An evaluation of five preservation techniques and conventional freezing temperatures of -20oC and -85oC for long-term preservation of Campylobacter jejuni

Addressing Challenges in Wildlife Rehabilitation: Antimicrobial-Resistant Bacteria from Wounds and Fractures in Wild Birds

Injuries and bone fractures are the most frequent causes of admission at wildlife rescue centers. Wild birds are more susceptible to open fractures due to their anatomical structure, which can lead to osteomyelitis and necrosis. Antibiotic therapy in these cases is indispensable, but the increase of antimicrobial-resistant isolates in wildlife has become a significant concern in recent years. In this context, the likelihood of antibiotic failure and death of animals with infectious issues is high. This study aimed to isolate, identify, and assess the antimicrobial resistance pattern of bacteria in wounds and open fractures in wild birds. To this end, injured birds admitted to a wildlife rescue center were sampled, and bacterial isolation and identification were performed. Then, antimicrobial susceptibility testing was assessed according to the disk diffusion method. In total, 36 isolates were obtained from 26 different birds. The genera detected were Staphylococcus spp. (63.8%), Escherichia (13.9%), Bacillus (11.1%), Streptococcus (8.3%), and Micrococcus (2.8%). Among Staphylococcus isolates, S. lentus and S. aureus were the most frequent species. Antimicrobial resistance was detected in 82.6% of the isolates, among which clindamycin resistance stood out, and 31.6% of resistant isolates were considered multidrug-resistant. Results from this study highlight the escalating scope of antimicrobial resistance in wildlife. This level of resistance poses a dual concern for wildlife: firstly, the risk of therapeutic failure in species of significant environmental value, and, secondly, the circulation of resistant bacteria in ecosystems.

Long-term preservation at low temperature of Escherichia coli cells embedded in egg white glass formed by slow drying at room temperature

Sterile homogeneous egg white (EW) is obtained through a three-step process, high-speed homogenization, centrifugation, and ultraviolet radiation. After incorporating 1.056 × 10¹⁰ CFU/g of Escherichia coli, the EW mixture was dehydrated by slow drying to form a brittle, water-soluble, and transparent bacteria-embedded egg white glass (BE-EWG). The BE-EWG stored at -20 °C for 4 months maintains almost all the cell growth functions and proliferation activities of the labeled E. coli, and most of the cell functions and 60 % of the proliferation activities are maintained for up to one year. The BE-EWG exhibits a porous hydrogel membrane structure after heat treatment, and many E. coli cells are accommodated in a grid with a pore size of 2-10 mm. The loss of bacteria-carrying viability after storage at room temperature may be related to the Maillard reaction between protein and glucose in EW, which results in the structural changes caused by protein cross-linking, darkened color and water insolubility of the BE-EWG. Therefore, the method of embedding E. coli cells in EWG as solid form at room temperature to avoid ice crystal formation during cryopreservation is more beneficial for storage, packaging and shipping at -20 °C.

Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds

As the world's leading cause of human gastro-enteritis, the food- and waterborne pathogen Campylobacter needs to be intensively monitored through a One Health approach. Particularly, wild birds have been hypothesized to contribute to the spread of human clinical recurring C. jejuni genotypes across several countries. A major concern in studying epidemiological dynamics is resolving the large genomic diversity of strains circulating in the environment and various reservoirs, challenging to achieve with isolation techniques. Here, we applied a passive-filtration method to obtain isolates and in parallel recovered genotypes from metagenomic sequencing data from associated filter sweeps. For genotyping mixed strains, a reference-based computational workflow to predict allelic profiles of nine extended-MLST loci was utilized. We validated the pipeline by sequencing artificial mixtures of C. jejuni strains and observed the highest prediction accuracy when including obtained isolates as references. By analyzing metagenomic samples, we were able to detect over 20% additional genetic diversity and observed an over 50% increase in the potential to connect genotypes across wild-bird samples. With an optimized filtration method and a computational approach for genotyping strain mixtures, we provide the foundation for future studies assessing C. jejuni diversity in environmental and clinical settings at improved throughput and resolution.

Perspective: Multiomics and Machine Learning Help Unleash the Alternative Food Potential of Microalgae

Food security has become a pressing issue in the modern world. The ever-increasing world population, ongoing COVID-19 pandemic, and political conflicts together with climate change issues make the problem very challenging. Therefore, fundamental changes to the current food system and new sources of alternative food are required. Recently, the exploration of alternative food sources has been supported by numerous governmental and research organizations, as well as by small and large commercial ventures. Microalgae are gaining momentum as an effective source of alternative laboratory-based nutritional proteins as they are easy to grow under variable environmental conditions, with the added advantage of absorbing carbon dioxide. Despite their attractiveness, the utilization of microalgae faces several practical limitations. Here, we discuss both the potential and challenges of microalgae in food sustainability and their possible long-term contribution to the circular economy of converting food waste into feed via modern methods. We also argue that systems biology and artificial intelligence can play a role in overcoming some of the challenges and limitations; through data-guided metabolic flux optimization, and by systematically increasing the growth of the microalgae strains without negative outcomes, such as toxicity. This requires microalgae databases rich in omics data and further developments on its mining and analytics methods.

