Multidrug-resistant Stenotrophomonas maltophilia: Description of new MLST profiles and resistance and virulence genes using whole-genome sequencing

Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia

BACKGROUND

Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient.

METHODS

These bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia.

RESULTS

Results showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR.

CONCLUSION

Our study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes.

Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates

Stenotrophomonas maltophilia is a rapidly evolving multidrug-resistant opportunistic pathogen that can cause serious infections in immunocompromised patients. Although phage therapy is one of promising strategies for dealing with MDR bacteria, the main challenges of phage therapeutics include accumulation of phage resistant mutations and acquisition of the phage defense systems. To systematically evaluate the impact of (pro)phages in shaping genetic and evolutionary diversity of S. maltophilia, we collected 166 S. maltophilia isolates from three hospitals in southern China to analyze its pangenome, virulence factors, prophage regions, and anit-viral immune systems. Pangenome analysis indicated that there are 1328 saturated core genes and 26961 unsaturated accessory genes in the pangenome, suggesting existence of highly variable parts of S. maltophilia genome. The presence of genes in relation to T3SS and T6SS mechanisms suggests the great potential to secrete toxins by the S. maltophilia population, which is contrary to the conventional notion of low-virulence of S. maltophilia. Additionally, we characterized the pan-immune system maps of these clinical isolates against phage infections and revealed the co-harboring of CBASS and anti-CBASS in some strains, suggesting a never-ending arms race and the co-evolutionary dynamic between bacteria and phages. Furthermore, our study predicted 310 prophage regions in S. maltophilia with high genetic diversity. Six viral defense systems were found to be located at specific position of the S. maltophilia prophage genomes, indicating potential evolution of certain site/region similar to bacterial 'defense islands' in prophage. Our study provides novel insights into the S. maltophilia pangenome in relation to phage-defense mechanisms, which extends our understanding of bacterial-phage interactions and might guide the application of phage therapy in combating S. maltophilia infections.

Evaluation of phenotypical and genotypical methods for the identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility

AIMS

Evaluate methods for identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility.

METHODS AND RESULTS

From 270 S. maltophilia strains identified by VITEK®2, 40 were selected and submitted to MALDI TOF-MS, 16S and 23S rRNA gene analysis, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and an antimicrobial susceptibility profile. 16S rRNA sequencing was able to identify 39 (97.5%) strains as Stenotrophomonas spp. and one (2.5%) as Luteimonas huabeiensis. MALDI TOF-MS identified 37 (92.5%) strains as S. maltophilia, and three (7.5%) were not identified. PCR targeting 23S rRNA yielded a positive result for 39 (97.5%) strains. However, after sequencing, two strains were identified as Stenotrophomonas rhizophila, showing false-positive results. The confirmed S. maltophilia strains (n = 37) showed 35 distinct ERIC-PCR profiles and exhibited sensitivity to minocycline and levofloxacin, and six (16.3%) showed intermediate resistance to sulfamethoxazole-trimethoprim.

CONCLUSION

Matrix-assisted laser desorption lonization-time of flight mass spectrometry (MALDI-TOF MS) was a satisfactory methodology for the identification of S. maltophilia, but expansion of the database is necessary for the identification of other species. 16S rDNA sequencing showed low resolution for Stenotrophomonas species differentiation. PCR targeting 23S rRNA could not differentiate S. maltophilia from S. rhizophila. ERIC-PCR was shown to be a useful tool for the microbial source tracking of S. maltophilia.

Global prevalence and distribution of antibiotic resistance among clinical isolates of Stenotrophomonas maltophilia: A systematic review and meta-analysis

OBJECTIVES

Stenotrophomonas maltophilia (S. maltophilia), an opportunistic pathogen, causes infection in patients undergoing immunosuppressive therapy, mechanical ventilation, or catheters and in long-term hospitalized patients. Due to its extensive resistance to various antibiotics and chemotherapeutic agents, S. maltophilia is challenging to treat. Using case reports, case series, and prevalence studies, the current study provides a systematic review and meta-analysis of antibiotic resistance profiles across clinical isolates of S. maltophilia.

