New Insight into Genotypic and Phenotypic Relatedness of Staphylococcus aureus Strains from Human Infections or Animal Reservoirs

A common human and animal opportunistic pathogen Staphylococcus aureus occurs mostly in the skin and/or nose vestibule mucous membrane as consistent of natural microflora in healthy individuals. Colonization can lead to an invasive mode of infection under particular conditions of a host organism, mostly immunodeficiency, surgical interventions or longitudinal hospitalization of patients (Malachowa et al. 2011; O’Gara 2017). The European Centre for Disease Prevention and Control alarms that the most antimicrobial-resistant healthcare-associated infections are caused by the methicillin-resistant S. aureus (MRSA). Estimating the level of distribution, the MRSA isolates are responsible for 10% to 25% of all staphylococcal infections in Poland; in Slovakia, these rates are even higher (25% to 50%). Moreover, an increasing problem is the expansion of community-acquired MRSA (ECDC 2015).

Staphylococcal strains carrying antimicrobial-resistance genes colonize a vast range of animal species, especially household or livestock animals, with clear evidence of the intra-species transmission of staphylococci (Angen et al. 2017; Kmet et al. 2018).

Under particular conditions, S. aureus causes infections, and become high-risk pathogens due to several virulence determinants such as toxins and enzymes combined with other survival strategies of bacteria like antibiotic resistance and biofilm production (Goldmann and Medina 2017). An important staphylococcal strategy is to damage host cell membranes, caused by hemolysins, bi-component leukocidins, and phenol soluble modulins. For example, α-hemolysin and bi-component leukocidins act as pore-forming toxins, while β-haemolysin is sphingomyelinase, which hydrolyzes lipids of plasma membrane into ceramide and phosphorylcholine (Herrera et al. 2016). Additionally, α-hemolysin and Panton-Valentine leucocidin (PVL) promote apoptosis of phagocytes (Seilie and Bubeck Wardenburg 2017). Another group of virulence factors is an enterotoxin superfamily. These toxins are responsible for staphylococcal food poisoning, but they also affect some immune system cells, with further consequences (Zhang et al. 2017).

S. aureus strains also secrete a variety of enzymes. Proteases include a vast group of secreted enzymes, such as aureolysin, serine proteases, and staphopains, which are engaged in the evasion of complement-mediated bacterial killing (Miedzobrodzki et al. 2002; Sabat et al. 2008; Otto 2014). Nuclease, another extracellular enzyme, degrades neutrophil extracellular traps (NETs), providing the strain resistant to NET-mediated killing (Zawrotniak and Rapala-Kozik 2013; Paharik and Horswill 2016). S. aureus also produces lipase, which lyses triglycerides to free fatty acids – but the biological function of this process is still unknown (Cadieux et al. 2014). Finally, extracellular urease is involved in biofilm regulation and protection against low pH. Urease catalyzes the hydrolysis of urea and neutralizes acids using ammonia (Vandecandelaere et al. 2017). Triggering calculus formation, an increased pH level plays a significant role in urinary tract diseases (Paharik and Horswill 2016).

The progress of S. aureus infections depends on the secretion of surface proteins, numerous extracellular toxins, and enzymes that destruct host cells and tissues (Kong et al. 2016). Due to this fact, this work aimed to recognize the characteristic properties of S. aureus strains based on phenotypic and genetic features such as the production of enzymes and toxins, their resistance profiles and MRSA detection. Firstly, the strains were genetically characterized by microarrays’ profiling and spa typing. Secondly, the human and animal strains were compared based on microarray testing and phenotypic manifestations, together with the analysis of their relatedness or differences between them.

Antibiotic susceptibility testing. All the S. aureus strains tested were susceptible to trimethoprim/sulfamethoxazole (Table II). Five human (19%) and ten animal (37%) strains were susceptible to all the antibiotics tested. Eight strains (15%), the Slovakian bovine strains together with one human strain originated from Kraków were multi-resistant (resistant to more than three antibiotics). The highest resistance rate was observed for penicillin (n = 33; 62%), with 17 human (65%) and 16 animal (59%) resistant strains. The detection of resistance to cefoxitin helped to identify nine strains (two from humans and seven from animals) as methicillin-resistant (MRSA), and one of them did not exhibit resistance to benzylpenicillin/ amoxicillin. Among the MRSA strains, bovine strains from Slovakia (n = 7) were resistant to other antibiotics. All of these strains demonstrated resistance to erythromycin and clindamycin, and they were classified to have an inducible MLS_B (macrolides-lincosamides-streptogramin B resistance) phenotype. Bovine strains of non-Slovakian origins were susceptible to the majority of antibiotics tested. Among methicillin-susceptible S. aureus (MSSA) strains, 18 (54%) demonstrated resistance only to penicillin/amoxicillin, two (6%) to penicillin and doxycycline, four (12%) to penicillin and erythromycin, and one to chloramphenicol and aminoglycosides. The susceptibility rate was high for both human and animal isolates. In both collections, however, the proportions of strains resistant to antimicrobials other than β-lactams were equal.

