Evaluation of six commercial and in-house phenotypic tests for detection of AmpC ß-lactamases: is routine detection possible?

Background: Phenotypic characterization of the prevalent AmpC ß-lactamases in clinical isolates is essential for making informed empirical decisions and critical for strengthening antimicrobial stewardship programmes. This study focused on assessing six assays, two in-house and four commercial phenotypic tests for detection of AmpC, to study the feasibility of making its detection a routine diagnostic microbiology laboratory activity. Methods: A total of 116 non-duplicate Gram-negative bacteria that were resistant to third-generation cephalosporins and amoxicillin/clavulanic acid, and resistant or susceptible to piperacillin/tazobactam and carbapenems, were screened by cefoxitin discs for AmpC. These isolates were subjected to two in-house (AmpC Tris-EDTA and disc approximation) methods and four commercial tests: D69C AmpC Detection Set; D72C ESBL, AmpC & Carbapenemase Detection Set; combination disc test: ESBL + AmpC Screen Disc Kit; and AmpC MIC Test Strip for confirmation of AmpC production. Ten whole-genome-sequenced AmpC-confirmed Gram-negative isolates were used as positive controls and one as a negative control. Results: The prevalence of AmpC ß-lactamases was 16%. Escherichia coli was a major carrier of plasmid-mediated AmpC (26.5%), followed by Klebsiella pneumoniae (23.4%). Phenotypically, 61% of AmpCs were detected by Tris-EDTA (accuracy: 73.8%), 76% by disc approximation (accuracy: 89.2%), 75% by the D69C AmpC Detection Set (accuracy: 95.4%), 74% by the D72C AmpC, ESBL & Carbapenemase Detection Set (accuracy: 95.4%), 76% by the combination disc test (accuracy: 95.4%) and 63% by AmpC MIC Test Strip (accuracy: 87.7%). The sensitivity and specificity of D69C were 97.9% and 88.2%, respectively, and 95.9% and 93.8% for the combination disc test, while for the disc approximation test and D72C they were 93.9% and 75%, and 93.9% and 100%, respectively. Screening by cefoxitin screening was less sensitive (75%) and specific (25%). Disc approximation and the combination disc test detect AmpC in Enterobacterales and also Pseudomonas aeruginosa and Acinetobacter species. Conclusions: We recommend the in-house disc approximation test and the commercial D69C, as well as the combination disc test, as excellent tools for detection of AmpC. The cefoxitin test overcalls AmpC and cannot be considered a good stand-alone test for AmpC detection.

Fusarium solani Necrotizing Fasciitis Complicating Treatment for Acute Lymphoblastic Leukemia: A Case Report.

Fungal infections due to Fusarium species are serious albeit rare and mostly occur in severely immunocompromised patients. The prognosis of such infections, especially of disseminated manifestations, is poor as a result of multi-antifungal resistance, particularly to azoles. We report a case of a rapidly progressive necrotizing fasciitis of the foot secondary to Fusarium solani in a young female patient with acute lymphoblastic leukemia on consolidation therapy. Surgical debridement was undertaken and liposomal amphotericin was given as definitive therapy for a total of six weeks followed by secondary prophylaxis that resulted in remarked clinical and radiological improvement. High clinical suspicion, prompt surgical intervention, rapid diagnosis, and timely initiation of appropriate antifungal therapy are crucial for a favorable outcome in this relatively uncommon life-threatening infection.

Favourable outcomes of non-O1, non-O139 Vibrio cholerae bacteraemia in vulnerable populations: a case series.

Background: Non-O1, non-O139 Vibrio cholerae (NOVC) bacteraemia is an uncommon infection and could be associated with life-threatening conditions in susceptible hosts. Definitive management guidelines are lacking. Aim: To describe the clinical spectrum, treatment practices and outcome of NOVC bacteraemia. Methods: Eight patients with NOVC bacteraemia admitted to two large tertiary care hospitals in Oman were identified over a 10-year period (2010-2020). Data were extracted retrospectively from the hospital patient data management. Results: Six (75.0%) patients were male, and the median age of patients was 67.5 years. The majority of cases (87.5%) were not associated with travel and no clear sources were identified. All patients had predisposing factors including diabetes mellitus, chronic liver disease or malignancies. Gastrointestinal symptoms were the predominant manifestations in 75.0% of cases, but diarrhoea was only reported in one patient. Conclusions: Early presentation (median interval from symptom onset to presentation 1.5 days), appropriate management and highly susceptible isolates may have contributed to the favourable outcome, as there were no cases of death or severe course of infection. All patients were discharged home after a median of 9 days of hospitalization.

