ABSTRACT
Methicillin-resistant Staphylococcus aureus isolates lacking mec genes (n = 32), collected from Belgian hospitals, were characterized for their β-lactamase production and the presence of mutations in pbp genes, the pbp4 promoter, and genes involved in penicillin-binding protein 4 overproduction (gdpP and yjbH). Twelve isolates were β-lactamase hyperproducers (BHPs), while 12 non-BHP isolates might produce an incomplete GdpP protein. Most isolates showed nucleotide missense mutations in pbp genes. A few isolates also showed mutations in the pbp4 promoter.
KEYWORDS: β-lactamase, BORSA, MODSA, PBP
TEXT
Methicillin-resistant Staphylococcus aureus (MRSA) strains carry penicillin-binding protein 2a (PBP2a), a low-affinity PBP encoded by mecA and homologues (1, 2). However, isolates with methicillin and/or oxacillin (OXA) resistance but without mec determinants (methicillin-resistant lacking mec [MRLM] strains) have been reported from the 1980s to recent years (3–10). Their phenotype can be caused by hyperproduction of β-lactamase, which partially hydrolyzes semisynthetic β-lactamase-resistant penicillins (5, 6). These β-lactamase hyperproducers (BHPs) recover full susceptibility to β-lactams in the presence of β-lactamase inhibitors (5, 6). Methicillin resistance has also been associated with multiple unlinked mutations in native pbp genes that reduce the affinity of PBPs for β-lactams, as well as with mutations in the pbp4 promoter and/or in genes (gdpP [phosphodiesterase c-di-AMP regulator] and yjbH [disulfide stress effector]) that lead to PBP4 overproduction (7–9, 11, 12). BHP isolates are usually named borderline oxacillin-resistant S. aureus (BORSA) (6), while isolates with resistance due to mutations are named modified S. aureus (MODSA) (3, 10); however, other authors have used the term BORSA for both BHP and MODSA isolates (4).
Data regarding the characteristics of MRLM strains are scarce (5–10), making their nomenclature difficult. In this study, we have determined the occurrence and characteristics, including β-lactamase hyperproduction and mutations in genes and regions involved in β-lactam resistance, of MRLM strains collected at the Belgian National Reference Centre (NRC) for Staphylococcus aureus.
The study was a retrospective analysis of 298 human S. aureus isolates that were collected from 73 Belgian laboratories and were sent to the NRC, due to diagnostic problems regarding their β-lactam resistance, in 2013 to 2015. The first selection identified isolates resistant to OXA and/or cefoxitin (FOX), as tested by Etest (bioMérieux), combined with the absence of mecA and mecC (13). Selected isolates were further tested for the presence of mecB (14) and PBP2a, by immunochromatographic assay after induction with OXA/FOX disks (13), using the Clearview Exact PBP2a assay (Alere). OXA- and/or FOX-resistant, mecA-, mecB-, mecC-, and PBP2a-negative isolates were studied further.
MICs for penicillin (PEN), ampicillin (AMP), amoxicillin (AMX), amoxicillin-clavulanic acid (AMC), ampicillin-sulbactam (SAM), and ceftaroline (CPT) were determined by the Etest method. MICs for PEN and CPT were interpreted according to EUCAST guidelines (15). β-Lactamase production was determined by the penicillin disk diffusion test (PDDT) (15). The presence of the β-lactamase gene blaZ was determined by PCR (16). Isolates were classified as BHPs if they were PDDT and blaZ positive with ≥2-fold MIC reductions for AMC and/or SAM, compared to AMX and AMP (5). The genes encoding native PBPs (pbp1, pbp2, pbp3, and pbp4), the pbp4 promoter, gdpP, and yjbH were amplified and sequenced by using primers described previously (see the supplemental material). Molecular typing was performed using multilocus sequence typing (MLST) (17).
Among the isolates in the S. aureus collection (n = 298), 32 isolates showed resistance to OXA (n = 8), FOX (n = 6), or OXA and FOX (n = 18) (Table 1) and were mecA, mecB, mecC, and PBP2a negative. This proportion of MRLM strains seemed high (10.7%), compared to other studies of clinical collections (6), but is probably biased by the sampling method (isolates were referred to the NRC because of discordance in OXA and/or FOX resistance results). The isolates were recovered from different patients attending 20 hospitals located in Flanders (n = 10), Wallonia (n = 4), or Brussels (n = 6). The isolates were recovered mostly from nasal/skin screening samples (n = 18) but also from wound/skin infection (n = 8), ear, nose, and throat (n = 3), blood (n = 1), urine (n = 1), and unknown (n = 1) samples. The carriage rates of BORSA isolates have been the subject of only a few studies, but they have been detected colonizing the nares of asymptomatic healthy carriers, as well as being involved in skin and soft tissue infections, surgical wounds, and urinary tract infections in hospital and community settings (10).
