Genomic Features of an MDR Escherichia coli ST5506 Harboring an IncHI2/In229/blaCTX-M-2 Array Isolated from a Migratory Black Skimmer

Migratory birds have contributed to the dissemination of multidrug-resistant (MDR) bacteria across the continents. A CTX-M-2-producing Escherichia coli was isolated from a black skimmer (Rynchops niger) in Southeast Brazil. The whole genome was sequenced using the Illumina NextSeq platform and de novo assembled by CLC. Bioinformatic analyses were carried out using tools from the Center for Genomic Epidemiology. The genome size was estimated at 4.9 Mb, with 4790 coding sequences. A wide resistome was detected, with genes encoding resistance to several clinically significant antimicrobials, heavy metals, and biocides. The blaCTX-M-2 gene was inserted in an In229 class 1 integron inside a ∆TnAs3 transposon located in an IncHI2/ST2 plasmid. The strain was assigned to ST5506, CH type fumC19/fimH32, serotype O8:K87, and phylogroup B1. Virulence genes associated with survival in acid conditions, increased serum survival, and adherence were also identified. These data highlight the role of migratory seabirds as reservoirs and carriers of antimicrobial resistance determinants and can help to elucidate the antimicrobial resistance dynamics under a One Health perspective.

Targeting the gut microbiota for cancer therapy

Growing evidence suggests that the gut microbiota modulates the efficacy and toxicity of cancer therapy, most notably immunotherapy and its immune-related adverse effects. The poor response to immunotherapy in patients treated with antibiotics supports this influential role of the microbiota. Until recently, results pertaining to the identification of the microbial species responsible for these effects were incongruent, and relatively few studies analysed the underlying mechanisms. A better understanding of the taxonomy of the species involved and of the mechanisms of action has since been achieved. Defined bacterial species have been shown to promote an improved response to immune-checkpoint inhibitors by producing different products or metabolites. However, a suppressive effect of Gram-negative bacteria may be dominant in some unresponsive patients. Machine learning approaches trained on the microbiota composition of patients can predict the ability of patients to respond to immunotherapy with some accuracy. Thus, interest in modulating the microbiota composition to improve patient responsiveness to therapy has been mounting. Clinical proof-of-concept studies have demonstrated that faecal microbiota transplantation or dietary interventions might be utilized clinically to improve the success rate of immunotherapy in patients with cancer. Here, we review recent advances and discuss emerging strategies for microbiota-based cancer therapies.

Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1

Ample evidence indicates that the gut microbiome is a tumor-extrinsic factor associated with antitumor response to anti-programmed cell death protein-1 (PD-1) therapy, but inconsistencies exist between published microbial signatures associated with clinical outcomes. To resolve this, we evaluated a new melanoma cohort, along with four published datasets. Time-to-event analysis showed that baseline microbiota composition was optimally associated with clinical outcome at approximately 1 year after initiation of treatment. Meta-analysis and other bioinformatic analyses of the combined data show that bacteria associated with favorable response are confined within the Actinobacteria phylum and the Lachnospiraceae/Ruminococcaceae families of Firmicutes. Conversely, Gram-negative bacteria were associated with an inflammatory host intestinal gene signature, increased blood neutrophil-to-lymphocyte ratio, and unfavorable outcome. Two microbial signatures, enriched for Lachnospiraceae spp. and Streptococcaceae spp., were associated with favorable and unfavorable clinical response, respectively, and with distinct immune-related adverse effects. Despite between-cohort heterogeneity, optimized all-minus-one supervised learning algorithms trained on batch-corrected microbiome data consistently predicted outcomes to programmed cell death protein-1 therapy in all cohorts. Gut microbial communities (microbiotypes) with nonuniform geographical distribution were associated with favorable and unfavorable outcomes, contributing to discrepancies between cohorts. Our findings shed new light on the complex interaction between the gut microbiome and response to cancer immunotherapy, providing a roadmap for future studies.