Basidiobolus omanensis sp. nov. Causing Angioinvasive Abdominal Basidiobolomycosis.

Human infectious fungal diseases are increasing, despite improved hygienic conditions. We present a case of gastrointestinal basidiobolomycosis (GIB) in a 20-year-old male with a history of progressively worsening abdominal pain. The causative agent was identified as a novel Basidiobolus species. Validation of its novelty was established by analysis of the partial ribosomal operon of two isolates from different organs. Phylogeny of ITS and LSU rRNA showed that these isolates belonged to the genus Basidiobolus, positioned closely to B. heterosporus and B. minor. Morphological and physiological data supported the identity of the species, which was named Basidiobolus omanensis, with CBS 146281 as the holotype. The strains showed high minimum inhibitory concentrations (MICs) to fluconazole (>64 µg/mL), itraconazole and voriconazole (>16 µg/mL), anidulafungin and micafungin (>16 µg/mL), but had a low MIC to amphotericin B (1 µg/mL). The pathogenic role of B. omanensis in gastrointestinal disease is discussed. We highlight the crucial role of molecular identification of these rarely encountered opportunistic fungi.

Mycobacterium farcinogenes osteomyelitis of the proximal tibia: A case report.

Non-tuberculous mycobacteria (NTM) are an unusual cause of osteomyelitis. Mycobacterium farcinogenes is an uncommon cause of human disease. We describe here the first case of M. farcinogenes osteomyelitis in a 49-year-old man who underwent left knee anterior cruciate ligament and medial meniscal repair which was complicated by recurrent septic arthritis and surgical site infection. As a consequence, he underwent multiple surgical debridements. Ultimately, left proximal tibial osteomyelitis was diagnosed and M. farcinogenes was recovered from the tissue biopsy culture. Clinical improvement was achieved following surgical removal of the prosthesis along with prolonged combination antimicrobial therapy.

Molecular detection of varicella zoster virus while keeping an eye on the budget.

Varicella zoster virus (VZV) PCR is highly sensitive compared to traditional detection methods like culture and direct fluorescent antibody testing (DFA); however, the high cost of commercial assays prohibits their use in many clinical laboratories. Major contributors to cost are the nucleic acid extraction and the PCR reagents. This study evaluated an "in-house" qualitative real-time PCR where the nucleic acid extraction was replaced by a crude extraction, homogenization and heat treatment. Three methods were compared: virus culture and DFA and real-time PCR following each extraction methods. The real-time PCR was highly specific for VZV, and the analytical sensitivity was equivalent following both extraction methods. In contrast, virus culture and DFA was approximately 10,000-fold less sensitive. Using 200 clinical specimens, the sensitivity for the real-time PCR following nucleic acid extraction or homogenization and heat treatment was essentially equivalent at 100% and 97.2%, respectively; whereas, virus culture and DFA was significantly less sensitive at 54.8%. Overall, homogenization and heat treatment combined with a qualitative in-house real-time PCR is a rapid, accurate and cost effective method for the detection of VZV.

A cost effective real-time PCR for the detection of adenovirus from viral swabs.

Compared to traditional testing strategies, nucleic acid amplification tests such as real-time PCR offer many advantages for the detection of human adenoviruses. However, commercial assays are expensive and cost prohibitive for many clinical laboratories. To overcome fiscal challenges, a cost effective strategy was developed using a combination of homogenization and heat treatment with an "in-house" real-time PCR. In 196 swabs submitted for adenovirus detection, this crude extraction method showed performance characteristics equivalent to viral DNA obtained from a commercial nucleic acid extraction. In addition, the in-house real-time PCR outperformed traditional testing strategies using virus culture, with sensitivities of 100% and 69.2%, respectively. Overall, the combination of homogenization and heat treatment with a sensitive in-house real-time PCR provides accurate results at a cost comparable to viral culture.