SEROVAR_CGMLST = f"{SISTR_PREFIX}serovar_cgmlst"
 
+
+#QC_MESSAGES Updates
+#Matches the non-actionable cgMLST loci found INFO message and strips it from qc_messages
+CGMLST_LOCI_INFO_PATTERN = re.compile(r"INFO: Number of cgMLST\d+ loci found \(n=\d+\)")
+def filter_qc_messages(qc_messages):
+    if not qc_messages:
+        return qc_messages
+    cleaned = CGMLST_LOCI_INFO_PATTERN.sub("", qc_messages)
+    # Collapse leftover separators/whitespace left behind by the removal
+    cleaned = re.sub(r"\s*\|\s*", " | ", cleaned)
+    cleaned = re.sub(r"^\s*\|\s*|\s*\|\s*$", "", cleaned)
+    cleaned = re.sub(r"\n\s*\n", "\n", cleaned)
+    return cleaned.strip()
+
+WZX_WZY_PATTERN = "Wzx/Wzy genes missing"
+WZX_WZY_WARNING_MESSAGE = "WARNING: Wzx/Wzy genes missing. Cannot determine O-antigen serogroup."
+
+def wzx_wzy_only_failure(qc_messages):
+    #Checks if a SISTR FAIL is solely due to missing Wzx/Wzy genes: does not affect serovar prediction and should not result in FAIL for typingQC
+    if not qc_messages:
+        return False
+    return WZX_WZY_PATTERN in qc_messages
+
 def H1_warning(qc_messages):
     # Check if SISTR WARNING contains identification of the inability to identify H1 antigens, and therefore, unable to predict serovar repliably
     if not qc_messages:
@@ -70,12 +94,16 @@ def H1_warning(qc_messages):
 
 def extract_sistr_qc(sample_data):
     qc_status = sample_data.get(QC_STATUS_KEY, "Unknown")
-    qc_messages = sample_data.get(QC_MESSAGES_KEY, "")
+    qc_messages = filter_qc_messages(sample_data.get(QC_MESSAGES_KEY, ""))
 
     if qc_status.upper() == "PASS":
         # For PASS samples, leave QUALITY_ANALYSIS column blank
         return ""
 
+    if qc_status.upper() == "FAIL" and wzx_wzy_only_failure(qc_messages):
+        # O-antigen serogroup couldn't be determined, but this doesn't block typingQC and reports it as a warning rather than the raw FAIL message.
+        return WZX_WZY_WARNING_MESSAGE
+
     elif qc_status.upper() == "WARNING":
         # If sample raises a WARNING in qc_status record the QC_message
         return qc_messages if qc_messages else "SISTR analysis completed with warnings. Please review results manually."
@@ -86,13 +114,16 @@ def extract_sistr_qc(sample_data):
 
 def build_typingQC_message(sample_data, reportable_serovars):
     qc_status = sample_data.get(QC_STATUS_KEY, "Unknown")
-    qc_messages = sample_data.get(QC_MESSAGES_KEY, "")
+    qc_messages = filter_qc_messages(sample_data.get(QC_MESSAGES_KEY, ""))
 
     # Check for H1 antigen warning from SISTR and treat it as an RDS [FAIL]
     if qc_status.upper() == "WARNING" and H1_warning(qc_messages):
         return "[SISTR_FAIL] Serotyping unsuccessful. RESEQUENCING or TRADITIONAL SEROTYPING is advised."
 