Metaphenotypes associated with recurrent genomic lineages of Campylobacter jejuni responsible for human infections in Luxembourg

Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. Although considered fragile, this microaerophilic bacterium is able to survive in various challenging environments, which subsequently constitutes multiple sources of transmission for human infection. To test the assumption of acquiring specific features for adaptation and survival, we established a workflow of phenotypic tests related to the survival and the persistence of recurrent and sporadic strains. A representative collection of 83 strains isolated over 13 years from human, mammal, poultry, and environmental sources in Luxembourg, representing different spreading patterns (endemic, epidemic, and sporadic), was screened for survival to oxidative stresses, for acclimating to aerobic conditions (AC), and for persistence on abiotic surfaces. Using the cgMLST Oxford typing scheme for WGS data, the collection was classified into genomic lineages corresponding to host-generalist strains (lineages A and D, CC ST-21), host-specific strains (lineage B, CC ST-257 and lineage C, CC ST-464) and sporadic strains. We established that when a strain survives concentrations beyond 0.25 mM superoxide stress, it is six times more likely to survive hyperoxide stress and that a highly adherent strain is 14 times more likely to develop a biofilm. Surprisingly, more than half of the strains could acclimate to AC but this capacity does not explain the difference between recurrent genomic lineages and sporadic strains and the survival to oxidative stresses, while recurrent strains have a significantly higher adhesion/biofilm formation capacity than sporadic ones. From this work, the genomic lineages with more stable genomes could be characterized by a specific combination of phenotypes, called metaphenotypes. From the functional genomic analyses, the presence of a potentially functional T6SS in the strains of lineage D might explain the propensity of these strains to be strong biofilm producers. Our findings support the hypothesis that phenotypical abilities contribute to the spatio-temporal adaptation and survival of stable genomic lineages. It suggests a selection of better-adapted and persistent strains in challenging stress environments, which could explain the prevalence of these lineages in human infections.

Development of miniaturized agar based assays in 96-well microplates applicable to high-throughput screening of industrially valuable microorganisms

High-throughput screening (HTS) is a present-day approach for assaying thousands of cultures in parallel. This miniaturization allows rapid screening of large number of microorganims capable of producing bio-based materials thereby meeting the demands of the ever evolving food, pharmaceutical and cosmetic industry. In this study, agar-based assays for phosphate solubilization, cellulose degradation and lactic acid production were developed in 96-well microplates using Biomek FX^P Automated Liquid Handling system. Techno-economic analysis from this study reveals the lower overall cost per assay using HTS as compared to conventional Petri plate assays. Though automated liquid handling workstations have been used to perform liquid-based assays, there are very few studies which report their use for agar-based microplate assays. These findings thus corroborate the establishment of rapid and efficient miniaturized, qualitative agar-based screening methods for identifying microorganisms with potential for commercial application.

Isolation and Characterization of Lytic Bacteriophages Specific for Campylobacter jejuni and Campylobacter coli

In this study, two lytic bacteriophages designated as vB_CjP and vB_CcM were isolated and evaluated for their ability to combat multidrug-resistant bacteria Campylobacter jejuni and Campylobacter coli, respectively. A morphological analysis of these phages by transmission electron microscopy revealed that the vB-CjP bacteriophage had a mean head dimension of 66.6 ± 2.1 nm and a short non-contractile tail and belongs to the Podoviridae family, whereas vB_CcM had a mean head dimension of 80 ± 3.2 nm, a contractile tail, and a length calculated to be 60 ± 2.5 nm and belongs to the Myoviridae family. The results of the host range assay showed that vB_CjP could infect 5 of 10 C. jejuni isolates, whereas vB_CcM could infect 4 of 10 C. coli isolates. Both phages were thermostable and did not lose their infectivity and ability to lyse their host following exposure to 60 °C for 10 min; furthermore, phage particles were relatively stable within a pH range of 6–8. A one-step growth curve indicated that the phages produced estimated burst sizes of 110 and 120 PFU per infected cell with latent periods of 10 and 15 min, for vB-CjP and vB-CcM, respectively. The lytic activity of these phages against planktonic Campylobacter showed that these phages were able to control the growth of Campylobacter in vitro. These results suggest that these phages have a high potential for phage applications and can reduce significantly the counts of Campylobacter spp. The lytic activity of vB-CjP and vB-CcM phages at different (MOIs) against multidrug resistance Campylobacter strains was evaluated. The bacterial growth was slightly delayed by both phages, and the highest efficiency of both phages was observed when MOI = 1 was applied.

Prevalence and antimicrobial resistance of Campylobacter from wild birds of prey in Spain

Wild birds have been identified as a relevant reservoir of Campylobacter spp., therefore, a potential source of infection in humans and domestic animals. The objective of this study was to determine the occurrence of Campylobacter spp. on birds of prey in Spain. In addition, antibiotic resistance profiles of the isolates were evaluated. A total of 689 specimens of 28 raptor species were analyzed, with a resulting individual prevalence of 7.5%. C. jejuni was the most frequently isolated species (88.5%), followed by C. coli and C. lari (3.8% each). The occurrence of Campylobacter was significantly higher (p < 0.05) in nocturnal birds of prey (15.3%), in spring season (12.2%) and in carnivorous species (9.4%). Isolates displayed a remarkable resistance to nalidixic acid (69.9%), ciprofloxacin (69.9%), and tetracycline (55.6%), and a low resistance to streptomycin (6.7%). Our findings highlight the importance of birds of prey as reservoirs of Campylobacter strains and their significant role as carriers of antimicrobial resistance.

Inter-trophic Interaction of Gut Microbiota in a Tripartite System

Gut microbiota can be transmitted either environmentally or socially and vertically at intraspecific level; however, whether gut microbiota interact along trophic levels has been largely overlooked. Here, we characterized the gut bacterial communities of weevil larvae of Curculio arakawai that infest acorns of Mongolian oak (Quercus mongolica) as well as acorn-eating mammals, Siberian chipmunk (Tamias sibiricus), to test whether consumption of seed-borne larvae remodels the gut bacterial communities of T. sibiricus. Ingestion of weevil larvae of C. arakawai significantly altered the gut bacterial communities of T. sibiricus. Consequently, T. sibiricus fed larvae of C. arakawai showed higher capability to counter the negative effects of tannins, in terms of body weight maintenance, acorn consumption, N content in feces, urine pH, and blood ALT activity. Our results may first show that seed-borne insects as hidden players have a potential to alter the gut microbiota of seed predators in the tripartite system.

Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes

Campylobacter jejuni is the leading cause of bacterial gastroenteritis, which has motivated the monitoring of genetic profiles circulating in Luxembourg since 13 years. From our integrated surveillance using a genotyping strategy based on an extended MLST scheme including gyrA and porA markers, an unexpected endemic pattern was discovered in the temporal distribution of genotypes. We aimed to test the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS) associated with comprehensive and internationally validated schemes. This pilot study assessed four WGS-based typing schemes to classify a panel of 108 strains previously identified as recurrent or sporadic profiles using this in-house typing system. The strain collection included four common lineages in human infection (N = 67) initially identified from recurrent combination of ST-gyrA-porA alleles also detected in non-human samples: veterinary (N = 19), food (N = 20), and environmental (N = 2) sources. An additional set of 19 strains belonging to sporadic profiles completed the tested panel. All the strains were processed by WGS by using Illumina technologies and by applying stringent criteria for filtering sequencing data; we ensure robustness in our genomic comparison. Four typing schemes were applied to classify the strains: (i) the cgMLST SeqSphere+ scheme of 637 loci, (ii) the cgMLST Oxford scheme of 1,343 loci, (iii) the cgMLST INNUENDO scheme of 678 loci, and (iv) the wgMLST INNUENDO scheme of 2,795 loci. A high concordance between the typing schemes was determined by comparing the calculated adjusted Wallace coefficients. After quality control and analyses with these four typing schemes, 60 strains were confirmed as members of the four recurrent lineages regardless of the method used (N = 32, 12, 7, and 9, respectively). Our results indicate that, regardless of the typing scheme used, epidemic or endemic signals were detected as reflected by lineage B (ST2254-gyrA9-porA1) in 2014 or lineage A (ST19-gyrA8-porA7), respectively. These findings support the clonal expansion of stable genomes in Campylobacter population exhibiting a multi-host profile and accounting for the majority of clinical strains isolated over a decade. Such recurring genotypes suggest persistence in reservoirs, sources or environment, emphasizing the need to investigate their survival strategy in greater depth.

Investigation of Campylobacter colonization in three Australian commercial free-range broiler farms

Campylobacter spp. contaminated poultry products are strongly associated with foodborne illnesses worldwide. Development of effective management strategies to reduce contamination by Campylobacter spp. requires an improved understanding of the numerous factors that drive these contamination processes. Currently, chicken farms are using more free-range chicken meat production systems in response to consumer preferences. However, Campylobacter spp. colonization has rarely been investigated on free-range broiler farms. The present study investigated the temporal and environmental factors influencing Campylobacter spp. colonization of free-range broilers as well as potential sources and genetic diversity of Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli) in commercial free-range broiler farms. Genetic linkages among the isolates were analyzed using flaA amplicon analysis. Campylobacter coli was first detected in fecal samples of a commercial free-range broiler flock on day 10 of rearing. Multiple genotypes of C. jejuni and C. coli were identified in this study. The farm environment was identified as a potential source of C. jejuni and C. coli colonization of free-range broilers. The dominant Campylobacter genotype varied between free-range broiler farms over time, with C. jejuni being the most frequently isolated species. These findings enhance the understanding of C. jejuni and C. coli colonization in free-range broiler farms and could inform the development of more effective intervention strategies to help control this important foodborne pathogen.

Microampere Electric Current Causes Bacterial Membrane Damage and Two-Way Leakage in a Short Period of Time

Physical agents, such as low electric voltage and current, have recently gained attention for antimicrobial treatment due to their bactericidal capability. Although microampere electric current was shown to suppress the growth of bacteria, it remains unclear to what extent the microampere current damaged the bacterial membrane. Here, we investigated the membrane damage and two-way leakage caused by microampere electric current (≤100 μA) with a short exposure time (30 min). Based on MitoTracker staining, propidium iodide staining, filtration assays, and quantitative single-molecule localization microscopy, we observed significant membrane damage, which allowed two-way leakage of ions, small molecules, and proteins. This study paves the way to new development of antimicrobial applications for ultralow electric voltage and current.IMPORTANCE Although electric voltage and current have been studied for a long time in terms of their ability to suppress the growth of bacteria and to kill bacteria, increasing interest has been aroused more recently due to the prevalence of antibiotic resistance of microbes in past decades. Toward understanding the antimicrobial mechanism of low electric voltage and current, previous studies showed that treating bacteria with milliampere electric currents (≥5 mA) for ≥72 h led to significant damage of the bacterial membrane, which likely resulted in leakage of cellular contents and influx of toxic substances through the damaged membrane. However, it remains unclear to what extent membrane damage and two-way (i.e., inward and outward) leakage are caused by lower (i.e., microampere) electric current in a shorter time frame. In this work, we set out to answer this question. We observed that the membrane damage was caused by microampere electric current in half an hour, which allowed two-way leakage of ions, small molecules, and proteins.

