Characterization of Knockdown Resistance in DDT-and Pyrethroid-Resistant Culex Quinquefasciatus Populations From Sri Lanka

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Characterization of knockdown resistance in DDT-and pyrethroid-resistant


Culex quinquefasciatus populations from Sri Lanka

Article  in  Tropical Medicine & International Health · May 2008


DOI: 10.1111/j.1365-3156.2008.02033.x · Source: PubMed

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Tropical Medicine and International Health doi:10.1111/j.1365-3156.2008.02033.x

volume 13 no 4 pp 548–555 april 2008

Characterization of knockdown resistance in DDT- and


pyrethroid-resistant Culex quinquefasciatus populations from
Sri Lanka
Charles S. Wondji1, W. A. P. Priyanka De Silva2, Janet Hemingway1, Hilary Ranson1 and S. H. P. Parakrama
Karunaratne2

1 Liverpool School of Tropical Medicine, Liverpool, UK


2 Department of Zoology, University of Peradeniya, Peradeniya, Sri Lanka

Summary DDT and pyrethroid resistance in Culex quinquefasciatus have been previously reported in Sri Lanka,
but the mechanisms involved have yet to be characterized. We report the presence of two mutant alleles
of the sodium channel gene, the target site for both DDT and pyrethroid insecticides. Both mutations
resulted in classic knockdown resistance (kdr) L1014F mutation because of either an A-to-T substitution
or an A-to-C substitution. We developed two alternative assays to distinguish between the two
mutations and used these to screen 214 individuals from nine geographic locations throughout Sri
Lanka. Very high levels of kdr mutations were found throughout the country. A predominance of the
A-to-C mutation was observed over the A-to-T with an average allele frequency of 50% and 2%,
respectively. In addition to these non-synonymous kdr substitutions, we also found an indel (TCACA) in
the intron downstream of the kdr mutation. After genotyping this indel in 136 individuals, we found no
evident correlation between kdr genotypes and intronic indel. The presence of two alternative kdr
mutations has implications for the reliance on single molecular diagnostics for detection of resistance in
field populations. Furthermore, the high levels of these kdr mutations in C. quinquefasciatus populations
throughout Sri Lanka are of concern for the future of pyrethroid-based control programmes on this
island.

keywords Culex quinquefasciatus, pyrethroid, insecticide resistance, sodium channel, knockdown


resistance, Sri Lanka

populations from Sri Lanka and prompted the current


Introduction
study (SHPP Karunaratne, unpublished data).
The mosquito Culex quinquefasciatus is an important Knockdown resistance (kdr), which results from muta-
vector of many parasitic and viral agents of human tions in the voltage-gated sodium channel, the target site of
diseases. In Sri Lanka, as in many countries in Southeast DDT and pyrethroid insecticides, is widespread in many
Asia, C. quinquefasciatus is the main vector of the insect species (Williamson et al. 1996; Dong 1997; Mar-
parasitic worm Wuchereria bancrofti, the agent of tinez-Torres et al. 1998, 1999). This resistance phenotype
lymphatic filariasis (LF) (Jayasekera et al. 1991). Control is most commonly caused by a substitution of a leucine
of this vector has relied extensively on the application of codon (1014) in the S6 hydrophobic segment of domain II
insecticides (McCarroll & Hemingway 2002) and hence which reduces the affinity of target site for insecticides
the emergence of insecticide resistance represents a major (O’Reilly et al. 2006). In Culex and Anopheles mosquitoes,
concern for plans to control or eradicate LF (Ottesen two alternative substitutions, L1014F and L1014S, both
et al. 1997). associated with pyrethroid resistance, have been detected
Resistance to organochlorine, organophosphate and (Martinez-Torres et al. 1998, 1999; Ranson et al. 2000).
carbamate insecticides is well documented and widespread Other metabolic resistance mechanisms involving P450
in populations of C. quinquefasciatus (Hemingway et al. monooxygenases, glutathione S-transferases and carboxy-
1990; Pasteur & Raymond 1996; Karunaratne & Hem- lesterases have also been implicated in pyrethroid resis-
ingway 2001). More recent bioassay data indicated a high tance in mosquitoes, but the detailed molecular basis of
level (around 80%) of pyrethroid resistance in Culex such resistance is unknown.