-    if qc_status.upper() in ["PASS", "WARNING"]:
+    # A FAIL solely due to missing Wzx/Wzy genes: fall through to the serovar reportability check below and prepend a warning instead of SISTR_FAIL
+    is_wzx_wzy_fail = qc_status.upper() == "FAIL" and wzx_wzy_only_failure(qc_messages)
+
+    if qc_status.upper() in ["PASS", "WARNING"] or is_wzx_wzy_fail:
         # Extract serovar predictions
         serovar = sample_data.get(SEROVAR_KEY, "")
         serovar_cgmlst = sample_data.get(SEROVAR_CGMLST, "")
diff --git a/bin/validate_serotypes.py b/bin/validate_serotypes.py
index 9880265..6200c50 100755
--- a/bin/validate_serotypes.py
+++ b/bin/validate_serotypes.py
@@ -39,28 +39,58 @@ def create_serotype_lookup(sample_data_list):
 
     return serotype_lookup
 
-def determine_validated_serotype(typingqc_message, sample_serotype, approve_verification=False):
-# Determine the validated serotype based on typingQC message and sample serotype.
+# Serovar rename mappings: predicted serovar -> validated reportable name (CDC)
+# Add new entried here as nomenclature changes are required
+SEROVAR_RENAME_MAP = {
+    "Panama": "Panama/Houston",
+    "Sendai": "Miami"
+}
+
+# Quality metrics warnings to append when a rename is applied
+SEROVAR_RENAME_WARNINGS = {
+    "Sendai": "WARNING: Predicted serovar Sendai has been reported as Miami to conform with current CDC serovar nomenclature."
+}
+
+def apply_serovar_rename(serotype, quality_metrics):
+# If serotype matched a knoen rename mappung, return the renamed validated serotype and updated quality_metrics string. Otherwsie return the inputs unchanged.
+    if serotype not in SEROVAR_RENAME_MAP:
+        return serotype, quality_metrics
+
+    renamed = SEROVAR_RENAME_MAP[serotype]
+    warning = SEROVAR_RENAME_WARNINGS.get(serotype)
+
+    if warning:
+        #Append warning to existing quality_metics content if present
+        updated_metrics = f"{quality_metrics}; {warning}" if quality_metrics.strip() else warning
+    else:
+        updated_metrics = quality_metrics
+
+    return renamed, updated_metrics
+
+def determine_validated_serotype(typingqc_message, sample_serotype, quality_metrics, approve_verification=False):
+# Determine the validated serotype based on typingQC message and sample serotype. Returns validated_serotype, updated_quality_metrics
     typingqc_upper = str(typingqc_message).upper()
 
     if 'FAIL' in typingqc_upper:
-        return 'pending'
+        return 'pending', quality_metrics
+
     elif 'WARNING' in typingqc_upper:
         if approve_verification:
             # If approving verification, treat like PASS
             if not sample_serotype or sample_serotype.strip() == '':
-                return ''
-            return sample_serotype
+                return '', quality_metrics
+            return apply_serovar_rename(sample_serotype, quality_metrics)
         else:
             # Default behavior for warnings
-            return 'verification needed'
+            return 'verification needed', quality_metrics
+
     elif 'PASS' in typingqc_upper:
         # If no serotype provided, leave blank
         if not sample_serotype or sample_serotype.strip() == '':
-            return ''
-        return sample_serotype
+            return '', quality_metrics
+        return apply_serovar_rename(sample_serotype, quality_metrics)
     else:
-        return 'unknown'
+        return 'unknown', quality_metrics
 
 def find_column_indices(header):
 # Find the indices of important columns in the CSV header.
@@ -68,6 +98,7 @@ def find_column_indices(header):
         'sample': None,
         'sample_name': None,
         'typingqc_message': None,
+        'quality_metrics': None,
         'validated_serotype': None
     }
 
@@ -79,13 +110,15 @@ def find_column_indices(header):
             indices['sample_name'] = i
         elif col_lower == 'typingqc_message':
             indices['typingqc_message'] = i
+        elif col_lower == 'quality_metrics':
+            indices['quality_metrics'] = i
         elif col_lower == 'validated_serotype':
             indices['validated_serotype'] = i
 
     return indices
 
 def process_csv_file(input_path, serotype_lookup, output_path, approve_verification=False):
-# Process the CSV file and add validated serotype column.
+    # Process the CSV file and add validated serotype column.
     rows = []
 
     with input_path.open('r', newline='', encoding='utf-8') as csvfile:
@@ -123,19 +156,27 @@ def process_csv_file(input_path, serotype_lookup, output_path, approve_verificat
             if col_indices['typingqc_message'] is not None and len(row) > col_indices['typingqc_message']:
                 typingqc_message = row[col_indices['typingqc_message']]
 
