Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying Novel Variant blaKPC-203, Cross-Resistant to Ceftazidime/Avibactam and Cefiderocol, but Susceptible to Carbapenems, Isolated in Italy, 2023.

BACKGROUND: Klebsiella pneumoniae is a concerning pathogen, responsible for hospital-associated outbreaks. Multi drug resistant (MDR) strains are especially hard to treat. We conducted whole-genome sequencing on a MDR K. pneumoniae strain in order to identify genomic features potentially linked to its phenotype. METHODS: DNA sequencing was performed on the Illumina iSeq 100 platform. Genome assembly was carried out with SPAdes. The genome was annotated with RASTtk. Typing was performed with MLST and Kaptive. Antibiotic resistance genes were detected with AMRFinderPlus and Abricate, and further verified with BLAST. RESULTS: The strain exhibited resistance to ceftazidime/avibactam and cefiderocol, but remained susceptible to carbapenems. The strain belonged to sequence type ST101, serotype O1:K17. The analysis of antibiotic resistance genes indicated that the strain carried a novel KPC variant, designated as KPC-203, featuring a EL deletion at amino acid position 166-167, within the Ω-loop, and a nine-amino-acid insertion (LAVYTRAPM) at position 259. Sequence alterations were found in porin genes ompK35 and ompK36. Unlike molecular testing, which was able to detect the KPC-203 variant, all phenotypic carbapenemase detection methods achieved negative results. CONCLUSIONS: KPC-203, a novel KPC variant, showed a sequence modification in a cephalosporin resistance-associated hotspot. Interestingly, such alterations typically correlate with the restoration of carbapenem susceptibility. We hypothesize that KPC-203 likely led to resistance to ceftazidime/avibactam and cefiderocol, while maintaining susceptibility to carbapenems.

The Impact of the Seasonal and Geographical Distribution of Tuberculosis in Sicily: A 6-Year Retrospective Study (2018-2023).

Background: Tuberculosis (TB) continues to be a major public health issue, with high mortality rates reported worldwide. It is worth noting that most of the hospitalizations for tuberculosis in the Sicilian region involve Italian-born individuals, underscoring the need to address this problem. Recent research on the geographic area and seasonality of infectious diseases, including tuberculosis, may aid in developing effective preventive measures. Objectives: This study aimed to evaluate the impact of the season and geographical area on tuberculosis disease prevalence in the Sicilian region. Methods: A retrospective study from January 2018 to May 2023 was conducted on patients with tuberculosis in the Sicilian region by analyzing computerized records on the Infectious Diseases Information System, currently named the Italian National Notification System (NSIS), of the Epidemiology Unit at Policlinico Paolo Giaccone University Hospital of Palermo and the Regional Reference Laboratory for Tuberculosis Surveillance and Control. Results: Eastern and Western Sicily were the geographical Sicilian areas with the highest frequency of patients with tuberculosis (52.2% and 42.6%, respectively). In comparison, Central Sicily had a significantly lower frequency of patients with tuberculosis (5.2%). Regarding the season, autumn was the season with the highest number of notification cases (28.9%), while spring was the season with the lowest frequency of patients with tuberculosis (19.7%). In autumn, we found significantly fewer patients with tuberculosis from Eastern Sicily (39.3%) and Central Sicily (1.5%), while Western Sicily had more patients with tuberculosis (59.3%). In spring, we found significantly more patients with tuberculosis from Eastern Sicily (64.1%), while Western and Central Sicily had significantly fewer patients with tuberculosis (23.9% and 12%, respectively). The presence of patients with tuberculosis did not significantly differ between geographical regions in summer and winter. Conclusions: Geographical area and seasonality significantly impact the distribution of tuberculosis cases in Sicily. These factors may be linked to different climatic conditions across the various geographical areas considered. Our findings suggest that climate can play a critical role in the spread of airborne infectious diseases, such as tuberculosis.

Validation of a Loop-Mediated Isothermal Amplification-Based Kit for the Detection of Legionella pneumophila in Environmental Samples According to ISO/TS 12869:2012.

