Complete genome sequence of invasive Streptococcus pneumoniae serotype 11A causing meningitis in an adult patient, Italy 2022.

Streptococcus pneumoniae is a major global health concern, being a common cause of meningitis in both children and adults. Here, we report the complete genome sequence of P10_PNE_LCR, a S. pneumoniae 11A strain isolated in Northern Italy from an adult patient diagnosed with meningitis.

Performance evaluation of Bruker UMIC® microdilution panel and disc diffusion to determine cefiderocol susceptibility in Enterobacterales, Acinetobacter baumannii, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter xylosoxidans and Burkolderia species.

PURPOSE: Cefiderocol susceptibility testing (AST) represents an open challenge for clinical microbiology. Herein, we evaluated the performance of the UMIC® Cefiderocol broth microdilution (BMD) test and disc diffusion on Gram-negative species. METHODS: UMIC® Cefiderocol BMD test, disc diffusion and reference BMD were in parallel performed on a collection of 256 clinical isolates. Categorical agreement (CA), essential agreement (EA), bias, major errors (MEs) and very major errors (VMEs) were calculated for both AST methods. RESULTS: The UMIC® Cefiderocol BMD strip exhibited an EA < 90% (85.5%), a CA higher than 90% (93.7%) and a low number of VMEs (n = 4, 4.2%) and MEs (n = 12, 7.4%). UMIC® Cefiderocol identified 96.2% of the resistant isolates [Enterobacterales, (39/40); P. aeruginosa (19/19); A. xylosoxidans (5/6); S. maltophilia (5/6); Burkholderia spp. (8/8)]. Disc diffusion showed a high CA (from 94.9 to 100%) regardless of disc manufacturer in Enterobacterales, P. aeuroginosa, A. baumannii and S. maltophilia. However, high rates of results falling in the area of technical uncertainty (ATU) were observed in Enterobacterales (34/90, 37.8%) and P. aeruginosa (16/40, 40%). Disc diffusion showed a poor performance in A. xylosoxidans and Burkholderia spp. if PK/PD breakpoint was used (overall, 5/9 VMEs; in contrast, the use of P. aeruginosa-specific breakpoints resulted in 100% of CA with 24.6% of results in the ATU). CONCLUSION: In conclusion, disc diffusion and UMIC® Cefiderocol are valid methods for the determination of cefiderocol susceptibility. Given the high number of results in the ATU by disc diffusion, a combined use of both AST methods may represent a solution to overcome the challenge of cefiderocol susceptibility testing in routine microbiology laboratories.

Clonal Dissemination of Candida auris Clinical Isolates in Northern Italy, 2021.

Candida auris is a concerning pathogen in health care due to its ability to spread in medical settings. In this study, we characterized the genome of three C. auris clinical isolates collected in the Emilia-Romagna region of Northeastern Italy from January 2020 to May 2021. Whole-genome sequencing was performed using Illumina iSeq 100 and Oxford Nanopore MinION systems. Genomes were assembled with Flye. Phylogenetic analysis was carried out with RaxML. The ERG11, TAC1b, and FKS1 genes were examined for known substitutions associated with resistance to azoles and caspofungin using Diamond. All three C. auris isolates belonged to clade I (South Asian lineage) and showed high minimum inhibitory concentrations for fluconazole. Two of the three isolates were closely related to the first Italian index case of C. auris occurred in the 2019 and carried similar mutations associated to azole resistance. The third isolate showed a greater phylogenetic distance from these strains and had a different genetic determinant not previously seen in Italy. Our data suggest that two C. auris clinical isolates may have been epidemiologically related to the first outbreak previously observed in Italy, while the remaining isolate may have originated from a different source. Further research is needed to understand C. auris transmission and resistance and to control its spread.

In Vitro Evaluation of Increasing Avibactam Concentrations on Ceftazidime Activity against Ceftazidime/Avibactam-Susceptible and Resistant KPC-Producing Klebsiella pneumoniae Clinical Isolates.

