Search Results (64)

Background/Objectives: Antimicrobial resistance (AMR) in Staphylococcus spp. associated with poultry production is an emerging concern with implications for animal and public health. This study aimed to characterize antimicrobial susceptibility patterns and detect targeted methicillin resistance determinants in Staphylococcus isolates recovered from broiler chickens affected by bacterial chondronecrosis with osteomyelitis (BCO). Methods: A total of 200 bacterial isolates were evaluated, of which 167 were confirmed as Staphylococcus spp. Species identification was performed using presumptive phenotypic characterization followed by 16S rRNA gene sequencing. Antimicrobial susceptibility was assessed using disk diffusion, while presumptive methicillin-resistant phenotypes were evaluated using oxacillin screening and CHROMagar MRSA. Targeted molecular detection of mecA and mecC was performed by PCR. Results: The isolates demonstrated substantial species diversity, with S. aureus as the predominant species. Antimicrobial resistance was mainly observed against β-lactam antibiotics, particularly penicillin (33.5%), whereas high susceptibility was retained for non-β-lactam agents, including ciprofloxacin, tetracycline, trimethoprim–sulfamethoxazole, and azithromycin. A targeted PCR detected mecA in 7.2% of isolates, while mecC was not detected. The detection of mecA in oxacillin-susceptible isolates suggested genotype–phenotype discordance. Conclusions: BCO-associated Staphylococcus spp. from broiler chickens showed diverse species distribution, penicillin-dominant resistance, and targeted mecA detection across multiple species, supporting the use of combined phenotypic and molecular approaches for methicillin resistance surveillance. Full article

Vulvovaginal candidiasis (VVC) is a common fungal infection among reproductive-age women and is increasingly challenged by the emergence of non-albicans Candida species and reduced azole susceptibility. This prospective cross-sectional study investigated 235 symptomatic reproductive-age women attending two healthcare facilities in Ho Chi Minh City, Vietnam, to determine VVC prevalence, Candida species distribution, pregnancy-associated patterns, antifungal susceptibility, and diagnostic performance. Vaginal swabs were cultured on Sabouraud Dextrose Agar and CHROMagar™ Candida, while species identification was confirmed by PCR-RFLP targeting the ITS region. Susceptibility to fluconazole and clotrimazole was assessed using the disk diffusion method. Candida spp. was detected in 55.7% of participants. C. albicans accounted for 50.3% of isolates, whereas non-albicans Candida species represented 49.7%, indicating a substantial species shift. VVC was more frequent among pregnant women, particularly in the third trimester. Most C. albicans, C. tropicalis, and C. parapsilosis isolates remained susceptible to azoles; however, C. glabrata showed markedly reduced susceptibility to fluconazole and clotrimazole. CHROMagar™ Candida reliably identified C. albicans but misclassified several non-albicans Candida isolates compared with PCR-RFLP. These findings highlight the need for routine species-level diagnosis, antifungal susceptibility testing, and strengthened VVC surveillance in reproductive and antenatal healthcare settings in Vietnam. Full article

Background: The emergence of alternative methods of obtaining groceries since the COVID-19 pandemic has raised new concerns regarding food safety. In this study, we sought to evaluate these concerns by evaluating how the procurement method of ground beef impacts the microbial load in the beef, as this has not been thoroughly studied. Methods: Specifically, we compared beef samples obtained from in-store shopping, grocery delivery, and meal kit delivery services to determine if these new, more convenient methods of grocery shopping impact the total microbial load or Escherichia coli present in the beef. We homogenized a total of 65 beef samples and plated dilutions on trypticase soy agar, MacConkey agar, and CHROMagar. Results: We found that in-store samples had the highest microbial load with an average of 5.06 log CFU/g, while grocery delivery samples resulted in an average of 4.76 log CFU/g and meal kit samples had an average of 4.23 log CFU/g when plated on TSA. This represents a 6.7-fold change between in-store samples and meal kit samples. These differences were not statistically significant (p = 0.1, ANOVA). When plated on MacConkey agar, in-store samples had a bacterial count at 3.0 log CFU/g, while grocery delivery samples had 2.99 log CFU/g and meal kit delivered samples had 3.05 log CFU/g. Suspected E. coli O157 colonies were detected using CHROMagar plates, as these plates function to change the coloration of positive E. coli O157 colonies to pink. Suspected E. coli O157 colonies were observed in three in-store samples, two grocery delivery samples, and one meal kit sample. After confirmatory agglutination testing, one meal kit sample was confirmed as E. coli O157. Conclusions: While trends suggest possible lower microbial contamination in delivery methods versus in-store shopping procurement, no statistical significance between methods was found. These findings indicate no significant changes in microbial loads in delivered ground beef, and the high variance suggests that all procurement methods still pose some level of risk. Full article

