Integrated analysis of intestinal microbial community and muscle transcriptome profile in rabbits

Intestinal microbial community plays an important part in maintaining health and skeletal muscle development in livestock. This study is the first of its kind in the world. In order to better understand the relationship between gut microbiota and gene expression in skeletal muscle of rabbits, caecum contents and longissimus dorsi tissues of rabbits at 0 d (S1), 35 d (S2) and 70d (S3) were collected and subjected for 16S rRNA sequencing and transcriptome sequencing. Our results showed that, among three groups of rabbits, Firmicutes and Bacteroidetes were the dominant phyla at the phylum level, while Akmansia, Bacteroides and Ruminobacter were the dominant genera at the genus level, and the relative abundance of Akmansia and Bacteroides increased firstly and then decreased from 0 d to 70 d. By analyzing the transcriptome sequencing data, we identified 2866, 2446 and 4541 differentially expressed genes (DEGs) in S1 vs S2, S2 vs S3 and S1 vs S3 groups, respectively. Finally, we performed correlation analysis between gut microbiota and the expression levels of muscle development-related genes of rabbits at 0 d and 70 d. Compared with 0 day old rabbits, in 70 day old rabbits Acinetobacter and Cronbacter with decreased abundance, and Ruminococcaceae_UCG-014 and Ruminococcus_1 with increase abundance is beneficial to caecum health in rabbits. These results will lay a foundation for further re-searches about the relationship between caecum microflora and muscle development in rabbits.

An integrated approach to explore the microbial biodiversity of natural milk cultures for cheesemaking

The use of natural milk culture (NMC) represents a key factor in Protected Designation of Origin (PDO) Montasio cheese, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMC is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMC collected from 10 PDO Montasio cheese dairies was investigated by employing colony counts and metagenomic analysis. Furthermore, residual sugars, organic acids, and volatile profiles were quantitatively investigated. Results showed that Streptococcus thermophilus was the dominant species in all NMC, and a subdominant population made of other streptococci and Ligilactobacillus salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMC. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staphylococcus aureus) as well as possible functional aspects (Next Generation Probiotics). Statistical analysis based on residual sugars, organic acids, and volatiles' content allowed to correlate the presence of specific microbial groups with metabolites of great technological and sensory relevance, which can contribute to giving value to the artisanal production procedures of NMC and clarify their role in the creation of the characteristics of PDO Montasio cheese.

Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features

The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.

Antimicrobial resistance profiles of common mastitis pathogens on large Chinese dairy farms

The primary objective of this study was to determine the antimicrobial resistance (AMR) profile of common mastitis pathogens on large Chinese dairy farms. A total of 673 isolates, including Staphylococcus aureus (14.41%, 97/673), coagulase-negative staphylococci (CNS, 52.30%, 352/673), Streptococcus agalactiae (5.64%, 38/673), non-agalactiae streptococci (7.42%, 50/673), Acinetobacter spp. (7.72%, 52/673), Escherichia spp. (6.39%, 43/673), and Klebsiella spp. (6.09%, 41/673), were collected from 15 large Chinese dairy farms in 12 provinces. The AMR profiles were measured using a microdilution method. Our results showed that more than 75% of Staph. aureus (87/97) and CNS (291/352) were resistant to penicillin (PEN). More than 30% of Escherichia spp. (15/43) showed resistance to ampicillin (AMP). However, less than 10% CNS and non-agalactiae streptococci showed resistance to amoxicillin/clavulanate (AMC; 1/352; 0/50), cephalexin (LEX; 1/352; 0/50), ceftiofur (EFT; 10/352; 0/50), and rifaximin (RIX; 21/352; 2/50); less than 10% Staph. aureus showed resistance to AMC (1/97), oxacillin (OX; 3/97), LEX (1/97), EFT (2/97), and RIX (2/97); less than 10% Strep. agalactiae showed resistance to PEN (3/38), AMC (0/38), LEX (0/38), EFT (0/38), and RIX (0/38); and less than 10% Escherichia spp. showed resistance to AMC (1/43) and EFT (4/43). These results suggested that most mastitis pathogens were susceptible to most antimicrobials with exceptions of Staph. aureus tested against penicillin or ampicillin and CNS against penicillin or oxacillin. To control the AMR threat in Chinese dairy farms, a nationwide surveillance program for AMR of bovine mastitis pathogens is needed.

The bacterial and archaeal communities of flies, manure, lagoons, and troughs at a working dairy

Background

Fundamental investigations into the location, load, and persistence of microbes, whether beneficial or detrimental, are scarce. Many questions about the retention and survival of microbes on various surfaces, as well as the load necessary for spread, exist. To answer these questions, we must know more about where to find various microbes and in what concentrations, the composition of the microbial communities, and the extent of dissemination between various elements. This study investigated the diversity, composition, and relative abundance of the communities associated with manure, lagoons, troughs, house flies, and stable flies present at a dairy, implementing two different free-stall management systems: flow-through and cross-vent. Shotgun metagenomics at the community level was used to compare the microbiomes within the dairy, allowing confident interpretation at the species level.

Results

The results showed that there were significant difference in microbial composition between not only each of the dairy elements but also management styles. The primary exceptions were the microbiomes of the house fly and the stable fly. Their compositions heavily overlapped with one another, but interestingly, not with the other components sampled. Additionally, both species of flies carried more pathogens than the other elements of the dairy, indicating that they may not share these organisms with the other components, or that the environments offered by the other components are unsatisfactory for the survival of some pathogens..

Conclusion

The lack of overlapping pathogen profiles suggests a lack of transfer from flies to other dairy elements. Dairy health data, showing a low incidence of disease, suggests minimal sharing of bacteria by the flies at a level required for infection, given the health program of this dairy. While flies did carry a multitude of pathogenic bacteria, the mere presence of the bacteria associated with the flies did not necessarily translate into high risk leading to morbidity and mortality at this dairy. Thus, using flies as the sole sentinel of dairy health may not be appropriate for all bacterial pathogens or dairies.

Association of milk microbiome with bovine mastitis before and after antibiotic therapy

Background and Aim

Mastitis is recognized as the most common disease in cattle and causes economic losses in the dairy industry. A number of opportunistic bacterial taxa have been identified as causative agents for this disease. Conventionally, antibiotics are used to treat mastitis; however, most bacteria are resistant to the majority of antibiotics. This study aimed to use molecular methods to identify milk microbiome patterns characteristic of mastitis that can help in the early diagnosis of this disease and in the development of new treatment strategies.

Materials and Methods

To evaluate the microbiome composition, we performed NGS sequencing of the 16S rRNA gene of the V3 region.

Results

An increase in the abundance of the bacterial genera Hymenobacter and Lachnospiraceae NK4A136 group is associated with the development of subclinical and clinical mastitis in dairy cows. These bacteria can be added to the list of markers used to detect mastitis in cows. Furthermore, a decrease in the abundance of Ralstonia, Lachnospiraceae NK3A20 group, Acetitomaculum, Massilia, and Atopostipes in cows with mastitis may indicate their role in maintaining a healthy milk microbiome. Antibiotics reduced the levels of Streptococcus in milk compared to those in the healthy group and cows before antibiotic treatment. Antibiotic therapy also contributed to an increase in the abundance of beneficial bacteria of the genus Asticcacaulis.

Conclusion

This study expands our understanding of the association between milk microbiota and mastitis.