METHODS

A systematic literature search was performed for original research articles published in Medline, Web of Science, and Embase databases from 2000 to 2022. Statistical analysis was performed using STATA 14 software to report antibiotic resistance of S. maltophilia clinical isolates worldwide.

RESULTS

223 studies (39 case reports/case series and 184 prevalence studies) were collected for analysis. A meta-analysis of prevalence studies demonstrated that the most antibiotic resistance worldwide was to levofloxacin, trimethoprim-sulfamethoxazole (TMP/SMX), and minocycline (14.4%, 9.2%, and 1.4%, respectively). Resistance to TMP/SMX (36.84%), levofloxacin (19.29%), and minocycline (1.75%) were the most prevalent antibiotic resistance types found in evaluated case reports/case series studies. The highest resistance rate to TMP/SMX was reported in Asia (19.29%), Europe (10.52%), and America (7.01%), respectively.

CONCLUSION

Considering the high resistance to TMP/SMX, more attention should be paid to patients' drug regimens to prevent the emergence of multidrug-resistant S. maltophilia isolates.

Genotypic Diversity, Antibiotic Resistance, and Virulence Phenotypes of Stenotrophomonas maltophilia Clinical Isolates from a Thai University Hospital Setting

Stenotrophomonas maltophilia is a multidrug-resistant organism that is emerging as an important opportunistic pathogen. Despite this, information on the epidemiology and characteristics of this bacterium, especially in Thailand, is rarely found. This study aimed to determine the demographic, genotypic, and phenotypic characteristics of S. maltophilia isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand. A total of 200 S. maltophilia isolates were collected from four types of clinical specimens from 2015 to 2016 and most of the isolates were from sputum. In terms of clinical characteristics, male and aged patients were more susceptible to an S. maltophilia infection. The majority of included patients had underlying diseases and were hospitalized with associated invasive procedures. The antimicrobial resistance profiles of S. maltophilia isolates showed the highest frequency of resistance to ceftazidime and the lower frequency of resistance to chloramphenicol, levofloxacin, trimethoprim/sulfamethoxazole (TMP/SMX), and no resistance to minocycline. The predominant antibiotic resistance genes among the 200 isolates were the smeF gene (91.5%), followed by bla_L1 and bla_L2 genes (43% and 10%), respectively. Other antibiotic resistance genes detected were floR (8.5%), intI1 (7%), sul1 (6%), mfsA (4%) and sul2 (2%). Most S. maltophilia isolates could produce biofilm and could swim in a semisolid medium, however, none of the isolates could swarm. All isolates were positive for hemolysin production, whereas 91.5% and 22.5% of isolates could release protease and lipase enzymes, respectively. In MLST analysis, a high degree of genetic diversity was observed among the 200 S. maltophilia isolates. One hundred and forty-one sequence types (STs), including 130 novel STs, were identified and categorized into six different clonal complex groups. The differences in drug resistance patterns and genetic profiles exhibited various phenotypes of biofilm formation, motility, toxin, and enzymes production which support this bacterium in its virulence and pathogenicity. This study reviewed the characteristics of genotypes and phenotypes of S. maltophilia from Thailand which is necessary for the control and prevention of S. maltophilia local spreading.

Phenotypic and Molecular Characteristics of the MDR Efflux Pump Gene-Carrying Stenotrophomonas maltophilia Strains Isolated in Warsaw, Poland

