Characterization of multidrug-resistant potential pathogens isolated from milk and some dairy products in Egypt

Objective

This study aimed to explore the incidence and antimicrobial resistance (AMR) of Escherichia coli, Staphylococcus aureus, and Bacillus cereus in raw milk and some Egyptian dairy products, namely Kariesh cheese and rice with milk.

Material and Methods

112 samples (70 raw milk, 30 Kariesh cheese, and 12 rice with milk) were randomly collected from different districts in Cairo and Giza, Egypt. The samples were examined for E. coli, S. aureus, and B. cereus presence. The susceptibility of the obtained isolates was tested against 11 antimicrobials using the disk diffusion method, and further, the presence of AMR genes was examined.

Results

The incidences of E. coli, S. aureus, and B. cereus were 69.64%, 12.5%, and 16.7% in the examined samples, respectively. The antibiogram indicated that E. coli isolates (n = 60) were resistant to gentamycin (73.33%), ampicillin (AM, 53.3%), and cefotaxime (CTX, 16.66%). Multidrug-resistant (MDR) E. coli strains (n = 5) were tested for β-lactams resistance genes. blaTEM was detected in all isolates, and two of them additionally carried blaCTX-M. Staphylococcus aureus isolates (n = 10) were resistant to AM (100%), followed by tetracycline (TE), CTX, and gentamycin (60% each). All MDR S. aureus strains (n = 4) carried blaZ and tetK, and three of them additionally carried aac(6')-aph (2''). Bacillus cereus isolates (n = 30) showed resistance to AM (100%), amoxicillin (20%), and TE (6.66%). bla and tetA genes were detected in all MDR B. cereus isolates (n = 6).

Conclusion

Our findings denote the high incidence of potential health hazards in raw milk and some of its products and the existence of AMR bacteria, including MDR strains, which can cause human illnesses that are difficult to treat.

Composition of Culturable Microorganisms in Dusts Collected from Sport Facilities in Finland during the COVID-19 Pandemic

Sport facilities represent extreme indoor environments due to intense cleaning and disinfection. The aim of this study was to describe the composition of the cultivated microbiota in dust samples collected in sport facilities during the COVID-19 pandemic. A dust sample is defined as the airborne dust sedimented on 0.02 m² within 28 d. The results show that the microbial viable counts in samples of airborne dust (n = 9) collected from seven Finnish sport facilities during the pandemic contained a high proportion of pathogenic filamentous fungi and a low proportion of bacteria. The microbial viable counts were between 14 CFU and 189 CFU per dust sample. In seven samples from sport facilities, 20-85% of the microbial viable counts were fungi. Out of 123 fungal colonies, 47 colonies belonged to the potentially pathogenic sections of Aspergillus (Sections Fumigati, Nigri, and Flavi). Representatives of each section were identified as Aspergillus fumigatus, A. flavus, A. niger and A. tubingensis. Six colonies belonged to the genus Paecilomyces. In six samples of dust, a high proportion (50-100%) of the total fungal viable counts consisted of these potentially pathogenic fungi. A total of 70 isolates were considered less likely to be pathogenic, and were identified as Aspergillus section Nidulantes, Chaetomium cochliodes and Penicillium sp. In the rural (n = 2) and urban (n = 7) control dust samples, the microbial viable counts were >2000 CFU and between 44 CFU and 215 CFU, respectively, and consisted mainly of bacteria. The low proportion of bacteria and the high proportion of stress tolerant, potentially pathogenic fungi in the dust samples from sport facilities may reflect the influence of disinfection on microbial communities.

Analysis of microbial diversity in the feces of Arborophila rufipectus

Introduction

Intestinal microbiota composition plays a crucial role in modulating the health of the host. This evaluation indicator is very sensitive and profoundly impacts the protection of endangered species. Currently, information on the gut microbiota of wild birds remains scarce. Therefore, this study aimed to describe the gut microbial community structure and potentially, the pathogen composition of wild Arborophila rufipectus.

Methods

To guarantee comprehensive data analysis, we collected fecal samples from wild A. rufipectus and Lophura nycthemera in their habitats for two quarters. The 16S rRNA gene was then sequenced using high-throughput sequencing technology to examine the intestinal core microbiota, microbial diversity, and potential pathogens with the aim of determining if the composition of the intestinal microflora varies seasonally.

Results and Discussion

The gut microbiota of A. rufipectus and L. nycthemera primarily comprised four phyla: Proteobacteria (45.98%), Firmicutes (35.65%), Bacteroidetes (11.77%), and Actinobacteria (3.48%), which accounted for 96.88% of the total microbial composition in all samples. At the genus level, core microorganisms were found, including Shigella (10.38%), Clostridium (6.16%), Pseudomonas (3.03%), and Rickettsiella (1.99%). In these genera, certain microbial species have been shown to be pathogenic. This study provides important indicators for analyzing the health status of A. rufipectus and formulating protective measures.

Dishwashers as an Extreme Environment of Potentially Pathogenic Yeast Species

The study aimed to compare the yeast species diversity in the specific environment of dishwashers, taking into account the potential risk for users. Yeasts were isolated from ten dishwashers and from tap water supplied to the appliances. Samples were collected for mycological analyses at the beginning of each month, from February to May 2016. Four dishwasher sites (rubber seals, detergent dispensers, sprinklers, and water drains) were analyzed. The microfungi were identified by the standard procedures applied in mycological diagnostics. To confirm species identification, molecular analysis was performed based on the sequences of the D1/D2 region. The presence of microfungi was detected in 70% of the investigated appliances. Rubber seals, detergent dispensers, and water drains were the most frequently colonized elements. Thirty-five yeast strains were isolated in this study, of which twenty-seven were obtained from dishwashers and eight from tap water. The strains belonged to six genera and six species (Candida parapsilosis, Clavispora lusitaniae, Dipodascus capitatus, Exophiala dermatitidis, Meyerozyma guilliermondii, and Rhodotorula mucilaginosa). Most of the strains came from rubber seals. In this way, it was demonstrated that the dishwashers’ condition is sufficient as an ecological niche for microfungi.

