Salud Pública de México

Genome misclassification of <i>Klebsiella variicola</i> and <i>Klebsiella quasipneumoniae</i> isolated from plants, animals and humans

ORIGINAL ARTICLE

Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans
[Clasificación errónea de aislados de Klebsiella variicola y Klebsiella quasipneumoniae obtenidos de plantas, animales y humanos]

Esperanza Martínez-Romero, PhD,(1) Nadia Rodríguez-Medina, M in C,(2) Marilu Beltrán-Rojel, Biol,(2) Jesús Silva-Sánchez, PhD,(2) Humberto Barrios-Camacho, PhD,(2) Ernesto Pérez-Rueda, PhD,(3,4) Ulises Garza-Ramos, PhD.(2)

(1) Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Cuernavaca, Morelos, México.
(2) Grupo de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México.
(3) Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. México.
(4) Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México. Mérida, Yucatán, México.

Martínez-Romero E, Rodríguez-Medina N, Beltrán-Rojel M, Silva-Sánchez J, Barrios-Camacho H, Pérez-Rueda E, Garza-Ramos U. Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans. Salud Publica Mex 2018;60:56-62. http://doi.org/10.21149/8149

Received on: August 22, 2016 • Accepted on: June 13, 2017
Corresponding author: Dr. Ulises Garza Ramos. Departamento de Diagnóstico Epidemiológico, Instituto Nacional de Salud Pública. Av. Universidad 655 col. Santa María Ahuacatitlán. 62100, Cuernavaca, Morelos, México.
E-mail: ulises.garza@insp.mx

CONTENT

  1. Abstract
  2. Resumen
  3. Introduction
  4. Material y methods
  5. Results ando discussion
  6. Final considerations
  7. Acknowledgments
  8. References

Abstract

Objective. Due to the fact that K. variicola, K. quasipneumoniae and K. pneumoniae are closely related bacterial species, misclassification can occur due to mistakes either in normal biochemical tests or during submission to public databases. The objective of this work was to identify K. variicola and K. quasipneumoniae genomes misclassified in GenBank database. Materials and methods. Both rpoB phylogenies and average nucleotide identity (ANI) were used to identify a significant number of misclassified Klebsiella spp. genomes. Results. Here we report an update of K. variicola and K. quasipneumoniae genomes correctly classified and a list of isolated genomes obtained from humans, plants, animals and insects, described originally as K. pneumoniae or K. variicola, but known now to be misclassified. Conclusions. This work contributes to recognize the extensive presence of K. variicola and K. quasipneumoniae isolates in diverse sites and samples.

Keywords: bacterial infections; Gram-negative bacterial infections; Enterobacteriaceae infections; nitrogen fixation

Resumen

Objetivo. Identificar genomas mal clasificados de K. variicola, y K. quasipneumoniae en la base de datos del GenBank. Material y métodos. En el presente estudio se usaron tanto análisis filogenéticos usando rpoB como la identidad media de nucleótidos (ANI, por sus siglas en ingles) para identificar un número significativo de genomas del género Klebsiella. Resultados. Se reportó una actualización de genomas de K. variicola y K. quasipneumoniae correctamente clasificados y una lista de aquellos aislamientos obtenidos de seres humanos, plantas, animales e insectos, descritos originalmente como K. pneumoniae o K. variicola pero ahora se conoce que están mal clasificados. Conclusiones. Este trabajo contribuye a la presencia extensiva de aislamientos de K. variicola y K. quasipneumoniae en diversos sitios y muestras.

