Successful treatment of persistent SARS-CoV-2 infection with nirmatrelvir/ritonavir plus sotrovimab in four immunocompromised patients.

Immunocompromised patients with leukemia/lymphoma often have a suboptimal response to vaccination against SARS-CoV-2 and, if infected, can develop a persistent infection.SARS-CoV-2 PCR was performed on nasopharingeal swabs and serum IgG anti-SARS-CoV-2 trimeric spike glycoprotein antibodies were measured during persistence of infection. Treatment with a combination of nirmatrelvir/ritonavir plus sotrovimab led to viral clearance in three patients with leukaemia or lymphoma with persistent SARS-CoV-2 and negative SARS-CoV-2 antibody tests. No standardized treatments for persistent infection with SARS-CoV-2 infection are available. We have reported the viral clearance in two immunocompromised patients treated with antiviral drug nirmatrelvir/ritonavir and monoclonal antibody sotrovimab. We suggest that this strategy should be tested in clinical trials to find the right strategy for a clinical problem with public health implications to SARS-CoV-2 evolution and immune escape in these sub-set of patients.

Artificial Intelligence Can Guide Antibiotic Choice in Recurrent UTIs and Become an Important Aid to Improve Antimicrobial Stewardship.

BACKGROUND: A correct approach to recurrent urinary tract infections (rUTIs) is an important pillar of antimicrobial stewardship. We aim to define an Artificial Neural Network (ANN) for predicting the clinical efficacy of the empiric antimicrobial treatment in women with rUTIs. METHODS: We extracted clinical and microbiological data from 1043 women. We trained an ANN on 725 patients and validated it on 318. RESULTS: The ANN showed a sensitivity of 87.8% and specificity of 97.3% in predicting the clinical efficacy of empirical therapy. The previous use of fluoroquinolones (HR = 4.23; p = 0.008) and cephalosporins (HR = 2.81; p = 0.003) as well as the presence of Escherichia coli with resistance against cotrimoxazole (HR = 3.54; p = 0.001) have been identified as the most important variables affecting the ANN output decision predicting the fluoroquinolones-based therapy failure. A previous isolation of Escherichia coli with resistance against fosfomycin (HR = 2.67; p = 0.001) and amoxicillin-clavulanic acid (HR = 1.94; p = 0.001) seems to be the most influential variable affecting the output decision predicting the cephalosporins- and cotrimoxazole-based therapy failure. The previously mentioned Escherichia coli with resistance against cotrimoxazole (HR = 2.35; p < 0.001) and amoxicillin-clavulanic acid (HR = 3.41; p = 0.007) seems to be the most influential variable affecting the output decision predicting the fosfomycin-based therapy failure. CONCLUSIONS: ANNs seem to be an interesting tool to guide the antimicrobial choice in the management of rUTIs at the point of care.

Early-onset fulminant neonatal sepsis caused by Multi-Drug Resistant and ESBL producing E. coli (CTX-M gene) in a late-preterm neonate: case report and literature review.

Neonatal sepsis is a systemic condition characterized by haemodynamic changes and other clinical manifestations due to a presence of pathogenic microorganisms (bacteria, viruses, or fungi) in nor- mally sterile fluid that occurs in an infant younger than 90 days old. Neonatal sepsis may be divided into two types: early-onset neonatal sepsis (EOS) and late-onset neonatal sepsis (LOS). Gram-posi- tive microorganisms are the etiological agents in 62% of EOS, and in 43% of the total the identified microorganism is GBS. Gram-negative microorganisms comprise 37% of the etiological agents of EOS, of which 29% are caused by Escherichia coli. ESBL-producing Enterobacteriaceae represent a major worldwide threat among drug-resistant bacteria in both hospital and community settings. ESBLs are often located on large plasmids that also harbour genes resistant to other antimicrobial classes, resulting in multidrug-resistant isolates. Plasmid-encoded ESBLs of the CTX-M-type are increasingly reported worldwide in Gram-negative rods and now account for most of the ESBLs found in Enterobacteriaceae. We present one case of EOS by Multi Drug Resistant (MDR) and ESBL producing E. coli (CTX-M gene) in a neonate born to a mother recently immigrated from Africa. Maternal blood culture grew the same bacteria.

On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy.

BACKGROUND: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. METHODS: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. RESULTS: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. CONCLUSIONS: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.

Management of Recurrent Cystitis in Women: When Prompt Identification of Risk Factors Might Make a Difference.

