Annals of Clinical Microbiology and Antimicrobials最新文献

Objectives: Rifamycin agents (rifampicin (RIF), rifapentine (RFP), rifabutin (RFB)) are the cornerstone of tuberculosis (TB) therapy. Rifamycins are metabolized into 25-deacetyl-metabolites, which have been described has active and may contribute to in vivo drug effect. However, little is known about the combined effect of rifamycins and their metabolites across different Mycobacterium tuberculosis complex (MTBC) lineages.

Methods: This study included 14 MTBC strains representing the main lineages. Minimum inhibitory concentrations (MICs) were determined using microdilution assays for the three rifamycins and their metabolites. A checkerboard assay was used to assess drug interactions, with the fractional inhibitory concentration (FIC) index calculated for synergy or antagonism.

Results: MICs varied across rifamycins, RIF and its metabolite showed the highest MICs, followed by RFP and RFB and their respective metabolites. FIC indices for rifamycin-metabolite combinations indicated additive effects (FIC between 0.5 and 1.25), with no antagonism observed, even at clinically relevant metabolite-to-parent drug ratios, and without impact of MTBC lineage.

Conclusions: Rifamycin metabolites exhibit additive effects with parent drugs, potentially enhancing bactericidal activity. This highlights that rifamycin susceptibility testing should account for both parent drugs and their metabolites, as these metabolites also exhibit antimicrobial activity. Additionally, these findings support further pharmacokinetic/pharmacodynamic studies to optimize TB treatment regimens, particularly in relation to metabolite-to-parent drug ratios in patients.

Background: The dissemination of multi-drug-resistant bacteria, particularly Methicillin-resistant Staphylococcus aureus (MRSA), necessitates exploring new alternatives for their control. Bacteriophages are promising antibiotic alternatives with unique features. Here, we have performed a comprehensive characterization of a newly isolated bacteriophage (PSK) and compared its therapeutic potential with vancomycin in vivo.

Methods: Sewage samples were processed and enriched with the MRSA S. aureus SK1 strain in a search for isolation of a lytic bacteriophage. The isolated bacteriophage was assessed in vitro in terms of thermal and pH stability and kinetic parameters using absorption and one step growth curve assays. Moreover, its potential antibacterial activity was evaluated against S. aureus SK1 lone and in combination of standard of care antibiotics used for treatment of wound infections. We further analyzed its genome to exclude the presence of any potential toxin or antibiotic resistance genes. Finally, its antibacterial potential and capability to alleviate wound infection were assessed using a murine wound-infection model.

Results: The lytic bacteriophage (PSK) was isolated as a new species of the genus Rosenblumvirus with a genome size of 17,571 bp that is free from potential resistance or virulence genes. PSK displays infectivity against 4/10 S. aureus strains including two vancomycin-resistant strains. Moreover, it demonstrates favorable infection kinetics of fast adsorption with latent period and burst size of 20 min and 123 PFU/infected cell, respectively. Stability analysis revealed thermal stability up to 60 °C with wide pH range stability (4-11). In vitro, PSK kills S. aureus SK1 with multiplicity of infection (MOI) as low as 10^- 4 with an overall mutation frequency of 2.47 × 10^- 6 CFU/mL that is further improved when combined with 0.25× MIC of oxacillin, fusidic acid or vancomycin. In vivo, a single dose of PSK in murine wound infection model exhibited a comparable performance to four doses of vancomycin, when treatment started 2 h post-infection. However, when applied 2 days post-infection, PSK demonstrates superior antibacterial activity (up to 4.58 log unit count reduction) and enhances wound closure and tissue healing.

Conclusion: These findings represent PSK as a potential vancomycin alternative effective in treating S. aureus- induced wound infections.

Background: An important knowledge gap exists on the epidemiology of blood stream infections (BSIs) in low-middle-income countries (LMICs). In this retrospective analysis, we evaluated the etiology, antimicrobial resistance (AMR) and trends of BSIs in Eritrea.

Methods: The study reviewed 9-year records (January 2014- December 2022) of 3153 patients with blood culture results available in the National Health Laboratory (NHL) archives. Relevant data included age, sex, hospital/care center, and year.