Palabras clave: infecciones bacterianas; infecciones por bacterias gramnegativas; fijación de nitrógeno


A recent taxonomic description of the genus Klebsiella spp. includes three taxonomic subspecies; K. pneumoniae subsp. pneumoniae (KpI), K. pneumoniae subsp. rhinoscleromatis and K. pneumoniae subsp. ozaenae and our novel species; Klebsiella variicola (KpIII), K. singaporensis, K. michiganensis and K. quasipneumoniae (KpII), which has two subspecies: Klebsiella quasipneumoniae subsp. quasipneumoniae (KpII-A) and K. quasipneumoniae subsp. similipneumoniae (KpII-B).1 For these bacterial species novel genome sequences have been described from the strains 07A044, 18A0691 and FIHV2014.2 The misclassification of K. variicola and Klebsiella spp. genomes was first identified by whole-genome and rpoB phylogenies.3,4 Subsequently by K. quasipneumoniae and other K. variicola genomes the misclassification was evidenced by Average Nucleotide Identity (ANI).5 The aim of this work was detect misclassified K. variicola and K. quasipneumoniae genomes. We used an rpoB gene phylogenetic analysis and the results were validated by ANI. We identified the isolates misclassified previously described5 and identified new isolates that corresponded to K. variicola and K. quasipneumoniae that were deposited as K. pneumoniae. Likewise, we identified one K. variicola genome misclassified that corresponds to K. quasipneumoniae subsp. similipneumoniae.

Materials and methods

Identification of the K. variicola and K. quasipneumoniae genomes

The complete nucleotide sequence of rpoB (KVR801 v1_470024) gene from K. variicola 801 (CDMV00000000) was downloaded from the European Nucleotide Archive database.6 The rpoB sequence was analyzed by the BLASTn option (with default values) against 419 complete and draft Klebsiella spp. (tax id: 570) genomes deposited in GenBank database (last analysis 13/07/2015).7 The rpoB genes from Escherichia coli K-12-MG1655, Salmonella enterica Ty21a, Klebsiella oxytoca KCTC1686, K. quasipneumoniae subsp. quasipneumoniae 18A069 (KpII-A), K. quasipneumoniae subsp. quasipneumoniae 01A030 (KpII-A) and K. quasipneumoniae subsp. similipneumoniae 07A044 (KpII-B) genomes1 were included in the phylogenetic analysis. Subsequently, the rpoB nucleotide sequences of K. pneumoniae genomes with 100% nucleotide identity were filtered out to exclude a possible bias. All strain genomes identified as K. variicola and K. quasipneumoniae were included. Finally, a phylogenetic reconstruction was performed using the maximum-likelihood method with a Tamura-Nei-parameter model and 1000 bootstrap replications (Mega v6.06).8

The ANI was determined using the Average Nucleotide Identity Calculator9 the default parameters. In total, thirty-one K. variicola, nine K. quasipneumoniae and two K. pneumonia genomes were downloaded from GenBank and analyzed (table I). K. variicola At-22 (CP001891), K. quasipneumoniae subsp. quasipneumoniae 18A069 (CBZM000000000), K. quasipneumoniae subsp. similipneumoniae 07A044 (CBZR000000000) and K. pneumoniae MGH78578 (CP000647) were used as reference genomes of the respective bacterial species.


Table I. Average nucleotide identity (ANI) between bacterial genomes from all isolates as queries, and K. variicola, K. pneumoniae and K. quasipneumoniae reference strain genomes

Average nucleotide identity (%)