The novel ß-lactam/ß-lactamase inhibitor combinations (ßL-ßLICs) are one of the last-line resources available against multidrug-resistant (MDR) Gram-negative bacteria. Among ßL-ßLICs, ceftazidime/avibactam (CAZ-AVI) demonstrated strong activity against carbapenem-resistant Enterobacterales (CRE). Avibactam was proven to restore bactericidal activity of ceftazidime, inhibiting both KPC and OXA-48-like ß-lactamases. Despite this, emergence of CAZ-AVI-resistant strains in Enterobacterales has been reported. Herein, we evaluated the in vitro ceftazidime activity in the presence of increasing concentrations of avibactam by the broth microdilution method against CAZ-AVI-susceptible and resistant genome-characterized KPC-producing K. pneumoniae (KPC-Kp) clinical isolates. Strains expressing KPC and co-expressing KPC/OXA-181 carbapenemase were selected on the basis of the different phenotypic traits for novel ßL-ßLICs and cefiderocol. Notably, avibactam at 8 mg/L maintained the MIC of ceftazidime above the clinical breakpoint in 14 out of 15 (93%) KPC-Kp resistant to CAZ-AVI. A high concentration of avibactam (i.e., 64 mg/L) is required to observe a bactericidal activity of ceftazidime against 9 out of 15 (60%) CAZ-AVI-resistant isolates. In vitro evaluation showed that with the increase in the concentration of avibactam, ceftazidime showed high activity against CAZ-AVI-susceptible strains. High concentrations of avibactam in vivo are required for ceftazidime to be active against CAZ-AVI-resistant KPC-Kp.

Could an optimized joint pharmacokinetic/pharmacodynamic target attainment of continuous infusion ceftazidime-avibactam be a way to avoid the need for combo therapy in the targeted treatment of deep-seated DTR Gram-negative infections?

The objective of this study was to assess the relationship between joint pharmacokinetic/pharmacodynamic (PK/PD) target attainment of continuous infusion (CI) ceftazidime-avibactam and the microbiological outcome of documented difficult-to-treat resistant (DTR) Gram-negative infections. A 2-year retrospective cohort study was performed in patients receiving CI ceftazidime-avibactam mono- or combo therapy for documented DTR Gram-negative infections and undergoing therapeutic drug monitoring of both ceftazidime and avibactam. The free fractions of steady-state concentrations (fCss) of ceftazidime and avibactam were calculated. The joint PK/PD target was considered optimal when both the fCss/MIC ratio for ceftazidime ≥4 (equivalent to 100% fT>4xMIC) and the fCss/CT ratio for avibactam >1 (equivalent to 100% fT >CT of 4.0 mg/L) were simultaneously achieved (quasi-optimal if only one of the two and suboptimal if neither of the two was achieved). Multivariate logistic regression analysis was applied for testing potential variables associated with microbiological failure. Fifty-eight patients were treated with CI ceftazidime-avibactam mono- (36) or combo therapy (22) for documented DTR Gram-negative infections [74.2% for primary or secondary bloodstream infections (BSIs)]. Combo therapy was administered more frequently to intensive care unit (ICU) patients (P = 0.023) or for pneumonia (P = 0.001) and less frequently for intra-abdominal infections and BSIs (P = 0.04). Microbiological failure occurred in five cases (8.6%, three in mono- and two in combo therapy). In the multivariate analysis, the suboptimal/quasi-optimal joint PK/PD target emerged as the only independent predictor of microbiological failure (odds ratio [OR] 11.11; 95% confidence interval [CI] 1.31-93.98; P = 0.023), whereas monotherapy was not (P = 0.99). Optimized joint PK/PD target attainment of CI ceftazidime-avibactam monotherapy could represent a way forward for allowing microbiological eradication of DTR Gram-negative infections and could render unnecessary combo therapy.

Clonal dissemination of Klebsiella pneumoniae resistant to cefiderocol, ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam co-producing KPC and OXA-181 carbapenemase.