Result: During the surveillance period, we examined data from 3153 patients (1797 (57.0%) men vs. 1356 (43.0%) females, and 1.2 years (Q1: 0.01 months - Q3: 15 years). Of the samples submitted, 1026 (35.5%) samples were positive for the presence of pathogens (663(64.6%) pathogens vs. 363 (35.4%)) potential contaminants. In decreasing frequency, the most common isolates were: Coagulase-negative Staphylococcus (CoNs), 189 (28.6%); Klebsiella spp., 120 (18.2%); Escherichia coli, 66 (10.0%); Citrobacter spp., 48 (7.3%); Staphylococcus aureus, 47(7.1%); Pseudomonas aeruginosa, 34 (5.1%); and Salmonella spp., 33(5.1). The relative prevalence of BSIs changed somewhat over time (p-value < 0.001) with the isolation of multiple isolates trending upward from 2018 and onwards. Additional findings included the likely presence of extended spectrum beta lactamase (ESBL), high frequency of methicillin resistant Staphylococcus aureus (MRSA) (37(80.4%) and high rate of resistance to gentamicin (363(62.5%) and fluoroquinolones. Furthermore, the multiple antimicrobial resistances (MAR) index was relatively high (mean = 0.55, SD: ±0.23) with wide species-level variation. In a related density cluster analysis, we demonstrated a time-dependent increase in the diversity of resistotypes.

Conclusion: This study highlights the considerable health burden of AMR/or MDR in BSIs in Eritrea. Additionally, it underscores the urgent need for enhanced laboratory capacity, surveillance, institutionalisation of antibiotic stewardship programs, and robust infection control programs in hospitals across the country. The need for multidisciplinary research was also highlighted.

Metagenomic next-generation sequencing (mNGS) has greatly improved our understanding of pathogens in infectious diseases such as pulmonary tuberculosis (PTB). However, high human DNA background (> 95%) impedes the detection sensitivity of mNGS in identifying intracellular Mycobacterium tuberculosis (MTB), posing a pressing challenge for MTB diagnosis. Therefore, there is an urgent need to improve MTB diagnosis performance in PTB patients. In this study, we optimized mNGS method for diagnosis of PTB. This led to the development of the host DNA depletion assisted mNGS (HDA-mNGS) technique, which we compared with conventional mNGS and the host DNA depletion-assisted Nanopore sequencing (HDA-Nanopore) in diagnostic performance. We collected 105 bronchoalveolar lavage fluid (BALF) samples from suspected PTB patients across three medical centers to assess the clinical performance of these methods. The results of our study showed that HDA-mNGS had the highest sensitivity (72.0%) and accuracy (74.5%) in PTB detection. This was significantly higher compared to mNGS (51.2%, 58.2%) and HDA-Nanopore (58.5%, 62.2%). Furthermore, HDA-mNGS provided an increased coverage of the MTB genome by up to 16-fold. Antibiotic resistance gene analysis indicated that HDA-mNGS could provide increased depth to the detection of Antimicrobial resistance (AMR) locus more effectively. These findings indicate that HDA-mNGS can significantly improve the clinical performance of PTB diagnosis for BALF samples, offering great potential in managing antibiotic resistance in PTB patients.

Objectives: While the reported incidence of non-tuberculous mycobacterial (NTM) infections is increasing, the true prevalence remains uncertain due to limitations in diagnostics and surveillance. The emergence of rare and novel species underscores the need for characterization to improve surveillance, detection, and management.

Methods: We performed whole-genome sequencing (WGS) and/or targeted deep-sequencing using the Deeplex Myc-TB assay on all NTM isolates collected in Slovakia and the Czech Republic between the years 2019 to 2023 that were unidentifiable at the species level by the routine diagnostic line probe assays (LPA) GenoType CM/AS and NTM-DR. Minimal inhibitory concentrations against amikacin, ciprofloxacin, moxifloxacin, clarithromycin, and linezolid were determined, and clinical data were collected.

