Foodborne Origin and Local and Global Spread of Staphylococcus saprophyticus Causing Human Urinary Tract Infections.

Staphylococcus saprophyticus is a primary cause of community-acquired urinary tract infections (UTIs) in young women. S. saprophyticus colonizes humans and animals but basic features of its molecular epidemiology are undetermined. We conducted a phylogenomic analysis of 321 S. saprophyticus isolates collected from human UTIs worldwide during 1997-2017 and 232 isolates from human UTIs and the pig-processing chain in a confined region during 2016-2017. We found epidemiologic and genomic evidence that the meat-production chain is a major source of S. saprophyticus causing human UTIs; human microbiota is another possible origin. Pathogenic S. saprophyticus belonged to 2 lineages with distinctive genetic features that are globally and locally disseminated. Pangenome-wide approaches identified a strong association between pathogenicity and antimicrobial resistance, phages, platelet binding proteins, and an increased recombination rate. Our study provides insight into the origin, transmission, and population structure of pathogenic S. saprophyticus and identifies putative new virulence factors.

Staphylococcus saprophyticus Causing Infections in Humans Is Associated with High Resistance to Heavy Metals.

Staphylococcus saprophyticus is a common pathogen of the urinary tract, a heavy metal-rich environment, but information regarding its heavy metal resistance is unknown. We investigated 422 S. saprophyticus isolates from human infection and colonization/contamination, animals, and environmental sources for resistance to copper, zinc, arsenic, and cadmium using the agar dilution method. To identify the genes associated with metal resistance and assess possible links to pathogenicity, we accessed the whole-genome sequence of all isolates and used in silico and pangenome-wide association approaches. The MIC values for copper and zinc were uniformly high (1,600 mg/liter). Genes encoding copper efflux pumps (copA, copB, copZ, mco, and csoR) and zinc transporters (zinT, czrAB, znuBC, and zur) were abundant in the population (20 to 100%). Arsenic and cadmium showed various susceptibility levels. Genes encoding the ars operon (arsRDABC), an ABC transporter and a two-component permease, were linked to resistance to arsenic (MICs ≥ 1,600 mg/liter; 14% [58/422]; P < 0.05). At least three cad genes (cadA or cadC and cadD-cadX or czrC) and genes encoding multidrug efflux pumps and hyperosmoregulation in acidified conditions were associated with resistance to cadmium (MICs ≥ 200 mg/liter; 20% [85/422]; P < 0.05). These resistance genes were frequently carried by mobile genetic elements. Resistance to arsenic and cadmium were linked to human infection and a clonal lineage originating in animals (P < 0.05). Altogether, S. saprophyticus was highly resistant to heavy metals and accumulated multiple metal resistance determinants. The highest arsenic and cadmium resistance levels were associated with infection, suggesting resistance to these metals is relevant for S. saprophyticus pathogenicity.

Genomic and Phenotypic Characterization of Campylobacter fetus subsp. venerealis Strains.

The pathogenesis mechanisms of Campylobacter fetus subsp. venerealis (Cfv), the etiologic agent of Bovine Genital Campylobacteriosis remain elusive. This study evaluated the virulence potential and biovar characteristics of Cfv isolates (n = 13) by PCR screening of putative virulence-factor (VF) genes, Multilocus Sequence Typing (MLST) analysis, antimicrobial susceptibility to tetracycline, penicillin, enrofloxacin and streptomycin testing and whole-genome sequencing (WGS; n = 5), also comparing the latter with 26 other whole-genome sequences of Cfv strains. The putative VF genes encoding type IV secretion system of Cfv (virB2-virB11/virD4) were absent in 92% of isolates, including isolates from aborted foetuses, evidencing that these VF genes are not essential for Cfv pathogenicity. The parA gene, used as a Cfv diagnostic molecular target, was detected in only 3 of 13 isolates, invalidating its use for diagnosis purposes. Three novel sequence types were identified by MLST. Although no in vitro antimicrobial resistance was detected, WGS identified antimicrobial resistance-related genes, including those encoding the multidrug efflux pumps CmeABC and YkkCD, indicating that their presence is not enough to provide antimicrobial resistance. The SNP and accessory protein families analysis segregated the Cfv and Cfv biovar intermedius (Cfvi) strains into different clusters. In conclusion, this study evidenced virulence potential and biovar characteristics of Cfv and Cfvi, which are of relevance for the control of Bovine Genital Campylobacteriosis.

Co-Inoculation with Staphylococcus equorum and Lactobacillus sakei Reduces Vasoactive Biogenic Amines in Traditional Dry-Cured Sausages.

