BioMed Research International

BioMed Research International / 2018 / Article

Research Article | Open Access

Volume 2018 |Article ID 4208762 | 9 pages | https://doi.org/10.1155/2018/4208762

Complex Clonal Diversity of Staphylococcus aureus Nasal Colonization among Community Personnel, Healthcare Workers, and Clinical Students in the Eastern Province, Saudi Arabia

Academic Editor: Klaus P. Hunfeld
Received21 Jul 2018
Accepted26 Nov 2018
Published18 Dec 2018

Abstract

Here, 210 healthy participants including community personnel (70), clinical students (68), and healthcare workers (HCWs) (72) from the eastern region of Saudi Arabia were studied. Sixty-three Staphylococcus aureus isolates were obtained from the nares of 37% of the community personnel and 26% of the clinical students and HCWs. Methicillin-resistant S. aureus (MRSA) was found in 16% (10 isolates) of the 63 isolates; six were from HCWs. Molecular characterization revealed high clonal diversity among the isolates, with 19 different spa types, 12 clonal complexes (CCs), and seven sequence types (STs) detected. The most common strain type was USA900, CC15, and t084, seen in 11 methicillin-susceptible S. aureus (MSSA) isolates. Moreover, three novel spa types in six isolates and one novel ST in two isolates were identified, most from HCWs. Interestingly, 29 isolates were mecA positive by PCR, whereas only 10 isolates were MRSA by disk diffusion (cefoxitin resistant). Of the 19 MSSA mecA-positive isolates, 16 were PBP2a negative, leaving three unique isolates from HCWs that were mecA and PBP2a positive yet cefoxitin susceptible. Our findings highlight the importance of phenotypically and genotypically characterizing S. aureus strains isolated from healthy communities to monitor the risk of possible cross-transmission to hospitalized patients. The identified strains showed a clonal lineage relationship with previously reported S. aureus and MRSA strains acquired from hospital settings.

1. Introduction

Staphylococcus aureus is among the most commonly isolated bacteria especially in hospitals. It causes different types of infections ranging from superficial lesions to life-threatening septicemia, endocarditis, and pneumonia [1]. Most S. aureus infections are caused by methicillin-sensitive strains (MSSA), although a worldwide increase in the number of infections and outbreaks caused by methicillin-resistant S. aureus (MRSA) are also evident [2]. Multiple body sites can be colonized by S. aureus, although in humans, the anterior nares are the most frequent carriage sites and are considered their native ecological niches. Although the nasal carriage of S. aureus does not indicate disease, it does increase the risk of acquiring staphylococcal infections. Consequently, it is used as an indicator to monitor the possibility of outbreaks and hospital-associated infections caused by this organism [3].

Healthcare workers (HCWs) including doctors, nurses, technicians, and diagnostic laboratory staff who have continuous hospital exposure represent an important reservoir for transmitting S. aureus. Similarly, clinical students during their internship are also potential sources for transferring the organism. Accordingly, screening the nasal carriage in these two cohorts is an important component of the control of S. aureus and MRSA in any healthcare facility [4, 5]. Although the community carriage rates of S. aureus are still low, they are rising rapidly in certain parts of the world [6], highlighting the importance of the rapid identification of carriers in order to appropriately control S. aureus infections.

The molecular characterization of S. aureus has become a routine tool for investigating circulating S. aureus clones, and the importance of detecting epidemic clones in hospitals as well as within the community has been well established. Pulsed-field gel electrophoresis (PFGE) has been considered the classical gold standard technique for molecular typing specifically for short-term epidemiology [7]. On the other hand, DNA sequence-based methods such as multilocus sequence typing (MLST) [8] and S. aureus protein A gene (spa)-typing [9] are replacing other molecular-typing techniques because of their ease of use in detecting international clones and exchanging results among laboratories via online databases [10].

The Kingdom of Saudi Arabia is the largest country in western Asia and the second largest in the Arab world. It occupies the bulk of the Arabian Peninsula. The city of Al-Ahsa is located in the eastern region of the kingdom. However, at present, the epidemiological and genetic characterization of S. aureus isolates, especially from healthy carriers, in regions of the Middle East including the Kingdom of Saudi Arabia remain insufficient. The aim of the current study was to determine the frequency of S. aureus and the predominant clones, especially including MRSA, carried in the anterior nares of an open population of community personnel, clinical students, and HCWs within the eastern region of the Kingdom of Saudi Arabia.

