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Appl. Microbiol., Volume 4, Issue 4 (December 2024) – 6 articles

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17 pages, 1127 KiB

Open AccessReview

Resistome Mapping in Foodborne Pathogens: Understanding Role in the Transmission Dynamics of Resistance Genes

by Muneer Oladipupo Yaqub, Chinedu Eucharia Joseph, Aashika Jain and Lekshmi K. Edison

Appl. Microbiol. 2024, 4(4), 1476-1492; https://doi.org/10.3390/applmicrobiol4040102 (registering DOI) - 19 Oct 2024

Abstract

The emergence of antimicrobial resistance (AMR) in pathogens transmitted through food poses a significant threat to global public health, complicating infection treatment and increasing mortality rates. This review explores the role of resistome mapping as a crucial tool for understanding the transmission dynamics of antimicrobial resistance genes (ARGs) in foodborne pathogens, such as Salmonella, Escherichia coli, Listeria monocytogenes, and Campylobacter spp., as well as various techniques for resistome mapping, such as metagenomic sequencing, PCR-based methods, and whole-genome sequencing (WGS), highlighting the significance of horizontal gene transfer (HGT) as a key mechanism for ARG dissemination in foodborne pathogens. Additionally, we investigated the influence of agricultural practices and environmental factors on AMR development, highlighting the critical need for improved surveillance, antibiotic stewardship, and global collaboration to mitigate the spread of resistant ARGs through the food chain. The perceptions gained from resistome mapping play an essential role in developing effective approaches to address AMR and to ensure food safety. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods, 2nd Edition)

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12 pages, 467 KiB

Open AccessArticle

Molecular Typing of Somatic Coliphage Groups and Their Occurrence and Survival in Sewage

by Heesuk Lee, Jeremy Chemla, Thomas A. Randall, Emily S. Bailey and Mark D. Sobsey

Appl. Microbiol. 2024, 4(4), 1464-1475; https://doi.org/10.3390/applmicrobiol4040101 (registering DOI) - 19 Oct 2024

Abstract

A conventional, group-specific PCR method was developed to identify each of the four previously defined major taxa (Myoviridae, Siphoviridae, Podoviridae and Microviridae) of somatic coliphages and used to classify isolates from sewage. Somatic coliphage infectivity detection, occurrence and survival in primary human sewage effluent was observed over time to further understand the presence and behavior of the groups of somatic coliphages at two environmental temperatures (4 and 25 °C). Over time, the taxonomic composition of the somatic coliphage population in sewage changed, with the Microviridae family becoming the most prevalent family in the sewage population after several weeks. Based on their persistence and prevalence in environmental waters, phages belonging to the Microviridae family provide supporting information on sewage contamination and possibly of human enteric viruses in sewage-contaminated water. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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11 pages, 2337 KiB

Open AccessArticle

Integration of Whole-Genome Sequencing with ddPCR Kit for Detection of Omicron Subvariants in Wastewater in the Upper Peninsula of Michigan

by Michelle M. Jarvie, Thu N. T. Nguyen, Benjamin Southwell and Derek Wright

Appl. Microbiol. 2024, 4(4), 1453-1463; https://doi.org/10.3390/applmicrobiol4040100 - 13 Oct 2024

Viewed by 375

Abstract

This study explores the integration of genome sequencing and digital droplet polymerase chain reaction (ddPCR)-based methods for tracking the diversity of COVID-19 variants in wastewater. The research focuses on monitoring various Omicron subvariants during a period of significant viral evolution. Genome sequencing, particularly using Oxford Nanopore Technology (ONT), provides a detailed view of emerging variants, surpassing the limitations of PCR-based detection kits that rely on known sequences. Of the 43 samples analyzed, 39.5% showed matching results between the GT Molecular ddPCR kits and sequencing, though only 4% were exact matches. Some mismatches occurred due to newer subvariants like XBB and BQ.1, which the ddPCR kits could not detect. This emphasized the limitations of ddPCR kits, which rely on known variant sequences, while sequencing provides real-time data on emerging variants, offering a more comprehensive view of circulating strains. This study highlights the effectiveness of combining these methodologies to enhance early detection and inform public health strategies, especially in regions with limited clinical sequencing capabilities. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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19 pages, 2313 KiB

Open AccessArticle

Recovery of Pasteurization-Resistant Vagococcus lutrae from Raw Seafoods Using a Two-Step Enrichment, Its Presumptive Prevalence, and Novel Classification Phenotypes

by Elizabeth F. Scruggs, Zaria Gulley, Guadalupe Steele, Mohammed Alahmadi, Asim Barnawi, Hussain Majrshi and Hung King Tiong

