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Antimicrobial Agents and Chemotherapy, May 2007, p. 1589-1595, Vol. 51, No. 5
0066-4804/07/$08.00+0 doi:10.1128/AAC.01545-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Horizontal Gene Transfer of ftsI, Encoding Penicillin-Binding Protein 3, in Haemophilus influenzae
Sho Takahata,*
Takashi Ida,
Nami Senju,
Yumiko Sanbongi,
Aiko Miyata,
Kazunori Maebashi, and
Shigeru Hoshiko
Pharmaceutical Research Center, Meiji Seika Kaisha, Ltd., 760 Morooka-cho, Kohoku-ku, Yokohama 222-8567, Japan
Received 12 December 2006/
Returned for modification 20 January 2007/
Accepted 15 February 2007

ABSTRACT
Horizontal gene transfer has been identified in only a small
number of genes in
Haemophilus influenzae, an organism which
is naturally competent for transformation. This report provides
evidence for the genetic transfer of the
ftsI gene, which encodes
penicillin-binding protein 3, in
H. influenzae. Mosaic structures
of the
ftsI gene were found in several clinical isolates of
H. influenzae. To identify the origin of the mosaic sequence,
complete sequences of the corresponding gene from seven type
strains of
Haemophilus species were determined. Comparison of
these sequences with mosaic regions identified a homologous
recombination of the
ftsI gene between
H. influenzae and
Haemophilus haemolyticus. Subsequently, ampicillin-resistant
H. influenzae strains harboring identical
ftsI sequences were genotyped by
pulsed-field gel electrophoresis (PFGE). Divergent PFGE patterns
among β-lactamase-nonproducing ampicillin-resistant (BLNAR)
strains from different hospitals indicated the potential for
the genetic transfer of the mutated
ftsI gene between these
isolates. Moreover, transfer of the
ftsI gene from BLNAR strains
to β-lactamase-nonproducing ampicillin-susceptible (BLNAS)
H. influenzae strains was evaluated in vitro. Coincubation of
a BLNAS strain (a rifampin-resistant mutant of strain Rd) and
BLNAR strains resulted in the emergence of rifampin- and cefdinir-resistant
clones at frequencies of 5.1
x 10
–7 to 1.5
x 10
–6.
Characterization of these doubly resistant mutants by DNA sequencing
of the
ftsI gene, susceptibility testing, and genotyping by
PFGE revealed that the
ftsI genes of BLNAR strains had transferred
to BLNAS strains during coincubation. In conclusion, horizontal
transfer of the
ftsI gene in
H. influenzae can occur in an intraspecies
and an interspecies manner.

INTRODUCTION
Haemophilus influenzae is naturally competent for DNA uptake
from the surrounding environment. Recognition and efficient
uptake of species-specific DNA molecules is mediated by the
presence of uptake signal sequences (USSs) in donor DNA. The
consensus sequence of the USS in
H. influenzae was identified
as 5'-AAGTGCGGT-3' (
6). A recent study has revealed that USSs
exist in the genomes of other species of the family
Pasteurellaceae,
suggesting that this element is utilized for the uptake and
exchange of DNA between
H. influenzae and related species (
2).
A total of 1,471 copies of the USS were found in the
H. influenzae Rd strain by searching its complete genome (
15). However, horizontal
gene transfer in
H. influenzae has been reported for a small
number of genes. For instance, the genetic transfer of
ompP2,
a gene encoding major outer membrane protein P2, was reported
among clinical isolates of
H. influenzae (
7,
16). Intergeneric
lateral transfer of the tryptophanase gene cluster between
Escherichia coli and
H. influenzae was also identified (
11).