+            # Get existing quality_metrics value
+            quality_metrics = ''
+            if col_indices['quality_metrics'] is not None and len(row) > col_indices['quality_metrics']:
+                quality_metrics = row[col_indices['quality_metrics']]
+
             # Get the serotype for this sample
             sample_serotype = serotype_lookup.get(sample_id, '')
 
-            # Determine validated serotype
-            validated_serotype = determine_validated_serotype(
+            # Determine validated serotype and updated quality_metrics
+            validated_serotype, updated_quality_metrics = determine_validated_serotype(
                 typingqc_message,
                 sample_serotype,
-                approve_verification
+                quality_metrics,
+                approve_verification,
             )
 
-            # Set the validated serotype in the appropriate column
+            # Write validated serotype and (possibly updated) quality_metrics back to row
             if col_indices['validated_serotype'] is not None:
                 row[col_indices['validated_serotype']] = validated_serotype
+            if col_indices['quality_metrics'] is not None:
+                row[col_indices['quality_metrics']] = updated_quality_metrics
 
             rows.append(row)
 
diff --git a/tests/data/CAMP001.flat_sample.json.gz b/tests/data/CAMP001.flat_sample.json.gz
index d672733..5c83cf0 100644
Binary files a/tests/data/CAMP001.flat_sample.json.gz and b/tests/data/CAMP001.flat_sample.json.gz differ
diff --git a/tests/data/EA001.flat_sample.json.gz b/tests/data/EA001.flat_sample.json.gz
index c9db6c0..26b9fe7 100644
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diff --git a/tests/data/EC001.flat_sample.json.gz b/tests/data/EC001.flat_sample.json.gz
index 7e16674..c632695 100644
Binary files a/tests/data/EC001.flat_sample.json.gz and b/tests/data/EC001.flat_sample.json.gz differ
diff --git a/tests/data/EC002.flat_sample.json.gz b/tests/data/EC002.flat_sample.json.gz
index 1a0d5ce..b0dc1c7 100644
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diff --git a/tests/data/EC004.flat_sample.json.gz b/tests/data/EC004.flat_sample.json.gz
index efbd668..da1d4c9 100644
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diff --git a/tests/data/EC005.flat_sample.json.gz b/tests/data/EC005.flat_sample.json.gz
index ef66afb..330f109 100644
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diff --git a/tests/data/EC006.flat_sample.json.gz b/tests/data/EC006.flat_sample.json.gz
index 13d262a..ff6d24c 100644
Binary files a/tests/data/EC006.flat_sample.json.gz and b/tests/data/EC006.flat_sample.json.gz differ
diff --git a/tests/data/EC007.flat_sample.json.gz b/tests/data/EC007.flat_sample.json.gz
index acc4142..e381c1c 100644
Binary files a/tests/data/EC007.flat_sample.json.gz and b/tests/data/EC007.flat_sample.json.gz differ
diff --git a/tests/data/LIST001.flat_sample.json.gz b/tests/data/LIST001.flat_sample.json.gz
index c898be9..f81985a 100644
Binary files a/tests/data/LIST001.flat_sample.json.gz and b/tests/data/LIST001.flat_sample.json.gz differ
diff --git a/tests/data/SALM001.flat_sample.json.gz b/tests/data/SALM001.flat_sample.json.gz
index 2823d99..5a2603b 100644
Binary files a/tests/data/SALM001.flat_sample.json.gz and b/tests/data/SALM001.flat_sample.json.gz differ
diff --git a/tests/data/SALM002.flat_sample.json.gz b/tests/data/SALM002.flat_sample.json.gz
index e779a3d..81ca2d7 100644
