Human campylobacteriosis: A public health concern of global importance

Cadmium exposure promotes inflammation through the PPAR signaling pathway in the small intestine and colon of Hu sheep

With the increase of cadmium content in the environment, the losses caused by cadmium-induced intestinal diseases to animal husbandry are increasing year by year. However, most of the on-going research activities focus on zoonotic diseases rather than exploring the mechanisms of animal disease occurrence from an anthropogenic environmental perspective. In this study, stressed Hu sheep under cadmium environmental exposure were selected to explore the mechanism of inflammatory bowel disease development. 16 s, untargeted metabolomics and transcriptomic multiomics were used to analyze the changes of their intestinal tract and intestinal contents. The results showed that the beneficial microorganisms (s_Ruminococcus_sp) in the Cd group were significantly decreased and the potentially harmful microorganisms were significantly enriched, and the changes of these microorganisms affected the changes of metabolites (caprylic acid) to a certain extent, resulting in a decrease in fatty acids in the intestine. Due to the combined effect of cadmium ion and fatty acid reduction, the PPAR signaling pathway was inhibited, and the fatty acid transport and binding were further reduced, causing very serious damage to the intestine. We revealed for the first time the mechanism of intestinal injury in Hu sheeps under cadmium environmental exposure and provided new prevention and treatment methods of intestinal diseases under the environmental exposure to trace metals.

Harnessing medicinal plant compounds for the control of Campylobacter in foods: a comprehensive review

Campylobacter is a major foodborne and zoonotic pathogen, causing severe human infections and imposing a substantial economic burden on global public health. The ongoing spread and emergence of multidrug-resistant (MDR) strains across various fields exacerbate therapeutic challenges, raising the incidence of diseases and fatalities. Medicinal plants, renowned for their abundance in secondary metabolites, exhibit proven efficacy in inhibiting various foodborne and zoonotic pathogens, presenting sustainable alternatives to ensure food safety. This review aims to synthesize recent insights from peer-reviewed journals on the epidemiology and antimicrobial resistance of Campylobacter species, elucidate the in vitro antibacterial activity of medicinal plant compounds against Campylobacter by delineating underlying mechanisms, and explore the application of these compounds in controlling Campylobacter in food. Additionally, we discuss recent advancements and future prospects of employing medicinal plant compounds in food products to mitigate foodborne pathogens, particularly Campylobacter. In conclusion, we argue that medicinal plant compounds can be used as effective and sustainable sources for developing new antimicrobial alternatives to counteract the dissemination of MDR Campylobacter strains.

Transmission of dominant strains of Campylobacter jejuni and Campylobacter coli between farms and retail stores in Ecuador: Genetic diversity and antimicrobial resistance

Thermotolerant Campylobacter is an important zoonotic pathogen known for causing gastroenteritis in humans, with poultry as its primary reservoir. A total of 468 samples were collected, of which 335 were chicken carcass samples (representing the food component), and 133 were chicken caeca samples (representing the animal component). These samples underwent culture, with colonies examined under a microscope. Species identification was achieved through multiplex PCR. Additionally, antimicrobial susceptibility profiles were determined using the Kirby-Bauer method, testing for sensitivity to gentamicin, ciprofloxacin, tetracycline, and erythromycin. Additionally, 55 C. jejuni (62.5%) and 33 C. coli (37.5%) isolates were selected for whole genome sequencing (WGS). A High prevalence of Campylobacter was observed, with rates of 95.5% (n = 127, CI95%: 92.5% - 98.5%) in the animal component and 72.5% (n = 243, CI95%: 69.9% - 75.1%) in the food component. Specifically, C. jejuni was detected in 33.1% (n = 42) of poultry farms and 38.3% (n = 93) of chicken carcasses, while C. coli was found in 64.6% (n = 82) of poultry farms and 60.5% (n = 147) of chicken carcasses. Antimicrobials with the highest rates of resistance (67%-100%) were ciprofloxacin and tetracycline, in both animal and food component isolates. Erythromycin resistance was notable, ranging from 22% to 33%, with only two C. jejuni isolates from retail were resistant to gentamicin. Furthermore, multidrug resistance was identified in 23% (20 isolates) of the Campylobacter isolates. Genetic analysis revealed the presence of fourteen resistance genes in both C. jejuni and C. coli isolates, including tet(O), blaOXA-460, blaOXA-184, blaOXA-489, blaOXA-193, blaOXA-784, blaOXA-603, aph(3')-IIIa, aad9, aph(2'')-If, aadE-Cc, sat4, and ant(6)-Ia. Additionally, twenty-five plasmids were detected in the 88 Campylobacter isolates examined. Interestingly, most isolates also harbored genes encoding putative virulence factors associated with pathogenicity, invasion, adherence, and production of cytolethal distending toxin (cdt): cheV, cheA, cheW, cheY, flaA, flgR, flaC, flaD, flgB, flgC, ciaB, ciaC. The WGS analysis showed the presence of several cgSTs in both animal and food components, with nine of them widely disseminated between components. Moreover, C. coli and C. jejuni isolates from different sources presented less than 11 single nucleotide polymorphisms (SNPs), suggesting clonality (16 isolates). Further analysis using SNP tree demonstrated widespread distribution of certain C. jejuni and C. coli clones across multiple farms and retail stores. This study presents, for the first-time, insights into the clonality, plasmid diversity, virulence, and antimicrobial resistance (AMR) of thermotolerant Campylobacter strains originating from the Ecuadorian poultry industry. The identification of AMR genes associated with the main antibiotics used in the treatment of campylobacteriosis in humans, highlights the importance of the prudent use of antimicrobials in the poultry industry. Additionally, this research remarks the need for regional studies to understand the epidemiology of this pathogen.

Novel Drug-like HsrA Inhibitors Exhibit Potent Narrow-Spectrum Antimicrobial Activities against Helicobacter pylori

Helicobacter pylori infection constitutes a silent pandemic of global concern. In the last decades, the alarming increase in multidrug resistance evolved by this pathogen has led to a marked drop in the eradication rates of traditional therapies worldwide. By using a high-throughput screening strategy, in combination with in vitro DNA binding assays and antibacterial activity testing, we identified a battery of novel drug-like HsrA inhibitors with MIC values ranging from 0.031 to 4 mg/L against several antibiotic-resistant strains of H. pylori, and minor effects against both Gram-negative and Gram-positive species of human microbiota. The most potent anti-H. pylori candidate demonstrated a high therapeutic index, an additive effect in combination with metronidazole and clarithromycin as well as a strong antimicrobial action against Campylobacter jejuni, another clinically relevant pathogen of phylum Campylobacterota. Transcriptomic analysis suggests that the in vivo inhibition of HsrA triggers lethal global disturbances in H. pylori physiology including the arrest of protein biosynthesis, malfunction of respiratory chain, detriment in ATP generation, and oxidative stress. The novel drug-like HsrA inhibitors described here constitute valuable candidates to a new family of narrow-spectrum antibiotics that allow overcoming the current resistome, protecting from dysbiosis, and increasing therapeutic options for novel personalized treatments against H. pylori.

A Decade of Antimicrobial Resistance in Human and Animal Campylobacter spp. Isolates

Objectives: Campylobacter spp. remain a leading cause of bacterial gastroenteritis worldwide, with resistance to antibiotics posing significant challenges to treatment and public health. This study examines profiles in antimicrobial resistance (AMR) for Campylobacter isolates from human and animal sources over the past decade. Methods: We conducted a comprehensive review of resistance data from studies spanning ten years, analyzing profiles in resistance to key antibiotics, ciprofloxacin (CIP), tetracycline (TET), erythromycin (ERY), chloramphenicol (CHL), and gentamicin (GEN). Data were collated from various regions to assess global and regional patterns of resistance. Results: The analysis reveals a concerning trend of increasing resistance patterns, particularly to CIP and TET, across multiple regions. While resistance to CHL and GEN remains relatively low, the high prevalence of CIP resistance has significantly compromised treatment options for campylobacteriosis. Discrepancies in resistance patterns were observed between human and animal isolates, with variations across different continents and countries. Notably, resistance to ERY and CHL showed regional variability, reflecting potential differences in antimicrobial usage and management practices. Conclusions: The findings underscore the ongoing challenge of AMR in Campylobacter, highlighting the need for continued surveillance and research. The rising resistance prevalence, coupled with discrepancies in resistance patterns between human and animal isolates, emphasize the importance of a One Health approach to address AMR. Enhanced monitoring, novel treatment strategies, and global cooperation are crucial for mitigating the impact of resistance and ensuring the effective management of Campylobacter-related infections.

Draft genomes of multidrug-resistant Campylobacter jejuni and Campylobacter coli strains from Brazil representing novel sequence types

Whole-genome sequencing identified three previously unidentified multilocus sequence types of Campylobacter jejuni (ST-12332) and Campylobacter coli (ST-12333 and ST-12663), harboring resistance genes for multiple antimicrobial classes. The sources of isolation highlight the circulation of resistance strains within animals and humans, emphasizing the need for preventive measures.

High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater

Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.