Occurrence of Campylobacter species from broiler chickens and chicken meat in Malaysia

Campylobacter is reported as a major cause of foodborne illness worldwide. Consumption of contaminated chicken meat is considered a significant risk factor of Campylobacter infection in humans. This study investigated the occurrence of non-Campylobacter jejuni-Campylobacter coli, in broiler chickens (n = 210) and chicken meat (n = 109). The samples were collected from seven broiler chicken farms (n = 210 cloacal swabs), 11 markets (n = 84 chicken meat), and 5 supermarkets (n = 25 chicken meat) located in different districts of Selangor State. Campylobacter were isolated from cloacal swabs using the Cape Town Protocol and from meat samples using the method of Duffy et al. (2007) with some modifications for Campylobacter isolations which were reported effective in the isolation of non-C. jejuni-C. coli Campylobacter species. The isolates were identified by Gram staining for cellular morphology, wet mount for motility and biochemical tests. Confirmation of presumed Campylobacter isolates was carried out using multiplex PCR (mPCR). One hundred seven (107/210) or 50.9% and twenty-nine (29/109) or 26.6% of chickens and chicken meat samples respectively were positive for Campylobacter species. Among the Campylobacter isolates from chickens, C. jejuni was the most predominantly isolated species (69.5%), followed by C. coli (16.2%). Campylobacter fetus and C. upsaliensis were the non-C. jejuni-C. coli Campylobacter species isolated in this study, at 9.3% and 2.5% respectively. Overall, the findings indicated broiler chickens were colonized not only by the common Campylobacter species but also by other Campylobacter species. We found the Cape Town Protocol useful to detect the occurrence of non-C. jejuni-C. coli isolates in chickens.

Disinfectant and Antimicrobial Susceptibility Profiles of Campylobacter coli Isolated in 1998 to 1999 and 2015 from Swine and Commercial Pork Chops

Susceptibility profiles were determined for 111 Campylobacter coli strains obtained in 1998 to 1999 and 2015 from market age pigs and pork chops against 22 disinfectants and 9 antimicrobials. Resistance to tetracycline (TET) was observed in 44.4% of 1998 to 1999 strains, and the antibiotic resistance profile was TET. But strains obtained in 2015 from swine and retail pork chops had 75% TET resistance and the antibiotic resistance profile was TET, followed by azithromycin-erythromycin-TET-telithromycin-clindamycin. Antimicrobial resistance increased in 2015 strains. All strains were resistant to triclosan, and 84.1% and 95.8% of strains in 1998 to 1999 and 2015, respectively, were chlorhexidine resistant. All strains were susceptible to benzalkonium chloride. There was a shift toward higher susceptibility to chlorhexidine, triclosan, P-128, OdoBan, CPB, and CPC in 2015 swine and pork chop strains compared with 1998 to 1999 strains. The disinfectants Tek-Trol and providone-iodine, tris(hydroxylmethyl)nitromethane (THN) and formaldehyde demonstrated the highest susceptibilities. Didecyldimethylammonium chloride (C10AC) appeared to be about equally effective as benzyldimethyltetradecylammonium chloride (C14BAC) for inhibiting C. coli, and both were more effective than C8AC and C12BAC, but C16BAC was not efficient at inhibiting C. coli. The BACs, C12BAC and C14BAC, were the most effective ingredients in DC&R. Also, C12BAC and C14BAC, or these two in synergy with C10AC were responsible for inhibition of C. coli at high P-128 MICs. No cross-resistance was observed between antibiotics and disinfectants. The continued use of THN and formaldehyde in DC&R should be evaluated since these components are not effective, and their inclusion adds unwanted chemicals in the environment. PRACTICAL APPLICATION: Campylobacter species cause diarrheal disease throughout the world. Disinfectants are often used on the farm, in veterinary medicine, by the food processing industry, in restaurants, and in consumer's homes. Limited information is available in the literature showing how disinfectants or disinfectant components may affect the many different foodborne pathogens, and, specifically, Campylobacter coli studied here. The knowledge generated in this study concerning the interactions of a broad array of disinfectants against C. coli may well affect the types of disinfectants and disinfectant formulations allowable for use by medical personnel, producers, food processors, restaurants, and consumers.

Characterisation and Antibiotic Resistance of Selected Bacterial Pathogens Recovered from Dairy Cattle Manure during Anaerobic Mono-Digestion in a Balloon-Type Digester

Dairy cattle manure serves as a potential source of contamination and infection of animals, humans and the environment. Manure samples withdrawn from a balloon-type digester during anaerobic digestion were evaluated for the presence of antibiotic-resistant bacterial pathogens. The bacterial load of the samples was determined via a viable plate count method and the recovered isolates were subjected to characterisation and identification. These isolates were employed in antibiotic susceptibility testing using a disc diffusion method against a suite of 10 conventional antibiotics. The multiple antibiotic resistance (MAR) index was calculated and MAR phenotypes were generated. Although all the bacterial pathogens showed a certain degree of resistance to the studied antibiotics, a marked resistance was demonstrated by Campylobacter sp. to co-trimoxazole (87.5%) and nalidixic acid (81.5%). Remarkably, a high resistance (82.42%) was demonstrated against the antibiotic class, macrolide, followed by beta-lactams (40.44%), suggesting that bacterial resistance depended on the chemical structure of the antibiotics. However, individual bacterial isolates varied in resistance to particular antibiotics. Of the 83 bacterial isolates, 40(48.19%) observed MAR > 0.2 and, thus, were described as multidrug-resistant isolates. A total of 28 MAR phenotypes were revealed with the highest frequency of MAR phenotypes (37.5%) expressed against 3 antibiotics. Results indicated a high risk of exposure to various antibiotics and wide diversity of antibiotic resistance.

Interactions of organic acids with Campylobacter coli from swine

Campylobacter coli is a bacterial species that is a major cause of diarrheal disease worldwide, and Campylobacter spp. are among the top 5 foodborne pathogens in the United States. During food production organic acids (OAs) are often used to remove bacteria from animal carcasses. The interactions of six OAs with 111 C. coli strains obtained from swine and retail pork chops were studied by determining the molar minimum inhibitory concentrations (MICMs) of the C. coli strains, and the pH at the MICMs. The Henderson-Hasselbalch equation was used to calculate the concentrations of the undissociated and dissociated OAs at the MICMs of the C. coli strains. The results for the 111 different C. coli strains obtained from different locations were treated as a single group for each OA since many of the C. coli strains behaved similarly to each different OA. Inhibition of C. coli was not dependent on pH or on the undissociated OA species, but C. coli inhibition correlated with the dissociated OA species. Therefore, if the concentration of the dissociated OAs decreases from optimum, one may then expect that C. coli bacteria would escape disinfection. The concentration of the dissociated OA should be carefully controlled in a carcass wash. We suggest maintaining a concentration of the dissociated acetic, butyric, citric, formic, lactic and propionic acids at 29, 23, 11, 35, 22 and 25 mM, respectively, when using a carcass wash with these OAs to remove C. coli bacteria. However, due to C. coli utilization of acetate, formate, lactate and propionate, these four OAs may not be the best choice to use for a carcass wash to remove C. coli contamination. Of the six OAs, citric acid was the most efficient at inhibiting C. coli.