Simple Summary

Nosocomial infections caused by Stenotrophomonas maltophilia have been increasing worldwide. These bacteria are intrinsically resistant to most antibiotics. The underestimated resistance mechanism of Gram-negative rods is an overexpression of multidrug-resistant (MDR) efflux pumps. The aim of this study was to analyze the genetic diversity of isolates derived from various clinical materials, including blood, and the prevalence of MDR efflux pump genes and susceptibility profiles to the anti-S. maltophilia drugs. The research was conducted on 94 S. maltophilia isolates derived from hospitalized patients and outpatients in Warsaw, Poland. All isolates were susceptible to trimethoprim-sulfamethoxazole and minocycline, while 44/94 isolates demonstrated reduction in susceptibility to levofloxacin. A large genetic variation was observed among these isolates. However, a clonal relationship was revealed among two groups of bloodstream isolates from one hospital ward: (1) nine isolates, (2) six isolates. Moreover, the presence of genes encoding ten different efflux pumps from the resistance-nodulation-division family and the ATP-binding cassette family was shown in the majority of the 94 isolates. The obtained knowledge about the prevalence of efflux pump genes in clinical S. maltophilia strains makes it possible to predict the scale of the risk of resistance emergence in strains as a result of gene overexpression.

Abstract

An increase of nosocomial infections caused by Stenotrophomonas maltophilia strains has recently been observed all over the world. The isolation of these bacteria from the blood is of particular concern. In this study we performed the phenotypic and genotypic characterization of 94 S. maltophilia isolates, including isolates from patients hospitalized in a tertiary Warsaw hospital (n = 79) and from outpatients (n = 15). All isolates were found to be susceptible to trimethoprim-sulfamethoxazole and minocycline, while 44/94 isolates demonstrated a reduction in susceptibility to levofloxacin. A large genetic variation was observed among the isolates tested by pulsed-field gel electrophoresis. A clonal relationship with 100% similarity was observed between isolates within two sub-pulsotypes: the first included nine bloodstream isolates and the second involved six. Multilocus sequence typing showed two new sequence types (ST498 and ST499) deposited in public databases for molecular typing. Moreover, the presence of genes encoding ten different efflux pumps from the resistance-nodulation-division family and the ATP-binding cassette family was shown in the majority of the 94 isolates. The obtained knowledge about the prevalence of efflux pump genes in clinical S. maltophilia strains makes it possible to predict the scale of the risk of resistance emergence in strains as a result of gene overexpression.

Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS

Background

Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS).

Methods

A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis.

Results

A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSL_B and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSL_B and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples.

Conclusion

High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSL_B and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.

Draft Genome Sequence of the Multidrug-Resistant Strain Stenotrophomonas maltophilia N0320, Isolated from a Commercial Nanoparticle Product

Stenotrophomonas maltophilia is an emerging opportunistic pathogen that is frequently associated with hospital infections. We report the 4.8-Mbp draft genome sequence of the oxidase-positive S. maltophilia strain N0320, an isolate from a commercial hydroxyapatite nanoparticle product.

Clinical Status of Efflux Resistance Mechanisms in Gram-Negative Bacteria

Antibiotic efflux is a mechanism that is well-documented in the phenotype of multidrug resistance in bacteria. Efflux is considered as an early facilitating mechanism in the bacterial adaptation face to the concentration of antibiotics at the infectious site, which is involved in the acquirement of complementary efficient mechanisms, such as enzymatic resistance or target mutation. Various efflux pumps have been described in the Gram-negative bacteria most often encountered in infectious diseases and, in healthcare-associated infections. Some are more often involved than others and expel virtually all families of antibiotics and antibacterials. Numerous studies report the contribution of these pumps in resistant strains previously identified from their phenotypes. The authors characterize the pumps involved, the facilitating antibiotics and those mainly concerned by the efflux. However, today no study describes a process for the real-time quantification of efflux in resistant clinical strains. It is currently necessary to have at hospital level a reliable and easy method to quantify the efflux in routine and contribute to a rational choice of antibiotics. This review provides a recent overview of the prevalence of the main efflux pumps observed in clinical practice and provides an idea of the prevalence of this mechanism in the multidrug resistant Gram-negative bacteria. The development of a routine diagnostic tool is now an emergency need for the proper application of current recommendations regarding a rational use of antibiotics.