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Tropical Medicine and International Health volume 13 no 4 pp 548–555 april 2008

C. S. Wondji et al. DDT and pyrethroid resistance in Culex quinquefasciatus

The objective of this study was to detect additional


kdr mutations other than the A-to-T already identified at
codon 1014 in C. quinquefasciatus and to develop tools to
rapidly detect these mutations and to assess their role in
conferring DDT and pyrethroid resistance in this species in
Sri Lanka. We designed two diagnostic methods. One is
applicable in all laboratories including those in resource-
poor settings and the other, while very robust and allowing
high throughput, requires specialized equipment not widely
available in tropical countries. We used these tools to
conduct a preliminary survey of the distribution of kdr
mutations in C. quinquefasciatus in Sri Lanka.

Materials and methods


Mosquito samples and bioassays
Samples of C. quinquefasciatus, which were used to study
the polymorphism of the sodium channel gene, were
collected from Kegalle and Kurunegala in Sri Lanka. For a
preliminary study of the distribution of the kdr mutation
in Sri Lanka, more samples were later collected in
Colombo, Hambantota, Matale, Kandy, Moneragala,
Puttalam and Anuradapura (Figure 1). Larvae of C.
quinquefasciatus were collected in different breeding sites
and reared in the insectary. Bioassays were performed on
3-day-old adults using the standard WHO test kit method
for both DDT at 4% for samples from Kegalle and
permethrin at 0.25% for 1 h for samples from Kurune-
gala. Control tests were carried out by exposing females to
untreated papers. Figure 1 Map of Sri Lanka with areas of mosquito collection.

Amplification and sequencing of sodium channel gene


sequencer. Sequences were searched for polymorphisms
fragment
using BioEdit and ClustalW alignment software (Thomp-
Genomic DNA from 20 adult females resistant to per- son et al. 1994).
methrin (from Kurunegala) and DDT (from Kegalle) was
extracted using the LIVAK method as described previously
New diagnostics for knockdown resistance in Culex
(Collins et al. 1987). A fragment of sodium channel gene
quinquefasciatus
from these mosquitoes was amplified by PCR using two
primers (kdr forward GTG GAT CGA ATC CAT GTG The hot ligation oligonucleotide assay (HOLA) method
and kdr reverse AGC AAG GCT AAG AAA AGG TT). Ten involves a PCR amplification of the target DNA fragment
picomole of each of these primers was added to a PCR followed by a heated oligonucleotide ligation in presence of
reaction containing 1· HotStar Taq Buffer, 0.2 mm a detector primer labelled with biotin and a reporter primer
dNTPs, 1.5 mm MgCl2, 1U HotStar Taq (Qiagen) and labelled with fluorescein. The mutation is detected after a
10 ng genomic DNA. Amplification was performed with coloured reaction in a plate’s well between a horseradish
the following conditions: 1 cycle at 95 C for 15 min; 35 peroxidase-conjugated anti-fluorescein and TMB
cycles of 94 C for 30 s, 52 C for 30 s and elongation at (3,3¢,5,5¢-Tetramethylbenzidine), which is its substrate.
72 C for 1 min; followed by 1 cycle at 72 C for 10 min. Detailed protocols describing this method have been
PCR products were purified using the QIAquick PCR published previously (Lynd et al. 2005; Wondji et al. 2005;
purification kit (Qiagen) and directly sequenced on both Black et al. 2006). A reporter primer and three nucleotide-
the strands using a Beckman CEQ 8000 automatic specific detector primers were designed and used for the

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Tropical Medicine and International Health volume 13 no 4 pp 548–555 april 2008