Impact of human-associated Escherichia coli clonal groups in Antarctic pinnipeds: presence of ST73, ST95, ST141 and ST131

There is growing concern about the spreading of human microorganisms in relatively untouched ecosystems such as the Antarctic region. For this reason, three pinniped species (Leptonychotes weddellii, Mirounga leonina and Arctocephalus gazella) from the west coast of the Antartic Peninsula were analysed for the presence of Escherichia spp. with the recovery of 158 E. coli and three E. albertii isolates. From those, 23 harboured different eae variants (α1, β1, β2, ε1, θ1, κ, ο), including a bfpA-positive isolate (O49:H10-A-ST206, eae-k) classified as typical enteropathogenic E. coli. Noteworthy, 62 of the 158 E. coli isolates (39.2%) exhibited the ExPEC status and 27 (17.1%) belonged to sequence types (ST) frequently occurring among urinary/bacteremia ExPEC clones: ST12, ST73, ST95, ST131 and ST141. We found similarities >85% within the PFGE-macrorrestriction profiles of pinniped and human clinic O2:H6-B2-ST141 and O16:H5/O25b:H4-B2-ST131 isolates. The in silico analysis of ST131 Cplx genomes from the three pinnipeds (five O25:H4-ST131/PST43-fimH22-virotype D; one O16:H5-ST131/PST506-fimH41; one O25:H4-ST6252/PST9-fimH22-virotype D1) identified IncF and IncI1 plasmids and revealed high core-genome similarities between pinniped and human isolates (H22 and H41 subclones). This is the first study to demonstrate the worrisome presence of human-associated E. coli clonal groups, including ST131, in Antarctic pinnipeds.

Isolation of Campylobacter spp. from Three Species of Antarctic Penguins in Different Geographic Locations

The presence of Campylobacter species was studied in three Antarctic penguin species, Adélie (Pygoscelis adeliae), chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua). A total of 390 penguins were captured in 12 different rookeries along the Antarctic Peninsula with differences in the amount of human visitation: six colonies were highly visited [Stranger Point, King George Island (P. papua and P. adeliae); Hannah Point, Livingston Island (P. papua and P. antarctica); Deception Island (P. antarctica); and Paradise Bay, Antarctic Peninsula (P. papua)], and six colonies were rarely visited [Devil's Point, Byers Peninsula, Livingston Island (P. papua); Cierva Cove, Antarctic Peninsula (P. papua); Rongé Island (P. papua and P. antarctica); Yalour Island (P. adeliae); and Avian Island (P. adeliae)]. A total of 23 strains were isolated from penguins from nine different rookeries. Campylobacter lari subsp. lari was isolated from eight samples (seven from P. papua and one from P. adeliae); C. lari subsp. concheus from 13 (ten from P. adeliae and three from P. antarctica) and C. volucris from two samples (both from P. papua). We did not find any significant differences in the prevalence of Campylobacter spp. between the populations in highly and rarely visited areas. This is the first report of C. lari subsp. concheus and C. volucris isolation from penguins in the Antarctic region.

Resistance of Campylobacter jejuni Isolated from Layer Farms in Northern Jordan Using Microbroth Dilution and Disc Diffusion Techniques

Campylobacter jejuni is an important pathogen of significant public health importance. This pathogen is associated with human infection and has been isolated from mammals and birds. Ninety-two cloacal C. jejuni isolates were identified from 35 layer farms in Northern Jordan. Antimicrobial susceptibility was determined using minimal inhibitory concentration (MIC) and disc diffusion techniques with variable suggested breakpoints. Using MIC and EUCAST cut-off values, the study revealed a significantly high resistance level (100%) among the layers' isolates against ciprofloxacin and tetracycline. A relatively high resistance (41%) toward gentamicin and amoxicillin and low resistance to nalidixic acid (21%), erythromycin (14%), and florfenicol (6.5%) were also found. This high level of resistance may indicate abuses in the handling of antibiotics, which may require stricter control in the local layer industry. A good agreement between the 2 techniques used was demonstrated and the disc diffusion technique could be used as a rapid screening test for antimicrobial susceptibility of C. jejuni to many antibiotics using specific Campylobacter breakpoints.