Antimicrobial Resistance and Genomic Characterization of Campylobacter jejuni and Campylobacter coli Isolated from Retail Chickens in Beijing, China

Objective Campylobacter species are the main causes of foodborne illness worldwide, posing significant threats to public health. This study aimed to investigate the antibiotic resistance and genomic characterization of C. jejuni/C.coli from retail chickens in Beijing. Methods Antimicrobial susceptibility testing was conducted on 126 C. jejuni/C. coli isolated from retail chickens in Beijing, following CLSI protocols. Whole genomes of all isolates were sequenced using the Illumina platform. Results More C. coli (83.82%) showed multi-drug resistance than C. jejuni (8.62%). Genomic analysis demonstrated 42 sequence types (STs) and 12 clonal complexes (CCs), from which CC828 and CC52 were dominant. cdtA, cdtB and cdtC encoding cytotoxic protein were present spontaneously in most C. jejuni but not found in any C. coli isolates. The abundances of antibiotic resistance genes (ARGs) and virulence genes (VGs) in C. jejuni and C. coli were significantly different, with ARGs numbered in C. coli and VGs in C. jejuni. Conclusions High prevalence of multi-drug resistance C. coli and C. jejuni isolated from Beijing chickens were challenging clinical antibiotic usages in the treatment of Campylobacter infection. The surveillance of particular C. jejuni and C. coli STs correlated with higher resistance and virulence needs to be strengthened in the future.

Campylobacteriosis: A rising threat in foodborne illnesses

Campylobacteriosis is a foodborne illness that is contracted by eating contaminated food, particularly animal products like meat from diseased animals or corpses tainted with harmful germs. The epidemiology of campylobacteriosis varies significantly between low-, middle-, and high-income countries. Campylobacter has a complicated and poorly known survival strategy for getting past host barriers and causing sickness in humans. The adaptability of Campylobacter to unfavorable environments and the host's immune system seems to be one of the most crucial elements of intestinal colonization. A Campylobacter infection may result in fever, nausea, vomiting, and mild to severe bloody diarrhea in humans. Effective and rapid diagnosis of Campylobacter species infections in animal hosts is essential for both individual treatment and disease management at the farm level. According to the most recent meta-analysis research, the main risk factor for campylobacteriosis is travel, which is followed by eating undercooked chicken, being exposed to the environment, and coming into close contact with livestock. Campylobacter jejuni, and occasionally Campylobacter coli, are the primary causes of Campylobacter gastroenteritis, the most significant Campylobacter infection in humans for public health. The best antibiotic medications for eradicating and decreasing Campylobacter in feces are erythromycin, clarithromycin, or azithromycin. The best strategy to reduce the number of human infections caused by Campylobacter is to restrict the amount of contamination of the poultry flock and its products, even if the majority of infections are contracted through handling or ingestion of chicken.

Selective depletion of Campylobacter jejuni via T6SS dependent functionality: an approach for improving chickens gut health

The targeted depletion of potential gut pathogens is often challenging because of their intrinsic ability to thrive in harsh gut environments. Earlier, we showed that Campylobacter jejuni (C. jejuni) exclusively uses the Type-VI Secretion System (T6SS) to target its prey such as Escherichia coli (E. coli), and phenotypic differences between T6SS-negative and T6SS-positive C. jejuni isolates toward bile salt sensitivity. However, it remains unclear how the target-driven T6SS functionality prevails in a polymicrobial gut environment. Here, we investigated the fate of microbial competition in an altered gut environment via bacterial T6SS using a T6SS-negative and -positive C. jejuni or its isogenic mutant of the hemolysin-coregulated protein (hcp). We showed that in the presence of bile salt and prey bacteria (E. coli), T6SS-positive C. jejuni experiences enhanced intracellular stress leading to cell death. Intracellular tracking of fluorophore-conjugated bile salts confirmed that T6SS-mediated bile salt influx into C. jejuni can enhance intracellular oxidative stress, affecting C. jejuni viability. We further investigated whether the T6SS activity in the presence of prey (E. coli) perturbs the in vivo colonization of C. jejuni. Using chickens as primary hosts of C. jejuni and non-pathogenic E. coli as prey, we showed a marked reduction of C. jejuni load in chickens cecum when bile salt solution was administered orally. Analysis of local antibody responses and pro-inflammatory gene expression showed a reduced risk of tissue damage, indicating that T6SS activity in the complex gut environment can be exploited as a possible measure to clear the persistent colonization of C. jejuni in chickens.

Campylobacter jejuni and Campylobacter coli infection, determinants and antimicrobial resistance patterns among under-five children with diarrhea in Amhara National Regional State, Northwest Ethiopia

BACKGROUND

Children with under-five year age disproportionally affected with foodborne illness. Campylobacteriosis is the most common foodborne disease next to Norovirus infection. Macrolides are commonly prescribed as the first line of treatment for Campylobacter gastroenteritis, with fluoroquinolone and tetracycline as secondary options. However, resistance to these alternatives has been reported in various regions worldwide.

OBJECTIVE

To determine the prevalence, associated risk-factors and antimicrobial resistance of Campylobacter jejuni and C. coli among under-five children with diarrhea.

METHODS

Institution-based cross-sectional study was conducted from November, 2022 to April 2023. The study sites were selected using a random sampling technique, while the study subjects were included using a convenient sampling technique. The data were collected using a structured questionnaire. Stool samples were inoculated onto modified charcoal cefoperazone deoxycholate agar and incubated for 48 hours. The suspected colonies were analyzed using matrix-assisted laser desorption ionization-time of flight mass spectrometry to confirm the species. Antimicrobial susceptibility testing was performed using a disc diffusion technique. All potential covariates (independent variables) were analyzed one by one using bivariate logistic regression model to identify candidate variables with P value < 0.25. Multivariable logistic analysis was used to identify potential associated factors using the candidate variables. A p value ≤ 0.05 at a 95% confidence interval was statistically significant.

RESULT

Among the 428 samples, 7.0% (CI: 4.5-9.3) were confirmed Campylobacter species. The prevalence of C. jejuni and C. coli among under-five children was 5.1% (CI: 3.0-7.0) and 1.9% (CI: 0.7-3.3), respectively. C. jejuni (73.3%) was dominant over C. coli (26.7%). The resident, contact with domestic animals, and parents/guardians education level were significantly associated with campylobacteriosis among under-five children. One-third of the Campylobacter isolates (33.3%, 10/30) were resistant to ciprofloxacin and tetracycline whereas 10.0% (3/30) were resistant to erythromycin. Furthermore, 3.3% (1/30) of the Campylobacter were found to be multidrug-resistant.

CONCLUSION

The prevalence of Campylobacter species was 7.0%. The resistance rate of Campylobacter species of ciprofloxacin and tetracycline-resistance strains was 33.3%. Peri-urban residence, contact with domestic animals, and low parental educational statuses were significantly associated factors with increased risk of Campylobacter infection. Continuous surveillance on antimicrobial resistance and health education of personal and environmental hygiene should be implemented in the community.

Short Variable Regions flaA Gene (SVR-flaA) Diversity and Virulence Profile of Multidrug-Resistant Campylobacter from Poultry and Poultry Meat in India

Human gastrointestinal infections caused by Campylobacter species is the second most important foodborne illness after salmonellosis worldwide. Poultry represent one of the main sources of Campylobacter organisms. In the present study, the short variable region of flagellin gene (SVR-flaA) typing was carried out to determine the variation among the circulating strains of Campylobacter jejuni and Campylobacter coli. The C. jejuni and C. coli isolated from poultry and poultry meat were screened for the presence of virulence determinants like cadF, flaA, cdtB, and wlaN gene. The screening for wlaN gene is crucial in view of the fact that most patients with Guillian Barre's (GB) syndrome with a preceding history of diarrheal illness have been found to harbor wlaN gene-positive C jejuni strains. Out of the 200 samples comprising poultry meat and cloacal swabs, 21.5% of samples were found to harbor Campylobacter spp. of which 2.5% were Campylobacter jejuni, and 19% were confirmed as Campylobacter coli. The cadF, flaA, cdtB virulence genes were detected in all the Campylobacter spp. isolated in the present study. The presence of the wlaN gene in the Campylobacter jejuni isolated in the present study may pose a public health threat with long-term human health implications. The SVR-flaA typing of twelve Campylobacter isolates obtained in the present study revealed that Campylobacter coli flaA sequence OL471375 is a new strain with a novel allele type 1,675 and peptide sequence 5 which stands deposited in pubMLST database for Campylobacter. The other flaA-SVR gene sequences identified in this study were OL471369, OL471370, OL471371, OL471372, OL471373, and OL471374. Among twelve Campylobacter spp., three distinct DdeI-RFLP patterns were observed, each varying in size from 100 to 1,000 base pairs. Antimicrobial profiling of the Campylobacter spp. isolated in the present study revealed that 50% of the strains were multidrug resistant. All the Campylobacter spp. were resistant to ciprofloxacin (CIP), ampicillin (AMP), penicillin (PEN), and nalidixic acid (NAL) whereas 57.1% of strains were resistant to tetracycline (TET) and erythromycin (ERY) 28% to amoxicillin (AMX) and enrofloxacin (ENO), 85% to amikacin (AMK). The high degree of resistance to fluoroquinolones observed in the present study is crucial in view of fluoroquinolones being drugs of choice for the treatment of human Campylobacter infections.