Dry-cured sausages are traditional in Mediterranean countries, and Paio do Alentejo (PA) is one of the most popular in South Portugal. The aim of the present work was to evaluate the effect of combined starters on the safety and quality of PA preserving its sensory quality. Physicochemical parameters, namely pH and water activity (aW), microbiological parameters, biogenic amines, color, texture, and sensory attributes were assessed. Three starter cultures were used, namely Staphylococcus equorum S2M7 and Lactobacillus sakei CV3C2, both separate and combined with the 2RB4 yeast strain at a concentration of 106 cfu/g. Dextrose 0.25% was added to the meat batter. Starters had a significant effect on the reduction of aW values (0.845 to 0.823). The treatment with L. sakei as well as the co-inoculation of L. sakei with S. equorum effectively reduced the L. monocytogenes counts to undetectable levels. Sausages co-inoculated with S. equorum S2M7/L. sakei CV3C2 showed a significant reduction in the content of vasoactive amines, namely tryptamine (26.21 to 15.70) and ß-phenylethylamine (4.80 to 3.69). Regarding texture, control PA showed higher hardness values, and the starters promoted the cohesiveness of the batter while reducing chewiness. The studied starters did not compromise the sensory characteristics of PA.

Staphylococcus saprophyticus From Clinical and Environmental Origins Have Distinct Biofilm Composition.

Biofilm formation has been shown to be critical to the success of uropathogens. Although Staphylococcus saprophyticus is a common cause of urinary tract infections, its biofilm production capacity, composition, genetic basis, and origin are poorly understood. We investigated biofilm formation in a large and diverse collection of S. saprophyticus (n = 422). Biofilm matrix composition was assessed in representative strains (n = 63) belonging to two main S. saprophyticus lineages (G and S) recovered from human infection, colonization, and food-related environment using biofilm detachment approach. To identify factors that could be associated with biofilm formation and structure variation, we used a pangenome-wide association study approach. Almost all the isolates (91%; n = 384/422) produced biofilm. Among the 63 representative strains, we identified eight biofilm matrix phenotypes, but the most common were composed of protein or protein-extracellular DNA (eDNA)-polysaccharides (38%, 24/63 each). Biofilms containing protein-eDNA-polysaccharides were linked to lineage G and environmental isolates, whereas protein-based biofilms were produced by lineage S and infection isolates (p < 0.05). Putative biofilm-associated genes, namely, aas, atl, ebpS, uafA, sasF, sasD, sdrH, splE, sdrE, sdrC, sraP, and ica genes, were found with different frequencies (3-100%), but there was no correlation between their presence and biofilm production or matrix types. Notably, icaC_1 was ubiquitous in the collection, while icaR was lineage G-associated, and only four strains carried a complete ica gene cluster (icaADBCR) except one that was without icaR. We provided evidence, using a comparative genomic approach, that the complete icaADBCR cluster was acquired multiple times by S. saprophyticus and originated from other coagulase-negative staphylococci. Overall, the composition of S. saprophyticus biofilms was distinct in environmental and clinical isolates, suggesting that modulation of biofilm structure could be a key step in the pathogenicity of these bacteria. Moreover, biofilm production in S. saprophyticus is ica-independent, and the complete icaADBCR was acquired from other staphylococci.

Effect of high hydrostatic pressure challenge on biogenic amines, microbiota, and sensory profile in traditional poultry- and pork-based semidried fermented sausage.

The processing of traditional poultry- and pork-based semidried fermented smoked sausages needs to be modernized to improve product quality and further extend its shelf life. The aim of the present study was to apply different combinations of high pressure (300 to 600 MPa) and time (154 to 1,800 s) on the sausages using an experimental design based on response surface methodology. The chemical, microbial, and sensory characteristics of sausages treated with high-pressure processing (HPP) were investigated. HPP application to semidried fermented sausages resulted in color changes, which could be dependent on the ingredients, formulation, and smoking conditions used. Nevertheless, none of the HPP treatments applied resulted in detectable changes in sensory properties, as tested in a triangle test and confirmed by the analysis of focus groups assessment. Significant differences were detected for lactic acid bacteria (LAB) counts from 344 MPa and 1,530 s onward, with a marked decrease for the combination of 600 MPa and 960 s (P < 0.05). Coagulase-negative staphylococci showed higher tolerance to the increase in pressure than LAB. HPP induced a microbial reduction on Enterobacteriaceae, molds, and yeasts, minimizing the production of the main biogenic amines. However, the polyamines (spermine and spermidine) increased since their metabolic use by microorganisms did not occur. Given the reduction of the main spoilage microbial indicators with no detectable sensory changes observed with the binomial condition of 600 MPa and 960 s, this was chosen as the optimal combination to be further applied. PRACTICAL APPLICATION: The results from sensory analysis revealed that any of the HPP treatments applied resulted in detectable changes in sensory properties, as tested in a triangle test and confirmed by the analysis of the focus groups speeches.

Assessment of Coagulase-Negative Staphylococci and Lactic Acid Bacteria Isolated from Portuguese Dry Fermented Sausages as Potential Starters Based on Their Biogenic Amine Profile.

