Explore the vast range of titles available.

Xiaorong Wang; Jianchu Zhang, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Number 1277, Jie Fang Rode, Wuhan, Hubei, 430022, People’s Republic of China, Tel + 86-27-85726707, Email rong-100@163.com; zsn0928@163.comPurpose: To investigate the molecular epidemiology and risk factors of carbapenem-resistant Klebsiella pneumoniae (CRKP) infection.Patients and Methods: Patient’s clinical data and CRKP strains were collected from November 2017 to December 2018 at a tertiary hospital in Wuhan, China. The antimicrobial susceptibilities, carbapenem-resistant genes, multi-locus sequence typing (MLST), homologous analysis, and risk factors for CRKP were determined.Results: A total of 203 CRKP strains were isolated, and 98.5% (200/203) of patients were nosocomially infected. The mortality rate was 17.7% (36/203). All 203 strains were confirmed as carbapenemases -producing strains. The most predominant carbapenemase gene was blaIMP-4 (81.3%, 165/203), followed by blaKPC-2 (25.1%, 51/203) and blaNDM-1 (23.2%, 47/205). Of the 203 strains, 28 (13.8%) had both blaKPC-2 and blaIMP-4 genes, 23 (11.3%) had both blaIMP-4 and blaNDM-1 genes, 20 (9.9%) had blaKPC-2, blaIMP-4 and blaNDM-1 three genes. MLST analysis showed that there were 48 ST typologies (including 7 new STs), of which ST-11 was the most prevalent (59.6%, 121/203). Phylogenetic analysis showed that 203 CRKP isolates came from 7 clusters and exhibited a strong correlation with the isolation source. eBURST analyses indicated that CRKP isolates have undergone different evolutionary processes. Patients with ST-11 CRKP underwent more mechanical ventilation (50% vs 32.9%, P=0.020) and gastric catheterization (15.7% vs 6.1%, P=0.042) within 3 months before sample collection, and also had higher drug-resistance rate than non-ST-11 CRKP. Comparing with CSKP (carbapenem-sensitive Klebsiella pneumoniae), gastrointestinal disease (odds ratio [OR]=6.168, P=0.003), nosocomial infection (OR=5.573, P=0.012), antibiotic exposure (OR=4.131, P=0.004), urinary catheterization (OR=3.960, P=0.031) and venous/arterial catheterization (OR=2.738, P=0.026) within the preceding 3 months were independent risk factors for CRKP infection.Conclusion: The IMP-4 was the most predominant carbapenemase and blaIMP-4 bearing Klebsiella pneumoniae ST-11 was spreading in the hospital. Nosocomial infections, antibiotic exposure, and urinary and venous/arterial catheterization within 3 months were the risk factors for developing CRKP infection.

The large and complex genome of Pseudomonas aeruginosa , which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P . aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P . aeruginosa isolated from two different infection types and countries.

Vibrio bacteria, particularly members of the Harveyi clade, are the most important pathogens of aquatic organisms that cause significant economic losses in the world. It is difficult to provide specific data on taxa of the Harveyi clade for biological research and prevention strategies. Therefore, we conducted an extensive phenotypic and antibiotic resistance study, as well as phylogenetic and molecular typing of 192 isolates of the Harveyi clade collection from 2000 to 2020 with a typical interannual difference from a coastal area in China. The isolates had a significant interspecific genetic and antibiotic resistance diversity. Based on the multilocus sequence analysis (MLSA) of housekeeping genes ( gyrB , pyrH , recA , and atpA ), 192 Harveyi clade isolates were rapidly and accurately classified into 10 species. The population of these isolates was composed of 95 sequence types (STs), of which 92 STs were newly identified, indicating a high degree of genetic diversity. ST327 ranked first, accounting for 11.5% of the total number of isolates (22 out of 192), followed by ST215 with 6.25%, while 63 STs included single isolates. At the metabolic level, the physiological and biochemical experiments revealed that all the Harveyi clade isolates were positive for oxidase and negative for melibiose. The isolates showed a varied tolerance to 11 antibiotics. No isolates were resistant to neomycin. The percentages of sulfadimidine-resistant strains (61 out of 192), sulfadiazine (44 out of 192), sulfamonomethoxine (44 out of 192), sulfamethoxazole (33 out of 192), thiamphenicol (34 out of 192), ciprofloxacin (52 out of 192), and enrofloxacin (31 out of 192) were 31.77%, 22.92%, 22.92%, 17.19%, 17.71%, 27.08%, and 16.15%, respectively. A proportion of 61.8% of the isolates presented a multiple antibiotic resistance index (MARI) lower than 0.1, indicating that the risk of antibiotic resistance transmission of most of the Harveyi clade is low in mariculture systems in China. These results provide substantial data to support further studies on the identification and genetic and metabolic diversity of Harveyi clade isolates in mariculture systems in China.