C. S. Wondji et al. DDT and pyrethroid resistance in Culex quinquefasciatus

hot ligation reaction (Table 1). Aliquots were made for genotype individuals for the presence of this indel follow-
each of the three oligonucleotide pairs containing 1 lm ing the protocol described earlier and using the primers
detector and 1 lm reporter. Three microlitres of PCR listed in Table 1.
product from the reaction described above was mixed with
2 ll of 10· ampligase buffer, 50 nm detector and reporter
Results
mix and 0.05 U ⁄ ll Ampligase enzyme (Epicentre, Mad-
ison, WI, USA) and water to bring the total volume of the Bioassays were carried out with samples from Kegalle and
reaction to 20 ll. The reaction conditions were 95 C for Kurunegala and resulted in 99% survival rate using 4%
5 min, 25 cycles of 94 C for 1 min, 63 C for 2 min, with DDT papers (149 alive over 150 tested) and 0.25%
a final hold at 4 C. Each specimen’s genotype was permethrin (148 alive over 150 tested).
determined following the protocol described in detail by A 400-bp fragment of the sodium channel gene was
Lynd et al. (2005). sequenced from 20 C. quinquefasciatus individuals from
For the pyrosequencing method, 3 sequence-specific Kurunegala, who had survived 1 h of exposure to 0.25%
primers were designed to genotype the kdr mutation permethrin. Two polymorphic sites were identified within
(Table 1) using the software provided by Pyrosequencing this sequence. The first site was at the third position of
AB (http://www.pyrosequencing.com). The sequence to codon 1014, where we observed the A-to-T mutation,
analyse was 5¢-TTA ⁄ C ⁄ TGTC GTGAGTATTCCAG-3¢ inducing a change of leucine to phenylalanine, as previ-
and the dispensation order was 5¢-TACaGTCGT-3¢. The ously reported by Xu et al. (2005) in the same species.
lower case of nucleotide ‘a’ means that it is negative However, some individuals contained an alternative
control and should not be incorporated in the target DNA. phenylalanine codon at this position, encoded by TTC.
A target DNA fragment was first amplified by PCR as This A-to-C kdr mutation has not been previously reported
described previously (Wondji et al. 2007) using the for- in mosquitoes (Davies et al. 2007). The second polymor-
ward and the biotinylated reverse primers presented in phic site was in the intron, around 260-bp downstream of
Table 1. Pyrosequencing reactions were performed as the kdr mutation, where we observed a 5-bp insertion
described by Wondji et al. (2007) according to the man- (TCACA) in 8 of the 15 individuals.
ufacturer’s instructions using the PSQ 96 SNP Reagent Kit
(Biotage AB) and the sequencing primer shown in Table 1.
Optimization of knockdown resistance diagnostics
The genotype was determined using the SNP Software
(Biotage AB). The pyrosequencing method monitors DNA synthesis in
real time by recording bioluminescence resulting from a
cascade of reactions triggered by the incorporation of a
Genotyping of intronic indel
nucleotide. In this study, the assay was used to detect the
A 5-bp indel was identified in the intronic region that three potential nucleotides (A ⁄ C ⁄ T) at the third coding
immediately follows the kdr mutation between base pairs position of the 1014 codon in a single reaction. The
253 and 257 of this intron. The pyrosequencer was used to histograms for each possible genotype at codon 1014 were

Table 1 Oligonucleotide sequences used


Primers Oligo sequences 5¢-3¢ Modifications in both pyrosequencing and HOLA
methods
kdr pyrosequencing
Forward TGTCCTGCATTCCGTTCTTC 5¢-Biotin
Reverse CTAATGCGCACACTAGATCATTCG
Sequencing CACCGTAGTGATAGGAAAT
HOLA method
Reporter AAATTTCCTATCACTACGGTG 5¢-Phosphorylation
3¢-Fluorescein
Detector ‘T’ CTTCAGACTGGAATACTCACGACA 5¢-Biotin
Detector ‘A’ CTTCAGACTGGAATACTCACGACT 5¢-Biotin
Detector ‘C’ CTTCAGACTGGAATACTCACGACG 5¢-Biotin
Indel pyrosequencing
Forward CCTAAAGGTGCAATTGTCTTGG 5¢-Biotin
Reverse CGCATGCGAGATTCCAATC
Sequencing CGTTGTTTTGACAGCTC

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Tropical Medicine and International Health volume 13 no 4 pp 548–555 april 2008