Legionella pneumophila is a freshwater opportunistic pathogen and the leading cause of severe pneumonia known as Legionnaires' disease. It can be found in all water systems and survives in biofilms, free-living amoebae, and a wide variety of facilities, such as air conditioning and showers in hospitals, hotels and spas. The reference cultural method allows for the isolation and identification in many days, and in addition, it does not detect viable but rather non-culturable bacteria, increasing the risk of infection. In this context, a new LAMP-based (loop-mediated isothermal amplification) kit was developed, allowing for the rapid, sensitive, and labor-saving detection of L. pneumophila. The kit, "Legionella pneumophila Glow", was validated according to ISO/TS 12869:2012, testing sensitivity, inclusivity and exclusivity, and kit robustness. Sensitivity showed that the "Legionella pneumophila Glow" kit can detect up to 28 plasmid copies/µL. Robustness tests showed consistent results, with both contamination levels and the matrices used giving reproducible results. Furthermore, real samples were evaluated to compare the performance of the two methods. The LAMP kit "Legionella pneumophila Glow" proved a useful option for the rapid, efficient, and labor-saving screening of different typologies of water samples, offering significant advantages over the traditional method, as it is characterized by a high sensitivity, ease of use for laboratory testing, and a large reduction in analysis time, making it an asset to official controls.

Enterobacterales carrying chromosomal AmpC ß-lactamases in Europe (EuESCPM): Epidemiology and antimicrobial resistance burden from a cohort of 27 hospitals, 2020-2022.

INTRODUCTION: The ESCPM group (Enterobacter species including Klebsiella aerogenes - formerly Enterobacter aerogenes, Serratia species, Citrobacter freundii complex, Providencia species and Morganella morganii) has not yet been incorporated into systematic surveillance programs. METHODS: We conducted a multicentre retrospective observational study analysing all ESCPM strains isolated from blood cultures in 27 European hospitals over a 3-year period (2020-2022). Diagnostic approach, epidemiology, and antimicrobial susceptibility were investigated. RESULTS: Our study comprised 6,774 ESCPM isolates. MALDI-TOF coupled to mass spectrometry was the predominant technique for bacterial identification. Susceptibility to new ß-lactam/ß-lactamase inhibitor combinations and confirmation of AmpC overproduction were routinely tested in 33.3% and 29.6% of the centres, respectively. The most prevalent species were E. cloacae complex (44.8%) and S. marcescens (22.7%). Overall, third-generation cephalosporins (3GC), combined third- and fourth-generation cephalosporins (3GC + 4GC) and carbapenems resistance phenotypes were observed in 15.7%, 4.6%, and 9.5% of the isolates, respectively. AmpC overproduction was the most prevalent resistance mechanism detected (15.8%). Among carbapenemase-producers, carbapenemase type was provided in 44.4% of the isolates, VIM- (22.9%) and OXA-48-enzyme (16%) being the most frequently detected. E. cloacae complex, K. aerogenes and Providencia species exhibited the most notable cumulative antimicrobial resistance profiles, with the former displaying 3GC, combined 3GC + 4GC and carbapenems resistance phenotypes in 15.2%, 7.4%, and 12.8% of the isolates, respectively. K. aerogenes showed the highest rate of both 3GC resistant phenotype (29.8%) and AmpC overproduction (32.1%), while Providencia species those of both carbapenems resistance phenotype (42.7%) and carbapenemase production (29.4%). ESCPM isolates exhibiting both 3GC and combined 3GC + 4GC resistance phenotypes displayed high susceptibility to ceftazidime/avibactam (98.2% and 95.7%, respectively) and colistin (90.3% and 90.7%, respectively). Colistin emerged as the most active drug against ESCPM species (except those intrinsically resistant) displaying both carbapenems resistance phenotype (85.8%) and carbapenemase production (97.8%). CONCLUSIONS: This study presented a current analysis of ESCPM species epidemiology in Europe, providing insights to inform current antibiotic treatments and guide strategies for antimicrobial stewardship and diagnostics.

Microbial profile in bile from pancreatic and extra-pancreatic biliary tract cancer.

