International Journal of Microbiology最新文献

Emerging and re-emerging infectious diseases and pathogens present a significant global public health threat that has led researchers to focus on discovering new antimicrobial agents in order to address the challenge. Sponges are a promising source of marine natural products, which can be used as lead molecules for drug discovery. This study was aimed at identifying marine sponges through morphological and molecular techniques and evaluate the bioactivity potential of their organic crude extracts against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans. Deoxyribonucleic acid (DNA) barcoding of the cytochrome c oxidase subunit I (COI) gene identified three genera of sponges (Carteriospongia, Callyspongia, and Paratetilla). Disk diffusion assay was used to determine the inhibition zone diameter (IZD) of the sponges' extracts. Minimum inhibitory concentrations (MICs) and the minimum bactericidal/fungicidal concentrations (MBCs/MFCs) of the most active sponge extracts were determined. The bioactive compounds were analyzed using gas chromatography-mass spectrometry (GC-MS). The dichloromethane extracts of Carteriospongia foliascens demonstrated the highest antifungal activity against C. albicans (31.33 ± 1.2 mg mL^-1), surpassing the standard drug fluconazole (29.33 ± 1.5 mg mL^-1). The MIC values for the sponge extracts ranged from 3.86 to 5.89 mg mL^-1, and the ethyl acetate extract of Callyspongia fallax had an MBC of 4.03 mg mL^-1 against S. aureus. GC-MS chromatogram identified 98 compounds across 41 classes in three sponge extracts. Notably, 9.2% of these compounds have been reported to exhibit antimicrobial activity against human pathogens. This study confirms that sponges are a source of useful biochemicals, which have potential for drug discovery. To the best of our knowledge, this is the first comprehensive study to report on the characterization of marine sponges from the Kenyan waters. Further research work to structurally elucidate and identify the most active bioactive compounds from the extracts of C. foliascens and C. fallax is recommended.

Background: Klebsiella pneumoniae is an opportunistic pathogen linked to a range of severe infections. It is classified into classic K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) forms, with hvKp showing enhanced virulence. This study examines Type VI secretion system (T6SS) presence and virulence factors in cKp and hvKp strains while assessing antimicrobial resistance. Methods: Eighty-three K. pneumoniae isolates were collected from hospitalized patients in Ilam, Iran, between June and December 2023. Antimicrobial susceptibility testing was conducted using the disk diffusion method. Hypervirulent K. pneumoniae isolates were identified by string test, tellurite resistance, and presence of peg-344, iucA, and iutA using polymerase chain reaction (PCR). Furthermore, PCR detected virulence, β-lactamases, and T6SS genes. Results: Of 83 isolates, 16.87% and 83.13% were hvKp and cKp, respectively. All isolates were multidrug-resistant (MDR), with 18.07% exhibiting carbapenem resistance. The pattern of antibiotic resistance in hvKp and cKp is not significantly different, except for ciprofloxacin, tetracycline, and azithromycin. Also, there was no significant difference between T6SS-positive and T6SS-negative isolates except for ciprofloxacin. T6SS presence did not significantly correlate with virulence or resistance genes, except for ciprofloxacin resistance (p = 0.0219). Conclusion: Surveillance, infection control, and targeted therapies are essential to combat hypervirulent and drug-resistant K. pneumoniae.

Background: Acanthamoeba is a free-living amoeba that is widely found in nature in different environments such as soil, water, and dust. This parasite is the cause of amoebic keratitis and granulomatous amoebic encephalitis. This study is aimed at investigating the prevalence and genotypes of Acanthamoeba in different wards of Gonabad Bohlool Hospital, northeastern Iran. Methods: One hundred and eighty-three samples were collected from equipment in various wards of Gonabad hospital in 2023; swabs were cultured in nonnutrient agar (NNA) medium with the addition of killed Escherichia coli. In positive samples containing stellate cysts, PCR molecular testing was performed using JDP1 and JDP2 primers. To confirm Acanthamoeba, genotyping and sequencing were also done. Results: Acanthamoeba sp. was observed in 114 out of 183 samples (62.30%). The highest percentage of Acanthamoeba contamination was in the emergency ward with 81.82%, and the lowest percentage was in the operating and imaging room with 50%. Moreover, the highest percentage of Acanthamoeba contamination was in staff areas and equipment with 66.67%, and the lowest percentage was 56.14% on medical equipment. Also, in this research, the Genotypes T4 (n = 10, 43.5%), T3 (n = 4, 17.4%), T5 (n = 4, 17.4%), T11 (n = 3, 13%), and T2 (n = 2, 8.7%) were determined. Conclusions: The findings of this study showed that Acanthamoeba is more common in the emergency ward and on the surfaces and equipment of the staff areas. Considering the dangerous complications caused by this amoeba, health education to increase awareness in the field of transmission as well as health measures to prevent contamination, including disinfection, is recommended.

The emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-producing E. coli) is a significant public health concern, particularly in developing countries like Indonesia, where reports on the prevalence and characteristics of these resistant strains are scarce. This lack of data hampers effective infection control and antibiotic stewardship efforts. This study is aimed at investigating the prevalence and assessing the antimicrobial susceptibility profiles of ESBL-producing E. coli isolated from clinical samples of Indonesian patients, thereby contributing to an understanding of antibiotic resistance patterns in this region. A cross-sectional study was conducted at RSUD dr. Adhyatma Hospital, Semarang, Indonesia, over 3 years (from January 2022 to December 2024). Clinical specimens were obtained from patients diagnosed with E. coli infections, and isolates were identified and assessed for antibiotic susceptibility utilizing the VITEK2 Compact system. Data were examined via the Fisher's exact test. Out of 449 E. coli isolates, 199 (44.3%) were identified as ESBL, with the highest prevalence in pus (35.6%) and urine (27.2%). ESBL-producing E. coli isolates demonstrated high sensitivity (above 90%) to amoxicillin-clavulanic acid, ceftazidime, ertapenem, meropenem, and tigecycline. Our study also underlined the higher prevalence of multidrug resistance (MDR) in ESBL compared to non-ESBL. The results highlight the urgent need for enhanced surveillance and infection control measures in healthcare settings to combat the spread of ESBL-producing E. coli. Healthcare professionals, including nurses and clinicians, must be aware of this resistance pattern to guide empirical treatment choices and improve patient outcomes in managing infections caused by these resistant strains.

Background: Candida albicans complex species are the main cause of candidiasis. Objectives: The purpose of this study was to report the prevalence and genetic diversity of C. albicans complex using hyphal wall protein 1 (HWP1) gene size polymorphism, as well as the susceptibility patterns to fluconazole and voriconazole. Methods: A total of 170 yeast isolates were obtained from vulvovaginal samples, and phenotypic and proteomic identification was performed. Results: Most clinical isolates were C. albicans complex (n = 153) followed by C. glabrata (n = 13), C. parapsilosis complex (n = 2), and Pichia kudriavzevii (n = 2). Among C. albicans complexes, all isolates were C. albicans sensu stricto and 2.61% and 4.58% were resistant to fluconazole and voriconazole, respectively. Conclusions: The presence of different alleles was confirmed, heterozygosity was more common than homozygosity (71.03% vs. 28.97%), and some isolates showed a homozygosis pattern not previously described. Despite these genetic diversities, no specific genotype was linked to azole resistance.

Enterococcus faecalis is a commensal and opportunistic pathogen increasingly recognized for its antimicrobial resistance (AMR) and zoonotic potential. This study employs whole-genome sequencing (WGS) to characterize E. faecalis isolates from retail meat samples, focusing on antimicrobial resistance genes (ARGs), virulence determinants, mobile genetic elements, and phylogenomic relationships. Fifty raw meat samples, including chicken (n = 18), beef (n = 17), and turkey (n = 15), were collected from retail markets in Akungba-Akoko, Nigeria. Confirmed isolates underwent antimicrobial susceptibility testing and WGS-based genomic analysis. Ten E. faecalis isolates were recovered, predominantly from chicken. All exhibited resistance to clindamycin, erythromycin, and tetracycline. Dominant AMR genes included aac(6⁣')-aph(2⁣^″), ant(6)-Ia, lsa(A), erm(B), tet(M), and tet(L). Plasmid replicons rep9c and repUS43 were associated with sequence types ST477 and ST16, respectively. MGEs such as IS3, IS6, IS256, and IS1380 colocalized with resistance and virulence genes. Phylogenomic analysis revealed two major lineages (ST477 and ST16) and indicated geographic clustering across African isolates. The co-occurrence of multidrug resistance, virulence factors, and MGEs in foodborne E. faecalis poses a public health concern due to the risk of horizontal gene transfer and zoonotic spread. These findings support the need for strengthened genomic surveillance and AMR control strategies in food systems, particularly within low- and middle-income countries.