K. variicola

At-22

K. pneumoniae

MGH78578

K. quasipneumoniae

18A069

K. variicola

At-22

100.00

94.07

92.90

223/14

99.18

94.14

92.98

B1

99.17

94.08

92.91

CH4

99.18

94.10

92.90

MGH20

99.18

94.08

92.94

MGH40

99.15

94.13

92.95

UCICRE10

99.19

94.14

92.91

UCI18

99.19

94.15

92.94

BIDMC61

99.16

94.05

92.95

MGH68

99.15

94.12

92.89

MGH76

99.19

94.15

93.03

MGH80

99.18

94.09

93.03

BIDMC88

99.14

94.12

92.94

BIDMC90

99.10

94.14

93.02

MGH114

99.19

94.12

92.93

MGH92

99.12

94.09

92.93

1.1.55

99.13

94.12

92.94

KTE92

99.13

94.13

92.95

342

99.08

94.13

92.93

KP5-1

99.13

94.07

92.89

BZ19

99.17

94.13

92.92

DX120E

99.19

94.13

92.91

DSM15968

99.13

94.13

92.90

CAG:634

99.17

94.01

92.90

801

99.16

94.09

92.95

8917

99.19

94.14

92.91

06-268

99.17

94.08

92.92

3

99.21

94.07

92.88

4880

99.18

94.02

92.92

6A2

99.21

94.03

92.93

T29A

99.16

94.08

92.93

K. quasipneumoniae

18A069*

92.90

93.27

100.00

01A030*

92.84

93.10

99.15

07A044‡

92.93

93.31

100.00§

UCICRE14*

92.88

93.23

99.22

12-3578‡

92.90

93.30

99.22§

ATCC 700603‡

92.92

93.31

99.32§

MGH44‡

92.91

93.39

99.06§

HKUOPLA‡

92.96

93.40

99.20§

HKUOPLC‡

92.95

93.40

99.19§

K. pneumoniae

MGH78578

94.07

100.00

93.27

NTUH-K2044

94.10

99.21

93.28

* Klebsiella quasipneumoniae subsp. quasipneumoniae

Klebsiella quasipneumoniae subsp. similipneumoniae

§ K. quasipneumoniae subsp. similipneumoniae 07A044 used as reference genome in ANI calculation


Results and discussion

Klebsiella spp. genomes that corresponded to K. variicola and K. quasipneumoniae

Both K. variicola as K. pneumoniae and K. quasipneumoniae isolates exhibit very similar biochemical features,1 and to date there are no reported biochemical tests for their appropriate differentiation.3,4,10,11 The phylogenetic analysis of the rpoB gene is more adequate than the 16S rRNA for Klebsiella spp. differentiation.12 Likewise, K. variicola DX120E was identified both by 16S rRNA as rpoB genes, however, a better resolution was obtained with rpoB gene analysis.13 In addition, K. variicola described in animals and plants was also included in the rpoB phylogenetic analysis.3 Previously concatenated housekeeping genes were proposed to differentiate of Klebsiella species.1,3 With this criterium K. pneumoniae 342 from maize,14 and K. pneumoniae KP5-1 from insect15 were found to be misclassified as K. pneumoniae.3 Actually the new K. variicola and K. pneumoniae isolates may now be properly identified by PCR. The first multiplex PCR, M-PCR-1 based on unique genes from each species would allow the differentiation in clinical laboratories of K. variicola and K. pneumoniae bacterial species.3 In the present study, the nucleotide BLAST analyses of rpoB gene sequence allowed the analysis of 419 Klebsiella spp. Genomes. All those strains with rpoB genes with 100% nucleotide identity to rpoB of K. pneumoniae MGH78578 were not further considered, as they had a correct taxonomic affiliation. 144 non-redundant DNA sequences were used for a phylogenetic analysis, showing seventeen putative K. pneumoniae strains corresponding to K. variicola bacterial species (figure 1). Their reported identification was K. pneumoniae MGH20, MGH40, MGH68, MGH76, MGH80, MGH92, MGH114, UCI18, BIDMC61, BIDMC88, BIDMC90, 223/14, KTE92, UCICRE10, B1, and CH4 and Klebsiella spp. 1.1.55. The Klebsiella spp. 1.1.55 clinical isolate was previously identified as a possible K. variicola.4 In addition, K. pneumoniae UCICRE14 corresponded to K. quasipneumoniae subsp. quasipneumoniae (KpII-A), whereas the K. pneumoniae 12-3578, ATCC 700603, MGH44 and HKUOPLC and K. variicola HKUOPLA corresponded to K. quasipneumoniae subsp. similipneumoniae (KpII-B) (figure 1).

