Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.

Xeruborbactam is a broad-spectrum boronate-type β-lactamase inhibitor. We aimed to evaluate its activity in combination with meropenem and compare it with other β-lactam/β-lactamase inhibitor combinations against Enterobacterales. The following isolates were screened: (i) an isogenic collection of 94 Escherichia coli isolates producing β-lactamases under wild-type and low-permeability conditions, (ii) 300 genetically diverse clinical Enterobacterales isolates producing the three main carbapenemase types (KPC-like, OXA-48-like, and metallo-β-lactamases), and (iii) two collections of isolates producing mechanisms of resistance to β-lactam/β-lactamase inhibitor combinations, such as KPC variants or PBP3 insertions combined with metallo-β-lactamases (MBLs). The MICs of meropenem, meropenem/xeruborbactam, meropenem/vaborbactam, imipenem, imipenem/relebactam, cefepime, cefepime/taniborbactam, ceftazidime, ceftazidime/avibactam, aztreonam, and aztreonam/avibactam were determined by reference broth microdilution and interpreted following the European Committee on Antimicrobial Susceptibility Testing guidelines, using the breakpoint of the β-lactam alone for not yet approved combinations. Resistance mechanisms of all clinical isolates were analyzed by whole genome sequencing. Meropenem/xeruborbactam had the broadest spectrum against the isogenic collection, although higher MICs were noted for transformants producing IMP-23, SPM-1, and NDM enzymes (these latter only when produced under low-permeability conditions). Meropenem/xeruborbactam displayed the most potent activity against the collection of 300 clinical strains (MIC _50/90 ≤0.06/≤0.06 mg/L). Xeruborbactam restored meropenem activity against the strains carrying resistance mechanisms to β-lactam/β-lactamase inhibitor combinations, including strains producing KPC variants or MBLs in combination with additional chromosomal alterations (MIC range: ≤0.06–0.25 and ≤0.06–4 mg/L, respectively). Our findings highlight the potential of xeruborbactam in combination with meropenem as a promising treatment against carbapenemase-producing Enterobacterales, including strains with emerging resistance to other β-lactam/β-lactamase inhibitor combinations.

Objectives: To generate in vitro ceftazidime-avibactam-resistant mutants derived from Klebsiella pneumoniae producing OXA-48 or OXA-48 derivatives OXA-131 and OXA-232 carbapenemases, to define their antimicrobial susceptibility phenotype and to analyse mutations potentially involved in resistance to ceftazidime-avibactam. Methods: Mutants were obtained by plating overnight bacterial cultures on Mueller-Hinton agar plates containing increasing concentrations of ceftazidime-avibactam (0.5/4–32/4 mg/L). MICs were determined using Sensititre™ DKMNG panels. Whole-genome sequencing of 8 parental strains and 31 mutant derivatives was performed with Illumina. Results: All parental strains were susceptible to ceftazidime-avibactam (MIC ≤ 0.5/4–2/4 mg/L) and either susceptible or resistant to meropenem (MIC 0.5 to >16 mg/L) and imipenem (MIC ≤ 0.5 to >16 mg/L). MICs of ceftazidime-avibactam for the mutants increased up to 4 to >16 mg/L, while MICs of meropenem and imipenem for most mutants either increased up to >16 mg/L or remained unchanged. Whole-genome sequencing of the mutants identified alterations in genes coding for proteins related to AcrAB-TolC (AcrB, AcrR), PBPs (PBP2, PBP3), porins (OmpK36, EnvZ) or the stress or stringent responses (RseB, CpxA, SpoT). No mutations were detected in genes coding for OXA-48-like enzymes or other β-lactamases. Conclusions: Ceftazidime-avibactam can select in vitro mutants of OXA-48-like carbapenemase-producing K. pneumoniae resistant to this combination and, in some cases, also to carbapenems. No mutations related to ceftazidime-avibactam resistance were found in genes coding OXA-48-like enzymes, but they were detected in genes related to active efflux, PBPs, permeability or proteins of the stress and stringent responses.