Enzymatic activity. In the S. aureus collection, 42 strains (79%) demonstrated β-hemolytic activity: 18 strains showed a double zone of hemolysis (Savini et al. 2013), and 24 strains presented a single zone of hemolysis; 11 strains (21%) did not demonstrate hemolysis (Fig. 1.1). Double-zone hemolysis occurred mostly in human strains (n = 12, 23%), and 17 animal strains showed regular β-hemolysis zone. Both human and animal populations showed similar number of β-hemolytic strains.

Fifty-two (98%) strains demonstrated proteolytic activity. Most of the strains showed low (n = 21, 40%) or moderate (n = 23, 43%) proteolysis. Seven (13%) strains, of which five were the human origin, showed high proteolytic activity. Most human (n = 12) and animal (n = 11) strains showed moderate while 14 animal strains (n = 14) showed low proteolytic activity (Fig. 1.2).

All the strains showed nuclease activity, usually high (n = 28, 53%) or moderate (n = 20, 38%). The animal strains (n = 22; 81%) showed higher nuclease activity than human strains, which mostly exhibited moderate activity (n = 16; 62%).

Twenty-nine (55%) strains showed lipase activity, high activity was presented by nine strains (16%; five were human and four animal), moderate activity exhibited 13 strains (25%; seven were human and six animal), and low activity – seven strains (13%; three were human and four animal). Twenty-four (45%) strains did not exhibit any lipase activity. The human and animal bacteria collections showed an almost identical rate of lipase activity.

Forty-four (83%) strains demonstrated urease activity, but in most cases (n = 19, 36%) it was low. Six animal and four human strains showed very high urease activity (n = 10, 19%), three human and seven animal strains showed high activity (n = 10, 19%), and eight human strains showed moderate activity (15%). Nine strains (five from animals and four from humans; n = 9; 17%) did not exhibit urease activity. Human and animal strains did not differ in terms of urease activity. Figure 1 shows the results of phenotypic testing.

Fig. 1.

The spa typing. Based on the spa typing, 35 S. aureus strains were assigned into 20 spa types (Table III). Eighteen singletons were found, including the following spa types: t053, t091, t127, t150, t335, t723, t793, t3165, t4087, t5447, t14393, t14394, t14403, and t14404. Table III shows bacterial isolates assigned to spa types and clonal complexes together with their resistance and virulence genes. Figure 2 presents the results of BURP analysis, which demonstrates the clonal complexes based on the spa gene sequence similarities. Interestingly, spa-CC 045 was previously described as spa-CC 002 using Ridom StaphType software version 1.4 (Ridom GmbH, Würzburg, Germany), but a further update to version 2.1.1 resulted in changing the founder strain within the clonal complex.

Fig. 2.

The human strains belonged into more different spa-CCs than animal strains did. Most human strains (n = 10) and only one animal strain were assigned to spa-CC 084. Interestingly, these ten human strains and one canine strain originated from the same city Gdańsk. Other spa-CCs of human strains were as follows: spa-CC 008.051 (n = 2), spa-CC 017 (n = 3), spa-CC 015.031 (n = 2), and spa-CC 026.2642 (n = 2). Among the animal strains, spa-CCs were also distinct, but there was a strong correlation between spa-CC and a place of strain isolation. The most numerous clonal complex was spa-CC 084 (n = 11). The geographic spa type division was distinctly observed among the strains originating from bovine mastitis infections. Four bovine strains originating from Tomaszów Lubelski were assigned to one spa-CC 14395.14396, four strains originating from Lęczna to spa-type t150, and two strains originating from Luków to spa-type t053. Among the bovine strains received from Kosice (Slovakia), two spa-CCs were reported: spa-CC 045 (n = 4) and spa-CC 2393.5163 (n = 3). The former spa-CC was also identified in Świdnik (n = 3).

