Frequency and diversity of Stenotrophomonas spp. carrying blaKPC in recreational coastal waters

Comparative resistomics analysis of multidrug-resistant Chryseobacteria

Chryseobacteria consists of important human pathogens that can cause a myriad of nosocomial infections. We isolated four multidrug-resistant Chryseobacterium bacteria from activated sludge collected at domestic wastewater treatment facilities in the New York Metropolitan area. Their genomes were sequenced with Nanopore technology and used for a comprehensive resistomics comparison with 211 Chryseobacterium genomes available in the public databases. A majority of Chryseobacteria harbor 3 or more antibiotic resistance genes (ARGs) with the potential to confer resistance to at least two types of commonly prescribed antimicrobials. The most abundant ARGs, including β-lactam class A (blaCGA-1 and blaCIA) and class B (blaCGB-1 and blaIND) and aminoglycoside (ranA and ranB), are considered potentially intrinsic in Chryseobacteria. Notably, we reported a new resistance cluster consisting of a chloramphenicol acetyltransferase gene catB11, a tetracycline resistance gene tetX, and two mobile genetic elements (MGEs), IS91 family transposase and XerD recombinase. Both catB11 and tetX are statistically enriched in clinical isolates as compared to those with environmental origins. In addition, two other ARGs encoding aminoglycoside adenylyltransferase (aadS) and the small multidrug resistance pump (abeS), respectively, are found co-located with MGEs encoding recombinases (e.g., RecA and XerD) or transposases, suggesting their high transmissibility among Chryseobacteria and across the Bacteroidota phylum, particularly those with high pathogenicity. High resistance to different classes of β-lactam, as well as other commonly used antimicrobials (i.e., kanamycin, gentamicin, and chloramphenicol), was confirmed and assessed using our isolates to determine their minimum inhibitory concentrations. Collectively, though the majority of ARGs in Chryseobacteria are intrinsic, the discovery of a new resistance cluster and the co-existence of several ARGs and MGEs corroborate interspecies and intergenera transfer, which may accelerate their dissemination in clinical environments and complicate efforts to combat bacterial infections.

New Delhi metallo-β-lactamase-1-producing Citrobacter portucalensis belonging to the novel ST264 causing fatal sepsis in a vulnerable migratory sea turtle

Olive ridley (Lepidochelys olivacea) turtles migrate across tropical regions of the Atlantic, Pacific, and Indian Oceans. Worryingly, olive ridley populations have been declining substantially and is now considered a threatened species. In this regard, habitat degradation, anthropogenic pollution, and infectious diseases have been the most notorious threats for this species. We isolated a metallo-β-lactamase (NDM-1)-producing Citrobacter portucalensis from the blood sample of an infected migratory olive ridley turtle found stranded sick in the coast of Brazil. Genomic analysis of C. portucalensis confirmed a novel sequence type (ST), named ST264, and a wide resistome to broad-spectrum antibiotics. The production of NDM-1 by the strain contributed to treatment failure and death of the animal. Phylogenomic relationship with environmental and human strains from African, European and Asian countries confirmed that critical priority clones of C. portucalensis are spreading beyond hospital settings, representing an emerging ecological threat to marine ecosystems.

Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps

S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.

Irrigation Ponds as Sources of Antimicrobial-Resistant Bacteria in Agricultural Areas with Intensive Use of Poultry Litter