Penicillin-binding protein 3 (PBP 3), which is encoded by the ftsI gene, is a transpeptidase needed for cross-linking of the septal cell wall peptidoglycan during cell division. The essentiality of this enzyme in H. influenzae was demonstrated by targeted gene disruption (18). A remarkable increase of β-lactamase-nonproducing ampicillin-resistant (BLNAR) H. influenzae strains has been reported in Japan (14). These resistant strains have been shown to possess various mutations in the ftsI gene, leading to amino acid substitutions responsible for β-lactam resistance, such as substitutions at positions 526 (Asn
Lys), 517 (Arg
His), 377 (Met
Ile), 385 (Ser
Thr), and 389 (Leu
Phe) in the PBP 3 protein (12, 19). Due to their rapid increase and nationwide spread, it is difficult to consider that BLNAR strains emerged independently by accumulating multiple mutations in the ftsI gene. Moreover, totally identical ftsI sequences from different BLNAR isolates have frequently been observed (14). These observations drove us to hypothesize that the genetic transfer of the ftsI gene occurs in H. influenzae strains. In this study, evidence for the genetic transfer of the ftsI gene in H. influenzae was obtained by carefully analyzing the nucleotide sequence of the ftsI genes from various clinical isolates and also by in vitro gene transfer experiments.

MATERIALS AND METHODS
Bacterial strains.
The strains used in this study are listed in Table
1.
H. influenzae Rd (ATCC 51907) and type strains of
Haemophilus species (
H. haemolyticus ATCC 33390,
H. parainfluenzae ATCC 33392,
H. aphrophilus ATCC 33389,
H. paraphrophilus ATCC 29241,
H. segnis ATCC 33393,
H. parahaemolyticus ATCC 10014, and
H. paraphrohaemolyticus ATCC 29237) were obtained from the American Type Culture Collection.
A spontaneous rifampin-resistant derivative of
H. influenzae Rd, designated
H. influenzae Rd
RIF, was obtained by selecting
a clone grown on chocolate agar containing 25 µg/ml of
rifampin. Complete sequencing of the
rpoB gene in this mutant
revealed a point mutation, G436T, that resulted in the replacement
of Val-146 to Phe-146 in the RpoB protein. Other
H. influenzae and
H. haemolyticus strains were clinical isolates collected
in Japan between 1997 and 2003 (
12,
14). The isolates were identified
through their requirements for β-NAD
+ (V factor) and hemin
(X factor) for growth, by the nucleotide sequence of the 16S
rRNA gene (
4), and also by hemolytic activity assessment.
Media, antimicrobial susceptibility testing, and antibacterial agents.
Chocolate II agar plates (Becton Dickinson, Sparks, MD) and
brain heart infusion broth supplemented with 2% defibrinated,
lysed horse blood plus 15 µg/ml β-NAD
+ (sBHI broth)
were routinely used for bacterial growth. MICs were determined
by the broth dilution method according to the guidelines of
the Clinical and Laboratory Standards Institute (
3). The following
antibiotics were used in this study: rifampin (Sigma Chemical
Co., St. Louis, MO), cefdinir (Kemprotec, Ltd., Middlesbrough,
United Kingdom), and fosfomycin (Meiji Seika Kaisha, Ltd., Tokyo,
Japan).
Determining the sequence of the ftsI genes from type strains of Haemophilus species.