TABLE 1.
Phenotypic and genotypic characteristics of methicillin-resistant isolates lacking mec genes
BORSA type and strain | MIC (mg/liter)a |
blaZ | PDDT | BHP | ST/lineageb | |||||
---|---|---|---|---|---|---|---|---|---|---|
OXA | FOX | PEN | AMP/SAM | AMX/AMC | CPT | |||||
BHP | ||||||||||
001 | 3 | 4 | >32 | 4/2 | 12/1 | 0.5 | + | + | + | ST25/CC25 |
002 | 3 | 4 | >32 | 8/2 | 12/1 | 0.38 | + | + | + | ST25/CC25 |
003 | 4 | 4 | >32 | 6/1.5 | 8/1 | 0.38 | + | + | + | ST25/CC25 |
005 | 8 | 4 | >32 | 4/1.5 | 8/1 | 0.38 | + | + | + | ST25/CC25 |
006 | 4 | 3 | 4 | 3/1.5 | 8/0.75 | 0.25 | + | + | + | ST3407/CC25 |
007 | 3 | 3 | >32 | 2/0.5 | 4/0.38 | 0.25 | + | + | + | ST30/CC30 |
008 | 6 | 4 | >32 | 16/3 | 24/1 | 0.38 | + | + | + | ST25/CC25 |
009 | 8 | 4 | >32 | 8/2 | 12/1 | 0.38 | + | + | + | ST8/CC8 |
010 | 6 | 6 | 0.75 | 4/2 | 4/2 | 0.38 | + | + | + | ST9/CC9 |
023 | 4 | 6 | >32 | 12/6 | 16/1 | 0.38 | + | + | + | ST25/CC25 |
030 | 4 | 6 | 3 | 3/1.5 | 6/1.5 | 0.38 | + | + | + | ST34/CC30 |
032 | 6 | 6 | 2 | 4/2 | 12/2 | 0.5 | + | + | + | ST7/CC7 |
Non-BHP | ||||||||||
004 | 12 | 6 | 4 | 2/2 | 3/1 | 0.38 | + | + | − | ST3405/CC8 |
011 | 4 | 8 | 1.5 | 1.5/2 | 2/1.5 | 0.5 | + | + | − | ST5/CC5 |
012 | 8 | 6 | 0.125 | 0.19/0.25 | 0.75/0.5 | 0.5 | + | + | − | ST582/CC15 |
013 | 4 | 6 | 2 | 2/2 | 3/1.5 | 1 | + | + | − | ST5/CC5 |
014 | 4 | 6 | 3 | 3/3 | 4/2 | 1 | + | + | − | ST7/CC7 |
015 | 6 | 6 | 6 | 2/2 | 3/1.5 | 1 | + | + | − | ST101/CC101 |
017 | 1.5 | 6 | 0.75 | 1/1.5 | 2/1 | 0.5 | + | + | − | ST1327/CC22 |
018 | 2 | 6 | 1.5 | 2/2 | 3/1.5 | 1 | + | + | − | ST45/CC45 |
019 | 4 | 8 | 0.75 | 1.5/1.5 | 2/1.5 | 1 | + | + | − | ST669/CC97 |
025 | 6 | 6 | 12 | 3/4 | 3/2 | 0.75 | + | + | − | ST3412/CC101 |
027 | 1 | 6 | 2 | 2/2 | 3/1 | 0.38 | + | + | − | ST3385/CC30 |
028 | 0.75 | 6 | 1.5 | 1/2 | 2/1 | 0.25 | + | + | − | ST109/CC9 |
029 | 0.5 | 6 | 0.75 | 1.5/1 | 2/1 | 0.5 | + | + | − | ST22/CC22 |
031 | 12 | 8 | 4 | 4/3 | 4/2 | 1 | + | + | − | ST3384/CC1 |
016 | 0.5 | 6 | 0.94 | 0.19/0.25 | 0.38/0.38 | 0.25 | − | − | − | ST3411/CC8 |
020 | 3 | 6 | 0.75 | 0.38/0.25 | 0.38/0.38 | 1 | − | − | − | ST101/CC101 |
021 | 8 | 6 | 0.38 | 0.38/0.19 | 1/1.5 | 0.50 | − | − | − | ST101/CC101 |
022 | 6 | 6 | 0.94 | 0.125/0.5 | 0.25/0.75 | 0.38 | − | − | − | ST1/CC1 |
024 | 4 | 6 | 0.19 | 0.50/0.75 | 0.75/0.75 | 1 | − | − | − | ST5/CC5 |
026 | 4 | 6 | 0.25 | 0.50/1 | 1/0.75 | 1 | − | − | − | ST398/CC398 |
Bold type indicates resistance values according to EUCAST (15).