BACKGROUND: Management of recurrent urinary tract infection (rUTI) is still challenging. A better understanding of the natural history of rUTI could help us reduce antibiotic use and improve antibiotic stewardship. OBJECTIVE: To describe the effect of risk identification, stratification, and counseling on the natural course of the disease in women with rUTI. DESIGN, SETTING, AND PARTICIPANTS: A total of 373 women affected by recurrent cystitis were enrolled in this longitudinal cohort study between December 2014 and December 2019. A systematic and standardized identification of risk factors was performed. INTERVENTION: As intervention, risk factors were treated or removed where possible. Patients with nonremovable risk factors were included in the control group. All patients were scheduled for follow-up visits every 6 mo. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The main outcome measures were the rate of symptomatic recurrences and improvement in questionnaire results from baseline to the end of the follow-up period. Reduction of antibiotic usage was regarded as a secondary outcome measure. RESULTS AND LIMITATIONS: Finally, 353 women were analyzed: 196 in the study group and 157 in the control group. At the end of the follow-up period, a statistically significant reduction in the symptomatic recurrence rate was found between the two groups (0.9 ± 0.2 and 2.6 ± 0.5; p < 0.001), as well as in quality of life and anxiety according to mean questionnaire results: quality of life (0.88 ± 0.06 and 0.63 ± 0.09; p < 0.001) and Spielberger State-Trait Anxiety Inventory-Form Y (32.7 ± 9.3 and 47.5 ± 14.3; p < 0.001). The use of antibiotics was significantly lower in the study group: 4410 versus 9821 (p < 0.001). A limitation to consider is the lack of a randomized design for the active approach in the high-risk group. CONCLUSIONS: Identification, counseling, and removal of risk factors, where possible, are able to change the natural history of rUTI, by reducing the number of symptomatic episodes and antibiotic use and improving quality of life. PATIENT SUMMARY: In this report, we analyzed a large cohort of women affected by recurrent urinary tract infections and followed for a long time period. We found that risk factor identification and counseling may change the natural history of recurrent urinary tract infections, concluding that this approach is able to reduce the number of symptomatic episodes, reduce antibiotic usage, and improve patients' quality of life.

A Community Study of SARS-CoV-2 Detection by RT-PCR in Saliva: A Reliable and Effective Method.

Efficient, wide-scale testing for SARS-CoV-2 is crucial for monitoring the incidence of the infection in the community. The gold standard for COVID-19 diagnosis is the molecular analysis of epithelial secretions from the upper respiratory system captured by nasopharyngeal (NP) or oropharyngeal swabs. Given the ease of collection, saliva has been proposed as a possible substitute to support testing at the population level. Here, we used a novel saliva collection device designed to favour the safe and correct acquisition of the sample, as well as the processivity of the downstream molecular analysis. We tested 1003 nasopharyngeal swabs and paired saliva samples self-collected by individuals recruited at a public drive-through testing facility. An overall moderate concordance (68%) between the two tests was found, with evidence that neither system can diagnose the infection in 100% of the cases. While the two methods performed equally well in symptomatic individuals, their discordance was mainly restricted to samples from convalescent subjects. The saliva test was at least as effective as NP swabs in asymptomatic individuals recruited for contact tracing. Our study describes a testing strategy of self-collected saliva samples, which is reliable for wide-scale COVID-19 screening in the community and is particularly effective for contact tracing.

Survey of diagnostic and typing capacity for enterovirus infection in Italy and identification of two echovirus 30 outbreaks.

BACKGROUND: Enterovirus infections can cause a variety of illnesses, ranging from asymptomatic infections to severe illness and death. AIM: To support polio eradication activities, in February 2019, the WHO Regional Reference Laboratory for polio in Italy, at the National Institute of Public Health (Istituto Superiore di Sanità), promoted an investigation on non-polio enterovirus laboratory capacity, with the support of the Italian Ministry of Health. The aim was to collect data on the assays used routinely for diagnostic purposes and to characterize enterovirus outbreaks strains by sequence analysis of the Viral Protein 1 region. METHODS: A questionnaire was administered to public health laboratories through all Italian Regions for 2018 and subsequently, an electronic form for lab-confirmed enterovirus infection reported from February 2019 to January 2020, including patients clinical characteristics, and laboratory data was distributed through 25 laboratories participating the survey. RESULTS: Overall, a homogenous laboratory capacity for enterovirus infection diagnosis was found and 21,000 diagnostic tests were retrospectively reported in 2018. Then, in 2019, two outbreaks of Echovirus 30 were identified and confirmed by molecular analyses. CONCLUSION: These results underline the need monitor the circulation of non-polio enterovirus to ascertain the real burden of the disease in the country.