Psychrotrophic Bacteria Equipped with Virulence and Colonization Traits Populate the Ice Cream Manufacturing Environment

Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures, producing biofilms that adhere to the surfaces and might embed other microorganisms, including spoilers and pathogens. There is increasing evidence that these communities can be transferred to the final product. To explore the microbial contamination routes in a facility producing ice creams, we collected foods and environmental swabs from industrial surfaces of equipment and tools and performed taxonomic and functional analyses of the microbial DNA extracted from the environmental samples. Our results suggest that complex communities dominated by psychrotrophic bacteria (e.g., Pseudomonas and Acinetobacter spp.) inhabit the food processing environment, and we demonstrate that these communities might be transferred from the surfaces to the products. Functional analysis performed on environmental samples highlighted the presence of several genes linked to antimicrobial resistance and adherence on abiotic surfaces; such genes were more abundant on food contact (FC) than on other surfaces. Metagenome-assembled genomes (MAGs) of Pseudomonas stutzeri showed genes linked with biofilm formation and motility, which are surely linked to colonizing capabilities in the processing lines. The study highlights clear potential advantages of applying microbiome mapping in the food industry for source tracking of microbial contamination and for planning appropriate ad hoc sanitization strategies. IMPORTANCE Several microbial species might permanently establish in food processing facilities, thus contributing to food loss. In fact, food contact surfaces might transfer microorganisms to intermediates and products, potentially representing a hazard to human health. In this work, we provide evidence of the existence of complex microbial communities overcoming sanitation in an ice cream-producing facility. These communities harbored several genes that could potentially lead to attachment to surfaces and antimicrobial resistance. Also, prediction of routes of contamination showed that several potential spoilage taxa might end up in the final product. Importantly, in this work, we show that mapping the environmental microbiome is a high-resolution technique that might help food business operators ensure food quality and safety through detection of potentially hazardous microorganisms.

Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin

Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.

Longitudinal Changes in Milk Microorganisms in the First Two Months of Lactation of Primiparous and Multiparous Cows

The present experiment was carried out to analyze the longitudinal changes in milk microorganisms. For this purpose, milk samples were collected from 12 healthy cows (n = 96; six primiparous cows and six multiparous cows) at eight different time points. The characteristics and variations in microbial composition were analyzed by 16S rRNA gene high-throughput sequencing. In the primiparous group, higher and more stable alpha diversity was observed in transitional and mature milk compared with the colostrum, with no significant difference in alpha diversity at each time point in the multiparous group. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota were the most dominant phyla, and Pseudomonas, UCG-005, Acinetobacter, Vibrio, Lactobacillus, Bacteroides, Serratia, Staphylococcus, and Glutamicibacter were the most dominant genera in both primiparous and multiparous cow milk. Some typically gut-associated microbes, such as Bacteroides, UCG-005, and Rikenellaceae_RC9_gut_group, etc., were enriched in the two groups. Biomarker taxa with the day in time (DIM) were identified by a random forest algorithm, with Staphylococcus showing the highest degree of interpretation, and the difference in milk microbiota between the two groups was mainly reflected in 0 d-15 d. Additionally, network analysis suggested that there were bacteria associated with the total protein content in milk. Collectively, our results disclosed the longitudinal changes in the milk microbiota of primiparous and multiparous cows, providing further evidence in dairy microbiology.

Microbial contamination, community diversity and cross-contamination risk of food-contact ice

Ice is widely used in the food industry, as an ingredient (edible ice) directly added to food or as a coolant (food-contact ice) for fresh food preservation along the cold chain. However, it has been shown that food-contact ice are easily polluted by pathogens, potentially endangering the public's health. In the present study, the hygiene status of food-contact ice collected from various sources (local farmer markets, supermarkets, and restaurants) was evaluated through the quantitative estimation of total bacterial counts and coliform counts as well as the prevalence of foodborne pathogenic bacteria (Staphylococcus aureus, Vibrio parahaemolyticus, Salmonella, Listeria monocytogenes, Shigella). The average levels of total bacterial counts in the ice for preserving the aquatic products, poultry meat and livestock meat are 4.88, 4.18 and 6.11 log₁₀ CFU/g, respectively. Over 90 % of the food-contact ice were positive for coliforms. The detection rate of S. aureus in all the food-contact ice samples was highest, followed by Salmonella, V. parahaemolyticus and L. monocytogenes, and Shigella was not detected. In addition, the bacterial community diversity of food-contact ice was analyzed with high-throughput sequencing. The dominant bacteria taxa in food-contact ice are heavily dependent on the environment of sampling sites. The predicted phenotypes of biofilm forming, oxidative stress tolerance, mobile element containing and pathogenesis were identified in the bacteria taxa of food-contact ice, which should be carefully evaluated in future work. Finally, the cross-contamination models of pathogen transfer during ice preservation were established. The results showed that the transfer rates of ice-isolated S. aureus between food and ice were significantly higher than that of V. parahaemolyticus. The binomial distribution B(n, p) exhibited a better fitness to describe the pathogen transfer during ice preservation when the transfer rate was low, in turn, the transfer rate-based probability model showed a better fit to the data when the transfer rate was high. Monte Carlo simulation with Latin-Hypercube sampling was carried out to predict the contamination levels of S. aureus and V. parahaemolyticus on food as the result of cross contamination during ice preservation ranging from -2.90 to 2.96 log₁₀ CFU/g with a 90 % confidence interval. The findings of this work are conducive to a comprehensive understanding of the current hygiene status of food-contact ice, and lay a theoretical foundation for the risk assessment of cross-contamination during ice preservation.

Characterization of Acinetobacter baumannii Isolated from Raw Milk

Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance and biofilm formation. Our findings revealed that, among the 100 samples, Acinetobacter spp. were found in 13 samples based on CHROM agar results. We further characterized them using rpoB and 16S-23SrRNA sequencing and gyrB multiplex PCR analysis and confirmed that 9 out of the 13 Acinetobacter spp. isolates were A. baumannii and 4 were other species. The A. baumannii isolates were resistant to β-lactam drugs, including cefotaxime (44%), ampicillin-sulbactam and levofloxacin (33.3% for each), imipenem, meropenem and aztreonam (22.2% for each). We observed different antimicrobial resistance patterns, with a multi-antibiotic resistant (MAR) index ranging from 0.2 to 0.3. According to the PCR results, bla_OXA-51 and bla_OXA-23 genes were amplified in 100% and 55.5% of the A. baumannii isolates, respectively, while the bla_OXA-58 gene was not amplified. Furthermore, the metallo-β-lactamases (MBL) genes bla_IMP and bla_NDM were found in 11.1% and 22.2% of isolates, respectively, while bla_VIM was not amplified. Additionally, eight A. baumannii isolates (88.8%) produced black-colored colonies on Congo red agar, demonstrating their biofilm production capacity. These results showed that, besides other foodborne pathogens, raw milk should also be examined for A. baumannii, which could be a public health concern.

Estimation of the post-mortem interval by modelling the changes in oral bacterial diversity during decomposition

AIMS

Decomposition, a complicated process, depends on several factors, including carrion insects, bacteria and the environment. However, the composition of and variation in oral bacteria over long periods of decomposition remain unclear. The current study aims to illustrate the composition of oral bacteria and construct an informative model for estimating the post-mortem interval (PMI) during decomposition.