Changes in the fecal microbiome of the Yangtze finless porpoise during a short-term therapeutic treatment

The fecal microbiome is an integral part of aquatic mammals, like an inner organ. But we know very little about this inner organ of the threatened aquatic species, Yangtze finless porpoise (YFP). Four YFPs were placed into a purse seine for skin ulceration treatment, and this opportunity was taken to nurse the animals closer. In particular, we collected the feces of the YFPs before and after the paired healing and therapeutic treatment, along with samples of their fish diet and water habitat, to explore the changes in their fecal microbiome. Firmicutes (20.9–96.1%), Proteobacteria (3.8–78.7%), Actinobacteria (0.1–35.0%) and Tenericutes (0.8–17.1%) were the most dominant phyla present in the feces. The proportion of Proteobacteria and Actinobacteria increased after the treatment. Firmicutes showed a significant decrease, and most potential pathogens were absent, which reflected the administration of ciprofloxacin hydrochloride. Moreover, environmental shifts can also contribute to changes in the fecal microbiome. These results indicate that certain microbial interactions can be affected by environmental shifts, dietary changes and health-care treatments, which can also help maintain the internal environment of YFPs. These findings will inform the future enhanced protection and management of endangered YFPs and other vulnerable aquatic animals.

Non-tuberculous Mycobacteria in South African Wildlife: Neglected Pathogens and Potential Impediments for Bovine Tuberculosis Diagnosis

Non-tuberculous mycobacteria (NTM) are not only emerging and opportunistic pathogens of both humans and animals, but from a veterinary point of view some species induce cross-reactive immune responses that hamper the diagnosis of bovine tuberculosis (bTB) in both livestock and wildlife. Little information is available about NTM species circulating in wildlife species of South Africa. In this study, we determined the diversity of NTM isolated from wildlife species from South Africa as well as Botswana. Thirty known NTM species and subspecies, as well as unidentified NTM, and NTM closely related to Mycobacterium goodii/Mycobacterium smegmatis were identified from 102 isolates cultured between the years 1998 and 2010, using a combination of molecular assays viz PCR and sequencing of different Mycobacterial house-keeping genes as well as single nucleotide polymorphism (SNP) analysis. The NTM identified in this study include the following species which were isolated from tissue with tuberculosis- like lesions in the absence of Mycobacterium tuberculosis complex (MTBC) implying their potential role as pathogens of animals: Mycobacterium abscessus subsp. bolletii, Mycobacterium gastri, Mycobacterium species closely related to Mycobacterium goodii/Mycobacterium smegmatis, Mycobacterium brasiliensis, Mycobacterium sinense JMD 601, Mycobacterium avium subsp. avium, Mycobacterium sp. GR-2007, Mycobacterium bouchedurhonense, and Mycobacterium septicum/M. peregrinum. Mycobaterium brasiliensis, Mycobacterium gastri, Mycobacterium sp. GR-2007, and a potential novel Mycobacterium species closely related to Mycobacterium goodii were found for the first time in this study to be potential pathogens of animals. Mycobacterium simiae was isolated from a sample originating from a tuberculin skin test positive reactor, demonstrating its potential to elicit inappropriate immune responses in animals that may interfere with diagnosis of tuberculosis by immunology. Mycobacterium abscessus subsp. bolletti was the most frequently detected NTM identified in 37 of the 102 isolates. Other NTM species were also isolated from animals not showing any pathological changes. Knowledge gained in this study contribute to the understanding of NTM species circulating in wild animals in South Africa and the pathogenic potential of certain species, whose role in disease causation need to be examined, as well as to a certain extent the potential of M. simiae to hamper the diagnosis of bTB.

Infection control in the pulmonary function test laboratory

Pulmonary function testing plays a crucial role in the diagnostic evaluation of patients with lung diseases. Cases of cross infection acquired from the pulmonary function laboratory, although rare, have been reported from various countries. It is therefore imperative to identify the risks and potential organisms implicated in cross infections in a pulmonary function test (PFT) laboratory and implement better and more effective infection control procedures, which will help in preventing cross infections. The infrastructure, the daily patient flow, and the prevalent disinfection techniques used in a PFT laboratory, all play a significant role in transmission of infections. Simple measures to tackle the cross infection potential in a PFT laboratory can help reduce this risk to a bare minimum. Use of specialized techniques and equipment can also be of much use in a set up that has a high turnover of patients. This review aims at creating awareness about the possible pathogens and situations commonly encountered in a PFT laboratory. We have attempted to suggest some relevant and useful infection control measures with regard to disinfection, sterilization, and patient planning and segregation to help minimize the risk of cross infections in a PFT laboratory. The review also highlights the lacuna in the current scenario of PFT laboratories in India and the need to develop newer and better methods of infection control, which will be more user-friendly and cost effective. Further studies to study the possible pathogens in a PFT laboratory and evaluate the prevalent infection control strategies will be needed to enable us to draw more precious conclusions, which can lead to more relevant, contextual recommendations for cross infections control in PFT lab in India.