1

Validation by average nucleotide identity analysis

The results obtained by phylogenetic analysis of rpoB gene were confirmed by determining the ANI value (table I). K. variicola At-22, K. quasipneumoniae 18A069, K. quasipneumoniae subsp. similipneumoniae 07A044 and K. pneumoniae MGH78578 were used as reference genomes in the ANI platform. This platform may use draft or complete genomes.7 When strains from the same subspecies were compared, ANI was >99%. Among the K. variicola genomes, an ANI value of >99.08 was obtained; similarly, an ANI value of >99.15% for the K. quasipneumoniae genomes was obtained. For the K. pneumoniae and Klebsiella spp. genomes that were identified as K. variicola in the present study, ANI values were <94.01% compared with those of K. pneumoniae MGH-78578. In contrast, an ANI value of >98.89% was obtained when K. variicola isolates were compared to K. variicola At-22 (table I). Previously, Chen and colleagues5 detected nine misclassified K. variicola and four K. quasipneumoniae genomes. This update of Klebsiella genomes highlight that not only K. pneumoniae are misclassified, but also, K. variicola.

Not only K. pneumoniae and K. variicola but also K. quasipneumoniae isolates are not differentiated by biochemical methods. To address this problem, Brisse and colleagues1 proposed a phylogenetic analysis based on five protein-coding genes (rpoB, fusA, gapA, gyrA, and leuS) that clearly differentiates K. variicola and K. quasipneumoniae from K. pneumoniae bacterial species. Nevertheless, we previously showed that the rpoB nucleotide partial gene sequence (501 bases) also supports the differentiation of K. variicola and K. pneumoniae.3 This work confirms the correct taxonomic affiliation using the complete rpoB gene sequence.

General characteristics of K. variicola and K. quasipneumoniae strains and genomes

Misclassified K. pneumoniae and K. variicola genomes, now know to corresponded to K. variicola or K. quasipneumoniae, were submitted to GenBank in 2009. Other misclassified strains, such as Klebsiella spp. 1.1.55, and K. pneumoniae 342 genomes were deposited in 2008 (table II). The latter was reported to correspond to K. variicola in subsequent studies.1,3,16 Genome submissions were mainly to USA, Mexico and Malaysia, with the USA as the major contributor (table II). These isolates were obtained from many different sources, such as humans (from urine, pus bile and other organic tisues), giant pandas (feces), different sites of plants, and from diverse insect species (table II). The majority of bacterial genomes were submitted as drafts with 12 to 400 contigs, using mostly Illumina technology. Five K. variicola genomes were completely sequenced using the Sanger shotgun, PacBio and 454 technologies (completed by Sanger sequencing of gaps), and the draft genomes contained from 24 to 464 contigs.


Table II. Characteristics of K. variicola, K. quasipneumoniae and K. pneumoniae genomes considered in the study

GenBank submission specie

Bacterial specie

Isolate

Origin of isolates

Submitted on public data base

Country

Sequencing

method

Contigs

N50

(coverage)

Genome

size

CDS or proteins

(total)

Accession

number data base

PUBMED

(PMID)

K. pneumoniae

K. pneumoniae

NTUH-K2044

Human (blood)

06-Jan-2004

Chine

Sanger shotgun

1

5 248 520

5 248 520

5 270

AP006725.1

19447910

K. pneumoniae

K. pneumoniae

MGH-78578

Human

06-Sep-2006

USA

Sanger shotgun

1

5 315 120

5 315 120

5 244

CP000647.1

Unpublished

K. pneumoniae

K. variicola

223/14

Human (pus)

07-Oct-2014

Malaysia

PacBio

13

5 584 553 (75X)

6 165 397

5 797

JRTV00000000

Unpublished

K. pneumoniae

K. variicola

B1

Plant (bitter gourd)

29-Oct-2014

Malaysia

Illumina HiSeq

90

152 679 (63X)