C. S. Wondji et al. DDT and pyrethroid resistance in Culex quinquefasciatus

predicted by the pyrosequencing software as shown in


Figure 2. As an example, for a T ⁄ T homozygote, a single
peak with a relative height of 3 is predicted. In T ⁄ C
heterozygotes, the relative height of the T peak will be
reduced to 2.5 (as T’s now represent 5 out of 6 bases in this
codon) and the C peak will have a relative height of 0.5. All
the six genotypes could be reliably scored using this
method (Figure 3).
Each of the three nucleotides observed at the third
coding position of codon 1014 could also be readily
detected by the HOLA method (Figure 4). Wild-type
individuals gave a positive signal only with the A detector
indicating the TTA genotype, whereas kdr individuals gave
a positive signal using the C and ⁄ or T detectors. The plates
were scored manually, and these results were confirmed
using a spectrophotometer at 650 nm.
For the preliminary study of kdr distribution, individual
C. quinquefasciatus collected from 9 field sites throughout
Sri Lanka were genotyped for the kdr mutation using both
the pyrosequencing and HOLA methods. In general, there
Figure 3 Representative pyrograms of the kdr mutation after the
was a high level of concordance between results obtained pyrosequencing assay. The observed genotypes are C ⁄ C, A ⁄ C,
from the two methods; although, after the initial run, A ⁄ A, A ⁄ T, C ⁄ T and T ⁄ T. The yellow areas indicate the nucleo-
discrepancies were observed in 21 out of 214 individuals. tides of interest (SNP).
For these 21 individuals, we suspected that a non-specific
ligation may have occurred in the HOLA method, and we
therefore increased the ligation temperature from 58 to

(a) (d)

(b) (e)
Figure 4 Example of the kdr genotype results from a HOLA
plate. Origin of samples used: Kegalle (1–3), Matale (4–6), Kandy
(7–9), Colombo (10–12); A ⁄ A, A ⁄ C, A ⁄ T and C ⁄ T, respectively,
indicate homozygote TTA, heterozygote TTA ⁄ TTC, heterozygote
TTA ⁄ TTT and TTC ⁄ TTT genotypes observed for the 12 samples
tested.

(c) (f)
63 C. This improved the concordance rate and left only 5
individuals showing a discrepancy in the genotype score
from the two methods. These 5 samples were sequenced
and the results confirmed scores from the pyrosequencer.
Details of these results are presented in Table 2.

Figure 2 Histograms of the kdr mutation pyrosequencing assay as


predicted by pyrosequencing software. The predicted genotypes Distribution of knockdown resistance frequencies
are C ⁄ C (A), A ⁄ C (B), A ⁄ A (C), A ⁄ T (D), C ⁄ T (E) and T ⁄ T (F).
The yellow areas indicate the nucleotides of interest (SNP). The Of the six potential genotypes (A ⁄ A, A ⁄ C, C ⁄ C, A ⁄ T, C ⁄ T,
sequence to the right is included as a control to verify that the T ⁄ T) that could have been observed at the third codon of
reaction is functioning correctly. residue 1014, A ⁄ A, A ⁄ C and C ⁄ C were by far the most

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C. S. Wondji et al. DDT and pyrethroid resistance in Culex quinquefasciatus

Table 2 Frequency distribution of kdr mutations in samples from Sri Lanka

Genotypes (%)

TTA TTA ⁄ C TTC TTA ⁄ T TTC ⁄ T TTT

Location Number tested SS SR RR SR RR RR

Kegalle 31 15 (48) 8 (25) 6 (19) 2 (6) 0 0


Kurunegala 25 2 (8) 12 (48) 11 (44) 0 0 0
Hambantota 27 9 (33.3) 12 (44.4) 6 (22.2) 0 0 0
Matale 20 3 (15) 8 (40) 7 (35) 1 (5) 1 (5) 0
Kandy 18 11 (61.1) 6 (33.3) 0 0 1 (5.6) 0
Colombo 20 3 (15) 10 (50) 6 (30) 1 (5) 0 0
Moneragala 30 1 (3.3) 20 (66.7) 9 (30) 0 0 0
Puttalam 21 4 (19) 12 (57.1) 5 (23.8) 0 0 0
Anuradapura 22 4 (18.2) 9 (40.9) 8 (36.4) 0 0 1 (4.5)
Total 214 52 (24.3) 97 (45.3) 58 (27.1) 4 (1.87) 2 (0.94) 1 (0.47)

