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Journal of Clinical Microbiology, October 2008, p. 3208-3214, Vol. 46, No. 10
0095-1137/08/$08.00+0 doi:10.1128/JCM.00221-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS),1 School of Pathology,2 School of Public Health, University of the Witwatersrand, Johannesburg, South Africa,3 Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia4
Received 4 February 2008/ Returned for modification 15 April 2008/ Accepted 14 July 2008
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Neisseria meningitidis contains three penicillin-binding proteins (PBPs): PBP1, encoded by ponA; PBP2, encoded by penA; and PBP3, encoded by pbp3 (2, 6, 19). In meningococci, penicillin nonsusceptibility is due to altered PBP2, causing intermediate resistance (MICs, 0.12 to 0.25 µg/ml) (4, 36), or, in rare cases, to the production of a plasmid-encoded β-lactamase, causing high-level resistance (MICs, >0.25 µg/ml) (9, 46).
Non-β-lactamase-producing penicillin-resistant meningococcal strains were first identified in Spain in 1985 (44). Subsequently, penicillin nonsusceptibility has been reported from several countries, although the frequency with which such isolates have been found varies widely. Surveillance studies of invasive isolates in the United Kingdom, Europe, and North America have reported prevalence rates for penicillin-nonsusceptible isolates ranging from 4% in the United States to 8% in Scotland, 23% in Sweden, and 30% and 38% in France and Portugal, respectively (3, 13, 25, 30, 35, 43). Seventeen percent of invasive isolates and 61% of carriage isolates showed decreased penicillin susceptibility in a study in Turkey (33).
Few studies have documented the existence of penicillin nonsusceptibility in Africa. A study in Casablanca, Morocco, reported an average rate of 4% for invasive meningococcal isolates intermediately resistant to penicillin from 1992 to 2000 (51), and strains from a meningitis outbreak in Ghana showed no evidence of resistance to penicillin (21). In 1987, β-lactamase-producing penicillin-resistant meningococcal isolates (MICs, >256 µg/ml) from two patients in South Africa were reported, but their mechanisms of resistance were never confirmed genotypically (9).
The aims of this study were to detect the prevalence of penicillin-nonsusceptible strains causing invasive disease in South Africa, to determine the clonality of these strains, and to examine the genetic diversity of their penA genes.
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Phenotypic strain characterization.
Bacteria were identified according to standardized procedures (48). Penicillin MICs for all viable isolates were determined by using the Etest (AB Biodisk, Solna, Sweden) on Mueller-Hinton agar supplemented with 5% sheep blood and incubating at 37°C under 5% CO2. Broth microdilution MICs were determined for those isolates for which the penicillin MICs by the Etest were
0.25 µg/ml. Results were interpreted using the following MIC breakpoints, recommended by the Clinical and Laboratory Standards Institute (CLSI) performance standards: susceptibility to penicillin (Pens),
0.06 µg/ml; intermediate resistance (Peni), >0.06 to 0.25 µg/ml; resistance (Penr),
0.5 µg/ml (15). Nitrocefin (Oxoid Ltd., Basingstoke, England) was used to test all submitted isolates for β-lactamase production. Ceftriaxone, chloramphenicol, and rifampin were tested using disk diffusion screening, and MICs for all resistant strains were determined using Etest methodology (15, 16). Screening for fluoroquinolone nonsusceptibility, using ofloxacin discs and the zone size breakpoints stipulated for Neisseria gonorrhoeae (32), was initiated in 2003. In 2005, ciprofloxacin Etest methodology was introduced, and results were interpreted using the new MIC breakpoints provided by the CLSI (15). Serogroups were determined by using slide agglutination with polyclonal antisera to capsular polysaccharides A, C, X, Y, Z, and W135 and a monoclonal antiserum to capsular polysaccharide B (Remel Biotech Limited, Dartford, England). PCR was used to confirm serogrouping for all Peni isolates (39).
Genotypic strain characterization. Isolates that were defined by their MICs (>0.06 µg/ml) as not susceptible to penicillin were selected for further characterization.
PFGE.