BACKGROUND: Dysbiotic biliary bacterial profile is reported in cancer patients and is associated with survival and comorbidities, raising the question of its effect on the influence of anticancer drugs and, recently, the suggestion of perichemotherapy antibiotics in pancreatic cancer patients colonized by the Escherichia coli and Klebsiella pneumoniae. OBJECTIVE: In this study, we investigated the microbial communities that colonize tumours and which bacteria could aid in diagnosing pancreatic and biliary cancer and managing bile-colonized patients. METHODS: A retrospective study on positive bile cultures of 145 Italian patients who underwent cholangiopancreatography with PC and EPC cancer hospitalized from January 2006 to December 2020 in a QA-certified academic surgical unit were investigated for aerobic/facultative-anaerobic bacteria and fungal organisms. RESULTS: We found that among Gram-negative bacteria, Escherichia coli and Pseudomonas spp were the most frequent in the EPC group, while Escherichia coli, Klebsiella spp, and Pseudomonas spp were the most frequent in the PC group. Enterococcus spp was the most frequent Gram-positive bacteria in both groups. Comparing the EPC and PC, we found a significant presence of patients with greater age in the PC compared to the EPC group. Regarding Candida spp, we found no significant but greater rate in the PC group compared to the EPC group (11.7% vs 1.96%). We found that Alcaligenes faecalis was the most frequent bacteria in EPC than the PC group, among Gram-negative bacterial species. CONCLUSIONS: Age differences in gut microbiota composition may affect biliary habitats in our cancer population, especially in patients with pancreatic cancer. Alcaligenes faecalis isolated in the culture of bile samples could represent potential microbial markers for a restricted follow-up to early diagnosis of extra-pancreatic cancer. Finally, the prevalence of Candida spp in pancreatic cancer seems to trigger new aspects about debate about the role of fungal microbiota into their relationship with pancreatic cancer.

Characterization of Listeria monocytogenes Strains Isolated in Palermo (Sicily and Italy) during the Years 2018-2020 from Severe Cases of Listeriosis.

Listeria monocytogenes (LM), the etiological agent of listeriosis, can cause foodborne zoonosis. In this study, we characterized 23 strains that caused human severe listeriosis in Palermo (Sicily, Italy) during the period of 2018-2020. In addition, we assessed the phenotypic susceptibility of clinical isolates to antibiotics in accordance with EUCAST guidelines. The serogroup was determined through the use of PCR, while MLST and MVLST were identified through the sequencing of housekeeping genes. Finally, susceptibility to antibiotics was assessed by means of the Phoenix automatic system. Patients hospitalized with listeriosis were predominantly males (56% vs. 44% of females). The cases not associated with pregnancy included patients >65 years of age (60%), two of whom were affected by cancer, while cases associated with pregnancy included two pregnant women and three preterm infants. The data collected showed that the main pathologies shown by patients were meningitis (60.9%) and bacteremia (39.1%). The LM strains were isolated from the blood (52%), cerebrospinal fluid (26%), cerebrospinal fluid + blood (13%), blood + a nasal swab (4%), and ascitic fluid (4%). The predominant serogroup was IVb (96%), whereas only one strain belonged to serogroup IIa (4%). Among the strains with serotypes 4b, 4d, and 4e, ST2/VT21 (92%) and ST6/VT19 (4%) were determined, while only isolates with serotypes 1/2a and3a show ST155/VT45 (CC155). This study reveals the widespread circulation of a clinical strain (ST2/VT21) associated with suspected food contamination, demonstrating the importance of carrying out molecular epidemiological surveillance. Our clinical isolates were susceptible to the beta-lactams assayed, in agreement with the literature data.

Analysis of Bacterial Stent Colonization: The Role of Urine and Device Microbiological Cultures.

In this study, we explored the incidence of double J (JJ) contamination of patients who underwent an endourological procedure for urinary stones and ureteral stenosis. We developed a prospective study between January 2019 and December 2021. Ninety-seven patients, 54 male and 43 female, were enrolled. Urine culture was taken during four steps: before stent insertion, a sample from selective renal pelvis catheterization, a sample two days after the JJ insertion and finally, after the stent removal procedure. At the time of the stent removal, 1 cm of proximal and distal ends were cut off and placed in the culture for bacterial evaluation. Cohen's kappa coefficient value (k) and concordance rates of microbiological culture results were evaluated. The study group comprised 56% of male patients. Proximal and distal stent cultures were positive in 81 and 78 patients. The concordance rate of microbiological cultures between proximal and distal double J stent is 88% (k 0.6). The most common pathogens isolated from urine and stent cultures were Enterococcus spp. in 52 cases and Klebsiella spp. in 27 cases.