SS, homozygote susceptible genotype; RS, heterozygote susceptible ⁄ resistant genotype; RR, homozygote-resistant genotype. The fre-
quencies of genotypes are given in brackets.

predominant with 52, 97 and 58 individuals, respectively,


Detection of indel
from the total sample size of 214. All the three genotypes
involving the T nucleotide were found only at a very low The TCACA indel identified in the intron downstream of
frequency (4, 2 and 1 for A ⁄ T, C ⁄ T and T ⁄ T, respectively) the kdr mutation was genotyped in 136 samples from the
in the total sample. These results indicate that an A-to-C 9 locations to look for correlations between this indel
rather than A-to-T substitution is the major mutation and the kdr mutation. A PCR product of size 67 bp was
conferring kdr in Sri Lanka. This differs from the situation first obtained using the forward and reverse biotinylated
in the USA (Xu et al. 2005) or in West Africa (Chandre primers (Table 1) before the pyrosequencing reaction.
et al. 1998; Corbel et al. 2007) as well as in C. pipiens The three expected genotypes (TCACA ⁄ TCACA, TCA-
(Martinez-Torres et al. 1999), where only the A-to-T CA ⁄ ) and ) ⁄ )) were clearly identified by the pyrose-
substitution has been reported. quencing assay with observed peaks corresponding to the
Thirty of 31 individuals collected from Kegalle survived expected histograms (Figure 5). The distribution of these
exposure to the diagnostic dose of DDT, and yet 15 of 3 genotypes (Table 3) conforms to the expected ratios
these possess the susceptible genotype suggesting that kdr is
not the major cause of DDT resistance in this location.
(a)
Indeed, this absence of kdr alleles in DDT-resistant
individuals suggests that other mechanisms of resistance
such as the metabolic resistance mechanism could be
operating in these samples through the over-expression of
some detoxifying genes. In Kurunegala, 22 individuals out
(b)
of 25 survived an hour exposure to 0.25% permethrin.
Twelve of these were homozygotes for the kdr mutation,
TTC, and the remainder were heterozygotes (TTC ⁄ TTA).
Of the 3 susceptible individuals (those dead after bioassay
test), 2 individuals were heterozygotes and 1 of them was
homozygote susceptible. (c)

For the 7 other collection sites, where no bioassay was


carried out, the kdr allele varied in frequency from 17% to
64% for the A-to-C mutation and from 0% to 5% for the
A-to-T mutation. The A ⁄ C genotype was predominant in
all 7 samples. These results indicate that the kdr mutation
is common in field populations of C. quinquefasciatus of Figure 5 Expected histograms and observed programs of the
Sri Lanka. TCACA indel of the sodium channel gene by pyrosequencing.

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C. S. Wondji et al. DDT and pyrethroid resistance in Culex quinquefasciatus

Table 3 Distribution of indel genotypes in relation with kdr mutations

kdr Genotypes

Location Number tested TTA TTA ⁄ C TTC TTA ⁄ T TTC ⁄ T TTT

Kegalle-DDT tested TCACA ⁄ TCACA 0 0 0 0 0 0 0


TCACA ⁄ ) 7 4 0 1 2 0 0
)⁄) 5 5 0 0 0 0 0
Kurunegala Permethrine tested TCACA ⁄ TCACA 1 0 1 0 0 0 0
TCACA ⁄ ) 11 0 5 6 0 0 0
)⁄) 7 1 4 2 0 0 0
Hambatota TCACA ⁄ TCACA 4 2 1 1 0 0 0
TCACA ⁄ ) 4 1 2 1 0 0 0
)⁄) 4 1 2 1 0 0 0
Kandy TCACA ⁄ TCACA 4 3 0 0 0 1 0
TCACA ⁄ ) 4 3 1 0 0 0 0
)⁄) 3 3 0 0 0 0 0
Colombo TCACA ⁄ TCACA 2 0 1 1 0 0 0
TCACA ⁄ ) 9 3 3 2 1 0 0
)⁄) 2 1 1 0 0 0 0
Moneragala TCACA ⁄ TCACA 10 1 5 4 0 0 0
TCACA ⁄ ) 7 0 2 5 0 0 0
)⁄) 2 0 2 0 0 0 0
Puttalama TCACA ⁄ TCACA 3 0 2 1 0 0 0
TCACA ⁄ ) 6 3 2 1 0 0 0
)⁄) 6 1 3 2 0 0 0
Anuradapura TCACA ⁄ TCACA 10 2 2 5 0 0 1
TCACA ⁄ ) 4 1 1 2 0 0 0
)⁄) 3 2 1 0 0 0 0
Matale TCACA ⁄ TCACA 2 0 0 2 0 0 0
1 (NG) – – – – – –
TCACA ⁄ ) 13 3 5 3 1 1 0
)⁄) 2 (NG) – – – – – –
Total TCACA ⁄ TCACA 36 8 12 14 0 1 1
1 (NG) – – – – – –
TCACA ⁄ ) 65 16 20 20 4 1 0
)⁄) 32 14 13 5 0 0 0
2 (NG) – – – – – –
136 38 45 39 4 2 1

