Paenibacillus spp. isolated from human and environmental samples in Spain: detection of 11 new species

Abstract

One hundred thirty-six isolates, 88 human and 48 environmental, that met the requirements to belong to the genus Paenibacillus were identified using a polyphasic taxonomic approach known as 16S rRNA plus phenotypic traits. Thirty-seven Paenibacillus species were identified; some had not been previously reported from clinical samples. The main species were P. pabuli (13 isolates), P. provencensis (11), P. phoenicis (9) and P. lautus (8). P. pabuli (11/13) and P. provencensis (8/11) were mainly environmental isolates, while P. phoenicis (9/9) and P. lautus (6/8) were mainly human isolates. Despite the difficulties in assigning to human Paenibacillus isolates a role as a pathogen or contaminant, here 25% of the isolates were involved in true infections, especially in those cases that affected abscesses, wound exudates, ocular infections and diverse fluids. In addition, 15 isolates were identified as 11 'Candidatus' to a new species, all of them from human specimens except one that was obtained from laboratory air. The antimicrobial susceptibility testing showed 95.6% of isolates were resistant to ampicillin, 44% were resistant to cotrimoxazole, 20 to 30% were resistant to cefotaxime and vancomycin and 13% were resistant to rifampicin and erythromycin.

Keywords: Clinical samples; Paenibacillus; environmental isolates; new species; polyphasic taxonomy.

Fig. 1

Neighbour-joining phylogenetic tree based on 16S rRNA gene sequence of Paenibacillus spp. type (T) and novel (bold type) strains highlighting position of P. phoenicis and nine novel strains found in our study relative to other phylogenetically close organisms. Numbers at nodes are percentages of bootstrap values (>50%) obtained by repeating analysis 1000 times to generate majority consensus tree. Bacillus subtilis DSM10 was used as outgroup. Scale bar indicates 0.01 nucleotide sequence divergence. Numbers in bold correspond to nine strains identified as P. phoenicis in our study.

Fig. 2

Transmission electron microscopy of Paenibacillus phoenicis strain CNM 1389-07 showing (a) oval endospores and (b) peritrichous flagella.

Fig. 3

Extended phylogenetic tree according to neighbour-joining method of genus Paenibacillus inferred from 16S rRNA gene sequences. Bootstrap values are expressed as percentage of 1000 replications. Numbers at nodes are percentages of bootstrap values (>50%). Scale bar represents 0.01 substitutions per nucleotide position. Bacillus subtilis strain DSM10 is used as outgroup. Eleven ‘Candidatus’ species are shown in bold type.