Editorial: Special Issue: "Legionella pneumophila: A Microorganism with a Thousand Faces".

Legionella pneumophila is a microorganism that is able to contaminate the freshwater environment and, consequently, human-made water systems [...].

Orogenital Human Papillomavirus Infection and Vaccines: A Survey of High- and Low-Risk Genotypes Not Included in Vaccines.

Knowledge of human papillomavirus transmission from the genital tract to the oral mucosa remains unsatisfactory, with poor and often inconsistent literature results. The increase in HPV-associated oral malignancies prompts further analysis of the simultaneous detection of the virus in the two anatomical areas and on the identification of genotypes to be included in future vaccines. Therefore, in this retrospective study, we evaluated orogenital HPV concurrence, hrHPV, lrHPV and type-concordance in 337 samples, as well as the prevalence of the most common genotypes not included in HPV vaccines. Concurrence was found in 12.5% (31/248) of cases, hr-concordance in 61.3% (19/31) and lr-concordance in 12.9% (4/31). Finally, type-concordance was found in 32.3% (10/31) of concurrent infections. Regarding the identification of non-vaccine genotypes, the significantly prevalent genotypes in the anogenital area were HPV66 (12.6%, p < 0.0001), HPV53 (11.1%, p < 0.0001), HPV51 (8.7%, p < 0.0001), HPV42 (8.2%, p < 0.0001) and HPV68 (5.6%, p = 0.0034) in women and HPV66 (14.6%, p = 0.0058), HPV42 (12.2%, p = 0.0428), HPV51 (12.2%, p = 0.0428), HPV53 (12.2%, p = 0.0428), HPV70 (12.2%, p = 0.0428) and HPV73 (12.2%, p = 0.0428) in men. Considering the results of our study, we recommend including the high-risk genotypes HPV51, HPV68, HPV53 and HPV66 in future HPV vaccine formulations.

Intestinal Lesions Due to Rhodococcus equi in a Patient With Advanced Retroviral Disease and Pulmonary Infection: A Case of Colonic Malakoplakia.

In humans, Rhodococcus equi (R. equi) is a zoonotic infection usually involving immunocompromised subjects, only rarely affecting immunocompetent subjects. Herein, we describe an R. equi infection in a 50-year-old Russian man with acquired immune deficiency syndrome (AIDS) who presented with pulmonary cavitary lesions and clinical manifestation of colonic malakoplakia. A colonoscopy examination showed ulceration and mucosal erosion, and the histological findings confirmed the colonic malakoplakia. The patient recovered from pulmonary and gastrointestinal disease after four weeks of antibiotic treatment with intravenous ciprofloxacin and oral azithromycin and also underwent subsequent long-term oral antibiotic treatment to achieve clinical and immune restoration after antiretroviral therapy. Infectious disease pathology subspecialties should always consider R. equi chronic infection as a cause of malakoplakia in patients with AIDS. As only a few cases of colonic malakoplakia associated with R. equi are reported in the literature, these cases are important to describe, especially for clinical and treatment management.

A Serological Analysis of the Humoral Immune Responses of Anti-RBD IgG, Anti-S1 IgG, and Anti-S2 IgG Levels Correlated to Anti-N IgG Positivity and Negativity in Sicilian Healthcare Workers (HCWs) with Third Doses of the mRNA-Based SARS-CoV-2 Vaccine: A Retrospective Cohort Study.