Bacterial resistance on farms can be driven by antimicrobial use. Less is known about inter-farm transfer of resistance genes and their persistence under low antimicrobial pressure. Over two years and nine visits, we examined the shedding of resistant indicator bacteria (Escherichia coli) on one lower- and one higher-antimicrobial-usage pig farm. There was a unidirectional transfer of some less healthy pigs from the former to the latter. Faecal pools (180) were cultured on Chromagar ECC, with and without added cefotaxime or ciprofloxacin. Presumptive E. coli were phenotyped, and many ciprofloxacin-resistant isolates were whole-genome sequenced. Comparing farms, there was more (p < 0.0001) phenotypic resistance to the antimicrobial panel from the higher-usage unit, and markedly more (about ten-fold) multi-resistance. Significantly elevated individual drug resistances on this unit correlated with recently used antimicrobials. Ciprofloxacin and/or cefotaxime-resistant isolates were often present, although in low proportions. Neither of these antimicrobial classes had been administered recently, except for one fluoroquinolone course late in the study. AMR genes were more diverse from the higher-usage farm, but some resistant and multi-resistant isolates were closely related between farms. Thus, we demonstrated the maintenance of resistance genes in strains present on farms, even where selective pressure was low. Full article

The threat of antimicrobial resistance in aquatic environments, particularly riverine systems, is escalating, in part due to effluents discharged from healthcare facilities. This issue has been recognized not only in Japan but also in other Asian countries such as Indonesia and Nepal. Nevertheless, existing research remains limited, prompting an investigation into the prevalence of antimicrobial-resistant bacteria in the upstream and downstream sites of environmental rivers. In 2024, six samples were collected from three rivers in Hyogo Prefecture, Japan; five samples from five river sites in Indonesia; and three samples from downstream sites of rivers in Kathmandu, Nepal. These samples were subjected to selective culture–based Next Generation Sequencing and resistome analyses, based exclusively on the selective culture of bacteria propagated on CHROMagar ESBL plates. In Japan and Indonesia, Pseudomonas, Stenotrophomonas and Acinetobacter were frequently detected, whereas Klebsiella was overwhelmingly predominant in Nepal. Significant differences in the similarity of bacterial community composition among sampling sites across the three countries were observed (p < 0.001). Notably, Nepal exhibited the highest abundance level of antimicrobial resistance genes among the three countries, largely consisting of β-lactam resistance genes. In conclusion, these analyses elucidated substantial differences in bacterial community composition and degrees of environmental contamination. Full article

Background/Objectives:  Candida infections constitute a significant category of healthcare-associated infections. In studies aiming to develop new antifungal agents against Candida species, the importance of their virulence factors has been emphasized. Methods: This study included 100 Candida isolates obtained from patients hospitalized in intensive care units. Standard microbiological and molecular methods were employed for species identification. Virulence factors were determined through protease, phospholipase, hemolysis, and biofilm activity assays per-formed on the Candida strains. The EUCAST liquid microdilution method was used to assess antifungal susceptibility. Results: Based on sequencing results, 39 isolates were identified as Candida albicans and 61 as non-albicans Candida species. The accuracy of species identification was found to be 71% for Chromagar Candida and 87% for the MALDI-TOF MS system, compared to sequencing. Protease activity was positive in 52% of the isolates, phospholipase in 42%, hemolytic activity in 77%, and biofilm formation in 48%. Kruskal–Wallis analysis revealed no statistically significant interspecies differences in MIC distributions for amphotericin B, fluconazole, itraconazole, or nystatin (p > 0.05), although species-specific trends were observed, with higher fluconazole MICs in C. albicans and lower MIC values in C. tropicalis.  Conclusions: Determining the distribution of Candida species, as well as their virulence factors and antifungal MIC profiles, is of great importance for developing appropriate treatment strategies and reducing related morbidity and mortality. Full article

