Identification of Yersinia enterocolitica isolates from humans, pigs and wild boars by MALDI TOF MS

Application of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Foodborne Pathogens: Current Developments and Future Trends

Foodborne pathogens have gained sustained public attention, exerted significant pressure on food manufacturers, and posed serious health risks to human. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been employed for quick and accurate identification of microorganisms in the prevention of foodborne epidemics in recent years. Herein, we first summarize the principle of MALDI and its workflow for foodborne pathogens. Subsequently, we review the recent progress and applications of MALDI-TOF MS in foodborne pathogen determination. Additionally, we outline the expanded utilization of MALDI-based techniques for the identification of closely related species. We also assess the current gaps and propose possible solutions to address the existing challenges. MALDI-TOF MS is a promising biotool for rapid and accurate identification of foodborne microbes at the species and genus level in food samples. Database expansion and direct quantification of spoilage microbes are two promising areas for future progress in MALDI-TOF MS applications.

An Update in Knowledge of Pigs as the Source of Zoonotic Pathogens

The available data indicate that the human world population will constantly grow in the subsequent decades. This constant increase in the number of people on the Earth will lead to growth in food demand, especially in food of high nutritional value. Therefore, it is expected that the world livestock population will also increase. Such a phenomenon enhances the risk of transmitting pathogens to humans. As pig production is one of the most significant branches of the world's livestock production, zoonoses of porcine origins seem to be of particular importance. Therefore, in this review, we aim to introduce the latest data concerning, among other things, epidemiology and available preventive measures to control the most significant porcine zoonoses of viral, bacterial, and parasitic origin.

Isolation, characterization and antimicrobial resistance of Yersinia enterocolitica from Polish cattle and their carcasses

BACKGROUND

Yersinia enterocolitica is a heterogeneous bacterial species that has been divided into six biotypes and more than 70 serotypes. Each year, the European Food Safety Authority classifies yersiniosis caused by Y. enterocolitica as one of the most important zoonotic diseases. The prevalence of Y. enterocolitica in cattle has not been thoroughly analyzed in Poland, and beef and bovine carcasses contaminated with antimicrobial resistant Y. enterocolitica pose a health risk for both, farm workers and consumers. Therefore, the aim of this study was to evaluate the prevalence of Y. enterocolitica in cattle and to determine the antimicrobial susceptibility of the isolated strains.

RESULTS

A total of 1020 samples were analyzed, including 660 rectal swabs collected from live cattle and 360 swabs from cold-stored beef carcasses. The results of this study indicate that Y. enterocolitica was isolated from three of the 15 examined cattle herds and the prevalence within these herds ranged from 0% to nearly 32%. Y. enterocolitica was isolated from 14.7% of the examined heifers, 7.4% of calves and 5.5% of adult cows. More than 65% of the strains were isolated from cold enrichment. The strains isolated from live cattle tested positive for the ystB gene, while ail and ystA genes were not found. Most of the isolated strains belonged to bioserotype 1A/NT. The majority of the isolated strains were resistant to ampicillin, cefalexin and amoxicillin with clavulanic acid, however these are expected phenotypes for Y. enterocolitica.

CONCLUSIONS

The results of this study indicate that Y. enterocolitica is present in cattle herds in Poland. The strains isolated from live cattle were ystB-positive, most of them belonged to bioserotype 1A/NT. The prevalence of Y. enterocolitica strains was generally low in cold-stored beef carcasses.

Prevalence of Multidrug-Resistant Bacteria (Enteropathogens) Recovered from a Blend of Pig Manure and Pinewood Saw Dust during Anaerobic Co-Digestion in a Steel Biodigester

South Africa adopts intensive livestock farming, embracing the employment of huge quantities of antibiotics to meet the increased demand for meat. Therefore, bacteria occurring in the animal products and manure might develop antibiotic resistance, a scenario which threatens public health. The study investigated the occurrence of Gram-negative bacteria from eighteen pooled samples withdrawn from a single-stage steel biodigester co-digesting pig manure (75%) and pine wood saw dust (25%). The viable counts for each bacterium were determined using the spread plate technique. The bacterial isolates were characterised based on cultural, morphological and biochemical characteristics, using the Analytical Profile Index 20 e test kit. In addition, isolates were characterised based on susceptibility to 14 conventional antibiotics via the disc diffusion method. The MAR index was calculated for each bacterial isolate. The bacterial counts ranged from 104 to 106 cfu/mL, indicating manure as a potential source of contamination. Overall, 159 bacterial isolates were recovered, which displayed diverse susceptibility patterns with marked sensitivity to amoxicillin (100% E. coli), streptomycin (96.15% for Yersinia spp.; 93.33% for Salmonella spp.) and 75% Campylobacter spp. to nitrofurantoin. Varying resistance rates were equally observed, but a common resistance was demonstrated to erythromycin (100% of Salmonella and Yersinia spp.), 90.63% of E. coli and 78.57% of Campylobacter spp. A total of 91.19% of the bacterial isolates had a MAR index > 0.2, represented by 94 MAR phenotypes. The findings revealed multidrug resistance in bacteria from the piggery source, suggesting they can contribute immensely to the spread of multidrug resistance; thus, it serves as a pointer to the need for the enforcement of regulatory antibiotic use in piggery farms. Therefore, to curb the level of multidrug resistance, the piggery farm should implement control measures in the study area.