METHODS AND RESULTS

Samples were collected from rats' oral cavities for 59 days, and 12 time points in the PMI were selected to detect bacterial community structure by sequencing the V3-V4 region of the bacterial 16S ribosomal RNA (16S rRNA) gene on the Ion S5 XL platform. The results indicated that microorganisms in the oral cavity underwent great changes during decomposition, with a tendency for variation to first decrease and then increase at day 24. Additionally, to predict the PMI, an informative model was established using the random forest algorithm. Three genera of bacteria (Atopostipes, Facklamia and Cerasibacillus) were linearly correlated at all 12 time points in the 59-day period. Planococcaceae was selected as the best feature for the last 6 time points. The R² of the model reached 93.94%, which suggested high predictive accuracy. Furthermore, to predict the functions of the oral microbiota, PICRUSt results showed that energy metabolism was increased on day 3 post-mortem and carbohydrate metabolism surged significantly on days 3 and 24 post-mortem.

CONCLUSIONS

Overall, our results suggested that post-mortem oral microbial community data can serve as a forensic resource to estimate the PMI over long time periods.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of the present study are beneficial for estimating the PMI. Identifying changes in the bacterial community is of great significance for further understanding the applicability of oral flora in forensic medicine.

Prevalence of classes 1 and 2 integrons in multidrug-resistant Acinetobacter baumanni isolates recovered from some aquatic environment in South Africa

The emergence of antibiotic-resistance genes (ARGs) by means of integrons in multidrug-resistant Acinetobacter baumannii (MDR A. baumannii) has become a significant challenge in the management of infections from this pathogen. In this paper, we report on the variable region of class 1 and 2 integrons observed in MDR A. baumanni isolates recovered from rivers in the Eastern Cape Province, South Africa. Class 1 and 2 integrons with their variable regions were evaluated with polymerase chain reaction techniques followed by sequencing. Antibiotic sensitivity testing, checkerboard assay, time-kill independent assay, and Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) were carried out using standard microbiological techniques. A total of fifty-six (56) isolates were examined, among which 45 (79%) tested positive for class 1 integron, and 7 (12.3%) had class 2 integron. None was found to be class 3 integron positive among the isolates. The variable region contained aadA1, aadA5, and aadA2 genes, which confer resistance against streptomycin and spectinomycin, aac(6')-Ib against amikacin/ tobramycin and dfrA17 genes against trimethoprim. The minimum inhibitory concentrations of the antimicrobials for one of the tested organisms were resistant against meropenem, colistin sodium methanesulfonate, tetracycline, ceftazidime, and ciprofloxacin (16, > 16, > 8, > 256, and 128 ug/mL respectively). The impact of colistin combined with quinolones (ciprofloxacin), with the FICIs (0.31) indicated synergistic effects against MDR A baumanni. However, when colistin was combined with meropenem and ceftazidime, additive effects with fractional inhibitory concentration (FIC) index ranging from 0.52 to 1 were observed. No antagonistic effect was evaluated among the examined isolates. ERIC-PCR analyses of A. baumanni isolates revealed significant genetic diversity, suggesting various sources of environmental contamination. We conclude that A. baumanni harbouring class 1 integrons in aquatic milieus are a significant source of ARGs and can transmit these elements to other organisms and consequently to man with significant public health implications.

Characterization of rumen, fecal, and milk microbiota in lactating dairy cows

Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p &lt; 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p &lt; 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p &lt; 0.001). While diversity indices were not linked (p &gt; 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.

Comparison of raw cow milk microbiota in two milking systems: a field study

This study investigated the effect of different milking systems on the milk composition and microbial community of raw milk in a commercial dairy farm. Raw milk samples from conventional milking system (CMS) and automatic milking system (AMS) were collected and the microbiota on each was assessed by 16S rRNA gene sequencing. Results showed that the acetone (P = 0.031) and β-hydroxybutyrate (P≤0.001) levels in the raw milk of the AMS group were increased compared with the CMS group. Principal component analysis, unweighted and weighted principal coordinates analysis, and heat map of microbial community composition in the raw milk showed a clear separation between two groups. AMS increased the abundance of the genera Acinetobacter (FDR = 0.004) and Staphylococcus (FDR = 0.004) in the raw milk compared with the CMS group. In contrast, the abundance of the genera Pseudomonas (FDR = 0.028), Lactococcus (FDR = 0.015), Sphingobacterium (FDR = 0.004), Brevundimonas (FDR = 0.005), and Chryseobacterium (FDR = 0.042) in the raw milk was reduced in the AMS group compared with the CMS group. The abundance of the genera Acinetobacter and Staphylococcus in the raw milk was positively correlated with the β-hydroxybutyrate, acetone, free fatty acid, citric acid, and urea nitrogen levels. Furthermore, the abundance of the genus Acinetobacter in the raw milk was negatively correlated with the somatic cell counts. The study demonstrates that the introduction of AMS in the dairy farm can regulate microbiota composition in the raw milk and this modification may exert an effect on reducing the somatic cell counts in the raw milk.

Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

BACKGROUND

Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing.

RESULTS

Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons.

CONCLUSIONS

These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective

Background

Acinetobacter baumannii ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole-genome sequencing (WGS) was applied to identify the acquired or mutational variants of antimicrobial resistance (AMR) genes in 85 German A. baumannii strains utilizing Illumina technology. Additionally, the whole genome of 104 German isolates deposited in the NCBI database was investigated.

Results

In-silico analysis of WGS data revealed wide varieties of acquired AMR genes mediating resistance mostly to aminoglycosides, cephalosporins, carbapenems, sulfonamides, tetracyclines and macrolides. In the 189 analyzed genomes, the ant (3″)-IIa conferring resistance to aminoglycosides was the most frequent (55%), followed by bla_ADC.25 (38.6%) conferring resistance to cephalosporin, bla_OXA-23 (29%) and the bla_OXA-66 variant of the intrinsic bla_OXA-51-likes (26.5%) conferring resistance to carbapenems, the sul2 (26%) conferring resistance to sulfonamides, the tet. B (19.5%) conferring resistance to tetracycline, and mph. E and msr. E (19%) conferring resistance to macrolides. bla_TEM variants conferring resistance to cephalosporins were found in 12% of genomes. Thirteen variants of the intrinsic bla_OXA-51 carbapenemase gene, bla_OXA-510 and bla_ADC-25 genes were found in isolates obtained from dried milk samples.

Conclusion

The presence of strains harboring acquired AMR genes in dried milk raises safety concerns and highlights the need for changes in producing dried milk. Acquired resistance genes and chromosomal gene mutation are successful routes for disseminating AMR determinants among A. baumannii. Identification of chromosomal and plasmid-encoded AMR in the genome of A. baumannii may help understand the mechanism behind the genetic mobilization and spread of AMR genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02270-7.

Levofloxacin in veterinary medicine: a literature review

A potent third-generation antimicrobial fluoroquinolone drug, levofloxacin was introduced into human clinical practice in 1993. Levofloxacin is also used in veterinary medicine, however its use is limited: it is completely banned for veterinary use in the EU, and used extralabel in only companion animals in the USA. Since its introduction to clinical practice, many studies have been published on levofloxacin in animal species, including pharmacokinetic studies, tissue drug depletion, efficacy, and animal microbial isolate susceptibility to levofloxacin. This literature overview highlights the most clinically relevant and scientifically important levofloxacin studies linked to the field of veterinary medicine.