Microarray testing. All the strains demonstrated positive results for the species markers: gapA (glyceraldehyde 3-phosphate dehydrogenase), katA (catalase), coa (coagulase), spa (Staphylococcus protein A), sbi (IgG-binding protein), nuc (thermostable nuclease), fnbA (fibronectin-binding protein A), vraS (sensor protein), sarA (staphylococcal accessory regulator A), eno (enolase), and saeS (histidine protein kinase). The presence of nuc gene was also confirmed phenotypically (Fig. 1). Five strains presented negative results, and two strains – ambiguous results for the 23S-rRNA gene, and they were probably caused by RNA contamination. The results for these strains were reliable because the number of ambiguous results did not exceed 3%. All isolates but one (n = 52; 98%) carried the tetEfflux gene, which encodes tetracycline efflux protein, and the fosB gene (n = 43; 81%), which confers resistance to fosfomycin and bleomycin. In 32 strains (17 from humans and 15 from animals), the genes involved in penicillin resistance by the production of β-lactamase (blaZ, blaI, and blaR) were detected; among these strains, eight were MRSA strains. Strains carrying the other resistance genes did not exceed 17%. The most prevalent resistance patterns were: tetEfflux, fosB, and blaZ/I/R, tetEfflux, fosB (Table III). The first one was carried by strains belonged to spa-CC 084 (n = 6; t084, t144, t9490), spa- CC 045 (n = 3; t010), and spa-CC 008.015 (n = 1, t008). Strains with spa type t010 were the only MSSA strains from the spa-CC 045. The other strain from spa-CC 008.015 (no. 23; t051), and two strains from spa-CC 084 (no. 9, 18), harbored the second most frequent pattern. The same resistance genes were present also in spa- CC 017 (n = 1; t021), and all of the strains from spa-CC 14395.14396. The animal strains of spa-CC 2393.5163 carried a unique resistance pattern among other strains from the collections (Table III).

These MRSA strains carried mecA or mecR, and associated with the SCCmec element genes for glicerophosphoryl-diester-phosphodiesterase (upgQ), and cassette chromosome recombinases (ccrA-2, ccrB-2). Four of these strains carried also potassium-transporting ATPases (kdp operon); a DNA-binding response regulator; the mecI gene; and xylR, encoding a pseudogene of xylose repressor. The most MRSA strains belonged to spa-CC 045 (n = 4), and spa-CC 2393.5163 (n = 3). Two strains carried the mecA gene and they were blaZ/I/R negative. One of them exhibited spa type t002 (spa- CC 045), and the other belonged to spa type t2642 (spa-CC 026.2642) (Table III).

All the 53 isolates harbored the δ-hemolysin gene, components of other hemolysins, and the leucocidin D component (lukF/S, lukY, hl, hld, hldIII). All but three strains carried also the gene for α-hemolysin (hlgA, n = 50; 94%); the β-hemolysin gene (hlb, n = 35, 66%); and the staphylokinase gene (sak, n = 24; 45%). The absence of both – hlb and sak genes was a characteristic feature of P-like pA+ genotype of the strains in comparison to other human strains which carried hlb (n = 11) and sak (n = 12) gene in more than 70%. Lack of the sak genes were observed also in animal stains from t010, and t14395. On the other hand, the hlb gene was absent in human spa-CCs 026.2642 and 015.031. Human P-like pA+ strains were in majority grouped in spa-CC 084 (t084, t9490, t491), and two of them were classified as singletons (t335, t793). The characteristic property of these stains was also lack of enterotoxins genes.

Fifteen enterotoxin genes frequently occurred in human and animal strains from most regions, including sea (n = 11; 21%), seb (n = 2; 4%), sec (n = 3; 6%) sed (n = 5; 9%), seg (n = 25; 47%), seh (n = 1; 2%), sei (n = 24; 45%), sej (n = 5; 9%), sel (n = 3; 6%), selm (n = 24; 45%), seln (n = 24; 45%), selo (n = 24; 45%), ser (n = 5; 9%), selu (n = 24; 45%), and ego-cluster (n = 24, 45%), which encodes enterotoxins seg, sei, selm, seln, selo, and selu. Although, strains from spa types t008, t2393, and t5163 carried only enterotoxin A gene (sea).

