Phase variation modulates the multi-phenotypes displayed by clinical Campylobacter jejuni strains

The high incidence and prevalence of Campylobacter spp. in the food supply chain entail the importance to understand their mechanisms developed to withstand harsh environmental conditions encountered. Different stress conditions and phenotypic approaches were evaluated to study the behaviour of five clinical C. jejuni isolates with different genotypes, including the tolerance to oxygen and the oxidants hydrogen peroxide and cumene hydroperoxide, the motility and the ability to form biofilm on polystyrene and stainless steel at different temperatures and atmospheres. Whole Genome Sequencing was performed to analyse the occurrence of 216 genes involved in these mechanisms plus phase variation. The isolates showed high tolerance to oxygen and peroxide stress with different swimming motility performances and biofilm formation abilities. Aerotolerance was related with a reduced sensitive to peroxide stress and a loss of motility that promotes biofilm formation depending on the material surface. Comparative genomics did not reveal any clear gene pattern, although phase variation occurring during host infection was observed to be crucial for the modulation of the different survival mechanisms adopted by the bacteria. These findings reveal that the bacteria can combine diverse and complex strategies in an efficient manner to survive and persist in the environment.

Genomic Characterization of Campylobacter jejuni Associated with Perimyocarditis: A Family Case Report

Campylobacter spp. is the leading cause of foodborne gastrointestinal infections in humans worldwide. This study reports the first case of four family members who had contact with the same source of Campylobacter jejuni contamination with different results. Only the little siblings were infected by the same C. jejuni strain, but with different symptoms. Whereas the daughter was slightly affected with mild enteritis, the son suffered a longer campylobacteriosis followed with a perimyocarditis. This is the first case of the youngest patient affected by C. jejuni-related perimyocarditis published to date. The genomes of both strains were characterized by whole-genome sequencing and compared with the C. jejuni NCTC 11168 genome to gain insights into the molecular features that may be associated with perimyocarditis. Various comparison tools were used for the comparative genomics analysis, including the identification of virulence and antimicrobial resistance genes, phase variable (PV) genes, and single nucleotide polymorphisms (SNPs) identification. Comparisons of the strains identified 16 SNPs between them, which constituted small but significant changes mainly affecting the ON/OFF state of PV genes after passing through both hosts. These results suggest that PV occurs during human colonization, which modulates bacteria virulence through human host adaptation, which ultimately is related to complications after a campylobacteriosis episode depending on the host status. The findings highlight the importance of the relation between host and pathogen in severe complications of Campylobacter infections.

CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

BACKGROUND

The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge.

RESULTS

To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation.

CONCLUSIONS

The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .

Easy Nitrite Analysis of Processed Meat with Colorimetric Polymer Sensors and a Smartphone App

We have developed an in situ methodology for determining nitrite concentration in processed meats that can also be used by unskilled personnel. It is based on a colorimetric film-shaped sensory polymer that changes its color upon contacting the meat and a mobile app that automatically calculates the manufacturing and residual nitrite concentration by only taking digital photographs of sensory films and analyzing digital color parameters. The film-shaped polymer sensor detects nitrite anions by an azo-coupling reaction, since they activate this reaction between two of the four monomers that the copolymer is based on. The sensory polymer is complemented with an app, which analyzes the color in two different digital color spaces (RGB and HSV) and performs a set of 32 data fittings representing the concentration of nitrite versus eight different variables, finally providing the nitrite concentration of the test samples using the best fitting curve. The calculated concentration of nitrite correlates with a validated method (ISO 2918: 1975) usually used to determine nitrite, and no statistically significant difference between these methods and our proposed one has been found in our study (26 meat samples, 8 prepared, and 18 commercial). Our method represents a great advance in terms of analysis time, simplicity, and orientation to use by average citizens.