Characterization of Chemical and Bacterial Compositions of Dairy Wastewaters

The dairy industry produces large amounts of wastewater, including white and cleaning wastewater originating principally from rinsing and cleaning-in-place procedures. Their valorization into process water and non-fat milk solids, in the case of white wastewater, or the renewal of cleaning solutions could be achieved using pressure-driven membrane processes. However, it is crucial to determine the intrinsic characteristics of wastewaters, such as proximate composition and bacterial composition, to optimize their potential for valorization. Consequently, white and cleaning wastewaters were sampled from industrial-scale pasteurizers located in two different Canadian dairy processing plants. Bacterial profiles of dairy wastewaters were compared to those of tap waters, pasteurized skim milk and unused cleaning solutions. The results showed that the physicochemical characteristics as well as non-fat milk solids contents differed drastically between the two dairy plants due to different processing conditions. A molecular approach combining quantitative real-time polymerase chain reaction (qPCR) and metabarcoding was used to characterize the bacteria present in these solutions. The cleaning solutions did not contain sufficient genomic DNA for sequencing. In white wastewater, the bacterial contamination differed depending on the dairy plant (6.91 and 7.21 log10 16S gene copies/mL). Psychrotrophic Psychrobacter genus (50%) dominated white wastewater from plant A, whereas thermophilic Anoxybacillus genus (56%) was predominant in plant B wastewater. The use of cold or warm temperatures during the pasteurizer rinsing step in each dairy plant might explain this difference. The detailed characterization of dairy wastewaters described in this study is important for the dairy sector to clearly identify the challenges in implementing strategies for wastewater valorization.

Surveillance of Extended-Spectrum β-Lactamase-, Cephalosporinase- and Carbapenemase-Producing Gram-Negative Bacteria in Raw Milk Filters and Healthy Dairy Cattle in Three Farms in Île-de-France, France

The aim of this work was to test a surveillance protocol able to detect extended-spectrum β-lactamase (ESBL)-, cephalosporinase (AmpC)- and carbapenemase (CP)-producing gram-negative bacteria in three conveniently chosen dairy farms with known prior occurrences of ESBL- and CP-producing strains. The protocol was applied monthly for a year. At each visit, 10 healthy lactating dairy cows were rectally swabbed, and raw milk filters (RMFs) were sampled in two of the three farms. Bacterial isolation was based on a first screening step with MacConkey agar supplemented with 1 mg/L cefotaxime and commercial carbapenem-supplemented media. We failed to detect CP-producing strains but showed that ESBL-Escherichia strains, found in one farm only (13 strains), were closely associated with multi-drug resistance (12 out of 13). The limited number of conveniently selected farms and the fact that RMFs could not be retrieved from one of them limit the validity of our findings. Still, our results illustrate that ESBL-status changes monthly based on fecal swabs and negative herds should be qualified as “unsuspected” as proposed by previous authors. Although surveillance of farm statuses based on RMF analysis could theoretically allow for a better sensitivity than individual swabs, we failed to illustrate it as both farms where RMFs could be retrieved were constantly negative. Determination of CP herd-level status based on RMFs and our surveillance protocol was hindered by the presence of intrinsically resistant bacteria or strains cumulating multiple non-CP resistance mechanisms which means our protocol is not specific enough for routine monitoring of CP in dairy farms.

Zooming Into the Microbiota of Home-Made and Industrial Kefir Produced in Greece Using Classical Microbiological and Amplicon-Based Metagenomics Analyses

Kefir is a high nutritional fermented dairy beverage associated with a wide range of health benefits. It constitutes a unique symbiotic association, comprising mainly lactic acid bacteria, yeasts, and occasionally acetic acid bacteria, which is strongly influenced by the geographical origin of the grains, the type of milk used, and the manufacture technology applied. Until recently, kefir microbiota has been almost exclusively studied by culture-dependent techniques. However, high-throughput sequencing, alongside omics approaches, has revolutionized the study of food microbial communities. In the present study, the bacterial, and yeast/fungal microbiota of four home-made samples (both grains and drinks), deriving from well spread geographical regions of Greece, and four industrial beverages, was elucidated by culture-dependent and -independent analyses. In all samples, classical microbiological analysis revealed varying populations of LAB and yeasts, ranging from 5.32 to 9.60 log CFU mL^–1 or g^–1, and 2.49 to 7.80 log CFU mL^–1 or g^–1, respectively, while in two industrial samples no yeasts were detected. Listeria monocytogenes, Salmonella spp. and Staphylococcus spp. were absent from all the samples analyzed, whereas Enterobacteriaceae were detected in one of them. From a total of 123 isolates, including 91 bacteria and 32 yeasts, Lentilactobacillus kefiri, Leuconostoc mesenteroides, and Lactococcus lactis as well as Kluvyeromyces marxianus and Saccharomyces cerevisiae were the mostly identified bacterial and yeast species, respectively, in the home-made samples. On the contrary, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lacticaseibacillus rhamnosus along with Debaryomyces hansenii and K. marxianus were the main bacterial and yeast species, respectively, isolated from the industrial beverages. In agreement with the identification results obtained from the culture-dependent approaches, amplicon-based metagenomics analysis revealed that the most abundant bacterial genera in almost all home-made samples (both grains and drinks) were Lactobacillus and Lactococcus, while Saccharomyces, Kazachstania, and Kluvyeromyces were the predominant yeasts/fungi. On the other hand, Streptococcus, Lactobacillus, and Lactococcus as well as Kluvyeromyces and Debaryomyces dominated the bacterial and yeast/fungal microbiota, respectively, in the industrial beverages. This is the first report on the microbiota of kefir produced in Greece by a holistic approach combining classical microbiological, molecular, and amplicon-based metagenomics analyses.

Acinetobacter baumannii as a community foodborne pathogen: Peptide mass fingerprinting analysis, genotypic of biofilm formation and phenotypic pattern of antimicrobial resistance

Acinetobacter baumannii (A. baumannii) is one of the most common Gram-negative pathogens that represent a major threat to human life. Because the prevalence of Multidrug-resistant biofilm-forming A. baumannii is increasing all over the world, this may lead to outbreaks of hospital infections. Nonetheless, the role of raw meat as a reservoir for A. baumannii remains unclear. Here our research was aimed to exhibit the frequency, precise identification, and genotyping of biofilm-related genes as well as antimicrobial resistance of A. baumannii isolates of raw meat specimens. Fifty-five A. baumannii strains were recovered from 220 specimens of different animal meat and then identified by Peptide Mass Fingerprinting Technique (PMFT). All identified isolates were genotyped by the qPCR method for the existence of biofilm-related genes (ompA, bap, blaPER-1, csuE, csgA, and fimH). In addition, the antimicrobial resistance against A. baumannii was detected by the Kirby-Bauer method. Based on our findings, the frequency rate of 55 A. baumannii isolates was 46.55%, 32.50%, 15.00%, and 9.68% of sheep, chicken, cow, and camel raw meat samples, respectively. The PMFT was able to identify all strains by 100%. the percentages of csuE, ompA, bla_PER-1, bap, and csgA genes in biofilm and non-biofilm producer A. baumannii were 72.73%, 60%, 58.2%, 52.74%, and 25.45%, respectively. In contrast, the fimH was not detected in all non-biofilm and biofilm producer strains. The ompA, bap, blaPER-1, csgA were detected only in biofilm-producing A. baumannii isolates. The maximum degree of resistance was observed against amoxicillin/clavulanic acid (89.10%), gentamicin (74.55%), tetracycline (72.73%), ampicillin (65.45%), and tobramycin (52.73%). In conclusion, our investigation demonstrated the high incidence of multi-drug resistant A. baumannii in raw meat samples, with a high existence of biofilm-related virulence genes of ompA, bap, blaPER-1, csgA. Therefore, it has become necessary to take the control measures to limit the development of A. baumannii.