Reported nucleotide sequences of the ftsI genes from species of the family Pasteurellaceae (H. influenzae Rd, H. ducreyi 35000HP, H. somnus 2336, Mannheimia succiniciproducens MBEL55E, Pasteurella multocida Pm70, and Actinobacillus pleuropneumoniae 4074 [GenBank accession nos. NC 00097, NC 002940, NZ AACJ01000008, NC 006300, NC 002663, and NZ AACK01000005, respectively]) were aligned in order to search for conserved regions. Degenerate oligonucleotide primers specific for the conserved regions upstream and downstream of the coding region of the ftsI gene were constructed. One of two upstream forward primers, primer PH1 (5'-TTGGTAAAGCNATTMWGCC-3') and primer PH2 (5'-GWAGTGCVRTATTACG-3'), was used for PCR amplification, along with a downstream reverse primer, primer PH3 (5'-TGATAATCNARATGATCRCG-3'). Primers PH2 and PH3 were used to amplify the full-length ftsI genes of H. haemolyticus, H. parainfluenzae, H. aphrophilus, and H. paraphrophilus. Primers PH1 and PH3 were used for H. segnis. The following two primers were constructed for specific amplification of the ftsI genes from H. parahaemolyticus and H. paraphrohaemolyticus: 5'-GTGAGGCAGAAATAGAGG-3' and 5'-AAAGGTTCTGCCATCCAC-3'. PCR amplifications were performed as follows: 30 s of denaturation at 98°C and 30 cycles of denaturation at 95°C for 30 s, annealing at 45 to 55°C for 30 s, and extension at 72°C for 3 min. The cycling reaction was performed with a GeneAmp PCR system 9700 (Applied Biosystems, Foster City, CA). Sequencing was carried out with a BigDye Terminator (version 1.1) cycle sequencing kit and a 3730 DNA analyzer (Applied Biosystems). The sequences were confirmed by sequencing at least two independent PCR products for each strain.
Nucleotide sequencing of the ftsI genes from clinical isolates.
The full-length ftsI genes were amplified by PCR with the following primers: 5'-CTCGTTATCCGTTACAGCAG-3' and 5'-GCCAAACCGTGTGATGAAAC-3'. PCR amplifications were performed as follows: 2 min of denaturation at 94°C and 30 cycles of denaturation at 94°C for 30 s, annealing at 53°C for 30 s, and extension at 72°C for 3 min. The cycling reaction and DNA sequencing were performed as described above.
PFGE.
The preparation of the plugs containing bacteria and pulsed-field gel electrophoresis (PFGE) were performed as described previously (13), with slight modifications. Briefly, cells grown in sBHI broth were collected and suspended in 10 mM EDTA buffer (pH 8.0). The suspension was mixed with an equivalent volume of 2% low-melting-point agarose to produce agarose plugs. After solidification, the plugs were incubated in 100 mM EDTA buffer containing 50 µg lysozyme per ml at 37°C for 1 h. Then the plugs were treated with 250 mM EDTA buffer containing 10 mg proteinase K per ml and 1% N-lauroylsarcosine overnight at 50°C. After the plugs were washed with extensive volumes of 10 mM Tris-HCl (pH 8.0)-1 mM EDTA buffer, the DNA was digested with SmaI. The resulting DNA fragments were subjected to PFGE in 0.5x TBE (0.045 M Tris-borate, 1 mM EDTA) buffer with a CHEF Mapper electrophoresis system (Bio-Rad Laboratories, Hercules, CA). The DNA fragments were visualized with ethidium bromide.
In vitro genetic transfer.
Cells grown on chocolate II agar were suspended in sBHI broth at a density of about 108 CFU/ml. After preincubation at 37°C for 1 h, H. influenzae RdRIF and one of the BLNAR strains (strain MSC06647, MSC06651, or MSC06663) were mixed at a ratio of 1:1. The effect of DNase I on transfer was assessed by adding 100 U of the enzyme (Takara Bio Inc., Otsu, Japan). The cell suspensions were incubated at 37°C for 2 h and plated on chocolate agar containing 16 µg/ml of rifampin and 0.5 µg/ml of cefdinir. Nucleotide sequencing of the ftsI gene from doubly resistant mutants was performed as indicated above.
Nucleotide sequence accession numbers.
The complete DNA sequences of the ftsI genes from type strains of Haemophilus species and from clinical isolates of H. influenzae and H. haemolyticus, as determined in the present study, appear in the DDBJ/EMBL/GenBank nucleotide sequence databases under the accession nos. AB267855 to AB267861 (for the type strains) and AB267863 to AB267867 (for the clinical isolates).

RESULTS
Determination of ftsI gene sequences from Haemophilus species.
