Understanding the distribution and prevalence of different M. tuberculosis lineages can help public health authorities and researchers track the spread of tuberculosis (TB). Some lineages are thought to be more virulent, transmissible, and prone to drug resistance. Here, we sought to find the major lineages and sublineages of M. tuberculosis circulating in Pakistan.

In 2017, a large outbreak of Legionnaires' disease, involving 58 patients, occurred in a public bath facility in Hiroshima Prefecture, Japan. We analyzed 94 Legionella pneumophila strains isolated from patients and the public bath facility using molecular typing methods, including Pulsed-Field Gel Electrophoresis, sequence-based typing, multi-locus variable number tandem repeat analysis, and Whole-Genome Sequencing (WGS). Genotypes obtained using these molecular epidemiological typing methods were highly correlated with each other. L. pneumophila strains of various genotypes were isolated from the public bath facility, of which only ST2398 and ST2399 were isolated from patients. ST2398 and ST2399, isolated from patients, bath water, and swabs, derived from one common circulating system at the bath facility out of seven were found to be novel genotypes and a highly clonal genetic lineage by single nucleotide variant (SNV) analysis based on WGS. The result of haplotype network analysis based on SNVs showed that ST2398 and ST2399 differed only approximately 30-42 SNVs, and some environmental strains that differed by only 0-3 SNVs from patient strains were isolated. These results demonstrated that this outbreak was caused by L. pneumophila assigned to the ST2398 and ST2399 clades. We found that at least three patients were co-infected with different clusters of L. pneumophila serogroup 1. Our results show that several strains must be isolated from a single sample to consider the accumulation of mutations in water and co-infection when investigating outbreaks.

Vancomycin-resistant Enterococcus faecium (VREfm) are multidrug-resistant pathogens that cause severe nosocomial infections. The knowledge of virulence profiles of VREfm for the development of invasive infections is still limited. The aim of this study was to analyse gene profiles and genetic variants of VREfm and their association with the development of VREfm bloodstream infections (VRE-BSI).

This study aimed to characterize the molecular epidemiology, antimicrobial resistance, virulence profiles, and clinical outcomes of Methicillin-resistant Staphylococcus aureus (MRSA) infections among intensive care unit (ICU) patients in southern China.

Acinetobacter baumannii (AB) is the most frequently isolated nosocomial pathogen, but severe infections by A. pittii, A. ursingii, and A. bereziniae are increasing. This study investigated the distribution and antibiotic resistance of Acinetobacter spp. strains from various clinical specimens.

The increased detection of Shiga toxin-producing Escherichia coli (STEC) O113:H4 among human cases in Belgium questions the importance of this serotype as an emerging pathogen. However, detailed information focusing on serotype O113:H4 from human and non-human sources remains limited. We analysed a collection of 140 STEC O113:H4 isolates and their whole genomes, originating from animal hosts (cattle, deer, goats, and sheep), food, and humans, to determine their genetic relationship and assess key virulence genes. All STEC O113:H4 genomes lacked the locus of enterocyte effacement (LEE) and belonged to Pasteur Sequence Type (pST) 367 complex, dominated by pST367 (ehxA, stx) and pST1729 (ehxA, stx). Compared to stx isolates, stx isolates carried on median more virulence factors, which might thus contribute to enhanced pathogenicity. Besides, humans appear to be infected with distinct subgroups of STEC O113:H4 carrying distinct stx subtypes and originating from potentially different sources: deer, goats, and sheep for STEC carrying stx (alone or in combination with stx) and mainly cattle for STEC carrying stx. Our results call for improved understanding and continuous surveillance of emerging STEC O113:H4.

KL57 Klebsiella pneumoniae (K. pneumoniae) is an emerging serotype with epidemiological characteristics and pathogenic mechanisms that remain incompletely understood. This study comprehensively analyzed the genomic features of KL57 K. pneumoniae strains isolated in Wuxi from 2016 to 2023, and investigated the global molecular epidemiology and population dynamics of KL57 K. pneumoniae.