BACKGROUND: With SARS-CoV-2 antibody tests on the market, healthcare providers must be confident that they can use the results to provide actionable information to understand the characteristics and dynamics of the humoral response and antibodies (abs) in SARS-CoV-2-vaccinated patients. In this way, the study of the antibody responses of healthcare workers (HCWs), a population that is immunocompetent, adherent to vaccination, and continuously exposed to different virus variants, can help us understand immune protection and determine vaccine design goals. METHODS: We retrospectively evaluated antibody responses via multiplex assays in a sample of 538 asymptomatic HCWs with a documented complete vaccination cycle of 3 doses of mRNA vaccination and no previous history of infection. Our sample was composed of 49.44% males and 50.56% females, with an age ranging from 21 to 71 years, and a mean age of 46.73 years. All of the HCWs' sera were collected from April to July 2022 at the Sant'Elia Hospital of Caltanissetta to investigate the immunologic responses against anti-RBD, anti-S1, anti-S2, and anti-N IgG abs. RESULTS: A significant difference in age between HCWs who were positive and negative for anti-N IgG was observed. For anti-S2 IgG, a significant difference between HCWs who were negative and positive compared to anti-N IgG was observed only for positive HCWs, with values including 10 (U/mL)-100 (U/mL); meanwhile, for anti-RBD IgG and anti-S1 IgG levels, there was only a significant difference observed for positive HCWs with diluted titers. For the negative values of anti-N IgG, among the titer dilution levels of anti-RBD, anti-S1, and anti-S2 IgG, the anti-S2 IgG levels were significantly lower than the anti-RBD and anti-S1 levels; in addition, the anti-S1 IgG levels were significantly lower than the anti-RBD IgG levels. For the anti-N IgG positive levels, only the anti-S2 IgG levels were significantly lower than the anti-RBD IgG and anti-S1 IgG levels. Finally, a logistic regression analysis showed that age and anti-S2 IgG were negative and positive predictors of anti-N IgG levels, respectively. The analysis between the vaccine type and mixed mRNA combination showed higher levels of antibodies in mixed vaccinated HCWs. This finding disappeared in the anti-N positive group. CONCLUSIONS: Most anti-N positive HCWs showed antibodies against the S2 domain and were young subjects. Therefore, the authors suggest that including the anti-SARS-CoV-2-S2 in antibody profiles can serve as a complementary testing approach to qRT-PCR for the early identification of asymptomatic infections in order to reduce the impact of potential new SARS-CoV-2 variants. Our serological investigation on the type of mRNA vaccine and mixed mRNA vaccines shows that future investigations on the serological responses in vaccinated asymptomatic patients exposed to previous infection or reinfection are warranted for updated vaccine boosters.

Staphylococcus aureus and Coagulase-Negative Staphylococci from Bloodstream Infections: Frequency of Occurrence and Antimicrobial Resistance, 2018-2021.

BACKGROUND: The abuse of antibiotics during the SARS-CoV-2 pandemic might have disrupted efforts to curb the further development and spread of the antimicrobial resistance of Staphylococcus aureus infection and Staphylococcus spp. coagulase-negative (CoNS) agents of nosocomial bloodstream infections (NBSIs). The purpose of our work was to study the resistance patterns of Staphylococcus aureus and CoNS through the analysis of blood cultures in hospitalized SARS-CoV-2-positive and SARS-CoV-2-negative patients (pts.). MATERIALS AND METHODS: During the period January 2018-June 2021, a retrospective case-control study was performed on blood cultures positive for Staphylococcus spp. detected in 177 adult pts. (≥18 years old) hospitalized for >48 hours at Sant'Elia Hospital, Caltanissetta. RESULTS: Staphylococcus aureus was isolated in 33.9% of blood culture samples, and among CoNS, the most frequent strains were Staphylococcus capitis (18.6%) and Staphylococcus hominis (18.1%). Patients aged ≥ 65 years, with a greater number of males, comprised the SARS-CoV-2-negative pts. (71.8% vs. 52.2%, p = 0.0154). Among the SARS-CoV-2-positive patients, the significant resistance of Staphylococcus aureus was only observed for erythromycin (57.1%). The oxacillin resistance of Staphylococcus capitis was higher in SARS-CoV-2-positive than in negative pts. (90% and 78.3%, respectively). Comparing the two groups, we found an increase in resistance in SARS-CoV-2-negative patients for the following antibiotics: gentamicin for Staphylococcus aureus (p = 0.007), clindamycin and erythromycin (p = 0.012) for Staphylococcus hominis and oxacillin and rifampicin for Staphylococcus haemoliticus (p = 0.012). CONCLUSIONS: Our study confirms the relevance of oxacillin-resistant Staphylococcus aureus in being responsible for bloodstream infection and draws attention to highly oxacillin-resistant CoNS such as Staphylococcus capitis. The presence of resistant strains of CoNS in hospitals can be worrying, as it limits treatment options and worsens outcomes. The Infection Control Committee (ICC) recommends new treatment strategies to decrease colonization and infections. As part of the implementation of a bloodstream infection prevention program, the authors encourage the introduction of a report on the antimicrobial resistance of hospital bacteremia due to CoNS.