Poultry litter is widely used worldwide as an organic fertilizer in agriculture. However, poultry litter may contain high concentrations of antibiotics and/or antimicrobial-resistant bacteria (ARB), which can be mobilized through soil erosion to water bodies, contributing to the spread of antimicrobial resistance genes (ARGs) in the environment. To better comprehend this kind of mobilization, the bacterial communities of four ponds used for irrigation in agricultural and poultry production areas were determined in two periods of the year: at the beginning (low volume of rainfall) and at the end of the rainy season (high volume of rainfall). 16S rRNA gene sequencing revealed not only significantly different bacterial community structures and compositions among the four ponds but also between the samplings. When the DNA obtained from the water samples was PCR amplified using primers for ARGs, those encoding integrases (intI1) and resistance to sulfonamides (sul1 and sul2) and β-lactams (blaGES, blaTEM and blaSHV) were detected in three ponds. Moreover, bacterial strains were isolated from CHROMagar plates supplemented with sulfamethoxazole, ceftriaxone or ciprofloxacin and identified as belonging to clinically important Enterobacteriaceae. The results presented here indicate a potential risk of spreading ARB through water resources in agricultural areas with extensive fertilization with poultry litter.

Poly(3-hydroxybutyrate) biosynthesis under non-sterile conditions: Piperazine as nitrogen substrate control switch

Poly(3-hydroxybutyrate) (PHB), as a kind of bioplastics for sustainable development, can be synthesized by various microorganisms, however, the high cost of its microbial fermentation is a challenge for its large-scale application. In this study, piperazine degrading strain, Paracoccus sp. TOH, was developed as an excellent chassis for open PHB fermentation with piperazine as controlling element. Whole-genome analysis showed that TOH possesses multi-substrate metabolic pathways to synthesize PHB. Next, TOH could achieve a maximum PHB concentration of 2.42 g L^-1, representing a yield of 0.36 g-PHB g^-1-glycerol when C/N ratio was set as 60:1 with 10 g L^-1 glycerol as substrate. Furthermore, TOH could even synthesize 0.39 g-PHB g^-1-glycerol under non-sterile conditions when piperazine was fed with a suitable rate of 1 mg L^-1 h^-1. 16S rRNA gene sequencing analysis showed that microbial contamination could be effectively inhibited through the regulation of piperazine under non-sterile conditions and TOH dominated the microbial community with a relative abundance of 72.3% at the end of the operational period. This study offers an inspired open PHB fermentation system with piperazine as the control switch, which will realize the goal of efficient industrial biotechnology as well as industrial wastewater treatment.

The Municipal Sewage Discharge May Impact the Dissemination of Antibiotic-Resistant Escherichia coli in an Urban Coastal Beach

To determine the potential of the recreational marine environment as a dissemination vector of antibiotic-resistant microorganisms, the dissemination of antibiotic-resistant E. coli strains isolated from an urban coastal beach was studied. Sixty-nine and thirteen E. coli strains were isolated from the seawater and sand, respectively, in Fujiazhuang bathing beach, China. The average Antibacterial Resistance Index (ARI) value detected in the seawater is approximately three times that in beach sand. All the isolates from the sand were grouped into one cluster and only the isolates from the municipal sewage outlet were classified into three antibiogram clusters that were observed in the hetero-sites of the E. coli isolates. The E. coli strains with multiple antibiotic resistance (58% of total) were prevalent in the seawater, whereas the isolates from the sand were not detected with multiple antibiotic resistance. A significant association (p < 0.05) between all phenotypic and relative genotypic resistance profiles was observed in the isolates, except in the quinolones resistance genotype. The presence of a class 1 integron was significantly correlated with the resistance of E. coli to sulfonamides, streptomycin, and levofloxacin (p < 0.01). This study revealed that the municipal sewage discharge may impact the dissemination of antibiotic-resistant strains in the urban coastal beach, and that the class 1 integrons play an important role in mediating the resistance of E. coli to sulfonamide antibiotics.