Group A Streptococcus (GAS) isolates with spontaneous mutations in covR and covS are frequently identified in patients with necrotizing fasciitis and toxic shock syndrome. CovR/CovS is a two-component regulator system, and the phosphorylation of CovR is solely modulated by CovS. Nonetheless, the phenotype of the ∆covS mutant and the ∆covR mutant is not entirely identical. It has been shown that the expression of SpeB protease is only detected in the ∆covR mutant, and the ∆covR mutant causes more severe local lesions than the ∆covS mutant in the mouse infection model. SpeB-mediated gasdermin A cleavage triggers keratinocyte death, resulting in sizeable lesion size but preventing invasive skin infection by GAS. This study, therefore, elucidated whether SpeB is a key factor related to trigger keratinocyte death after the ∆covR mutant infection. Although the ∆covR mutant caused more keratinocyte deaths than the ∆covS mutant, this difference was not contributed by SpeB but mediated by streptolysin S (SLS). Moreover, SLS in the ∆covR mutant contributed to increased macrophage cell death and elevated IL-1β levels. Similar to the SpeB expression profile, SLS was upregulated in the ∆covR mutant but repressed in the ∆covS mutant. In a mouse subcutaneous infection model, the SLS-deficient ∆covR mutant exhibited reduced lesion size and mortality compared to the ∆covR mutant, suggesting that SLS repression does not contribute to GAS immune evasion or invasive skin infection. This finding may help explain the differential presentations after ∆covR mutant and ∆covS mutant infection and why clinical GAS isolates more frequently harbor spontaneous mutations in covS rather than in covR.

This study aims to generate the first complete genome of Pantoea septica and provide a thorough genomic characterisation of this under-documented species. The study seeks to enhance understanding of P. septica, clarifying features relevant to opportunistic infection in vulnerable cohorts.

Mycetoma is a neglected tropical disease characterized by large tumorous lesions. It can be caused by fungi (eumycetoma) or bacteria (actinomycetoma). The hallmark of mycetoma is the formation of grains by the causative agent. Grains can only be formed in vivo; therefore, in vivo models are crucial to studying mycetoma. In vivo, grain models have been developed in the invertebrate Galleria mellonella for eumycetoma, but not for actinomycetoma. Here, we aimed to develop the first actinomycetoma grain model in G. mellonella larvae. Actinomadura madurae strains DSM43236 and DSM44005 were used to infect G. mellonella larvae. Larval survival was monitored over 10 days. Grain formation was studied histologically and compared to grains in human tissues. The efficacy of trimethoprim-sulfamethoxazole and amikacin, the current standard treatment for actinomycetoma, was determined. A. madurae infection decreased the survival of G. mellonella larvae in a concentration-dependent manner. Grains were formed within 24 h post-infection. After 72 h these grains became melanised. No significantly enhanced survival was noted with trimethoprim-sulfamethoxazole, amikacin, or a combination thereof. In this model, the melanised A. madurae grains did differ from human grains, most likely due to the immune system of G. mellonella. The lack of therapeutic efficacy could be caused by this melanin or the fact that A. madurae grains, in general, are less susceptible to these drugs. More research will be needed to address this question.

Elizabethkingia anophelis is an emerging multidrug-resistant Gram-negative pathogen that can cause severe nosocomial infections. Although multidrug resistance complicates the clinical management of E. anophelis, the ecological impact of stress responses, including antibiotic pressure, is unclear. We demonstrated that exposure to sub-inhibitory concentrations of imipenem promoted the secretion of antibiotic-induced outer membrane vesicles (iOMVs) by E. anophelis. This study analyzed the physical and functional characteristics of iOMVs produced by a drug-resistant clinical isolate of E. anophelis treated with imipenem and assessed the potential of E. anophelis iOMVs to modulate biofilm formation in other clinically relevant Gram-negative bacteria. High-resolution imaging and biofilm assays showed that iOMVs inhibited biofilm formation and reduced biofilm density. The inhibitory effect did not affect other nosocomial pathogens such as Pseudomonas aeruginosa, Enterobacter cloacae, or Klebsiella pneumoniae. Imipenem-induced vesiculation may inadvertently impair E. anophelis' biofilm resilience while altering microbial competition, reshaping survival dynamics in polymicrobial environments. These results demonstrate the paradoxical effect of antibiotic stress and suggest that vesicle-mediated interactions strongly affect nosocomial pathogen ecology.

This study aimed to investigate the identification of bla-positive multidrug-resistant Mixta calida isolates from human hosts and to elucidate their genomic determinants in a species-wide context.

