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Background. Non-tuberculous mycobacterial infective endocarditis (NTM-IE) is an uncommon but increasingly recognized aetiology of culture-negative endocarditis, particularly in the context of healthcare exposure. Rapidly growing non-tuberculous mycobacteria (NTM) species present significant diagnostic and therapeutic challenges due to their indolent nature and clinical similarity to tuberculosis. Case summary. We describe a case series of three patients with native valve infective endocarditis caused by rapidly growing NTM following recent percutaneous coronary intervention. All patients initially presented with prolonged fever and systemic inflammatory signs, and routine microbiological workup results were negative. The diagnosis was based on repeated blood and/or urine cultures with the detection of rapidly growing NTM, exclusion of Mycobacterium tuberculosis by PCR analysis and echocardiography demonstrating valvular vegetations. Cultures were performed on consecutive days at a single reference laboratory according to established protocols to reduce the risk of sample contamination. Species-level identification was not feasible because of limited resources. All patients received combination antimicrobial therapy guided by the available susceptibility data and expert consultation. Despite multidrug treatment, clinical outcomes were poor in these cases. Two patients died before definitive surgical intervention could be performed, and one patient died during the induction of the valve replacement surgery. Conclusion. This case series highlights the difficulties in diagnosing NTM-IE and its high mortality rate. NTM infection should be considered in patients with chronic fever after invasive cardiovascular procedures or with prolonged culture-negative endocarditis. Medical therapy is frequently inadequate, and a combined medical-surgical approach may be necessary.

Actinopolyspora saharensis DSM 46666 (=H244), a rare actinomycete, was isolated from Palm grove in the Oasis of Inghid in the Mzab region of the Algerian Sahara and deposited in the German Collection of Microorganisms and Cell Cultures (DSMZ). Here, we report the draft genome sequence of strain DSM 46666, with a size of 4.67 Mbp and a G+C content of 69.5 %. Bioinformatic analysis of the genomic sequence revealed the carbohydrate-active enzyme gene repertoires involved in carbohydrate metabolism and the occurrence of 14 biosynthetic gene clusters disclosing the secondary metabolite capacity of strain DSM 46666.

Brevibacterium sediminis strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond near the Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium at a salinity of 20. Phylogenetic analysis based on 16S rRNA sequencing showed a 99.67% identity with Brevibacterium linens AE038-8 from the International Nucleotide Sequence Database Collaboration DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing on the Oxford Nanopore MinION platform, with genome annotation performed against the NCBI Reference Sequence Database and The Genome Taxonomy Database databases. The genome is ~4.1 Mb in size, with a G+C content of 64.59 mol%. Functional analysis of the genome revealed genes related to complex carbon utilization, nitrogen and phosphate metabolism and metal transport. Additionally, the genome encodes secondary metabolites, including ε-poly-l-lysine, ectoine, terpene and phenazine, which could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.

Micromonospora ureilytica DSM 120150, Nocardiopsis akebiae DSM 120151, Streptomyces fildesensis DSM 41987^T, Streptomyces hypolithicus DSM 41950^T and Streptomyces albidoflavus DSM 120149 are five Antarctic strains. Here, we present the high-quality genome sequences of DSM 120150, DSM 120151, DSM 41987^T, DSM 41950^T and DSM 120149 with sizes of 7.51 Mbp, 6.90 Mbp, 8.91 Mbp, 6.01 Mbp and 6.85 Mbp, respectively.

Peri-implant mucositis is a reversible inflammatory lesion of the mucosa surrounding a dental implant, caused by the accumulation of bacterial plaque and biofilm formation, without bone loss. If peri-implant mucositis is not addressed, it can progress to peri-implantitis, characterized by significant inflammation and infection of the peri-implant mucosa accompanied by the loss of supporting bone. Clinical evidence suggests that the management of peri-implant infections consists of mechanical debridement of the implant, surgical intervention and the administration of antibiotics. However, limited information is available regarding antibiotic resistance in bacteria causing peri-implant diseases. This study is focused on assessing the antibiotic resistance of bacteria isolated from explanted dental implants with peri-implant infections to amoxicillin, clindamycin and metronidazole. To this end, biofilms were recovered using titanium curettes from dental implants of 10 patients with peri-implant infections: patients with peri-implant mucositis (n=4) exhibited redness, swelling or bleeding and absence of bone loss; patients with peri-implantitis (n=6) were diagnosed based on probing depth ≥6 mm and presence of bone loss. Antibiotic sensitivity was assessed using the Kirby-Bauer disc diffusion method in accordance with the Clinical and Laboratory Standards Institute at 10 µg per disc of amoxicillin, 30 µg per disc of clindamycin and metronidazole at a concentration of 50 µg per disc. The results were expressed as the diameters of inhibition zones for each antibiotic. Two peri-implant bacteria were identified by sequencing of their 16S rRNA. Peri-implant bacteria showed resistance to amoxicillin and metronidazole at 100% (10 out of 10). All isolates from dental implants with peri-implant infections (10 out of 10) were sensitive to clindamycin. Two isolates, M29 and P30 strains, were identified as Streptococcus salivarius by 16S rRNA sequencing. Our findings reveal emerging resistance to amoxicillin and metronidazole in clinical isolates from implants with peri-implant infections, yet bacterial susceptibility to clindamycin remains.