Emergence of Plasmid-Mediated Quinolone Resistance (PMQR) Genes in Campylobacter coli in Tunisia and Detection of New Sequence Type ST13450

The aim of this study is to investigate the occurrence of plasmid mediated quinolone resistance (PMQR) determinants in Campylobacter coli isolates collected from broilers, laying hens and poultry farm environments. One hundred and thirty-nine C. coli isolates were isolated from broilers (n = 41), laying hens (n = 53), eggs (n = 4) and the environment (n = 41) of 23 poultry farms located in northeastern of Tunisia. Antimicrobial susceptibility testing was performed on all isolates according to the recommendation of the European Committee on Antimicrobial Susceptibility Testing guidelines. The detection of PMQR genes: qnrA, qnrB, qnrC, qnrD, qnrS, qepA, and aac(6)-Ib gene was performed using polymerase chain reaction (PCR) and specific primers. aac(6')-Ib amplicons were further analyzed by digestion with BtsCI to identify the aac(6')-Ib-cr variant. Mutations in GyrA and the occurrence of RE-CmeABC efflux pump were determined by mismatch amplification mutation assay (MAMA) PCR and PCR, respectively. In addition, eleven isolates were selected to determine their clonal lineage by MLST. The 139 C. coli isolates were resistant to ciprofloxacin, and 86 (61.8%) were resistant to nalidixic acid. High rates of resistance were also observed toward erythromycin (100%), azithromycin (96.4%), tetracycline (100%), chloramphenicol (98.56%), ampicillin (66.1%), amoxicillin-clavulanic acid (55.39%), and kanamycin (57.55%). However, moderate resistance rates were observed for gentamicin (9.35%) and streptomycin (22.3%). All quinolone-resistant isolates harbored the Thr-86-Ile amino acid substitution in GyrA, and the RE-CmeABC efflux pump was detected in 40.28% of isolates. Interestingly, the qnrB, qnrS, qepA, and aac(6')-Ib-cr were detected in 57.7%, 61.15%, 21.58%, and 10% of isolates, respectively. The eleven isolates studied by MLST belonged to a new sequence type ST13450. This study described for the first time the occurrence of PMQR genes in C. coli isolates in Tunisia and globally.

Survival Time of Campylobacter jejuni in Broiler Crops

Lactobacillus spp. inhibit the growth of Campylobacter spp. in vitro. However, in chicken crops, in which Lactobacillus spp. predominate, such inhibition of Campylobacter has not been confirmed. In our previous study, feeding paddy rice to broiler chicks increased the residence time of the food, which might enhance the bactericidal activity of the crop. Here, the bactericidal activity against the remaining Campylobacter spp. in broiler crops was evaluated. A suspension prepared by mixing Campylobacter jejuni and titanium dioxide (TiO2) was inoculated into the pharynx of 26-day-old broiler chicks fed a paddy rice-based diet. The crop contents were sampled at 20-min intervals. The TiO2 residual ratio in the crop gradually decreased with time after inoculation, with 57% of the inoculated TiO2 remaining in the crop 60 min after inoculation. The survival fraction of C. jejuni in the crops was 11% at 40 min, only 1% at 60 min, and was undetectable at 80 min. Most of the inoculated C. jejuni died in the crop before entering the next segment. These data indicated that bacterial death occurred between 30 min and 40 min after inoculation. The average survival time of C. jejuni in the crop was calculated to be 37.1 min. Thus, C. jejuni remaining in a chicken crop for more than 40 min died.

Campylobacteriosis and Control Strategies against Campylobacters in Poultry Farms

Campylobacteriosis is a significant foodborne illness caused by Campylobacter bacteria. It is one of the most common bacterial causes of gastroenteritis worldwide, with poultry being a major reservoir and source of infection in humans. In poultry farms, Campylobacters colonize the intestinal tract of chickens and contaminate meat during processing. Vaccines under development against Campylobacters in poultry showed partial or no protection against their cecal colonization. Therefore, this review will elaborate on campylobacteriosis and emphasize the control strategies and recent vaccine trials against Campylobacters in poultry farms. The epidemiology, diagnosis, and treatment of Campylobacter infection, along with specific mention of poultry Campylobacter contamination events in Malaysia, will also be discussed.

Campylobacter gastroenteritis and bacteremia in an asplenic patient with a recent history of Yersinia Enterocolitis: Case report and literature review

In this case report, we present a patient with a history of splenectomy and two recent hospital admissions for severe gastroenteritis with sepsis. The first hospital admission was for Yersinia enterocolitica and the second admission was for Campylobacter fetus gastroenteritis with bacteremia. During both admissions, the patient was treated with a prolonged course of antibiotics and later discharged with full recovery. In our review, we address the risk of enterocolitis in splenectomized patients.

Investigation of Potential Gut Health Biomarkers in Broiler Chicks Challenged by Campylobacter jejuni and Submitted to a Continuous Water Disinfection Program

The exploration of novel biomarkers to assess poultry health is of paramount importance, not only to enhance our understanding of the pathogenicity of zoonotic agents but also to evaluate the efficacy of novel treatments as alternatives to antibiotics. The present study aimed to investigate potential gut health biomarkers in broiler chicks challenged by Campylobacter jejuni and subjected to a continuous water disinfection program. A total of 144 one-day-old hatched broiler chicks were randomly allocated to four treatment groups with four replicates each, according to the following experimental design: Group A received untreated drinking water; Group B received drinking water treated with 0.01-0.05% v/v Cid 2000™ (hydrogen peroxide, acetic acid and paracetic acid); Group C was challenged by C. jejuni and received untreated drinking water; and Group D was challenged by C. jejuni and received drinking water treated with 0.01-0.05% v/v Cid 2000™. The use of Cid 2000™ started on day 1 and was applied in intervals until the end of the experiment at 36 days, while the C. jejuni challenge was applied on day 18. Potential biomarkers were investigated in serum, feces, intestinal tissue, intestinal content, and liver samples of broilers. Statistical analysis revealed significant increases (p < 0.001) in serum cortisol levels in C. jejuni-challenged broilers. Serum fluorescein isothiocyanate dextran (FITC-d) increased significantly (p = 0.004) in broilers challenged by C. jejuni and treated with drinking water disinfectant, while fecal ovotransferrin concentration also increased significantly (p < 0.001) in broilers that received the drinking water disinfectant alone. The gene expression levels of occludin (p = 0.003) and mucin-2 (p < 0.001) were significantly upregulated in broilers challenged by C. jejuni, while mucin-2 significantly increased in birds that were challenged and received the drinking water disinfectant (p < 0.001). TLR-4 expression levels were significantly (p = 0.013) decreased in both groups that received the drinking water disinfectant, compared to the negative control group. Finally, the C. jejuni challenge significantly increased (p = 0.032) the crypt depth and decreased (p = 0.021) the villus height-to-crypt-depth ratio in the ileum of birds, while the tested disinfectant product increased (p = 0.033) the villus height in the jejunum of birds. Furthermore, the counts of C. jejuni in the ceca of birds (p = 0.01), as well as its translocation rate to the liver of broilers (p = 0.001), were significantly reduced by the addition of the water disinfectant. This research contributes to novel insights into the intricate interplay of water disinfection and/or C. jejuni challenge with potential intestinal biomarkers. In addition, it emphasizes the need for continued research to unveil the underlying mechanisms, expands our understanding of broiler responses to these challenges and identifies breakpoints for further investigations.

Prediction of edapho-climatic parameters in the incidence of Campylobacter spp. in northwestern Mexico

Campylobacter spp. is one of the main causes of enteric zoonotic infections worldwide. In Mexico, although a commonly detected pathogen in both children and adults, there is limited surveillance and few studies. The northern part of Mexico stands out for an unnoticed outbreak of Campylobacter jejuni due to contaminated drinking water, which caused an abrupt increase in Guillain-Barré syndrome in the local population. Although it is suggested that its distribution in nature is related to edaphic and climatic factors, this relationship is scarcely known. To understand abiotic factors driving the occurrence and prevalence of Campylobacter spp. in three municipalities from three states in northwestern Mexico (Chihuahua, Sonora, and Baja California), we used the kriging interpolation method of unsampled areas and the correspondence analysis of 23 environmental variables. Of the three municipalities evaluated, Janos in Chihuahua (CHIH), has the highest number of geographic areas classified as high and medium incidence, followed by Santa Cruz, Sonora (SON) and Mexicali, Baja California (BC). Mexicali (BC) edaphic variables limit the potential incidence of the bacterium, mainly due to the lack of soil moisture and its difficulty of surviving on dry surfaces, related to electrical conductivity and salinity. Janos (CHIH) presents limitations in terms of soil water availability, although its presence is more heterogeneous (2 to 8 months). Santa Cruz (SON) has the highest soil water availability (4 to 5 months), and presents pH, texture and low percentage of salinity conditions for the potential incidence of Campylobacter spp. Mexicali (BC) reports a temperature in the warmest month of up to 43°C, which could influence the presence of thermophilic species. The annual precipitation is another limiting factor for the potential incidence of Campylobacter spp. since it does not exceed 509.5 mm, contributing to Janos (CHIH) as the municipality with the highest potential incidence of this bacterium.

Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria

Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.

Identification of novel small molecule inhibitors of twin arginine translocation (Tat) pathway and their effect on the control of Campylobacter jejuni in chickens

Introduction

Control of Campylobacter from farm to fork is challenging due to the frequent emergence of antimicrobial-resistant isolates. Furthermore, poultry production systems are known reservoirs of Campylobacter. The twin-arginine translocation (Tat) pathway is a crucial bacterial secretion system that allows Campylobacter to colonize the host intestinal tract by using formate as the main source of energy. However, Tat pathway is also a major contributing factor for resistance to copper sulfate (CuSO4).

Methods

Since mammals and chickens do not have proteins or receptors that are homologous to bacterial Tat proteins, identification of small molecule (SM) inhibitors targeting the Tat system would allow the development of safe and effective control methods to mitigate Campylobacter in infected or colonized hosts in both pre-harvest and post-harvest. In this study, we screened 11 commercial libraries (n = 50,917 SM) for increased susceptibility to CuSO4 (1 mM) in C. jejuni 81-176, a human isolate which is widely studied.

Results

Furthermore, we evaluated 177 SM hits (2.5 μg/mL and above) that increased the susceptibility to CuSO4 for the inhibition of formate dehydrogenase (Fdh) activity, a Tat-dependent substrate. Eight Tat-dependent inhibitors (T1-T8) were selected for further studies. These selected eight Tat inhibitors cleared all tested Campylobacter strains (n = 12) at >10 ng/mL in the presence of 0.5 mM CuSO4in vitro. These selected SMs were non-toxic to colon epithelial (Caco-2) cells when treated with 50 μg/mL for 24 h and completely cleared intracellular C. jejuni cells when treated with 0.63 μg/mL of SM for 24 h in the presence of 0.5 mM of CuSO4. Furthermore, 3 and 5-week-old chicks treated with SM candidates for 5 days had significantly decreased cecal colonization (up to 1.2 log; p < 0.01) with minimal disruption of microbiota. In silico analyses predicted that T7 has better drug-like properties than T2 inhibitor and might target a key amino acid residue (glutamine 165), which is located in the hydrophobic core of TatC protein.

Discussion

Thus, we have identified novel SM inhibitors of the Tat pathway, which represent a potential strategy to control C. jejuni spread on farms.

The Transmission of Campylobacter Strains in Dairy Herds in Different Housing Systems

Cattle are frequent carriers of Campylobacter spp.; therefore, these bacteria may be transmitted to humans through meat or milk. Campylobacter spp. in raw milk derives most commonly from secondary fecal contamination during the milking process; however, the udder excretion of Campylobacter may be a cause of milk-borne infection. Studies were carried out on a Campylobacter-positive farm with two different housing systems (with free-stall and tie-stall systems). The sampling process comprised several stages, including samples being taken from animals, such as from raw milk and feces, and from the environment, such as the from floor in the milking parlor and from teat cups. None of the individual raw milk samples or swabs from the floor in the parlor before the milking process were positive for Campylobacter spp. Simultaneously, Campylobacter spp. was isolated from all swabs from the floor after the milking process and in the bulk tank milk samples from the two farms. The incidence of Campylobacter isolated from fecal and teat swab samples ranged from 15.4% to 26.7% and from 8.9% to 25%, respectively. Altogether, 59 recovered Campylobacter isolates were classified, based on sequencing of the flaA short variable region, showing 15 different allele types, and the majority of them were distributed among one farm. Analysis of the virulence and antimicrobial properties showed that genes related to adherence, invasion and cytotoxicity were widely distributed among the Campylobacter recovered strains. In relation to AMR, multidrug resistance was noted in 16.1% of strains.

Microbial Metabolite Trimethylamine N-Oxide Promotes Campylobacter jejuni Infection by Escalating Intestinal Inflammation, Epithelial Damage, and Barrier Disruption

The interactions between Campylobacter jejuni , a critical foodborne cause of gastroenteritis, and the intestinal microbiota during infection are not completely understood. The crosstalk between C. jejuni and its host is impacted by the gut microbiota through mechanisms of competitive exclusion, microbial metabolites, or immune response. To investigate the role of gut microbiota on C. jejuni pathogenesis, we examined campylobacteriosis in the IL10KO mouse model, which was characterized by an increase in the relative abundance of intestinal proteobacteria, E. coli , and inflammatory cytokines during C. jejuni infection. We also found a significantly increased abundance of microbial metabolite Trimethylamine N-Oxide (TMAO) in the colonic lumens of IL10KO mice. We further investigated the effects of TMAO on C. jejuni pathogenesis. We determined that C. jejuni senses TMAO as a chemoattractant and the administration of TMAO promotes C. jejuni invasion into Caco-2 monolayers. TMAO also increased the transmigration of C. jejuni across polarized monolayers of Caco-2 cells, decreased TEER, and increased C. jejuni -mediated intestinal barrier damage. Interestingly, TMAO treatment and presence during C. jejuni infection of Caco-2 cells synergistically caused an increased inflammatory cytokine expression, specifically IL-1β and IL-8. These results establish that C. jejuni utilizes microbial metabolite TMAO for increased virulence during infection.

Identification and functional characterization of putative ligand binding domain(s) of JlpA protein of Campylobacter jejuni

Among the major Surface Exposed Colonization Proteins (SECPs) of Campylobacter jejuni (C. jejuni), Jejuni lipoprotein A (JlpA) plays a crucial role in host cell adhesion specifically by binding to the N-terminal domain of the human heat shock protein 90α (Hsp90α-NTD). Although the JlpA binding to Hsp90α activates NF-κB and p38 MAP kinase pathways, the underlying mechanism of JlpA association with the cellular receptor remains unclear. To this end, we predicted two potential receptor binding sites within the C-terminal domain of JlpA: one spanning from amino acid residues Q332-A354 and the other from S258-T295; however, the latter exhibited weaker binding. To assess the functional attributes of these predicted sequences, we generated two JlpA mutants (JlpAΔ1: S258-T295; JlpAΔ2: Q332-A354) and assessed the Hsp90α-binding affinity-kinetics by in vitro and ex vivo experiments. Our findings confirmed that the residues Q332-A354 are of greater importance in host cell adhesion with a measurable impact on cellular responses. Further, thermal denaturation by circular dichroism (CD) confirmed that the reduced binding affinity of the JlpAΔ2 to Hsp90α is not associated with protein folding or stability. Together, this study provides a possible framework for determining the molecular function of designing rational inhibitors efficiently targeting JlpA.

The antibacterial mechanism of (-)-epigallocatechin-3-gallate (EGCG) against Campylobacter jejuni through transcriptome profiling

(-)-Epigallocatechin-3-gallate (EGCG) has been shown antibacterial activity against Campylobacter jejuni; however, the relevant antibacterial mechanism is unknown. In this study, phenotypic experiments and RNA sequencing were used to explore the antibacterial mechanism. The minimum inhibitory concentration of EGCG on C. jejuni was 32 µg/mL. EGCG-treated was able to increase intracellular reactive oxygen species levels and decline bacterial motility. The morphology and cell membrane of C. jejuni after EGCG treatment were observed collapsed, broken, and agglomerated by field emission scanning electron microscopy and fluorescent microscopy. The RNA-seq analysis presents that there are 36 and 72 differential expressed genes after C. jejuni was treated by EGCG with the concentration of 16 and 32 µg/mL, respectively. EGCG-treated increased the thioredoxin expression, which was a critical protein to resist oxidative stress. Moreover, downregulation of the flgH and flgM gene in flagellin biosynthesis of C. jejuni was able to impair the flagella, reducing cell motility and virulence. The primary antibacterial mechanism revealed by RNA-seq is that EGCG with iron-chelating activity competes with C. jejuni for iron, causing iron deficiency in C. jejuni, which potentially impacts the survival and virulence of C. jejuni. The results suggested a new direction for exploring the activity of EGCG against C. jejuni in the food industry. PRACTICAL APPLICATION: A deeper understanding of the antibacterial mechanism of EGCG against C. jejuni was more beneficial in improving the food safety, eliminating concerns about human health caused by C. jejuni in future food, and promoting the natural antibacterial agent EGCG application in the food industry.