Immunoinformatic Approach for the Identification of Potential Epitopes Against Stenotrophomonas maltophilia: A Global Opportunistic Pathogen

Background:

Stenotrophomonas maltophilia is an aerobic, non-fermentative, gram negative, multidrug resistant and opportunistic nosocomial pathogen. It is associated with high morbidity and mortality in severely immunocompromised paediatric patients, including neonates. Immunoinformatic analysis paved a new way to design epitope-based vaccines which resulted in a potential immunogen with advantages such as lower cost, specific immunity, ease of production, devoid of side effects, and less time consumption than conventional vaccines. Till date, there is no development in the vaccines or antibody-based treatments for S. maltophilia-associated infections.

Introduction:

Currently, epitope-based peptide vaccines against pathogenic bacteria have grasped more attention. In our present study, we have utilized various immunoinformatic tools to find a prominent epitope that interacts with the maximum number of HLA alleles and also with the maximum population coverage for developing a vaccine against Stenotrophomonas maltophilia.

Methods:

This study has incorporated an immunoinformatic based screening approach to explore potential epitope-based vaccine candidates in Stenotrophomonas maltophilia proteome. In this study, 4365 proteins of the Stenotrophomonas maltophilia K279a proteome were screened to identify potential antigens that could be used as a good candidate for the vaccine. Various immunoinformatic tools were used to predict the binding of the promiscuous epitopes with Major Histocompatibility Complex (MHC) class I molecules. Other properties such as allergenicity, physiochemical properties, adhesion properties, antigenicity, population coverage, epitope conservancy and toxicity were analysed for the predicted epitope.

Results:

This study helps in finding the prominent epitope in Stenotrophomonas infections. Hence, the main objective in this research was to screen complete Stenotrophomonas maltophilia proteome to recognize putative epitope candidates for vaccine design. Using computational vaccinology and immunoinformatic tools approach, several aspects are obligatory to be fulfilled by an epitope to be considered as a vaccine candidate. Our findings were promising and showed that the predicted epitopes were non-allergenic and fulfilled other parameters required for being a suitable candidate based on certain physio-chemical, antigenic and adhesion properties.

Conclusion:

The epitopes LLFVLCWPL and KSGEGKCGA have shown the highest binding score of −103 and −78.1 kcal/mol with HLA-A*0201 and HLA-B*0702 MHC class I allele, respectively. They were also predicted to be immunogenic and non-allergenic. Further various immunological tests, both in vivo and in vitro methods, should be performed for finding the efficiency of the predicted epitope in the development of a targeted vaccine against Stenotrophomonas maltophilia infection.

Tetracycline-Resistant Bacteria Selected from Water and Zebrafish after Antibiotic Exposure

The emergence of antibiotic-resistant pathogens due to worldwide antibiotic use is raising concern in several settings, including aquaculture. In this work, the selection of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) was evaluated after exposure of zebrafish to oxytetracycline (OTC) for two months, followed by a recovery period. The selection of ARB in water and fish was determined using selective media. The abundance of tetA genes was estimated through qPCR. Higher prevalence of ARB was measured in all samples exposed to the antibiotic when compared to control samples, although statistical significance was only achieved five days after exposure. Isolates recovered from samples exposed to the antibiotic were affiliated with Pseudomonas and Stenotrophomonas. Various antibiotic susceptibility profiles were detected and 37% of the isolates displayed multidrug resistance (MDR). The selection of the tetA gene was confirmed by qPCR at the highest OTC concentration tested. Two MDR isolates, tested using zebrafish embryos, caused significant mortality, indicating a potential impact on fish health and survival. Overall, our work highlights the potential impact of antibiotic contamination in the selection of potential pathogenic ARB and ARGS.

