Letters in Applied Microbiology最新文献

Clostridioides difficile is an opportunistic pathogen of the gastrointestinal tract that can cause illnesses ranging from diarrhea to pseudomembranous colitis. Recurrent Clostridioides difficile infection remains a major clinical challenge, with substantial relapse rates after standard antibiotic therapy. Emerging evidence suggests that rifaximin can be used after the conventional therapy to reduce risk of the recurrence. However, rifaximin resistance in Clostridioides difficile remains the primary concern. The aim of this systematic review and meta-analysis is to estimate the risk of rifaximin resistance in Clostridioides difficile infection and among different ribotypes. The search included PubMed, Scopus, Web of Science, and Cochrane Library for studies reporting rifaximin resistance in Clostridioides difficile isolates. After systematically screening 731 records from all databases and excluding 664 studies, a total of 67 studies were included in the meta-analysis. The findings of the meta-analaysis indicated a resistance rate of 15.1% (95%CI,12.0%-18.9%) for rifaximin and/or rifampicin and 12.8% (95%CI,8.8%-18.2%) for rifaximin alone. Ribotype-specific analysis revealed high rifaximin resistance in RT017(72.3%), RT027(47.0%), and RT018(20.9%), while RT012, RT002, RT112, and RT014/020 demonstrated low resistance. The study finding indicate that rifaximin/rifamycin resistance in Clostridioides difficile is concerning and not randomly distributed but is more frequently associated with certain ribotypes.

Mycobacterium avium ssp. paratuberculosis (MAP) is an intestinal pathogen which is excreted fecally and can be spread in the environment through contaminated manure. Lactic acid fermentation (LAF) was evaluated as a method to inactivate MAP in cattle manure. As carbohydrate (CHO) sources oats and saccharose were used. After mixing, manure was incubated at 21°C for 8 weeks. The microbial shift was determined using cultural methods. The results showed different suitability of the selected CHOs for inactivation of MAP by LAF. Using squeezed oats as an additive, culturable MAP was reduced to below the detection limit after 35 and 42 days of fermentation. Additional saccharose decreased the reduction time to 21 days. With saccharose only addition, inactivation of MAP was not successful and bacterial counts did not differ from the negative control. Detection of IS900 genome fragments using RT-PCR showed that the number of gene copies in the manure did not decrease during the course of the experiments. This study showed that LAF is a valuable option for decontaminating cattle manure with natural resources in the case of paratuberculosis.

Studies have revealed the presence of Listeria species on food and non-food contact surfaces in apple packing facilities. However, the occurrence of Listeria in controlled atmosphere (CA) storage facilities has not been well characterized. This two-year longitudinal study assessed the prevalence, diversity, and distribution of Listeria spp. within nine CA storage rooms at three different facilities (A, B, and C), focusing on Zone 3 non food contact surfaces. A total of 304 samples were collected, and 5.9% (18) were positive for Listeria spp., predominantly on floors below condenser units. Of 18 positive sample sites, L. monocytogenes was the main species detected, accounting for 61.1% (11/18), followed by L. seeligeri at 22.2% (4/18). None of the facilities showed repeated detection of the same Listeria subtype at the same location during the 2-year period. However, in Facility A, L. monocytogenes was repeatedly detected on the floor below condenser units, although the isolates belonged to different subtypes. Our findings highlight the importance of preventive measures such as environmental monitoring and sanitation programs that may mitigate Listeria spp. contamination in CA storage environments, considering the microbes ability to survive in low temperature modified atmosphere conditions conducive to long-term apple storage.

Microbial source tracking (MST) using Bacteroidales markers provides information on faecal contamination in environmental waters. The marker BacUni targets a range of sources, while HF183 is primarily associated with human faeces. Duplex quantitative PCR (qPCR) assays allow simultaneous detection of both markers, though competition between primer-probe sets can affect accuracy. Digital PCR (dPCR) offers absolute quantification and higher sensitivity, but multiplexing can be challenging when marker concentrations differ. This study compared HF183 and BacUni quantification across singleplex and duplex qPCR formats and duplex dPCR. Synthetic standards revealed variability due to gBlock design and probe orientation, whereas environmental samples showed minimal format-dependent effects. Duplex qPCR provided comparable results to singleplex, with minor underestimation relative to dPCR. These small differences likely reflect the use of dPCR-quantified standards for qPCR calibration, rather than using DNA concentration-based calibration methods. Low-copy HF183 samples highlighted dPCR's superior sensitivity near detection limits. GoTaq qPCR was the most economical option, especially in duplex format, whereas dPCR offered competitive costs for duplexed samples with the advantage of absolute quantification. These findings demonstrate that duplex qPCR assays reliably quantify HF183 and BacUni in environmental waters, with dPCR serving as a robust complementary method for low-abundance or confirmatory analyses.