5 484 200

5 212

JSWX00000000

Unpublished

K. pneumoniae

K. variicola

CH4

Plant (chili)

29-Oct-2014

Malaysia

Illumina HiSeq

95

131 443 (74X)

5 480 893

5 223

JSXA00000000

Unpublished

K. pneumoniae

K. variicola

MGH20

Human (respiratory)

06-Sep-2013

USA

Illumina HiSeq 2000

25

665 487 (145X)

5 651 060

5 237

AYJK00000000

Unpublished

K. pneumoniae

K. variicola

MGH40

Missing (urine)

06-Sep-2013

USA

Illumina

14

858 351 (143X)

5 379 986

4 978

AYIX00000000

Unpublished

K. pneumoniae

K. variicola

UCICRE10

missing

06-Sep-2013

USA

Illumina HiSeq 2000

12

1 342 103 (135X)

5 376 506

4 959

AYIF00000000

Unpublished

K. pneumoniae

K. variicola

UCI18

Human (urine)

10-Jan-2014

USA

Illumina

18

540 261 (136X)

6 035 862

5 643

JCML00000000

Unpublished

K. pneumoniae

K. variicola

BIDMC61

Human (urine)

25-Apr-2014

USA

Illumina

24

493 486 (135X)

5 580 642

5 170

JMWB00000000

Unpublished

K. pneumoniae

K. variicola

MGH68

Human (urine)

25-Apr-2014

USA

Illumina HiSeq 2000

25

398 006 (135X)

5 521 224

5 124

JMZD00000000

Unpublished

K. pneumoniae

K. variicola

MGH76

Human (bile)

25-Apr-2014

USA

Illumina

400

57 253 (46X)

5 960 376

5 327

JMZK00000000

Unpublished

K. pneumoniae

K. variicola

MGH80

Human (urine)

25-Apr-2014

USA

Illumina

36

341 150 (139X)

5 775 155

5 394

JMZM00000000

Unpublished

K. pneumoniae

K. variicola

BIDMC88

Human (missing)

10-Jun-2015

USA

Illumina HiSeq 2000

30

1 342 103 (135X)

5 376 506

5 399

LFBA00000000

Unpublished

K. pneumoniae

K. variicola

BIDMC90

Human (missing)

10-Jun-2015

USA

Illumina

48

445 357 (132X)

6 478 359

6 153

LFBC00000000

Unpublished

K. pneumoniae

K. variicola

MGH114

Human

10-Jun-2015

USA

Illumina

96

293 076 (23X)

6 023 346

5 644

LFAP00000000

Unpublished

K. pneumoniae

K. variicola

MGH92

Human (missing)

10-Jun-2015

USA

Illumina

98

130 603 (55X)

5 642 554

5 199

LFAD00000000

Unpublished

Klebsiella sp.

K. variicola

1.1.55

Human (missing)

08-Oct-2009

USA

454 GS-FLX

96

110 877 (20X)

5 459 739

5 010

ACXA00000000

Unpublished

Klebsiella sp.

K. variicola

KTE92

Human (missing)

22-Feb-2013

USA

Illumina

34

344 789 (129X)

5 471 343

5 043

ASQN00000000

Unpublished

K. pneumoniae

K. variicola

342

Plant (maize stems)

05-Mar-2008

USA

Sanger shotgun

1

5 641 239 (8X)

5641 239

5 813

CP000964.1

18654632

K. pneumoniae

K. variicola

KP5-1

Insect (Nezara viridula)

04-Jun-2014

USA

454 GS-Junior

1

5 365 144 (16X)

5 365 144

5 198

CP008700.1

25146146

K. variicola

K. variicola

BZ19

Human (Faeces)

21-Aug-2014

Brazil

454

208

55 792 (14X)

5 543 565

5 003

JDWA00000000

25135672

K. variicola

K. variicola

DX120E

Plant (banana roots)