A mathematical modeling approach to the quantification of lactic acid bacteria in vacuum-packaged samples of cooked meat: Combining the TaqMan-based quantitative PCR method with the plate-count method

The TaqMan-based quantitative Polymerase Chain Reaction (qPCR) method and the Plate Count (PC) method are both used in combination with primary and secondary mathematical modeling, to describe the growth curves of Leuconostoc mesenteroides and Weissella viridescens in vacuum-packaged meat products during storage under different isothermal conditions. Vacuum-Packaged Morcilla (VPM), a typical cooked blood sausage, is used as a representative meat product, with the aim of improving shelf-life prediction methods for those sorts of meat products. The standard curves constructed by qPCR showed good linearity between the cycle threshold (C_T) and log₁₀ CFU/g, demonstrating the high precision and the reproducible results of the qPCR method. The curves were used for the quantification of L. mesenteroides and W. viridescens in artificially inoculated VPM samples under isothermal storage (5, 8, 13 and 18 °C). Primally, both the qPCR and the PC methods were compared, and a linear regression analysis demonstrated a statistically significant linear correlation between the methods. Secondly, the Baranyi and Roberts model was fitted to the growth curve data to estimate the kinetic parameters of L. mesenteroides and W. viridescens under isothermal conditions, and secondary models were used to establish the dependence of the maximum specific growth rate on the temperature. The results proved that primary and secondary models were adequate for describing the growth curves of both methods in relation to both bacteria. In conclusion, the results of all the experiments proved that the qPCR method in combination with the PC method can be used to construct microbial growth kinetics and that primary and secondary mathematical modeling can be successfully applied to describe the growth of L. mesenteroides and W. viridescens in vacuum-packaged morcilla and, by extension, other cooked meat products with similar characteristics.

Characterization of Virulence and Persistence Abilities of Listeria monocytogenes Strains Isolated from Food Processing Premises

We report the characterization of 15 Listeria monocytogenes strains isolated from various food processing plants by multivirulence locus sequence typing to determine virulence types (VTs) and epidemic clones. Molecular mechanisms involved in adaptation to food processing environments and related to virulence were also studied. Phenotypic behaviors associated with various antimicrobials, biofilm formations, and invasiveness were assessed. There were 11 VTs among the 15 L. monocytogenes strains. Strains belonging to six VTs were stress survival islet 1 (SSI-1) and one strain of VT94 was SSI-2. Tn6188 was found in VT6 and VT94 strains, and bcrABC cassette genes were identified in VT21, VT60, and VT63 strains. Only one strain, in VT20, showed llxS, whereas a full-size inlA was detected in strains belonging to VT8, VT20, VT21, and VT63. VT10, VT20, VT21, VT60, and VT63 strains were the most tolerant to studied disinfectants. A VT6 strain showed the strongest biofilm formation ability in polyvinyl chloride, and strains belonging to VT10, VT11, VT20, and VT94 had moderate abilities. Antimicrobial sensitivity tests showed that all the L. monocytogenes strains were multidrug resistant. F tests revealed that only strains of VT10, VT60, and VT94 were significantly noninvasive (P < 0.05) in Caco-2 cells. Our findings illustrate how L. monocytogenes isolates exploit diverse mechanisms to adapt to adverse conditions. Consequently, detailed characterization of L. monocytogenes isolates is required for comprehensive elimination of this pathogenic bacterium in food processing environments.

Distribution and Persistence of Listeria monocytogenes in a Heavily Contaminated Poultry Processing Facility

We studied the colonization and distribution of Listeria monocytogenes in a heavily contaminated poultry processing plant over a 1-year period. A total of 180 nonfood contact surfaces, 70 food contact surfaces, 29 personnel, and 40 food samples were analyzed. L. monocytogenes isolates were subtyped by PCR serotyping, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing. L. monocytogenes was detected in samples collected at every visit to the plant, and 43.8% (visit 4) to 65.6% (visit 7) of samples were positive, for an overall prevalence of 55.2%. The deboning area had the highest prevalence of positive samples (83.3%), and the processing area had the highest diversity of PFGE types. Ninety percent of the final products were positive for L. monocytogenes. Most of the isolates belonged to well-known persistent L. monocytogenes sequence types (ST9 and ST121). This study illustrates a well-established L. monocytogenes contamination problem in a poultry processing plant associated with a generalized failure of the food safety system as a whole. These findings reflect the potential for L. monocytogenes contamination when the food safety and quality management system is unsatisfactory, as described in the present study. It is essential to revise food safety and quality management systems to eliminate L. monocytogenes from food processing facilities, to control the entrance of sporadic sequence types, and to prevent L. monocytogenes spread within such facilities, especially in those premises with higher L. monocytogenes prevalence in the environment and final food products.