Assessment of the Role of Free-living and Farmed Fallow Deer (Dama dama) as A Potential Source of Human Infection with Multiple-Drug-Resistant Strains of Yersinia enterocolitica and Yersinia pseudotuberculosis

Yersinia enterocolitica and Y. pseudotuberculosis are Gram-negative, facultative anaerobic bacteria that cause yersiniosis—one of the most important zoonotic diseases of the digestive tract. The aim of this study was to determine the prevalence of potentially human-pathogenic Y. enterocolitica and Y. pseudotuberculosis strains in free-living and farmed fallow deer, and to evaluate their sensitivity to chemotherapeutics. A total of 372 rectal swabs were analyzed, including 262 from free-living and 110 from farmed fallow deer. Due to the psychrophilic properties of Yersinia, two samples were collected from each animal. Seven Y. enterocolitica strains were isolated from free-living fallow deer, while two strains were isolated from farmed fallow deer. Yersinia pseudotuberculosis strains were not identified. All isolated Y. enterocolitica strains were ystB-positive, and phylogenetic analysis based on the nucleotide sequences of this gene revealed the presence of two phylogenetic groups. Yersinia enterocolitica strains isolated from fallow deer belonged to biotype 1A, and serotyping analysis demonstrated that the vast majority did not agglutinate with any diagnostic sera. All strains were multiple drug resistant and were not sensitive to at least four of the tested chemotherapeutics (amoxicillin with clavulanic acid, ampicillin, cefalexin, and streptomycin). One Y. enterocolitica strain isolated from a free-living animal was resistant to nine out of the 13 analyzed chemotherapeutics and was intermediately sensitive to the four remaining chemotherapeutics. The highest sensitivity was noted in case of ciprofloxacin (five strains) and trimethoprim-sulfamethoxazole (three strains). Only one strain isolated from a free-living animal was sensitive to three out of the 13 examined antibiotics, whereas the remaining strains were sensitive to only one drug or were not sensitive to any of the chemotherapeutics used. The results of this study indicate that multiple drug-resistant Y. enterocolitica strains can be carried by free-living and farmed fallow deer. This observation gives serious cause for concern because the meat of fallow deer and other ruminants is often consumed semi-raw (steak) or raw (tartar steak).

Prevalence and Persistence of Multidrug-Resistant Yersinia enterocolitica 4/O:3 in Tonsils of Slaughter Pigs from Different Housing Systems in Croatia

Yersinia enterocolitica is one of the priority biological hazards in pork inspection. Persistence of the pathogen, including strains resistant to antimicrobials, should be evaluated in pigs from different housing systems for risk ranking of farms. In this 2019 study, tonsils were collected from 234 pigs, of which 69 (29.5%) were fattened on 3 big integrated farms, 130 (55.5%) on 10 medium-sized farms, and 35 (15%) on 13 small family farms. In addition, 92 pork cuts and minced meat samples from the same farms were tested for the presence of Y. enterocolitica using the culture method. Phenotypic and genetic characteristics of the isolates were compared with previously collected isolates from 2014. The overall prevalence of Y. enterocolitica in pig tonsils was 43% [95% CI 36.7−49.7]. In pigs from big integrated, medium-sized, and small family farms, the prevalence was 29%, 52%, and 40%, respectively. All retail samples of portioned and minced pork tested negative for pathogenic Y. enterocolitica, likely due to high hygienic standards in slaughterhouses/cutting meat or low sensitivity of culture methods in these matrices. The highest recovery rate of the pathogen from tonsils was found when alkali-treated PSB and CIN agar were combined. The biosecurity category of integrated and medium farms did not affect the differences in prevalence of Y. enterocolitica (p > 0.05), in contrast to family farms. Pathogenic ail-positive Y. enterocolitica biotype 4 serotype O:3 persisted in the tonsils of pigs regardless of the type of farm, slaughterhouse, and year of isolation 2014 and 2019. PFGE typing revealed the high genetic concordance (80.6 to 100%) of all the Y. enterocolitica 4/O:3 isolates. A statistically significant higher prevalence of multidrug-resistant Y. enterocolitica 4/O:3 isolates was detected in the tonsils of pigs from big integrated farms compared to the other farm types (p < 0.05), with predominant and increasing resistance to nalidixic acid, chloramphenicol, and streptomycin. This study demonstrated multidrug resistance of the pathogen in pigs likely due to more antimicrobial pressure on big farms, with intriguing resistance to some clinically relevant antimicrobials used in the treatment of yersiniosis in humans.