Background/objective(s)/introduction Acne vulgaris, a prevalent dermatological concern, has shown a consistent increase in reported cases from 2016 to 2019, according to data from the Institute of Dermatology, Thailand. This condition not only causes physical and psychological discomfort but also poses treatment challenges, including the potential development of antibiotic resistance. However, the precise role and distribution of Propionibacterium acnes , an acne-associated bacterium, remain unclear among the Thai population. This study aimed to investigate the prevalence of different P. acnes groups in facial samples from Thai individuals. Materials and methods Facial swabbing was performed to collect bacterial samples from facial skin of Thai individuals. The 16 S rRNA gene was analyzed for species identification. Multi-locus sequence typing (MLST8) was employed to classify sequence types (STs), clonal complexes (CCs), and phylotypes. Results Among the 65 P. acnes isolates, five closely matched sequence types (ST22, ST36, ST53, ST101, and ST115), five corresponding clonal complexes (CC1, CC2, CC3, CC5, and singleton type IA2), and three phylogroups (IA1, IA2, and IB) were identified. Notably, substantial differences were observed in the Thai samples analyzed in this study compared to findings from previous research. Specifically, CC2 (type IA2) emerged as the predominant type, in contrast to the predominance of CC1 (type IA1) reported in other studies. Furthermore, phylotype II, which has been documented elsewhere, was not detected in the present study. These variations in P. acnes prevalence highlight considerable genetic diversity across studies, potentially influenced by factors such as anatomical sampling sites and geographical regions. Conclusion The isolates identified in this study will serve as valuable resources for future research on P. acnes diversity and for the development of population-specific acne treatments, particularly tailored to Thai individuals.

Multidrug-resistant (MDR) Klebsiella pneumoniae is a common infectious pathogen. We performed whole-genome sequencing (WGS) of 39 randomly selected, geographically diverse MDR K. pneumoniae from nine Egyptian hospitals. Clinical sources, phenotypic antibiotic resistance, and hyper-mucoviscosity were documented. WGS data were epidemiologically interpreted and tested for the presence of antibiotic resistance and virulence genes. Based on WGS data, we identified 18 classical multi-locus sequence types (MLST), the most common type being ST101 (23.1%) followed by ST147 (17.9%). Phylogenetic analyses identified small numbers of closely related isolates in a few of the centers, so we mostly documented independent nosocomial acquisition or import from public sources. The most common acquired resistance gene found was blaCTX-M-15, detected in 27 isolates (69.2%). Carbapenemase genes encountered were blaNDM-1 (n = 13), blaNDM-5 (n = 1), blaOXA-48 (n = 12), blaOXA-181 (n = 2), and blaKPC2 (n = 1). Seven strains (18%) contained more than a single carbapenemase gene. While searching for virulence-associated genes, sixteen wzi alleles were identified with wzi137, wzi64, and wzi50 most commonly found in ST101, ST147, and ST16, respectively. Yersiniabactin was the most common virulence factor (69.2%). Hyper-mucoviscosity was documented for 6 out of 39 isolates.This is the first genomic study of MDR K. pneumoniae from Egypt. The study revealed a clear spread of well-known international clones and their associated antimicrobial resistance and (hyper)virulence traits. The clinical situation in Egypt seems to reflect the scenario documented in many other countries and requires close attention.

Klebsiella pneumoniae is a common pathogen capable of causing a wide range of infections. Antibiotic resistance complicates treatment of these infections significantly. We are comparing resistance levels and genotypes among two collections of K. pneumoniae clinical isolates from Alexandria Main University Hospital (AMUH). We used disc diffusion and Minimum Inhibitory Concentration (MIC) by microbroth dilution to assess resistance levels and performed whole genome sequencing (WGS) to describe multilocus sequence types (MLST) and resistance gene presence. Among a collection of 56 K. pneumoniae clinical isolates (19 from 2019 to 37 from 2021), multidrug resistance (MDR) was 33% and 10%, extended drug resistance (XDR) was 24% and 46% and pan-drug resistance (PDR) was 43% and 43%, respectively. We identified 15 MLST STs including two novel types (ST-6118 and ST-6119 ). ST-101 and ST-383 were common between the two collections; ST-101 was the most common genotype in 2019 (28.6%) and ST-147 was most common in 2021 (25%). Ampicillin/sulbactam, amikacin, cefepime, ceftriaxone and ertapenem MICs were significantly higher in 2021. Prevalence of aph(3’) – Ia , aph(3’)-VI , mphA was significantly higher in 2021. The increasing resistance levels and the persistence of some MDR/XDR genotypes is concerning. Understanding mechanisms of resistance will inform infection control and antimicrobial stewardship plans to prevent evolution and spread of XDR and PDR strains.

The yeast Candida glabrata has emerged, second only to Candida albicans , to be one of the most frequently isolated fungi in clinical specimen from human. Its frequent resistance towards azole antifungal drugs and the high capacity to form biofilms on indwelling catheters of individual isolates render it an often difficult to treat pathogen. Hence, there is a notably increasing scientific and clinical interest in this species. This has led to the development of a variety of molecular tools for genetic modification, strain collections, and last but not least different approaches to analyse the population structure among isolates of different geographical and clinical contexts. Often, these are used to study correlations (or the absence thereof) with different pathogenicity, virulence, or drug resistance traits. Three molecular methods have been used to type within the C. glabrata population on a genetic level by multiple studies: multi-locus sequence typing, microsatellite length polymorphisms, and clustering of whole-genome sequencing data, and these are subject of this review.