Candida viswanathii has been sporadically reported in Asia and South America but not in Europe. This study reports the first European outbreak of C. viswanathii in a paediatric hospital, outlining diagnostic challenges and containment measures. Fifteen C. viswanathii isolates were recovered from blood cultures of consecutive pediatric patients admitted to intensive care units between April and August 2025. Identification was performed using MALDI-TOF MS, chromogenic media, Fourier-transform infrared (FT-IR) spectroscopy, and whole-genome sequencing (WGS). Antifungal susceptibility testing was performed by broth microdilution. All isolates were initially misidentified as C. tropicalis by MALDI-TOF MS and undetected by the FilmArray BCID2 panel. WGS confirmed C. viswanathii, and FT-IR analysis revealed clonally related strains, indicating an outbreak. Colonies displayed a distinct deep-blue color on chromogenic CHROMagar™ medium. Elevated fluconazole minimum inhibitory concentrations were observed, while isolates remained susceptible to echinocandins and amphotericin B. A multidisciplinary infection-control response halted transmission within four weeks. This investigation documents the first C. viswanathii outbreak in Europe, highlighting diagnostic limitations of current commercial tools and the need for updated databases. Integration of FT-IR spectroscopy and WGS facilitated outbreak detection and containment, underscoring the importance of advanced diagnostics and surveillance for emerging fungal pathogens. Full article

Yeasts of the Candida genus are part of the normal human microbiota but can cause infections (candidiasis) under certain conditions. While Candida albicans remains the most common etiological agent, the prevalence of non-albicans Candida species—such as C. glabrata, C. tropicalis, C. krusei, C. parapsilosis, C. kefyr, C. lusitaniae, and the emerging multidrug-resistant C. auris—has been increasing. Effective treatment of candidiasis requires rapid and accurate identification of the causative species, particularly due to species-specific antifungal agent resistance patterns. The aim of this study was to evaluate the usefulness of five chromogenic media for the differentiation of Candida species: BD CHROMagar Candida (Becton Dickinson), CHROM ID Candida (bioMérieux), CHROMAgar Candida Plus (CHROMAgar France, Biomaxima), CHROMAgar Candida Plus (GRASO Biotech), and Brilliance Candida Agar (OXOID). A total of 175 strains from the following species were tested: C. albicans, C. parapsilosis, C. dubliniensis, C. lusitaniae, C. tropicalis, C. glabrata, C. kefyr, C. krusei, and C. auris. Species identification was confirmed by MALDI-TOF mass spectrometry using the MALDI Biotyper system (Bruker). Colony morphology, especially color characteristics, was assessed on each medium. The morphological features of most Candida species were consistent with the manufacturer’s descriptions and allowed for presumptive species-level identification. However, some species showed reproducible but previously undescribed morphological traits, including variations in colony shade. Notably, C. auris could not be reliably identified using BD, bioMérieux, or OXOID media. In conclusion, while chromogenic media are a helpful preliminary diagnostic tool, subtle differences in colony coloration can complicate interpretation. Diagnostic caution is recommended, and confirmatory methods such as MALDI-TOF remain essential for reliable identification, especially for emerging or less common Candida species. Full article

Background: Pigs and cattle have been implicated as reservoirs of antimicrobial resistance genes (ARGs) that can spread to humans, and houseflies are considered potential carriers of bacteria with ARGs that could contribute to their spread to the environment, including food, animals, and humans. Methods: In this study, 107, 145, and 127 Escherichia coli strains were isolated from houseflies, pigs, and cattle, respectively, from a slaughterhouse in Lima, Peru. Antimicrobial susceptibility testing was performed using the Kirby–Bauer method, where thirteen antibiotics were used. Strains were also plated on CHROMagar COL-APSE agar, and colistin’s minimum inhibitory concentration (MIC) was determined. Colistin-resistant E. coli strains were subjected to whole genome sequencing. Results: 7.8% (8/107), 1.38% (2/145), and 0.79% (1/127) of E. coli strains isolated from houseflies, pigs, and cattle, respectively, were resistant to colistin (MIC ≥ 4 µg/mL). ARGs associated with resistance to more than 6 different antibiotic classes were identified, including tetracyclines, beta-lactams, fluoroquinolones, nitroimidazoles, trimethoprim and amphenicols. Conclusions: This study suggests that flies could contribute to the dissemination of ARG carrying bacteria and shows the potential risk of animals and meat production systems as reservoirs of ARG carrying bacteria. Full article