Abstract LB062: Efficacy of Responder-derived Fecal Microbiota Transplant (R-FMT) and Pembrolizumab in Anti-PD-1 Refractory Patients with Advanced Melanoma

Background: Monoclonal antibodies (mAb) targeting the programmed cell death protein 1 (PD-1) receptor provide durable long-term benefit in a subset of patients (pts) with advanced melanoma with response rates of 35-42% and 4-year progression-free survival (PFS) rate of 27%. Separately, the composition of the gut microbiota has been shown to correlate with anti-PD-1 efficacy in human cancer pts with melanoma, renal cell cancer and non-small cell lung cancer (NSCLC) although the precise organisms differ considerably across various studies. In preclinical models, responder-derived fecal microbiome and microbiome consortia produce anti-tumor responses. The effect of microbiome modulation in pts with anti-PD-1 refractory melanoma has not been evaluated. Methods: To evaluate whether primary resistance to anti-PD-1 immunotherapy could be overcome by intestinal microbiome modulation, we designed and conducted a phase II study (NCT03341143). We enrolled pts with primary refractory metastatic melanoma with best response of short-term stable disease (≤6 months) or progressive disease (PD) to prior anti-PD-1 based immunotherapy. Pts received single-administration of responder-derived fecal microbiota transplantation (R-FMT) together with pembrolizumab. Candidate donors were pts with advanced melanoma treated with anti-PD-1 immunotherapy with durable partial or complete response (PR, CR). Pembrolizumab was continued till intolerable toxicity or disease progression. Safety and clinical activity (based on RECIST v1.1) were main objectives; while progression-free survival (PFS) was a key secondary endpoint. Results: As of December 1, 2020, 16 pts with primary refractory melanoma were enrolled, of whom 15 were evaluable. LDH was elevated in 14/15 pts; and the median number of prior therapies was 2. Recipient pts were seromatched to receive a single R-FMT from one of eight candidate donors (5 CR; 3 PR; median PFS 58 months, range 43-70). R-FMT was administered via colonoscopy after bowel preparation with no use of antibiotics. Pembrolizumab was administered IV per label. R-FMT/pembrolizumab was well-tolerated, with no unusual toxicity signals. R-FMT induced rapid and durable microbiota perturbation in most pts; while 6 of 15 evaluable pts had evidence of clinical benefit. Response to R-FMT/pembrolizumab was associated with an increased abundance of taxa previously shown to be associated with response to anti-PD-1, increased CD8+ T cell activation, and decreased frequency of IL-8 expressing myeloid cells. Responders had distinct proteomic and metabolomic signatures, and transkingdom network analyses confirmed that the gut microbiome regulated these changes. Conclusions: In pts with anti-PD-1 primary refractory melanoma, R-FMT/pembrolizumab changed the gut microbiome and reprogrammed the tumor microenvironment to overcome resistance to anti-PD-1 immunotherapy. Response was associated with CD8 T cell induction and reduction of IL-8 expressing myeloid cells.

Citation Format: Diwakar Davar, Amiran Dzutsev, John A. McCulloch, Richard R. Rodrigues, Joe-Marc Chauvin, Robert M. Morrison, Richelle N. Deblasio, Carmine Menna, Quanquan Ding, Ornella Pagliano, Bochra Zidi, Shuowen Zhang, Jonathan H. Badger, Marie Vetizou, Alicia M. Cole, Miriam R. Fernandes, Stephanie Prescott, Raquel G. Costa, Ascharya K. Balaji, Andrey Morgun, Ivan Vujkovic-Cvijin, Hong Wang, Amir A. Borhani, Marc B. Schwartz, Howard M. Dubner, Scarlett J. Ernst, Amy Rose, Yana G. Najjar, Yasmine Belkaid, John M. Kirkwood, Giorgio Trinchieri, Hassane M. Zarour. Efficacy of Responder-derived Fecal Microbiota Transplant (R-FMT) and Pembrolizumab in Anti-PD-1 Refractory Patients with Advanced Melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB062.

Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients

Anti-programmed cell death protein 1 (PD-1) therapy provides long-term clinical benefits to patients with advanced melanoma. The composition of the gut microbiota correlates with anti-PD-1 efficacy in preclinical models and cancer patients. To investigate whether resistance to anti-PD-1 can be overcome by changing the gut microbiota, this clinical trial evaluated the safety and efficacy of responder-derived fecal microbiota transplantation (FMT) together with anti-PD-1 in patients with PD-1-refractory melanoma. This combination was well tolerated, provided clinical benefit in 6 of 15 patients, and induced rapid and durable microbiota perturbation. Responders exhibited increased abundance of taxa that were previously shown to be associated with response to anti-PD-1, increased CD8⁺ T cell activation, and decreased frequency of interleukin-8-expressing myeloid cells. Responders had distinct proteomic and metabolomic signatures, and transkingdom network analyses confirmed that the gut microbiome regulated these changes. Collectively, our findings show that FMT and anti-PD-1 changed the gut microbiome and reprogrammed the tumor microenvironment to overcome resistance to anti-PD-1 in a subset of PD-1 advanced melanoma.

