Proposta de uma nova nomenclatura para os genes de resistência plasmidial à fosfomicina do tipo fos e análise retrospectiva da distribuição geográfica desses genes no mundo
Data
2023-06-30
Autores
Leite, Mariana Isabela 
Orientadores
Silva, Rodrigo Cayô da
Tipo
Trabalho de conclusão de curso
Título da Revista
ISSN da Revista
Título de Volume
Resumo
A fosfomicina é um antimicrobiano antigo que, através de pesquisas recentes, tem se
mostrado um importante aliado no tratamento de infecções causadas por bactérias
multirresistentes (MDR). A resistência à fosfomicina através de enzimas inativadoras se dá,
principalmente, por metaloenzimas denominadas Fos. Os genes plasmidiais codificadores
dessas enzimas, chamados fos, têm sido reportados em vários países do mundo e em
diferentes espécies bacterianas. Entretanto, sua classificação e nomenclatura não seguem
um padrão bem estabelecido, o que resulta na dificuldade quando um novo gene fos é
reportado. Tendo em vista que a atual classificação e nomenclatura não levam em
consideração as identidades nucleotídicas entre os genes fos plasmidiais reportados, a
descrição de novos genes ou novas variantes alélicas fica comprometida, assim como a real
frequência desses genes nas diferentes regiões geográficas. Além disso, com o aumento do
uso de fosfomicina, bem como o de relatos de genes fos pelo mundo, vê-se a necessidade
de mapeamento desses determinantes de resistência. Este estudo buscou mapear as
variantes do gene fos plasmidiais previamente reportadas em todo o mundo, bem como
sugerir uma nova classificação e nomenclatura desses determinantes de resistência,
procurando solucionar as inconsistências verificadas no sistema atual. Foram utilizados para
a coleta de dados as plataformas GenBank/NCBI e BLASTp. As sequências de genes fos
recuperadas foram submetidas a critérios de seleção e exclusão, para posterior alinhamento
e análise filogenética, utilizando o programa DNAstar Lasergene MegAling versão 7.0.0
(DNAStar, Madison, EUA). Para tanto, foram coletados dados sobre as variantes de fos
previamente reportadas como: fosA1-fosA10 e fosC2; fosB1-fosB9; fosC; fosD; fosE; fosF;
fosG; fosH; fosI; fosK; fosL1-fosL2; fosM1-fosM3; e fosX. Ainda, a nova classificação e
nomenclatura sugerida neste estudo foi construída com base na identidade nucleotídica
apresentada por cada um dos genes fos descritos até o momento. Do total de 980
sequências coletadas, 780 foram selecionadas para a análise filogenética, bem como a
avaliação da distribuição dos genes fos plasmidiais globalmente. Dentre todos os genes fos
plasmidiais descritos até o momento, os mais frequentes foram fosA3 (47.44%),
principalmente no continente asiático, seguido por fosX (8.36%) e fosA7 (8.16%). A grande
maioria dos isolados foram descritos na Ásia (61,15%), seguido pela América (21,7%) e
Europa (13,6%). Na análise da frequência de genes fos por país, verificamos um predomínio
de registros na China (28%) e Japão (18%), além de outros países como EUA (5%), França
(4%), Alemanha (4%) e Paquistão (3%) que também estão entre os países com maior
número de registros de genes fos no mundo. Ao todo, genes fos já foram descritos em 38
espécies bacterianas diferentes, sendo 22 espécies gram-negativas e 16 espécies grampositivas, com destaque para os gêneros Staphylococcus spp. (n=10 espécies),
Pseudomonas spp. (n=5 espécies) e Enterobacter spp. (n=4 espécies). A nova classificação
e nomenclatura propostas no presente estudo agrupou os genes fos em 15 famílias (fosAfosP), 25 grupos (fosA1-fosA3, fosB1-fosB2, fosC1, fosD1, fosE1, fosF1-fosF2, fosG1-fosG2,
fosH1-fosH2, fosI1-fosI2, fosJ1, fosK1, fosL1-fosL3, fosM1, fosN1, fosO1 e fosP1) e 50
variantes alélicas, das quais 16 são novas. O mapeamento da ocorrência dos genes fos
permitiu uma melhor compreensão de sua distribuição mundial, assim como a detecção de
áreas de maior frequência, denominados “hotspots” para o surgimento e disseminação
desses determinantes de resistência à fosfomicina. Da mesma maneira, a nova classificação
e nomenclatura sugeridas permitiu a organização dos genes fos, corrigindo inconsistências
importantes.