Significant higher airborne antibiotic resistance genes and the associated inhalation risk in the indoor than the outdoor

Inhalation of airborne antibiotic resistance genes (ARGs) can lead to antimicrobial resistance and potential health risk. In modern society, increasing individuals stay more indoors, however, studies regarding the exposure to airborne ARGs in indoor environments and the associated risks remain limited. Here, we compared the variance of aerosol-associated ARGs, bacterial microbiomes, and their daily intake (DI) burden in dormitory, office, and outdoor environments in a university in Tianjin. The results indicated that compared to outdoor aerosols, indoors exhibited significantly higher absolute abundance of both ARG subtypes and mobile genetic elements (MGEs) (1-7 orders of magnitude), 16S rRNA genes (2-3 orders), and total culturable bacteria (1-3 orders). Furthermore, we observed that significantly different airborne bacterial communities are the major drivers contributing to the variance of aerosol-associated ARGs in indoor and outdoor aerosols. Notably, the high abundances of total bacteria, potential pathogenic genera, and ARGs (particularly those harbored by pathogens) in indoor and outdoor aerosols, especially in indoors, may pose an increased exposure risk via inhalation. The successful isolation of human pathogens such as Elizabethkingia anopheles, Klebsiella pneumonia, and Delftia lacustris resistant to the "last-resort" antibiotics carbapenems and polymyxin B from indoor aerosols further indicated an increased exposure risk in indoors. Together, this study highlights the potential risks associated with ARGs and their inhalation to human health in indoor environments.

Discrimination of biofilm-producing Stenotrophomonas maltophilia clinical strains by matrix-assisted laser desorption ionization-time of flight

Stenotrophomonas maltophilia is a Gram-negative drug-resistant pathogen responsible for healthcare-associated infections. The aim was to search for biomarker peaks that could rapidly detect biofilm production in S. maltophilia clinical isolates obtained from two tertiary care hospitals in Mexico. Isolates were screened for the presence of biofilm-associated genes, in which the fsnR gene was associated with biofilm production (p = 0.047), whereas the rmlA+ genotype was associated with the rpfF- genotype (p = 0.017). Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectra comparison yielded three potential biomarker peaks (4661, 6074, and 6102 m/z) of biofilm-producing rmlA+ and rpfF- genotypes with >90% sensitivity (p<0.001). MALDI-TOF MS analyses showed a correlation between the relative abundance of 50S ribosomal proteins (L30 and L33) and the presence of the fnsR, rmlA and rpfF-2 genes, suggested to play a role in biofilm formation. Isolates obtained in the intensive care unit showed low clonality, suggesting no transmission within the hospital ward. The detection of biomarkers peaks by MALDI-TOF MS could potentially be used to early recognize and discriminate biofilm-producing S. maltophilia strains and aid in establishing appropriate antibiotic therapy.

Cluster of S. maltophilia among patients with respiratory tract infections at an intensive care unit

Background

Stenotrophomonas maltophilia is associated with respiratory tract infections in immunocompromised patients, and it has emerged as an important nosocomial pathogen, with admission to intensive care units (ICUs) and ventilators as recognized risk factors.

Aim

To describe the investigation of a sudden increase in patients with pneumonia caused by S. maltophilia at a Swedish ICU and the control measures taken.

Methods

Lower respiratory tract cultures from patients admitted to the ICU were obtained, and environmental cultures were collected from sink drains and medical equipment. Isolates identified as S. maltophilia were subjected to antibiotic susceptibility testing and whole genome sequencing (WGS).

Findings

A total of 17 S. maltophilia isolates were found (four from patients and 13 from the environment). The WGS identified two outbreak clones, sequence type (ST) 361 and ST138, and seven unique ones. Most likely, the outbreak clones originated from two sinks, and transmission was enhanced by a calorimeter. After changing the sink and calorimeter routines, no more cases were registered.

Conclusion

Acquisition of S. maltophilia from the hospital environment appears to be easy, especially if water is involved. To control this bacterium, better knowledge of its transmission routes in hospital environments is required.