All the 53 isolates harbored the V8-protease gene (sspA) and staphopain A and B (sspP, sspB), and 47 strains (89%) carried the aureolysin gene (aur). Genes for serine proteases also were detected frequently: 20 human and 21 animal strains (n = 41; 77%) carried the splA and splB genes. Additionally, 10 animal and 20 human strains (n = 30; 57%) carried the splE gene, encoding serine protease E.

Adhesin and biofilm formation genes frequently occurred in the strains analyzed. All of them exhibited following genes: icaA/C (intercellular adhesion protein A/C), icaD (biofilm PIA synthesis protein D), clfA/B (clumping factor A/B), ebh/ebpS (cell wall-associated fibronectin-binding proteins), eno (enolase), fib/fnbA (fibrinogen binding proteins), and vwb (Willebrand factor). Strains from spa-CC 015.031, and spa-CC 017 carried cna (collagen-binding adhesin) genes, which differentiated them from other strains from the collections.

All the 53 isolates harbored the clumping factor genes (clfA, clfB), cell wall-associated fibronectin-binding protein gene ( ebh, ebpS), enolase gene (eno), fibrinogen-binding protein (fib), fibronectin-binding protein (fnb), immunodominant antigen B (isaB), heme/ transferrin-binding protein (isdA), putative transporter protein (ImrP), and hyaluronate lyase A1 (hysA1). The capsule-5 encoding gene (capsule 5) occurred mostly in animal strains while the capsule-8 encoding gene’s (capsule 8) rate was higher in human strains.

The research presented here aimed to characterize the properties of isolates of two particular collections of human and livestock S. aureus strains, using phenotypic and genetic methods, and to assess the compatibility of results between microarray and phenotypic manifestations. The investigation focused on the comparison of human and animal strains because studies have shown that animals are a reservoir of pathogens for people (Petinaki and Spiliopoulou 2012). Therefore, dogs have been reported as hosts for MRSA strains, genetically closely related to human strains (Strommenger et al. 2006; Nienhoff et al. 2009).

The next group of animal strains originated from cows. Transmission of bovine strains from cows and cow milk to people and the other way round has been reported as a result of close contact in the dairy environment (Schmidt et al. 2017). Other authors reported a high share of nasal MRSA colonization among volunteers working in farms. However, only 6% MRSA contaminations survive more than 48 hours (Angen et al. 2017). It has been shown that high persistence of multi-resistant isolates increases the importance of monitoring of intra-species strains transmission (Petinaki and Spiliopoulou 2012).

Another way of bovine strains transmission is the contamination of dairy products (Kummel et al. 2016; Nunes and Caldas 2017), and as a result, foodborne infections in human. There was also shown that laboratory investigation detected S. aureus in stool samples of 15 patients who had gastrointestinal symptoms, and the strains isolated harbored the seg, sei, selm, seln, selo, and selu genes (Umeda et al. 2017). These results provided the convincing evidence of potential foodborne outbreaks caused by S. aureus strains, underlining the significance of bovine strain monitoring to human health prevention.

It was epidemiologically crucial to estimate the resistance to antibiotics for both human and animal pathogens, although the collected strains exhibited low rates of resistance. The low number of MRSA likely resulted from the origin of strains, because all the human strains were received from outdoor patients, and from canine or bovine strains usually presented methicillin-susceptible profiles (Kronenberg et al. 2011; Jagielski et al. 2014). The human and animal collections did not differ in resistance profiles, despite methicillin resistance, which was higher in animal strains.

Detection of the appropriate genes with microarrays also tested all the strains’ antibiotic resistance. MRSA strains (n = 9, 17%) were correctly identified by phenotypic antibiotic tests because all of these strains showed the presence of the mecA gene. Other genetic traits of antibiotic resistance differed from these phenotypically observed. For the blaZ/I/R genes, such differences occurred for three strains (two from humans and one from an animal). Two of them did not carry blaZ/I/R genes, but phenotyping showed their resistance to penicillin, and one of them presented an opposite correlation (there was no phenotypic resistance and the appropriate genes were present). The second situation probably resulted from the phenotypic method drawback, so the presence of blaZ/I/R genes confirmed by microarrays was recognized as a correct result. For some strains the antibiotic resistance genes presence did not correlate with the phenotypic manifestation: for chloramphenicol (n = 2), doxycycline (n = 6), erythromycin (n = 7), amikacin (n = 3), and gentamicin (n = 7). These data partially agree with results by others in which the occurrence rate of resistance genes was higher than the corresponding phenotypic manifestation of resistance (Li et al. 2015). In the present research, the resistance to antibiotics detected by phenotypic methods only, without any confirmation of the presence of resistance genes, was possibly a result of mutations or a novel or not tested resistance gene presence.