The aim of this study was to evaluate the decarboxylase activity of coagulase-negative staphylococci (CNS) and lactic acid bacteria (LAB) involved in meat products fermentation, in order to characterize and select the strains most suitable to be used as safe starter cultures. Isolates were obtained from traditional Portuguese dry fermented meat sausages, identified by PCR and characterized according to their technological properties. Lactobacilli and enterococci were assessed for their bacteriocinogenic potential. Biogenic amines (BA) were screened by culture method and analyzed by RP-HPLC/UV. The screening method, compared with chromatographic analysis, was not reliable for CNS and LAB strains selection. Tyramine decarboxylase activity was present in CNS strains, with a slight production of amines. No other hazardous BA were produced. Among lactobacilli, moderate production of tyramine was related only to Lactobacillus curvatus, with some strains producing putrescine or 2-phenylethylamine. Enterococci were high and moderate producers of tyramine and 2-phenylethylamine, respectively. Staphylococcus xylosus, Staphylococcus equorum, and Staphylococcus carnosus, independent of their genetic and technological profiles and BA production, were adequate for use in meat products, according to the data. Lactobacillus plantarum and Lactobacillus sakei strains could also be selected for starters. PRACTICAL APPLICATION: The selection of coagulase-negative staphylococci and lactic acid bacteria (LAB) isolates were based on their production of biogenic amines in order to avoid this potential hazard production in meat products. The most suitable isolates could be used as safe starter cultures in meat products industry. The staphylococci and LAB selected will achieve particular organoleptic characteristics in meat products and bioprotection from pathogens.

Characterization and Technological Features of Autochthonous Coagulase-Negative Staphylococci as Potential Starters for Portuguese Dry Fermented Sausages.

The manufacture of dry fermented sausages is an important part of the meat industry in Southern European countries. These products are usually produced in small shops from a mixture of pork, fat, salt, and condiments and are stuffed into natural casings. Meat sausages are slowly cured through spontaneous fermentation by autochthonous microbiota present in the raw materials or introduced during manufacturing. The aim of this work was to evaluate the technological and safety features of coagulase-negative staphylococci (CNS) isolated from Portuguese dry fermented meat sausages in order to select autochthonous starters. Isolates (n = 104) obtained from 2 small manufacturers were identified as Staphylococcus xylosus, Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus carnosus. Genomically diverse isolates (n = 82) were selected for further analysis to determine the ability to produce enzymes (for example, nitrate-reductases, proteases, lipases) and antibiotic susceptibility. Autochthonous CNS producing a wide range of enzymes and showing low antibioresistance were selected as potential starters for future use in the production of dry fermented meat sausages.

Human, food and animal Campylobacter spp. isolated in Portugal: high genetic diversity and antibiotic resistance rates.

Infections by Campylobacter jejuni and Campylobacter coli are considered the major cause of bacterial gastroenteritis in humans, with food being the main source of infection. In this study, a total of 196 Campylobacter strains (125 isolates from humans, 39 from retail food and 32 from food animal sources) isolated in Portugal between 2009 and 2012 were characterised by multilocus sequence typing (MLST) and flaA short variable region (SVR) typing. Susceptibility to six antibiotics as well as the mechanisms underlying antibiotic resistance phenotypes was also studied. Based on MLST typing, C. coli strains were genetically more conserved, with a predominant clonal complex (CC828), than C. jejuni strains. In contrast, C. coli isolates were genetically more variable than C. jejuni with regard to flaA-SVR typing. A high rate of resistance was observed for quinolones (100% to nalidixic acid, >90% to ciprofloxacin) and, in general, resistance was more common among C. coli, especially for erythromycin (40.2% vs. 6.7%). In addition, most isolates (86%) were resistant to multiple antimicrobial families. Besides the expected point mutations associated with antibiotic resistance, detected polymorphisms in the cmeABC locus likely play a role in the multiresistant phenotype. This study provides for the first time an overview of the genetic diversity of Campylobacter strains from Portugal. It also shows a worrying antibiotic multiresistance rate and the emergence of Campylobacter strains resistant to antibiotics of human use.

Genetic diversity, antibiotic resistance and biofilm-forming ability of Arcobacter butzleri isolated from poultry and environment from a Portuguese slaughterhouse.

The genus Arcobacter is an emerging pathogen associated with several clinical symptoms. This genus is widely distributed and has been isolated from environmental, animal, food and human samples, where poultry is considered the major source. In this study, forty three Arcobacter butzleri strains isolated from poultry and environment of a Portuguese slaughterhouse, were characterized by pulsed field gel electrophoresis (PFGE) and assessed for antimicrobial susceptibility and ability to form biofilms. PFGE patterns obtained using restriction enzymes SmaI and SacII revealed high genetic diversity, with 32 distinct PFGE patterns. Most of A. butzleri isolates presented multiple antimicrobial resistance, exhibiting four different resistance profiles. All 43 isolates were susceptible to gentamicin and 2.3% were resistant to chloramphenicol, in contrast to twenty four (55.8%) that were resistant to ciprofloxacin. Among 36 selected isolates, 26 strains presented biofilm-forming ability, which was dependent on the atmosphere and initial inoculum density. Overall, the results showed that A. butzleri displays a high genetic diversity, and presents resistance to several antibiotics, which together with its biofilm formation ability may represent a potential hazard for foodborne infections and a considerable risk for human health.