NG, not genotyped.

under the model of Hardy–Weinberg equilibrium in 7


Discussion
out of the 9 localities (P > 0.05 for each sample after
chi-square test). A deviation from the expected ratio was In this study, we analysed partial sequences of sodium
observed in the two localities of Moneragala and channel gene in field samples of C. quinquefasciatus to
Anuradapura (v2 = 8.1, P = 0.018 and v2 = 10.5, determine the prevalence of kdr alleles in Sri Lanka.
P = 0.005, respectively) with an excess of the TCA- Surprisingly, we identified two alternative substitutions at
CA ⁄ TCACA genotype. No departure from the expected the third position of codon 1014, both of which result in
ratios was observed for the total sample of 136 the replacement of leucine with phenylalanine. As far as we
individuals. We did not observe a significant correlation are aware, this is the first report of the occurrence of two
between this indel and the different kdr genotypes. The alternative phenylalanine codons at position 1014 in the
TCACA ⁄ TCACA and the heterozygote indel genotype sodium channel gene within an insect species. A recent
were observed with five of the six kdr genotypes and the comparative study of voltage-gated sodium channels in 65
homozygote ) ⁄ ) genotype was observed with three of insect species has shown that the A-to-C mutation was
the kdr genotypes (Table 3). present only in 2 species (Davies et al. 2007). These species

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C. S. Wondji et al. DDT and pyrethroid resistance in Culex quinquefasciatus

are Blattella germanica, the German cockroach (Dong equipment, not readily available in disease endemic coun-
1997) and Myzus persicae, the green peach aphid (Marti- ties. By contrast, the HOLA method is very easy to set up
nez-Torres et al. 1999). But the A-to-T mutation was not and implement in any basic laboratory and is a cheap
detected in these two species confirming that the co- diagnostic method for field studies.
occurrence of the A-to-T and A-to-C mutations in C. The present study highlights the genetic plasticity of
quinquefasciatus is the first observation in insects so far. It mosquito species and supports the need to constantly
may be interesting to investigate in future studies if the A- monitor field populations of vectors across their geo-
to-C mutation could confer a different level of pyrethroid graphical distribution for mutations conferring insecticide
resistance than the A-to-T mutation despite the fact that resistance. Populations of C. quinquefasciatus should be
both the mutations lead to the same amino acid change. monitored around the world with one of the two methods
Further investigation could also assess the level of resis- presented in this study to accurately detect the presence of
tance conferred by the simultaneous co-occurrence of A-to- the kdr mutation. This accurate detection will improve
C and A-to-T mutations in a population or in an control programmes on this vector.
individual. Previously, in mosquitoes, two mutations have
been observed in the 1014 codon, but these lead to
Acknowledgements
alternative substitutions, either a serine or phenylalanine
(Martinez-Torres et al. 1999; Ranson et al. 2000). The authors would like to acknowledge Stuart Hall for
The presence of these two alleles shows that kdr technical help.
mutation in C. quinquefasciatus has arisen at least twice.
The high predominance of the A-to-C mutation over the A-
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Corresponding Author Charles S. Wondji, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
Tel.: +44 151 705 3107; Fax: +44 151 705 3369; E-mail: c.s.wondji@liverpool.ac.uk

ª 2008 Blackwell Publishing Ltd 555


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