Pulsed-field gel electrophoresis (PFGE) was carried out using the NheI restriction enzyme according to a previously described method (23), and restriction profiles were analyzed using GelCompar software (version 4.1; Applied Maths, Kortrijk, Belgium). Dendrograms were created using the unweighted-pair group method with arithmetic averages. The banding patterns were analyzed with the Dice coefficient. Optimization of 1.5% and a position tolerance of 1% were used for the band migration distance. PFGE profiles were visually inspected, and clusters were designated based on differences of
3 bands (42). This was congruent with a similarity index of approximately 80%. A PFGE cluster was therefore defined as three or more isolates sharing
80% similarity on the dendrogram. An arbitrary number was assigned to each cluster. The patterns of Peni isolates were compared to existing patterns for Pens meningococcal isolates stored in the database from previous studies (17, 47).
MLST. Multilocus sequence typing (MLST) was performed on 18 isolates arbitrarily selected from each of the PFGE clusters and unrelated isolates. Sequence types (STs) were determined through the MLST website (http://pubmlst.org/neisseria) (27).
Restriction fragment length polymorphism (RFLP) of penA.
A 511-bp fragment of the transpeptidase region (3' end) of the penA gene was amplified by PCR using previously described primers AA-1 and 99-2 (1). PCR products were subjected to TaqI restriction endonuclease digestion and electrophoresed through 2% agarose gels in order to determine the efficiency of this method in accurately differentiating Pens from Peni or Penr isolates (41). Eight penicillin-susceptible clinical isolates were included as controls (MICs,
0.06 µg/ml).
DNA sequencing of penA. penA gene polymorphisms were determined by sequencing a 511-bp fragment of the transpeptidase region (3' end) of the penA gene. Amplified products were purified using the QIAquick PCR purification kit (Qiagen Inc., Valencia, CA) and were sequenced using BigDye Terminator chemistry (version 3.1; Applied Biosystems, Foster City, CA) and an ABI 3130 capillary sequencer. Sequence analysis and alignment were carried out using DNAStar Lasergene software (version 7). penA alleles were assigned allele numbers based on the nomenclature described by Taha et al. (40) by comparing sequences with those currently available in the penA database (http://neisseria.org/perl/agdbnet/agdbnet.pl?file=penA.xml).
Statistical analysis. Univariate analysis was performed using Fisher's exact test or the Mantel-Haenszel test for comparison of categorical variables. Analysis was performed with Epi Info software, version 6.04d (18), and Stata, version 9 (StataCorp Limited). Two-sided P values of <0.05 were considered significant throughout.
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During the period analyzed, 6% (87/1,381) of isolates were intermediately resistant to penicillin, with MICs ranging from 0.094 to 0.25 µg/ml (the MIC at which 50% of Peni isolates were inhibited was 0.125 µg/ml). No isolates tested fully resistant to penicillin or tested positive for β-lactamase production. Annual prevalences for the Peni isolates were 6% (14/231), 4% (8/192), 13% (33/264), 7% (20/281), and 3% (12/413) for 2001 to 2005, respectively. All Peni isolates were susceptible to chloramphenicol, ceftriaxone, and rifampin. Similarly, all Pens isolates were susceptible to chloramphenicol and ceftriaxone, and 0.3% (4/1,293) were not susceptible to rifampin. All isolates were susceptible to fluoroquinolones.
Invasive meningococcal disease caused by Peni strains did not differ from that caused by Pens strains with regard to the percentage of cases in which patients were children less than 5 years old (50% [42/84] of Peni cases versus 44% [526/1,200] of Pens cases; P = 0.27) or male (52% [44/84] of Peni cases versus 58% [730/1,255] of Pens cases; P = 0.3). The prevalence of Peni was lower among cases in which N. meningitidis was isolated from CSF (5%; 59/1,075) than among those in which the organism was isolated from other sterile sites (9%; 28/306) (P = 0.02). During the period of enhanced surveillance (2003 to 2005), only five patients from whom Peni meningococci were isolated were tested for HIV; of these, 1 patient was HIV positive compared to 79/183 (43%) Pens patients. The in-hospital case fatality rate was 4/23 (17%) for Peni cases compared to 57/359 (16%) for Pens cases (P = 0.85).