Objectives: Herein, we describe the epidemiology of carbapenemase-producing Enterobacterales (CPE) before and during the COVID-19 pandemic. Also, we report the emergence of an outbreak of Klebsiella pneumoniae strains co-producing KPC and OXA-181 carbapenemase, resistant to novel ß-lactam/ß-lactamase inhibitors (ßL-ßLICs) and cefiderocol. Methods: CPE were collected during a period of 3 years from 2019 to 2021. Antimicrobial susceptibility testing for novel ßL-ßLICs and cefiderocol was performed by MIC test strips and microdilution with iron-depleted broth. WGS was performed on 10 selected isolates using the Illumina platform, and resistome analysis was carried out by a web-based pipeline. Results: Between January 2019 and December 2021, we collected 1430 carbapenemase producers from 957 patients with infections due to CPE. KPC was the most common carbapenemase, followed by VIM, OXA-48 and NDM. During 2021, we identified 78 K. pneumoniae co-producing KPC and OXA-181 carbapenemases in 60 patients, resistant to meropenem/vaborbactam and imipenem/relebactam. Resistance to ceftazidime/avibactam and cefiderocol was observed respectively in 7 and 8 out of the 10 sequenced K. pneumoniae. Genome analysis showed that all isolates were clonally related, shared a common porin and plasmid content, and carried blaOXA-181 and blaKPC carbapenemases. Specifically, 4 out of 10 isolates carried blaKPC-3, while 6 harboured mutated blaKPC. Of note, KPC producers resistant to ceftazidime/avibactam and harbouring mutated blaKPC exhibited higher MICs of cefiderocol (median MIC 16 mg/L, IQR 16-16) than strains harbouring WT blaKPC-3 (cefiderocol 9 mg/L, IQR 1.5-16). Conclusions: Our results highlight the need for continuous monitoring of CPE to limit widespread MDR pathogens carrying multiple mechanisms conferring resistance to novel antimicrobial molecules.

Pharmacokinetics/pharmacodynamics of cefiderocol administered by continuous infusion in a case series of critically ill patients with carbapenem-resistant Acinetobacter baumannii infections undergoing continuous venovenous haemodiafiltration (CVVHDF).

OBJECTIVES: To assess the pharmacokinetics/pharmacodynamics (PK/PD) of cefiderocol administered by continuous infusion (CI) in a case series of critically ill patients with carbapenem-resistant Acinetobacter baumannii (CRAB) infections undergoing continuous venovenous haemodiafiltration (CVVHDF). METHODS: Critically ill patients receiving cefiderocol by CI during CVVHDF for documented bloodstream infections (BSIs), ventilator-associated pneumonia (VAP), and/or complicated intrabdominal infections (cIAIs) caused by CRAB and undergoing therapeutic drug monitoring (TDM) from February 2022 to January 2023 were retrospectively assessed. Cefiderocol concentrations were determined at steady-state, and the free fraction (fCss) was calculated. Cefiderocol total clearance (CLtot) was determined at each TDM assessment. fCss/MIC ratio was selected as a PD determinant of cefiderocol efficacy and defined as optimal (>4), quasi-optimal (1-4), and suboptimal (<1). RESULTS: Five patients with documented CRAB infections (two BSI+VAP, two VAP, and one BSI+cIAI) were included. The maintenance dose of cefiderocol was 2 g q8h over 8 h by CI. Median average fCss was 26.5 mg/L (21.7-33.6 mg/L). Median CLtot was 4.84 L/h (2.04-5.22 L/h). Median CVVHDF dose was 41.1 mL/kg/h (35.5-44.9 mL/kg/h), and residual diuresis was reported in 4/5 cases. Optimal PK/PD target was attained in all cases, with a median cefiderocol fCss/MIC ratio of 14.9 (6.6-33.6). CONCLUSION: CI of full doses of cefiderocol could be a useful strategy to attain aggressive PK/PD targets for the treatment of severe CRAB infections in critically ill patients undergoing high-intensity CVVHDF and who have residual diuresis.

