Long-term intensive care unit outbreak of carbapenemase-producing organisms associated with contaminated sink drains.

BACKGROUND: Between 2018 and 2022, a Belgian tertiary care hospital faced a growing issue with acquiring carbapenemase-producing organisms (CPO), mainly VIM-producing P. aeruginosa (PA-VIM) and NDM-producing Enterobacterales (CPE-NDM) among hospitalized patients in the adult intensive care unit (ICU). AIM: To investigate this ICU long-term CPO outbreak involving multiple species and a persistent environmental reservoir. METHODS: Active case finding, environmental sampling, whole-genome sequencing (WGS) analysis of patient and environmental strains, and implemented control strategies were described in this study. FINDINGS: From 2018 to 2022, 37 patients became colonized or infected with PA-VIM and/or CPE-NDM during their ICU stay. WGS confirmed the epidemiological link between clinical and environmental strains collected from the sink drains with clonal strain dissemination and horizontal gene transfer mediated by plasmid conjugation and/or transposon jumps. Environmental disinfection by quaternary ammonium-based disinfectant and replacement of contaminated equipment failed to eradicate environmental sources. Interestingly, efflux pump genes conferring resistance to quaternary ammonium compounds were widespread in the isolates. As removing sinks was not feasible, a combination of a foaming product degrading the biofilm and foaming disinfectant based on peracetic acid and hydrogen peroxide has been evaluated and has so far prevented recolonization of the proximal sink drain by CPO. CONCLUSION: The persistence in the hospital environment of antibiotic- and disinfectant-resistant bacteria with the ability to transfer mobile genetic elements poses a serious threat to ICU patients with a risk of shifting towards an endemicity scenario. Innovative strategies are needed to address persistent environmental reservoirs and prevent CPO transmission.

Hepatitis C virus among blood donors in Lubumbashi, DRC: Seroprevalence and molecular characterisation.

OBJECTIVES: To date, no study has been done yet on the distribution of Hepatitis C virus genotypes in Lubumbashi, Democratic Republic of Congo. The objective of this work was to determine the seroprevalence and study the distribution of hepatitis C virus (HCV) genotypes among blood donors in Lubumbashi, DRC. METHODS: This was a cross-sectional descriptive study among blood donors. The detection of anti-HCV antibodies was carried out by rapid diagnostic test (RDT) then confirmed by Chemiluminescent immuno-assay (CLIA). Viral load was determined by Nucleic Acid Amplification test (NAT) on Panther system and genotyping by Next Generation Sequencing (NGS) on Sentosa platform. RESULTS: The obtained seroprevalence was 4.8%. Genotypes 3a (5.0%), 4 (90.0%) and 7 (5.0%) and a few drug resistance mutations were identified in the study population. Significant disturbances of some studied biochemical parameters (HDL-cholesterol, direct bilirubin, transaminases, ALP, GGT and albumin) have been observed in positive HCV blood donors. Irregular family and volunteer donors have been found as the socio-demographic characteristics associated with hepatitis C. CONCLUSION: With a seroprevalence of 4.8% obtained among blood donors, Lubumbashi is in an area with medium endemicity for HCV, highlighting the need to implement strategies aiming to improve transfusion safety among blood recipients in Lubumbashi. This study reports for the first time the presence of HCV strains of genotypes 3a, 4 and 7. These results might allow better therapeutic management of HCV infections and contribute to the development of the mapping of HCV genotypes in Lubumbashi and DRC as well.

Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria.

The rpoB gene codes for the RNA polymerase ß subunit, which is the target of rifampicin, an essential drug in the treatment of tuberculosis and other mycobacterial infections. This gene is present in all bacteria, but its length and nucleotide sequence vary between bacterial species, including mycobacteria. Mutations in the rpoB gene alter the structure of this protein and cause drug resistance. To describe the resistance-associated mutations, the scientific and medical communities have been using, since 1993, a numbering system based on the Escherichia coli sequence annotation. Using E. coli reference for describing mutations in mycobacteria leads to misunderstandings, particularly with the increasing use of whole genome sequencing, which brought an alternative numbering system based on the Mycobacterium tuberculosis rpoB sequence. We propose using a consensus numbering system for the reporting of resistance mutations based on the reference genomes from the species interrogated (such as strain H37Rv for M. tuberculosis). This manuscript provides the necessary figures and tables allowing researchers, microbiologists and clinicians to easily convert other annotation systems into one common language.

Genotypic evaluation of etravirine sensitivity of clinical human immunodeficiency virus type 1 (HIV-1) isolates carrying resistance mutations to nevirapine and efavirenz.