Biofilm formation, virulence and antimicrobial resistance of different Campylobacter jejuni isolates from a poultry slaughterhouse

The fastidious requirement of the zoonotic pathogen Campylobacter jejuni contrasts with its ability to overcome harsh conditions. Different strategies might be involved in the survival and persistence of C. jejuni through the poultry food chain. Therefore, the aims of this study were to get insights in the survival strategies in the poultry slaughterhouse environment by (i) characterizing factors such as biofilm formation, virulence and antimicrobial resistance in environmental isolates and (ii) understanding the possible link between the phenotypic and genetic characterization using whole genome sequencing (WGS). Results have shown that three STs: ST 443 (PFGE A), ST 904 (PFGE C) and ST 3769 (PFGE G), out of the six studied, formed biofilms with variable intensity according to different conditions (temperatures -37 °C, 30 °C, 25°C- and materials -stainless steel and plastic-). High levels of antimicrobial resistance were found in isolates to ciprofloxacin, nalidixic acid and tetracycline as well as to two common detergents used in the slaughterhouse. A combination of several changes in the genome of ST 904 (PFGE C) including mutations, insertions in antimicrobial resistance genes, the presence of T6SS and a set of genes related to virulence factors might explain its ability to form biofilm and persist longer in the environment. However, the complexity of the survival strategies adopted by the different strains of C. jejuni suggests that multiple mechanisms may exist that allow these organisms to persist and ultimately cause disease in humans.

Listeria monocytogenes colonization in a newly established dairy processing facility

The presence and colonization of Listeria monocytogenes were investigated in a newly established dairy processing plant during a one-year period. A total of 250 non-food contact surfaces, 163 food contact surfaces, 46 personnel and 77 food samples were analyzed in two different buildings according to the cheese production chain. Initial steps, including salting, are performed in building I (old facility), while the final steps, including ripening, cutting and packaging, are performed in building II (new facility). Overall, 218 samples were collected from building I and 318 from building II. L. monocytogenes isolates were subtyped by PFGE and MLST, and a questionnaire about quality measures was completed. The overall prevalence of L. monocytogenes was 8.40%, and while the presence of the pathogen was observed just during the first sampling in building I, L. monocytogenes was found in building II at the third sampling event. The salting area in building I had the highest proportion of positive samples with the highest diversity of PFGE types. Moreover, L. monocytogenes PFGE type 3 (sequence type -ST- 204) was first detected in building II in the third visit, and spread through this building until the end of the study. The answers to the questionnaire implied that lack of hygienic barriers in specific parts of the facilities and uncontrolled personnel flow were the critical factors for the spread of L. monocytogenes within and between buildings. Knowledge of the patterns of L. monocytogenes colonization can help a more rational design of new cheesemaking facilities, and improve the food safety within current facilities.

Campylobacter in the Food Chain

Currently Campylobacter is the most commonly reported zoonosis in developed and developing countries. In the European Union, the number of reported confirmed cases of human campylobacteriosis was 246,307 in 2016, which represents 66.3 cases per 100,000 population. The genus Campylobacter includes 31 species with 10 subspecies. Within the genus Campylobacter, C. jejuni subsp. jejuni and C. coli are most frequently associated with human illness. Mainly, the infection is sporadic and self-limiting, although some cases of outbreaks have been also reported and some complications such as Guillain-Barré syndrome might appear sporadically. Although campylobacters are fastidious microaerophilic, unable to multiply outside the host and generally very sensitive, they can adapt and survive in the environment, exhibiting aerotolerance and resistance to starvation. Many mechanisms are involved in this, including pathogenicity, biofilm formation, and antibiotic resistant pathways. This chapter reviews the sources, transmission routes, the mechanisms, and strategies used by Campylobacter to persist in the whole food chain, from farm to fork. Additionally, different strategies are recommended for application along the poultry food chain to avoid the public health risk associated with this pathogen.