Colistin, a polymyxin antibiotic used as a last-resort treatment for serious infections, exhibits efficacy against multidrug-resistant organisms. Colistin-resistant bacteria limit the treatment options and increase the risk of untreatable infections. In this study, we investigated various antimicrobial-resistant Escherichia coli strains isolated from broiler cecal feces. In the primary screening using CHROMagar C3GR and ESBL, 147 E. coli isolates were obtained from 231 broiler cecal samples at five domestic poultry farms in Japan in 2024. Of the 147 isolates tested for antimicrobial susceptibility, 20 (13.6%) showed resistance to colistin. Moreover, whole-genome sequencing detected the colistin resistance gene, mcr-1.1 (phosphoethanolamine transferase), in the colistin-resistant E. coli strains isolated from the tested five poultry farms. Multilocus sequence typing revealed that all strains belonged to ST1485, indicating that the cloned strains had spread to multiple poultry farms. Subsequent core-genome comparison analysis with global ST1485 strains indicated that the ST1485 isolates in this study were highly identical, whereas the global strains were distinct. The complete genome sequence of BroCaecum-55 contained mcr-1.1 in a 62,716 bp IncI2 replicon plasmid (pBroCa-55-p2). In conclusion, mcr-1.1-positive colistin-resistant E. coli strains, which are rarely reported in Japan, were isolated from Japanese broilers, indicating that colistin resistance persisted even after the ban on colistin use as a feed additive in Japan in 2018. Our findings highlight the need for continuous monitoring of colistin-resistant bacteria in livestock to reduce the transmission risk to humans. Full article

Background: Poultry litter is the main waste of poultry farming and is widely used as an agricultural fertilizer. However, owing to the use of antimicrobials in animal production, it can accumulate antimicrobial residues, antimicrobial-resistant bacteria (ARB), and antimicrobial resistance genes (ARGs). This study aimed to evaluate the impact of poultry litter use on the microbiome and resistome of agricultural soils. Methods: Soil samples from fertilized and unfertilized plots were collected from two horticultural farms that intensively use poultry litter. Microbiome composition was assessed using 16S rRNA sequencing. A culture-dependent method was used to isolate resistant strains on CHROMagar plates supplemented with sulfamethoxazole or ciprofloxacin. ARGs and integrase-encoding genes were identified by PCR. Results: Microbiome analysis revealed significant differences in structure and composition between poultry litter-fertilized and unfertilized soils. Fertilized soils exhibited greater alpha diversity and richness. Bacillota, commonly found in the avian gastrointestinal tract, were more abundant in fertilized soils. A total of 62 resistant strains were isolated, and 23 clinically relevant strains harbored ARGs, including fluoroquinolone (qnrA and qnrB) and β-lactam (bla_GES, bla_TEM, and bla_SHV) resistance genes. Class 1 and 2 integron-associated genes (intI1 and intI2) were also detected. Notably, the rare bla_GES gene was detected in Bacillus sp. from unfertilized soil. Similarly, qnrA co-occurred with bla_SHV in a Bosea sp. strain from unfertilized soil. Conclusions: These findings highlight the potential for ARB dissemination in agricultural environments, where ARB and ARGs, once introduced into soils, may spread by weathering and other environmental factors, complicating negative control selection in in situ studies. Full article

Background/Objectives: Ulcerative colitis (UC) and Crohn’s disease (CD) are the usual clinical forms of inflammatory bowel disease (IBD). Changes in the oral microbiota, especially the presence of emerging fungi and herpesviruses, have been shown to worsen the clinical aspects of IBD. The aim of this study was to screen for emerging pathogens in the oral yeast microbiota and the presence of herpesvirus in IBD patients. Methods: Oral swabs of seven UC or CD patients were collected. The samples were plated on Sabouraud Dextrose Agar and subcultured on CHROMagar Candida and CHROMagar Candida Plus. Polyphasic taxonomy was applied and identified using molecular tools, such as MALDI-TOF MS and ITS partial sequencing. Multiplex qPCR was used to identify the herpesvirus. Results: The mean age was 38.67 ± 14.06 years, 57.14% were female, and two had diabetes. The CD patients presented with Rhodotorula mucilaginosa, Candida orthopsilosis and Kodamaea jinghongensis, while the UC patients presented with Cutaneotrichosporon dermatis, Candida glabrata, Candida lusitanea and Candida tropicalis. Two UC individuals had at least one herpesvirus. In the first individual, a co-detection of Herpes Simplex Virus 1 (HSV-1) and C. lusitaniae was observed. The second presented with co-infections of Epstein–Barr virus (EBV), Human Herpesvirus 7 (HHV-7) and C. tropicalis. Conclusions: We identified rarely described yeasts and co-infections in IBD patients, highlighting the need to identify emerging pathogens in the oral microbiota, as they may contribute to opportunistic infections. Full article