09-Sep-2014

Chine

PacBio

1

5 501 013 (96X)

5 501 013

5 172

CP009274

Unpublished

K. variicola

K. variicola

DSM15968

Plant (banana roots)

13-Jan-2015

Chine

PacBio

1

5 521 203 (185X)

5 521 203

4 979

CP010523

Unpublished

K. variicola

K. variicola

CAG:634

Human (gut)

28-Nov-2012

Denmark

Not founded

464

19 584

5 182 156

4 879

CBBA000000000

Unpublished

K. variicola

K. variicola

801

Human (blood)

15-Jan-2015

Mexico

454 GS-FLX Titanium

91

131 409 (15X)

5 790 474

5 620

CDMV00000000

25886267

K. variicola

K. variicola

8917

Human (sputum)

18-Feb-2015

Mexico

454 GS-FLX Titanium

103

257 189 (20X)

5 686 491

5 621

CEGG00000000

25858850

K. variicola

K. variicola

06-268

Human (abscess)

24-Jul-2015

Mexico

454 GS-FLX Plus

19

407 879 (30X)

5 431 857

5 278

CXOZ00000000

This work

K. variicola

K. variicola

3

Plant (maize shoots)

24-Jul-2015

Mexico

454 GS-FLX Plus

24

374 829 (25X)

5 512 858

5 387

CXOY00000000

26358599

K. variicola

K. variicola

4880

Human (blood)

24-Jul-2015

Mexico

454 GS-FLX Titanium

88

220 017 (19X)

5 415 715

5 258

CXPB00000000

This work

K. variicola

K. variicola

6A2

Plant (banana root)

24-Jul-2015

Mexico

454 GS-FLX Titanium

206

168 242 (15X)

5 925 914

5 906

CXPC00000000

26358599

K. variicola

K. variicola

T29A

Plant (sugar cane stem)

24-Jul-2015

Mexico

454 GS-FLX Titanium

126

213 313 (18X)

5 865 668

5 751

CXPA00000000

26358599

K. variicola

K. variicola

At-22

Insect (fungus matrix)

26-Jan-2010

USA

454 GS-FLX

1

5 458 505

5 458 505

5 309

CP001891.1

19965433

K. quasipneumoniae*

K. quasipneumoniae

01A030

Human (blood)

16-May-2014

Austria

Illumina

65

151 149

5 465 736

5 287

CCDF00000000

Unpublished

K. quasipneumoniae*

K. quasipneumoniae

18A069

Human

08-Jan-2014

Spain

Illumina

476

24 320

5 387 733

5 007

CBZM000000000

24958762

K. quasipneumoniae

K. quasipneumoniae

07A044

Human

08-Jan-2014

Germany

Illumina

46

257 097

5 109 717

4 927

CBZR000000000

24958762

K. pneumoniae

K. quasipneumoniae*

UCICRE14

missing

06-Sep-2013

USA

Illumina

24

(140X)

5 517 176

5 054

AYIC00000000

Unpublished

K. pneumoniae

K. quasipneumoniae

12-3578

Human (blood)

15-Apr-2013

Chine

Illumina HiSeq

183

136 195 (62X)

5 742 061

0

AQOC00000000

Unpublished

K. pneumoniae

K. quasipneumoniae

ATCC 700603

Human

15-Jan-2013

USA

Illumina HiSeq

103

226 688 (800X)

5 461 663

5 231

AOGO00000000

23723407

K. pneumoniae

K. quasipneumoniae

MGH44

missing (respiratory)

06-Sep-2013

USA

Illumina

11

922 744 (273X)

5 240 541

4 832

AYIV00000000

Unpublished

K. variicola

K. quasipneumoniae

HKUOPLA

Panda (feces)

31-Jul-2015

Chine

Illumina MiSeq

1

5 062 551 (61X)