Helicobacter pylori and Epstein-Barr Virus Co-Infection in Gastric Disease: What Is the Correlation with p53 Mutation, Genes Methylation and Microsatellite Instability in a Cohort of Sicilian Population?

Genetic predisposition, environmental factors, and infectious agents interact in the development of gastric diseases. Helicobacter pylori (Hp) and Epstein-Barr virus (EBV) infection has recently been shown to be correlated with these diseases. A cross-sectional study was performed on 100 hospitalized Italian patients with and without gastric diseases. The patients were stratified into four groups. Significant methylation status differences among CDH1, DAPK, COX2, hMLH1 and CDKN2A were observed for coinfected (Hp-EBV group) patients; particularly, a significant presence of COX2 (p = 0.0179) was observed. For microsatellite instability, minor stability was described in the Hp-HBV group (69.23%, p = 0.0456). Finally, for p53 mutation in the EBV group, exon 6 was, significantly, most frequent in comparison to others (p = 0.0124), and in the Hp-EBV group exon 8 was, significantly, most frequent in comparison to others (p < 0.0001). A significant positive relationship was found between patients with infection (Hp, EBV or both) and p53 mutation (rho = 0.383, p = 0.0001), methylation status (rho = 0.432, p < 0.0001) and microsatellite instability (rho = 0.285, p = 0.004). Finally, we observed among infection and methylation status, microsatellite instability, and p53 mutation a significant positive relationship only between infection and methylation status (OR = 3.78, p = 0.0075) and infection and p53 mutation (OR = 6.21, p = 0.0082). According to our analysis, gastric disease in the Sicilian population has different pathways depending on the presence of various factors, including infectious agents such as Hp and EBV and genetic factors of the subject.

Aggregatibacter aphrophilus and Eikenella corrodens: a case of brain abscess.

We report a case of a 26-year-old female who developed a brain abscess that was strongly suspected to be caused by Staphylococcus epidermidis, A. aphrophilus, and E. corrodens species. In general, A. aphrophilus and E. corrodens, members of the HACEK group (Haemophilus spp., Aggregatibacter spp., C. hominis, E. corrodens, and K. kingae), have been associated with the development of endocarditis, meningitis, sinusitis, otitis media, pneumonia, osteomyelitis, peritonitis, and wound infections. Cerebral abscesses are a rare manifestation of these bacteria; only a few cases are described in the literature, generally related to the diffusion of these organisms through the bloodstream after a dental procedure or a heart disease. Our case is unique because the rarity of the infection site appeared apparently in absence of risk factors. The patient underwent surgery to drain the abscess and was subsequently put on intravenous antibiotic treatment with ceftriaxone, vancomycin, and metronidazole. After 6 months, brain imaging revealed that the lesion had disappeared. The patient achieved excellent results with this approach.

Multicentre Surveillance of Candida Species from Blood Cultures during the SARS-CoV-2 Pandemic in Southern Europe (CANCoVEU Project).