φYeO3-12 phage tail fiber Gp17 as a promising high specific tool for recognition of Yersinia enterocolitica pathogenic serotype O:3

Yersiniosis is an infectious zoonotic disease caused by two enteropathogenic species of Gram-negative genus Yersinia: Yersinia enterocolitica and Yersinia pseudotuberculosis. Pigs and other wild and domestic animals are reservoirs for these bacteria. Infection is usually spread to humans by ingestion of contaminated food. Yersiniosis is considered a rare disease, but recent studies indicate that it is overlooked in the diagnostic process therefore the infections with this bacterium are not often identified. Reliable diagnosis of Yersiniosis by culturing is difficult due to the slow growth of the bacteria easily overgrown by other more rapidly growing microbes unless selec-tive growth media is used. Phage adhesins recognizing bacteria in a specific manner can be an excellent diagnostic tool, es-pecially in the diagnosis of pathogens difficult for culturing. In this study, it was shown that Gp17, the tail fiber protein (TFP) of phage φYeO3-12, specifically recognizes only the pathogenic Yersinia enterocolitica serotype O:3 (YeO:3) bacteria. The ELISA test used in this work confirmed the specific interaction of this protein with YeO:3 and demonstrated a promising tool for developing the pathogen recognition method based on phage adhesins.

Genetic Diversity and Distribution of Virulence-Associated Genes in Y. enterocolitica and Y. enterocolitica-Like Isolates from Humans and Animals in Poland

Yersinia enterocolitica, widespread within domestic and wild-living animals, is a foodborne pathogen causing yersiniosis. The goal of this study was to assess a genetic similarity of Y. enterocolitica and Y. enterocolitica-like strains isolated from different hosts using Multiple Locus Variable-Number Tandem Repeat Analysis (MLVA) and Pulsed-Field Gel Electrophoresis (PFGE) methods, and analyze the prevalence of virulence genes using multiplex-Polymerase Chain Reaction (PCR) assays. Among 51 Yersinia sp. strains 20 virulotypes were determined. The most common virulence genes were ymoA, ureC, inv, myfA, and yst. Yersinia sp. strains had genes which may contribute to the bacterial invasion and colonization of the intestines as well as survival in serum. One wild boar Y. enterocolitica 1A strain possessed ail gene implying the possible pathogenicity of 1A biotype. Wild boar strains, represented mainly by 1A biotype, were not classified into the predominant Variable-Number Tandem Repeats (VNTR)/PFGE profile and virulotype. There was a clustering tendency among VNTR/PFGE profiles of pig origin, 4/O:3, and virulence profile. Pig and human strains formed the most related group, characterized by ~80% of genetic similarity what suggest the role of pigs as a potential source of infection for the pork consumers.

Biofilm formation and extracellular microvesicles-The way of foodborne pathogens toward resistance

Almost all known foodborne pathogens are able to form biofilms as one of the strategies for survival under harsh living conditions, to ward off the inhibition and the disinfection during food production, transport and storage, as well as during cleaning and sanitation of corresponding facilities. Biofilms are communities where microbial cells live under constant intracellular interaction and communication. Members of the biofilm community are embedded into extracellular matrix that contains polysaccharides, DNA, lipids, proteins, and small molecules that protect microorganisms and enable their intercellular communication under stress conditions. Membrane vesicles (MVs) are produced by both Gram positive and Gram negative bacteria. These lipid membrane-enveloped nanoparticles play an important role in biofilm genesis and in communication between different biofilm members. Furthermore, MVs are involved in other important steps of bacterial life like cell wall modeling, cellular division, and intercellular communication. They also carry toxins and virulence factors, as well as nucleic acids and different metabolites, and play a key role in host infections. After entering host cells, MVs can start many pathologic processes and cause serious harm and cell death. Prevention and inhibition of both biofilm formation and shedding of MVs by foodborne pathogens has a very important role in food production, storage, and food safety in general. Better knowledge of biofilm formation and maintaining, as well as the role of microbial vesicles in this process and in the process of host cells' infection is essential for food safety and prevention of both food spoilage and host infection.

Pleural empyema due to Salmonella in a patient with bronchogenic carcinoma: the first case report from a cancer hospital in Egypt

Background

Salmonella species are motile, Gram-negative facultative anaerobic bacilli, which belong to the family Enterobacteriaceae. The most common clinical presentations of Salmonella infection are gastroenteritis and enteric fever. Detection of Salmonella organisms in empyema is very rare.