2. Materials and Methods

2.1. Subjects

A total of 210 healthy participants were included in the study: 70 were non-hospital personnel (adults in the community), 68 were clinical students, and 72 were HCWs. The non-hospital personnel were between 18 and 30 years old and had not been hospitalized, subjected to dialysis and/or surgery, implanted with a permanent indwelling catheter, or even administered an invasive medical device within the last year. Clinical students were pharmacy students who had clinical exposure during their internship in the eastern region of Saudi Arabia. All community personnel and clinical student participants were of Saudi nationality. The HCWs (doctors, nurses, and diagnostic laboratory staff) included different nationalities working in various clinical departments of six different hospitals in Al-Ahsa, Saudi Arabia. The participants who took part in the study were asked to sign a consent form.

2.2. Sampling Methods

Nasal samples were collected from the anterior nares of the three participant groups, HCWs, clinical students, and community personnel, using a transport swab moistened with sterile normal saline solution. Swabs were then placed in tubes containing Amies medium and transferred within 24 h for laboratory culture. The swabs were used to inoculate mannitol salt agar plates, which were then incubated at 37°C for 24 h. S. aureus was characterized by yellow colonies on MSA due to fermentation of mannitol and a positive coagulase and catalase tests. One representative isolate of S. aureus from each plate was subcultured, screened for coagulase (Staphaurex, Remel, Lenexa, KS, USA), and preserved at -80°C.

2.3. Antimicrobial Susceptibility Testing

S. aureus isolates were screened for their susceptibility to six antibiotics (erythromycin, 15 μg; ampicillin, 10 μg; cefoxitin, 30 μg; amoxicillin/clavulanic acid, 20/10 μg; linezolid, 30 μg; and clindamycin, 2 μg) using the disk diffusion method (Oxoid Ltd, Basingstoke, UK) following the Clinical Laboratory Standards Institute (CLSI) guidelines [11]. Disk diffusion analysis of cefoxitin resistance to detect MRSA was performed according to CLSI recommendations.

2.4. Expression of the mecA Gene (i.e., PBP2a Production)

Penicillin Binding Protein 2a (PBP2a) was assessed by either rapid latex agglutination (Oxoid PBP2a Latex Agglutination Test, Oxoid Microbiology Products, Basingstoke, Hampshire, UK) or rapid immunochromatographic qualitative assay (Alere PBP2a, Alere™, Waltham, MA, USA).

2.5. Molecular Characterization
2.5.1. PFGE Analysis

For each isolate, chromosomal DNA was extracted, digested by SmaI restriction endonuclease in agarose plugs, and analyzed as previously described [12]. Isolates with a PFGE profile similarity of 80% or higher (Dice coefficient, UPGMA clustering) were considered to be related as per Tenover et al. [7].

2.5.2. PCR Amplification of the mecA Gene

Genomic DNA was extracted and utilized for PCR amplification of the mecA gene as described by Fey et al. [13].

2.5.3. Staphylococcal Cassette Chromosome mec (SCCmec) Typing

SCCmec typing was performed on mecA-positive isolates using previously described multiplex PCR protocols [14, 15].

2.5.4. spa Typing

PCR for spa typing was performed using the primers and thermal cycling conditions of the European Network of Laboratories for Sequenced Based Typing of Microbial Pathogens (SeqNet [http://www.seqnet.org]). The spa typing plug-in tool of BioNumerics v7.5 was used for analysis of spa sequences and assignment of spa types, which were confirmed via the freely available Ridom Spa Server (http://spa.ridom.de/index.shtml).

2.5.5. MLST

MLST was performed according to the protocol on the S. aureus MLST website (http://saureus.mlst.net/misc/info.asp).