Research investigating the microbial community of an ecosystem or animal can involve a range of methodologies, including sequencing technology, bioinformatic software and taxonomy database. Researchers may utilise short-read sequencing on Illumina MiSeq or long-read sequencing on platforms like Oxford Nanopore to obtain different research outcomes, for example, enhanced identification of microbes at species or strain level with Nanopore. However, replicability across these techniques is not well studied, while the technique used to process reads into microbial taxa may also result in different taxonomy assignments. In this study, we analyse an existing, real-world dataset which had low genus-level identification with Illumina sequencing and analysis with the SILVA database and compare sequencing with Nanopore on the same samples. We pair this with multiple bioinformatic approaches and taxonomy databases for each sequencing technique to compare phylum- and genus-level assignments and use mock communities to identify which combination of sequencing technique, bioinformatic approach and taxonomy database provides the most accurate taxonomy. We found that Nanopore reads processed with either utilised bioinformatic approach or taxonomy database provided higher accuracy in the assignment of a mock community than any technique combination with Illumina. We also found that the Top 10 genera assigned to a real-world database were substantially different across technique combinations and varied more by taxonomy database than either bioinformatic approach or sequencing technology.

Some members of the lactic acid bacteria (LAB) have been used as probiotics. Ethiopian honey wine, Tej, may be a useful source of potential probiotic bacteria. However, LABs from this source have not yet been evaluated for their probiotic properties. This study was conducted to evaluate the in vitro probiotic properties of LAB isolated from Ethiopian honey wine, Tej. For this purpose, 30 samples were collected from Southwest Ethiopia. LAB isolates were first tested for their antimicrobial activity and those with this property were evaluated for probiotic properties, such as tolerance to acid, salt, and bile, adherence properties, anticholesterol activity, antioxidant activity, and antibiotic susceptibility. The antibacterial activity of the LAB isolates against test organisms was assessed by the agar well diffusion method. Acid, salt, and bile tolerance were evaluated by the plate count method. Adhesion properties were assessed by the determination of bacterial hydrophobicity to the nonpolar solvent p-xylene. Anticholesterol was determined by measuring the remaining cholesterol in the spent broth. The antioxidant capacity was assessed by the 1,1-diphenyl-2-picrylhydrazyl free radical-scavenging capacity, and the antibiotic susceptibility of isolates was tested by the disk diffusion method. A total of 143 LABs were isolated from Tej samples. The LAB count was ranged between 7.4 and 6.5 log cfu/mL. Of the 143 LAB isolates, 37 exhibited different levels of antimicrobial activity. Eight of these were identified to species level by 16S ribosomal genes sequence analysis. The greatest inhibition was against Shigella boydii ATCC 25931 with 19 ± 4.2 mm, and the least inhibitory activity was against Escherichia coli ATTC 25922 and Staphylococcus aureus ATTC 25913 with 8.0 ± 1.4. All except two isolates survived at pH 2 and pH 3 (18.4%-89.6%). Then, 37 isolates survived in more than 50% bile and 54%-67% adhesion capacity. The cholesterol-lowering and 1,1-diphenyl-2-picrylhydrazyl free radical-scavenging capacities ranged from 8% to 54% and 13% to 33%, respectively. Most isolates were susceptible to antibiotics, except for one isolate that resisted all tested antibiotics. This study shows that many LABs isolated from Ethiopian honey wine, Tej have probiotic properties and they can be considered as probiotic candidates. We recommend evaluation of in vivo probiotic properties of the LAB isolates to provide strong supporting evidence.

