Abstract

Stenotrophomonas belongs to the family gamma-proteobacteria, which are Gram-

negative bacteria. Their recovery from patients and intrinsic ability to resist many
antimicrobial agents make them of clinical importance though they are opportunistic
pathogens. Stenotrophomonas possess vast metabolic capacities, which enhances its
survival in many habitats. They can grow in harsh conditions, including
antimicrobial agents. Stenotrophomonas abilities have been exploited in
bioremediation, dye decolorization and plant growth promotion. Although
Stenotrophomonas can cause infections in patients with underlying disease
conditions, their beneficial applications should not be ignored. Isolation and
characterization of new isolates can lead to the discovery of novel species with more
benefits and also provide the possible ways for controlling antibiotic-resistant
behaviors. This study therefore focuses on the isolation and genomic
characterization of Stenotrophomonas species from different environments in
Mexico to understand their diversity, evolution and the potential for application.

Stenotrophomonas species were isolated from different parts of Mexico using both
double layer agar-plating technique and selective medium (StenoVIA agar). Isolates
were identified with bacterial biochemical feature using the conventional techniques,
Maldi-TOF spectrometry and the partial16S rRNA sequence. Evolution and
diversity of isolates were inferred by phylogentic analysis using the sequenced genes
and REP-PCR & ERIC finger printing technique respectively. The antimicrobial
susceptibility pattern of the isolates was evaluated using both disc-diffusion and
MIC based susceptibility studies according to the CLSI standard. Further analysis
based on Stenotrophomonas’ phenotype such as degradation assay were evaluated
in minimal medium with PAH as carbon source. The sequencing of the genomes
revealed the genes that are involved in the degradation of PAH, dye decolorization
and antibiotic resistance.

The results showed that 54 Stenotrophomonas isolates were recovered from soil,
sewage and clinical specimens from about 300 samples. Varied biochemical
characteristics were observed in the isolates. As some Stenotrophomonas
maltophilia strains preferred arabinose and mannitol as their unique carbon source,
in contrast to the trait for this species. The strains recovered from crude oil-
contaminated sites and textile effluent successfully degraded polycylic aromatic
hydrocarbon (PAH) and decolorized textile dyes respectively in degradation and
decolorization experiments. The UPLC-MS and GC-MS analysis of their
metabolites showed that they completely degraded PAH and decolorized textile dye
respectively. The degradation of PAH by the Stenotrophomonas produced catechol
(molecular weight, 110.03) as the metabolite determined from UPLC spectrometry.
Stenotrophomonas isolates were resistant to most antibiotics tested. They showed
100% resistance to ampicillin, doxycycline and amoxycillin but were susceptible to
fluoroquinolones. They were also resistant to Trimethoprim-Sulfamethoxazole
(80%), which is the first drug of choice for the treatment of Stenotrophomonas
maltophilia’ infections. The multiple antibiotic resistant index (MARI) showed that
the clinical strains were more resistant to the tested antibiotic agents with an average
MARI index of 0.8. Isolates from sewage and soil had average MARI index of 0.65
and 0.7 respectively. Five genomes were sequenced because they showed special
characteristics such as the degradation of PAH (PEMSOL, ASS1 and SVIA2),
Textile dye decolorization (TEPEL), possible plant growth promotion (ATCM1_4).
The sequence assemblage resulted in 1 contigs and 1 scaffold in PEMSOL, ASS1
and SVIA2 while ATCM1_4 and TEPEL has 8 contigs and six contigs respectively.
The coding proteins in the genomes identified are 3905, 4108, 4028, 3681 and 3905
respectively. The size of the genome is between 4.2 Mb and 4.5 Mb. Each genome
has between 19 and 27 genomic islands. Further analysis showed that some genes
associated with their phenotypes were also found on the genomes. Alcohol
dehydrogenase encoding gene, catechol 2, 3 dioxygenase, lactoylgluthatione lyase
are important for the degradation of PAHs. Tyrosinase and Azo R1 oxidoreductase
are required for the degradation of Azo dyes and textile dye. We also identified some
genes in the genome that may be involved in resistance to antimicrobial agents such
as the ampC genes, gnl|TC-DB|Q4LDT6|2.A.6.2.34 RND multidrug efflux
transporter.

Stenotrophomonas is a genus of economically important bacteria. Their benefit can

be better exploit and applied for large scale use, if we understand the mechanisms
involved in their survival. Genome analysis of some strains in the study gave insight
to some of the important genes which assist them to survive and use toxic substances
for growth. The identification of the genes involved in bioremediation and antibiotic
resistance in Stenotrophomonas will give insight to how they can be manipulated to
halt the resistant menace and hence, can be applied for bioremediation purposes

In conclusion, Stenotrophomonas are highly diverse and their phenotypic properties

can be evolutionally slectected by their environment. For example, isolates from
crude oil contaminated sites possess the ability to use PAH for growth. Also, the
resistant behavior of the isolates under the impact of the environment was
characterized in this study. An important result from this study indicates the need
for better public hygiene because the environment could be a reservoir for drug
resistant bacteria among Stenotrophomonas strians. There is also a need to review
the drug use for the treatment of Stenotrophomonas infection because of the high
occurrence of resistant strains to SXT, which is the primary drug of choice