3. Results

3.1. S. aureus Nasal Carriage and Antimicrobial Susceptibility Testing

S. aureus was isolated from 26 (37%) of the non-hospital community personnel, 18 (26%) of the clinical students, and 19 (26%) HCWs, for a total of 63 isolates. As shown in Table 1, methicillin resistance was found in 16% of the S. aureus isolates (one from the community, six from HCWs, and three from clinical students). Multiresistant S. aureus (resistant to three antibiotics) was isolated from two HCWs (one was MRSA), one community personnel and one clinical student (both isolates were MRSA). Resistance to ampicillin was the most prevalent in all population groups (90% of isolates). No resistance to linezolid was detected, whereas amoxicillin/clavulanic acid and clindamycin remained potent antimicrobials, with 92% and 98% potency, respectively. Five isolates were fully susceptible, three isolated from clinical students and two from community personnel, whereas there were no fully susceptible isolates from HCWs.


CohortIsolate codeAge (years)SexRelatives in healthcare facilityHospitalization during last yearUse of Ab in the last yearResistance pattern

Non-hospital personnel (community)2C20FNNYAMP, E
3C21FNNYAMP
6C21FYNNAMP
7C20FNNYAMP
10C19FNNYAMP
13C21FYNYAMP
14C21FYNNAMP, AMC
15C21FNNNAMP
17C19FNNYAMP
18C19FNNN -
19C22FNNYAMP, AMC
22C22MNNYAMP
24C21MNNYAMP
25C21MYNNAMP
27C22MNNYAMP
29C22MYNNAMP
35C21MNNNAMP
41C23FNNNAMP
45C20FNNNAMP
50C24FNNY -
54C22FNNYAMP, AMC, FOX
56C22FNNNAMP
57C22FYNNAMP
63C20FNNNAMP
67C19FNNNAMP
69C21FNNNAMP

Healthcare workers2W26FYNNAMP, FOX
12W27MNNNAMP
15W26FNNYAMP
17W32MNNYE
23W24MYNNAMP
28W27FNYNAMP, FOX
30W25FNNNAMP, E
31W26MNNNAMP
33W25FNNYAMP
38W23MNNNAMP
49W23MYNNAMP
50W24MNNYAMP
55W40FY YNAMP, FOX
57W59MNNNAMP, E, DA
58W53MYNNAMP, FOX
63W31MNYNAMP, FOX
68W42MYNNAMP, AMC, FOX
70W34MNNNAMP
73W23MNNNAMP

Clinical students3S23FYYYAMP
5S22FYNYAMP
10S22FNYY -
11S22FNNN -
16S21FNNNAMP
17S23FYYYAMP, FOX
19S22FYYYAMP
24S23FNNYAMP, E
26S22FNNYAMP
30S22FYNYAMP
35S23MYNNAMP
37S23MYNYAMP
38S23MNNYAMP
39S22MNNN -
45S25MNNNAMP
48S22MNNYAMP
58S21FNYYAMP, AMC, FOX
68S22MYNYAMP, FOX

M: male; F: female.
Y: yes; N: no.
resistance determined by disk diffusion method, interpreted according to CLSI guidelines [11].
E: erythromycin, 15 μg; AMP: ampicillin, 10 μg, FOX: cefoxitin, 30 μg; AMC: amoxicillin/clavulanic acid, 20/10 μg; LZD: linezolid, 30 μg; DA: clindamycin, 2 μg.
no resistance detected.
3.2. S. aureus Molecular Characterization and Typing

The S. aureus strain types recovered from the different participant groups are summarized in Table 2 and Figure 1. Isolates were initially characterized by PFGE (see supplemental file (available here)) and, where possible, assigned to known S. aureus strain types. Uncertain assigned isolates to known international PFGE types were further characterized by spa typing, from which the MLST clonal complex (CC) or sequence type (ST) was either inferred or specifically determined.


Genotype (PFGE, MLST, spa) / no. of isolates (from C, S, W)No. of MSSA No. of MRSA (SCCmec) / isolate codes

USA900, CC15, t084 / 11 (8, 2, 1)110

EU ST80, CC80, t131 / 6 (3, 2, 1)42 (IV) / 58S, 68W

EMRSA-15, CC22, t1328 / 6 (1, 3, 2)4 (3 mecA pos with SCCmec IV but PBP2a neg)2 (IV) / 28W, 63W

USA200, CC30, t274 / 6 (2, 2, 2)60

USA600, CC45, t065 / 5 (2, 3, 0)50

USA800, CC5, t688 / 3 (0, 0, 3)1 (mecA pos with SCCmec IV and PBP2a pos)2 (IV) / 2W, 55W