International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil

CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried blaCTX-M -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.

Identification and genomic features of halotolerant extended-spectrum-β-lactamase (CTX-M)-producing Escherichia coli in urban-impacted coastal waters, Southeast Brazil

We report the occurrence and genomic analysis of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in anthropogenically polluted coastal waters of Southeast Brazil. E. coli strains belonging to sequence types (STs) ST10, ST38, ST155 and ST1284 exhibited a wide resistome, with genes conferring resistance to medically relevant antimicrobials and heavy metals, and a halophilic behavior (tolerance to 9-10% NaCl). These findings suggest a heavy contamination in this area by critical priority bacteria adapted to marine environments, which might have negative impacts on human and ocean health.

Wild owls colonized by international clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli and Salmonella Infantis in the Southern Cone of America

Extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriaceae have been classified as critical priority pathogens by the World Health Organization (WHO). We have conducted a microbiological and genomic surveillance study, in order to investigate the occurrence and features of antibiotic-resistant bacteria in wild birds admitted to a wildlife rescue and rehabilitation centre in Chile. This study reports for the first time the occurrence of highly virulent ESBL-producing Escherichia coli and Salmonella enterica serovar Infantis in wild owls inhabiting the Southern Cone of America. Genomic analysis revealed a wide resistome (for antibiotics, heavy metals and disinfectants) among international lineages of E. coli belonging to ST345 and ST2705, and S. Infantis ST32, producing CTX-M-8 or CTX-M-65 ESBLs. On the other hand, wide virulome was associated with a highly virulent behaviour in the Galleria mellonella infection model. Worryingly, all these lineages have been previously reported in humans, supporting that wide resistome and virulome could be contributing to rapid adaptation and dissemination of these clones at the human-animal-environment interface. In summary, wild owls can constitute environmental reservoirs of international clones of ESBL (CTX-M)-producing E. coli and S. Infantis carrying a wide resistome and virulome, in the Southern Cone of America, with potential risks to human, animal and environmental health.

Antimicrobial blue light inactivation of international clones of multidrug-resistant Escherichia coli ST10, ST131 and ST648

BACKGROUND

International clones of multidrug-resistant Escherichia coli have been a leading cause of human and animal infections worldwide. Microbial inactivation by blue light has been proposed as an effective treatment for superficial infections and surface contamination.

AIM

To evaluate the inactivation efficacy of blue light irradiation against high-risk multidrug-resistant strains of E. coli.

METHODS

Blue LED light (λ = 410 nm) was used to inactivate in vitro suspensions of colistin- broad-spectrum cephalosporin-, or carbapenem-resistant E. coli strains belonging to sequence types (STs) ST10, ST131 and ST648, carrying mcr-1, bla_CTX-M or bla_KPC-2 genes.

RESULTS

Our results showed that all E. coli strains were susceptible to blue light irradiation, independently of antibiotic resistance and virulence profiles. In addition, blue light irradiation induced a strain-specific and dose-dependent bacterial effect.

CONCLUSION

Our results support use of blue light as a promising antimicrobial option against MDR pathogens, including high-risk clones of E. coli displaying resistance to polymyxins or broad-spectrum β-lactam antibiotics.

VanA-type vancomycin-resistant Enterococcus faecium ST1336 isolated from mussels in an anthropogenically impacted ecosystem

We report the occurrence and genomic features of multidrug-resistant vancomycin-resistant Enterococcus faecium vanA belonging to a novel sequence type (designated ST1336), carrying a Tn1546-like element, in marine brown mussels (Perna perna) from anthropogenically affected coastal waters of the Atlantic coast of Brazil, highlighting a potential source of dissemination for related ecosystems, with additional consequences for seafood safety and quality.

Zooanthroponotic Transmission of Drug-Resistant Pseudomonas aeruginosa, Brazil

We recovered VIM-2 carbapenemase-producing Pseudomonas aeruginosa isolates from an infected dog, its owner, and the domestic environment. Genomic investigation revealed household transmission of the high-risk hospital clone sequence type 233 in the human–animal–environment interface. Results suggest zooanthroponotic transmission of VIM-2–producing P. aeruginosa in the household following the patient's hospital discharge.