A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni

MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this study was to enhance strain level resolution for Campylobacter jejuni through the optimization of spectrum processing parameters using a series of designed experiments. A collection of 172 strains of C. jejuni were collected from Luxembourg, New Zealand, North America, and South Africa, consisting of four groups of antibiotic resistant isolates. The groups included: (1) 65 strains resistant to cefoperazone (2) 26 resistant to cefoperazone and beta-lactams (3) 5 strains resistant to cefoperazone, beta-lactams, and tetracycline, and (4) 76 strains resistant to cefoperazone, teicoplanin, amphotericin, B and cephalothin. Initially, a model set of 16 strains (three biological replicates and three technical replicates per isolate, yielding a total of 144 spectra) of C. jejuni was subjected to each designed experiment to enhance detection of antibiotic resistance. The most optimal parameters were applied to the larger collection of 172 isolates (two biological replicates and three technical replicates per isolate, yielding a total of 1,031 spectra). We observed an increase in antibiotic resistance detection whenever either a curve based similarity coefficient (Pearson or ranked Pearson) was applied rather than a peak based (Dice) and/or the optimized preprocessing parameters were applied. Increases in antimicrobial resistance detection were scored using the jackknife maximum similarity technique following cluster analysis. From the first four groups of antibiotic resistant isolates, the optimized preprocessing parameters increased detection respective to the aforementioned groups by: (1) 5% (2) 9% (3) 10%, and (4) 2%. An additional second categorization was created from the collection consisting of 31 strains resistant to beta-lactams and 141 strains sensitive to beta-lactams. Applying optimal preprocessing parameters, beta-lactam resistance detection was increased by 34%. These results suggest that spectrum processing parameters, which are rarely optimized or adjusted, affect the performance of MALDI-TOF MS-based detection of antibiotic resistance and can be fine-tuned to enhance screening performance.

Low temperature adaptation and the effects of cryoprotectants on mesorhizobia strains

In this study, the tolerance of Mesorhizobium sp. ACMP18, Mesorhizobium sp. USDA3350, and Mesorhizobium temperatum LMG23931 strains, to cold and freezing were investigated. The ability to withstand freezing at -20 °C and -70 °C for 24 months was different among the studied strains and depended on the cryoprotectant used. The survivability of mesorhizobial strains at -20 °C and -70 °C was significantly improved by some cryoprotectans (glycerol and sucrose/peptone). It is worth noting that the greatest resistance to freezing was detected when stress treatments were performed in glycerol as a cryoprotectant. Using PCR analysis, cspA genes were identified in the studied strains. Their nucleotide sequences were most similar to the sequences of the corresponding genes of the Mesorhizobium species. The expression of the cspA gene in the studied bacteria was analyzed using the RT-PCR technique. The fatty acid composition of the mesorhizobia was determined at 5, 10, 15, and 28 °C. It was noticed that growth temperature significantly affected the fatty acid composition and the amounts of unsaturated fatty acids, especially that of cis-vaccenic acid (18:1ɷ(11)), increased markedly in bacterial cells cultivated at 5, 10, and 15 °C.

Fluorescent microbead-based immunoassay for anti-Erysipelothrix rhusiopathiae antibody detection in cetaceans

A fluorescent microbead-based immunoassay (FMIA) for detection of anti-Erysipelothrix rhusiopathiae antibodies in pigs was adapted for use in cetaceans. The FMIA was validated and adjusted using serum samples from 10 vaccinated captive bottlenose dolphins Tursiops truncatus collected between 1 and 13 mo after immunization. The technique was then used to analyze specimens from 15 free-ranging cetaceans stranded alive on the Valencian Mediterranean coast between 2006 and 2014: 11 striped dolphins Stenella coeruleoalba, 3 Risso's dolphins Grampus griseus and 1 bottlenose dolphin Tursiops truncatus. One of these wild animals was confirmed to have died from E. rhusiopathiae septicemia, but no anti-E. rhusiopathiae antibodies were detected in its serum, pericardial fluid or milk samples. Another free-ranging individual, which lacked any signs or lesions that might be indicative of E. rhusiopathiae infection, showed high fluorescence intensity similar to that measured in captive dolphins at 6-13 mo after vaccination. These results suggest that this animal underwent an E. rhusiopathiae infection several months before stranding. The findings in the present study suggest that FMIA can be useful for detecting anti-E. rhusiopathiae antibodies in cetaceans, and its application to free-ranging animals is particularly interesting because of the great value of these specimens. Furthermore, the FMIA can be multiplexed to allow the determination of up to 100 analytes per sample in a single well, thereby reducing the cost, time and sample volume needed.

Evaluation and histological examination of a Campylobacter fetus subsp. venerealis small animal infection model

Bovine genital campylobacteriosis (BGC), caused by Campylobacter fetus subsp. venerealis, is associated with production losses in cattle worldwide. This study aimed to develop a reliable BGC guinea pig model to facilitate future studies of pathogenicity, abortion mechanisms and vaccine efficacy. Seven groups of five pregnant guinea pigs (1 control per group) were inoculated with one of three strains via intra-peritoneal (IP) or intra-vaginal routes. Samples were examined using culture, PCR and histology. Abortions ranged from 0% to 100% and re-isolation of causative bacteria from sampled sites varied with strain, dose of bacteria and time to abortion. Histology indicated metritis and placentitis, suggesting that the bacteria induce inflammation, placental detachment and subsequent abortion. Variation of virulence between strains was observed and determined by culture and abortion rates. IP administration of C. fetus subsp. venerealis to pregnant guinea pigs is a promising small animal model for the investigation of BGC abortion.

Investigating the host specificity of Campylobacter jejuni and Campylobacter coli by sequencing gyrase subunit A

BACKGROUND

Surveillance and field investigations of Campylobacter infections require molecular tools with genetic markers appropriate for tracing purposes, i.e. based on the principle that some Campylobacter lineages acquire a host signature under adaptive selection pressure. We developed a sequence-based method targeting the quinolone resistance determining region within the subunit A of DNA gyrase (gyrA). Host specificity was evaluated by characterizing two collections of Campylobacter jejuni (N = 430) and Campylobacter coli (N = 302) originating from surface waters, domestic mammals and poultry.