USA100/800, CC5, t002 / 1 (0, 0, 1)1 (mecA pos with SCCmec II but PBP2a neg)0

USA300/500, CC8, t008 / 1 (0, 1, 0)10

USA300/500, CC8, t024 / 1 (1, 0, 0)10

USA500, CC97, t267 / 1 (1, 0, 0)10

USA400, CC1, t128 / 1 (1, 0, 0)01 (IVa) / 54C

PFGE A, ST1291, unknown spa / 2 (0, 0, 2)2 (1 mecA pos with SCCmec V and PBP2a pos; 1 mecA pos with SCCmec V but PBP2a neg)0

PFGE B, ST2196, t5078 / 1 (1, 0, 0)1 (mecA pos with SCCmec I but PBP2a neg)0

PFGE C, CC101, t5078 / 4 (2, 1, 1)4 (3 mecA pos with SCCmec I but PBP2a neg)0

PFGE D, ST291, t937 / 2 (0, 1, 1)2 (1 mecA pos with SCCmec I and PBP2a pos; 1 mecA pos with SCCmec I but PBP2a neg)0

PFGE E, SLV1292, t1149 / 2 (0, 0, 2)2 (mecA pos with SCCmec V but PBP2a neg)0

PFGE F, ST6, t304 / 2 (0, 1, 1)02 (II) / 17S, 58W

PFGE G, ST789, unknown spa / 3 (1, 1, 1)3 (mecA pos with SCCmec I but PBP2a neg)0

PFGE H, CC22, t349 / 1 (1, 0, 0)10

PFGE I, ST152, t355 / 1 (1, 0, 0)10

PFGE J, ST2816, unknown spa / 1 (0, 0, 1)1 (mecA pos with SCCmec IV but PBP2a neg)0

PFGE K, CC88, t1339 / 1 (0, 1, 0)01 (IV) / 68S

PFGE L, CC121, t159 / 1 (1, 0, 0)10

PFGE designations either indicate a relationship to known strain types or, where unknown, an arbitrarily assigned alphabetical designation
MRSA as determined by resistance to cefoxitin
unknown spa type (SLV of t11096) 04-12-17-20-17-12-17-17-16
unknown spa type (SLV of t2505) 07-23-21-17-13-323-23-02-12-23
unknown spa type 07-23-12-12-17-13-22-16-16-23
C: community personnel; W: health care workers; S: clinical students
pos: positive; neg: negative.

The 26 community isolates included 14 different strain types (Figure 1(a); Table 2), which in some cases were related to well-known epidemic MRSA types (e.g., CC80 t131; CC8 t024); however, only one was methicillin resistant (CC1 t128). The overwhelming majority of isolates (20 of 26, 77%) were “true” MSSA, known by cefoxitin susceptibility in disk diffusion test, and the most common strain type was CC15 t084 (8 isolates). Five isolates representing four different strain types were phenotypically methicillin susceptible but carried a presumably inactive mecA gene, as evidenced by the susceptible cefoxitin disk diffusion inhibition zone size and the absence of a PBP2a product.

The 18 clinical student isolates (Figure 1(b); Table 2) included 11 different strain types, which in most cases were the same as those isolated from the community personnel. However, three isolates with three different genetic backgrounds were methicillin resistant (ST6 t304, CC88 t1339, and CC80 t131). In addition, five isolates representing four different strain types (three of which were also seen in the community personnel group) exhibited phenotypic methicillin susceptibility, despite carriage of a presumably inactive mecA gene.

The 19 isolates from HCWs (Figure 1(c); Table 2) comprised 13 different strain types. This group had the highest number of “true” MRSA (known by cefoxitin resistance in disk diffusion analysis), 32%: six isolates representing four different strain types and exhibiting greater genetic variability than the two other groups. Six isolates representing four different strain types were phenotypically methicillin susceptible with an inactive mecA gene; one of these strain types was seen in another group (ST789 SLV-t2505). However, the HCW group was unique in yielding three isolates representing three different strain types that were phenotypically methicillin susceptible but mecA positive and PBP2a positive.