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diff --git a/tests/data/SALM003.flat_sample.json.gz b/tests/data/SALM003.flat_sample.json.gz
index b5fb15b..bfc6cf5 100644
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diff --git a/tests/data/SALM004.flat_sample.json.gz b/tests/data/SALM004.flat_sample.json.gz
index fbfd51d..dc500a6 100644
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diff --git a/tests/data/SALM005.flat_sample.json.gz b/tests/data/SALM005.flat_sample.json.gz
index 35947d5..f2afbf8 100644
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diff --git a/tests/data/SALM007.flat_sample.json.gz b/tests/data/SALM007.flat_sample.json.gz
index a187676..c711a19 100644
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diff --git a/tests/data/SALM008.flat_sample.json.gz b/tests/data/SALM008.flat_sample.json.gz
index 7c5e090..415fffe 100644
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diff --git a/tests/data/SALM009.flat_sample.json.gz b/tests/data/SALM009.flat_sample.json.gz
index db0438a..f81819b 100644
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diff --git a/tests/data/SALM010.flat_sample.json.gz b/tests/data/SALM010.flat_sample.json.gz
index e5f6dca..291094a 100644
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diff --git a/tests/data/SALM011.flat_sample.json.gz b/tests/data/SALM011.flat_sample.json.gz
index 58c4a57..1524f95 100644
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diff --git a/tests/data/SALM012.flat_sample.json.gz b/tests/data/SALM012.flat_sample.json.gz
index 3e7bd95..5f8fdf5 100644
Binary files a/tests/data/SALM012.flat_sample.json.gz and b/tests/data/SALM012.flat_sample.json.gz differ
diff --git a/tests/data/SALM013.flat_sample.json.gz b/tests/data/SALM013.flat_sample.json.gz
new file mode 100644
index 0000000..983e6ca
Binary files /dev/null and b/tests/data/SALM013.flat_sample.json.gz differ
diff --git a/tests/data/SALM014.flat_sample.json.gz b/tests/data/SALM014.flat_sample.json.gz
new file mode 100644
index 0000000..d3a3377
Binary files /dev/null and b/tests/data/SALM014.flat_sample.json.gz differ
diff --git a/tests/data/samplesheets/samplesheet1.csv b/tests/data/samplesheets/samplesheet1.csv
index c89375f..8562f92 100644
--- a/tests/data/samplesheets/samplesheet1.csv
+++ b/tests/data/samplesheets/samplesheet1.csv
@@ -1,8 +1,8 @@
 sample,sample_name,mikrokondo_data,predicted_identification_name,qc_status_overall,predicted_primary_type_name
-SAMPLE1,EC001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC001.flat_sample.json.gz,Escherichia coli,PASSED,O157:H7
-SAMPLE2,EC002,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC002.flat_sample.json.gz,Escherichia coli,PASSED,O55:H7
-SAMPLE3,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM001.flat_sample.json.gz,Salmonella houtenae,PASSED,IV Y:gz51:-
-SAMPLE4,SALM004,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM004.flat_sample.json.gz,Salmonella enterica,PASSED,Gallinarum
-SAMPLE5,SALM003,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM003.flat_sample.json.gz,Salmonella enterica,FAILED,Kentucky
-SAMPLE6,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED,
-SAMPLE7,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED,
+SAMPLE1,EC001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC001.flat_sample.json.gz,Escherichia coli,PASSED,O157:H7
+SAMPLE2,EC002,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC002.flat_sample.json.gz,Escherichia coli,PASSED,O55:H7
+SAMPLE3,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM001.flat_sample.json.gz,Salmonella houtenae,PASSED,IV Y:gz51:-