Acinetobacter spp. in food and drinking water - A review

Acinetobacter spp. has emerged as a pathogen of major public health concern due to their increased resistance to antibiotics and their association with a wide range of nosocomial infections, community-acquired infections and war and natural disaster-related infections. It is recognized as a ubiquitous organism however, information about the prevalence of different pathogenic species of this genus in food sources and drinking water is scarce. Since the implementation of molecular techniques, the role of foods as a source of several species, including the Acinetobacter baumannii group, has been elucidated. Multidrug resistance was also detected among Acinetobacter spp. isolated from food products. This highlights the importance of foods as potential sources of dissemination of Acinetobacter spp. between the community and clinical environments and reinforces the need for further investigations on the potential health risks of Acinetobacter spp. as foodborne pathogens. The aim of this review was to summarize the published data on the occurrence of Acinetobacter spp. in different food sources and drinking water. This information should be taken into consideration by those responsible for infection control in hospitals and other healthcare facilities.

Genome Sequences of Four Strains of Acinetobacter bereziniae Isolated from Human Milk Pumped with a Personal Breast Pump and Hand-Washed Milk Collection Supplies

Acinetobacter bereziniae, formerly Acinetobacter genomospecies 10, is an opportunistic pathogen possessing resistance to multiple antibiotics, and it has been reported to be responsible for hospital-associated infections in immunocompromised individuals. We report the draft genome sequences of four Acinetobacter bereziniae strains that were isolated from a single human milk sample collected with a personal breast pump and a hand-washed milk collection kit.

Acinetobacter bereziniae, formerly Acinetobacter genomospecies 10, is an opportunistic pathogen possessing resistance to multiple antibiotics, and it has been reported to be responsible for hospital-associated infections in immunocompromised individuals. We report the draft genome sequences of four Acinetobacter bereziniae strains that were isolated from a single human milk sample collected with a personal breast pump and a hand-washed milk collection kit.

Snapshot of Cyprus Raw Goat Milk Bacterial Diversity via 16S rDNA High-Throughput Sequencing; Impact of Cold Storage Conditions

In general, it is a common practice among dairy producers to store the milk in the refrigerator directly after milking, in order to preserve it and prevent the development of spoilage microbes. However, the impact of keeping the milk in the refrigerator overnight on milk microbial diversity has been poorly investigated. This study aimed to provide a snapshot of the bacterial composition of goat milk after direct storage at −80 °C and after being kept overnight at 4 °C and then in storage at −80 °, using high-throughput sequencing (HTS). Goat milk samples from four different farms were analyzed, to reveal that milk bacterial diversity differed between the two different storage conditions. Goat milk directly stored at −80 °C was characterized by the presence of the Gram-negative contaminants Pseudomonas and Acinetobacter, in addition to the genera Corynebacterium, Chryseobacterium, Bacteroides and Clostridium. Milk samples that were kept overnight at 4 °C were characterized by a reduction in their bacterial biodiversity and the predominance of the Gram-negative, aerobic Phyllobacterium. Overall, HTS methodologies provide an in-depth identification and characterization of the goat raw milk microbiome. Further, they offer a better understanding of the contribution of cold storage conditions to milk microbiota formation. This study may assist dairy producers in improving raw milk and raw milk cheeses quality and guaranteeing consumers’ safety.

From food to hospital: we need to talk about Acinetobacter spp

Some species of the genus Acinetobacter are admittedly important hospital pathogens. Additionally, various animal and plant foods have been linked to the presence of Acinetobacter, including resistant strains. However, due to isolation difficulties and the lack of official standard methods, there is a dearth of work and epidemiological data on foodborne diseases caused by this microorganism. Considering that Acinetobacter spp. may represent a serious public health problem, especially because of their resistance to carbapenems and colistin, and because of the fact that these pathogens may transfer resistance genes to other bacteria, studies are needed to evaluate the pathogenicity of both food and clinical isolates and to search for them using control strategies, such as the adoption of more efficient disinfection measures and use of antimicrobial substances (AMS). In contrast, AMS production by strains of the genus Acinetobacter has already been described, and its potential for application against other Gram-negative food or clinical pathogens, reveals a new field to be explored.

The prevalence of pathogens causing bovine mastitis and their associated risk factors in 15 large dairy farms in China: An observational study

The primary objective of this study was to determine the distribution of major pathogens causing mastitis and analyze the association of the main pathogens with the type of milk {milk samples collected from cows with mastitis of different severities, which consisted of subclinical mastitis (Lanzhou Mastitis Test weak positive, positive, and strong positive) and clinical mastitis}, region, season, bedding material, parity and lactation stage on large dairy farms. Fifteen large dairy farms in twelve major milk-producing provinces of China were enrolled in the study for approximately one year; 1,153 mastitis milk samples were collected and processed. The most frequently isolated pathogens were Staphylococcus spp. (39.03 %), Streptococcus spp. (11.01 %), Bacillus spp. (8.24 %), Aerococcus viridans (6.76 %), and Acinetobacter spp. (3.38 %), and most of these pathogens were environmental bacteria (67.53 %). Contagious pathogens (Staphylococcus aureus and Streptococcus agalactiae) were more prevalent in milk samples from bovine clinical mastitis cases than in milk samples from bovine subclinical mastitis cases. The percentages of Staphylococcus spp. and Bacillus spp. might be higher in northeastern farms than in farms located in other regions. A higher percentage of Staphylococcus spp. was observed in summer, while a lower proportion of Streptococcus spp. was detected in fall. Streptococcus agalactiae and Streptococcus uberis were more frequently isolated in farms using sand bedding, whereas Staphylococcus aureus, Staphylococcus haemolyticus and Bacillus licheniformis were more prevalent in farms using organic bedding. No obvious associations were found between the main mastitis pathogens and parity or lactation stage. Based on these findings, the dominant pathogens, types of milk, regions, seasons and bedding materials should be considered when designing mastitis prevention and control programs at large Chinese dairy farms.

Drug resistance and virulence traits of Acinetobacter baumannii from Turkey and chicken raw meat

Acinetobacter baumannii (A. baumannii) is a miscellaneous bacterium with ability of extensive antibiotic resistance. A. baumannii strains have also been isolated from animal origins. The objective of our atudy was characterization of A. baumannii antibiotic resistance and virulence traits from turkey and chicken raw meat. Of 576 turkey and 424 chicken specimens during 2017-2019, 200 (120 from turkey and 80 from chicken) isolates were identified as A. baumannii. Virulence factors and antibiotic resistance patterns of A. baumannii were determined using polymerase chain reaction (PCR) technique and Kirby-Bauer test. All the isolates were resistant to tetracycline and cefoxitin and 81 % and 56 % of them produced ESBLs and carbapenemases. Also 74 % of them (34 % from chicken and 40 % from turkey) were multidrug-resistant (MDR) A. baumannii. Colistin and fosfomycin non-susceptibility was detected among 12 % and 10 % of them, respectively. The existence of tetA, dfrA, tetB, bla_oxa-51-like, bla_oxa-23-like, sul1, bla_oxa-24-like, bla_oxa-58-like, fosA3 and mcr-1 genes accounted for 80 %, 71 %, 70.5 %, 66 %, 62 %, 43 %, 34 %, 22 %, 11 % and 13 % of them, repectively. Additionally, predominant virulence factors included the fimH, afa/draBC, sfa/foc DE, cnfI and cnf2 genes. The rate of antibiotic resistance genes and virulence factors was not significantly different between turkey and chicken (p > 0.05). High rate of antibiotic non-susceptibility even against last-line resorts in poultry products is a concern and suggest that animals play a potential role as reservoirs of transmission of MDR A. baumannii.