Objective: In the present study, we used phenotypic and molecular methods to determine susceptibility to oxacillin in coagulase-negative staphylococci (CoNS) and estimate the prevalence of strains with low-level resistance to oxacillin, mecA-positive oxacillin-susceptible methicillin-resistant (OS-MRCoNS), and borderline oxacillin-resistant (BORCoNS). Methods: One hundred one CoNS strains were screened for oxacillin and cefoxitin susceptibility using phenotypic (disk diffusion, agar dilution, latex agglutination, and chromagar) and molecular (detection of mecA, mecB, and mecC) methods. Staphylococcal cassette chromosome mec (SCCmec) typing was performed. Results: Sixteen (15.8%) CoNS strains were mecA-positive, and 85 (84.2%) were mec-negative. Seven (6.9%) were classified as OS-MRCoNS, accounting for 43.8% of all mecA-positive strains. Twelve (11.9%) mec-negative strains were classified as borderline oxacillin resistant (BORCoNS). Compared with MRCoNS and BORCoNS, OS-MRCoNS strains demonstrated lower resistance to non-beta-lactams. SCCmec type I cassette was predominant. The disc-diffusion method with oxacillin accurately predicted OS-MRCoNS strains but did not provide reliable results for BORCoNS strains. Meanwhile, the latex agglutination test and CHROMagar culture accurately identified BORCoNS but not OS-MRCoNS. Conclusions: Finally, our findings imply that the recognition of methicillin resistance in CoNS requires a meticulous approach and that further research is needed to develop unified laboratory diagnostic algorithms to prevent the misreporting of borderline CoNS. Full article

Introduction: Shiga toxin-producing Escherichia coli (STEC), particularly E. coli O157:H7, is a major contributor to foodborne outbreaks globally. Both E. coli O157 and non-O157 strains can lead to severe health issues, including hemolytic colitis and hemolytic uremic syndrome, which can result in kidney failure. Methods: Two hundred and one frozen beef samples were purchased from various supermarkets located in the Eastern Province of Saudi Arabia and subsequently enriched in tryptic soy broth (TSB). From the enriched samples in TSB, 1 mL portion was mixed with immunomagnetic beads (IMB) coated with specific antibodies targeting the E. coli O157 O antigen. The beads, which contained the captured bacteria, were then streaked onto CHROMagar O157 and Sorbitol MacConkey (SMAC) agar. The DNA extracted from these samples was examined using multiplex PCR to identify potential virulence gene markers, specifically stx-1, stx-2, and eae. Results: Of the 201 examined samples, 88 (43.8%) and 106 (52.7%) were positive for E. coli and produced colorless and mauve colonies on SMAC agar and CHROMagar O157, respectively. Out of 298 isolates in total, 174 isolates of E. coli were isolated with IMB enrichment. The highest detection rate of virulence gene markers was found among isolates that had been isolated using IMB enrichment, where 25 (8.4%), 2 (0.7%) and 12 (4%) isolates tested positive for stx1, stx2, and eae genes respectively. Among 42 isolates harboring potential virulence gene markers, 11 isolates were identified as E. coli O157 (stx₁⁺/eae⁺ or stx₂⁺/eae⁺). ERIC-PCR genotyping was able to determine the genetic relatedness among 42 isolates of E. coli O157 and E. coli non-O157 into 10 types with four identical related clusters and a genetic similarity rate above 90% homology from the identified isolates. Conclusions: The present study gives a clear perspective on STEC contamination in imported frozen beef marketed in Saudi Arabia. Because of the many possibilities of STEC contamination in imported frozen beef, further studies on the spread of STEC at various levels of imported frozen meat are needed on a long-term basis. Full article

Vulvovaginal candidiasis (VVC) can lead to multiple complications when it occurs during pregnancy, so it is necessary to diagnose it promptly for effective treatment. Traditional methods for identifying Candida spp. are often too time-consuming and have limited specificity and sensitivity. In this work, we evaluated the diagnostic utility of an endpoint PCR assay (Cand PCR) in vaginal swab specimens. Using a cotton swab, 108 vaginal swab samples were taken from pregnant women who consented to participate in the study. The samples were inoculated in Sabouraud agar plates (the gold standard) and subsequently used to extract DNA directly from the exudate. The yeasts isolated from the Sabouraud agar were identified in CHROMagar™ Candida. DNA extracted from vaginal swabs was amplified by Cand PCR. Based on the results of the Cand PCR and the gold standard, sensitivity (S), specificity (E), positive predictive values (PPVs), and negative predictive values (NPVs) were determined. Cand PCR presented an S = 65%, E = 100%, PPV = 100% and NPV = 91%. Cand PCR showed low sensitivity for detecting Candida spp. directly from vaginal swabs, but it was useful for identifying the etiologic agent and reducing the time to obtain the result, which is usually at least 48 h. Full article