Lactic acid bacteria as protective cultures in fermented pork meat to prevent Clostridium spp. growth

In meat fermented foods, Clostridium spp. growth is kept under control by the addition of nitrite. The growing request of consumers for safer products has led to consider alternative bio-based approaches, the use of protective cultures being one of them. This work is aimed at checking the possibility of using two Lactobacillus spp. strains as protective cultures against Clostridium spp. in pork ground meat for fermented salami preparation. Both Lactobacillus strains displayed anti-clostridia activity in vitro using the spot agar test and after co-culturing them in liquid medium with each Clostridium strain. Only one of them, however, namely L. plantarum PCS20, was capable of effectively surviving in ground meat and of performing anti-microbial activity in carnis in a challenge test where meat was inoculated with the Clostridium strain. Therefore, this work pointed out that protective cultures can be a feasible approach for nitrite reduction in fermented meat products.

Comparison of polymerase chain reaction methods and plating for analysis of enriched cultures of Listeria monocytogenes when using the ISO11290-1 method

Analysis for Listeria monocytogenes by ISO11290-1 is time-consuming, entailing two enrichment steps and subsequent plating on agar plates, taking five days without isolate confirmation. The aim of this study was to determine if a polymerase chain reaction (PCR) assay could be used for analysis of the first and second enrichment broths, saving four or two days, respectively. In a comprehensive approach involving six European laboratories, PCR and traditional plating of both enrichment broths from the ISO11290-1 method were compared for the detection of L. monocytogenes in 872 food, raw material and processing environment samples from 13 different dairy and meat food chains. After the first and second enrichments, total DNA was extracted from the enriched cultures and analysed for the presence of L. monocytogenes DNA by PCR. DNA extraction by chaotropic solid-phase extraction (spin column-based silica) combined with real-time PCR (RTi-PCR) was required as it was shown that crude DNA extraction applying sonication lysis and boiling followed by traditional gel-based PCR resulted in fewer positive results than plating. The RTi-PCR results were compared to plating, as defined by the ISO11290-1 method. For first and second enrichments, 90% of the samples gave the same results by RTi-PCR and plating, whatever the RTi-PCR method used. For the samples that gave different results, plating was significantly more accurate for detection of positive samples than RTi-PCR from the first enrichment, but RTi-PCR detected a greater number of positive samples than plating from the second enrichment, regardless of the RTi-PCR method used. RTi-PCR was more accurate for non-food contact surface and food contact surface samples than for food and raw material samples especially from the first enrichment, probably because of sample matrix interference. Even though RTi-PCR analysis of the first enrichment showed less positive results than plating, in outbreak scenarios where a rapid result is required, RTi-PCR could be an efficient way to get a preliminary result to be then confirmed by plating. Using DNA extraction from the second enrichment broth followed by RTi-PCR was reliable and a confirmed result could be obtained in three days, as against seven days by ISO11290-1.

Characterization by culture-dependent and culture-independent methods of the bacterial population of suckling-lamb packaged in different atmospheres

This study offers insight into the dynamics of bacterial populations in fresh cuts of suckling lamb under four different atmospheric conditions: air (A), and three Modified Atmosphere Packaging (MAP) environments, 15%O2/30%CO2/55%N2 (C, commercial), 70%O2/30%CO2 (O), and 15%O2/85%CO2 (H) for 18 days. Microbial analyses by both conventional methods and PCR-DGGE were performed. Controversial and surprising results emerged from comparing both methods in relation to the genus Pseudomonas. Thus, conventional methods detected the presence of high numbers of Pseudomonas colonies, although PCR-DGGE only detected this genus in air-packaged samples. PCR-DGGE detected higher microbial diversity in the control samples (A) than in the modified atmospheres (C, O, H), having atmosphere H the fewest number of species. Brochothrix thermosphacta, LAB (Carnobacterium divergens and Lactobacillus sakei), and Escherichia spp. were detected in all the atmospheres throughout storage. Moreover, previously undescribed bacteria from lamb meat such as Enterobacter hormaechei, Staphylococcus equorum and Jeotgalicoccus spp. were also isolated in this study by DGGE. Additionally, qPCR analysis was used to detect and characterize strains of Escherichia coli. Virulence genes (stx1, stx2 and eae) were detected throughout storage in 97% of the samples. A high CO2 atmosphere was the most effective packaging combination doubling storage time in comparison with commercial atmosphere.