Analysis of the nucleotide sequences of the
ftsI genes from
621
H. influenzae isolates revealed that at least 10 strains
harbored mosaic structures of the
ftsI gene which contained
a sequence divergent from that of the Rd strain. The nucleotide
sequences of these regions showed no similarity with those of
the reported
ftsI genes. To identify the origin of the mosaic
sequence, the complete sequence of the
ftsI genes of
Haemophilus species, whose natural host is only humans, was determined.
Figure
1 shows the deduced amino acid sequences of PBP 3 for
type strains of seven
Haemophilus species. The PBP 3 sequences
of
H. haemolyticus and
H. parainfluenzae showed high degrees
of homology with that of
H. influenzae. The identities of the
amino acid sequences were 92.5% and 83.1%, respectively. The
ftsI genes of
H. parahaemolyticus and
H. paraphrohaemolyticus were quite different from that of
H. influenzae and much closer
to those of
H. ducreyi and
Actinobacillus pleuropneumoniae.
Recombination of the ftsI gene between H. influenzae and H. haemolyticus.
Comparison of the mosaic
ftsI genes with the corresponding genes
of
Haemophilus species (
H. parainfluenzae,
H. haemolyticus,
H. aphrophilus,
H. paraphrophilus,
H. segnis,
H. parahaemolyticus,
and
H. paraphrohaemolyticus) indicated that homologous recombination
between
H. haemolyticus and
H. influenzae had occurred in some
isolates (Fig.
2). While the overall divergence of the nucleotide
sequences between
H. haemolyticus ATCC 33390 and
H. influenzae Rd was 12.7% (233 bp of 1,833 bp), both genes possessed two
USSs at the same position. One of the
H. influenzae isolates
(isolate MSC07169) possessed a sequence at the 3'-terminal region
(positions 1647 to 1833) almost identical to that of
H. haemolyticus ATCC 33390. Another
H. influenzae isolate (isolate MSC07771)
was also found to have an
H. haemolyticus-derived sequence at
positions 402 to 831. Furthermore, an
H. haemolyticus isolate
(isolate MSC07286) harboring a partial
ftsI gene of
H. influenzae at the 3'-terminal region (positions 897 to 1833) was also identified
among the culture collection. These data provide direct evidence
for the homologous recombination of the
ftsI gene between
H. influenzae and
H. haemolyticus.
Evidence for intraspecies genetic transfer of the ftsI gene.
To investigate the genetic transfer of the
ftsI gene between
H. influenzae strains, particularly among ampicillin-resistant
variants, BLNAR and β-lactamase-positive ampicillin-clavulanic
acid-resistant (BLPACR) strains possessing
ftsI genes with identical
nucleotide sequences were selected for genotyping by PFGE (Table
1, strains 1 to 10). Four strains isolated from different hospitals
(strains MSC02070, MSC01869, MSC01400, and MSC01855) possessed
identical nucleotide sequences for
ftsI (sequence 1). Another
ftsI sequence (sequence 2) was found in three strains isolated
from three separate hospitals (strains MSC07237, MSC02104, and
MSC02149). Strains MSC02022, MSC01363, and MSC01432 were isolated
at the same hospital and harbored
ftsI genes with identical
sequences (sequence 3). As shown in Fig.
3A, strains isolated
from different hospitals harboring identical
ftsI genes exhibited
distinctive PFGE patterns (lanes 1 to 4 and lanes 5 to 7), indicating
that these isolates are phylogenetically independent, despite
the identity of their
ftsI genes. On the other hand, three BLNAR
strains harboring identical
ftsI genes from the same hospital
showed the same PFGE pattern (lanes 8 to 10), suggesting their
clonal spread.
In vitro transfer of ftsI gene from BLNAR to BLNAS.
