Access microbiology最新文献

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.

Enterococcus faecalis is a gram-positive bacterium and a common cause of hospital-associated infections. Three major CRISPR loci have been discovered in this species, namely, CRISPR1-cas, CRISPR2 and CRISPR3-cas. We developed novel primers which target the CRISPR1-cas loci in E. faecalis and tested these primers on 26 E. faecalis isolates isolated from diverse settings from Segamat, Malaysia. Half of the isolates were found to carry the CRISPR1-cas9 locus, and the CRISPR1 array was successfully amplified in 12 out of 13 isolates that contained the cas9 gene. Characterization of the CRISPR array shows that CRISPR1-cas shares similar array length and typical repeat sequences with CRISPR2 but differs significantly in terms of spacer identities and terminal repeat (TR) sequences. Most CRISPR spacers encode for chromosomal DNA sequences. Genotype characterization based on ancestral spacer (AS) and TR sequences indicates that E. faecalis with the same CRISPR1-AS genotype do not always harbour the same CRISPR2-AS genotypes and vice versa. A combined CRISPR1-cas and CRISPR2 typing offers comparable discriminatory power to MLST, suggesting its potential to be used in short-term strain identification and epidemiological surveillance at a lower sequencing cost. Our study provides a genetic reference for future studies in Southeast Asia.

Assessment of the pathogenic potential (virulence and toxicity) in non-pathogenic bacterial species is a challenge as it relies on methods developed for assessment of species known to be pathogenic. Here, we have applied and evaluated some of these methods on industrially relevant bacteria to differentiate between 'true' virulence factors applying only to pathogens and niche factors being defined as promoting colonization and survival rather than pathogenicity and as being present also in non-pathogenic bacteria. We examined the pathogenicity of 49 strains from 9 industrially relevant bacterial species (Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus delbrueckii, Lacticaseibacillus rhamnosus, Limosilactobacillus fermentum, Latilactobacillus curvatus, Ligilactobacillus salivarius, Staphylococcus carnosus and Staphylococcus xylosus), including 14 clinical isolates of the same species, through genomic screening and phenotypically through assays established for pathogenic bacteria. The genomes were screened against the Virulence Factor Database (VFDB), and thresholds (>80% nucleotide or protein identity, >70% coverage) provided by the European Food Safety Authority (EFSA) were adopted to differentiate between genes of potential concern and genes of no concern. Core genome analysis was performed to determine whether the clinical isolates were phylogenetically related to the industrial isolates. The genotypic assessment did not reveal the presence of true virulence factors in the examined strains, and in the core genome analysis, the clinical isolates could not be distinguished from the industrial strains. Furthermore, cytotoxicity toward Vero cells, negative impact on Caco-2 cell viability and haemolytic activity on blood agar plates were examined, and none of the tested strains exhibited any activity in these assays. Overall, the results suggest that VFDB screening with the EFSA thresholds can be used to differentiate between true virulence factors and niche factors. Furthermore, the use of phenotypic assays supports the genotypic assessment, albeit expert knowledge is required to interpret the results.

Here, we report the draft sequence of a rapid-growing nontuberculous Mycobacterium isolated from a urine sample at the Scottish Mycobacteria Reference Laboratory, Royal Infirmary of Edinburgh, UK. The reported genome has a length of 6,749,454 bp, a G+C content of 67.2 mol% and 6,336 protein CDSs. Average nucleotide identity (ANI) analysis identified Mycobacterium vanbaalenii PYR-1 as the closest relative (83.32% ANI), indicating that this isolate likely represents a novel species within the genus. Notably, phenotypic characterization revealed a distinct antimicrobial resistance (AMR) profile. This assembly provides a valuable resource for studying the evolution of AMR mechanisms in nontuberculous mycobacteria and offers insight into resistance phenotypes observed in clinical isolates.

Tuberculosis (TB) is an infectious disease that affects humans and animals. The pathogens that cause TB belong to the Mycobacterium tuberculosis complex (MTBC), with M. tuberculosis and Mycobacterium bovis as the main representatives of human- and animal-adapted strains, respectively. One key genetic regulator of the MTBC members is the PhoPR system, which controls many processes, including the stress response, lipid metabolism and pathogenesis, among others. Previous studies identified a key G71I substitution in the M. bovis PhoR orthologue relative to M. tuberculosis PhoR and suggested that PhoPR might be non-functional in animal-adapted strains, but recent work has highlighted the functionality of PhoPR in M. bovis despite the G71I substitution. Here, we compare the transcriptional effects of the PhoPR system of M. tuberculosis H37Rv and M. bovis AF2122/97 on an M. bovis AF2122/97 ΔphoPR knockout background. Our results show common patterns of gene expression between the two orthologues, but also clear differences in the expression of rubredoxin genes and lipid biosynthetic loci. This work adds to the evidence that the PhoPR system is indeed functional in M. bovis and suggests that PhoPR controls differential transcriptional programmes that are important in the adaptation to human or animal hosts.