+SAMPLE4,SALM004,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM004.flat_sample.json.gz,Salmonella enterica,PASSED,Gallinarum
+SAMPLE5,SALM003,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM003.flat_sample.json.gz,Salmonella enterica,FAILED,Kentucky
+SAMPLE6,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED,
+SAMPLE7,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED,
diff --git a/tests/data/samplesheets/samplesheet_ectyper.csv b/tests/data/samplesheets/samplesheet_ectyper.csv
index 20ea5f1..12e5c6e 100644
--- a/tests/data/samplesheets/samplesheet_ectyper.csv
+++ b/tests/data/samplesheets/samplesheet_ectyper.csv
@@ -1,8 +1,8 @@
 sample,sample_name,mikrokondo_data,predicted_identification_name,qc_status_overall,predicted_primary_type_name
-SAMPLE1,EC001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC001.flat_sample.json.gz,Escherichia coli,PASSED,O157:H7
-SAMPLE2,EC002,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC002.flat_sample.json.gz,Escherichia coli,PASSED,O55:H7
-SAMPLE3,EC004,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC004.flat_sample.json.gz,Escherichia coli,FAILED,O103:H2
-SAMPLE4,EC005,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC005.flat_sample.json.gz,Escherichia coli,PASSED,O2/O137:H41
-SAMPLE5,EC006,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC006.flat_sample.json.gz,Escherichia coli,PASSED,-:H21
-SAMPLE6,EC007,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC007.flat_sample.json.gz,Escherichia coli,PASSED,O111:H8
-SAMPLE8,EA001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EA001.flat_sample.json.gz,Escherichia coli,PASSED,
+SAMPLE1,EC001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC001.flat_sample.json.gz,Escherichia coli,PASSED,O157:H7
+SAMPLE2,EC002,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC002.flat_sample.json.gz,Escherichia coli,PASSED,O55:H7
+SAMPLE3,EC004,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC004.flat_sample.json.gz,Escherichia coli,FAILED,O103:H2
+SAMPLE4,EC005,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC005.flat_sample.json.gz,Escherichia coli,PASSED,O2/O137:H41
+SAMPLE5,EC006,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC006.flat_sample.json.gz,Escherichia coli,PASSED,-:H21
+SAMPLE6,EC007,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC007.flat_sample.json.gz,Escherichia coli,PASSED,O111:H8
+SAMPLE8,EA001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EA001.flat_sample.json.gz,Escherichia coli,PASSED,
diff --git a/tests/data/samplesheets/samplesheet_exclusions.csv b/tests/data/samplesheets/samplesheet_exclusions.csv
index 1073149..d9b34ee 100644
--- a/tests/data/samplesheets/samplesheet_exclusions.csv
+++ b/tests/data/samplesheets/samplesheet_exclusions.csv
@@ -1,5 +1,5 @@
 sample,sample_name,mikrokondo_data,predicted_identification_name,qc_status_overall,predicted_primary_type_name
-SAMPLE1,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM001.flat_sample.json.gz,Salmonella houtenae,PASSED,"IV Y:g,z51:-"
-SAMPLE2,SALM004,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM004.flat_sample.json.gz,Salmonella enterica,PASSED,Gallinarum
-SAMPLE4,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED,
-SAMPLE5,CAMP001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/CAMP001.flat_sample.json.gz,Campylobacter_coli,FAILED,
+SAMPLE1,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM001.flat_sample.json.gz,Salmonella houtenae,PASSED,"IV Y:g,z51:-"
+SAMPLE2,SALM004,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM004.flat_sample.json.gz,Salmonella enterica,PASSED,Gallinarum