ST, sequence type.
Most isolates (n = 26 [81%]) carried an active β-lactamase (blaZ), but only 12 were PDDT positive and BHPs (Table 1). Although their β-lactam resistance phenotype may be due β-lactamase hyperproduction, they carried mutations (Table 2) that cannot be disregarded as influencing the resistance phenotype. The remaining 20 isolates (including 14 blaZ-positive/PDDT-positive isolates and 6 blaZ-negative/PDDT-negative isolates) were non-BHPs and had diverse mutations (Table 2).
TABLE 2.
Location of mutations in the pbp4 promoter and AA substitutions in the pbp, yjbH, and gdpP genes identified in methicillin-resistant isolates lacking mec genesa
Lineage and strain | Location of mutations/AA substitutions |
||||||
---|---|---|---|---|---|---|---|
PBP1 (pbp1) | PBP2 (pbp2) | PBP3 (pbp3) | Upstream of pbp4 start codon | PBP4 (pbp4) | YjbH (yjbH) | GdpP (gdpP) | |
CC1 | |||||||
031 | − | − | − | − | − | − | A109T, Q163b |
022 | − | − | − | − | R200L | − | R504b |
CC5 | |||||||
011 | − | − | − | − | − | − | D105b |
013 | − | − | − | − | − | − | D105N, P392S, A601E |
024 | − | T284I | − | − | − | − | D105N, P392S, V609b |
CC7 | |||||||
014 | − | Q629P | − | − | − | − | E396b |
032 | − | Q629P | − | − | − | − | I203N |
CC8 | |||||||
004 | − | − | − | − | − | − | V490E |
009 | − | P10L, A405V | N685K, K686N, K687b | − | − | − | F54L, P312L |
016 | − | − | P659c | − | − | − | − |
CC9 | |||||||
010 | T39I, Y336C, T371I, H499Y | A132V, L451I | S634F | T→A at 266 bp | − | − | − |
028 | − | − | D195N | − | − | − | T307I |
CC15 | |||||||
012 | − | H200Y | − | − | − | − | M313I, E314b |
CC22 | |||||||
029 | S629T, S664T | T439V, T691A | K584N | C→T at 407 bp, C→T at 298 bp, G→T at 62 bp | D98E | − | − |
017 | S629T, S664T | T439V, T691A | K584N | C→T at 407 bp, C→T at 298 bp, G→T at 62 bp | D98E | − | V430b |
CC25 | |||||||
001 | D149E | Q629P | K6N | − | − | − | − |
002 | D149E | Q629P | K6N | − | − | − | − |
003 | D149E | Q629P | K6N | − | − | − | − |
005 | D149E | Q629P | K6N | − | − | − | − |
006 | D149E | G142C, Q629P, S679T | K6N, D644G | − | − | − | − |
008 | D149E | Q629P | K6N, F24L | − | − | − | − |
023 | D149E | Q629P | K6N | − | − | − | − |
CC30 | |||||||
007 | − | N81S | − | − | − | − | F54L |
027 | − | − | − | C→T at 171 bp | − | − | V609D |
030 | − | − | − | C→T at 171 bp | − | − | G208S, S403I |
CC45 | |||||||
018 | D480E, S664T | E269Q | S225A, L201F, M376V, D599E | G→T at 62 bp | Y208F, V381F, R430I | − | Q56b |
CC97 | |||||||
019 | H499Y, S571G | − | S634F | − | − | − | A210S |
CC101 | |||||||
015 | D593E | A591T | − | − | E218K | − | Q258b |
020 | D593E | A591T | − | − | E218K | − | Q293b |
021 | D593E | T117C, A591T | − | − | E218K | K259I | Q642b |
025 | D593E | A591T | − | − | E218K | − | E486K |
CC398 | |||||||
026 | F405L, D480E, D662N, S664T | D270E, D489E, T439V, T691A | D684N | A→G at 371 bp, G→A at 265 bp, A→G at 72 bp | − | − | D231Tn |
The isolates are grouped according to their lineage and/or AA substitutions. AA substitutions in the transglycosylase and transpeptidase domain of the PBPs are in italics and bold, respectively. The methicillin-sensitive Staphylococcus aureus strains ATCC 25923, ATCC 9144, NCTC8325, and MSSA476 were used as references for the pbp1, pbp2, pbp3, pbp4 (including its promoter), yjbH, and gdpP genes. The AA substitutions A405V and Q629P in PBP2, affecting β-lactam resistance, were described previously (7, 9, 21). The AA substitutions Y336C, T371I, and H499Y in PBP1 and S364F in PBP3 were detected previously in MRLM strains (9). Some AA substitutions in GdpP (D105N and P392S) are also present in MRSA CC5 reference strains (N315, Mu3, and Mu50). Tn, insertion of a putative IS30 family transposase; −, absence of mutations or amino acid substitutions.
