Kayoko Hayakawa

Chryseobacterium species are environmental bacteria occasionally implicated in human infections; however, their clinical and genomic features are not fully characterized. This study investigated the clinical, genotypic, and phenotypic characteristics of Chryseobacterium strains collected through the MultiDrug-Resistant Organisms Clinical Research Network, a multicenter prospective study of patients with carbapenem-resistant gram-negative bacilli isolated at tertiary care hospitals in Japan between April 2019 and March 2024. Among 18 patients with Chryseobacterium spp. confirmed by whole-genome sequencing (WGS), 5 had infection, and 13 were colonized. Bacteremia and pneumonia were the common types of infection. The isolates comprised five species, with Chryseobacterium indologenes and Chryseobacterium culicis being the most frequently detected. Compared with WGS, 16S rRNA gene sequencing demonstrated the highest species-level identification accuracy (93.8%), followed by MALDI Biotyper (50.0%), VITEK-MS (31.3%), and VITEK 2 Blue (31.3%). All systems correctly identified C. indologenes , but other species were frequently misidentified or remained unidentified because of limited database coverage. All isolates exhibited broad β-lactam resistance, including resistance to carbapenems, which was associated with species-specific combinations of metallo-β-lactamase and extended-spectrum β-lactamase genes. Minocycline, trimethoprim-sulfamethoxazole, and cefiderocol retained activity across all species. These findings highlight that diverse Chryseobacterium species, including uncommon ones, can be associated with human infections. Incorporating genomic approaches such as WGS or 16S rRNA gene analysis can improve species-level identification, especially for rare or emerging species. IMPORTANCE: Chryseobacterium species are emerging opportunistic pathogens that pose a diagnostic and therapeutic challenge as they are intrinsically resistant to most β-lactams, including carbapenems, and are often misidentified by routine clinical laboratory systems. In this multicenter study, we show that clinical Chryseobacterium isolates represent greater species diversity than is typically recognized, extending beyond Chryseobacterium indologenes to include uncommon species associated with both infection and colonization. Whole-genome sequencing clarified species assignments, revealed species-specific β-lactamase profiles, and highlighted the limitations of commonly used identification platforms, particularly for species absent from commercial databases. Despite broad β-lactam resistance, cefiderocol, minocycline, and trimethoprim-sulfamethoxazole retained in vitro activity across species. These findings emphasize the need for genomic or sequence-based identification to accurately define the clinical spectrum of Chryseobacterium species, guide interpretation of antimicrobial susceptibility, and improve recognition of these organisms as emerging healthcare-associated pathogens.

We aimed to identify genomically defined strain transmission events of carbapenem-resistant Gram-negative bacteria (CRGNB) in hospitals, estimate species-specific transmission rates and identify risk factors for transmission. The study included 708 patients from a Japanese prospective multicentre cohort study, the MultiDrug-Resistant organisms clinical research network, from whom at least one CRGNB isolate was collected between 2019 and 2024 (750 isolates in total). Clinical data were retrieved from electronic medical records, and microbiological analyses were performed at a central reference laboratory. Transmission events were determined via whole-genome sequencing data and single-nucleotide polymorphism-based genomic clustering. We identified 37 genomic clusters associated with intrahospital transmission and 1 associated with interhospital transmission. Ninety-four patients (13%) carried at least one isolate involved in intrahospital transmission, and each transmission event involved two to six patients. Patients with Acinetobacter spp. (60% involved in intrahospital transmission), Enterobacter cloacae complex (23%) and Klebsiella oxytoca complex (59%) were significantly associated with intrahospital transmission and were considered high-risk species groups. Patients with Enterobacterales isolates carrying acquired carbapenemase genes had higher intrahospital transmission rates relative to those without (31% vs. 2%). In multivariable analysis, independent risk factors for patients with intrahospital transmission were overlap in ward and time with other CRGNB-positive patients, carriage of high-risk species groups and acquired carbapenemase genes. In this Japanese multicentre cohort, intrahospital transmission of CRGNB was associated with both microbiological characteristics and patient- and healthcare-related factors, underscoring the need for targeted surveillance and infection prevention strategies.

