Download Distribution of antibiotic resistance genes in a

Distribution of antibiotic resistance genes in a global
Neisseria genome collection
E. Orton1, C. Brehony1 and M.C.J. Maiden1
1Department of Zoology, University of Oxford, Oxford, UK
Introduction
Fig. 1: Proportion of
resistant/reduced
susceptibility alleles
within the global dataset
for each of the four
antibiotic
resistance/reduced
susceptibility loci
analysed.
Although antibiotic resistance in Neisseria meningitidis (Nm) is not as
widespread a problem as it is for N. gonorrhoeae (Ng), the possibility of
increased resistance is always a concern. Specific mutations in four genes have
been shown to be associated with increased resistance to specific antibiotics:
rpoB (rifampicin), penA (penicillin G), gyrA (ciprofloxacin) and folP
(sulphonamide) (1-5). These genes were analysed in a collection of publically
accessible Neisseria species genomes on the PubMLST database
http://pubmlst.org/neisseria/. There were 1505 isolates in the collection
analysed and comprised 22 species of which 73.1% were Nm, 13.8% Ng and 7.4%
N. lactamica (Nl). The time period spanned by the collection was 1937-2013 and
included isolates from six continents and 50 countries. Analyses were carried
out using the embedded database tools. The temporal and geographic
distribution of resistance/reduced susceptibility associated alleles was analysed
along with their presence amongst other Neisseria species.
Temporal and geographic patterns
Fig. 2: Global
distribution of
resistant folP
alleles.
• Many resistant folP alleles (1, 4, 5, 8) in Nm have been in circulation for >40
years whilst some (37, 130, 162, 203) have shorter lifespans of 10-20 years.
• The resistant folP allele (112) identified in Nl had a lifespan of 21 years.
• All the resistant gyrA alleles identified (50, 71, 74, 128, 151) were within a
single isolate and have been recorded since 2000.
• Two of the reduced susceptibility penA alleles (7, 12) had a lifespan of <10
years, and two (9, 14) <20 years.
• All the prevalent resistant folP alleles were identified in Europe, though
many were also present in Africa and N. America (Fig. 2).
• The resistant Nm gyrA alleles were present in N. America (74, 151) or Asia
(71), whilst the resistant gyrA allele in Nl was identified in Europe
• All of the reduced susceptibility penA alleles were found in Europe (7, 9, 12,
14); two were also found in N. America (7, 14) and one also in Africa (14).
Fig. 3: Neighbour Joining Tree of
folP nucleotide allele sequences in
different Neisseria species.
Resistance associated alleles are
denoted by a hollow symbol.
Species distribution of resistance associated
alleles
• Several non Nm folP resistance alleles were interspersed with Nm alleles
implying recombination and potential reservoir of resistance alleles amongst
species (Fig. 3).
• Nm, Ng and Nl were the only species with resistant gyrA alleles.
• The cluster of reduced susceptibility penA alleles in N. subflava included one
resistant Nm allele.
• There was one resistant rpoB allele within Ng.
Typing associations
• 74.6% serogroup W folP alleles were resistance associated and 41.1% of
serogroup B alleles were resistance associated.
• Association of folP resistance alleles varied among the major hyperinvasive
clonal complexes (cc) (Table 1): 100% of alleles associated with ST-32cc were
resistant; 5.9% in ST-269cc.
• Each of the resistant gyrA alleles with typing data was a different serogroup:
A (74), B (151) and C (71).
• One isolate with a resistant gyrA allele was found within each of ST-5, ST162, ST-624 and ST-4821 ccs.
• Serogroup W had the highest frequency of reduced susceptibility penA alleles
(n=8), followed by serogroup C (n=3) and serogroup B (n=3).
• There was limited association between reduced susceptibility penA alleles
and the major hyperinvasive ccs; only 10.6% of penA alleles associated with
ST-269, and 0% for ST-1, ST-4 and ST-5 ccs.
Table 1:
Prevalence of
resistant folP
alleles associated
with
hyperinvasive
ccs.
References:
1. Taha MK, et al. 2010. Multicenter study for defining the breakpoint for rifampin resistance in Neisseria meningitidis by rpoB sequencing. Antimicrob. Agents Chemother. 54:3651-8.
2. Hong E, et al. 2013. Target gene sequencing to define the susceptibility of Neisseria meningitidis to ciprofloxacin. Antimicrob. Agents Chemother.:In press.
3. Qvarnstrom Y, Swedberg G. 2000. Additive effects of a two-amino-acid insertion and a single-amino-acid substitution in dihydropteroate synthase for the development of
sulphonamide-resistant Neisseria meningitidis. Microbiology 146 ( Pt 5):1151-6.
4. Fiebelkorn KR, et al. 2005. Mutations in folP associated with elevated sulfonamide MICs for Neisseria meningitidis clinical isolates from five continents. Antimicrob. Agents
Chemother. 49:536-40.
5. Taha MK, et al. 2007. Target gene sequencing to characterize the penicillin G susceptibility of Neisseria meningitidis. Antimicrob. Agents Chemother. 51:2784-92.
Multiple resistance
• Five isolates had multi-drug resistance (i.e. at least 3 loci) and were Ng or Nl.
• 107 isolates had two resistance associated alleles.
• Several folP and penA resistant/reduced susceptibility isolates were found,
mostly in Nm.
• Two were two Nm isolates with resistant folP and gyrA alleles.
• There was evidence of a pool of folP and penA resistance/reduced
susceptibility diversity within other Neisseria species, which could have
spread into Nm isolates.
Conclusions
This dataset enabled antibiotic resistance/reduced susceptibility to
sulphonamides, penicillin G, ciprofloxacin and rifampicin to be assessed on a
global scale and in a range of Neisseria species. The analysis demonstrated the
wide temporal and geographical spread of sulphonamide and penicillin G
antibiotic resistance/reduced susceptibility which was not the case for
ciprofloxacin and rifampicin. However, the potential for horizontal gene
transfer of resistance between different Neisseria species was evident and a
cause for close monitoring. This type of approach using NGS for molecular
epidemiology can greatly assist in such surveillance.