Results: Twenty-eight cultures from different patients were included, of which 9 (32.1%) met the clinically relevant NTM disease criteria. The majority of those had pulmonary involvement, while two children presented with lymphadenitis. Antimycobacterial resistance rates were low. In total, 15 different NTM species were identified, predominantly rare NTM like M. neoaurum, M. kumamotonense and M. arupense. Notably, clinically relevant M. chimaera variants were also identified with WGS and Deeplex-Myc TB, which, unlike other M. chimaera strains, appeared to be undetectable by LPA assays. Deeplex detected four mixed infections that were missed by WGS analysis. In contrast, WGS identified two novel species, M. celatum and M. branderi, which were not detected by Deeplex-Myc TB. Importantly, one of these novel species strains was associated with clinically relevant pulmonary disease.

Discussion: Our study demonstrates the clinical relevance of uncommon NTM and the effectiveness of targeted deep-sequencing combined with WGS in identifying rare and novel NTM species.

Background: Recurrent urinary tract infections (rUTIs) occur in over 20% of patients, with postmenopausal women (over 50 years old) carrying the highest risk for recurrence compared to younger women. Virulence factors such as type 1 fimbriae adhesin FimH, the outer membrane protease OmpT, and the secreted pore-forming toxin α-hemolysin (HlyA) have been shown to support the formation of intracellular bacterial communities (IBCs) within bladder epithelial cells (BECs), facilitating persistence. This study aims to characterize the virulence expression and intracellular persistence of ESBL-producing uropathogenic E. coli (E-UPEC) strains isolated from postmenopausal women with recurrent or single episode infections.

Methods: Study strains included 72 E-UPEC strains collected from patients (36 recurrent; 36 single episode) with a confirmed UTI diagnosis and control UPEC strains (CFT073 and UTI89). Patient demographics and clinical course were collected. Presence of hlyA, ompT, and fimH genes were confirmed by colony PCR, and qRT-PCR was performed using extracted RNA from a subset of 18 strains (12 recurrent; 6 single episode) grown in Luria-Bertani media and isolated from infected BECs to characterize gene expression. Bladder cell line 5637 was infected with study strains at MOI 15 for 2 h, treated with amikacin for 2 h to remove extracellular bacteria, then lysed to enumerate intracellular CFU counts.

Results: No differences in clinical characteristics between patient groups were observed. Overall prevalence of fimH, ompT, and hlyA was 99% (71/72), 82% (59/72), and 26% (19/72) respectively; presence of all three genes did not differ between recurrent and single-episode strains. Notably, all recurrent strains had significantly more intracellular CFUs compared to single episode strains (median 16,248 CFU/mL vs. 4,118 CFU/mL, p = 0.018). Intracellular expression ompT was significantly increased (p = 0.0312) in the recurrent group compared to LB media, while fimH was significantly decreased (p = 0.0365) in the single episode group compared to expression in LB media.

Conclusion: Our findings indicate strain-specific ability to persist inside BECs with the recurrent strains exhibiting increased ompT expression inside BECs and higher intracellular bacterial burden compared to strains causing single episode UTI. These results emphasize the potential microbial contributions to recurrence in postmenopausal women and warrant future investigations on the impact of antibiotic therapy and host response on IBC-supportive UPEC virulence.

Background: Mycobacterium abscessus (MABS) causes difficult-to-treat pulmonary and extra-pulmonary infections. A combination therapy comprising amikacin, cefoxitin, and a macrolide agent is recommended, but its antimicrobial activity and clinical efficacy is uncertain. Inducible resistance to macrolides (macrolides-iR) has been associated with poor clinical response in pulmonary infections, whilst for extra-pulmonary infections data are scarce.

Objectives: Herein, the aim was to evaluate the effect of the amikacin, cefoxitin, and clarithromycin combination against macrolides-iR MABS in a hollow-fiber infection model.

Methods: The hollow-fiber system was inoculated with M. abscessus subsp. abscessus type strain ATCC 19977 and treated during 10 days with the antibiotics combination. Two level of macrolide concentrations were evaluated mimicking the pharmacokinetics profiles of free (i.e. unbound) drug in blood and lung.