Campylobacter jejuni extracellular vesicles harboring cytolethal distending toxin bind host cell glycans and induce cell cycle arrest in host cells

Cytolethal distending toxins (CDTs) are released by Gram-negative pathogens into the extracellular medium as free toxin or associated with extracellular vesicles (EVs), commonly known as outer membrane vesicles (OMVs). CDT production by the gastrointestinal pathogen Campylobacter jejuni has been implicated in colorectal tumorigenesis. Despite CDT being a major virulence factor for C. jejuni, little is known about the EV-associated form of this toxin. To address this point, C. jejuni mutants lacking each of the three CDT subunits (A, B, and C) were generated. C. jejuni cdtA, cdtB, and cdtC bacteria released EVs in similar numbers and sizes to wild-type bacteria, ranging from 5 to 530 nm (mean ± SEM = 118 ±6.9 nm). As the CdtAC subunits mediate toxin binding to host cells, we performed "surface shearing" experiments, in which EVs were treated with proteinase K and incubated with host cells. These experiments indicated that CDT subunits are internal to EVs and that surface proteins are probably not involved in EV-host cell interactions. Furthermore, glycan array studies demonstrated that EVs bind complex host cell glycans and share receptor binding specificities with C. jejuni bacteria for fucosyl GM1 ganglioside, P1 blood group antigen, sialyl, and sulfated Lewisx. Finally, we show that EVs from C. jejuni WT but not mutant bacteria induce cell cycle arrest in epithelial cells. In conclusion, we propose that EVs are an important mechanism for CDT release by C. jejuni and are likely to play a significant role in toxin delivery to host cells.

IMPORTANCE

Campylobacter jejuni is the leading cause of foodborne gastroenteritis in humans worldwide and a significant cause of childhood mortality due to diarrheal disease in developing countries. A major factor by which C. jejuni causes disease is a toxin, called cytolethal distending toxin (CDT). The biology of this toxin, however, is poorly understood. In this study, we report that C. jejuni CDT is protected within membrane blebs, known as extracellular vesicles (EVs), released by the bacterium. We showed that proteins on the surfaces of EVs are not required for EV uptake by host cells. Furthermore, we identified several sugar receptors that may be required for EV binding to host cells. By studying the EV-associated form of C. jejuni CDT, we will gain a greater understanding of how C. jejuni intoxicates host cells and how EV-associated CDT may be used in various therapeutic applications, including as anti-tumor therapies.

Epoxide-Mediated Trans-Thioglycosylation and Application to the Synthesis of Oligosaccharides Related to the Capsular Polysaccharides of C. jejuni HS:4

The enzyme-resistant thioglycosides are highly valuable immunogens because of their enhanced metabolic stability. We report the first synthesis of a family of thiooligosaccharides related to the capsular polysaccharides (CPS) of Campylobacter jejuni HS:4 for potential use in conjugate vaccines. The native CPS structures of the pathogen consist of a challenging repeating disaccharide formed with β(1→4)-linked 6-deoxy-β-D-ido-heptopyranoside and N-acetyl-D-glucosamine; the rare 6-deoxy-ido-heptopyranosyl backbone and β-anomeric configuration of the former monosaccharide makes the synthesis of this family of antigens very challenging. So far, no synthesis of the thioanalogs of the CPS antigens have been reported. The unprecedented synthesis presented in this work is built on an elegant approach by using β-glycosylthiolate as a glycosyl donor to open the 2,3-epoxide functionality of pre-designed 6-deoxy-β-D-talo-heptopyranosides. Our results illustrated that this key trans-thioglycosylation can be designed in a modular and regio and stereo-selective manner. Built on the success of this novel approach, we succeeded the synthesis of a family of thiooligosaccharides including a thiohexasaccharide which is considered to be the desired antigen length and complexity for immunizations. We also report the first direct conversion of base-stable but acid-labile 2-trimethylsilylethyl glycosides to glycosyl-1-thioacetates in a one-pot manner.

Analysis of two cross-contamination cases of Campylobacter jejuni foodborne disease in fragile subjects in the territory of a Local Health Authority in Tuscany, Italy

Campylobacteriosis is the most reported foodborne disease in the European Union, with more than 100,000 confirmed cases annually. Human infection can be caused by a low infectious dose, and in fragile populations, the food disease can manifest itself in acute and severe forms. This study aims to analyze two cases of campylobacteriosis in fragile people caused by Campylobacter jejuni in 2023 in Tuscany and the actions of the Local Health Competent Authority. From the results of the related investigations, it was possible to attribute both cases of foodborne diseases to unsafe food management during preparation/administration. Given the peculiar characteristics of the etiological agent, it is necessary to focus the attention of the population, especially those who deal with fragile subjects, on the good hygiene practices to be followed both at home and in collective catering.

Overview of Ecology and Aspects of Antibiotic Resistance in Campylobacter spp. Isolated from Free-Grazing Chicken Tissues in Rural Households

Rural households all over the world rear backyard chicken mainly for their own consumption and, to a lesser extent, for barter trade. These chickens represent a staple dish with numerous culinary variations and a cheap source of protein. Although some Campylobacter species, and particularly Campylobacter jejuni and Campylobacter coli, have been associated with industrial poultry carcasses, studies concerning the ecology of this genus in rural households do not exist. To assess the prevalence of Campylobacter species in the tissues of backyard chickens, samples were collected from birds Gallus domesticus bred in households in the rural area of Epirus (Greece), and Campylobacter strains were isolated by quantitative methods at 37 °C and 42 °C. In total, 256 strains were identified, belonging to 17 Campylobacter species, with C. jejuni and C. coli being the most prevalent. From the four ecological parameters studied (size of the flock, presence of small ruminants in the same household, presence of other poultry species in the same household, and feeding leftovers of the household), the size of the flock and the presence of small ruminants and/or pigs in the same household mostly affected the distribution of these strains. To study the phenotypical resistance against 14 antibiotics, 215 strains were selected. The results showed a high prevalence of multidrug-resistance (MDR) strains extending to all classes of antibiotics. Further genome analysis revealed the presence of genes coding resistance (blaOxA-61, tet(O), tet(A) cmeA, cmeB, cmeC, and gyrA (Thr-86-Ile mutation)), with the efflux pump CmeABC being the most prevalent. All antimicrobial resistance-encoded genes co-circulated, except for blaOXA-61, which moved independently. The minimum inhibitory concentration (MIC) values of two out of three antibiotics (representing different classes) were reduced when the strains tested were exposed to carbonyl cyanide 3-chlorophenylhydrazone (CCCP), a known efflux pump inhibitor. The same result was obtained with the addition of CCCP to the MIC values of bile salts. These results lead to the conclusion that Campylobacter species are present in an impressive diversity in backyard chicken tissues and that they exert a significant resistance to antibiotics, raising a potential danger for public health.

Integrating meta-analysis with a quantitative microbial risk assessment model to investigate Campylobacter contamination of broiler carcasses

This study investigated the prevalence and associated risk factors of Campylobacter in South Korean broilers using a random-effects meta-analysis. Subsequently, to facilitate the design of preventive measures, the prevalence estimate from the meta-analysis was incorporated into a stochastic risk assessment model to quantify the Campylobacter contamination levels on broiler carcasses. The baseline model was developed based on the most common practices along the South Korean broiler processing line, with no interventions. Meta-analysis results revealed Campylobacter prevalence across the chicken supply chain in the following order: farms (60.6 % [57.3-63.4]), retail markets (43.90 % [24.81-64.99]), slaughterhouses (27.71 % [18.56-39.21]), and processing plants (14.50 % [3.96-41.09]). The model estimated a 52 % (36.1-70.8) Campylobacter prevalence at the end of chilling, with an average contamination level of 4.62 (2.50-6.74) log CFU/carcass. Sensitivity analysis indicated that Campylobacter fecal shedding (r = 0.95) and the amount of feces on bird exteriors (r = 0.17) at pre-harvest were the main factors for carcass contamination, while soft scalding (r = -0.22) and air chilling (r = -0.12) can serve as critical control points (CCPs) at harvest. Scenario analysis indicated that a combination of hard scalding, inside-outside bird washing, spray washing, and chlorinated water immersion chilling can offer a 30.9 % reduction in prevalence and a reduction of 2.23 log CFU/carcass in contamination levels compared to the baseline model. Apart from disinfection and sanitation interventions carried out during meat processing, the implementation of robust control measures is indispensable to mitigate Campylobacter prevalence and concentration at broiler farms, thereby enhancing meat safety and public health. Furthermore, given the high Campylobacter prevalence in the retail markets, future studies should explore the potential risk of cross-contamination at post-harvest stage.

A hybrid receptor binding protein enables phage F341 infection of Campylobacter by binding to flagella and lipooligosaccharides

Flagellotropic bacteriophages are interesting candidates as therapeutics against pathogenic bacteria dependent on flagellar motility for colonization and causing disease. Yet, phage resistance other than loss of motility has been scarcely studied. Here we developed a soft agar assay to study flagellotropic phage F341 resistance in motile Campylobacter jejuni. We found that phage adsorption was prevented by diverse genetic mutations in the lipooligosaccharides forming the secondary receptor of phage F341. Genome sequencing showed phage F341 belongs to the Fletchervirus genus otherwise comprising capsular-dependent C. jejuni phages. Interestingly, phage F341 encodes a hybrid receptor binding protein (RBP) predicted as a short tail fiber showing partial similarity to RBP1 encoded by capsular-dependent Fletchervirus, but with a receptor binding domain similar to tail fiber protein H of C. jejuni CJIE1 prophages. Thus, C. jejuni prophages may represent a genetic pool from where lytic Fletchervirus phages can acquire new traits like recognition of new receptors.