Background. Carbapenem and third-generation cephalosporin (3GC) resistance among Gram-negative bacteria poses a serious threat to human and animal health. This study aimed to identify and characterize carbapenem- and 3GC-resistant Enterobacterales isolated from poultry in Lusaka Province, Zambia. Methods. Ninety pooled cloacal samples were collected from market-ready broiler chickens in the Chongwe and Chilanga districts of Lusaka Province. The isolates were screened for 3GC and carbapenem resistance using the disc diffusion and broth microdilution methods. PCR and Sanger sequencing were performed for species identification and detection of β-lactamase-encoding (bla) genes, including bla _CTX-M, bla _TEM, bla _OXA-1 and bla _SHV. Hierarchical clustering was used to assess phenotypic and genotypic relationships. Results. A total of 83 3GC-resistant Gram-negative isolates were recovered, of which 12% were also carbapenem resistant. Escherichia coli was the most prevalent species, followed by Klebsiella pneumoniae and Enterobacter spp., then Pseudomonas aeruginosa, other Pseudomonas spp., Acinetobacter baumannii, Citrobacter freundii and Aeromonas caviae. Multidrug resistance occurred in 84.3% of the isolates, with the highest resistance to ampicillin, tetracycline and co-trimoxazole. Overall, 80.7% of the isolates harboured at least one of the four tested bla genes, with bla _CTX-M and bla _TEM being the most common. Hierarchical clustering revealed that isolates from both districts shared similar phenotypic and genotypic resistance patterns. Conclusions. The presence of multidrug- and carbapenem-resistant Enterobacterales from poultry highlights the emergence of carbapenem resistance in Zambia's food production sector. The detection of imipenem-resistant isolates indicates the potential for transmission of resistance genes between animals and humans. These findings underscore the need for prudent antimicrobial use, strengthened stewardship and a One Health surveillance approach to contain the spread of carbapenem resistance genes.

Capnocytophaga canimorsus is a fastidious Gram-negative bacterium found in the mouths of dogs and cats. It is a rare cause of infective endocarditis, when it is often associated with dog bites. We present a case of C. canimorsus infective endocarditis complicated by aortic regurgitation and root abscess in a patient with a history of previous infective endocarditis. The patient underwent redo aortic valve surgery with aortic valve replacement. Blood cultures and 16S ribosomal ribonucleic acid gene amplification and sequencing from the excised valve tissue confirmed C. canimorsus as the cause. The patient was treated with beta-lactam antibiotics and discharged home. Rather than secondary to a dog bite, infection most likely occurred due to a dog licking an open wound. It is important to remember that dog contact, often perceived as innocuous, such as being licked, can be a source of serious infection, particularly in the context of an open wound. Over a third of households in the UK own a dog as a pet. With C. canimorsus infections thought to be on the rise, in part due to increased pet ownership, there is a need to ensure pet owners, particularly those at risk of infections and chronic skin wounds, are educated on such risks and the appropriate preventative steps.

The intracellular autophagy receptor p62 (also known as Sequestosome-1) plays a dual role in autophagic flux and downstream Toll-like receptor signalling and has been implicated in modulating immune responses. However, its specific function in controlling intracellular bacterial survival, particularly in macrophages, remains less well characterized. Salmonella enterica serovar Typhimurium (S. Tm) is a major global pathogen and a leading cause of gastroenteritis-associated morbidity. We have previously demonstrated that host restriction of S. Tm in macrophages involves the GTPase Rab32 and the BLOC-3 complex. In the present study, we identify a novel interaction between p62 and Rab32. Notably, p62 restricts Salmonella survival independently of the Rab32/BLOC-3 pathway. Indeed, p62-knockdown in macrophages resulted in significantly increased intracellular bacterial survival, an effect that did not correlate with altered recruitment of canonical autophagy-related proteins, as assessed by fluorescence microscopy. Through real-time polymerase chain reaction (RT-qPCR) and infection assays, we further show that p62-depleted macrophages exhibit a dampened pro-inflammatory response, which corresponds with the increased bacterial burden. These findings provide new mechanistic insight into the role of p62 in modulating the macrophage inflammatory response during Salmonella infection, highlighting its contribution to host defence beyond its canonical functions in autophagy.