Open aquaculture systems represent a strategic environment for the study of antibiotic resistance dynamics, given the interactions between bacteria from humans, animals and the environment. The genomic investigation of eight Pseudomonas isolated from rainbow trout in a previous study demonstrated that non-wild-type and resistance phenotypes to several antibiotics (oxytetracycline, sulphonamides and florfenicol) were predominantly attributable to the presence of related genes [tet(Y), sul2 and floR]. Phylogenetic analyses revealed that several species of Pseudomonas iridis harboured these genes on mobile genetic elements, including integrative conjugative elements (ICE) on the chromosome or plasmids with a high degree of sequence similarity (>99%) between the genetic structures. Furthermore, comparisons between isolates with low and high MIC values to colistin showed mutations in the amino acid sequences of the PhoP/Q two-component system and a lack of the pmrA/B system. A wide diversity of known LPS-modifying genes involved in colistin resistance was also detected in resistant isolates. This study provided insights into the dynamics of antibiotic resistance in aquaculture systems. It demonstrated the presence of genes located on an ICE inserted into a chromosome or plasmid in P. iridis, which was isolated from healthy rainbow trout in different farms within the same watershed. Our study raises questions about the ability of environmental Pseudomonas bacteria to spread their antibiotic resistance genes to other bacterial species that are of interest in terms of human or animal surveillance.

Introduction. Alongshan virus (ALSV) is a tick-borne Flaviviridae. It has been detected in Ixodes ricinus and Ixodes persulcatus across China, Russia, Finland, Switzerland and Germany. Hypothesis/Gap Statement. However, the clinical relevance and the pathogenicity of ALSV in humans remain unclear. Sensitive and specific molecular tools are needed to support surveillance and to enable clinical investigations of ALSV in suspected cases of tick-borne meningoencephalitis. Aim. We aimed to develop, validate and integrate two ALSV-specific TaqMan real-time quantitative PCR (qPCR) assays on our open, high-throughput molecular diagnostic platform. Methodology. We designed assays targeting conserved regions of the NS3 (helicase-protease) and NS5 (RNA-dependent RNA polymerase) genes, incorporating degenerate bases and locked nucleic acid modifications where needed to accommodate documented viral diversity and to harmonize the annealing temperature with TaqMan probe-related technologies and our platform. Analytical sensitivity and reproducibility were assessed using synthetic plasmids carrying the targets; specificity was evaluated against 41 cerebrospinal fluid (CSF) pathogens and 30 winter CSF specimens from patients with suspected central nervous system infection. ALSV-positive Swiss tick extracts served as biological positives. Results. Detection frequencies for NS3 PCR were 100%, 100%, 92%, 72%, 20%, 28 and 0% at 1,000, 100, 10, 5, 2, 1 and 0.1 copies per reaction, respectively. For NS5, the detection frequencies were 100%, 100%, 92%, 88%, 40%, 20% and 0% at the same concentrations. Using a priori definition of limit of detection (LoD) as ≥95% positive replicates, LoD was 100 copies per reaction for both real-time qPCRs. However, as the PCRs are performed in triplicate in our platform, the LoD can be estimated at five copies per reaction for the NS3 real-time qPCR and two copies per reaction for the NS5 PCR. Intra- and inter-run reproducibility across five independent runs met diagnostic standards. Specificity was 100% (71/71). ALSV-positive tick samples were detected by both assays, with lower cycle thresholds for NS5. Conclusions. We validated two ALSV real-time qPCR assays suitable for integration into open molecular diagnostic platforms. These assays enable syndromic testing alongside other encephalitis-associated viruses (e.g., Tick-borne encephalitis virus and West Nile virus) and will facilitate timely clinical management of suspected cases, high-throughput tick surveillance and future clinical studies of potential ALSV pathogenic role.