The Clinical Trial of Sarilumab in Adults With COVID-19 (SARICOR) showed that patients with coronavirus disease 2019 (COVID-19) pneumonia and increased levels of interleukin (IL)-6 might benefit from blockade of the IL-6 pathway. However, the benefit from this intervention might not be uniform. In this subanalysis, we sought to determine if other immunoactivation markers, besides IL-6, could identify which subgroup of patients benefit most from this intervention. The SARICOR trial was a phase II, open-label, multicenter, controlled trial (July 2020–March 2021) in which patients were randomized to receive usual care (UC; control group), UC plus a single dose of sarilumab 200 mg (sarilumab-200 group), or UC plus a single dose of sarilumab 400 mg (sarilumab-400 group). Patients who had baseline serum samples for cytokine determination (IL-8, IL-10, monocyte chemoattractant protein–1, interferon-inducible protein [IP]-10) were included in this secondary analysis. Progression to acute respiratory distress syndrome (ARDS) according to cytokine levels and treatment received was evaluated. One hundred one (88%) of 115 patients enrolled in the SARICOR trial had serum samples (control group: n = 33; sarilumab-200: n = 33; sarilumab-400: n = 35). Among all evaluated biomarkers, IP-10 showed the strongest association with treatment outcome. Patients with IP-10 ≥2500 pg/mL treated with sarilumab-400 had a lower probability of progression (13%) compared with the control group (58%; hazard ratio, 0.19; 95% CI, 0.04–0.90; P = .04). Conversely, patients with IP-10 40 pg/mL. Importantly, IP-10 value <2500 pg/mL might discriminate those individuals who might not benefit from sarilumab therapy among those with high IL-6 levels.

Background/Objectives: Ceftazidime-avibactam (CAZ/AVI) and cefiderocol (FDC) retain activity against most clinical isolates of KPC-producing Klebsiella pneumoniae (KPC-Kp). Nevertheless, the emergence of cross-resistance between both agents has become an increasing clinical concern. In this study, the development of resistance to both CAZ/AVI and FDC was retrospectively investigated in KPC-Kp isolates recovered from patients treated with CAZ/AVI between 2014 and 2023. Methods: Twenty-two isolates (pre- and post-therapy) obtained from nine patients were included. Demographic and clinical data were collected. FDC susceptibility testing was determined for both clinical isolates and E. coli TOP10 transformants by reference broth microdilution using iron-depleted medium, and MICs were interpreted according to EUCAST breakpoints. Resistance mechanisms were characterized using whole genome sequencing. Results: Cross-resistance to both CAZ/AVI and FDC emerged in six patients (66.7%) during CAZ/AVI therapy, after a median treatment duration of 12.8 ± 7.6 days. The presence of different KPC-3 variants in the CAZ/AVI-FDC resistant isolates was revealed by genomic analysis. Furthermore, the role of KPC-28, KPC-31, KPC-47, KPC-94, KPC-95, and KPC-148 in mediating reduced susceptibility to CAZ/AVI and FDC was confirmed by AST of transformants carrying bla_KPC variants. However, differences in MIC values compared with those obtained for the corresponding clinical isolates supported the relevance of additional mechanisms of co-resistance. The presence of ferric citrate transport (FEC) system was also associated with higher FDC MICs. Mutations in genes coding siderophore-iron transporter, PBPs, sensor histidine kinase or Tol-Pal system were also found in some of the isolates. Conclusions: These findings highlight the ability of KPC-Kp to develop co-resistance to both CAZ/AVI and FDC during CAZ/AVI therapy.

Background/Objectives: The susceptibility of Corynebacterium spp. to antimicrobial agents is species-related, with increasing levels of resistance to fluoroquinolones in several species related to their continued use in clinical practice. The objectives were to determine the in vitro activity of delafloxacin in comparison with other fluoroquinolones against clinical isolates of Corynebacterium spp., to compare MICs of delafloxacin obtained with gradient strips and with reference microdilution, and to investigate the mechanisms related to fluoroquinolone resistance in the tested strains. Methods: Fifty-three clinical isolates, assigned to five species of Corynebacterium spp., were evaluated using reference microdilution for delafloxacin, ciprofloxacin, levofloxacin, and moxifloxacin (with and without reserpine or phenylalanine-arginine β-naphthylamide), and gradient strips for delafloxacin. The QRDR of the gyrA gene was amplified using primers specific to the different species, and mutations were defined after aligning against the corresponding reference sequences. Results: Delafloxacin was the most active compound with MIC₅₀/MIC₉₀ values of 0.5/8 mg/L. Single mutations at the QRDR were observed in isolates, with MICs of delafloxacin ranging from 0.016 to 4 mg/L, while double mutations occurred in isolates, with MICs ranging from 0.125 to 16 mg/L. The delafloxacin gradient strips showed an essential agreement of 88.7%, bias of −5%, and a Kappa index of 0.848. Conclusions: Increased MICs of delafloxacin against Corynebacterium spp. are related to the presence of non-conservative mutations in the QRDR of gyrA. Delafloxacin gradient strips could be a reasonable alternative for use in the clinical routine of the microbiology laboratory. Delafloxacin could represent an alternative for treating infections due to some species of Corynebacterium.