Case report of Usutu virus infection in an immunocompromised patient in Italy, 2022.

Usutu virus (USUV) is an arthropod-borne flavivirus emerged in Africa in 1950s and in Eruope in 1990s causing a massive number of birds' deaths. The role of USUV as human pathogen has been only recently hypothesized and cases of USUV infection in humans remain limited and often related to immunocompromised subjects. Herein, we report a case of USUV meningoencephalitis infection in an immunocompromised patient with no history of previous flavivirus infection. The infection due to USUV evolved rapidly since hospital admission thus resulting fatal in few days after symptoms onset and, although not proven, a suspected bacteria co-infection has been hypothesized. Based on these findings, we suggested that when USUV meningoencephalitis is suspected in countries endemic, careful attention should be applied to neurological syndromes during summer months especially among immunocompromised patients.

Synergistic Activity of Cefiderocol in Combination with Piperacillin-Tazobactam, Fosfomycin, Ampicillin-Sulbactam, Imipenem-Relebactam and Ceftazidime-Avibactam against Carbapenem-Resistant Gram-Negative Bacteria.

Limited treatment options are among the main reasons why antimicrobial resistance has become a leading major public health problem. In particular, carbapenem-resistant Enterobacteriales (CRE), Pseudomonas aeruginosa and Acinetobacter baumannii have been included by the World Health Organization (WHO) among the pathogens for which new therapeutic agents are needed. The combination of antibiotics represents an effective strategy to treat multidrug-resistant (MDR) pathogen infections. In this context, the aim of this study is to evaluate the in vitro activity of cefiderocol (CFD) in combination with different antimicrobial molecules against a collection of well-characterized clinical strains, exhibiting different patterns of antimicrobial susceptibility. Clinical strains were genomically characterized using Illumina iSeq100 platform. Synergy analyses were performed by combining CFD with piperacillin-tazobactam (PIP-TAZ), fosfomycin (FOS), ampicillin-sulbactam (AMP-SULB), ceftazidime-avibactam (CAZ-AVI), meropenem-vaborbactam (MER-VAB) and imipenem-relebactam (IMI-REL). Our results demonstrated the synergistic effect of CFD in combination with FOS and CAZ-AVI against CRE and carbapenem-resistant Acinetobacter baumannii (CR-Ab) clinical strains owing CFD-resistant profile, while the CFD and AMP-SULB combination was effective against CR-Pa strain displaying AMP-SULB-resistant profile. Moreover, the combination of CAZ-AVI/SULB showed synergistic activity in CAZ-AVI-resistant CRE strain. In conclusion, although further analyses are needed to confirm these results, our work showed the efficacy of CFD when used for synergistic formulations.

A descriptive pharmacokinetic/pharmacodynamic analysis of continuous infusion ceftazidime-avibactam for treating DTR gram-negative infections in a case series of critically ill patients undergoing continuous veno-venous haemodiafiltration (CVVHDF).

PURPOSE: To explore pharmacokinetic/pharmacodynamic (PK/PD) profile of continuous infusion (CI) ceftazidime-avibactam for treating difficult-to-treat resistant Gram-negative (DTR-GN) infections in critical patients undergoing continuous venovenous haemodiafiltration (CVVHDF). MATERIALS AND METHODS: Patients treated with CI ceftazidime-avibactam for DTR-GN infections during CVVHDF were retrospectively assessed. Ceftazidime and avibactam concentrations were measured at steady-state and the free fraction (fCss) was calculated. Total clearance (CLtot) of both agents were calculated and the impact of CVVHDF intensity was assessed by linear regression. The joint PK/PD target of ceftazidime-avibactam was defined as optimal when both fCss/MIC≥4 for ceftazidime and fCss/CT > 1 for avibactam were achieved. Relationship between ceftazidime-avibactam PK/PD targets and microbiological outcome was assessed. RESULTS: Eight patients with DTR-GN infections were retrieved. Median fCss were 84.5 (73.7-87.7 mg/L) for ceftazidime and 24.8 mg/L (20.7-25.8 mg/L) for avibactam. Median CLtot was 2.39 L/h (2.05-2.96 L/h) for ceftazidime and 2.56 L/h (2.12-2.98 L/h) for avibactam. Median CVVHDF dose was 38.6 mL/h/kg (35.9-40.0 mL/kg/h). CLtot were linearly correlated with CVVHDF dose (r = 0.53;p = 0.03, and r = 0.64;p = 0.006, respectively). The joint PK/PD targets were optimal granting microbiological eradication in all the assessable cases. CONCLUSION: CI administration of 1.25-2.5 g q8h ceftazidime-avibactam may allow prompt attainment and maintenance of optimal joint PK/PD targets during high-intensity CVVHDF.