Stop codon.
Absence of amino acid.
The 32 isolates were associated with 13 lineages, with a predominance of clonal complex 25 (CC25) (n = 7 [21.8%]). CC25 has been described as the most frequent lineage with the MRLM phenotype in Canada (7), but this clone is rarely found in Belgian hospitals (18). MRLM strains belonging to CC1, CC8, CC15, and CC45 in clinical settings and strains belonging to CC45 and CC398 in livestock were described previously (9, 19, 20).
Amino acid (AA) substitutions in the transglycosylase and transpeptidase domains of native PBPs may have different effects on β-lactam resistance. Certain AA substitutions affecting β-lactam resistance (A405V and Q629P in PBP2) were described previously (7, 9, 21). Some AA substitutions (Y336C, T371I, and H499Y in PBP1 and S364F in PBP3) were detected previously in MRLM strains from CC1, CC8, and CC15 (9). The non-BHP CC22 (CPT MIC of 0.5 mg/liter) showed AA substitutions (S629T and S664T in PBP1, T691A in PBP2, and D98E in PBP4) in common with CPT-intermediate-resistant (CPT MIC of 2 mg/liter) MRSA CC22, although the former carried additional mutations not present in MRLM strains (17). Isolates of CC25 and CC101 showed specific mutations that may have lineage origins.
Overexpression and/or mutations in PBP4 have been associated with low-level methicillin resistance (11). PBP4 overexpression can be mediated via mutations in its promoter (12) or via AA substitutions and/or loss of function of GdpP and YjbH proteins (22–24). In our study, a few isolates showed mutations in the pbp4 promoter, although no duplications or deletions were detected. One promoter mutation (a nucleotide change from C to T 298 bp upstream of the pbp4 start codon) was located between the −35 and −10 promoter sequences. Only one isolate showed AA substitutions in YjbH, but most carried AA substitutions in GdpP. In fact, 12 of the 20 non-BHP isolates may produce an incomplete GdpP. Among them, one isolate carried a gdpP gene interrupted by the insertion of a putative IS30 family transposase. GdpP is a phosphodiesterase that controls the intracellular levels of the secondary messenger c-di-AMP, which influences cell wall architecture, biofilm formation, and resistance/tolerance to β-lactams (24–26). The deletion of gdpP results in increased levels of c-di-AMP, which increase pbp4 transcript levels (24, 25). Moreover, mutations in this gene have been related to CPT tolerance (27, 28). Interestingly, some (n = 7) of the non-BHP isolates producing an incomplete GdpP have a borderline CPT MIC (1 mg/liter).
The clinical importance of MRLM strains is still unclear. However, these isolates have been involved in cases of clinical failure (29) and outbreaks (19), and they have been observed at high incidence rates in different patient populations (5, 30, 31). In Belgium, MRLM strains represent a heterogeneous group, with different patterns of resistance against β-lactams. Their overall prevalence may be underestimated due to the general use of the FOX test as a unique marker of methicillin resistance. Some isolates were BHPs, but most may be a mixture of BHP and MODSA, underlining the difficulties in their nomenclature.
Accession number(s).
The pbp1, pbp2, pbp3, pbp4, yjbH, and gdpP sequences generated in this study were deposited in GenBank under accession numbers MF070915 to MF071106 (see the supplemental material).
Supplementary Material
ACKNOWLEDGMENTS
We thank our microbiologist colleagues for sending their staphylococcal strains to the NRC.
We have no conflicts to declare.
Footnotes
Supplemental material for this article may be found at https://doi.org/10.1128/AAC.00091-18.
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