P18 Audit on compliance with the preventive measures on Clostridioides difficile

Background

Clostridioides (Clostridium) difficile persists to be a significant pathogen for healthcare acquired infections. Antibiotic usage is the main cause for the overgrowth of this organism and resulting in C. difficile infections (CDI). Other factors that are known to contribute are usage of proton pump inhibitors, laxatives usage and poor compliance with infection prevention control guidance in health care settings. The audit was carried out to analyse if the local guidance is followed on recognition of new onset of diarrhoea in an inpatient.

Objectives

Analyse compliance rate with our local guidance in Mayo University Hospital to be followed when inpatient has a new onset of diarrhoea. This to include reviewing of medications; such as laxatives, proton pump inhibitor (PPI) and antibiotics; prompt isolation and CDI precautions were commenced, samples sent for testing and commencing stool chart.

Methods

The data of patients was collected by reviewing the chart and collected data was stored and analysed using excel spreadsheet.

Results

The audit was carried out over a 4 month period from 10.06.22 until 14.10.22 in 7 wards. 31 patients were recorded as having diarrhoea with 69% (n=19) female and 39% (n=12) males during their inpatient stay. Majority of the recorded patients, which is 29% (n=9) were in medical male ward. The age of the patients ranged from 24 to 92 years of age with a median of 68 years. The median number of days from the admission until onset of diarrhoea was 5. On identifying new onset of diarrhoea, 32% (n=10) had recorded documentation of medications review. Out of 31 patients, 90% (n=28) were on PPI and only 21% (n=6) of them were held, while 7% (n=2) of them had their medication reviewed and was advised to continue the PPI as for clinical indication. Ninety percent (n=28) of patients were on regular laxatives and after the onset of diarrhoea only 39% (n=11) had the laxatives held. Of all the recorded patients, 32% (n=10) of patients had documentation of medication review and 19% (n=6) were continued on antibiotics for organisms other than CDI after discussion with clinical microbiology team. Fifty-five percent (n=17) of patients were isolated after the onset of new diarrhoea while the rest remained in a shared bay as per the discussion with clinical teams, while awaiting the stool results. Sixty-five percent (n=20) had a stool culture sent for CDI testing after the onset of new diarrhoea. Of these patients, 25% (n=5) tested positive for C. difficile.

Conclusions

Compliance to local guidance should be followed more strictly to avoid development of hospital acquired CDI and to prevent outbreaks in the healthcare setting.

Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) α-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of "extra-target" RAS suggests the need for RAS screening in all three DAA target regions.

Deep-sequencing study of HCV G4a resistance-associated substitutions in Egyptian patients failing DAA treatment

PURPOSE

 To study resistance-associated substitutions using next-generation sequencing in Egyptian hepatitis C virus-infected patients failing direct-acting antiviral treatment.

METHODS

 The current study describes three cases of treatment failure in patients referred to Zagazig Viral Hepatitis Treatment Center (ZVHTC), Sharkia Governorate, Egypt. RAS were identified and characterized using deep sequencing. The first patient had breakthrough while receiving a daclatasvir (DCV)+sofosbuvir (SOF) regimen, patient 2 relapsed after treatment with DCV+SOF+ribavirin (RBV), and patient 3 relapsed after DCV+SOF therapy. A serum sample was collected from each patient at failure and sent to Vall d'Hebron Research Institute at Hospital Universitari Vall d'Hebron in Barcelona (Spain) for deep-sequencing study to identify and characterize the RAS present in the samples.

RESULTS

 The following were identified: L28M, L30S and L28M+L30S in patient 1, L30R in patient 2, and R155C, D168E, L28M, L30H, L30S, L28M+L30H, and L28M+L30S in patient 3.

CONCLUSION

To the best of our knowledge, this is the first report from Egypt of patients failing DAA-based therapy, describing the associated RAS. This information will be of help to understand the natural history of HCV in Egyptian patients and guide the proper choice of retreatment protocols.

New hepatitis C virus genotype 1 subtype naturally harbouring resistance-associated mutations to NS5A inhibitors

Hepatitis C virus (HCV) is a highly divergent virus currently classified into seven major genotypes and 86 subtypes (ICTV, June 2017), which can have differing responses to therapy. Accurate genotyping/subtyping using high-resolution HCV subtyping enables confident subtype identification, identifies mixed infections and allows detection of new subtypes. During routine genotyping/subtyping, one sample from an Equatorial Guinea patient could not be classified into any of the subtypes. The complete genomic sequence was compared to reference sequences by phylogenetic and sliding window analysis. Resistance-associated substitutions (RASs) were assessed by deep sequencing. The unclassified HCV genome did not belong to any of the existing genotype 1 (G1) subtypes. Sliding window analysis along the complete genome ruled out recombination phenomena suggesting that it belongs to a new HCV G1 subtype. Two NS5A RASs (L31V+Y93H) were found to be naturally combined in the genome which could limit treatment possibilities in patients infected with this subtype.

Baseline hepatitis C virus resistance-associated substitutions present at frequencies lower than 15% may be clinically significant

BACKGROUND

Controversy is ongoing about whether a minority mutant present at frequencies below 15% may be clinically relevant and should be considered to guide treatment.

METHODS

Resistance-associated substitution (RAS) studies were performed in patients before and at failure of antiviral treatments using Next-generation hepatitis C virus (HCV) sequencing (NGS).

RESULTS

We have found two patients with genotype 1a infection having RAS in 3.5%-7.1% of the viral population at baseline that were selected during ledipasvir + sofosbuvir treatment. Co-selection of RAS located in a region not directly affected by the antiviral treatment also occurred. This observation calls into question, the recommendations to guide RAS-based direct-acting antiviral (DAA) treatment only when RAS are present in >15% of the sequences generated.

CONCLUSION

Our results suggests that RAS study should include all three HCV DAA target proteins and minority mutants should be considered as clinically relevant.

Assessment of a Novel Automatic Real-Time PCR Assay on the Cobas 4800 Analyzer as a Screening Platform for Hepatitis C Virus Genotyping in Clinical Practice: Comparison with Massive Sequencing

The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of high-resolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by transferring non-1a/1b samples to a center where HRCS is available, if further characterization is needed.