Oral Probiotics Alleviate Intestinal Dysbacteriosis for People Receiving Bowel Preparation

Background: Bowel preparation is necessary for successful colonoscopy, while it can seriously affect intestinal microbial composition and damage the intestinal mucosal barriers in humans.

Methods: To figure out whether probiotics can sustain intestinal homeostasis and guard people's health, the probiotic drug of Bifidobacterium Tetragenous viable Bacteria Tablets (P group, n = 16) or placebo (C group, n = 16) was used for volunteers receiving bowel preparation, and high-throughput sequencing method was applied to monitor their intestinal microbial changes.

Results: The present results suggested that bowel preparation obviously reduced the intestinal microbial diversity, while taking probiotics significantly restored it to normal level. In addition, probiotics sharply reduced the abundance of pathogenic Proteobacteria, and obviously lowered the ratio of Firmicutes/Bacteroidetes compared with control group at phylum level (P < 0.05). And probiotics markedly decreased the abundance of pathogenic Acinetobacter and Streptococcus, while greatly enriched the relative abundance of beneficial bacteria Bacteroides, Roseburia, Faecalibacterium, and Parabacteroides at genus level (P < 0.05).

Conclusion: Probiotic drugs, e.g., Bifidobacterium Tetragenous viable Bacteria Tablets, can be used to restore intestinal dysbacteriosis caused by bowel preparation, and reduce side effects during colonoscopy.

Prevalence and molecular analysis of multidrug-resistant Acinetobacter baumannii in the extra-hospital environment in Mthatha, South Africa

Introduction

The presence of Acinetobacter baumannii outside hospitals remains unclear. This study aimed to determine the prevalence of multidrug-resistance (MDR) A. baumannii in the extra-hospital environment in Mthatha, South Africa and to investigate the frequency of carbapenemase-encoding genes.

Material and Methods

From August 2016 to July 2017 a total of 598 abattoir samples and 689 aquatic samples were collected and analyzed presumptively by cultural methods for the presence of A. baumannii using CHROMagar™ Acinetobacter medium. Species identification was performed by autoSCAN-4 (Dade Behring Inc., IL) and confirmed by the detection of their intrinsic bla_OXA-51 gene. Confirmed MDR A. baumannii isolates were screened for the presence of carbapenemase-encoding genes, ISAba1 insertion sequence and integrase intI1.

Results

In total, 248 (19.3%) Acinetobacter species were isolated. Acinetobacter. baumannii was detected in 183 (73.8%) of which 85 (46.4%) and 98 (53.6%) were recovered from abattoir and aquatic respectively. MDR A. baumannii was detected in 56.5% (48/85) abattoir isolates and 53.1% (52/98) aquatic isolates. Isolates showed high resistance to antimicrobials most frequently used to treat Acinetobacter infections such as piperacillin/tazobactam; abattoir (98% of isolates resistant), aquatic (94% of isolates resistant), ceftazidime (84%, 83%), ciprofloxacin (71%, 70%), amikacin (41%, 42%), imipenem (75%, 73%), and meropenem (74%, 71%). All the isolates were susceptible to tigecycline and colistin. All the isolates carried bla_OXA-51-like. The bla_OXA-23 was detected in 32 (66.7%) abattoir isolates and 11 (21.2%) aquatic isolates. The bla_OXA-58-like was positive in 7 (14.6%) and 4 (7.7%) abattoir and aquatic isolates, respectively. Both groups of isolates lacked bla_OXA-24-like, bla_IMP-type, bla_VIM-type, bla_NDM-1,bla_SIM, bla_AmpC, ISAba1 and inI1. Isolates showed high level of Multiple Antibiotic Resistance Index (MARI) ranging from 0.20-0.52.

Conclusion

Extra-hospital sources such as abattoir and aquatic environments may be a vehicle of spread of MDR A. baumannii strains in the community and hospital settings.

Microbiome and Metabolome Analyses of Milk From Dairy Cows With Subclinical Streptococcus agalactiae Mastitis-Potential Biomarkers

The microbial ecosystem in the udders of dairy cows directly influences the flavor and quality of milk. However, to our knowledge, no published research has analyzed the complex relationship between the udder microbiome and its associated metabolism in animals with subclinical mastitis. We identified the bacterial species and measured relative population numbers in the milk of cows with subclinical Streptococcus agalactiae mastitis (GBS) and compared this information to that from the milk of healthy cows. Metabolite profiles were determined to investigate correlations between the milk microbiota and metabolic factors in healthy vs. GBS dairy cows. Six milk samples from GBS cows and six from healthy cows were subjected to 16S rRNA gene sequencing to identify the microbial species using a MiSeq high-throughput sequencing apparatus. The metabolites present in the milk were identified by gas chromatography time-of-flight mass spectrometry. Both principal component analysis and orthogonal partial least squares discriminant analysis indicated that the metabolites were well-separated from each other in the milk samples from the two groups. GBS dramatically altered microbial diversity, and the GBS group had significantly fewer Proteobacteria, Actinobacteria, and Acidobacteria than the CON group, with greater relative abundance of Firmicutes (p < 0.01). Several bacterial genera, such as Streptococcus, were significantly more abundant in milk from the GBS group than in milk from the CON group, and there was a tendency for greater abundance of Turicibacter (p = 0.07) and Enterococcus spp. (p = 0.07) in the GBS group. The levels of five milk metabolites were significantly higher in the GBS group than in the CON group: phenylpyruvic acid, the homogentisic acid: 4-hydroxyphenylpyruvic acid ratio, the xanthine: guanine ratio, uridine and glycerol. Metabolic pathway analysis of the different metabolites revealed that the following were enriched in both groups: galactose metabolism; pentose and glucuronate interconversion; starch and sucrose metabolism; alanine, aspartate and glutamate metabolism; arginine biosynthesis; citrate cycle (TCA cycle); D-glutamine and D-glutamate metabolism; and the neomycin, kanamycin, and gentamicin biosynthesis pathways. Several typical metabolites were highly correlated with specific ruminal bacteria, such as Streptococcaceae, Lachnospiraceae, Lactobacillaceae and Corynebacteriaceae, demonstrating the functional correlations between the milk microbiome and associated metabolites. These findings revealed that the milk microbiota and metabolite profiles were significantly different between the two groups of cows, raising the question of whether the microbiota associated with the bovine mammary gland could be related to mammary gland health. There was also a relationship between milk quality and the presence of spoilage bacteria. Other bacterial taxa should be investigated, as related information may provide insights into how perturbations in milk metabolomics profiles relate to differences in milk synthesis between healthy cows and those with subclinical mastitis.