Background Acinetobacter baumannii has emerged as a significant global pathogen, and community-acquired infections are concerning due to their severe clinical outcomes and high mortality. Despite this, the molecular epidemiology and phenotypic characteristics of community-acquired/community-onset A. baumannii (CAAB/COAB) strains remain poorly understood. This study analyzed the genotypes, virulence traits, and clinical manifestations of 32 COAB isolates collected in Taiwan between 2015 and 2017. Methods Capsular types (KLs), sequence types (STs) from the Oxford and Pasteur schemes, and international clones (ICs) were identified among the 32 COAB isolates. In vitro virulence was assessed by evaluating biofilm formation, motility, resistance to desiccation and serum, and in vivo virulence was confirmed in a Galleria mellonella larvae model. Associations between KL/ST types and virulence phenotypes, as well as between KL/ST types and the clinical manifestations of patients, were also analyzed. Results The results showed that among the tested COAB isolates, KL49 was the predominant capsular type, representing 18.8% ( n  = 6) of samples, and ST10 Pas /IC8 (ST10 Pas : ST10 under the Pasteur scheme, IC8: international clone 8) was the major clone (15.6%, n  = 5). Interestingly, we found that KL49/ST10 Pas , which is predominant in America and Australia but has never been reported for CAAB/COAB in Taiwan, had a hypervirulent phenotype with high serum resistance and high mortality in the G. mellonella larvae model. Furthermore, clinical records showed higher incidences of chronic obstructive pulmonary disease, pneumonia, elevated Pitt bacteremia scores, and 30-day mortality for patients with KL49/ST10 Pas infections than for patients with non-KL49/ST10 Pas infections. Conclusions This is the first report identifying KL49/ST10 Pas as a major clone of COAB in Taiwan. Its high virulence was demonstrated, highlighting a potential public health threat. This study lays a foundation for understanding the molecular epidemiology of COAB in Taiwan and supports future research on virulence and disease control strategies.

Toxoplasma gondii is an obligate intracellular parasite associated with severe disease, especially in the immunosuppressed. It is also a cause of congenital malformation and abortion in both animals and humans and is considered one of the most important foodborne pathogens worldwide with different strains showing variable distribution and differing pathogenicity. Thus, strain-level differentiation of T. gondii isolates is an essential asset in the understanding of parasite’s diversity, geographical distribution, epidemiology and health risk. Here, we designed and implemented an Oxford Nanopore MinION protocol to analyse genomic sequence variation including single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (InDel’s) of four different genomic loci, part of protein coding genes SAG2, SAG3, ROP17 and ROP21. This method provided results with the sequencing depth necessary for accurate differentiation of T. gondii strains and represents a rapid approach compared to conventional techniques which we further validated against environmental samples isolated from wild wood mice. In summary, multi-locus sequence typing (MLST) of both highly conserved and more polymorphic areas of the genome, provided robust data for strain classification in a platform ready for further adaption for other strains and pathogens.Key pointsTyping of T. gondii is essential for understanding the epidemiology and spread of more virulent strains. Multi-locus sequence typing (MLST) provides several advantages, including accuracy and specificity, over conventional approaches.The portable Nanopore-based approach described here represents a cheaper, quicker and less technically demanding approach to MLST in T. gondii.

This study describes the clinical and microbiological features associated with group B Streptococcus (GBS) bone and joint infections (BJIs). It was a retrospective analysis of adult cases of GBS BJIs reported to the French National Reference Center for Streptococci from January 2004 to December 2014. Clinical data and GBS molecular characteristics are reported. Strains were collected from 163 patients. The most frequent comorbidities were: solid organ cancer ( n  = 21, 21%) and diabetes mellitus ( n  = 20, 20%). The main infection sites were knee (47/155 = 30%) and hip (43/155 = 27%), and occurred on orthopedic devices in 71/148 cases (48%). CPS III ( n  = 47, 29%), Ia ( n  = 26, 16%) and V ( n  = 40, 25%) were predominant. Resistance to erythromycin, clindamycin and tetracycline was detected in 55/163 (34%), 35/163 (21%) and 132/163 (81%) strains, respectively. The most frequent sequence types were ST-1 ( n  = 21, 25%), ST-17 ( n  = 17, 20%) and ST-23 ( n  = 11, 13%). The rate of resistance to erythromycin was 0% for ST-17 strains, 52% ( n  = 11) for ST-1 and 44% ( n  = 7) for ST-23 ( p  < 0.001). GBS bone and joint infections predominantly occur in patients aged >50 years and/or with comorbidities such as cancer and diabetes mellitus. CPS type distribution and MLST are very similar to that of other adult GBS invasive infections.