The most common genotype was USA900, CC15, and t084, which was detected in 11 MSSA isolates: eight from community personnel, two from clinical students, and one from HCWs. The next most frequent types (six isolates each) were USA200, CC30, t274; EU ST80, CC80, and t131; and EMRSA-15, CC22, and t1328 (Table 2). One-third of the S. aureus isolates (21 of 63) did not correspond to any known PFGE strain type and were thus assigned to 12 different PFGE groups (A to L). SCCmec typing was performed for all 29 mecA-positive isolates, with SCCmecIV being the most common, and represented by 13 isolates. Eight of the 10 MRSA (cefoxitin resistant) isolates were SCCmec type IV, and the remaining two were SCCmec II (Table 2). Three novel spa types were found in six isolates as well as one novel ST (SLV “single locus variant” 1292) in two isolates; six of the eight isolates were from HCWs.

4. Discussion

The striking finding in the present study was the higher than expected nasal colonization rate (37%, 26 of 70) of S. aureus among the community personnel compared to clinical students (26%) and HCWs (26%), all of whom had clinical exposure. On the other hand, the rate of MRSA was the highest among HCWs (six isolates out of 19, 32%), whereas it was the lowest among community personnel (one isolate out of 26, 4%). Two studies reported the characterization of S. aureus from nasally colonized HCWs and medical students in Saudi Arabia [[16, 17], respectively]. In the first study, 40% (80 of 200) of HCWs (primarily nurses) were S. aureus carriers, with 36 of 80 isolates (45%) MRSA. In the second study, 25% (38 of 150) of students were nasal carriers of S. aureus, 10 of them (all from interns who underwent clinical training) being MRSA carriers as determined by detection of the mecA gene. These data are similar to ours, in which most MRSA isolates (nine of 10 isolates) were found among HCWs and clinical students, indicating that hospital exposure may lead to acquiring MRSA strains. Furthermore, Zakai [16] used the CLSI 2010 guidelines when reporting that only two of 10 mecA-positive isolates were oxacillin resistant by disk diffusion, whereas we identified MRSA as cefoxitin resistant by disk diffusion following the CLSI 2015 recommendations.

A study by Laman et al. has reported a nasal colonization of S. aureus in 44 (17.1%) of 257 samples with four isolates being methicillin resistant [18]. In another recent study, Heckel and coworkers reported an overall MRSA carriage rate of 4.1% in a German specialist palliative care setting and the prevalence rate of MRSA in PCU patients was higher than in general acute hospital populations [19]. Moreover, in a study from Taiwan [20], 26% of high school students were found to carry S. aureus in their noses, 14% of which were MRSA. This finding differs from our results for community personnel, among whom there was a 37% (26 of 70) rate of nasal carriage of S. aureus but with only one MRSA isolate (4%).

The current study revealed a high clonal diversity among S. aureus isolates from the three cohorts of healthy nonpatient individuals (community personnel, clinical students, and HCWs). The highest degrees of diversity and genetic variability were seen in the HCW group. Nineteen different spa types, 12 CCs, and seven STs were detected (Table 2), confirming the large genetic variability of isolates found in clinical settings. This is in contrast to a previous report noting a greater diversity of MRSA strains acquired from the community in comparison to those from a hospital setting [10]. In a study from Korea by Kang and colleagues, they reported a concordance rate of 94.2% between colonizing and clinical isolates by methicillin susceptibility with ST72-SCCmec type IV being the most predominant clone [21].

This study underscores the potential for the international dissemination of known epidemic S. aureus strain types to the eastern region of Saudi Arabia because two-thirds of the isolates (42 of 63) corresponded to well-known PFGE types (see supplemental file). It should be noted that the majority of these known types (32 of 42) were from community personnel and clinical students, who were all of Saudi nationality. Although the PFGE characterization of S. aureus isolates from Saudi Arabia has been performed previously [2224], no comparison of relatedness with known international strains was reported (e.g., for MRSA isolates), making it difficult to compare that data with our findings. On the other hand, an 18-year-old study by Van Belkum et al. [25] found that the overwhelming majority of Saudi Arabian MRSA strains (93%) at that time clustered into one predominant type with no relationship to any known epidemic clone. Okoye et al. reported a potential reduction (3-fold reduction) in the prevalence of MRSA nasal colonization in children admitted to Driscoll Children’s Hospital. They also reported that, out of 360 children, 21% were colonized with S. aureus and 14% of those isolates were MRSA [26].