5 090 052

4 757

CP012252

26472841

K. pneumoniae

K. quasipneumoniae

HKUOPLC

Panda (feces)

04-Aug-2015

Chine

Illumina MiSeq

1

5 088 873 (43X)

5 088 873

4 962

CP012300

Unpublished

*Klebsiella quasipneumoniae subsp. quasipneumoniae

Klebsiella quasipneumoniae subsp. similipneumoniae


The K. quasipneumoniae genomes were submitted in 2013 and 2015 from different countries, including Austria, China, Germany, Spain and USA. All of these genomes were isolated from humans and were sequenced using the Illumina platform, with contigs from 1 to 476 and genome sizes >5 Mb and a content of CDS or proteins of 4 757 to 5 287 (table II).

Final considerations

It is a fact that Klebsiella spp. isolates have been misclassified. Several isolates of both K. variicola and K. quasipneumoniae from various sources were identified as K. pneumoniae. We report here, on a genomic basis, on misclassified K. pneumoniae, K. quasipneumoniae and K. variicola isolates from humans, animals, plants and insects. Nevertheless, the recent use of different methods such as PCR, phylogenetic analysis of rpoB gene and ANI for the proper differentiation of K. variicola and K. quasipneumoniae from K. pneumoniae will help the adequate classification of Klebsiella species. This work contributes to recognizing the extensive presence of K. variicola and K. quasipneumoniae in diverse sites and samples. The correct identification of K. variicola in the hospital setting could contribute to a more appropriate medical treatment.17 Notably, some K. variicola18,19 and K. quasipneumoniae,20 respectively, have acquired carbapenem resistance and virulence factors.

Acknowledgments

This work was supported by grant CB-2015-01-256988 from SEP-Conacyt (Secretaría de Educación Pública-Consejo Nacional de Ciencia y Tecnología). We thank Angelina Quiterio for her excellent laboratory assistance and Michael Dunn and J. Martinez-Romero for their help in reviewing the manuscript. EP-R was supported by a grant (IN-201117) from PAPIIT-DGAPA, UNAM.

Declaration of conflict of interests. The authors declare that they have no conflict of interests.

References

1. Brisse S, Passet V, Grimont PA. Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola. Int J Syst Evol Microbiol 2014;64(Pt 9):3146-3152. https://doi.org/10.1099/ijs.0.062737-0

2. Arena F, Henrici De Angelis L, Pieralli F, Di Pilato V, Giani T, Torricelli F, et al. Draft Genome Sequence of the First Hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae Isolate from a Bloodstream Infection. Genome Announc 2015;3(5):pii: e00952-15. https://doi.org/10.1128/genomeA.00952-15

3. Garza-Ramos U, Silva-Sanchez J, Martinez-Romero E, Tinoco P, Pina-Gonzales M, Barrios H, et al. Development of a multiplex-PCR probe system for the proper identification of Klebsiella variicola. BMC Microbiol 2015;15:64. https://doi.org/10.1186/s12866-015-0396-6

4. Hazen TH, Zhao L, Sahl JW, Robinson G, Harris AD, Rasko DA, et al. Characterization of Klebsiella sp. strain 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates. Antimicrob Agents Chemother 2014;58(4):1879-1888. https://doi.org/10.1128/AAC.01605-13

5. Chen M, Li Y, Li S, Tang L, Zheng J, An Q. Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae. J Basic Microbiol 2016;56(1):78-84. https://doi.org/10.1002/jobm.201500415

6. European Nucleotide Archive [cited 2016 Jan]. Available from: http://www.ebi.ac.uk/ena

7. Basic Local Alignment Search Tool (BLAST) [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information [cited 2016 Jan]. Available from: https://blast.ncbi.nlm.nih.gov/Blast.cgi

8. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28(10):2731-2739. https://doi.org/10.1093/molbev/msr121

9. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57(Pt 1):81-91 [cited 2016 January]. Available from: http://enve-omics.ce.gatech.edu/ani/

