2 The Genus Leptospira: A Blooming Tree
The genus Leptospira forms a deep unique branch of spirochetes
and is classified in the family Leptospiraceae which is currently
divided into the genera Leptospira, Turneriella, and Leptonema.
The genera Turneriella and Leptonema each contain a single species, and relative to Leptospira, very little information is available for
these species [3]. The genus Leptospira is highly diverse and comprises 64 different species, which have been identified since the
isolation of L. interrogans in 1915 [4, 5]. The availability of a new
selective medium [6], the advent of relatively cheap whole-genome
sequencing (WGS), and increased interest in metagenomic studies
and soil microbial communities have resulted in expanding the
number of Leptospira species from 22 in 2018 [7] to 64 in
2019 [4].
Phylogenetic analysis, initially based on 16S rRNA gene
sequencing but now on whole-genome sequences, showed that
the genus is separated in two clades: “saprophytes” containing
species isolated in the natural environment and not responsible
for infections and “pathogens” containing all the species responsible for infections in humans and/or animals, plus environmental
species for which the pathogenicity remains unclear [4]. The two
clades are further subdivided in four subclades called P1, P2, S1,
and S2 [4]. The subclade P1 (formerly described as the pathogen
group) comprises 17 species (L. mayottensis, L. alexanderi,
L. kirschneri, L. kmetyi, L. alstonii, L. adleri, L. barantonii,
L. ellisii, L. dzianensis, L. gomenensis, L. putramalaysiae,
L. tipperaryensis, L. borgpetersenii, L. interrogans, L. noguchii,
L. santarosai, L. weilii). Some species, such as L. kmetyi, L. adleri,
L. ellisii, L. gomenensis, L. barantonii, L. dzianensis, and
L. putramalaysiae, first identified in the environment, have never
been isolated from infected animals or patients, suggesting that
they are not true pathogens [4, 8]. The subclade S2, also called
intermediate species, forms a group of 21 species distinct from the
pathogens (L. broomii, L. licerasiae, L. fainei, L. venezuelensis,
L. wolffii, L. haakeii, L. hartskeerlii, L. saintgironsiae,
L. neocaledonica, L. perolatii, L. dzoumogneensis, L. fletcheri,
L. fluminis, L. johnsonii, L. koniamboensis, L. langatensis,
L.
sarikeiensis,
L.
selangorensis,
L.
semungkisensis,
L. andrefontaineae, L. inadai). Most of these species have been
isolated from the environment, and their virulence status has not
been proven in animal models. The saprophytes are then subdivided in subclades S1 (L. terpstrae, L. vanthielii, L. yanagawae,
L. brenneri, L. harrisiae, L. levettii, L. kemamanensis,
L. bandrabouensis, L. bourretii, L. bouyouniensis, L. congkakensis,
L. ellinghausenii, L. jelokensis, L. kanakyensis, L. montravelensis,
L. mtsangambouensis, L. noumeaensis, L. perdikensis, L. biflexa,
272
Mathieu Picardeau
The genus Leptospira forms a deep unique branch of spirochetes
and is classified in the family Leptospiraceae which is currently
divided into the genera Leptospira, Turneriella, and Leptonema.
The genera Turneriella and Leptonema each contain a single species, and relative to Leptospira, very little information is available for
these species [3]. The genus Leptospira is highly diverse and comprises 64 different species, which have been identified since the
isolation of L. interrogans in 1915 [4, 5]. The availability of a new
selective medium [6], the advent of relatively cheap whole-genome
sequencing (WGS), and increased interest in metagenomic studies
and soil microbial communities have resulted in expanding the
number of Leptospira species from 22 in 2018 [7] to 64 in
2019 [4].
Phylogenetic analysis, initially based on 16S rRNA gene
sequencing but now on whole-genome sequences, showed that
the genus is separated in two clades: “saprophytes” containing
species isolated in the natural environment and not responsible
for infections and “pathogens” containing all the species responsible for infections in humans and/or animals, plus environmental
species for which the pathogenicity remains unclear [4]. The two
clades are further subdivided in four subclades called P1, P2, S1,
and S2 [4]. The subclade P1 (formerly described as the pathogen
group) comprises 17 species (L. mayottensis, L. alexanderi,
L. kirschneri, L. kmetyi, L. alstonii, L. adleri, L. barantonii,
L. ellisii, L. dzianensis, L. gomenensis, L. putramalaysiae,
L. tipperaryensis, L. borgpetersenii, L. interrogans, L. noguchii,
L. santarosai, L. weilii). Some species, such as L. kmetyi, L. adleri,
L. ellisii, L. gomenensis, L. barantonii, L. dzianensis, and
L. putramalaysiae, first identified in the environment, have never
been isolated from infected animals or patients, suggesting that
they are not true pathogens [4, 8]. The subclade S2, also called
intermediate species, forms a group of 21 species distinct from the
pathogens (L. broomii, L. licerasiae, L. fainei, L. venezuelensis,
L. wolffii, L. haakeii, L. hartskeerlii, L. saintgironsiae,
L. neocaledonica, L. perolatii, L. dzoumogneensis, L. fletcheri,
L. fluminis, L. johnsonii, L. koniamboensis, L. langatensis,
L.
sarikeiensis,
L.
selangorensis,
L.
semungkisensis,
L. andrefontaineae, L. inadai). Most of these species have been
isolated from the environment, and their virulence status has not
been proven in animal models. The saprophytes are then subdivided in subclades S1 (L. terpstrae, L. vanthielii, L. yanagawae,
L. brenneri, L. harrisiae, L. levettii, L. kemamanensis,
L. bandrabouensis, L. bourretii, L. bouyouniensis, L. congkakensis,
L. ellinghausenii, L. jelokensis, L. kanakyensis, L. montravelensis,
L. mtsangambouensis, L. noumeaensis, L. perdikensis, L. biflexa,
272
Mathieu Picardeau