Introduction: Surveillance of Candida species isolates from blood cultures (BCs) in Europe is considered fragmented, unable to allow the definition of targets of antifungal stewardship recommendations especially during the SARS-CoV-2 pandemic. Methods: We performed a multicentric retrospective study including all consecutive BC Candida isolates from six Southern European tertiary hospitals (1st January 2020 to 31st December 2021). Etiology, antifungal susceptibility patterns, and clinical setting were analyzed and compared. Results: C. albicans was the dominant species (45.1%), while C. auris was undetected. Candida species positive BC events increased significantly in COVID-19 ICUs in 2021 but decreased in other ICUs. Resistance to azole increased significantly and remained very high in C. albicans (fluconazole from 0.7% to 4.5%, p = 0.03) and C. parapsilosis complex (fluconazole up to 24.5% and voriconazole up to 8.9%), respectively. Resistance to caspofungin was remarkable in C. tropicalis (10%) and C. krusei (20%), while resistance to at least one echinocandin increased in 2021, especially in C. parapsilosis complex (from 0.8% to 5.1%, p = 0.05). Although no significant differences were observed over the study period, fluconazole and echinocandin resistance increased in COVID-19 ICUs by up to 14% and 5.8%, respectively, but remained undetected in non-intensive COVID-19 wards. Conclusions: Antifungal stewardship activities aimed at monitoring resistance to echinocandin in C. tropicalis and C. krusei, and against the spread of fluconazole resistant C. parapsilosis complex isolates are highly desirable. In COVID-19 patients, antifungal resistance was mostly present when the illness had a critical course.

Multicenter study on the prevalence of colonization due to carbapenem-resistant Enterobacterales strains before and during the first year of COVID-19, Italy 2018-2020.

Background: Among multidrug-resistant (MDR) bacteria able to threaten human health, carbapenem-resistant Enterobacterales (CRE) have become a major public health threat globally. National and international guidelines point out the importance of active routine surveillance policies to prevent CRE transmission. Therefore, defining lines of intervention and strategies capable of containing and controlling the spread of CRE is considered determinant. CRE screening is one of the main actions to curb transmission and control outbreaks, outlining the presence and also the prevalence and types of carbapenemase enzymes circulating locally. Objective: The purpose of this study was to outline the epidemiology of CRE colonization in Italy, detecting CRE-colonized patients at admission and during hospitalization, before and during the first year of COVID-19. Materials and methods: A total of 11,063 patients admitted to seven different hospitals (Bologna, Catania, Florence, Genoa, Naples, Palermo, and Turin) in Intensive Care Units (ICU) and other wards (non-ICU) located in the North, Center, and South of Italy were enrolled and screened for CRE carriage at admission (T0) and during the first 3 weeks of hospitalization (T1-T3). The study spanned two periods, before (September 2018-Septemeber 2019, I observational period) and during the COVID-19 pandemic (October 2019-September 2020, II observational period). Results: Overall, the prevalence of CRE-colonized patients at admission in ICU or in other ward, ranged from 3.9 to 11.5%, while a percentage from 5.1 to 15.5% of patients acquired CRE during hospital stay. There were large differences between the I and II period of study according to the different geographical areas and enrolling centers. Overall, comparison of prevalence of CRE-positive patients showed a significant increased trend between I and II observational periods both in ICU and non-ICU wards, mostly in the Southern participating centers. KPC-producing Klebsiella pneumoniae was the most frequent CRE species-carbapenemase combination reported in this study. In particular, the presence of KPC-producing K. pneumoniae was reported in period I during hospitalization in all the CRE-positive patients enrolled in ICU in Turin (North Italy), while in period II at admission in all the CRE-positive patients enrolled in ICU in Catania and in 58.3% of non-ICU CRE-positive patients in Naples (both centers in South Italy). Conclusion: The prevalence of CRE in Italy highly increased during the COVID-19 pandemic, mostly in the Southern hospital centers. KPC-producing K. pneumoniae was the most frequent colonizing CRE species reported. The results of our study confirmed the crucial value of active surveillance as well as the importance of multicenter studies representing diverse geographical areas even in endemic countries. Differences in CRE colonization prevalence among centers suggest the need for diversified and center-specific interventions as well as for strengthening efforts in infection prevention and control practices and policies.

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease.

