Evaluation of virulence factors profiles and antimicrobials resistance of Escherichia coli isolated from bulk tank milk and raw milk filters

Extended-spectrum beta-lactamase-producing Klebsiella pneumoniae and risk factors associated with high total bacterial count in bulk tank milk from dairy farms in Colombia

The objective of the study was to evaluate the frequency and genetic characteristics of ESBL-producing Escherichia coli and Klebsiella spp. and the risk factors associated with a high total bacterial count in bulk tank milk samples of dairy farms in three municipalities of the Antioquia Department, Colombia. Fifteen samples were positive for E. coli and Klebsiella spp. Subsequent analysis of the 16 S rRNA gene sequences confirmed these isolates included E. coli (n = 3), K. oxytoca (n = 11), and K. pneumoniae (n = 1). None of the isolates was positive for ESBL identification by phenotypic methods, but the only the isolate of K. pneumoniae was positive for the blaSHV61 gene by sequence analysis. The antibiotic susceptibility evaluation for all Klebsiella spp. isolates identified resistance to fosfomycin (50%; 6/12) and ampicillin (100%; 12/12). While most of the herds maintain adequate hygienic quality, specific risk factors such as having more than 60 milking cows, frequent changes in milkers, milking in paddocks, and using a chlorinated product for pre-dipping have been identified as associated with a high total bacterial count > 100,000 CFU/mL in bulk tank milk. However, certain variables including the milker being the owner of the animals and the proper washing and disinfection of the milking machine contribute to maintain a high level of hygiene and quality in the raw milk stored in the tanks. In conclusion, the frequency of ESBL producers was relatively low, with only K. pneumoniae testing positive for the blaSHV ESBL type. The presence of these bacteria in milk tanks represents a potential risk to public health for consumers of raw milk and its derivatives.

Antibiograms, multidrug resistance, and milk-related parameters of bacteria isolated from milk of dairy cattle in Phatthalung, Thailand

Background and Aim

Milk, a nutritious food, is widely consumed in human diets; however, contamination by micro-organisms can negatively impact its quality and consumer health. Contamination by micro-organisms affects the quality of milk, which can affect the quality of the milk production chain. This study aimed to determine the changes in milk composition and antibiotic susceptibility related to bacteria isolated from dairy cow milk.

Materials and Methods

Raw milk samples were collected from 72 dairy cows. All milk samples were subjected to the California Mastitis Test (CMT) for CMT score determination. We also investigated milk composition, bacterial culture (BC), and antibiotic susceptibility.

Results

About 47.22% and 30.56% of dairy cattle were positive for CMT + BC and automatic somatic cell count (ASCC) + BC, respectively. Fecal appearance and animal age were found to be risk factors for ASCC + BC positivity in dairy cattle. Bacteria were found in approximately 76% of milk samples, with the most common isolated species being α-hemolytic Streptococcus spp., coagulase-negative Staphylococcus spp., and Escherichia coli. Of these, 70% are resistant to at least one antibiotic. Variation in the multidrug resistance pattern was high in Klebsiella spp.

Conclusions

Fecal appearance and animal age are risk factors for ASCC + BC positivity in dairy cattle. This study identified antibiotic and multidrug resistance patterns, which require comprehensive studies and effective surveillance systems. Remarkably, the use of antibiotic therapy in dairy cattle should be monitored.

Contamination of Kazakhstan cheeses originating from Escherichia coli and its resistance to antimicrobial drugs

Background and Aim

Escherichia coli, a commensal intestine bacterium of vertebrates, is widely distributed in the environment and indicates the microbiological quality of food products in relation to coliforms. In addition, virulent strains, particularly E. coli O157:H7, cause outbreaks of toxic infections caused by consuming dairy products. Because food safety studies regarding E. coli have not been conducted in Central Asia, this research aimed to study the characteristics of contamination, microbiological and genotypic properties, and resistance to antimicrobial agents of E. coli strains that contaminate various types of commercialized cheeses originating from Kazakhstan.

Materials and Methods

In retail outlets, 207 samples of three types of cheese produced by 22 industrial and eight small enterprises in the central, eastern, southern, and northern regions of Kazakhstan were selected in 2020-2023. E. coli contamination was examined using standard microbiological, mass spectrometric, and molecular genetic methods. The discodiffuse European Committee on Antimicrobial Susceptibility Testing method was used to test the resistance of the identified E. coli isolates (65/207; 31.4%) to 20 antibacterial drugs. The Shiga toxin-producing E. coli (VT1 and VT2) and E. coli O157:H7 (eae) genes were investigated in all E. coli isolates using multiplex polymerase chain reaction.

