Damien Jacot

Castellaniella defragrans is an environmental Gram-negative, non-fermenting β-proteobacterium that is not known as a human pathogen. Here, we report the first documented case of C. defragrans bacteraemia in an 82-year-old man with monoclonal B-cell lymphocytosis, subsequently diagnosed with chronic lymphocytic leukaemia, who presented with fever, confusion and clinical signs of sepsis. Blood cultures showed sustained growth of C. defragrans for 7 days. Imaging revealed pulmonary consolidations and mediastinal infiltration suggestive of mediastinitis. Further investigations did not identify a clear additional infectious focus. In addition, an immunological evaluation revealed severe cellular and humoral immunosuppression. Antimicrobial therapy with high-dose meropenem led to bacteraemia clearance and progressive clinical improvement. Treatment was completed with oral sulfamethoxazole–trimethoprim for a total of five weeks. This case highlights the potential of environmental microorganisms to cause severe infections in immunocompromised hosts.

Dientamoeba fragilis is a protozoan of the human digestive tract, yet its transmission and pathogenic role remain poorly understood. This study aimed to evaluate its impact on the efficacy and safety of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI). This longitudinal cohort study analyzed stool samples from FMT donors and recipients pre-treatment and at 2 and 8 weeks post-FMT. All samples were retrospectively tested using real-time PCR. Shotgun metagenomics was also performed on selected donor–recipient pairs to explore transmission. CDI cure rates, gastrointestinal adverse events (AEs), and serious adverse events (SAEs) were assessed prospectively. A total of 53 FMT were analyzed (179 samples), with 23 (43%) derived from D. fragilis-positive donor stool (4 of 10 donors, 40%). Four of 52 recipients (18.2%), initially negative and who received treatment from positive donors, tested positive post-FMT. Shotgun metagenomics could not definitely confirm transmission due to the lack of a good reference genome. No significant differences in efficacy, AE, or SAE were observed between FMT from D. fragilis-positive versus -negative donors, even in immunocompromised patients. No SAEs were attributed to FMT. D. fragilis may be transmitted via FMT without evidence of short-term clinical impact. Consequently, RT-PCR detection should be interpreted cautiously in the context of donor exclusion decisions.

Introduction: Dientamoeba fragilis is a protozoan of the human digestive tract, yet its transmission and pathogenic role remain poorly understood. This study aimed to evaluate its impact on the efficacy and safety of FMT in treating recurrent Clostridioides difficile infection (rCDI). Patients and methods: This longitudinal cohort study analyzed stool samples from FMT donors and recipients pre-treatment and at 2 and 8 weeks post-FMT. All samples were retrospectively tested using real-time PCR. Shotgun metagenomics was also performed on selected donor-recipient pairs to explore transmission. CDI cure rates, gastrointestinal adverse events (AE), and serious adverse events (SAE) were assessed prospectively. Results: A total of 53 FMT were analysed (179 samples), with 23 (43%) derived from D. fragilis -positive donor stool (4 of 10 donors, 40%). Four of 52 recipients (18.2%), initially negative and who received treatment from positive donors, tested positive post-FMT. Shotgun metagenomics could not definitely confirm transmission due to the lack of a good reference genome. No significant differences in efficacy, AE, or SAE were observed between FMT from D. fragilis -positive versus -negative donors, even in immunocompromised patients. No SAE were attributed to FMT. Conclusion: D. fragilis may be transmitted via FMT without clinical impact, highlighting the need to reconsider donor exclusion and aligning with growing evidence of its questionable pathogenicity.

Ralstonia mannitolilytica, an opportunistic pathogen commonly present in water, was identified in three hospitalized patients over a short period of time. The comparison of draft genomes of 12 isolates from patients and water sprays showed fewer than 10 single-nucleotide polymorphisms, indicating that water sprays were the contamination source.