The prevalence of Peni isolates for the 5-year period differed by serogroup, with serogroup A demonstrating the lowest prevalence (7/295; 2%); other prevalences were 8% (24/314) for serogroup B, 8% (9/117) for serogroup C, 9% (22/248) for serogroup Y, and 6% (25/396) for serogroup W135 (P = 0.02). Prevalence fluctuated within serogroups over the years; for example, Peni prevalences in serogroup W135 were 15% (2/13), 4% (1/24), 12% (3/26), 12% (9/77), and 4% (10/256) for 2001 to 2005, respectively. The prevalences of Peni in serogroup B ranged from 2% (1/58) in 2005 to 13% (10/76) in 2003. The Peni isolates were identified in all nine provinces of South Africa. The percentages of Peni isolates in the different provinces were as follows: 13% (7/52) in the Eastern Cape, 9% (9/99) in Free State, 5% (42/813) in Gauteng, 11% (5/46) in KwaZulu-Natal, 5% (1/19) in Limpopo, 5% (2/43) in Mpumalanga, 6% (1/16) in Northern Cape, 4% (2/51) in Northwest, and 7% (18/242) in the Western Cape. The relative percentages of Peni and Pens isolates did not differ between provinces (P = 0.23).
Molecular characterization. PFGE patterns were obtained for 82/87 Peni isolates and were grouped into 9 clusters and 19 unrelated isolates (Fig. 1). Cluster 1 (22/82; 27%) comprised W135 strains isolated mostly during 2004 and 2005, all of which also belonged to a larger Pens PFGE cluster representing 93% of all W135 isolates collected nationally during 2000 to 2005 (47). Cluster 2 (14/82; 17%) comprised isolates belonging to serogroup Y. The serogroup Y isolates in this cluster were related by PFGE to a larger clone including serogroup Y Pens isolates, analyzed for this time period. Cluster 3 comprised five serogroup Y isolates (6%). Cluster 4 consisted of five serogroup A isolates, all of which belonged to a larger clone, including Pens isolates, originating from Gauteng Province. Cluster 5 (4/82; 5%) comprised serogroup B and C isolates. Cluster 6 consisted of three serogroup C isolates and one serogroup Y isolate (4/82; 5%). The remaining three clusters were made up of three isolates each, which belonged to serogroups C, B, and W135, respectively. Nineteen isolates were unrelated to the nine clusters and belonged to serogroups B (n = 15), C (n = 2), Y (n = 1), and W135 (n = 1). When analyzed together with Pens isolates, serogroup B and C Peni isolates were found to be heterogeneous and to belong to several different clusters (data not shown).
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FIG. 1. Dendrogram representing the PFGE patterns of 82 N. meningitidis isolates intermediately resistant to penicillin that caused invasive disease in South Africa in 2001 to 2005. Similarity values are given on the dendrogram branches. SG, serogroup; CC, clonal complex.
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RFLP of the penA gene for 87 Peni isolates revealed four restriction endonuclease patterns (Fig. 1). All isolates for which the MIC was
0.094 µg/ml (n = 27) had the same pattern (wild type, or RFLP-1). Forty-eight isolates for which the MIC was 0.125 µg/ml displayed either the RFLP-1 (n = 35) or the RFLP-2 or -3 (n = 13) pattern. Isolates for which the MIC was
0.19 µg/ml (n = 12) had altered patterns (RFLP-2, -3, or -4). Eight penicillin-susceptible control isolates all displayed the wild-type pattern.
DNA sequence analysis of the transpeptidase region of the penA gene from 87 Peni isolates identified 24 different alleles by using the online database, including 9 novel penA alleles that were not listed in the database and were assigned new allele types (Fig. 1 and 2). Amino acid substitutions were observed in PBP2 of only 25/87 (29%) Peni isolates. Twelve isolates for which the MIC was equal to 0.125 µg/ml and all isolates for which the MIC was greater than 0.125 µg/ml (n = 13) displayed altered penA alleles with 10 to 15% nucleotide variation in the transpeptidase region, resulting in 9 to 17 amino acid substitutions in PBP2 (Fig. 2). Eight amino acid substitutions were common to 23 of the 25 isolates; the remaining 2 isolates (isolates 10267 and 13544) harbored six of the eight common substitutions. Twelve isolates harbored an additional Asn residue inserted between residues Thr572 and Ala573 at the 3' end of the fragment.