Complete genome sequence and antimicrobial resistance analysis of ESBL-producing Shigella sonnei carrying small cryptic plasmids isolated in northern Italy.

OBJECTIVES: Herein, we sequenced and assembled the genome of a Shigella sonnei isolate carrying several small plasmids using a hybrid approach that combined Oxford Nanopore Technologies and Illumina platforms. METHODS: Whole-genome sequencing was conducted using the Illumina iSeq 100 and Oxford Nanopore MinION systems, and the resulting reads were used for hybrid genome assembly via Unicycler. Coding sequences were annotated using RASTtk, while genes involved in antimicrobial resistance and virulence were identified using AMRFinderPlus. Plasmid nucleotide sequences were aligned to the NCBI non-redundant database using BLAST, and replicons were identified using PlasmidFinder. RESULTS: The genome consisted of 1 chromosome (4 801 657 bp), 3 major plasmids (212 849 bp, 86 884 bp, and 83 425 bp, respectively) and 12 small cryptic plasmids (ranging from 8390 bp to 1822 bp). BLAST analysis revealed that all plasmids were highly similar to previously deposited sequences. Genome annotation predicted 5522 coding regions, including 19 antimicrobial resistance genes and 17 virulence genes. Four of the antimicrobial resistance genes were located in small plasmids, and four of the virulence genes were located in a large virulence plasmid. CONCLUSION: The presence of antimicrobial resistance genes in small cryptic plasmids may represent an overlooked mechanism for the propagation of these genes among bacterial populations. Our work provides new data on these elements that may inform the development of new strategies to control the spread of extended spectrum ß-lactamase-producing bacterial strains.

Comparison of Broth Microdilution, Disk Diffusion and Strip Test Methods for Cefiderocol Antimicrobial Susceptibility Testing on KPC-Producing Klebsiella pneumoniae.

The aim of this study was to compare the reference broth microdilution (BMD) method with the Disk Diffusion (DD) test and strip test against a collection of 75 well-characterized Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) clinical strains to assess cefiderocol (CFD) antimicrobial activity. Whole-genome sequencing was performed on KPC-Kp strains by Illumina iSeq100 platform. The Categorical Agreement (CA) between the BMD method and DD test was 92% (69/75) with a Major Error (ME) of 16.7% (6/36). Additionally, the CA between the BMD method and test strip was 90.7% (68/75) with a Very Major Error (VME) of 17.9% (7/39) and 82.7% (62/75) between the strip test and DD with a ME of 30.2%. KPC-Kp strains showing resistance to CFD were 27 out of 75 (36%) by three methods. Specifically, 51.9% (14/27) of KPC-Kp resistant to CFD harbored blaKPC-3, while 48.1% (13/27) harbored mutated blaKPC-3. Moreover, KPC-Kp strains carrying a mutated blaKPC-3 gene exhibited high MIC values (p value < 0.001) compared to wild-type blaKPC-3. In conclusion, the DD test resulted as a valid alternative to the BMD method to determine the in vitro susceptibility to CFD, while the strip test exhibited major limitations.

Whole Genome Sequencing of a Chlamydia trachomatis Strain Responsible for a Case of Rectal Lymphogranuloma Venereum in Italy.