Results

An average of 31.4% samples of commercial Kazakhstani cheeses of various types were found to be contaminated with E. coli in almost all geographical regions of Kazakhstan, regardless of the productivity of the dairy enterprises. Soft cheeses produced by small farms (80% of samples) packaged at the retail site (100%) were the most contaminated with E. coli. The microbiological index (colony-forming unit/g) was unsatisfactory and unsuitable in 6.2% of such cheese samples. For the first time in Central Asia, the enteropathogenic strain E. coli O157:H7 was detected in 0.5% of cheese samples. E. coli isolates from cheese samples were resistant to 65% of antibacterial drugs and contained resistance genes to β-lactams, sulfonamides, and quinolones groups. At the same time, 25% of the E. coli isolates were multi-resistant to three or more antimicrobial agents.

Conclusion

The high level of contamination caused by multi-antibiotic resistant E. coli strains, including pathogenic pathogens, poses a risk to public health and highlights the need for further research on the monitoring and control of coliform enteropathogens in food products.

Occurrence of diarrheagenic Escherichia coli pathotypes from raw milk and unpasteurized buttermilk by culture and multiplex polymerase chain reaction in southwest Iran

BACKGROUND

In developing countries including Iran, there are limited data on diarrheagenic Escherichia coli (DEC) contamination in milk and unpasteurized buttermilks. This study aimed to determine the occurrence of DEC pathotypes by culture and multiplex polymerase chain reaction (M-PCR) in some dairy products from southwest Iran.

METHODS AND RESULTS

In this cross-sectional study (September to October 2021), 197 samples (87 unpasteurized buttermilk and 110 raw cow milk) were collected from dairy stores of Ahvaz, southwest Iran. The presumptive E. coli isolates were primarily identified using biochemical tests and then confirmed by PCR of uidA gene. The occurrence of 5 DEC pathotypes: enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and enteroinvasive E. coli (EIEC) were investigated using M-PCR. Overall, 76 (76/197, 38.6%) presumptive E. coli isolates were identified by biochemical tests. Using uidA gene, only 50 isolates (50/76, 65.8%) were confirmed as E. coli. DEC pathotypes were detected in 27 of 50 (54.0%) E. coli isolates (74.1%, 20/27 from raw cow milk and 25.9%, 7/27 from unpasteurized buttermilk). The frequency of DEC pathotypes was as follows: 1 (3.7%) EAEC, 2 (7.4%) EHEC, 4 (14.8%) EPEC, 6 (22.2%) ETEC, and 14 (51.9%) EIEC. However, 23 (46.0%) E. coli isolates had only the uidA gene and were not considered DEC pathotypes.

CONCLUSION

Possible health risks for Iranian consumers can be attributed to the presence of DEC pathotypes in dairy products. Hence, serious control and prevention efforts are needed to stop the spread of these pathogens.

Evaluation of Virulence Factors, Antibiotic Resistance, and Biofilm Formation of Escherichia coli Isolated from Milk and Dairy Products in Isfahan, Iran

Diarrheagenic E. coli (DEC) strains are important causes of gastrointestinal diseases worldwide, especially in developing countries. This study aimed to investigate the presence, antibiotic resistance, and potential biofilm formation in dairy products in Isfahan, Iran. A total of 200 samples, including traditional and pasteurized dairy products, were analyzed. In 200 samples, 54 E. coli isolates, including (48/110) and (6/90) positive samples of traditional and pasteurized dairy products, were detected. Furthermore, pathogenic strains were isolated from 30% of traditional dairy products and 5.55% of pasteurized dairy products. Most isolates were classified as enteropathogenic E. coli (EPEC). Moreover, antibiotic resistance was evaluated using the disk diffusion method for pathogenic E. coli. Overall, 73.68% of contaminated samples by pathogenic strains were resistant to at least one antibiotic. The highest resistance was observed against streptomycin (57.9%), followed by tetracycline (50%). Additionally, all isolates were sensitive to amikacin. For evaluating biofilm formation, the violet crystal assay was applied on a polystyrene microplate well for pathogenic isolates. In total, 68.42% of isolates were able to form biofilms. The presence of E. coli in dairy products indicates potential health risks for Iranian consumers. Serious measures are needed to control and prevent the spread of this pathogen.

A large-scale pico-droplet array for viable bacteria digital counting and dynamic tracking based on a thermosetting oil

A simple and rapid method was developed for real-time monitoring and digital counting of bacterial growth, and it can provide dynamic information at high resolution in the process.