Genetic Variants of the DSF Quorum Sensing System in Stenotrophomonas maltophilia Influence Virulence and Resistance Phenotypes Among Genotypically Diverse Clinical Isolates

The pathogenicity of Stenotrophomonas maltophilia is regulated in part by its quorum sensing (QS) system. The main QS signaling molecule in S. maltophilia is known as diffusible signal factor (DSF), and the rpf gene cluster is responsible for its synthesis and perception. Two cluster variants have been previously described, rpf-1 and rpf-2, which differ basically in the conditions under which DSF is produced. Here, correlations between the rpf variant and antibiotic susceptibility, LPS electrophoretic profiles and virulence-related phenotypes were evaluated for a collection of 78 geographically and genetically diverse clinical strains of S. maltophilia. In general there were associations between previously established genogroups and the genetic variant of the rpf cluster. However, only few genotype-phenotype correlations could be observed. Resistance to the β-lactam antibiotics ceftazidime and ticarcillin was associated with strains carrying the rpf-1 variant, whereas strains of variant rpf-2, particularly those of genogroup C, showed higher resistance levels to colistin. Strains of variant rpf-2 were also significantly more virulent to Galleria mellonella larvae than those of rpf-1, most likely due to an increased ability of rpf-2 strains to form biofilms. A comparative genomic analysis revealed the presence of proteins unique to individual genogroups. In particular, the strains of genogroup C share an operon that encodes for a new virulence determinant in S. maltophilia related to the synthesis of an alternative Flp/Tad pilus. Overall, this study establishes a link between the DSF-based QS system and the virulence and resistance phenotypes in this species, and identifies potential high-risk clones circulating in European hospitals.

Complete genome sequence data of multidrug-resistant Stenotrophomonas sp. strain SXG-1

Objectives A multidrug-resistant bacterium, Stenotrophomonas sp. SXG-1, was isolated from the liver of diseased hybrid sturgeon from Guizhou province, China. Methods Whole-genome sequencing was performed on the Illumina HiSeq 2500-PE125 platform with MPS (massively parallel sequencing) Illumina technology. All good quality paired reads were assembled using the SOAPdenovo into a number of scaffolds. PHI (Pathogen Host Interactions), VFDB (Virulence Factors of Pathogenic Bacteria) and ARDB (Antibiotic Resistance Genes Database) were used to analyses pathogenicity and drug resistance. Results Here we reported the complete genome sequence of Stenotrophomonas sp. SXG-1, which comprised 4534,602bp in 4077 coding sequences (CDS) with a G+C content of 66.42%. The genome contained 4 gene islands, 72 tRNAs and 13 rRNAs. According to the annotation analysis, strain SXG-1 encoded 22 genes related to the multidrug resistance. In addition to 10 genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, 12 genes of efflux pumps were presented, 9 of which were reported for the first time in Stenotrophomonas maltophilia. Conclusion This was the first complete genome sequence of Stenotrophomonas sp. isolated from the sturgeon. The complete genome sequence of Stenotrophomonas sp. strain SXG-1 may provide insights into the mechanism of antimicrobial resistance and prevent disease.

Mechanisms of antimicrobial resistance in Stenotrophomonas maltophilia: a review of current knowledge

Introduction: Stenotrophomonas maltophilia is a prototype of bacteria intrinsically resistant to antibiotics. The reduced susceptibility of this microorganism to antimicrobials mainly relies on the presence in its chromosome of genes encoding efflux pumps and antibiotic inactivating enzymes. Consequently, the therapeutic options for treating S. maltophilia infections are limited.Areas covered: Known mechanisms of intrinsic, acquired and phenotypic resistance to antibiotics of S. maltophilia and the consequences of such resistance for treating S. maltophilia infections are discussed. Acquisition of some genes, mainly those involved in co-trimoxazole resistance, contributes to acquired resistance. Mutation, mainly in the regulators of chromosomally-encoded antibiotic resistance genes, is a major cause for S. maltophilia acquisition of resistance. The expression of some of these genes is triggered by specific signals or stressors, which can lead to transient phenotypic resistance.Expert opinion: Treatment of S. maltophilia infections is difficult because this organism presents low susceptibility to antibiotics. Besides, it can acquire resistance to antimicrobials currently in use. Particularly problematic is the selection of mutants overexpressing efflux pumps since they present a multidrug resistance phenotype. The use of novel antimicrobials alone or in combination, together with the development of efflux pumps' inhibitors may help in fighting S. maltophilia infections.