Toxoplasma gondii infection during pregnancy: a ten-year observation in the province of Trento, Italy.

The study analysed the trend of toxoplasmosis infection in pregnancy by using antenatal serological screening and the incidence of the congenital condition in newborns in the province of Trento, Italy. Data from pregnant women who gave birth at local maternity units between 2009 and 2018 were obtained. The serological test results were collected from birth attendance certificates (BACs), the main - and mandatory - source of information used to monitor pregnancies, births and neonatal health in Italy. The BAC used in the province of Trento acquires the results of serological tests for a vast range of infections in pregnancy. The data collected from the BACs were integrated with those provided by the Hospital Information System (HIS), which was also used to collect data on the trimester in which the seroconversion occurred. A total of 45,492 pregnant women were analysed, of whom 24% were foreigners. The average coverage of serological screening in pregnancy was 99.7%. Mean overall prevalence of Toxoplasma gondii infection was 21.7% (95% CI: 21.3-22.1): in Italians the prevalence was 17.9% (95% CI: 17.5-18.30) and in foreign nationals 32.7% (95% CI: 32.26-33.13). The mean annual seroconversion rate was 0.35% (95% CI: 3.0-4.2) of susceptible women and 0.27% (95% CI: 2.2-3.4) of all pregnant women who were screened. The seroconversion rate was higher amongst foreign women (0.32%, 95% CI: 3.0-3.6) than Italian women (0.24%, 95% CI: 2.1-2.8). In all, 91.0% of seroconverted women were treated during pregnancy in accordance with the anti-toxoplasma protocol. Five cases of congenital infection were identified (2 amongst Italians and 3 amongst foreign women), amounting to an overall transmission rate of 4.0% (2.3% in Italians and 8.8% in foreigners). Transmission risk ranged from 0.0% in the first trimester to 19% in the third. The incidence of congenital toxoplasmosis, over the entire study period, was 0.012% live births (0.011% in Italians and 0.016% in foreigners). Data collection on infections in pregnancy through BAC allows area-based assessment. Although the quality of the data recorded in the BAC can be considered satisfactory, it was also necessary to access other information sources. The screening coverage was very high. The prevalence of toxoplasmosis infection was found to be higher in foreign mothers than in Italians, as well as seroconversion. The extent of serological screening and the high treatment rate helped to keep the risk of infection transmission to the foetus low and to achieve a very low rate of congenital infection.

Clinical Utility of a Highly Sensitive Lateral Flow Immunoassay as determined by Titer Analysis for the Detection of anti-SARS-CoV-2 Antibodies at the Point-of-Care.

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), became a pandemic in early 2020. Lateral flow immunoassays for antibody testing have been viewed as a cheap and rapidly deployable method for determining previous infection with SARS-CoV-2; however, these assays have shown unacceptably low sensitivity. We report on nine lateral flow immunoassays currently available and compare their titer sensitivity in serum to a best-practice enzyme-linked immunosorbent assay (ELISA) and viral neutralization assay. For a small group of PCR-positive, we found two lateral flow immunoassay devices with titer sensitivity roughly equal to the ELISA; these devices were positive for all PCR-positive patients harboring SARS-CoV-2 neutralizing antibodies. One of these devices was deployed in Northern Italy to test its sensitivity and specificity in a real-world clinical setting. Using the device with fingerstick blood on a cohort of 27 hospitalized PCR-positive patients and seven hospitalized controls, ROC curve analysis gave AUC values of 0.7646 for IgG. For comparison, this assay was also tested with saliva from the same patient population and showed reduced discrimination between cases and controls with AUC values of 0.6841 for IgG. Furthermore, during viral neutralization testing, one patient was discovered to harbor autoantibodies to ACE2, with implications for how immune responses are profiled. We show here through a proof-of-concept study that these lateral flow devices can be as analytically sensitive as ELISAs and adopted into hospital protocols; however, additional improvements to these devices remain necessary before their clinical deployment.

Coverage and outcomes of antenatal tests for infections: a population based survey in the Province of Trento, Italy.