+SAMPLE4,LIST001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/LIST001.flat_sample.json.gz,Listeria monocytogenes,PASSED,
+SAMPLE5,CAMP001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/CAMP001.flat_sample.json.gz,Campylobacter_coli,FAILED,
diff --git a/tests/data/samplesheets/samplesheet_incorrectJSON.csv b/tests/data/samplesheets/samplesheet_incorrectJSON.csv
index 1265cf8..8ad83b9 100644
--- a/tests/data/samplesheets/samplesheet_incorrectJSON.csv
+++ b/tests/data/samplesheets/samplesheet_incorrectJSON.csv
@@ -1,2 +1,2 @@
 sample,sample_name,mikrokondo_data,predicted_identification_name,qc_status_overall,predicted_primary_type_name
-SAMPLE1,SALM002,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM001.flat_sample.json.gz,Salmonella_houtenae,PASSED,Souza|Madjorio|Liverpool
+SAMPLE1,SALM002,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM001.flat_sample.json.gz,Salmonella_houtenae,PASSED,Souza|Madjorio|Liverpool
diff --git a/tests/data/samplesheets/samplesheet_sequence.csv b/tests/data/samplesheets/samplesheet_sequence.csv
index 145849d..fd55b6f 100644
--- a/tests/data/samplesheets/samplesheet_sequence.csv
+++ b/tests/data/samplesheets/samplesheet_sequence.csv
@@ -1,6 +1,6 @@
 sample,sample_name,mikrokondo_data,predicted_identification_name,qc_status_overall,predicted_primary_type_name
-SAMPLE1,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM001.flat_sample.json.gz,Salmonella_houtenae,PASSED,"IV Y:g,z51:-"
-SAMPLE2,SALM002,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM002.flat_sample.json.gz,Salmonella_enterica,FAILED,Souza|Madjorio|Liverpool
-SAMPLE4,SALM005,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM005.flat_sample.json.gz,Salmonella_enterica,PASSED,Paratyphi A
-SAMPLE6,CAMP001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/CAMP001.flat_sample.json.gz,Campylobacter coli,FAILED,
-SAMPLE7,EC004,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/EC004.flat_sample.json.gz,Escherichia coli,FAILED,O103:H2
+SAMPLE1,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM001.flat_sample.json.gz,Salmonella_houtenae,PASSED,"IV Y:g,z51:-"
+SAMPLE2,SALM002,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM002.flat_sample.json.gz,Salmonella_diarizonae,FAILED,"IIIb T:z35:z35"
+SAMPLE4,SALM005,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM005.flat_sample.json.gz,Salmonella_enterica,PASSED,Paratyphi A
+SAMPLE6,CAMP001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/CAMP001.flat_sample.json.gz,Campylobacter coli,FAILED,
+SAMPLE7,EC004,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/EC004.flat_sample.json.gz,Escherichia coli,FAILED,O103:H2
diff --git a/tests/data/samplesheets/samplesheet_sistr.csv b/tests/data/samplesheets/samplesheet_sistr.csv
index c6fd300..3f78501 100644
--- a/tests/data/samplesheets/samplesheet_sistr.csv
+++ b/tests/data/samplesheets/samplesheet_sistr.csv
@@ -1,10 +1,12 @@
 sample,sample_name,mikrokondo_data,predicted_identification_name,qc_status_overall,predicted_primary_type_name
-SAMPLE1,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM001.flat_sample.json.gz,Salmonella_houtenae,PASSED,"IV Y:g,z51:-"
-SAMPLE2,SALM002,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM002.flat_sample.json.gz,Salmonella_enterica,FAILED,Souza|Madjorio|Liverpool
-SAMPLE3,SALM005,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM005.flat_sample.json.gz,Salmonella_enterica,PASSED,Paratyphi A