Appl. Microbiol. 2024, 4(4), 1434-1452; https://doi.org/10.3390/applmicrobiol4040099 - 4 Oct 2024

Viewed by 437

Abstract

V. lutrae is an emerging human pathogen attributed to increasing hospitalization cases in humans; however, its biology and epidemiology are under-explored. The present study explored V. lutrae recovery, prevalence, and biology. A two-step enrichment method (i.e., step 1, nourishment; step 2, heat, 80 °C, 20 min) and thiosulfate–citrate–bile salts–sucrose (TCBS) agar were employed for recovering V. lutrae in raw seafood. Bacterial colonies were streaked for purification before 16S rRNA bacterial identification. Confirmed V. lutrae isolates were analyzed for their culture-challenged turbidity and virulence. Of 41 bacterial isolates, 9 confirmed V. lutrae, including regular (33%; nourished 24 h) and heat-resistant (67%; nourished 48 h plus heating) isolates, were exclusively from yellow colonies (i.e., TCBS) and were exclusively recovered from nourished shrimp (78%) and crab (22%) only. The culture and virulence biology revealed that they could diversely tolerate salinity (i.e., 0–17.5% additional NaCl), pasteurization (63 °C, 8 h), oxygen availability, and antibiotic sensitivity (i.e., erythromycin, gentamicin, and vancomycin). Further, this pathogen exhibited no visible hemolytic and alkalization activities. Emerging foodborne pathogens could readily evade the established food safety regime. The present study reveals systematic investigation and diverse phenotypes of V. lutrae to enhance its detection and contribute to public health initiatives. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 1124 KiB

Open AccessReview

The Rumen and Gastrointestinal Microbial Environment and Its Association with Feed Efficiency and Pregnancy in Female Beef Cattle

by M. Gabbi Martin, Juan F. Cordero-Llarena, Brynn H. Voy, Kyle J. McLean and Phillip R. Myer

Appl. Microbiol. 2024, 4(4), 1422-1433; https://doi.org/10.3390/applmicrobiol4040098 - 27 Sep 2024

Viewed by 639

Abstract

With the anticipated population growth by 2050, the demand for high-quality protein for human consumption is set to rise. To enhance the sustainability of U.S. cattle production, producers and researchers have traditionally concentrated on improving the feed efficiency of steers through advancements in genetics, nutrition, and microbiome tools, resulting in a more marketable beef product. However, without successful pregnancies, there would be no marketable animals to feed. Despite extensive research on hormonal impacts on cattle physiology, including nutrition and reproduction, there is limited knowledge about how the rumen microbial environment is impacted by pregnancy and feed efficiency in female beef cattle. Understanding the rumen microbiome’s role in feed efficiency and its response to hormonal changes during pregnancy is crucial for advancing sustainable beef cattle production. Therefore, this review highlights the importance of understanding the microbial dynamics in the rumen of pregnant beef females. Although progress has been made, gaps remain in understanding how varying nutritional requirements throughout pregnancy affect the rumen microbiome, highlighting the need for continued research. Addressing these areas will lead to more efficient and sustainable cattle production practices, benefiting beef production and contributing to global food security. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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11 pages, 2040 KiB

Open AccessArticle

Exploring the Intriguing World of Fungal Diversity in the Oral Cavities of a Native Community in Siltepec, Chiapas, Mexico

by Orquídea Pérez-González, Franco Valencia-Ampudia, Myriam A de la Garza-Ramos and Victor E. Aguirre-Arzola

Appl. Microbiol. 2024, 4(4), 1411-1421; https://doi.org/10.3390/applmicrobiol4040097 - 24 Sep 2024

Viewed by 576

Abstract

This study explores the relationship between filamentous fungi and dental caries in isolated indigenous communities in Siltepec, Chiapas, Mexico. A total of 37 oral swabs were collected, with 22 participants harboring filamentous fungi, primarily from the genus Cladosporium. Statistical analysis using Student’s t-test and the Mann–Whitney U test revealed a significant reduction in extensive and fully cavitated caries (p < 0.0001) in individuals with fungi, while those without fungi exhibited higher rates of dental decay. Participants with fungi had a higher prevalence of healthy teeth and incipient caries. The findings suggest that traditional maize-based diets, particularly fermented beverages like pozol, may promote the growth of beneficial fungi in the oral microbiome, offering a protective effect against dental caries through microbial competition and the alteration of the oral environment. These results underline the need for further research into the long-term impact of traditional diets on oral health and the potential use of natural substances, such as probiotics and plant-based antimicrobials, to maintain oral homeostasis and prevent caries. Full article

(This article belongs to the Special Issue Current Trends in the Applications of Probiotics and Other Beneficial Microbes)

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