Ensuring the sterility of pharmaceutical products, particularly those administered parenterally, is crucial for patient safety. Conventional sterility testing methods, while reliable, require incubation periods of up to 14 days, delaying product release. Therefore, exploring alternative rapid microbiological methods is essential for improving testing efficiency and reducing the time-to-result (TTR). This study evaluates the Red One™ system, a novel rapid method utilizing solid-phase cytometry and esterase-based activity staining, which reduces the TTR to just 96 h. Our results demonstrate the non-inferiority of the Red One™ system compared to traditional culture-based techniques by assessing key performance parameters, including limit of detection, accuracy, robustness, and ruggedness for various microorganisms, including slow-growing species such as Cutibacterium acnes. Our results indicate that this alternative system is an effective method for rapid sterility testing in the pharmaceutical industry.

Burkholderia cepacia complex (Bcc) bacteria are opportunistic pathogens that particularly affect people with cystic fibrosis and other immunosuppressed patients. These bacteria are also frequent contaminants of industrial products such as medicines and cosmetics, posing a risk to patients and raising public health concerns. Due to numerous outbreaks caused by contaminated products reported worldwide, the absence of Bcc in drugs has become mandatory under various codifications. For example, the US Pharmacopoeia recently incorporated testing for Bcc detection in non-sterile products (USP < 60 >). Detection of Bcc usually involves the use of the Burkholderia cepacia selective agar (BCSA), a selective but non-differential culture medium. In this study, we compared a recently developed chromogenic agar, CHROMagar™ B.cepacia, with BCSA for the recovery of Bcc and inhibition of non-Bcc species. We also evaluated both media for the detection of Bcc in artificially contaminated pharmaceutical and cosmetic samples. Both media exhibited similar inhibitory properties. Notably, all Bcc isolates in this study developed blue-green colonies on CHROMagar™ B.cepacia, enabling rapid and presumptive identification. These results suggest that CHROMagar™ B.cepacia could be a valuable tool for the rapid detection of Bcc in industrial samples.

Quinoa (Chenopodium quinoa Willd.) is a climate-resilient Andean crop with high nutritional value and strategic importance for food security in high-altitude regions. However, its productivity in low-input farming systems remains limited. This study developed scalable strategies for propagation and formulation of a Serratia sp. strain as a biofertilizer, using brewery spent yeast (BSY) as growth substrate. Microwave-assisted extraction (MAE) at 1200 W for 15 min significantly (P ≤ 0.05) enhanced soluble protein release from BSY, and MAE-treated media with a C:N ratio of 24:1 supported optimal bacterial growth. Carrageenan-based bio-bead formulations produced at 40°C with 96 g L⁻¹ carrageenan yielded the highest bacterial viability and moisture retention. In a field trial in the Bolivian Altiplano, bio-beads containing Serratia sp. applied at branching stage increased quinoa yield by up to 3.4-fold (P ≤ 0.01) compared with the control. The formulation control also substantially improved yield (2.2-fold), indicating that both the carrier matrix and bacterial inoculation contributed to growth enhancement. These findings demonstrate the potential of biofertilizer technologies based on agri-food by-product valorization to improve crop performance under extreme and resource-limited agricultural conditions.

As Salmonella is known to be able to persist in processing environments, we investigated whether the detection of Salmonella clusters from retail poultry can be linked to a persistent source. A total of 69 Salmonella Infantis isolates from retail poultry products from four different producers between 2008 and 2020 were sequenced and their sensitivity to antibiotics was determined. The six phylogenetic clusters spanning multiple months identified by sequence analysis indicate persistence of Salmonella. In addition, the pESI megaplasmid, which is known to harbor a diversity of resistance and persistence factors, was identified in 53 of the 69 isolates. The pESI plasmid was shown to be more prevalent among more recent strains and was shown to be present in isolates from five out of six clusters. The identification of clusters by whole genome sequencing analyses helps to identify persistent strains, as was shown in this study for S. Infantis. Moreover, the detection of pESI in these S. Infantis isolates suggests that pESI has a role in persistence and thus in the further spread and increased prevalence of S. Infantis.