-SAMPLE4,SALM008,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM008.flat_sample.json.gz,Salmonella enterica,PASSED,IIIb Y:z52:z
-SAMPLE5,SALM009,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM009.flat_sample.json.gz,Salmonella_enterica,PASSED,Senftenberg
-SAMPLE6,SALM010,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM010.flat_sample.json.gz,Salmonella enterica,PASSED,Umhlali|Adime|Birkenhead|Kivu|Norwich|Kastrup|Menston|Garoli|Daytona|Mkamba|Winston|Nigeria|Oyonnax|Eschweiler|Tienba|Planckendael|Massilia|Wohlen|Brindisi|Adamstua|Heerlen|Sharon|Remete
-SAMPLE7,SALM007,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM007.flat_sample.json.gz,Salmonella_enterica,PASSED,
-SAMPLE8,SALM011,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM011.flat_sample.json.gz,Salmonella enterica,PASSED,Adelaide|Agodi
-SAMPLE9,SALM012,https://raw.githubusercontent.com/phac-nml/typingQC/dev/tests/data/SALM012.flat_sample.json.gz,Salmonella_enterica,PASSED,Ibadan|Mississippi
+SAMPLE1,SALM001,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM001.flat_sample.json.gz,Salmonella_houtenae,PASSED,"IV Y:g,z51:-"
+SAMPLE2,SALM002,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM002.flat_sample.json.gz,Salmonella_diarizonae,FAILED,"IIIb T:z35:z35"
+SAMPLE3,SALM005,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM005.flat_sample.json.gz,Salmonella_enterica,PASSED,Paratyphi A
+SAMPLE4,SALM008,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM008.flat_sample.json.gz,Salmonella enterica,PASSED,IIIb Y:z52:z
+SAMPLE5,SALM009,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM009.flat_sample.json.gz,Salmonella_enterica,PASSED,Senftenberg
+SAMPLE6,SALM010,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM010.flat_sample.json.gz,Salmonella enterica,PASSED,Umhlali|Adime|Birkenhead|Kivu|Norwich|Kastrup|Menston|Garoli|Daytona|Mkamba|Winston|Nigeria|Oyonnax|Eschweiler|Tienba|Planckendael|Massilia|Wohlen|Brindisi|Adamstua|Heerlen|Sharon|Remete
+SAMPLE7,SALM007,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM007.flat_sample.json.gz,Salmonella_enterica,PASSED,
+SAMPLE8,SALM011,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM011.flat_sample.json.gz,Salmonella enterica,PASSED,Adelaide|Agodi
+SAMPLE9,SALM012,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM012.flat_sample.json.gz,Salmonella_enterica,PASSED,Ibadan|Mississippi
+SAMPLE10,SALM013,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM013.flat_sample.json.gz,Salmonella enterica,PASSED,Panama
+SAMPLE11,SALM014,https://raw.githubusercontent.com/phac-nml/typingQC/update/tests/data/SALM014.flat_sample.json.gz,Salmonella enterica,PASSED,Sendai
diff --git a/tests/pipelines/main.nf.test b/tests/pipelines/main.nf.test
index 9caf0c1..249a01b 100644
--- a/tests/pipelines/main.nf.test
+++ b/tests/pipelines/main.nf.test
@@ -92,10 +92,10 @@ nextflow_pipeline {
             assert values[0] == "SAMPLE2"
             assert values[1] == "SALM002"
             assert values[2].contains("[SEQ_FAIL] Sample may be contaminated.")
-            assert values[3].contains("[FAILED n50_value] 2038")
-            assert values[3].contains("[FAILED nr_contigs] 1712")
-            assert values[3].contains("[FAILED length] 3525632")
-            assert values[3].contains("[FAILED checkm_contamination] 4.2")
+            assert values[3].contains("[FAILED n50_value] 87033")
+            assert values[3].contains("[FAILED nr_contigs] 257")
+            assert values[3].contains("[FAILED length] 6443773")
+            assert values[3].contains("[FAILED checkm2_contamination] 6.35")
 