Immunoinformatics-driven approach for development of potential multi-epitope vaccine against the secreted protein FlaC of Campylobacter jejuni

Campylobacter jejuni causes a leading human gastrointestinal infection which is associated with foodborne diarrhea, stomach cramping, and fever. In the recent years, numerous multidrug-resistant strains of C. jejuni has evolved and is considered in the priority pathogens category. Therefore, an increasing demand exists to develop an effective vaccine against Campylobacteriosis. The T cell and B cell epitopes from the FlaC protein were predicted using comprehensive immunoinformatics tools. The predicted epitopes were chosen based on their antigenicity, allergenicity, and toxicity profiles. Using the bioinformatics approach various physicochemical properties of the constructed vaccine were determined. The molecular docking analysis of the vaccine with the TLRs demonstrated that TLR5 has a higher binding affinity of -1159.0 kcal/mol. Molecular dynamics simulation has confirmed the stable association of the vaccine with TLR5. The immune response of the constructed vaccine was validated using immunostimulation. Based on this study, we recommend the formulation of a multi-epitope vaccine as a promising agent to effectively combat the dreadful campylobacteriosis infection.Communicated by Ramaswamy H. Sarma.

Whole Genome Sequences, De Novo Assembly, and Annotation of Antibiotic Resistant Campylobacter jejuni Strains S27, S33, and S36 Newly Isolated from Chicken Meat

Campylobacter is a leading bacterial cause of gastrointestinal infections in humans and has imposed substantial medical and public health burdens worldwide. Among a total of 39 species in the Campylobacter genus, C. jejuni is the most important species responsible for approx. 90% of human Campylobacter illness. Most cases of the infection were acquired by ingesting undercooked poultry meat due to the high prevalence of Campylobacter in the products. Here, we reported the dataset of raw sequences, de novo assembled and annotated genomes of C. jejuni strains S27, S33, and S36 recently isolated from retail chicken by using PacBio highly accurate long-read sequencing technology combined with bioinformatics tools. Our data revealed several virulence and antibiotic resistance genes in each of the chromosomes, a type IV secretion system in the plasmid (pCjS33) of C. jejuni S33, and a type VI secretion system and a phage in the plasmid (pCjS36) of C. jejuni S36. This study not only provides new sequence data but also extends the knowledge pertaining to the genomic and functional aspects of this important foodborne pathogen, including the genetic determinants of virulence and antibiotic resistance.

Infant diarrheal disease in rhesus macaques impedes microbiome maturation and is linked to uncultured Campylobacter species

Diarrheal diseases remain one of the leading causes of death for children under 5 globally, disproportionately impacting those living in low- and middle-income countries (LMIC). Campylobacter spp., a zoonotic pathogen, is one of the leading causes of food-borne infection in humans. Yet to be cultured Campylobacter spp. contribute to the total burden in diarrheal disease in children living in LMIC thus hampering interventions. We performed microbiome profiling and metagenomic genome assembly on samples collected from over 100 infant rhesus macaques longitudinally and during cases of clinical diarrhea within the first year of life. Acute diarrhea was associated with long-lasting taxonomic and functional shifts of the infant gut microbiome indicative of microbiome immaturity. We constructed 36 Campylobacter metagenomic assembled genomes (MAGs), many of which fell within 4 yet to be cultured species. Finally, we compared the uncultured Campylobacter MAGs assembled from infant macaques with publicly available human metagenomes to show that these uncultured species are also found in human fecal samples from LMIC. These data highlight the importance of unculturable Campylobacter spp. as an important target for reducing disease burden in LMIC children.

Design of dot-blot hybridization assay for simultaneous detection of Campylobacter jejuni and Campylobacter coli: a preliminary study

Objectives

Campylobacters are a major cause of gastroenteritis worldwide. These are fastidious in culture and false negative results are seen in many clinical laboratories. Among molecular methods, the dot-blot technique is widely used for a variety of purposes, especially diagnostics. So, the authors aimed to detect C. jejuni and C. coli simultaneously using a dot-blot assay.

Methods

After evaluating the bioinformatics studies, a cadF-conserved fragment was selected for the design of primers and probe. DNAs from standard strains and a recombinant plasmid, prepared in this study, were used to assess the technique. The specificity of the method was also surveyed using DNAs from other enteric bacteria. The limit of detection was evaluated by recombinant plasmid and different concentrations of the designed probe.

Results

A 95-bp fragment of cadF was selected, and in silico analysis studies showed that it is conserved between both species. Also, the non-specific annealing of the primers and probe with other bacteria was not seen theoretically. The technique with recombinant plasmid as well as DNAs of standard strains created black spots on the membrane, confirming that the probe was correctly synthesized. No non-specific reactions with other bacterial species were observed (specificity=100%). The limit of detection of the test was determined to be 50 µg/ml.

Conclusions

This is the first study to simultaneously detect two important pathogens in the Campylobacter genus and was able to detect C. jejuni and C. coli with acceptable sensitivity and specificity.

Animal and In Vitro Models as Powerful Tools to Decipher the Effects of Enteric Pathogens on the Human Gut Microbiota

Examining the interplay between intestinal pathogens and the gut microbiota is crucial to fully comprehend the pathogenic role of enteropathogens and their broader impact on human health. Valid alternatives to human studies have been introduced in laboratory practice to evaluate the effects of infectious agents on the gut microbiota, thereby exploring their translational implications in intestinal functionality and overall health. Different animal species are currently used as valuable models for intestinal infections. In addition, considering the recent advances in bioengineering, futuristic in vitro models resembling the intestinal environment are also available for this purpose. In this review, the impact of the main human enteropathogens (i.e., Clostridioides difficile, Campylobacter jejuni, diarrheagenic Escherichia coli, non-typhoidal Salmonella enterica, Shigella flexneri and Shigella sonnei, Vibrio cholerae, and Bacillus cereus) on intestinal microbial communities is summarized, with specific emphasis on results derived from investigations employing animal and in vitro models.

Global trends in antimicrobial resistance on organic and conventional farms

The important hypothesis that organic livestock management reduces the prevalence of antimicrobial resistance is either fiercely supported or bitterly contested. Yet, empirical evidence supporting this view remains fragmentary, in part because relationships between antimicrobial use and drug resistance vary dramatically across contexts, hosts, pathogens, and country-specific regulations. Here, we synthesize global policies and definitions of 'organic' and ask if organic farming results in notable reductions in the prevalence of antimicrobial resistance when directly examined alongside conventional analogs. We synthesized the results of 72 studies, spanning 22 countries and five pathogens. Our results highlight substantial variations in country-specific policies on drug use and definitions of 'organic' that hinder broad-scale and generalizable patterns. Overall, conventional farms had slightly higher levels of antimicrobial resistance (28%) relative to organic counterparts (18%), although we found significant context-dependent variation in this pattern. Notably, environmental samples from organic and conventional farms often exhibited high levels of resistance to medically important drugs, underscoring the need for more stringent and consistent policies to control antimicrobial contaminants in the soil (particularly on organic farms, where the application of conventional manure could faciliate the spread antimicrobial resistance). Taken together, these results emphasize the challenges inherent in understanding links between drug use and drug resistance, the critical need for global standards governing organic policies, and greater investment in viable alternatives for managing disease in livestock.

Metabolomic signatures of intestinal colonization resistance against Campylobacter jejuni in mice

Introduction

Campylobacter jejuni stands out as one of the leading causes of bacterial enteritis. In contrast to humans, specific pathogen-free (SPF) laboratory mice display strict intestinal colonization resistance (CR) against C. jejuni, orchestrated by the specific murine intestinal microbiota, as shown by fecal microbiota transplantation (FMT) earlier.

Methods

Murine infection models, comprising SPF, SAB, hma, and mma mice were employed. FMT and microbiota depletion were confirmed by culture and culture-independent analyses. Targeted metabolome analyses of fecal samples provided insights into the associated metabolomic signatures.

Results

In comparison to hma mice, the murine intestinal microbiota of mma and SPF mice (with CR against C. jejuni) contained significantly elevated numbers of lactobacilli, and Mouse Intestinal Bacteroides, whereas numbers of enterobacteria, enterococci, and Clostridium coccoides group were reduced. Targeted metabolome analysis revealed that fecal samples from mice with CR contained increased levels of secondary bile acids and fatty acids with known antimicrobial activities, but reduced concentrations of amino acids essential for C. jejuni growth as compared to control animals without CR.

Discussion

The findings highlight the role of microbiota-mediated nutrient competition and antibacterial activities of intestinal metabolites in driving murine CR against C. jejuni. The study underscores the complex dynamics of host-microbiota-pathogen interactions and sets the stage for further investigations into the mechanisms driving CR against enteric infections.

Impact of Season on Intestinal Bacterial Communities and Pathogenic Diversity in Two Captive Duck Species

Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4-V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds.