Microbiotas are the range of microorganisms (mainly bacteria and fungi) colonizing multicellular, macroscopic organisms. They are crucial for several metabolic functions affecting the health of the host. However, difficulties hamper the investigation of microbiota composition in cultivating microorganisms in standard growth media. For this reason, our knowledge of microbiota can benefit from the analysis of microbial macromolecules (DNA, transcripts, proteins, or by-products) present in various samples collected from the host. Various omics technologies are used to obtain different data. Metagenomics provides a taxonomical profile of the sample. It can also be used to obtain potential functional information. At the same time, metatranscriptomics can characterize members of a microbiome responsible for specific functions and elucidate genes that drive the microbiotas relationship with its host. Thus, while microbiota refers to microorganisms living in a determined environment (taxonomy of microorganisms identified), microbiome refers to the microorganisms and their genes living in a determined environment and, of course, metagenomics focuses on the genes and collective functions of identified microorganisms. Metabolomics completes this framework by determining the metabolite fluxes and the products released into the environment. The gallbladder is a sac localized under the liver in the human body and is difficult to access for bile and tissue sampling. It concentrates the bile produced in the hepatocytes, which drains into bile canaliculi. Bile promotes fat digestion and is released from the gallbladder into the upper small intestine in response to food. Considered sterile originally, recent data indicate that bile microbiota is associated with the biliary tract's inflammation and carcinogenesis. The sample size is relevant for omic studies of rare diseases, such as gallbladder carcinoma. Although in its infancy, the study of the biliary microbiota has begun taking advantage of several omics strategies, mainly based on metagenomics, metabolomics, and mouse models. Here, we show that omics analyses from the literature may provide a more comprehensive image of the biliary microbiota. We review studies performed in this environmental niche and focus on network-based approaches for integrative studies.

Impact of Mycobacterium tuberculosis Infection on Human B Cell Compartment and Antibody Responses.

Tuberculosis (TB) remains one of the most important health challenges worldwide. Control of the TB epidemic has not yet been achieved because of the lack of an effective vaccine and rapid and sensitive diagnostic approaches, as well as the emergence of drug-resistant forms of M. tuberculosis. Cellular immunity has a pivotal role against M. tuberculosis infection, but the role of humoral immunity is still controversial. We analyzed the frequency, absolute counts, and phenotypic and functional subsets of B lymphocytes in the peripheral blood of patients with active TB and subjects with latent infection compared to healthy donors. Moreover, we analyzed serum levels of total Ig and their IgA, IgM, and IgG isotypes and the titers of preexisting antibodies against a pool of common viral pathogens. FlowCT and unsupervised clusterization analysis show that patients with active TB and LTBI subjects have modest non-significant reduction in the numbers of circulating B lymphocytes as compared to healthy donors. Moreover, LTBI subjects had high percentages of atypical B cell population and lower percentages of naive and switched memory B cells. These findings were supported by gene expression and GSEA analysis. Moreover, there were no differences between active TB patients, LTBI subjects and HD, either in serum levels of total Ig isotypes or in preexisting IgG antibody titers, to ten different antigens from eight common pathogenic viruses, clearly demonstrating that either active or latent M. tuberculosis infection preserves the antibody production capacity of long-lived plasma cells. Thus, our results agree with previous studies reporting unaltered B cell frequencies in the blood of active TB patients and LTBI individuals as compared to healthy controls.

Clostridium difficile Induced Inflammasome Activation and Coagulation Derangements.

C. difficile enterocolitis (CDAC) is the most common hospital infection, burdened by an increased incidence of coagulation-related complications such as deep vein thrombosis (DVT) and disseminated intravascular coagulation (DIC) as well as a significant sepsis-related mortality. In this review, we analyzed the available data concerning the correlation between coagulation complications related to C. difficile infection (CDI) and inflammasome activation, in particular the pyrin-dependent one. The little but solid available preclinical and clinical evidence shows that inflammasome activation increases the risk of venous thromboembolism (VTE). As proof of this, it has been observed that in vitro inhibition of the molecules (e.g., tissue factor) mainly involved in coagulation activation could block the process. In vivo studies show that it could be possible to reduce the incidence of complications associated with C. difficile infection (CDI) and mortality due to a state of hypercoagulability. A personalized therapeutic approach to reduce the inflammatory activity and prevent thromboembolic complications could be preliminarily defined to reduce mortality.

Spread of Multidrug-Resistant Microorganisms.

Multidrug-resistant organisms (MDRO) are bacteria that exhibit acquired resistance to multiple antibiotics, reducing the efficacy of antimicrobial therapies [...].