The next approach was to compare the phenotypic profiles to genetic ones, and for 23 isolates they differed. The hla gene was detected in 51 (96%) and hlb gene in 35 (66%) strains. These results suggest that hemolysin genes are widespread in staphylococcal populations, even if they do not show any phenotypic manifestation. Thus, there is a strong need to introduce molecular analyses into the hospital and veterinary laboratories, without which many strains may go unnoticed during standard laboratory examinations of patients and ill animals (Moraveji et al. 2014). However, nuclease and protease phenotypic testing gave similar results to molecular analysis.

Furthermore, the human and animal strains were compared based on the microarray patterns, and as it was shown in other investigation, this was the most discriminatory method for strain characterization (Kosecka-Strojek et al. 2016). No specific feature clearly differentiated them when based on the microarray results that concerned resistance genes, virulence genes, adhesion and biofilm formation genes, and immune evasion assay. However, bovine mastitis strains from Poland harbored less resistance and virulence genes than human strains did; this result was in agreement with the recent studies by Schmidt et al. (2017). Interestingly, the bovine strains from Slovakia showed multi-resistant profile. Microarray patterns also demonstrated the close similarity between strains originated from the same geographical places of isolation. However, the human P-like pA+ strains originated from Gdańsk showed slightly different microarray patterns than other strains. The reports have shown that the characteristic property of the P-like pA+ strains was lack of hlb and sak genes, and the present study confirmed this thesis (Piechowicz and Garbacz 2016). Therefore, these strains did not contain any enterotoxin genes in opposite to other human strains of the collections among which most the strains (67%) included genes of egccluster. Other investigation confirmed a high number of enterotoxin genes (n = 90, 56%) of the strains from Kraków (Ilczyszyn et al. 2016). Interestingly, animal strains from Gdańsk showed a low level of those genes (n = 1). This suggests that the P-like pA+ strains are less virulent than other human strains and that virulence is more comparable to animal strains. As widely known, colonization of various hosts by staphylococci requires adaptive changes, which in turn can be reflected by the acquisition of new genetic characteristics. Against the above data, it cannot be excluded that the P-like pA+ isolates described hereby are animal strains that are at a certain stage of the evolutionary process aimed at transforming them into human strains.

The human and animal strains were also compared based on the spa typing, and both collections had different spa types and spa-CCs. The only exception was spa-CC 084, containing ten human strains and an animal strain but all ten strains originated from Gdańsk. Among both human and animal strains, spa-CC strongly correlated with the place of strain isolation. Only one spa-CC 045 was identified in Świdnik (Poland) and Kosice (Slovakia), but according to Ridom SpaServer (www.ridom.de), it is one of the most common spa-CCs, with a global frequency of 6.03%. Our study showed that similarities between strains were more due to their geographic origin than due to the host species from which they originated. According to Ridom SpaServer (www.ridom.de) the most frequent spa-types in the world are t032, t003, t002, and t008. Asadollahi et al. (2018) have analyzed the most prevalent spa-types occurred human strains in particular continents and countries. Authors presented that the most prevalent spa-types in Europe are t008, t002, and t003, while in Poland the most frequent are spa-types are t003, t037, t053, t127, and t021. In contrast, in our study, the majority of human strains belonged to t084, and t9490 of spa-CC084.

The animal strains mostly belonged to t14395, and t010, and bovine strains were grouped. According to Ridom SpaServer (www.ridom.de) the spa type t010 belongs to ST5, whereas in Europe the most frequent are ST97, ST126, ST133, ST151, ST497, and ST771 (Holmes and Zadoks 2011).

The human and animal S. aureus collections were characterized by the phenotypic and molecular methods. The results obtained showed that phenotypically demonstrated resistance profiles and virulence factors were comparable to microarray’s profiling.

Analysis of human and animal strains did not demonstrate any specific marker clearly differentiating them in the microarray results. However, human P-like pA+ strains were characterized by lack of hlb, sak, and enterotoxin genes in comparison to other human strains. Moreover, the bovine mastitis strains from Poland showed sensitivity to almost all antibiotics used in the project in opposite to the Slovakian ones that demonstrated a broad range of antibiotic resistance.

Our study showed that similarities between strains were more due to their geographic origin than due to the host species from which they were isolated.