10. Alves MS, Dias RC, de Castro AC, Riley LW, Moreira BM. Identification of clinical isolates of indole-positive and indole-negative Klebsiella spp. J Clin Microbiol 2006;44(10):3640-3646. https://doi.org/10.1128/JCM.00940-06

11. van Veen SQ, Claas EC, Kuijper EJ. High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J Clin Microbiol 2010;48(3):900-907. https://doi.org/10.1128/JCM.02071-09

12. Martinez J, Martinez L, Rosenblueth M, Silva J, Martinez-Romero E. How are gene sequence analyses modifying bacterial taxonomy? The case of Klebsiella. Int Microbiol 2004;7(4):261-268.

13. Chun-Yan W, Li L, Li-Jing L, Yong-Xiu X, Chun-Jin H, Li-Tao Y, et al. Endophytic nitrogen-fixing Klebsiella variicola strain DX120E promotes sugarcane growth. Biol Fertil Soils 2014;50(4):657-666. https://doi.org/10.1007/s00374-013-0878-3

14. Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, et al. Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet 2008;4(7):e1000141. https://doi.org/10.1371/journal.pgen.1000141

15. Medrano EG, Forray MM, Bell AA. Complete genome sequence of a Klebsiella pneumoniae strain isolated from a known cotton insect boll vector. Genome Announc 2014;2(4):pii: e00850-14. https://doi.org/10.1128/genomeA.00850-14

16. Rosenblueth M, Martinez L, Silva J, Martinez-Romero E. Klebsiella variicola, a novel species with clinical and plant-associated isolates. Syst Appl Microbiol 2004;27(1):27-35. https://doi.org/10.1078/0723-2020-00261

17. Maatallah M, Vading M, Kabir MH, Bakhrouf A, Kalin M, Naucler P, et al. Klebsiella variicola is a frequent cause of bloodstream infection in the stockholm area, and associated with higher mortality compared to K. pneumoniae. PloS One 2014;9(11):e113539. https://doi.org/10.1371/journal.pone.0113539

18. Di DY, Jang J, Unno T, Hur HG. Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-β-lactamase, in an urban river in South Korea. J Antimicrob Chemother 2017;72(4):1063-1067. https://doi.org/10.1093/jac/dkw547

19. Hopkins KL, Findlay J, Doumith M, Mather B, Meunier D, D’Arcy S, et al. IMI-2 carbapenemase in a clinical Klebsiella variicola isolated in the UK. J Antimicrob Chemother 2017;72(7):2129-2131. https://doi.org/10.1093/jac/dkx103

20. Breurec S, Melot B, Hoen B, Passet V, Schepers K, Bastian S, et al. Liver Abscess Caused by Infection with Community-Acquired Klebsiella quasipneumoniae subsp. quasipneumoniae. Emerg Infect Dis 2016;22(3):529-531. https://doi.org/10.3201/eid2203.151466

Enlaces refback





Salud Pública de México es una publicación periódica electrónica, bimestral, publicada por el Instituto Nacional de Salud Pública (con domicilio en Avenida Universidad núm. 655, col. Santa María Ahuacatitlán, Cuernavaca, Morelos, C.P. 62100, teléfono 329-3000, página web, www.insp.mx), con ISSN: 1606-7916 y Reserva de Derechos al Uso Exclusivo con número: 04-2012-071614550600-203, ambos otorgados por el Instituto Nacional del Derecho de Autor. Editor responsable: Carlos Oropeza Abúndez. Responsable de la versión electrónica: Subdirección de Comunicación Científica y Publicaciones, Avenida Universidad núm. 655, planta baja, col. Santa María Ahuacatitlán, Cuernavaca, Morelos, C.P. 62100, teléfono 329 3000. Fecha de última modificación: 11 de abril de 2019. D.R. © por el sitio: Instituto Nacional de Salud Pública.

Gestionando el conocimiento