Virulence factors and antimicrobial resistance profiles of Campylobacter isolates recovered from consecutively reused broiler litter

IMPORTANCE

Campylobacter is a leading cause of foodborne illness in the United States due to consumption of contaminated or mishandled food products, often associated with chicken meat. Campylobacter is common in the microbiota of avian and mammalian gut; however, acquisition of antimicrobial resistance genes (ARGs) and virulence factors (VFs) may result in strains that pose significant threat to public health. Although there are studies investigating the genetic diversity of Campylobacter strains isolated from post-harvest chicken samples, there are limited data on the genome characteristics of isolates recovered from preharvest broiler production. Here, we show that Campylobacter jejuni and Campylobacter coli differ in their carriage of antimicrobial resistance and virulence factors may also differ in their ability to persist in litter during consecutive grow-out of broiler flocks. We found that presence/absence of virulence factors needed for evasion of host defense mechanisms and gut colonization played an integral role in differentiating Campylobacter strains.

Wastewater-based epidemiology of Campylobacter spp.: A systematic review and meta-analysis of influent, effluent, and removal of wastewater treatment plants

Campylobacter spp. is one of the four leading causes of diarrhoeal diseases worldwide, which are generally mild but can be fatal in children, the elderly, and immunosuppressed persons. The existing disease surveillance for Campylobacter infections is usually based on untimely clinical reports. Wastewater surveillance or wastewater-based epidemiology (WBE) has been developed for the early warning of disease outbreaks and the detection of the emerging new variants of human pathogens, especially after the global pandemic of COVID-19. However, the WBE monitoring of Campylobacter infections in communities is rare due to a few large data gaps. This study is a meta-analysis and systematic review of the prevalence of Campylobacter spp. in various wastewater samples, primarily the influent of wastewater treatment plants. The results showed that the overall prevalence of Campylobacter spp. was 53.26 % in influent wastewater and 52.97 % in all types of wastewater samples. The mean concentration in the influent was 3.31 ± 0.39 log10 gene copies or most probable number (MPN) per 100 mL. The detection method combining culture and PCR yielded the highest positive rate of 90.86 %, while RT-qPCR and qPCR were the two most frequently used quantification methods. In addition, the Campylobacter concentration in influent wastewater showed a seasonal fluctuation, with the highest concentration in the autumn at 3.46 ± 0.41 log10 gene copies or MPN per 100 mL. Based on the isolates of all positive samples, Campylobacter jejuni (62.34 %) was identified as the most prevalent species in wastewater, followed by Campylobacter coli (30.85 %) and Campylobacter lari (4.4 %). These findings provided significant data to further develop and optimize the wastewater surveillance of Campylobacter spp. infections. In addition, large data gaps were found in the decay of Campylobacter spp. in wastewater, indicating insufficient research on the persistence of Campylobacter spp. in wastewater.

Assessment of risk of exposure to Campylobacter species and their antibiotic-resistant genes from selected rivers in the Eastern Cape, South Africa

Contaminated rivers play a critical role in the transmission of Campylobacter and antibiotic-resistant genes (ARGs) in many parts of the world. South Africa is a water-scarce country which relies on its freshwater systems such as rivers for recreation, irrigation, and domestic activities. This study assesses the potential human exposure to Campylobacter and its ARGs from rivers through the ingestion route in two South African rivers. The concentration of viable Campylobacter and ARGs in selected rivers was determined using quantitative PCR. The concentrations were then used to estimate the number of gene copies a person could ingest after swimming in the contaminated water for 1 h (intake burden). The human intake burden of Campylobacter 16 S rRNA copies per 1-h swimming event ranged from 7.1 × 105-3.7 × 106 copies/h for the Bloukrans River, and 9.9 × 101-2.3 × 105 copies/h for the Swartkops River. The intake burden of Campylobacter ARGs ranged from 1.64 × 104-5.8 × 105 copies/h for cmeB; 1.0 × 103-5.7 × 104 copies/h for tetO for the Bloukrans River, and 3.6 × 102-1.551 × 105 copies/h (cmeB) and 9.98 × 102-5.7 × 104 copies/h (tetO) for the Swartkops River. Ingestion of water from contaminated rivers during recreation, cultural, or religious activities may lead to human exposure to ARGs, posing a health risk. In many communities in the world, rivers play an important role in the social and cultural lives of people, and so it is important to monitor the quality of river water. Studies such as these will help prevent the spread of antibiotic-resistant genes and waterborne diseases caused by pathogens such as Campylobacter.

Genotyping and antibiotic susceptibility of Campylobacter species isolated from raw milk samples in Qazvin, Iran

OBJECTIVE

Campylobacter species are major causes of foodborne illnesses, with unpasteurized milk being a significant carrier of these bacteria, posing a public health risk. One of the challenges in managing Campylobacter infections is the emergence and spread of antibiotic resistance. We conducted a study in Qazvin, Iran, testing 84 raw cow's milk samples to determine the frequency of C. jejuni and C. coli using culture-based and multiplex PCR methods. Additionally, the disk diffusion and RAPD-PCR approaches were utilized to evaluate the phenotypic antibiotic resistance profile and genetic diversity of Campylobacter strains.

RESULTS

The findings indicated that Campylobacter spp. was present in 19.05% of the samples, with C. coli being the predominant isolate. We tested eight antibiotic agents, and the resistance levels of the isolates were as follows: erythromycin 100%, tetracycline 75%, doxycycline 56.25%, ceftriaxone 43.75%, chloramphenicol 37.5%, amoxicillin-clavulanic acid 25%, nalidixic acid 12.5%, and azithromycin 6.25%. Genetic diversity analysis categorized Campylobacter isolates into 39 clusters, indicating a wide diversity among strains. However, no significant correlation was observed between antibiotic resistance and cluster patterns. These findings underscore the role of raw milk as a reservoir for Campylobacter spp. and highlight the substantial antibiotic resistance and genetic diversity within the species population.

A South African Perspective on the Microbiological and Chemical Quality of Meat: Plausible Public Health Implications

Meat comprises proteins, fats, vitamins, and trace elements, essential nutrients for the growth and development of the body. The increased demand for meat necessitates the use of antibiotics in intensive farming to sustain and raise productivity. However, the high water activity, the neutral pH, and the high protein content of meat create a favourable milieu for the growth and the persistence of bacteria. Meat serves as a portal for the spread of foodborne diseases. This occurs because of contamination. This review presents information on animal farming in South Africa, the microbial and chemical contamination of meat, and the consequential effects on public health. In South Africa, the sales of meat can be operated both formally and informally. Meat becomes exposed to contamination with different categories of microbes, originating from varying sources during preparation, processing, packaging, storage, and serving to consumers. Apparently, meat harbours diverse pathogenic microorganisms and antibiotic residues alongside the occurrence of drug resistance in zoonotic pathogens, due to the improper use of antibiotics during farming. Different findings obtained across the country showed variations in prevalence of bacteria and multidrug-resistant bacteria studied, which could be explained by the differences in the manufacturer practices, handling processes from producers to consumers, and the success of the hygienic measures employed during production. Furthermore, variation in the socioeconomic and political factors and differences in bacterial strains, geographical area, time, climatic factors, etc. could be responsible for the discrepancy in the level of antibiotic resistance between the provinces. Bacteria identified in meat including Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, Campylobacter spp., Salmonella spp., etc. are incriminated as pathogenic agents causing serious infections in human and their drug-resistant counterparts can cause prolonged infection plus long hospital stays, increased mortality and morbidity as well as huge socioeconomic burden and even death. Therefore, uncooked meat or improperly cooked meat consumed by the population serves as a risk to human health.

Fecal Microbiota Transplantation Reduces Campylobacter jejuni Colonization in Young Broiler Chickens Challenged by Oral Gavage but Not by Seeder Birds

Campylobacter spp., particularly C. jejuni and C. coli, are major food safety concerns, transmitted to humans mainly via contaminated poultry meat. In a previous study, we found that some commercial broiler farms consistently produced Campylobacter-free flocks while others consistently reared Campylobacter-colonized flocks, and significant differences in the gut microbiota compositions between the two types of farm categories were revealed. Therefore, we hypothesized that gut microbiota influences Campylobacter colonization in poultry and that the microbiota from Campylobacter-free flocks may confer colonization resistance to Campylobacter in the chicken intestine. In this study, two fecal microbiota transplantation (FMT) trials were performed to test the hypothesis. Newly hatched chicks were given FMT via oral gavage of the cecal content of Campylobacter-free adult chickens (treatment groups) or PBS (control groups) before the feed consumption. Approximately two weeks after the FMT, the birds were challenged with C. jejuni either by oral gavage (trial 1) or by co-mingling with Campylobacter-colonized seeder birds (trial 2) to evaluate the potential protective effect of the FMT. Cecal contents were collected (3 times, 5 days apart) to determine the Campylobacter colonization levels via culture and microbiota compositions via 16S rRNA gene sequencing. FMT reduced cecal Campylobacter colonization significantly (log10 1.2-2.54 CFU/g) in trial 1 but not in trial 2, although FMT significantly impacted the diversity and compositions of the gut microbiota in both trials. Several genera, such as Butyricimonas, Parabacteroides, Parasutterella, Bilophila, Fournierella, Phascolarctobacterium, and Helicobacter, had increased abundance in the FMT-treated groups in both trials. Furthermore, Campylobacter abundance was found to be negatively correlated with the Escherichia and Ruminococcus_torques_group genera. These findings indicate that even though FMT with adult cecal microbiota can positively affect the subsequent development of the gut microbiota in young broilers, its inhibitory effect on Campylobacter colonization varies and appears to be influenced by the challenge models.