Extraintestinal Pathogenic Escherichia coli: Virulence Factors and Antibiotic Resistance

The One Health approach emphasizes the importance of antimicrobial resistance (AMR) as a major concern both in public health and in food animal production systems. As a general classification, E. coli can be distinguished based on the ability to cause infection of the gastrointestinal system (IPEC) or outside of it (ExPEC). Among the different pathogens, E. coli are becoming of great importance, and it has been suggested that ExPEC may harbor resistance genes that may be transferred to pathogenic or opportunistic bacteria. ExPEC strains are versatile bacteria that can cause urinary tract, bloodstream, prostate, and other infections at non-intestinal sites. In this context of rapidly increasing multidrug-resistance worldwide and a diminishingly effective antimicrobial arsenal to tackle resistant strains. ExPEC infections are now a serious public health threat worldwide. However, the clinical and economic impact of these infections and their optimal management are challenging, and consequently, there is an increasing awareness of the importance of ExPECs amongst healthcare professionals and the general public alike. This review aims to describe pathotype characteristics of ExPEC to increase our knowledge of these bacteria and, consequently, to increase our chances to control them and reduce the risk for AMR, following a One Health approach.

Molecular characteristics of Escherichia coli from bulk tank milk in Korea

Background

Escherichia coli, which causes subclinical or clinical mastitis in cattle, is responsible for transmitting antimicrobial resistance via human consumption of raw milk or raw milk products.

Objectives

The objective of this study was to investigate the molecular characteristics of 183 E. coli from bulk tank milk of five different dairy factories in Korea.

Methods

The molecular characteristics of E. coli such as serogroup, virulence, antimicrobial resistance, and integron genes were detected using polymerase chain reaction and antimicrobial susceptibility were tested using the disk diffusion test.

Results

In the distribution of phylogenetic groups, group D was the most prevalent (59.6%) and followed by group B1 (25.1%). The most predominant serogroup was O173 (15.3%), and a total of 46 different serotypes were detected. The virulence gene found most often was fimH (73.2%), and stx1, fimH, incC, fyuA, and iutA genes were significantly higher in isolates of phylogenetic group B1 compared to phylogenetic groups A, B2, and D (p < 0.05). Among 64 E. coli isolates that showed resistance to at least one antimicrobial, the highest resistance rate was observed for tetracyclines (37.5%). All 18 integron-positive E. coli carried the integron class I (int1) gene, and three different gene cassette arrangements, dfrA12+aadA2 (2 isolates), aac(6′)-Ib3+aac(6′)-Ib-cr+aadA4 (2 isolates), and dfrA17+aadA5 (1 isolate) were detected.

Conclusions

These data suggest that the E. coli from bulk tank milk can be an indicator for dissemination of antimicrobial resistance and virulence factors via cross-contamination.

Review on the occurrence of the mcr-1 gene causing colistin resistance in cow's milk and dairy products

Both livestock farmers and the clinic use significant amount of antibiotics worldwide, in many cases the same kind. Antibiotic resistance is not a new phenomenon, however, it is a matter of concern that resistance genes (mcr - Mobilized Colistin Resistance - genes) that render last-resort drugs (Colistin) ineffective, have already evolved. Nowadays, there is a significant consumption of milk and dairy products, which, if not treated properly, can contain bacteria (mainly Gram-negative bacteria). We collected articles and reviews in which Gram-negative bacteria carrying the mcr-1 gene have been detected in milk, dairy products, or cattle. Reports have shown that although the incidence is still low, unfortunately the gene has been detected in some dairy products on almost every continent. In the interest of our health, the use of colistin in livestock farming must be banned as soon as possible, and new treatments should be applied so that we can continue to have a chance in fighting multidrug-resistant bacteria in human medicine.

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.

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics—ampicillin, cefotaxime, ciprofloxacin and gentamicin–for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together. They also clustered separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might support a better one-health approach for AR in Germany.

Detection of Antimicrobial Resistance Genes in the Milk Production Environment: Impact of Host DNA and Sequencing Depth