Accelerated biodegradation of polyethylene terephthalate by Thermobifida fusca cutinase mediated by Stenotrophomonas pavanii

Polyethylene terephthalate (PET) is a general plastic that produces a significant amount of waste due to its non-biodagradable properties. We obtained four bacteria (Stenotrophomonas pavanii JWG-G1, Comamonas thiooxydans CG-1, Comamonas koreensis CG-2 and Fulvimonas soli GM-1) that utilize PET as a sole carbon source through a novel stepwise screening and verification strategy. PET films pretreated with S. pavanii JWG-G1 exhibited weight loss of 91.4% following subsequent degradation by Thermobifida fusca cutinase (TfC). S. pavanii JWG-G1 was able to colonize the PET surface and maintain high cell viability (over 50%) in biofilm, accelerating PET degradation. Compared with PET films with no pretreatment, pretreatment with S. pavanii JWG-G1 caused the PET surface to be significantly rougher with greater hydrophilicity (contact angle of 86.3 ± 2° vs. 96.6 ± 2°), providing better opportunities for TfC to contact and act on PET. Our study indicates that S. pavanii JWG-G1 could be used as a novel pretreatment for efficiently accelerating PET biodegradation by TfC.

The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance

Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.

Appearance of mcr-9, blaKPC, cfr and other clinically relevant antimicrobial resistance genes in recreation waters and sands from urban beaches, Brazil

The co-occurrence of mcr-like and carbapenemase-encoding genes have been reported mainly in humans and animals, whereas, in the environment, studies are gradually increasing due to the One Health approach. In this study, we investigated antimicrobial resistance genes (ARGs) in water and sand samples from marine environments in Brazil. Total DNA from 56 samples (33 sands and 23 waters) was obtained and 27 different ARGs were detected, highlighting the presence of mcr-9, bla_KPC and cfr genes. Additionally, the microbiological analysis revealed that sand samples of all analyzed beaches were not recommended for primary use, whereas water samples from most beaches were classified as unsuitable for bathing. The presence of clinically relevant ARGs in urban beaches suggests the presence of antimicrobial-resistant bacteria. Furthermore, to the best of our knowledge, this is the first report of mcr-9 and cfr genes in the environment from Brazil and recreational areas worldwide.

Prevalence and antimicrobial susceptibility of Gram-negative bacilli in subgingival biofilm associated with periodontal diseases

BACKGROUND

This cross-sectional study aimed to determine the prevalence and antimicrobial susceptibility of Gram-negative bacilli (GNB) isolated from subgingival biofilm of individuals with different periodontal conditions.

METHODS

Subgingival biofilm was obtained from 362 individuals with periodontal health (PH) (n = 83), gingivitis (n = 74), and periodontitis (n = 205), cultivated in broth and selective media. Isolated strains were identified by mass spectrometry. Antimicrobial susceptibility was determined by the Clinical and Laboratory Standards Institute disk diffusion guidelines. Production of extended-spectrum beta-lactamase (ESBL) and carbapenemases were evaluated by double disk synergy test and spectrophotometric detection of imipenem hydrolysis, respectively. ESBL and carbapenemase encoding genes were surveyed by Polymerase chain reaction (PCR). Differences among groups were examined by Chi-square, Kruskal-Wallis or Mann-Whitney tests.

RESULTS

GNB were isolated from 36.2% of all subgingival biofilm samples, with a significantly greater prevalence and species diversity (P < 0.001) in patients with periodontitis (45.9%) compared with individuals with PH (24.1%) and gingivitis (22.9%). Pseudomonas aeruginosa (27.5%), Enterobacter cloacae (16.8%), and Enterobacter asburiae (10.7%) were the most predominant species. Resistance/reduced sensitivity to at least 1 antimicrobial was detected in 60% of the strains, but only 4.6% were multidrug resistant. Serratia marcescens, E. cloacae, and Enterobacter kobei presented high rates of intrinsic resistance (>40%) to amoxicillin-clavulanate and first/second-generations of cephalosporins. One strain of Klebsiella pneumoniae isolated from periodontitis was resistant to imipenem, but no ESBL encoding genes or ESBL phenotype was detected.

CONCLUSION

High prevalence and diversity of GNB, with low susceptibility to β-lactams are observed in the subgingival microbiota associated with periodontitis.