Background. Listeria monocytogenes is a common foodborne organism identified as a causative agent of multiple clinical conditions in unique circumstances such as pregnancy and immunocompromise. It is a Gram-positive rod and a facultative anaerobic organism. This paper presents a study over a timeline of 5 years in retrospect and explores the incidence of listeriosis amongst patients of different age groups, along with its associated risk factors and clinical outcomes. Materials and methods. This study was conducted in retrospect from June 2019 to June 2024 at Shifa International Hospital, Islamabad. Ninety-seven cases of listeriosis were identified. These cases were culture-positive listeriosis where the pathogen was isolated from various samples such as blood and cerebrospinal fluid. Important risk factors associated with the clinical presentations were also documented, which included diabetes mellitus, chronic kidney disease and malignancy. The mean±sd was calculated for the continuous variable. Frequency and percentage were calculated for categorical variables. Chi-square tests were performed to assess associations with mortality and foetal outcomes. Results. A total of 97 culture-confirmed listeriosis cases, comprising 44 (45.5%) males and 53 (54.6%) females, were obtained. Fifteen of the females were pregnant. Fever was the most common presenting symptom across all groups, with pregnant patients also reporting abdominal pain, vomiting and foetal complications, while non-pregnant patients showed a wider range, including neurological, respiratory and gastrointestinal complaints. Of the 97 patients, 86 had comorbidities - most commonly hypertension and diabetes - while 15 total adult deaths occurred. Eight pregnancies resulted in foetal losses. Descriptive trends in pregnant patients suggested worse foetal outcomes with higher C-reactive protein, total leukocyte count and maternal comorbidities. Ampicillin-based regimens were the most frequently used treatments, and all isolates were sensitive to the tested antibiotics. Conclusion. This study highlights how listeriosis poses substantial morbidity and mortality risk, especially in pregnant cases. There is also a critical data gap, emphasizing the need for better diagnostic strategies, timely and targeted interventions, awareness of the clinical team and public health surveillance to reduce the burden of this often-overlooked infection in Pakistan.

This Technical Resource presents genome sequence data for three strains of the bacterial pathogen Xanthomonas euvesicatoria pv. euvesicatoria (Xeu) collected in Serbia. We isolated these strains from pepper crops showing bacterial spot symptoms in 2016 at the municipality of Irig, in the Srem district. The presented data comprise raw sequencing reads and annotated, contig-level genome assemblies. We checked for the presence of sequences of known type-3 secretion system (T3SS) effector genes and plasmid-like sequences. Phylogenomic reconstruction revealed that the three strains fell in the same clade within Xeu. Strain X13 is most closely related to strain 66b, collected in Bulgaria in 2012. Strains X22 and X31 are most closely related to Tu-10 collected in the Southeastern Anatolia region of Türkiye in 2020. In common with other members of the clade, all three strains share a 75 kb plasmid that carries T3SS effector genes avrBs3, xopBA, xopAQ and xopE. Additionally, strain X13 shares extensive sequence similarity to the pXCV183 plasmid, including T3SS effector gene xopAX, and shares extensive sequence similarity with plasmid pXap41, including T3SS effector gene xopE3. This difference in plasmid content might contribute to the observed difference in virulence among the Serbian Xeu strains. The three Serbian strains lack a 31 kb plasmid, pLMG730.4, that is seen in several Vietnamese and Canadian strains within this clade of Xeu. The data presented will be a useful resource for future molecular epidemiology and genomic surveillance of this pathogen in the Balkan region, augmenting the previously available draft genome sequences of Xeu strains 66b (Bulgaria) and 83M (North Macedonia).

Background. Salmonella enterica subsp. arizonae is an uncommon zoonotic pathogen primarily associated with reptiles. While most infections are gastrointestinal, invasive infections such as bacteraemia, osteomyelitis, meningitis and septic arthritis have been reported, particularly in immunocompromised individuals. Pulmonary infections are exceedingly rare. Case presentation. A 66-year-old woman with rheumatoid arthritis on a tumour necrosis factor-alpha inhibitor presented with a 2 week history of progressive cough and dyspnoea. She reported prolonged exposure to a pet snake. Sputum cultures confirmed S. enterica subsp. arizonae, with susceptibility to ciprofloxacin. Imaging revealed the right lower lobe infiltrate without cavitation. She was successfully treated with ciprofloxacin for 2 weeks, with resolution of symptoms. Conclusion. This case highlights an uncommon presentation of Salmonella infection in an immunocompromised patient with bronchiectasis. With increasing exotic pet ownership, clinicians should maintain a high index of suspicion for Salmonella enterica subsp. arizonae in patients with known reptile exposure.