Methicillin-resistant Staphylococcus aureus (MRSA) remains a global health threat, with livestock-associated (LA-)MRSA ST398/t011 emerging in regions with human-animal contact. This study reports the first detection of ST398/t011 in clinical isolates from Bojnurd, northeastern Iran, alongside the hospital-associated ST239/t037 clone.

The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as the causative agent of COVID-19 precipitated a global health crisis of unprecedented scale. SARS-CoV-2 has been shown to interfere specifically with S phase progression during early stages of infection. Nucleocapsid (N) is an important structural protein. The abundance and early presence of N suggest that the N protein may play a pivotal role in determining the fate of host cells post-infection, including in cell cycle regulation. Our observations reveal that the SARS-CoV-2 N protein actually induces S phase arrest by promoting S phase entry and simultaneously blocking exit from this phase, which is different from previous report G1/S blockage, others describe G1 and G2/M arrest. Prolonged cell cycle arrest is frequently linked to cell death, while our data suggests the N protein curtails cell proliferation, slowing down cell growth without actively triggering cell death. Intriguingly, removing the N-arm, SR-rich region, CTD, or C-tail each abolishes the N protein's ability to suppress cell growth, whereas deletion of the NTD does not impact this capability, nor does it affect S phase arrest. All told, the SARS-CoV-2 N protein emerges as a multifunctional actor, not only driving key aspects of viral replication but also exerting significant effects on host cell physiology by modulating cell cycle progression and growth.

Staphylococcus lugdunensis, an emerging coagulase-negative Staphylococcus (CoNS) pathogen, has garnered increasing interest due to its production of lugdunin, a thiazolidine-containing antimicrobial peptide. However, standardized protocols for directly assessing lugdunin activity produced by S. lugdunensis remain lacking. In this study, we examined the effects of pH and incubation duration on lugdunin activity and evaluated the antibacterial spectrum of lugdunin produced by S. lugdunensis isolates against a panel of gram-positive and gram-negative bacterial strains. The optimal conditions for lugdunin antibacterial activity of isolate CGMH-SL85 were identified as pH 7.5 and a 72-h incubation period. Under the tested conditions, the lugdunin produced by CGMH-SL85 exhibited antimicrobial activity against five gram-positive strains, including Staphylococcus aureus ATCC29213 and Staphylococcus haemolyticus CGMH-SH53, followed by Enterococcus faecium EF029 and EF081-2 and Listeria monocytogenes ATCC10403S. However, no antibacterial activity was observed against any of the 11 tested gram-negative bacterial species. Furthermore, four distinct lugdunin susceptibility phenotypes were observed among 47 lugdunin-nonproducing S. lugdunensis strains (14 sequence type (ST)4, 27 ST27, and 6 ST29 strains), including Type A characterized by large, clear inhibition zones; Type B with smaller, clear zones; Type C displaying halo-like inhibition zones; and Type D showing no detectable activity. Moreover, 20 S. lugdunensis strains (42.6 %) exhibited the Type C phenotype. Notably, all six ST29 strains displayed the Type C phenotype, while the Type A phenotype was observed only among ST27 strains (3 strains). In conclusion, we developed a standardized protocol for evaluating lugdunin activity, using pH 7.5 and a 72-h incubation period, and found that different S. lugdunensis strains exhibited distinct lugdunin susceptibility phenotypes.

Hepatitis B virus (HBV) infection seems to be related to gut microbiota. This study aims to explore the effects of HBV infection on gut microbiota and possible immunological mechanisms using the Chinese woodchuck model. Nine adult woodchucks were randomly divided into Cyclosporine A (CsA) or Control group. Animals were orally treated with CsA and saline for 2 weeks before WHV inoculation, and continued until 8 weeks after that. Blood CsA concentrations were tested at 2 weeks after administration and before discontinuation. Quantitative PCR was used to detect serum WHV DNA. Flow cytometry was used to detect T cell immune response. Feces were collected for 16S rRNA sequencing. The result shows CsA oral administration can reach effective blood drug concentration in woodchucks and successfully prolong WHV replication. After 2 weeks of oral treatment, there was no significant difference in the gut microbiota between the two groups. At the clearance period of serum WHV, the relative abundance of Prevotella and Prevotella genera in the phylum Bacteroidetes significantly increased, while the relative abundance of Firmicutes significantly decreased. Meanwhile, the CD107a degranulation of CD4-T cells in peripheral blood showed a decreasing trend, while there was no significant difference in the frequency of PD-1+ CD4-T cells. In Conclusion, oral administration of CsA can significantly prolong the replication time of WHV in Chinese woodchucks. The gut microbiota of Chinese woodchuck undergoes significant changes during serum WHV clearance, which implies the Chinese woodchuck model can be used to study the interaction between HBV infection and gut microbiota.