Lymphogranuloma venereum (LGV) is a systemic sexually transmitted infection caused by Chlamydia trachomatis serovars L1 to L3. The current LGV cases in Europe are mainly characterized by an anorectal syndrome, spreading within men who have sex with men (MSM). Whole-genome sequencing of LGV strains is crucial to the study of bacterial genomic variants and to improve strategies for contact tracing and prevention. In this study, we described the whole genome of a C. trachomatis strain (LGV/17) responsible for a case of rectal LGV. LGV/17 strain was isolated in 2017 in Bologna (North of Italy) from a HIV-positive MSM, presenting a symptomatic proctitis. After the propagation in LLC-MK2 cells, the strain underwent whole-genome sequencing by means of two platforms. Sequence type was determined using the tool MLST 2.0, whereas the genovariant was characterized by an ompA sequence evaluation. A phylogenetic tree was generated by comparing the LGV/17 sequence with a series of L2 genomes, downloaded from the NCBI website. LGV/17 belonged to sequence type ST44 and to the genovariant L2f. Nine ORFs encoding for polymorphic membrane proteins A-I and eight encoding for glycoproteins Pgp1-8 were detected in the chromosome and in the plasmid, respectively. LGV/17 was closely related to other L2f strains, even in the light of a not-negligible variability. The LGV/17 strain showed a genomic structure similar to reference sequences and was phylogenetically related to isolates from disparate parts of the world, indicative of the long-distance dynamics of transmission.

A novel method to evaluate ceftazidime/avibactam therapy in patients with carbapenemase-producing Enterobactericeae (CPE) bloodstream infections.

INTRODUCTION: This study reports experience managing eight patients with bloodstream infections treated with a continuous infusion of ceftazidime-avibactam. METHODS: Patients who were treated for documented CPE BSIs susceptible to CAZ-AVI and who underwent real-time therapeutic drug monitoring were retrospectively assessed. Ceftazidime MICs were assessed in presence of increasing concentrations of avibactam by the broth microdilution method. An inhibitory sigmoid Emax model was used to characterize ceftazidime MIC reduction as a function of avibactam concentration, and the MICi was derived by conditioning the best-fit model using steady-state avibactam concentrations (Css). Ceftazidime fCss/MICi ratio was calculated for each patient and correlated to microbiological outcome. RESULTS: By adopting the innovative concept of effective MIC with an inhibitor (MICi), a trend towards higher microbiological failure and resistance development was found in patients with a lower ceftazidime fCss/MICi ratio (2/3 vs. 0/5). CONCLUSION: Assessment of changes in the ceftazidime MIC in relation to increasing avibactam concentration could represent a more robust pharmacokinetic/pharmacodynamic method for predicting microbiological failure given beta-lactam/beta-lactamase inhibitor combinations.

Severe Escherichia coli infections in critical adult patients: two case reports and genomic analysis.

Pathogenic Escherichia coli strains can infect a variety of body sites due to the expression of virulence factors necessary to overcome the host defenses. Here, we present two cases of E. coli infection in adults and discuss the associated genomic features. Whole-genome sequencing was performed using both Illumina iSeq 100 and Oxford Nanopore MinION systems. Assembly was carried out with Unicycler using a hybrid approach. The genomes were annotated with RASTtk and scanned for genes involved in antimicrobial resistance, virulence and stress response with AMRFinderPlus. Sequence analysis was conducted using tools from the Center for Genomic Epidemiology (CGE) website. The two strains, named SO80 and SO81, carried a genome of 5,229,956 and 5,437,935 base pairs, respectively. SO80 belonged to ST70 and carried 13 virulence factors, 6 of which were located on a 170 Kb plasmid, while SO81 belonged to ST69 and carried 29 virulence factors, 5 of which were located on a 113 Kb plasmid. Our work highlights key factors which may have contributed to the complicated clinical status of these patients, and provides new in-depth data on E. coli infections with few precedents in the literature.