Over the past decades, antimicrobial resistance (AMR) has been recognized as one of the most serious threats to public health. Although originally considered a problem to human health, the emerging crisis of AMR requires a "One Health" approach, considering human, animal, and environmental reservoirs. In this regard, the extensive use of antibiotics in the livestock production systems to treat mastitis and other bacterial diseases can lead to the presence of AMR genes in bacteria that contaminate or naturally occur in milk and dairy products, thereby introducing them into the food chain. The recent development of high-throughput next-generation sequencing (NGS) technologies is improving the fast characterization of microbial communities and their functional capabilities. In this context, whole metagenome sequencing (WMS), also called shotgun metagenomic sequencing, allows the generation of a vast amount of data which can be interrogated to generate the desired evidence, including the resistome. However, the amount of host DNA poses a major challenge to metagenome analysis. Given the current absence of literature concerning the application of WMS on milk to detect the presence of AMR genes, in the present study, we evaluated the effect of different sequencing depths, host DNA depletion methods and matrices to characterize the resistome of a milk production environment. WMS was conducted on three aliquots of bulk tank milk and three aliquots of the in-line milk filter collected from a single dairy farm; a fourth aliquot of milk and milk filter was bioinformatically subsampled. Two commercially available host DNA depletion methods were applied, and metagenomic DNA was sequenced to two different sequencing depth. Milk filters proved to be the most suitable matrices to evaluate the presence of AMR genes; besides, the pre-extraction host DNA depletion method was the most efficient approach to remove host reads. To our knowledge, this is the first study to evaluate the limitations posed by the host DNA in investigating the milk resistome with a WMS approach, confirming the circulation of AMR genes in the milk production environment.

Green one-step synthesis of carbon quantum dots from orange peel for fluorescent detection of Escherichia coli in milk

Carbon quantum dots (CQDs) prepared by a green one-step approach was used for sensitive and selective assay of Escherichia coli O157: H7 (E. coli). CQDs was synthesized from orange peel as a carbon source via a microwave-assisted method. The CQDs displayed strong green fluorescence under excitation wavelength of 420 nm. A fluorescent probe (CQDs-MNPs) for E. coli was fabricated based on CQDs labeled with aptamer (aptamer-CQDs) and magnetic nanoparticles labeled with complementary DNA (cDNA-MNPs). Fluorescent intensity of the CQDs-MNPs was decreased with addition of E. coli. The linearity between fluorescent intensity and E. coli concentration was used for developing a fluorescent method with detecting range of 500-10⁶ CFU/mL and detection limit of 487 CFU/mL. Milk samples contaminated by E. coli were analyzed by this method, and the results agreed with that achieved by plate-counting methods. This fluorescent probe exhibits great potential in guaranteeing food quality and safety.

Molecular characterization of virulence and drug resistance genes-producing Escherichia coli isolated from chicken meat: Metal oxide nanoparticles as novel antibacterial agents

Escherichia coli is a major global foodborne pathogen, infecting a wide range of animals and contaminating their meat products. E. coli, can lead to high morbidity and mortality with a huge economic loss especially if foodborne diseases are associated with multidrug resistant (MDR)- and multivirulent-producing pathogens. Due to the increased resistance to common antimicrobials used to treat livestock animals and human infections, the discovery of new and innovative nanomaterials are in high demand. Recently, metal oxides can be considered as effective inorganic agents with antimicrobial features. Hence, this study might be the first to evaluate the efficiency of metal oxide nanoparticles (MO-NPs) as novel antibacterial agents against MDR/multivirulent E. coli pathogens isolated from chicken meat. The occurrence of pathogenic E. coli was determined in fresh warm chicken meat parts (breast, thigh, liver and gizzard). Ninety-one of 132 (69%) chicken meat parts were Escherichia -positive with E. coli as the only species isolated. Out of identified 240 E. coli strains, 72.5% (174/240) were classified as MDR E. coli strains. Fifty-five profile patterns were obtained. From each pattern, one strain was randomly selected for further analysis of virulence and resistance genes. Extracted DNA was assessed for the presence of antibiotic resistance genes (bla_IMP-7, bla_IMP-25, bla_TEM, bla_SHV, bla_OXA-2, tetA, aadA, and aac(3)-IV) and virulence genes (stx1, stx2, hlyA, eaeA, aggR, eltB, estIb, papA, afa and hlyD). Clustering analyses revealed that 10 E. coli harboring the highest number of virulence and resistance genes were shifted together into one cluster designated as cluster X. The average activities of zinc peroxide nanoparticles (ZnO₂-NPs) were higher than that of zinc oxide nanoparticles (ZnO-NPs) and titanium dioxide nanoparticles (TiO₂-NPs) by 20% and 29%, respectively. The anti-inflammatory activity of ZnO₂-NPs in comparison with aspirin was assessed using membrane stabilization, albumin denaturation, and proteinase inhibition methods. Significant anti-inflammatory activity of ZnO₂-NPs was achieved at concentration levels of 500-1000 μg/ml. It seems that MO-NPs are effective alternative agents, since they exhibited a competitive antibacterial capability against MDR/multivirulent-producing E. coli pathogens isolated from chicken meat. Hence, ZnO₂-NPs are a promising nanoparticles-based material for controlling foodborne pathogens, thereby valued for food safety applications.