Prevalence and phenotypic pattern of antibiotic resistance of Acinetobacter baumannii isolated from different types of raw meat samples in Isfahan, Iran

Resistant Acinetobacter baumannii isolates are not only known as opportunistic nosocomial bacteria but may also be regarded as emerging bacterial contaminants in foods of animal origins. The present investigation was done to assess the prevalence and antibiotic resistance pattern of A. baumannii isolated from different types of raw meat samples. One hundred and ninety-four raw meat samples were collected and cultured for A. baumannii isolates. Culture-positive bacteria were also approved using the loop-mediated isothermal amplification (LAMP) technique. The disc diffusion method was used for antibiotic susceptibility testing. Out of 194 raw meat samples, 39 (20.10%) were positive for A. baumannii isolates. Ovine raw meat was the most commonly contaminated samples (32.14%). All of the culture-positive A. baumannii isolates were also approved using the LAMP assay. A. baumannii isolates harboured the highest prevalence of resistance against gentamicin (87.17%), tetracycline (79.48%), erythromycin (74.35%), azithromycin (66.66%), ciprofloxacin (58.97%), trimethoprim/sulphamethoxazole (56.41%) and rifampin (51.28%). The lowest prevalence of resistance was found against imipenem (17.94%) and chloramphenicol (28.20%). Raw bovine, ovine, caprine, camel and poultry meat samples were considered as the important sources of isolates resistant to some of the categories of antimicrobials used to treat infections caused by A. baumannii. Further studies are required to find the exact role of resistant A. baumannii isolates in the dissemination of antibiotic resistance to human population.

Acinetobacter baumannii in sheep, goat, and camel raw meat: virulence and antibiotic resistance pattern

Acinetobacter genus belongs to a group of Gram-negative coccobacillus. These bacteria are isolated from human and animal origins. Antimicrobial agents play a vital role in treating infectious diseases in both humans and animals, and Acinetobacter in this regard is defined as an organism of low virulence. The current study aimed to evaluate antibiotic resistance properties and virulence factor genes in Acinetobacterbaumannii strains isolated from raw animal meat samples. Fresh meat samples from 124 sheep, 162 goat, and 95 camels were randomly collected from Isfahan and Shahrekord cities in Iran. Most A. baumannii strains isolated from sheep meat samples represented fimH (82.35%), aac(3)-IV (78.43%), sul1 (78.43%) and Integron Class I (96.07%) genes. Moreover, more than 50% of A. baumannii strains isolated from sheep samples were resistant to streptomycin (54.90%), gentamycin (74.50%), co-trimoxazole (70.58%), tetracycline (82.35%), and trimethoprim (62.74%). Current findings revealed significant association between the presence of fimH, cnfI, afa/draBC, dfrA1, sulI, aac(3)-IV genes in sheep samples. Furthermore, significant association was observed between fimH, cnfI, sfa/focDE and dfrA1genes in goat meat samples. In sheep meat samples, significant differences were identified in resistance to gentamicin, tetracycline, and co-trimoxazole in comparison with other antibiotics. Finally, there were statistically significant differences between the incidences of resistance to gentamicin, tetracycline, and co-trimoxazole in comparison with other antibiotics in all strains. In conclusion, the presence of virulence factors and antibiotic resistance in A. baumannii strains isolated from animal meat samples showed that animals should be considered as a potential reservoir of multidrug-resistant A. baumannii.

Acinetobacter baumannii - a neglected pathogen in veterinary and environmental health in Germany

The emergence and global spread of drug resistant Acinetobacter (A.) baumannii is a cause of great concern. The current knowledge on antibiotic resistance in A. baumannii from animal origin is mostly based on few internationally published case reports, investigations of strain collections and several whole genome analyses. This lack of data results in a somewhat sketchy picture on how to assess the possible impact of drug resistant A. baumannii strains on veterinary and public health in Germany. Consequently, there is an urgent need to intensify the surveillance of A. baumannii in pet animals, the farm animal population and wildlife.

Spoilage potential of psychrotrophic bacteria isolated from raw milk and the thermo-stability of their enzymes

The storage and transportation of raw milk at low temperatures promote the growth of psychrotrophic bacteria and the production of thermo-stable enzymes, which pose great threats to the quality and shelf-life of dairy products. Though many studies have been carried out on the spoilage potential of psychrotrophic bacteria and the thermo-stabilities of the enzymes they produce, further detailed studies are needed to devise an effective strategy to avoid dairy spoilage. The purpose of this study was to explore the spoilage potential of psychrotrophic bacteria from Chinese raw milk samples at both room temperature (28 °C) and refrigerated temperature (7 °C). Species of Yersinia, Pseudomonas, Serratia, and Chryseobacterium showed high proteolytic activity. The highest proteolytic activity was shown by Yersinia intermedia followed by Pseudomonas fluorescens (d). Lipolytic activity was high in isolates of Acinetobacter, and the highest in Acinetobacter guillouiae. Certain isolates showed positive β-galactosidase and phospholipase activity. Strains belonging to the same species sometimes showed markedly different phenotypic characteristics. Proteases and lipases produced by psychrotrophic bacteria retained activity after heat treatment at 70, 80, or 90 °C, and proteases appeared to be more heat-stable than lipases. For these reasons, thermo-stable spoilage enzymes produced by a high number of psychrotrophic bacterial isolates from raw milk are of major concern to the dairy industry. The results of this study provide valuable data about the spoilage potential of bacterial strains in raw milk and the thermal resistance of the enzymes they produce.

Uterine Microbiota of Dairy Cows With Clinical and Subclinical Endometritis

The objective of this study was to characterize the uterine microbiota of dairy cows with clinical and subclinical endometritis and to identify the potential bacterial genera as well as their interactions associated with uterine disease. Uterine flush samples (n = 27) were collected from 13 healthy, 5 subclinical endometritic (SE), and 9 clinical endometritic (CE) cows at 30 days postpartum. Microbial DNA from uterine flush samples was subjected to sequencing of the 16S rRNA gene on the Illumina MiSeq platform. The uterine microbiota of healthy, SE, and CE cows had similarly complex microbial diversity, and shared 293 of 445 operational taxonomic units. However, endometritic and healthy cows could be discriminated by the relative abundance of bacterial genera. In CE cows, the uterine microbiota was characterized by increased abundance of Fusobacterium and unique presence of Trueperella and Peptoniphilus. For SE cows, known intrauterine pathogens were almost absent and the uterine microbiota was characterized by enrichment of Lactobacillus and Acinetobacter. Analysis of correlations between bacterial genera showed that the uterine microbiota exhibited two co-occurrence groups (i.e., the Lactococcus and the Fusobacterium COGs), indicating that the synergistic effect by co-occurred bacteria may be an important aspect of pathogenesis. Our findings support that common uterine pathogens are not associated with subclinical endometritis at 30 days postpartum and indicate the need of investigating the role of commensal bacteria such as Lactobacillus, and Acinetobacter in the inflammatory process of uterine endometrium.

Insights Into the Bovine Milk Microbiota in Dairy Farms With Different Incidence Rates of Subclinical Mastitis

Bovine mastitis continues to be a complex disease associated with significant economic loss in dairy industries worldwide. The incidence rate of subclinical mastitis (IRSCM) can show substantial variation among different farms; however, the milk microbiota, which have a direct influence on bovine mammary gland health, have never been associated with the IRSCM. Here, we aimed to use high-throughput DNA sequencing to describe the milk microbiota from two dairy farms with different IRSCMs and to identify the predominant mastitis pathogens along with commensal or potential beneficial bacteria. Our study showed that Klebsiella, Escherichia-Shigella, and Streptococcus were the mastitis-causing pathogens in farm A (with a lower IRSCM), while Streptococcus and Corynebacterium were the mastitis-causing pathogens in farm B (with a higher IRSCM). The relative abundance of all pathogens in farm B (22.12%) was higher than that in farm A (9.82%). However, the genus Bacillus was more prevalent in farm A. These results may be helpful for explaining the lower IRSCM in farm A. Additionally, the gut-associated genera Prevotella, Ruminococcus, Bacteroides, Rikenella, and Alistipes were prevalent in all milk samples, suggesting gut bacteria can be one of the predominant microbial contamination in milk. Moreover, Listeria monocytogenes (a foodborne pathogen) was found to be prevalent in farm A, even though it had a lower IRSCM. Overall, our study showed complex diversity between the milk microbiota in dairy farms with different IRSCMs. This suggests that variation in IRSCMs may not only be determined by the heterogeneity and prevalence of mastitis-causing pathogens but also be associated with potential beneficial bacteria. In the future, milk microbiota should be considered in bovine mammary gland health management. This would be helpful for both the establishment of a targeted mastitis control system and the control of the safety and quality of dairy products.