RESULTS

Based on nucleotide identity, a total of 80 gyrA alleles were observed. Thirty nine alleles assigned to C. coli encoding two peptides fell into three clades: two associated with surface waters and one associated with domestic mammals and poultry. The variability in GC content generated by synonymous mutations suggested that surface waters isolates originated from two distinct ecological niches. A total of 42 alleles were recorded from C. jejuni strains and encoded 8 peptides including one lying in a distinct lineage associated with wildlife. Seven of the 23 alleles encoding peptide #1 displayed the synonymous mutation G408A not identified in poultry isolates. By contrast, the substitution Ser22Gly observed in 4 different peptide groups was significantly associated with domestic birds (P = 0.001). The change in amino acid sequences Thr86Ile conferring resistance to quinolones was significantly associated with poultry (P < 0.001) in both C. jejuni and C. coli with 38.7% and 67.9% of quinolone-resistant strains, respectively.

CONCLUSIONS

The gyrA typing method presented here is an informative tool as sequences appear to be predictive of particular ecological niches. Combined with multi-locus sequence typing, it could increase the resolution of source attribution, and combined with porA/flaA typing it could be suitable for detecting temporal clusters of human cases. All gyrA alleles identified were deposited in the freely accessible online database http://pubmlst.org/campylobacter.

Survival of Campylobacter jejuni in naturally and artificially contaminated laying hen feces

Infected laying hens regularly excrete large amounts of Campylobacter jejuni with their feces, which represent a reservoir of infection within the flock and for animals in the region. However, the knowledge about survival times of C. jejuni in these feces is still scarce. Therefore, orienting laboratory experiments were carried out under controlled conditions to estimate the survival times of C. jejuni both in artificially and naturally contaminated laying hen feces. In 6 different laying hen flocks (3 Campylobacter-free and 3 Campylobacter-positive flocks), fresh excreta were randomly collected and pooled in 20-g samples per flock. In the laboratory, each of the 3 pooled samples from the Campylobacter-free barns were homogenized and mixed with 10 mL of a freshly prepared C. jejuni suspension (3 × 10(8) cfu/mL). The other 3 samples were homogenized only. The 6 samples were stored at 20 ± 1°C and 40 to 60% RH in 2 different incubators. Specimens of 2 g were taken from all 6 samples 1 h after storage and daily at the same time during the next 10 consecutive days and investigated on culturable C. jejuni. The survival times of culturable C. jejuni ranged from 72 to 96 h in artificially inoculated feces and varied from 120 to 144 h in naturally colonized flocks. The flaA typing by RFLP confirmed that the isolates from the artificially contaminated feces were identical with the added strain. A total of 5 different flaA types were identified from the naturally contaminated feces, and survival of these isolates was dependent on flaA type. The demonstrated survival times indicate that contaminated fresh feces are an important reservoir of C. jejuni, representing a permanent source of infection over at least 6 d after excretion. It shows the considerable potential of fresh feces in transmitting the agent within and between flocks during that period. This 6-d span should be considered when poultry manure is applied to land as organic fertilizer.

Anaerobic oral flora in the North American black bear (Ursus americanus) in eastern North Carolina

Microbial flora can provide insight into the ecology and natural history of wildlife in addition to improving understanding of health risks. This study examines the anaerobic oral flora of hunter killed black bears (Ursus americanus) in eastern North Carolina. Oral swabs from the buccal and lingual supragingival tooth surfaces of the first and second mandibular and maxillary molars of 22 black bears were inoculated onto Brucella Blood Agar plates supplemented with hemin and vitamin K after transport from the field using reduced oxoid nutrient broth. Sixteen anaerobic bacterial species, representing nine genera were identified using the RapID ANA II Micromethod Kit system and a number of organisms grown that could not be identified with the system. The most frequently identified anaerobes were Peptostreptococcus prevotii, Streptococcus constellatus, and Porphyromonas gingivalis. The diversity in the anaerobic oral flora of black bear in eastern North Carolina suggests the importance of including these organisms in basic health risk assessment protocols and suggests a potential tool for assessment of bear/habitat interactions.

Collection and preservation of frozen microorganisms

The storage of the different microorganisms over long periods is necessary to ensure reproducible results and continuity in research and in biomedical processes and also for commercial purposes. Effective storage means that a microorganism is maintained in a viable state free of contamination or genetic drift and must be easily restored without genotypic or phenotypic alterations to its original characteristics and properties. To this end, different techniques have been described and advances in cryopreservation technology have led to methods that allow low-temperature maintenance of a variety of cell types, minimizing the risks of genetic change and are now recommended for long-term storage of most microorganisms.This chapter summarizes the most important steps and components in the process of low- and -ultra-low temperatures freezing of bacteria, parasites, yeasts and fungi, viruses, and recombinant microorganisms.

Isolation and characterization of Campylobacter spp. from Antarctic fur seals (Arctocephalus gazella) at Deception Island, Antarctica

The presence of Campylobacter spp. was investigated in 41 Antarctic fur seals (Arctocephalus gazella) and 9 Weddell seals (Leptonychotes weddellii) at Deception Island, Antarctica. Infections were encountered in six Antarctic fur seals. The isolates, the first reported from marine mammals in the Antarctic region, were identified as Campylobacter insulaenigrae and Campylobacter lari.

Multilocus sequence typing, pulsed-field gel electrophoresis, and fla short variable region typing of clonal complexes of Campylobacter jejuni strains of human, bovine, and poultry origins in Luxembourg

Campylobacter jejuni is the most common cause of bacterial gastroenteritis in Luxembourg, with a marked seasonal peak during summer. The majority of these infections are thought to be sporadic, and the relative contribution of potential sources and reservoirs is still poorly understood. We monitored human cases from June to September 2006 (n = 124) by molecular characterization of isolates with the aim of rapidly detecting temporally related cases. In addition, isolates from poultry meat (n = 36) and cattle cecal contents (n = 48) were genotyped for comparison and identification of common clusters between veterinary and human C. jejuni populations. A total of 208 isolates were typed by sequencing the fla short variable region, macrorestriction analysis resolved by pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). We observed a high diversity of human strains during a given summer season. Poultry and human isolates had a higher diversity of sequence types than isolates of bovine origin, for which clonal complexes CC21 (41.6%) and CC61 (18.7%) were predominant. CC21 was also the most common complex found among human isolates (21.8%). The substantial concordance between PFGE and MLST results for this last group of strains suggests that they are clonally related. Our study indicates that while poultry remains an important source, cattle could be an underestimated reservoir of human C. jejuni cases. Transmission mechanisms of cattle-specific strains warrant further investigation.