Introduction: Bacterial infection is a considerable problem in hospitals. Thus, this study was executed to appraise the rampancy of bacterial infections, antimicrobial susceptibility patterns, and molecular characterization of isolates among patients in Bafgh Hospital in Yazd, Iran, in 2020. Methods: In the current study, we surveyed 103 isolates of 400 clinical specimens from early March 2020 to September 2020 in Bafgh Hospital. We assessed phenotypic traits and antibiotic resistance with standard microbiological methods. Phenotypic methods were also performed to identify extended-spectrum beta-lactamases (ESBLs) in Gram-negative bacilli, inducible clindamycin resistance, and methicillin resistance in Staphylococcus according to CLSI guidelines. Molecular identification of isolates was done by conventional PCR 16S rRNA gene sequencing. Furthermore, we investigated the prevalence of resistant genes including bla _TEM, bla _PER-2, bla _CTX-M, bla _SHV, and bla _VEB-1 in Gram-negative bacteria and the mecA gene in staphylococcal species. Results: From 400 different clinical specimens, 103 isolates of Gram-positive and Gram-negative bacteria were isolated. Based on phenotypic and molecular methods, most common isolates were Escherichia coli (53 isolates), followed by Klebsiella spp. (18 isolates), and Staphylococcus aureus (16 isolates). The highest resistance was found in Gram-positive bacteria to erythromycin (66.67%) and penicillin (55.56%), while considering Gram-negative bacteria, the most resistant was cefixime (49.41%) and trimethoprim-sulfamethoxazole (47.05%). In addition, out of 16 S. aureus isolates, 62.5% and 17.65% were resistant to methicillin and clindamycin, respectively. Among 83 Gram-negative isolates, 22.89% were ESBL-positive. The prevalence of bla _SHV, bla _PER2, bla _TEM, bla _CTX-M, and bla _VEB-1 genes was 78.31%, 59.03%, 40.96%, 30.12%, and 0%, respectively. Conclusions: The outbreak of bacterial infections is relatively high in hospitals. Recognizing risk agents for bacterial infections and restricting the administration of multidrug-resistant antibiotics is a substantial measure that must be taken to prevent patient mortality.

Background: Surgical site infections (SSIs) remain a critical challenge globally and are aggravated by rising antimicrobial resistance (AMR). Here, we evaluated the bacterial profile, AMR patterns, and ESβL characterization of isolates from patients diagnosed with SSI after trauma orthopedic surgery. Methods: This prospective study was carried out at Tamale Teaching Hospital from September 2023 to May 2024. Patients were asked to provide demographic data. Samples were also collected from patients suspected of SSI and cultured for bacterial isolation, identification, and AMR characterization. Results: In all, 210 patients were recruited for this study, and 14 (6.7%) out of 19 suspected cases developed SSI. Of 19 specimens, 14 (73.68%) were culture-positive, yielding 22 isolates. Monomicrobial growth were 7 (50.0%) and polymicrobial growth 7 (50.0%). Among the isolates, 3 (13.64%) were Gram-positive and 19 (86.36%) were Gram-negative bacilli. Pseudomonas aeruginosa (5, 22.73%) were the most common isolates, followed by Klebsiella spp. (4, 18.18%). ESβL-positive isolates were 3 (23.08%). PCR confirmed the expression of CTXM and SHV genes by two Klebsiella spp. and the CTXM gene by Proteus vulgaris. Conclusion: Gram-negative bacteria, particularly Pseudomonas aeruginosa, were the dominant isolates from surgical sites after trauma orthopedic surgery. Among the Gram-positives, Staphylococcus aureus was dominant. Among the Enterobacterales isolates, ESBL production was detected in three cases (23.08%), with two Klebsiella spp. harboring CTXM and SHV resistance genes, and CTXM in one Proteus vulgaris. The current study has revealed varied resistant patterns of AMR, with CTXM and SHV as common ESβL genes among the isolates. The clinical identification of CTX-M and SHV genes could guide clinicians to consider alternative treatments to optimize therapeutic outcomes and limit the spread of resistant pathogens.