Genotyping and distribution of putative virulence factors and antibiotic resistance genes of Acinetobacter baumannii strains isolated from raw meat

Background

Acinetobacter baumannii strains with multiple antimicrobial resistance are primarily known as opportunistic nosocomial bacteria but they may also be regarded as emerging bacterial contaminants of food samples of animal origin. Here we aimed to study the molecular characteristics of the A. baumanni strains isolated from raw meat samples.

Methods

A total of 22 A. baumanni strains were isolated from 126 animal meat samples and were genotyped by ERIC-PCR method and by PCR detection of their virulence and antimicrobial resistance determinants. A. baumannii strains with 80% and more similarities were considered as one cluster.

Results

Sixteen different genetic clusters were found amongst the 22 A. baumanni strains. Of the 22 strains, 12 (54.54%) had similar genetic cluster. A. baumannii strains exhibited the highest percentage of resistance against tetracycline (90.90%), trimethoprim (59.09%), cotrimoxazole (54.54%) and gentamicin (50.00%). TetA (81.81%), tetB (72.72%), dfrA1 (63.63%), aac(3)-IV (63.63%), sul1 (63.63%) and aadA1 (45.45%) were the most commonly detected antibiotic resistance genes. FimH (81.81%), afa/draBC (63.63%), csgA (63.63%), cnf1 (59.09%), cnf2 (54.54%) and iutA (50.00%) were the most commonly detected virulence factors. A. baumannii strains isolated from the chicken meat samples had the highest similarities in the genetic cluster.

Conclusions

A. baumannii strains with similar genetic cluster (ERIC-Type) had the same prevalence of antibiotic resistance, antibiotic resistance genes and virulence factors. Genetic cluster of the A. baumannii strains is the main factor affected the similarities in the genotypic and phenotypic properties of the A. baumannii strains.

The natural environment as a reservoir of pathogenic and non-pathogenic Acinetobacter species

Acinetobacter is a genus of Gram-negative bacteria, which are oxidase-negative, exhibiting a twitching motility under a magnifying lens. Besides being important soil microorganisms, due to their contribution to the soil fertility, Acinetobacter species, particularly A. baumannii, hold a prominent place within the genus because, it is the most virulent among the other species, causing varying degrees of human infections in clinical environments. However, results of different research have shown that Acinetobacter species can be isolated from such natural environments as surface water, wastewater and sewage, healthy human skin, plant, animal and food material as well as domestic appliances. The presence of some other Acinetobacter species in the natural environment has been associated with beneficial roles including soil improvement, detoxification of oil spillages and as microflora in human and plant bodies. In this paper, we carried out an overview of various natural ecological niches as reservoirs of pathogenic and non-pathogenic Acinetobacter species.

Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany

Forty-seven Acinetobacter spp. isolates from milk powder obtained from a powdered milk producer in Germany were investigated for their antibiotic resistance susceptibilities, in order to assess whether strains from food harbor multiple antibiotic resistances and whether the food route is important for dissemination of resistance genes. The strains were identified by 16S rRNA and rpoB gene sequencing, as well as by whole genome sequencing of selected isolates and their in silico DNA-DNA hybridization (DDH). Furthermore, they were genotyped by rep-PCR together with reference strains of pan-European groups I, II, and III strains of Acinetobacter baumannii. Of the 47 strains, 42 were identified as A. baumannii, 4 as Acinetobacter Pittii, and 1 as Acinetobacter calcoaceticus based on 16S rRNA gene sequencing. In silico DDH with the genome sequence data of selected strains and rpoB gene sequencing data suggested that the five non-A. baumannii strains all belonged to A. pittii, suggesting that the rpoB gene is more reliable than the 16S rRNA gene for species level identification in this genus. Rep-PCR genotyping of the A. baumannii strains showed that these could be grouped into four groups, and that some strains clustered together with reference strains of pan-European clinical group II and III strains. All strains in this study were intrinsically resistant toward chloramphenicol and oxacillin, but susceptible toward tetracycline, tobramycin, erythromycin, and ciprofloxacin. For cefotaxime, 43 strains (91.5%) were intermediate and 3 strains (6.4%) resistant, while 3 (6.4%) and 21 (44.7%) strains exhibited resistance to cefepime and streptomycin, respectively. Forty-six (97.9%) strains were susceptible to amikacin and ampicillin-sulbactam. Therefore, the strains in this study were generally not resistant to the clinically relevant antibiotics, especially tobramycin, ciprofloxacin, cefepime, and meropenem, suggesting that the food route probably poses only a low risk for multidrug resistant Acinetobacter strains or resistance genes.

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions

Milk microbiota has a great influence on the safety and quality of dairy products. However, few studies have investigated the variations of bacterial composition in raw milk. In this study, raw milk samples were collected in 12 successive months, and their bacterial compositions were determined by 16 S rRNA gene sequencing. The highest diversity of bacterial composition was detected in June, while the lowest was in December. Firmicutes, Proteobacteria and Actinobacteria were the most abundant phyla and exhibited a counter-balanced relationship. Pseudomonas, Lactococcus and Acinetobacter were the most prevalent genera (>1%), and a tiny core microbiota (Acinetobacter and Pseudomonas) was observed. Temperature and humidity were the determining factors for most variation in bacterial compositions at both the phylum and genus levels. Higher abundances of Pseudomonas, Propionibacterium and Flavobacterium were correlated with low temperature. Furthermore, Pseudomonas/Propionibacterium and Lactobacillus/Bifidobacterium were two pairs of genera that had synergistic effects. Associations between the microbiota and milk quality parameters were analyzed. The abundances of Propionibacterium and Pseudoalteromonas were negatively correlated to total bacterial count, which meant that they helped to maintain milk quality, while a series of environmental microorganisms contributed to the spoilage of raw milk.

Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors

The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures.

Diversity of Acinetobacter species isolated from different environments in Lebanon: a nationwide study

Aim: To investigate the extrahospital reservoirs of Acinetobacter spp. in Lebanon. Materials & methods: Two thousand three hundred and sixty-one samples from different ecological niches were analyzed by culture methods. Species identification was confirmed by rpoB-gene sequencing. Multilocus sequence typing was used to characterize the Acinetobacter baumannii clones. Results & conclusion: Acinetobacter spp. were detected in 14% of environmental samples and 8% of food samples. Furthermore, 9% of animals and 3.4% of humans were colonized. Non-baumannii Acinetobacter were the most common species isolated and newly susceptible A. baumannii clones were detected. Interestingly, 21 isolates were not identified at the species level and were considered as putative novel species. To our knowledge, this is the largest epidemiological study investigating the epidemiology of Acinetobacter spp. outside hospitals.