Influence of surface copper content on Stenotrophomonas maltophilia biofilm control using chlorine and mechanical stress

This work aimed to evaluate the action of materials with different copper content (0, 57, 96 and 100%) on biofilm formation and control by chlorination and mechanical stress. Stenotrophomonas maltophilia isolated from drinking water was used as a model microorganism and biofilms were developed in a rotating cylinder reactor using realism-based shear stress conditions. Biofilms were characterized phenotypically and exposed to three control strategies: 10 mg l^-1 of free chlorine for 10 min, an increased shear stress (a fluid velocity of 1.5 m s^-1 for 30s), and a combination of both treatments. These shock treatments were not effective in biofilm control. The benefits from the use of copper surfaces was found essentially in reducing the numbers of non-damaged cells. Copper materials demonstrated better performance in biofilm prevention than chlorine. In general, copper alloys may have a positive public health impact by reducing the number of non-damaged cells in the water delivered after chlorine exposure.

Prolonged exposure of Stenotrophomonas maltophilia biofilms to trace levels of clofibric acid alters antimicrobial tolerance and virulence

The presence of pharmaceuticals in water sources, including in drinking water (DW), is increasingly being recognized as an emerging and global concern for the environment and public health. Based on the principles of the "One Health" initiative, the present work aims to understand the effects of clofibric acid (CA), a lipid regulator, on the behavior of a selected bacterium isolated from drinking water (DW). Biofilms of the opportunistic pathogen Stenotrophomonas maltophilia were exposed to CA for 12 weeks at 170 and 17000 ng/L. The effects of CA were evaluated on planktonic S. maltophilia susceptibility to chlorine and antibiotics (amoxicillin, ciprofloxacin, erythromycin, kanamycin, levofloxacin, oxacillin, spectinomycin, tetracycline and trimethoprim-sulfamethoxazole), biofilm formation, motility, siderophores production and on the adhesion and internalization of the human colon adenocarcinoma cell line (HT-29). It was found that CA did not affect planktonic S. maltophilia tolerance to chlorine exposure. Additionally, no effects were observed on biofilm formation, motility and siderophores production. However, biofilms formed after CA exposure were more tolerant to chlorine disinfection and lower CFU reductions were obtained. Of additional concern was the effect of CA exposure on S. maltophilia increased tolerance to erythromycin. CA exposure also slightly reduced S. maltophilia ability to invade HT-29 cells. In conclusion, this work reinforces the importance of studying the effects of non-antibiotic contaminants on the behavior of environmental microorganisms, particularly their role as drivers affecting resistance evolution and selection.

Characterization of Acquired Antimicrobial Resistance Genes in Environmental Stenotrophomonas maltophilia Isolates from Brazil

Stenotrophomonas maltophilia is an opportunist pathogen that has intrinsic resistance to the majority of antibiotics and has a high ability to adapt in different environments; however, there are few reports of acquired resistance genes in S. maltophilia. The aim of this study was to investigate the antimicrobial resistance profile, the presence of mutations in the quinolone-resistance determining region, the presence of acquired resistance genes, and the different plasmid families in S. maltophilia isolated from Brazilian soils. A total of 16 isolates were obtained from a variety of agricultural soils with different cultures of Brazil and they were nonsusceptible to most of the antibiotics tested. No mutations were detected in the gyrA gene and only one (Ser-80-Ile) was detected in the parC gene. A diversity of acquired resistance genes was found, including the qnrA, qnrB, qnrS, oqxA, oqxB, bla_SHV, bla_CTX-M-Gp1, bla_PER, bla_OXA-1-like, bla_OXA-48-like, and sul1. All isolates presented ColE-like plasmids and only one presented IncL/M. These results show, for the first time, the presence of qnrA and oqxAB genes and the presence of qnrB and qnrS genes for the second time in the world in S. maltophilia.