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FIG. 2. Amino acid alignment showing substitutions in the transpeptidase region of PBP2 for 25 N. meningitidis isolates from South Africa, 2001 to 2005, with intermediate resistance to penicillin. Dashes indicate residues identical to those in the sequence of the Pens strain. The conserved KTG motif in the Pens strain is underlined. Boldfaced residues are common to all 25 isolates. An asterisk marks the position where some isolates have an Asn insertion.
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Overall, the Peni isolates analyzed for this period did not differ from the Pens isolates with regard to patient characteristics such as age or gender, and there was no association with outcome or HIV infection. During the study period evaluated for outcome (2003 to 2005), extended-spectrum cephalosporins were available in clinics and hospitals for empirical treatment of acute bacterial meningitis and were recommended for both children and adults (31); this may have influenced the lack of association with outcome that we observed. In our study, Peni isolates were more likely to be isolated from blood culture specimens than from CSF specimens. Oral antibiotics given to ill patients prior to admission may affect bacteremic organisms, rendering blood sterile, with less impact on organisms in the CSF. Our sample of bacteremic isolates may therefore be biased toward the more resistant strains.
PFGE showed a high degree of genetic diversity among the South African Peni isolates, with no dominant clone. Isolates clustered mostly according to serogroup. Previous work has shown that serogroup B and C isolates are genetically diverse in South Africa (17), and similarly, the Peni isolates belonging to these serogroups were genetically heterogeneous. In contrast, serogroup A, W135, and Y isolates are highly clonal in South Africa (17), and the Peni isolates belonging to these serogroups mimicked this trend. Several STs were identified among the Peni isolates, some of which have been described in Pens isolates (17, 47). Several studies have, like ours, found Peni strains to be genetically diverse (3, 25, 36). However, some studies have reported the emergence and spread of virulent clones intermediately resistant to penicillin (7, 12, 38). A Peni serogroup C clone caused an outbreak in Saskatchewan, Canada, in 1993 (7). A surveillance study in Portugal in 2000 to 2001 showed that penicillin resistance was significantly associated with serogroup C isolates displaying the C:2b:P1.2 phenotype (12). In Italy, an increase in serogroup C disease occurred in 2000 to 2003 (38). The majority of isolates (42%) belonged to a penicillin-nonsusceptible serogroup C clone (C:2b:P1.5) similar to that found in Portugal.
Some studies have suggested that restriction digestion of the penA gene is a rapid and reliable method for screening for penicillin nonsusceptibility in cultures (1, 29) and may also be useful for determining penicillin nonsusceptibility in culture-negative cases of meningococcal infection. However, our data show that only those Peni isolates that harbored penA alleles with nonsynonymous mutations displayed restriction profiles different from that of the wild type. Several Peni isolates displayed restriction patterns identical to those for Pens isolates, indicating that they would have been misclassified as Pens by use of this screening method.
penA sequences from non-penicillin-susceptible strains have been shown to be variable and highly divergent from those of wild-type strains, particularly in the 3' transpeptidase-encoding region (2). A MIC of >0.06 µg/ml has been established as the breakpoint for defining intermediate resistance to penicillin by use of broth microdilution (15). Our data show that all isolates for which the Etest MIC was
0.19 µg/ml had polymorphic penA alleles. The majority of isolates for which the Etest MIC was 0.125 µg/ml had penA alleles that were almost identical to the wild-type allele, differing by only a few nucleotide substitutions. Other studies have shown that a MIC of
0.125 µg/ml was associated with polymorphic penA genes (29, 43). Arreaza et al. have suggested that a MIC of 0.094 µg/ml should be used to define the intermediate breakpoint for penicillin (5). All of the South African isolates for which the MIC was
0.094 µg/ml had wild-type penA alleles. Phenotypic antibiotic susceptibility testing is, however, difficult to compare between laboratories in different countries because of differences in reagents and methodology (45).
