Annals of Clinical Microbiology and Antimicrobials最新文献

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.

We describe pulmonary cryptococcosis in a 28-year-old previously healthy man. Exhaustive immunological investigations revealed a primary NK cell deficiency associated with a secondary impaired anti-Cryptococcus CD8 lymphocyte response and the expansion of a CD8Vβ14 + T cell clone. This case illustrates the potential role of NK cells in immunity against Cryptococcus.

Objective: To examine the characteristics and spatiotemporal changes in the phenotypes and genotypes of extended-spectrum β-lactamases (ESBLs) in Escherichia coli strains isolated from bloodstream infections (BSIs) across China between 2014 and 2021.

Methods: 983 ESBL-positive E. coli strains were collected from BSIs in 66 hospitals across different geographic regions in China from 2014 to 2021. The phenotypic confirmation of ESBL was performed through the double-disc diffusion method. The genetic type was determined using polymerase chain reaction (PCR) followed by DNA sequencing.

Results: Between 2014 and 2021, the prevalence of ESBL-positive E. coli steadily decreased from 61.2 to 49.6%. Among 983 phenotypically confirmed ESBL-positive E. coli, 763 (77.6%) were confirmed to carry ESBL genes, with the majority being of the CTX-M type, which is further divided into 23 subtypes and dominated by the CTX-M-9 and CTX-M-1 groups, with 457/763 and 333/763, respectively. Other ESBLs and ampC genes, such as bla_OXA-1, bla_CMY, and bla_DHA-1, often coexisted with either the CTX-M-9 or CTX-M-1 groups. bla_CTX-M-14 (34.3%, 157/457) and bla_CTX-M-55 (45.9%, 153/333) were the dominant subtypes in the CTX-M-9 and CTX-M-1 groups, respectively. A notable increase in bla_CTX-M-27 was observed, particularly from 2019 to 2021, with 26.4%, 23.1%, and 25.8% in all genotypes. Regarding the geographical distribution of the ESBLs, the highest rate of ESBL genetic positivity was observed in Southwest China, accounting for 84.9% (45/53), and the lowest was observed in Northeast China, with 73.2% (30/41). The abundance of the bla_CTX-M-27 genotype, in particular, exhibited a notable increase in Southwest China, with 31.4% (14/45) of the strains exhibiting this genotype, followed by the CTX-M-55 genotype, with 13.6% (6/45) of the strains exhibiting this genotype.

Conclusions: This study demonstrated a steadily decreasing trend in the incidence of ESBLs and predominant CTX-M type ESBLs, particularly the CTX-M-9 and CTX-M-1 groups, in E. coli strains across China, a notable increase in the bla_CTX-M-27 genotype and regional variations in the ESBL gene distribution were detected.

Background: Nemonoxacin is a new quinolone with an antibacterial efficacy against methicillin-resistant Staphylococcus aureus (MRSA). Certain sequence types (STs) have been emerging in Taiwan, including fluoroquinolone-resistant ST8/USA300. It's an urgent need to determine nemonoxacin susceptibility against ST8/USA300 and other emerging lineages, if any. Additionally, molecular characterization of nemonoxacin resistance among different lineages has yet to be defined.

Methods: Non-duplicated MRSA blood isolates from five hospitals during 2019-2020 were collected and genotyped by pulsed-field gel electrophoresis, and further correlated to their STs. Antimicrobial susceptibility testing for all antibiotics was performing by using Sensititre standard panel, except nemonoxacin by using agar dilution method. Selected isolates with nemonoxacin MICs ≥ 0.5 mg/mL were sequenced for quinolone resistance-determining regions (QRDRs).

Results: Overall, 915 MRSA isolates belonged to four major lineages, ST8 (34.2%), ST59 (23.5%), ST239 (13.9%), and clonal complex 45 (13.7%). Two-thirds of tested isolates were non-susceptible to moxifloxacin, especially ST8/USA300 and ST239. Of them, proportions of nemonoxacin non-susceptibility by a tentative clinical breakpoint (tCBP) of 1 µg/mL among four major lineages appeared to be different (P = 0.06) and highest in ST239 (22.2%), followed by ST8/USA300 (13.5%). Among 89 isolates sequenced, 44.1% of ST8 and all ST239 isolates had ≥ 3 amino acid substitutions (AAS) in gyrA/parC (group A) or 2 AAS in gyrA/parC with additional AAS in gyrB/parE (group B). Compared to other AAS patterns, isolates in group A had the greatest non-susceptible proportions to nemonoxacin (86.9%; overall/pair-wised comparisons, P < 0.05).

Conclusions: Our study confirmed ST8/USA300 MRSA has disseminated in Taiwan. Using a tCBP defined by a higher parenteral daily dosage, nemonoxacin retained potency against moxifloxacin non-susceptible isolates. Patterns of AAS in QRDRs among different lineages may contribute to difference of nemonoxacin susceptibility.