Therapeutic Effects of Oral Application of Menthol and Extracts from Tormentil (Potentilla erecta), Raspberry Leaves (Rubus idaeus), and Loosestrife (Lythrum salicaria) during Acute Murine Campylobacteriosis

Human food-borne infections with the enteropathogen Campylobacter jejuni are becoming increasingly prevalent worldwide. Since antibiotics are usually not indicated in campylobacteriosis, alternative treatment regimens are important. We here investigated potential disease-alleviating effects of menthol and of extracts from tormentil, raspberry leaves, and loosestrife in acute murine campylobacteriosis. Therefore, C. jejuni-infected microbiota-depleted IL-10-/- mice were orally treated with the compounds alone or all in combination from day 2 until day 6 post-infection. Whereas neither treatment regimen affected gastrointestinal pathogen loads, the combination of compounds alleviated C. jejuni-induced diarrheal symptoms in diseased mice on day 6 post-infection. Furthermore, the therapeutic application of tormentil and menthol alone and the combination of the four compounds resulted in lower colonic T cell numbers in infected mice when compared to placebo counterparts. Notably, pro-inflammatory cytokines measured in mesenteric lymph nodes taken from C. jejuni-infected mice following tormentil, menthol, and combination treatment did not differ from basal concentrations. However, neither treatment regimen could dampen extra-intestinal immune responses, including systemic pro-inflammatory cytokine secretion on day 6 post-infection. In conclusion, the combination of menthol and of extracts from tormentil, raspberry leaves, and loosestrife constitutes an antibiotic-independent approach to alleviate campylobacteriosis symptoms.

Prevalence and risk factors associated with the occurrence of Campylobacter sp. in children aged 6-24 months in peri-urban Nairobi, Kenya

Introduction

Campylobacter bacteria is a major cause of foodborne-related bacterial gastroenteritis in humans worldwide. It is known to cause diarrhea in young children which has been shown to directly affect their weight and height as a result of malnutrition. Severe cases of diarrhea can also lead to death. Most of the burden is experienced in resource-limited countries in Africa and Southeast Asia where the disease is linked to poor hygiene and sanitation. The objective of this study was to determine the prevalence of Campylobacter in children aged between 6 and 24 months in Nairobi, Kenya and identify potential risk factors associated with their occurrence.

Methods

A cross-sectional study was carried out between May to December 2021. A total of 585 randomly selected households were visited in two wards (Uthiru/Ruthimitu and Riruta) in Dagoretti South sub-county, Nairobi. A questionnaire regarding how children's food is handled, the major foods consumed, sanitation and hygiene, and animal ownership was conducted among caregivers to identify associated risk factors. Stool samples were collected from 540/585 children and screened for the presence of Campylobacter using culture-based methods and confirmed through PCR.

Results

Of the 540 children's stool samples processed, Campylobacter isolates were detected in 4.8% (26/540). Campylobacter jejuni (C. jejuni) was the most common species in 80.8% of positive samples compared to Campylobacter coli (C. coli) in 26.9% of samples. In six samples, both C. jejuni and C. coli were isolated, while in four samples, it was not possible to speciate the Campylobacter. Drinking cow's milk (OR 4.2, 95% CI 1.4 - 12.6) and the presence of animal feces in the compound (OR 3.4, 95% CI 1.1 - 10.3) were found to be statistically associated with Campylobacter carriage in children.

Discussion

The carriage of Campylobacter in children in this community indicates a need for further investigation on source attribution to understand transmission dynamics and inform where to target interventions. Awareness creation among caregivers on good personal and food hygiene is needed, including boiling milk before consumption. Implementation of biosecurity measures at the household level is highly recommended to reduce contact between animals and humans.

Phenotypic and Genomic Characteristics of Campylobacter gastrosuis sp. nov. Isolated from the Stomachs of Pigs in Beijing

Campylobacter is among the four main causes of gastroenteritis worldwide. Most reported Campylobacter infections are caused by C. jejuni and C. coli. However, other emerging Campylobacter pathogens have been recognized as important pathogens in humans and animals. A novel bacterial strain, PS10T, was isolated from the gastric mucous of pigs in 2022 in Beijing, China. The cell was Gram-negative, microaerobic, motile, and negative for catalase, oxidase, and urease. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and core genome indicated that this isolate belongs to the genus Campylobacter. There were low dDDH relatedness and ANI values shared within this strain and its closest species C. mucosalis below the cut-off values generally recognized for isolates of the same species. The draft genome size of PS10T is 2,240,910 bp in length with a percentage of DNA G+C contents of 37.72%. Comparing the phenotypic and phylogenetic features among this isolate and its related organisms, strain PS10T represents a novel species within the genus Campylobacter, for which the name Campylobacter gastrosuis sp. nov. (Type strain PS10T = GDMCC 1.3686T = JCM 35849T) is proposed.

Aerotolerance and Multi-Locus Sequence Typing of Campylobacter jejuni Isolated from Commercial Broiler Processing Plants

Campylobacter jejuni is one of the leading causes of acute diarrhea in the United States. Despite being a microaerophilic pathogen, C. jejuni continues to endure within the domain of food production, especially in poultry processing. Recent research on aerotolerance indicates that close monitoring of this pathogen is necessary. A total of 40 C. jejuni isolates previously obtained from commercial broiler processing plants were analyzed for aerotolerance and genetic diversity. In addition, the effect of aerotolerance and storage time (days) on the survival of C. jejuni on broiler drumsticks at refrigeration (4 °C) and freezing conditions (-20 °C) was also evaluated. Out of 40 isolates, 25 (62.5%) were aero-sensitive (AS), 10 (25%) were intermediately aerotolerant (IAT), and 5 (12.5%) were hyper aerotolerant (HAT). The isolates belonged to four clonal complexes (CCs) and six sequence types, with the majority of isolates assigned to the CC-353 clonal complex. C. jejuni counts were reduced by 0.40 log CFU/g after 7 days at 4 °C and by 1.50 log CFU/g after 14 days at -20 °C, respectively, irrespective of aerotolerance (p < 0.001). At both refrigeration (p < 0.013) and freezing (p < 0.001), HAT showed greater reductions as compared to AS and IAT. These findings suggest that both refrigeration and freezing reduce C. jejuni counts.

Porcine carcasses as an underestimated source of antimicrobial resistant Campylobacter coli

Introduction

Campylobacteriosis is the most common human foodborne bacterial infection worldwide and is caused by bacteria of the Camplylobacter genus. The main source of these bacteria is poultry, but other food-producing animals such as pigs are also responsible for human infections. An increasing number of strains with resistance to fluoroquinolones and other antimicrobials such as macrolides were recently noted. The aim of the study was to investigate Campylobacter contamination of porcine carcasses and determine the antimicrobial resistance of the obtained isolates.

Material and Methods

A total of 534 swabs from carcasses of pigs slaughtered in Poland during 2019-2022 were tested for Campylobacter spp.

Results

Campylobacter was detected in 164 (30.7%) carcasses; among them 149 (90.8%) were classified as C. coli and the remaining 15 (9.2%) samples were C. jejuni-positive. Because a low number of C. jejuni isolates were identified, only the C. coli isolates were subjected to antimicrobial resistance analysis. The majority of these isolates were resistant to streptomycin (94.0%), ciprofloxacin (65.8%) and tetracycline (65.1%). A total of 94 (63.1%) strains displayed antimicrobial multiresistance patterns and were mainly resistant to fluoroquinolones, aminoglycosides and tetracyclines (74; 49.7% of the isolates tested).

Conclusion

The obtained results showed that pig carcasses may be contaminated with antimicrobial-resistant C. coli.

Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients

During the COVID-19 pandemic, impaired immunity and medical interventions resulted in cases of secondary infections. The clinical difficulties and dangers associated with secondary infections in patients necessitate the exploration of their microbiome. Metaproteomics is a powerful approach to study the taxonomic composition and functional status of the microbiome under study. In this study, the mass spectrometry (MS)-based data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. We have established a robust bioinformatics workflow within the Galaxy platform, which includes (a) generation of a tailored database of the common respiratory tract pathogens, (b) database search using multiple search algorithms, and (c) verification of the detected microbial peptides. The microbial peptides detected in this study, belong to several opportunistic pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Rhizopus microsporus, and Syncephalastrum racemosum. Microbial proteins with a role in stress response, gene expression, and DNA repair were found to be upregulated in severe patients compared to negative patients. Using parallel reaction monitoring (PRM), we confirmed some of the microbial peptides in fresh clinical samples. MS-based clinical metaproteomics can serve as a powerful tool for detection and characterization of potential pathogens, which can significantly impact the diagnosis and treatment of patients.