Case presentation

We report the case of a 66-year-old female patient with bronchogenic carcinoma who developed empyema, and Salmonella was identified from the culture of pleural fluid. After antimicrobial therapy and other therapeutic measures, including the insertion of an intercostal tube, oxygen supplementation, frequent suction of respiratory secretions, and chest physiotherapy, the patient's condition improved. To the best of our knowledge, this is the first case to be reported in Egypt.

Conclusions

Our case sheds light on the role of Salmonella in immunocompromised patients in general and cancer patients in specific. We recommend further study of this role, since it may lead to a better understanding of the pathogenicity of this organism in these patients.

Cloacal Gram-Negative Microbiota in Free-Living Grass Snake Natrix natrix from Poland

Reptiles appear to be an important vector for Gram-negative pathogens, therefore, they are epidemiologically relevant. However, the composition of reptilian microbiota has been poorly recognized so far. The majority of studies concern exotic reptiles as asymptomatic carriers of Salmonella serovars. Studies of other intestinal bacteria of reptiles are rare. Only recently, the microbiota of free-living European reptiles have been investigated, however, on the basis of small samples, mainly in protected areas. Here, we aim to investigate cloacal Gram-negative microbiota of free-living Natrix natrix. Snakes (N = 45) used in the study were collected in Kraków (Poland) and its vicinity. Nineteen species of Gram-negative bacteria were isolated. The most common species were: Aeromonas hydrophila, Morganella morganii, Proteus vulgaris, Salmonella spp. The bacteria prevalent in N. natrix cloacal swabs are likely to represent the natural intestinal Gram-negative microbiota of the examined snakes. Importantly, the identified bacteria are pathogenic to humans, which clearly highlights the epidemiological potential of free-living N. natrix. The risk of infection is high for immunocompromised humans, children (under 5 years old), elderly persons, and pregnant women. Our study provides the largest dataset on intestinal Gram-negative microbiota of wild snakes. The presence of multiple human pathogens determined by us calls for the necessity of further studies on reptile-transmitted bacteria in anthropogenic environments.

An overview of Yersinia enterocolitica and related species in samples of different origin from San Luis, Argentina

This study is aimed at offering an overview of the prevalence of Yersinia enterocolitica and related species in San Luis, Argentina, from samples of diverse origin received in our laboratory between 1984 and 2014, and providing an analysis of the distribution of Yersinia isolates according to their isolation sources, highlighting bioserotypes and potential reservoirs and vehicles of transmission to humans. From a total of 4572 samples of human, animal, food and environmental origins analyzed by traditional culture methods and molecular techniques, 229 (5%) samples were Yersinia positive. The highest frequency of Yersinia isolates was observed in environmental specimens (14.3%), followed by animal (9.2%), food (5%) and human (0.6%) samples. A total of 255 Yersinia isolates were characterized, including 183 Y. enterocolitica and 72 isolates of other Yersinia species. Biotype 1A associated to several serotypes was identified in Y. enterocolitica isolates from environment (100%), animals (95.5%), foods (71.7%) and human samples (40%); bioserotype 2/O:9 was identified in isolates from foods (25.5%), and biotype 3 was associated with strains from humans (60%), animals (4.5%) and foods (2.8%). This biotype included three strains O:3 and six strains O:5. The data highlight animals and foods as the main Y. enterocolitica sources in our region.

Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization

The genus Yersinia comprises species that differ widely in their pathogenic potential and public-health significance. Yersinia pestis is responsible for plague, while Yersinia enterocolitica is a prominent enteropathogen. Strains within some species, including Y. enterocolitica, also vary in their pathogenic properties. Phenotypic identification of Yersinia species is time-consuming, labour-intensive and may lead to incorrect identifications. Here, we developed a method to automatically identify and subtype all Yersinia isolates from their genomic sequence. A phylogenetic analysis of Yersinia isolates based on a core subset of 500 shared genes clearly demarcated all existing Yersinia species and uncovered novel, yet undefined Yersinia taxa. An automated taxonomic assignment procedure was developed using species-specific thresholds based on core-genome multilocus sequence typing (cgMLST). The performance of this method was assessed on 1843 isolates prospectively collected by the French National Surveillance System and analysed in parallel using phenotypic reference methods, leading to nearly complete (1814; 98.4 %) agreement at species and infra-specific (biotype and serotype) levels. For 29 isolates, incorrect phenotypic assignments resulted from atypical biochemical characteristics or lack of phenotypic resolution. To provide an identification tool, a database of cgMLST profiles and reference taxonomic information has been made publicly accessible (https://bigsdb.pasteur.fr/yersinia). Genomic sequencing-based identification and subtyping of any Yersinia is a powerful and reliable novel approach to define the pathogenic potential of isolates of this medically important genus.