BACKGROUND: Etravirine is a second-generation non-nucleoside reverse transcriptase inhibitor (NNRTI) with a pattern of resistance mutations quite distinct from the current NNRTIs. METHODS: We collected all routine samples of HIV-1 patients followed in the AIDS reference laboratory of UCLouvain (in 2006 and 2007) carrying resistance-associated mutations to nevirapine (NVP) or efavirenz (EFV). The sensitivity to Etravirine was estimated using three different drug resistance algorithms: ANRS (July 2008), IAS (December 2008) and Stanford (November 2008). We also verified whether the mutations described as resistance mutations are not due to virus polymorphisms by the study of 58 genotypes of NNRTI-naive patients. RESULTS: Sixty one samples harboured resistance to NVP and EFV: 41/61 had at least one resistance mutation to Etravirine according to ANRS-IAS algorithms; 42/61 samples had at least one resistance mutation to Etravirine according to the Stanford algorithm. 48 and 53 cases were fully sensitive to Etravirine according to ANRS-IAS and Stanford algorithms, respectively. Three cases harboured more than three mutations and presented a pattern of high-degree resistance to Etravirine according to ANRS-IAS algorithm, while one case harboured more than three mutations and presented high degree resistance to Etravirine according to the Stanford algorithm. The V1061 and V179D mutations were more frequent in the ARV-naive group than in the NNRTI-experienced one. CONCLUSIONS: According to the currently available algorithms, Etravirine can still be used in the majority of patients with virus showing resistance to NVP and/or EFV, if a combination of other active drugs is included.

HIV-1 proviral resistance mutations: usefulness in clinical practice.

OBJECTIVES: Transmitted HIV strains may harbour drug resistance mutations. HIV-1 drug resistance mutations are currently detected in plasma viral RNA. HIV-1 proviral DNA could be an alternative marker, as it persists in infected cells. METHODS: This was a prospective study assessing the prevalence and persistence of HIV-1 drug resistance mutations in DNA from CD4 cells before and after protease inhibitor (PI)- or nonnucleoside reverse transcriptase inhibitor (NNRTI)-based therapy initiation in 69 drug-naïve patients. RESULTS: Before therapy, 90 and 66% of detected mutations were present in CD4 cells and plasma, respectively. We detected seven key mutations, and four of these (M184M/V, M184M/I, K103K/N and M46M/I) were only found in the cells. When treatment was started, 40 patients were followed; the mutations detected at the naïve stage remained present for at least 1 year. Under successful treatment, new key mutations emerged in CD4 cells (M184I, M184M/I and Y188Y/H). CONCLUSIONS: The proportion of mutations detected in the DNA was statistically significantly higher than that detected in standard RNA genotyping, and these mutations persisted for at least 1 year irrespective of therapy. The pre-existence of resistance mutations did not jeopardise treatment outcome when the drug concerned was not included in the regimen. Analysis of HIV-1 DNA could be useful in chronic infections or when switching therapy in patients with undetectable viraemia.

Definition of clinical threshold for CMV real-time PCR after comparison with PP65 antigenaemia and clinical data.

BACKGROUND: pp65 antigenaemia and real-time PCR are two methods that are used to diagnose CMV infection in its early stages and, thereby, to facilitate initiation of pre-emptive therapy. OBJECTIVES: Firstly, to compare PCR with antigenaemia and clinical outcome in order to define a clinical threshold for starting pre-emptive therapy. Secondly, to study the impact of the transplant recipient's serological status on the viral load and on the cut-offs. STUDY DESIGN: Sixty-two patients were analysed using antigenaemia (APAAP method) and real-time PCR. ROC curves were established with antigenaemia or clinical outcome as reference. Patients were divided into primo-infection or reactivation on the basis of the serological status. RESULTS: PCR correlated better with the clinical data (AUC closer to 1 and best sensitivity, PPV and NPV) than antigenaemia. Furthermore, the performance of qPCR was even better in the reactivation patients. CONCLUSIONS: This work suggests that transplant recipients should be divided according to their serological status. Indeed, replacing antigenaemia by real-time PCR for decisions regarding initiation of pre-emptive therapy is of particular appeal in patients with positive serology. As a result of this work, we have set our clinical threshold at 1500 copies/ml for reactivation.

Seroepidemiology of herpes simplex type 2 in pregnant women in Belgium.

OBJECTIVE: The objective of this study was to study the prevalence of herpes simplex virus (HSV) type 2 in pregnant women in Belgium. STUDY DESIGN: The serum of 1000 consecutive women was collected. HSV-1 and HSV-2 control sera were added to the study. HSV-2 antibodies were tested with the HerpeSelect 2 enzyme-linked immunosorbent assay (ELISA; Focus) based on the use of the recombinant gG-2 antigen. RESULTS: The 21 HSV-2 control subjects were positive. Among the HSV-1 control subjects, 18 were negative and 4 were positive. Among the pregnant women, 80.3% were negative, 1.5% had equivocal results, and 18.2% were positive. No statistical difference was observed according to the origin (European or African) of the women. CONCLUSIONS: The results obtained with the control sera indicate a high sensitivity of the Focus ELISA, as well as a capacity to discriminate between HSV-1/HSV-2 infection. The HSV-2 prevalence in the studied population raises the question of the possible benefit of a specific preventive program in pregnant women.