             def outputFile2 = path("$launchDir/results/sequenceqc/EC004_sequenceQC.csv")
             assert outputFile2.exists()
@@ -181,6 +181,7 @@ nextflow_pipeline {
             assert path("$launchDir/results/merge/TypingQC_inputs.csv").exists()
             assert path("$launchDir/results/sequenceqc/SALM002_sequenceQC.csv").exists()
             assert path("$launchDir/results/sistrqc/SALM012_sistrQC.csv").exists()
+            assert path("$launchDir/results/sistrqc/SALM014_sistrQC.csv").exists()
 
             def outputFile_salm = path("$launchDir/results/sistrqc/SALM001_sistrQC.csv")
             assert outputFile_salm.exists()
@@ -291,9 +292,60 @@ nextflow_pipeline {
             assert header_salm8 == ["sample", "sample_name", "typingQC_message", "quality_metrics"]
             assert values_salm8[0] == "SAMPLE2"
             assert values_salm8[1] == "SALM002"
-            assert values_salm8[2].contains("[SISTR_FAIL] Serotyping unsuccessful. RESEQUENCING or TRADITIONAL SEROTYPING is advised.")
-            assert values_salm8[3].contains("FAIL: Large number of cgMLST330 loci missing (n=149 > 30)")
-        }
+            assert values_salm8[2].contains("[TYPE_FAIL]")
+            assert values_salm8[3].contains("WARNING: Input genome size (6443773 bp) not within expected range of 4000000-6000000 (bp) for Salmonella")
+
+            def outputFile_salm9 = path("$launchDir/results/sistrqc/SALM013_sistrQC.csv")
+            assert outputFile_salm9.exists()
+
+            // Read CSV into rows
+            def csv_salm9 = outputFile_salm9.readLines()
+            def header_salm9 = csv_salm9[0].split(",")
+            def values_salm9 = csv_salm9[1].split(",",4) // Only split first 3 commas (4 columns)
+
+            assert header_salm9 == ["sample", "sample_name", "typingQC_message", "quality_metrics"]
+            assert values_salm9[0] == "SAMPLE10"
+            assert values_salm9[1] == "SALM013"
+            assert values_salm9[2].contains("[SISTR_PASS]")
+
+            def outputFile_salm10 = path("$launchDir/results/sistrqc/SALM014_sistrQC.csv")
+            assert outputFile_salm10.exists()
+
+            // Read CSV into rows
+            def csv_salm10 = outputFile_salm10.readLines()
+            def header_salm10 = csv_salm10[0].split(",")
+            def values_salm10 = csv_salm10[1].split(",",4) // Only split first 3 commas (4 columns)
+
+            assert header_salm10 == ["sample", "sample_name", "typingQC_message", "quality_metrics"]
+            assert values_salm10[0] == "SAMPLE11"
+            assert values_salm10[1] == "SALM014"
+            assert values_salm10[2].contains("[SISTR_PASS]")
+            assert values_salm10[3].contains("WARNING: Wzx/Wzy genes missing. Cannot determine O-antigen serogroup.")
+
+            // check TypingQC_report csv file to ensure serovar updates are successful for sistrQC
+
+            def outputFileQC = path("$launchDir/results/serotype/TypingQC_report.csv")
+            assert outputFileQC.exists()
+
+            // Read CSV into rows
+            def csvQC = outputFileQC.readLines()
+            def headerQC = csvQC[0].split(",")
+            def valuesQC = csvQC[2].split(",", 7)
+            def valuesQC2 = csvQC[3].split(",", 7)
+
+            assert headerQC == ["sample", "sample_name", "typingQC_message", "quality_metrics", "Validated_Toxins", "Validated_STXSubtypes", "Validated_Serotype"]
+            assert valuesQC[0] == "SAMPLE10"
+            assert valuesQC[1] == "SALM013"
+            assert valuesQC[2].contains("[SISTR_PASS]")
+            assert valuesQC[3].isEmpty()
+            assert valuesQC[6].contains("Panama/Houston")
+            assert valuesQC2[0] == "SAMPLE11"
+            assert valuesQC2[1] == "SALM014"
+            assert valuesQC2[2].contains("[SISTR_PASS]")
+            assert valuesQC2[3].contains("WARNING: Wzx/Wzy genes missing. Cannot determine O-antigen serogroup.; WARNING: Predicted serovar Sendai has been reported as Miami to conform with current CDC serovar nomenclature.")
+            assert valuesQC2[4].isEmpty()
+            assert valuesQC2[6].contains("Miami")
+            }
     }
 
     test("SISTR module without reportable serovar input"){