A spontaneous rifampin-resistant mutant of
H. influenzae Rd,
designated Rd
RIF (a β-lactamase-nonproducing ampicillin-susceptible
[BLNAS] strain), and three BLNAR isolates (isolates MSC06647,
MSC06651, and MSC06663) were used to evaluate the genetic transfer
of the
ftsI gene in vitro. The spontaneous rates of rifampin
resistance in the BLNAR strains were 4.3
x 10
–9 to 8.7
x 10
–9. After the cultures of Rd
RIF and one of the BLNAR
strains were mixed, mutants resistant to both rifampin and cefdinir
were selected. Doubly resistant mutants were obtained after
the coincubation of Rd
RIF with MSC06647, MSC06651, and MSC06663
at frequencies of 5.1
x 10
–7, 1.2
x 10
–6, and 1.5
x 10
–6, respectively (Table
2). Treatment with DNase I
at 100 U totally abolished the emergence of doubly resistant
mutants (below the lower limit of detection). Nucleotide sequencing
of the
ftsI genes from doubly resistant mutants revealed that
the mutants possessed sequences identical to that of each parent
BLNAR strain (data not shown). As shown in Table
3, the susceptibilities
of the mutant clones (clones Rd
RIF/MSC06647, Rd
RIF/MSC06651,
and Rd
RIF/MSC06663) to rifampin and fosfomycin were equivalent
to those of Rd
RIF. Moreover, as predicted from the
ftsI sequence,
the susceptibility of these mutants to cefdinir was reduced
to a level similar to that of each of the parent BLNAR strains,
suggesting that doubly resistant mutants were derivatives of
the Rd
RIF strain that acquired the
ftsI gene from each BLNAR
strain. The genotypes of the doubly resistant mutants were confirmed
by PFGE (Fig.
3B). Doubly resistant mutants (lanes 15 to 17)
had the same pattern with Rd
RIF (lane 14) and had patterns that
were divergent from those of the BLNAR strains (lanes 11 to
13).

DISCUSSION
The nucleotide sequences of the
ftsI gene of BLNAR strains are
quite different from that of the
H. influenzae Rd strain. For
instance, the sequences of
ftsI from strains MSC02070 (sequence
1; GenBank accession no. AB267863), MSC07237 (sequence 2; GenBank
accession no. AB257096), and MSC02022 (sequence 3; GenBank accession
no. AB267864), the strains used in PFGE analysis, differed from
that of Rd by 2.7% (49 bp of 1,833 bp), 3.0% (55 bp of 1,833
bp), and 5.6% (102 bp of 1,833 bp), respectively. The existence
of genotypically divergent strains harboring identical
ftsI genes (Fig.
3A) strongly suggests the occurrence of genetic
transfer of the
ftsI gene in
H. influenzae. The existence of
USSs in the middle of and just downstream of the
ftsI gene supports
the efficient uptake and recombination of this gene (Fig.
2),
resulting in horizontal gene transfer among species.
Extensive sequence analysis of the ftsI genes from numerous clinical isolates of H. influenzae identified a mosaic structure of the ftsI gene in some strains. Complete sequences of the ftsI genes from Haemophilus species other than H. influenzae, such as H. parainfluenzae, H. haemolyticus, H. aphrophilus, H. paraphrophilus, and H. segnis, were determined and compared with that of the mosaic ftsI gene. Homologous recombination of the ftsI gene derived from H. haemolyticus was identified in some isolates (Fig. 2). Moreover, an H. haemolyticus strain harboring a partial ftsI gene from H. influenzae was also found. This is the first report describing the homologous recombination of the gene encoding a PBP in H. influenzae. It has been reported that other naturally competent gram-negative bacteria, Neisseria species (Neisseria gonorrhoeae and N. meningitidis), develop resistance to β-lactams by acquiring a mosaic-like structure of PBP 2, encoded by the penA gene. PBP 2 of Neisseria species is a homologue of PBP 3 in H. influenzae (36% amino acid sequence identity). It has been suggested that the horizontal genetic exchange of penA genes between commensal Neisseria species, such as N. cinerea, N. perflava, and N. flavescens, resulted in the mosaic structure of PBP 2 in N. gonorrhoeae and N. meningitidis (17). As H. haemolyticus is often recovered from the oropharyngeal area (10), it is possible that genetic exchange between colocalized H. influenzae and H. haemolyticus isolates or other Haemolyticus species takes place.