Carbapenem-resistant Enterobacterales (CRE) pose a global threat due to limited treatment options and high mortality. Difficult-to-treat resistance (DTR), defined as non-susceptibility to all conventional β-lactams and fluoroquinolones, has primarily been applied to Pseudomonas aeruginosa . However, its relevance for Enterobacterales remains unclear, particularly in regions with a distinct carbapenemase landscape, such as Japan where IMP-type metallo-β-lactamases predominate. We analyzed the MultiDrug-Resistant organisms clinical research network (MDRnet) cohort, a multicenter prospective study conducted at 13 Japanese hospitals between April 2019 and March 2024. This analysis included patients with clinically indicated cultures yielding CRE. Clinical characteristics and outcomes assessed using the desirability of outcome ranking (DOOR) framework and genomic epidemiology characterized by whole-genome sequencing were compared between DTR and non-DTR groups. Among 196 CRE cases, 64 (32.7%) represented infections, including 12 DTR cases (18.8%). Carbapenemase genes were detected in 34/64 infections (53.1%), with similar prevalence in the DTR and non-DTR groups (50.0% vs 53.8%). bla _IMP-1 was the most frequently identified carbapenemase gene ( n = 28). The overall 30-day mortality rate was 21.9%, with 16.7% (95% confidence interval [CI], 2.1%–48.4%) in the DTR group and 23.1% (95% CI, 12.5%–36.8%) in the non-DTR group. DOOR outcomes were similar between groups. Appropriate empiric and definitive therapy was less frequently administered in the DTR group. In this cohort, where IMP-type carbapenemases and non-DTR CRE are prevalent, DTR classification did not appear to correlate with 30-day mortality or DOOR outcomes. These findings underscore the importance of regional molecular epidemiology when interpreting clinical outcomes of CRE infections. IMPORTANCE: Difficult-to-treat resistance (DTR) is increasingly used to assess the clinical impact of antimicrobial resistance, but its significance in carbapenem-resistant Enterobacterales (CRE) may vary across molecular epidemiologic settings. In this prospective multicenter study from Japan, where IMP-type carbapenemases predominated, most CRE infections were classified as non-DTR. Whole-genome sequencing also revealed a distinct local clonal structure. DTR was not associated with 30-day mortality or desirability of outcome ranking despite lower rates of appropriate empiric and definitive therapy. Our study highlights the importance of interpreting DTR in CRE within the context of regional molecular epidemiology and supports the need for continued regional multicenter studies to evaluate its clinical utility.

Stenotrophomonas maltophilia is a carbapenem-resistant Gram-negative pathogen increasingly responsible for difficult-to-treat nosocomial infections. To describe the contemporary clinical characteristics and genome epidemiology of patients colonized or infected by S. maltophilia in a multicentre, prospective cohort. All patients with a clinical culture growing S. maltophilia were enrolled at six tertiary hospitals across Japan between April 2019 and March 2022. The clinical characteristics, outcomes, antimicrobial susceptibility and genomic epidemiology of cases with S. maltophilia were investigated. In total, 78 patients were included representing 34 infection and 44 colonization cases. The median age was 72.5 years (IQR, 61–78), and males accounted for 53 cases (68%). The most common comorbidity was localized solid malignancy (39%). Nearly half of the patients (44%) were immunosuppressed, with antineoplastic chemotherapy accounting for 31%. The respiratory tract was the most common site of colonization (86%), whereas bacteraemia accounted for most infection cases (56%). The 30 day all-cause mortality rate was 21%, which was significantly higher in infection cases than colonization cases (35% versus 9%; adjusted HR, 3.81; 95% CI, 1.22–11.96). Susceptibility rates to ceftazidime, levofloxacin, minocycline and sulfamethoxazole/trimethoprim were 14%, 65%, 87% and 100%, respectively. The percentage of infection ranged from 13% in the unclassified group to 86% in genomic group 6A. The percentage of non-susceptibility to ceftazidime ranged from 33% in genomic group C to 100% in genomic groups 6 and 7 and genomic group geniculate. In this contemporary multicentre cohort, S. maltophilia primarily colonized the respiratory tract, whereas patients with bacteraemia had the highest the mortality from this pathogen. Sulfamethoxazole/trimethoprim remained consistently active, but susceptibility to levofloxacin was relatively low. The proportions of cases representing infection and susceptibility to ceftazidime differed significantly based on genomic groups.

Cefmetazole is active against extended-spectrum β-lactamase-producing Escherichia coli (ESBLEC) and is a potential candidate for carbapenem-sparing therapy. This multicenter, observational study included patients hospitalized for invasive urinary tract infection due to ESBLEC between March 2020 and November 2021 at 10 facilities in Japan, for whom either cefmetazole or meropenem was initiated as a definitive therapy within 96 h of culture collection and continued for at least 3 d. Outcomes included clinical and microbiological effectiveness, recurrence within 28 d, and all-cause mortality (14 d, 30 d, in-hospital). Outcomes were adjusted for the inverse probability of propensity scores for receiving cefmetazole or meropenem. Eighty-one and forty-six patients were included in the cefmetazole and meropenem groups, respectively. Bacteremia accounted for 43% of the cefmetazole group, and 59% of the meropenem group. The crude clinical effectiveness, 14 d, 30 d, and in-hospital mortality for patients in the cefmetazole and meropenem groups were 96.1% vs 90.9%, 0% vs 2.3%, 0% vs 12.5%, and 2.6% vs 13.3%, respectively. After propensity score adjustment, clinical effectiveness, the risk of in-hospital mortality, and the risk of recurrence were similar between the two groups ( P = 0.54, P = 0.10, and P = 0.79, respectively). In all cases with available data (cefmetazole : n = 61, meropenem : n = 22), both drugs were microbiologically effective. In all isolates, bla _CTX-M was detected as the extended-spectrum β-lactamase gene. The predominant CTX-M subtype was CTX-M-27 (47.6%). Cefmetazole showed clinical and bacteriological effectiveness comparable to meropenem against invasive urinary tract infection due to ESBLECs.