Optimising the viability during storage of freeze-dried cell preparations of Campylobacter jejuni

Freeze-dried cultures of Campylobacter jejuni are used in the food and microbiological industry for reference materials and culture collections. However, C. jejuni is very susceptible to damage during freeze-drying and subsequent storage and it would be useful to have longer-lasting cultures. The survival of C. jejuni during freeze-drying and subsequent storage was investigated with the aim of optimising survival. C. jejuni was freeze-dried using cultures of different age (24-120 h), various lyoprotectants (10% phytone peptone, proteose peptone, peptonized milk, trehalose, soytone and sorbitol), various storage (air, nitrogen and vacuum) and re-hydration (media, temperature and time) conditions. One-day-old cultures had significantly greater survival after freeze-drying than older cultures. The addition of trehalose to inositol broth as a lyoprotectant resulted in almost 2 log(10) increase in survival after 2 months storage at 4 degrees C. Storage in a vacuum atmosphere and re-hydration in inositol broth at 37 degrees C increased recovery by 1-2 log(10) survival compared to re-hydration in maximal recovery diluent (MRD) after storage at 4 degrees C. Survival during storage was optimal when a one-day-old culture was freeze-dried in inositol broth plus 10% (w/v) trehalose, stored under vacuum at 4 degrees C and re-hydrated at the same incubation temperature (37 degrees C) in inositol broth for 30 min. The results demonstrate that the survival of freeze-dried cells of C. jejuni during storage can be significantly increased by optimising the culture age, the lyoprotectant, and the storage and re-hydration conditions. The logarithmic rate of loss of viability (K) followed very well an inverse dependence on the absolute temperature, i.e., the Arrhenius rate law. Extrapolation of the results to a more typical storage temperature (4 degrees C) predicted a very low K value of 1.5 x 10(-3). These results will be useful to the development of improved reference materials and samples held in culture collections.

Influence of inoculation levels and processing parameters on the survival of Campylobacter jejuni in German style fermented turkey sausages

This study investigated the influence of inoculum levels and manufacturing methods on the survival of Campylobacter (C.) jejuni in raw fermented turkey sausages. Sausages were prepared and inoculated with C. jejuni. After inoculation, these sausages were processed and ripened for 8 days. Samples were taken throughout the ripening process. The presence of C. jejuni was established bacteriologically. Additionally, lactic acid bacteria were enumerated, pH values and water activity were measured to verify the ripening process. To detect changes in genotype and verify the identity of the recovered clones, AFLP analysis was carried out on the re-isolated strains. Whereas no C. jejuni were detectable when inoculating the sausages with the lowest inoculum (0.08-0.44 log(10) cfu/g sausage emulsion), C. jejuni were detectable for 12-24h by enrichment when inoculated with approximately 2 log(10) cfu/g. After inoculation with 4 and 6 log(10) cfu/g respectively, C. jejuni were detectable without enrichment for 12-48 h and by enrichment for 144 h at the most. The greatest decrease of the C. jejuni population occurred during the first 4 h of ripening. Only a very high inoculum level allowed the survival of the organism during a fermentation process and during ripening to pose a potential risk for consumers. Lower initial Campylobacter inoculums will be eliminated during proper ripening of the sausages, if sufficient decrease in water activity and pH-value is ensured.

Changes of viability and composition of the Escherichia coli flora in faecal samples during long time storage

Long-time storage of faecal samples is necessary for investigations of intestinal microfloras. The aim of the present study was to evaluate how the viability and the composition of the Escherichia coli flora are affected in faecal samples during different storage conditions. Four fresh faecal samples (two from calves and two from infants) were divided into sub-samples and stored in four different ways: with and without addition of glycerol broth at -20 degrees C and at -70 degrees C. The viability and the phenotypic diversity of the E. coli flora in the sub-samples were evaluated after repeated thawings and after storage during 1 year. The samples stored for 1 year without thawing were also kept at room temperature for 5 days and subsequently analysed. According to phenotyping (PhP analysis) of 32 isolates per sample on day 0, all four samples contained two dominating strains of E. coli each, and between one and eight less common strains. Samples that were stored at -70 degrees C in glycerol broth showed equal or even higher bacterial numbers as the original samples, even after repeated thawings, whereas samples stored at -20 degrees C showed a considerably lower survival rate, also with addition of glycerol. Sub-samples containing glycerol broth that were kept at room temperature after storage for 1 year showed a clear increase in the number of viable cells as well as in diversity. The diversities in each sub-sample showed a tendency to decrease after several thawings as well as after storage. Generally, the E. coli populations in samples stored at -20 degrees C were less similar to the population of the original sample than that in samples stored at -70 degrees C. Samples that had been mixed with glycerol broth had an E. coli flora more similar to that in the original sample than those without glycerol broth. Furthermore, the sub-samples that were kept at room temperature after storage for 1 year generally were more similar to the original samples than if they were processed directly. We conclude that for long time storage of faecal samples, storage at -70 degrees C is preferable. If samples have to be thawed repeatedly, addition of glycerol is preferable both for samples stored at -70 degrees C and for samples stored at -20 degrees C. Our data also have indicated that when E. coli isolates from faecal samples are selected for, e.g. analysis of virulence factors, it is necessary to pick several isolates per sample in order to obtain at least one isolate representing the dominating strain(s).