In the present study, 17% of isolates (11 of 63) were identified as the CC15, t084 clone, and all were MSSA. This is in accordance with a previous study from Ghana [27], where 19% (57 of 308) of their isolates were CC15, 37 were t084, and all were MSSA. The CC15 t084 clone was also detected in 27% of MSSA isolates in a Swedish study [28]. It is worth mentioning that, in both of these previous studies, the MSSA isolates were clinical isolates in contrast to our study where all isolates were from healthy personnel, suggesting the cross-dissemination of clones between community and hospital settings. In Saudi Arabia, CC15 (t084, t085) was also detected at a high incidence (27%) in MSSA and MRSA clinical isolates from the AL-Qassim district, which is located in the center of Saudi Arabia, indicating the successful movement and persistence of this clone [29]. The other less commonly identified clonal complexes in our study (CC30, CC80, CC22, and CC45) have also been reported in clinical MRSA isolates from Riyadh (in middle region and the capital city of Saudi Arabia), whereas CC22 was the most prevalent clone (28%) [30]. In the present study, 13 of the 29 (45%) mecA-positive isolates were SCCmecIV. This result is in contrast to data from the city of Makkah (in the western region of Saudi Arabia), where SCCmecIII was the most prevalent (47%) followed by type IV (29%) [31]. However, another study from Saudi Arabia reported that SCCmecIV represented 75% (80 of 107) of isolates [30].

In another study done in Riyadh, Saudi Arabia;,17 clonal complexes were identified in S. aureus isolated from medical students, namely, CC15-MSSA, CC1-MSSA-SCCfus, CC8-MSSA, CC22-MSSA, CC25-MSSA, CC101-MSSA, CC5-MSSA, CC6-MSSA, CC30-MSSA, CC45-MSSA, CC96-MSSA, CC188-MSSA, CC398-MSSA, CC942-MSSA/PVL+, CC1290-MSSA, ST2482-MSSA, and CC80-MRSA-IV/PVL+ [32].

We found 19 MSSA isolates (30%) that carried the mecA gene but were still cefoxitin susceptible; 16 of these were PBP2a negative, leaving three unique MSSA isolates from HCWs that were positive for both mecA and PBP2a yet cefoxitin susceptible. These results illustrate the dynamic interrelationship between the presence or the absence of SCCmec and its expression in S. aureus strains. Previous reports have shown that MRSA and MSSA may contain similar genetic backgrounds, with the intermittent acquisition of SCCmec in MSSA populations [e.g., [33]]. In addition, the spontaneous excision of SCCmec, which encodes the protein responsible for methicillin resistance, may convert MRSA strains to MSSA, which could aid in the treatment of serious infections with resistant strains [34]. The latex agglutination test for PBP2a may show false positive reactions with MSSA [35], which although infrequent may explain our three unique isolates. However, the presence of mecA and PBP2a in MSSA strains deserves further investigation. With regard to susceptibility testing, these data suggest that the cefoxitin disk diffusion test is the most reliable means of identifying functionally active MRSA even though it takes longer than the latex agglutination test for PBP2a and PCR detection of mecA.

5. Conclusion

The diversity and complexity of the S. aureus strains isolated in our study, which were more related to previously known epidemic strains, underscore the need for the routine screening of healthy carriers to prevent infections caused by cross transmission. This study also highlights the importance of both the phenotypic and genotypic characterization of MRSA to better identify the carriers of resistant strains, especially among healthcare staff and clinical students who may serve as a reservoir of MRSA.

Data Availability

The data used to support the findings of this study are included within the article.

Conflicts of Interest

The authors declare no conflicts of interest.

Acknowledgments

The authors extend their appreciation to the Deanship of Scientific Research at King Saud University for funding this work through research group Project no. RGP-038 and Deanship of Scientific Research at King Faisal University, Project no. 150197. They are also grateful to Ms. Mariam R. Buhulaiqah and Ms. Dua’a M. Al-Hamdan for their technical work during the swabbing of the participants and bacterial isolation.

Supplementary Materials

PFGE dendogram for molecular typing of the isolates. (Supplementary Materials)

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Copyright © 2018 Taghrid S. El-Mahdy et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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