Tuberculosis (TB), caused by bacteria of the Mycobacterium tuberculosis complex (MTBC), remains a global health challenge, exacerbated by multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains.

Enteroinvasive Escherichia coli (EIEC) is a diarrhoeagenic E. coli pathotype that shares key virulence traits with Shigella, including the invasion plasmid (pINV). In Thailand, an outbreak caused by the EIEC serotype O8:H19-the first reported in the country-occurred in 2023, affecting over 150 patients. To elucidate the emergence, clinical relevance, and epidemiological distribution of EIEC in Thailand, we conducted a comprehensive investigation. We isolated and genomically characterised 63 isolates, comprising 28 EIEC (eight serotypes, including O96:H19 from a 2024 outbreak) and 35 Shigella (25 S. sonnei and 10 S. flexneri), along with 85 global reference strains. Comparative genomics revealed that the 2023 and 2024 EIEC outbreak isolates, along with a novel OX18:H25 EIEC lineage, harboured highly similar pINV plasmids with conserved invasion genes and complete conjugation elements. These isolates retained several biochemical traits that were more typical of commensal E. coli than classical EIEC. Limited chromosomal genome reduction-a hallmark of Shigella- was observed, which suggests that these lineages are in an early stage of adaptation toward a pathogenic lifestyle. Phylogenomic analysis showed that OX18:H25 is closely related to livestock-associated E. coli, supporting the hypothesis that pINV was recently acquired via horizontal gene transfer. These findings highlight the active circulation of putatively conjugative virulence plasmids among E. coli populations and the ongoing emergence of novel EIEC clones with epidemic-inducing potential.

Infections caused by hypervirulent Klebsiella pneumoniae (hvKp) are often characterised by severe, metastatic and relapsing infections. Initially described in Asia, this pathotype has now expanded worldwide. Convergent strains combining hypervirulence with multidrug resistance additionally aggravate the situation. However, only sparse data are available on the occurrence of hvKp in European countries. Therefore, this study investigated the prevalence of hvKp in a tertiary medical centre in Germany.

Bacteriophage therapy offers a promising solution to combat antibiotic-resistant infections, yet its potential against biofilm-associated pathogens in oral diseases remains underexplored. This study investigates the opportunistic bacterium Cutibacterium acnes, an overlooked contributor to dental implant and prosthetic joint infections. Biofilms formed by C. acnes are highly resilient and resistant to antibiotics, complicating treatment. Two novel lytic bacteriophages, Ristretto and Corretto, targeting C. acnes, were isolated from human saliva, with morphological analysis confirming their classification as siphoviruses. Their genome sequencing revealed no harmful antimicrobial resistance or virulence genes, making them suitable for therapeutic use. Remarkably, phage Corretto demonstrated a broad host range and achieved near-complete eradication of mature biofilms across multiple C. acnes strains, outperforming Ristretto in efficacy and strain coverage. The activity of these phages was dosage-dependent and varied across bacterial strains, revealing potential strain-specific resistance mechanisms within biofilms. These findings highlight bacteriophage therapy's potential to disrupt persistent biofilms where antibiotics fail, offering a new approach for treating biofilm-driven infections in dental and medical implantology. This study underscores the need for further research into phage-based strategies to address the growing global challenge of antimicrobial resistance and improve outcomes in biofilm-related diseases.

COVID-19-associated-pulmonary-aspergillosis (CAPA) is a severe superinfection mostly affecting critically ill COVID-19 patients. Early diagnosis and clinical management of CAPA remain major clinical challenges. Here, we evaluated different approaches to classify culture-positive CAPA at its peak season, assessed incidence and mortality, identified risk factors and analysed clinical and laboratory CAPA-management of three German tertiary care hospitals.