The molecular evolution of BLNAR strains has been considered to occur through the acquisition of point mutations in the ftsI gene by antibiotic pressure. However, our results raise the possibility of the development of resistance through homologous recombination from related species, which is a well-recognized mechanism known in N. gonorrhoeae (17) and Streptococcus pneumoniae (5, 9). As shown in Fig. 4, the nucleotide sequences of BLNAR strains are highly similar to that of H. haemolyticus around the region encoding the conserved SSN motif. Indeed, PBP 3 of H. haemolyticus, as well as those of BLNAR strains, possesses 377-Ile, which is identified as the amino acid residue associated with β-lactam resistance. Therefore, the ftsI gene of H. haemolyticus and/or related species might be the source of BLNAR. On the other hand, no sequence homology was observed in the region downstream of the KTG motif between BLNAR strains and H. haemolyticus or other Haemophilus species. These observations suggest that primary mutations of BLNAR, i.e., Asn526Lys and Arg517His, have emerged from the point mutation during antibiotic pressure.
A recent study of the bacterial flora in patients with acute
upper respiratory tract infections and healthy subjects revealed
that
H. influenzae strains are frequently detected in the nasopharynges
from both groups aged 6 years or younger (
8). Therefore, the
colocalization of or coinfection with multiple
H. influenzae strains could happen in some children, giving the opportunity
for
H. influenzae strains to exchange DNA. In Japan, oral cephalosporins
are extensively used for the treatment of upper respiratory
tract infections in children. BLNAR strains harboring mutations
in PBP 3 are resistant to most of the oral cephems but are not
resistant to cefditoren. The use of those cephems with poor
activities against BLNAR strains not only results in the failure
of the treatment (i.e., the failure to eliminate BLNAR strains)
but also leads to the selection of BLNAR strains mediated by
genetic transfer of the mutated
ftsI gene to BLNAS (i.e., the
failure to prevent the emergence of BLNAR strains).
Direct evidence for horizontal gene transfer of the ftsI gene between H. influenzae strains was obtained from in vitro gene transfer experiments. Coincubation of BLNAS and BLNAR strains resulted in the transfer of the ftsI gene from BLNAR to a BLNAS strain and recombination (Table 2). Addition of DNA fragments of the ftsI gene derived from BLNAR strains by PCR amplification, at final concentrations of 1 to 10 ng/ml, to the culture of BLNAS (strain RdRIF) had equivalent effects on the emergence of rifampin- and cefdinir-resistant mutants as coincubation of BLNAR and BLNAS strains (data not shown). Treatment with 100 U of DNase I abolished the emergence of resistant mutants not only after the transformation of DNA fragments to RdRIF strain but also after the coincubation of BLNAS and BLNAR strains. Although cell-to-cell contact has previously been implicated in chromosomal gene transfer (1), the mechanism of in vitro gene transfer of the ftsI gene was found to involve classical transformation.
In conclusion, horizontal transfer of the ftsI gene in H. influenzae was identified for the first time. The transfer of mutated ftsI genes might be associated with the rapid increase in BLNAR strains in Japan. Additionally, in vitro gene transfer experiments will be useful in evaluating the evolution of BLNAR strains.

ACKNOWLEDGMENTS
We thank Kimiko Ubukata (Kitasato University) for kindly providing
clinical isolates of
H. influenzae.

FOOTNOTES
* Corresponding author. Mailing address: Pharmaceutical Research Center, Meiji Seika Kaisha, Ltd., 760 Morooka-cho, Kohoku-ku, Yokohama 222-8567, Japan. Phone: 81-45-545-3139. Fax: 81-45-541-1768. E-mail:
sho_takahata{at}meiji.co.jp 
Published ahead of print on 26 February 2007. 

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Antimicrobial Agents and Chemotherapy, May 2007, p. 1589-1595, Vol. 51, No. 5
0066-4804/07/$08.00+0 doi:10.1128/AAC.01545-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
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