Impact of selective reporting of wound cultures on microbiology reports and antimicrobial-drug use on a wound-care ward in Finland: a retrospective cohort study.

BACKGROUND: Selective reporting is a promising tool for antimicrobial stewardship, but in wound cultures, its effects on the use of antimicrobials are unknown. Our HUS Diagnostic Center Bacteriology laboratory refined its selective reporting protocol for wound cultures during 2017-2018. In this study we aimed to show our protocol's impact on the frequency of antimicrobial escalation. METHODS: We performed a retrospective cohort study of patients in the wound-care ward of a primary-care hospital in Helsinki, Finland, from 2014 to 2016 (pre-intervention) and from 2019 to April 2021 (post-intervention). With the inclusion criterion being wound-culture collection, this provided us with 299 patients, of which 152 were in the pre-intervention group, and 147 were post-intervention. We collected the data from medical records and compared the pre-intervention- with the post-intervention group in terms of patient profiles, microbiology reports, antimicrobial treatment, and treatment outcomes. FINDINGS: In the pre-intervention group 40% of the patients were male and 60% female and in the post-intervention group 49% and 51% respectively. The frequency of AST reported had decreased from 63% in the pre-intervention group to 37% post-intervention (OR 0.35, p < 0.001). The post-intervention group demonstrated lower frequencies of antimicrobial treatment 7 d after wound culture collection, 82% pre-intervention vs 58% post-intervention (OR 0.31, p < 0.001), and antimicrobial escalation, 42% vs 20% (OR 0.35, p < 0.001) respectively. Length of hospital stay, and all-cause mortality were similar between the groups. INTERPRETATION: Selective reporting of wound cultures appears an effective and safe measure to reduce the use of antimicrobials. FUNDING: HUS Diagnostic Center.

Successful treatment of persisting SARS-CoV-2 infection in an immunocompromised patient with repeated nirmatrelvir/ritonavir courses: a case report.

BACKGROUND: In immunocompromised patients, persistent SARS-CoV-2 viral shedding and relapsing COVID-19 pneumonia have been described. Currently, little is known about the management of persisting COVID-19, and immunocompromised patients are recommended to be treated using antivirals and immunomodulatory therapies at similar doses and durations as the general population. Previous case reports have described treatment with repeated and prolonged courses of remdesivir and some evidence is emerging in the use of nirmatrelvir/ritonavir combination (NMV/r). METHODS: We describe a patient with recent chemotherapy including rituximab for follicular lymphoma with persisting SARS-CoV-2 infection. Polymerase chain reaction tests (PCR), cycle threshold values and blood SARS-CoV-2 antigen levels were evaluated. RESULTS: The patient presented with persisting SARS-CoV-2 with relapsing COVID-19 pneumonia. The patient was treated successfully with repeated courses of NMV/r without any observed adverse effects. After the third, prolonged course, the patient remained afebrile and PCR negative, and no relapses have been observed four months after the third NMV/r course. CONCLUSIONS: Nirmatrelvir-ritonavir could offer a more accessible alternative to remdesivir. Further research and guidelines for persisting SARS-CoV-2 infection in immunocompromised patients are urgently needed.

The phylodynamics of SARS-CoV-2 during 2020 in Finland.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other European nations, Finland has had a low incidence of SARS-CoV-2. To gain insight into the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020, we investigated the phylogeographic and -dynamic history of the virus. Methods: The origins of SARS-CoV-2 introductions were inferred via Travel-aware Bayesian time-measured phylogeographic analyses. Sequences for the analyses included virus genomes belonging to the B.1 lineage and with the D614G mutation from countries of likely origin, which were determined utilizing Google mobility data. We collected all available sequences from spring and fall peaks to study lineage dynamics. Results: We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain. Conclusions: A single introduction from Spain might have seeded one-third of cases in Finland during spring in 2020. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and the effects of early intervention and public health measures.

Real-life clinical sensitivity of SARS-CoV-2 RT-PCR test in symptomatic patients.

BACKGROUND: Understanding the false negative rates of SARS-CoV-2 RT-PCR testing is pivotal for the management of the COVID-19 pandemic and it has implications for patient management. Our aim was to determine the real-life clinical sensitivity of SARS-CoV-2 RT-PCR. METHODS: This population-based retrospective study was conducted in March-April 2020 in the Helsinki Capital Region, Finland. Adults who were clinically suspected of SARS-CoV-2 infection and underwent SARS-CoV-2 RT-PCR testing, with sufficient data in their medical records for grading of clinical suspicion were eligible. In addition to examining the first RT-PCR test of repeat-tested individuals, we also used high clinical suspicion for COVID-19 as the reference standard for calculating the sensitivity of SARS-CoV-2 RT-PCR. RESULTS: All 1,194 inpatients (mean [SD] age, 63.2 [18.3] years; 45.2% women) admitted to COVID-19 cohort wards during the study period were included. The outpatient cohort of 1,814 individuals (mean [SD] age, 45.4 [17.2] years; 69.1% women) was sampled from epidemiological line lists by systematic quasi-random sampling. The sensitivity (95% CI) for laboratory confirmed cases (repeat-tested patients) was 85.7% (81.5-89.1%) inpatients; 95.5% (92.2-97.5%) outpatients, 89.9% (88.2-92.1%) all. When also patients that were graded as high suspicion but never tested positive were included in the denominator, the sensitivity (95% CI) was: 67.5% (62.9-71.9%) inpatients; 34.9% (31.4-38.5%) outpatients; 47.3% (44.4-50.3%) all. CONCLUSIONS: The clinical sensitivity of SARS-CoV-2 RT-PCR testing was only moderate at best. The relatively high false negative rates of SARS-CoV-2 RT-PCR testing need to be accounted for in clinical decision making, epidemiological interpretations, and when using RT-PCR as a reference for other tests.

SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department: evaluation and utility.

BACKGROUND: Rapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed. OBJECTIVES: We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert® Xpress SARS-CoV-2 and Mobidiag Novodiag® Covid-19, in comparison to a combination reference of three large-scale PCR tests. Moreover, utility of the Novodiag® test in tertiary care emergency departments was assessed. RESULTS: In the preliminary evaluation, analysis of 90 respiratory samples resulted in 100% specificity and sensitivity for Xpert®, whereas analysis of 107 samples resulted in 93.4% sensitivity and 100% specificity for Novodiag®. Rapid SARS-CoV-2 testing with Novodiag® was made available for four tertiary care emergency departments in Helsinki, Finland between 18 and 31 May, coinciding with a rapidly declining epidemic phase. Altogether 361 respiratory specimens, together with relevant clinical data, were analyzed with Novodiag® and reference tests: 355/361 of the specimens were negative with both methods, and 1/361 was positive in Novodiag® and negative by the reference method. Of the 5 remaining specimens, two were negative with Novodiag®, but positive with the reference method with late Ct values. On average, a test result using Novodiag® was available nearly 8 hours earlier than that obtained with the large-scale PCR tests. CONCLUSIONS: While the performance of novel sample-to-answer PCR tests need to be carefully evaluated, they may provide timely and reliable results in detection of SARS-CoV-2 and thus facilitate patient management including effective cohorting.

DNA vaccination boosts Bacillus Calmette-Guérin protection against mycobacterial infection in zebrafish.

Despite the widespread use of the current Bacillus Calmette-Guérin (BCG) vaccine, tuberculosis is still a major cause of morbidity and mortality worldwide. Vaccination with BCG does not prevent a Mycobacterium tuberculosis infection, nor does it inhibit the reactivation of latent tuberculosis. Here, we show that adult zebrafish are modestly and variably protected from a mycobacterial infection by BCG vaccination. An intraperitoneal (i.p.) BCG vaccination was associated with enhanced survival upon a high-dose (20,000 bacteria) Mycobacterium marinum infection. In addition, BCG-vaccinated fish were more able to restrict a low-dose (30 bacteria) intraperitoneal infection with M. marinum, as indicated by lower bacterial loads at six weeks post infection (wpi). However, the vaccination could not completely prevent an infection. A qRT-PCR analysis comparing BCG-vaccinated and unvaccinated fish upon a mycobacterial infection indicated that the induction of Tumor necrosis factor (TNF) was more modest in vaccinated fish. The partial protection gained by BCG could be boosted by a DNA vaccine combining Ag85B, ESAT6 and a resuscitation-related gene RpfE, suggesting that this combination of antigens could be useful for a future BCG booster vaccine. We conclude that zebrafish is a useful early-phase preclinical model for studying subunit vaccines designed for boosting the effects of BCG.

An adult zebrafish model for preclinical tuberculosis vaccine development.

Tuberculosis remains a major global health challenge despite extensive vaccination schemes with the current live vaccine, Bacillus Calmette-Guérin. Tuberculosis vaccine research has been hampered by a scarcity of animal models which replicate human disease and are suitable for large-scale studies. We have shown recently that Mycobacterium marinum, a close relative of Mycobacterium tuberculosis, causes an infection resembling human tuberculosis in adult zebrafish (Danio rerio). In the present study we use this model to show that BCG vaccination as well as DNA vaccination with selected mycobacterial antigens (Ag85B, CFP-10 and ESAT-6) protects adult zebrafish from mycobacterial infection. Using a low-dose (∼20-30 bacteria) intraperitoneal M. marinum infection, both the number of granulomas and the amount of infected organs were reduced in the DNA vaccinated fish. Likewise, when infecting with a lethal infection dose (∼20,000-27,000 bacteria), vaccination significantly reduced both mortality and bacterial counts in a manner dependent on the adaptive immune response. Protective effects of vaccination were associated with enhanced expression of interferon gamma. Our results indicate that the zebrafish is a promising new model for preclinical tuberculosis vaccine research.