Fosfomycin is an old antimicrobial that, through recent research, has proven to be an important ally in the treatment of infections caused by multidrugresistant bacteria (MDR). Resistance to fosfomycin via inactivating enzymes is mainly via the metalloenzymes Fos. The plasmid genes encoding these enzymes, named fos, have been reported in several countries around the world and in different bacterial species. However, their classification and nomenclature did not follow a wellestablished standard, which results in difficulty when a new fos gene is reported. Since the current classification and nomenclature does not consider the nucleotide identities among the reported plasmidial fos genes the detection of these determinants, for example, is also affected. Furthermore, with the increased use of fosfomycin, as well as reports of fos genes around the world, there is a need for mapping of these resistance determinants. This study sought to map the plasmid fos gene variants previously reported worldwide, as well as suggest a new classification and nomenclature of these resistance determinants. GenBank/NCBI and BLASTp platforms were used for data collection. The recovered fos gene sequences were submitted to selection and exclusion criteria, for further alignment and phylogenetic analysis, using the DNAstar Lasergene MegAling version 7.0.0 program (DNAStar, Madison, USA). To this aim, data were collected on the previously reported fos variants as: fosA1fosA10 and fosC2; fosB1fosB9; fosC; fosD; fosE; fosF; fosG; fosH; fosI; fosK; fosL1fosL2; fosM1fosM3; and fosX. Furthermore, the new classification and nomenclature suggested in this study was constructed based on the nucleotide identity presented by each of the fos genes described up to now. From the total of 980 sequences collected, 780 were selected for phylogenetic analysis as well as evaluation of the distribution of plasmid fos genes globally. Among all plasmid fos genes described so far, the most frequent ones were fosA3 (47.44%), mainly in the Asian continent, followed by fosX (8.36%) and fosA7 (8.16%). Most isolates were described in Asia (61.15%), followed by America (21.7%) and Europe (13.6%). In the analysis of the frequency of fos genes by country, we found a predominance of records in China (28%) and Japan (18%), in addition to other countries such as USA (5%), France (4%), Germany (4%) and Pakistan (3%), which are also among the countries with the highest number of fos gene records in the world. In all, fos genes have been described in 38 different bacterial species, 22 gramnegative and 16 grampositive species, with emphasis on the genera Staphylococcus spp. (n=10 species), Pseudomonas spp. The new classification and nomenclature grouped the variants into 17 families (fosAfosP), 25 groups (fosA1fosA3, fosB1fosB2, fosC1, fosD1, fosE1, fosF1fosF2, fosG1fosG2, fosH1fosH2, fosI1fosI2, fosJ1, fosK1, fosL1fosL3, fosM1, fosN1, fosO1, and fosP1) and 50 allelic variants, among which 16 are new. The mapping of the occurrence of fos genes has allowed a better understanding of their worldwide distribution, as well as the detection of areas of higher frequency, called "hotspots" for the emergence and dissemination of these determinants of resistance to fosfomycin. Likewise, the new classification and nomenclature suggested allowed the organization of the fos genes, correcting important errors.
Fosfomycin is an old antimicrobial that, through recent research, has proven to be an important ally in the treatment of infections caused by multidrugresistant bacteria (MDR). Resistance to fosfomycin via inactivating enzymes is mainly via the metalloenzymes Fos. The plasmid genes encoding these enzymes, named fos, have been reported in several countries around the world and in different bacterial species. However, their classification and nomenclature did not follow a wellestablished standard, which results in difficulty when a new fos gene is reported. Since the current classification and nomenclature does not consider the nucleotide identities among the reported plasmidial fos genes the detection of these determinants, for example, is also affected. Furthermore, with the increased use of fosfomycin, as well as reports of fos genes around the world, there is a need for mapping of these resistance determinants. This study sought to map the plasmid fos gene variants previously reported worldwide, as well as suggest a new classification and nomenclature of these resistance determinants. GenBank/NCBI and BLASTp platforms were used for data collection. The recovered fos gene sequences were submitted to selection and exclusion criteria, for further alignment and phylogenetic analysis, using the DNAstar Lasergene MegAling version 7.0.0 program (DNAStar, Madison, USA). To this aim, data were collected on the previously reported fos variants as: fosA1fosA10 and fosC2; fosB1fosB9; fosC; fosD; fosE; fosF; fosG; fosH; fosI; fosK; fosL1fosL2; fosM1fosM3; and fosX. Furthermore, the new classification and nomenclature suggested in this study was constructed based on the nucleotide identity presented by each of the fos genes described up to now. From the total of 980 sequences collected, 780 were selected for phylogenetic analysis as well as evaluation of the distribution of plasmid fos genes globally. Among all plasmid fos genes described so far, the most frequent ones were fosA3 (47.44%), mainly in the Asian continent, followed by fosX (8.36%) and fosA7 (8.16%). Most isolates were described in Asia (61.15%), followed by America (21.7%) and Europe (13.6%). In the analysis of the frequency of fos genes by country, we found a predominance of records in China (28%) and Japan (18%), in addition to other countries such as USA (5%), France (4%), Germany (4%) and Pakistan (3%), which are also among the countries with the highest number of fos gene records in the world. In all, fos genes have been described in 38 different bacterial species, 22 gramnegative and 16 grampositive species, with emphasis on the genera Staphylococcus spp. (n=10 species), Pseudomonas spp. The new classification and nomenclature grouped the variants into 17 families (fosAfosP), 25 groups (fosA1fosA3, fosB1fosB2, fosC1, fosD1, fosE1, fosF1fosF2, fosG1fosG2, fosH1fosH2, fosI1fosI2, fosJ1, fosK1, fosL1fosL3, fosM1, fosN1, fosO1, and fosP1) and 50 allelic variants, among which 16 are new. The mapping of the occurrence of fos genes has allowed a better understanding of their worldwide distribution, as well as the detection of areas of higher frequency, called "hotspots" for the emergence and dissemination of these determinants of resistance to fosfomycin. Likewise, the new classification and nomenclature suggested allowed the organization of the fos genes, correcting important errors.