Total laboratory automation (TLA) is a valuable component of microbiology laboratories and a growing number of publications suggest the potential impact of automation in terms of analysis standardization, streaking quality, and the turnaround time (TAT). The aim of this project was to perform a detailed investigation of the impact of TLA on the workflow of commonly treated specimens such as urine. This is a retrospective observational study comparing two time periods (pre TLA versus post TLA) for urine specimen culture processing. A total of 35,864 urine specimens were plated during the pre-TLA period and 47,283 were plated during the post-TLA period. The median time from streaking to identification decreased from 22.3 h pre TLA to 21.4 h post TLA (p < 0.001), and the median time from streaking to final validation of the report decreased from 24.3 h pre TLA to 23 h post TLA (p < 0.001). Further analysis revealed that the observed differences in TAT were mainly driven by the contaminated and positive samples. Our findings demonstrate that TLA has the potential to decrease turnaround times of samples in a laboratory. Nevertheless, changes in laboratory workflow (such as extended opening hours for plate reading and antibiotic susceptibility testing or decreased incubation times) might further maximize the efficiency of TLA and optimize TATs.

In clinical bacteriology laboratories, reading and processing of sterile plates remain a significant part of the routine workload (30%–40% of the plates). Here, an algorithm was developed for bacterial growth detection starting with any type of specimens and using the most common media in bacteriology. The growth prediction performance of the algorithm for automatic processing of sterile plates was evaluated not only at 18–24 h and 48 h but also at earlier timepoints toward the development of an early growth monitoring system. A total of 3,844 plates inoculated with representative clinical specimens were used. The plates were imaged 15 times, and two different microbiologists read the images randomly and independently, creating 99,944 human ground truths. The algorithm was able, at 48 h, to discriminate growth from no growth with a sensitivity of 99.80% (five false-negative [FN] plates out of 3,844) and a specificity of 91.97%. At 24 h, sensitivity and specificity reached 99.08% and 93.37%, respectively. Interestingly, during human truth reading, growth was reported as early as 4 h, while at 6 h, half of the positive plates were already showing some growth. In this context, automated early growth monitoring in case of normally sterile samples is envisioned to provide added value to the microbiologists, enabling them to prioritize reading and to communicate early detection of bacterial growth to the clinicians.

Introduction. In early January 2020, the pandemic of COVID-19 (coronavirus disease 2019) rapidly spread from China and caused a worldwide pandemic. Hypothesis. Healthcare workers represent a high-risk group for acquiring COVID-19 and for nosocomial transmission of severe acute respiratory coronavirus 2 (SARS-CoV-2). Aim. We aimed to investigate over a 1 year period, across two pandemic waves, the SARS-CoV-2 seroprevalence in employees at a Western Switzerland public hospital. Methodology. A prospective observational SARS-CoV-2 seroprevalence study was proposed to all hospital employees who enrolled on a voluntary basis. Results. Out of 594 participants recruited on a voluntary basis, 269 volunteers (45.3 %) had anti-SARS-CoV-2 antibodies: this seroprevalence was twice higher than that reported in the local community. Healthcare workers with prolonged exposure to patients with COVID-19 showed a significantly higher odds ratio (OR) of having a positive SARS-CoV-2 serology [OR 3.19, 95 % confidence interval (CI) 2.16–4.74]. Symptoms showing the highest association with a positive serology were anosmia (OR 11.9, 95 % CI 5.58–30.9) and ageusia (OR 10.3, 95 % CI 4.8–26.3). A total of 17.1 % (95 % CI 12.2–21.1 %) of SARS-CoV-2 seropositive volunteers did not report a suspicion of COVID-19 in their personal history. Conclusion. Overall, we observed that the impact of the second SARS-CoV-2 pandemic wave was considerable and significantly affected healthcare workers with prolonged exposure to patients with COVID-19.

RT-PCRs to detect SARS-CoV-2 RNA is key to manage the COVID-19 pandemic. We analyzed SARS-CoV-2 viral loads from 22’323 RT-PCR results according to samples types, gender, age, and health units. Viral load did not show any difference across age and appears to be a poor predictor of disease outcome. SARS-CoV-2 viral load showed similar high viral loads than the one observed for RSV and influenza B. The importance of viral load to predict contagiousness and to assess disease progression is discussed.

On April 25 ^th , corresponding to the first deconfinement phase after the end of the lockdown in Switzerland, a universal admission screening strategy for COVID-19 was introduced in our hospital. All patients, including asymptomatic patients were tested for SARS-CoV-2 by quantitative reverse transcription polymerase chain reaction (RT-PCR). In addition to a qualitative answer, providing viral load values to the RT-PCR results not only helped the clinician to evaluate the stage of the infection but addressed patient contagiousness and guided infection control decisions. Here, we discuss the importance of reporting viral load values when a shift from a symptomatic to a universal screening strategy was performed.