Results: Using blood concentrations, the combination failed to prevent bacterial growth. Using lung concentrations, the combination had a limited but significant effect on bacterial growth from day 2 to day 10. Moreover, increasing clarithromycin concentrations stabilized the amikacin-tolerance level: amikacin minimal inhibitory concentration of amikacin-tolerant strains increased over time using blood concentrations while it remained stable using lung concentrations.

Conclusions: Our finding confirms the low activity of the amikacin, cefoxitin, and clarithromycin combination against macrolide-iR MABS infection, and suggest the influence of clarithromycin concentrations on response. The low concentration of clarithromycin in blood may hamper efficacy for the treatment of extra-pulmonary MABS infection. Consequently, it should not be considered as an active molecule in the chosen antibiotic combination, as recently recommended for pulmonary infections.

Aim: Located in the Southwest Indian Ocean area (SIOA), the two French overseas territories (FOTs) of Reunion and Mayotte islands are heavily impacted by antimicrobial resistance. The aim of this study was to investigate all cases of NDM-5 and OXA-181 carbapenemase-producing Escherichia coli (CPEc) in these two FOTs between 2015 and 2020, to better understand the regional spread of these last-line treatment resistant bacteria.

Methods: All E. coli isolates not susceptible to ertapenem from various public and private hospitals on Reunion and Mayotte islands were screened for carbapenemase production. Clinical and microbiological data were collected for each case. Genotypic analysis of the isolates was carried out using WGS to determine the clonality relationship between the isolates and the genetic support of the carbapenemase-encoding genes.

Results: A total of 92 isolates of NDM-5 (n = 67) and OXA-181 (n = 25) CPEc was collected from Reunion (n = 55) and Mayotte (n = 37) islands. Whole-genome sequencing identified 4 majors STs (ST58, ST167, ST405 and ST410). Genotypic analysis demonstrated numerous intra-ST possible cross transmission events, including strains isolated in both islands. Finally, all isolates (100%) carried the bla_NDM-5 or bla_OXA-181 genes on plasmids (IncF2, IncX3), most of which were conserved and identified in various STs.

Conclusion: We highlighted the dual dissemination of successful plasmids and the worrying circulation of high-risk clones via patients transfer between these two FOTs. It is therefore essential to effectively screen these patients for CPEc carriage on admission and to take these plasmids into account when investigating intra- or inter-hospital CPEc outbreaks.

Background: Highly frequent colorectal cancer (CRC) is predicted to have 3.2 million novel cases by 2040. Tumor microenvironment (TME) bacteriome and metabolites are proposed to be involved in CRC development. In this regard, we aimed to investigate the bacteriome and metabolites of healthy, adenomatous polyp, and CRC tissues.

Methods: Sixty samples including healthy (H), adenomatous polyps (AP), adenomatous polyps-adjacent (APA), cancer tumor (CT), and cancer tumor-adjacent (CA) tissues were collected and analyzed by 16 S rRNA sequencing and ¹H NMR spectroscopy.

Results: Our results revealed that the bacteriome and metabolites of the H, AP, and CT groups were significantly different. We observed that the Lachnospiraceae family depleted concomitant with acetoacetate and beta-hydroxybutyric acid (BHB) accumulations in the AP tissues. In addition, some bacterial species including Gemella morbillorum, and Morganella morganii were enriched in the AP compared to the H group. Furthermore, fumarate was accumulated concomitant to Aeromonas enteropelogenes, Aeromonas veronii, and Fusobacterium nucleatum subsp. animalis increased abundance in the CT compared to the H group.

Conclusion: These results proposed that beneficial bacteria including the Lachnospiraceae family depletion cross-talk with acetoacetate and BHB accumulations followed by an increased abundance of driver bacteria including G. morbillorum, and M. morganii may reprogram polyp microenvironment leading to tumor initiation. Consequently, passenger bacteria accumulation like A. enteropelogenes, A.veronii, and F. nucleatum subsp. animalis cross-talking fumarate in the TME may aggravate cancer development. So, knowledge of TME bacteriome and metabolites might help in cancer prevention, early diagnosis, and a good prognosis.