BACKGROUND: Rubella, syphilis, toxoplasmosis, cytomegalovirus (CMV), hepatitis B (HBV) and C (HCV), HIV, and Group B Streptococcus (GBS) infections may have very severe outcomes during pregnancy, and for this reason, monitoring of infections in pregnant women is a requirement of prenatal assistance. AIMS: To describe coverage and outcome of the screening for rubella, syphilis, toxoplasmosis, CMV, HBV, HCV, HIV, and Group B Streptococcus in pregnancy in the Autonomous Province of Trento, Northern Italy (538,600 inhabitants). METHODS: We analysed the coverage and outcome of the above-mentioned screenings among women who delivered in the hospitals of the Province of Trento between 2007 and 2014 (N = 38,712). Screenings were grouped according to characteristics such as recommendation by national and local guidelines, scheduling of the tests, operating methods, and charge. We also estimated odds ratios (ORs) for missing screening for selected infections through multiple logistic regression. RESULTS: Estimated uptake of antenatal screening was 99.7% for rubella, 99.3% for syphilis, 99.7% for toxoplasmosis, 98.1% for HIV infection, 99.0% for HBV, 98.9% for HCV, 94.0% for GBS infection, and 75.4% for CMV infection. The overall prevalence of immunity was 94.1% for rubella, 24.2% for toxoplasmosis, and 64.2% for CMV. The rate of seroconversion in pregnant women was 0.02% for rubella, 0.29% for toxoplasmosis, and 0.75% for CMV. The overall prevalence of infection was 0.94% for HBV, 0.53% for HCV, 22.3% for GBS, 0.29% for syphilis, and 0.13% for HIV. We found a significant positive association for all screening tests, between lack of testing and late first medical examination in pregnancy (ORs ranging from 1.20 to 1.66 for the first medical visit in the second trimester and ORs ranging from 1.60 to 5.88 for the first medical visit in third trimester, compared to early medical visit in the first trimester). Compared to Italian citizenship, foreign citizenship of the mother was also positively associated with absence of screening (ORs ranging from 1.30 to 1.53). A significant inverse association was observed for calendar year of delivery (ORs ranging from 0.71 to 0.97, for 1 year increment). Less educated mothers and pluriparae were also at higher risks of not being tested. Analysis of the association with mother age showed different heterogeneous effects. CONCLUSIONS: Our study indicates that the attention to screening and detecting infected cases is growing over the time. In addition, care delivered during pregnancy has a leading role in determining coverage of the examinations. Immigrant, pluriparous and less educated women need particular attention.

Characterization of a novel plasmid encoding F4-like fimbriae present in a Shiga-toxin producing enterotoxigenic Escherichia coli isolated during the investigation on a case of hemolytic-uremic syndrome.

In February 2017 a case of Hemolytic-Uremic Syndrome (HUS) was reported to the National Registry of HUS in an adult living in Northern Italy. Stool specimens from the patient and his family contacts were collected and the analyses led to the isolation of a Locus of Enterocyte Effacement (LEE)-negative Shiga toxin 2 (Stx2)-producing Escherichia coli. The epidemiological investigations performed brought to collect fecal samples from the animals reared in a farm held by the case's family and a mixture of bovine and swine feces proved positive for Shiga toxin-producing E. coli (STEC) and yielded the isolation of a LEE-negative stx2-positive E. coli strain. Further characterization by whole genome sequencing led to identify the isolates as two identical O2:H27 hybrid Enterotoxigenic Shiga toxin-producing E. coli (ETEC-STEC). Sequencing of a high molecular weight plasmid present in the human isolate disclosed a peculiar plasmid harboring virulence genes characteristic for both pathotypes, including the enterohemolysin-coding gene and sta1, encoding the heat stable enterotoxin. Moreover, a complete fae locus encoding the ETEC F4 fimbriae could be identified, including a novel variant of faeG gene responsible for the production of the main structural subunit of the fimbriae. This novel faeG showed great diversity in the nucleotidic sequence when compared with the reference genes encoding the swine F4 allelic variants, whereas at the amino acid sequence level the predicted protein sequence showed some similarity with FaeG from E. coli strains of bovine origin. Further investigation on the plasmid region harboring the newly identified faeG allelic variant allowed to identify similar plasmids in NCBI sequence database, as part of the genome of other previously uncharacterized ETEC-STEC strains of bovine origin, suggesting that the novel F4-like fimbriae may play a role in bovine host specificity.