The alteration of only one PBP suggests that penicillin resistance in N. meningitidis is still evolving, and the accumulation of additional altered PBPs may confer a higher level of resistance. Nucleotide sequencing of the penA gene showed a high degree of sequence diversity among the Peni isolates in this study, suggesting that these genes have arisen independently. The majority of Peni isolates harbored penA alleles with synonymous nucleotide substitutions, resulting in no amino acid alterations in PBP2. Approximately one-third of the Peni isolates had an altered PBP2. Eight amino acid changes were common to all isolates that had an altered penA allele (except for two isolates that had only six of these substitutions). The eight substitutions were the same as those previously described by Antignac et al. (2) and have been shown to correlate with the same region in Streptococcus pneumoniae PBP2X, which forms part of the active site for β-lactam binding. These investigators also showed that a PCR-amplified fragment harboring these eight mutations was sufficient to confer resistance on a penicillin-susceptible strain. Transformation studies with N. gonorrhoeae have shown that the presence of an additional aspartic acid residue in PBP2 results in a decreased affinity for penicillin; however, the presence of any other additional amino acids did not confer resistance (10). The significance of the Asn insertion in PBP2 of some of the South African N. meningitidis isolates is unclear, since it was present only in some altered penA alleles.
Nonsusceptibility to rifampin, chloramphenicol, and ceftriaxone has been reported previously but remains rare, with studies reporting either no reduced susceptibility or low prevalences (22, 26, 37, 51). Similarly, we report no reduced susceptibility to chloramphenicol or ceftriaxone and an extremely low prevalence of nonsusceptibility to rifampin. In 2007 to 2008, three cases of infection with epidemiologically and genotypically linked fluoroquinolone-resistant serogroup B meningococci were reported from the North Dakota-Minnesota region of the United States (14). The use of ciprofloxacin for chemoprophylaxis was subsequently suspended in this region, until further notice. We report no fluoroquinolone resistance among our meningococcal isolates.
To our knowledge, this is the first publication describing meningococci from sub-Saharan Africa that are intermediately resistant to penicillin. These isolates do not, at this time, appear to be due to the spread of a single clone. Continued surveillance, in South Africa and elsewhere in Africa, is necessary for monitoring ongoing trends in antimicrobial susceptibility, in particular the emergence of resistant strains that may pose therapeutic problems.
We also thank the following members of GERMS-SA: Sandeep Vasaikar (University of Transkei, Mthatha, Eastern Cape); Nolan Janse van Rensberg and Peter Smith (University of the Free State, Bloemfontein, Free State); Khatija Ahmed, Anwar Hoosen, Ruth Lekalakala, and Pyu Pyu Sein (University of Limpopo—Medunsa Campus, Garankuwa, Gauteng); Heather Crewe-Brown, Charles Feldman, Alan Karstaedt, Olga Perovic, and Jeannette Wadula (University of the Witwatersrand, Johannesburg, Gauteng); Mike Dove, Kathy Lindeque, Linda Meyer, and Gerhard Weldhagen (University of Pretoria, Pretoria, Gauteng); Wim Sturm and Trusha Vanmali (University of KwaZulu-Natal, Durban, KwaZulu-Natal); Ken Hamese (Polokwane/Mankweng Hospital Complex, Polokwane, Limpopo); Keith Bauer, Greta Hoyland, and Charles Mutanda (National Health Laboratory Service, Mpumalanga); Rena Hoffmann and Lynne Liebowitz (University of Stellenbosch, Stellenbosch, Western Cape); Denise Roditi, John Simpson, and Andrew Whitelaw (University of Cape Town, Cape Town, Western Cape); Adrian Brink (AMPATH Laboratories, Johannesburg, Gauteng); Claire Heney (Lancet Laboratories, Johannesburg, Gauteng); Marthinus Senekal (PathCare Laboratories, Cape Town, Western Cape); and John Frean, Karen Keddy, Kerrigan McCarthy, Elizabeth Prentice, Vanessa Quan, and Koshika Soma (National Institute for Communicable Diseases, Johannesburg, Gauteng).
This study was funded by the Medical Research Council, the National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), and the University of the Witwatersrand, South Africa, and by funds from the U.S. Agency for International Development's Antimicrobial Resistance Initiative, transferred via a cooperative agreement (U60/CCU022088) from the Centers for Disease Control and Prevention (CDC), Atlanta, GA. The contents are solely the responsibility of the authors and do not necessarily represent the official views of the CDC.
Published ahead of print on 23 July 2008. ![]()
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