Genetic background of CTX-M-15-producing Enterobacter hormaechei ST114 and Citrobacter freundii ST265 co-infecting a free-living green turtle (Chelonia mydas)

CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have become identified in marine ecosystem constituting a serious ecological issue. In this respect, although contamination of coastal waters and seafood, and even colonization of seabirds and fishes have been increasingly reported, molecular data are lacking to elucidate the clinical impact of ESBL producers in infected marine animals. In this study, using a genomic approach, we have analysed the genetic background of CTX-M-15-producing Enterobacter hormaechei (belonging to the international human clone ST114) and Citrobacter freundii (ST265) co-infecting a free-living green turtle (Chelonia mydas) suffering from septic arthritis, which progressed to generalized coelomitis and death. Wide resistome of these pathogens contributed to treatment failure and death of the animal.

Effective treatment and decolonization of a dog infected with carbapenemase (VIM-2)-producing Pseudomonas aeruginosa using probiotic and photodynamic therapies

BACKGROUND

Carbapenem-resistant bacterial infections are a critical problem in veterinary medicine with limited treatment options.

OBJECTIVE

To describe effective probiotic and photodynamic therapy of a dog with gut colonization and ear infection caused by a hospital-associated lineage of carbapenemase (VIM-2)-producing Pseudomonas aeruginosa.

ANIMALS

A 5-year-old Lhasa apso dog presented with otitis externa.

METHODS AND MATERIALS

Unilateral otitis externa caused by carbapenem-resistant P. aeruginosa was treated with antimicrobial photodynamic therapy (aPDT) using methylene blue as photosensitizer [wavelength 660 nm, fluence 140 J/cm2 , 8 J and 80 s per point (six equidistant points), 100 mW, spot size 0.028 cm2 and fluence rate 3.5 W/cm2 ]. The isolated bacterial strain also was tested for susceptibility to in vitro aPDT where the survival fraction was quantified by colony forming unit counts after exposure to increasing light doses. For decolonization, probiotic supplements were orally administered (once daily) for 14 days. Effectiveness of probiotics and photodynamic therapy was evaluated by clinical and microbiological culture assays.

RESULTS

Complete resolution of clinical signs was achieved by Day 7 after aPDT. Samples collected immediately and after seven and 14 days following aPDT were negative for VIM-2-producing P. aeruginosa. Oral and rectal swabs collected on days 7, 14 and 21 after probiotic therapy, confirmed effective gastrointestinal decolonization.

CONCLUSIONS AND CLINICAL IMPORTANCE

Combined use of aPDT and probiotics could be a promising therapeutic strategy for treatment of superficial infections produced by carbapenem-resistant bacteria, while avoiding recurrent infection due to intestinal bacterial carriage of these multidrug-resistant pathogens.

Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232

OBJECTIVES

Genomic characterization of the internationally spread sequence type (ST) 16 carbapenem-resistant Klebsiella pneumoniae.

METHODS

The complete genomes of three carbapenem producing ST16 K. pneumoniae from Italian patients were analysed by single-nucleotide polymorphism-based phylogeny, core genome multilocus sequence typing, resistance, plasmid, and virulence content and compared with ten genomes of ST16 strains isolated in other countries. Plasmids carrying bla_NDM-1 or bla_OXA-232 carbapenemase genes were assembled and sequences were analysed.

RESULTS

The internationally spread ST16 K. pneumoniae clone showed variability in terms of distribution of NDM-1 and OXA-232 type carbapenemases. In some ST16 strains, up to six plasmids can be simultaneously present in the same cell, including ColE-like plasmids carrying bla_OXA-232 and IncF plasmids carrying bla_NDM-1. The differences observed in plasmid, resistance, and virulence content and core genome suggested that there is not a unique, highly conserved ST16 clone, but instead different variants of this lineage circulate worldwide.

CONCLUSIONS

The ST16 K. pneumoniae clone has spread worldwide and may become a high-risk clone.

Genomic features of a multidrug-resistant Enterobacter cloacae ST279 producing CTX-M-15 and AAC(6')-Ib-cr isolated from fatal infectious stomatitis in a crossed pit viper (Bothrops alternatus)

OBJECTIVES

The widespread dissemination of extended-spectrum β-lactamase-producing Enterobacteriaceae has become a major issue in veterinary medicine. However, until now, there has been no report of bacteria with such a phenotype in infected snakes. The aim of this study was to report the first draft genome sequence of an Enterobacter cloacae isolate (SERP1) recovered from a snake with infectious stomatitis.

METHODS

The whole genome of E. cloacae strain SERP1 was sequenced on an Illumina NextSeq platform and was de novo assembled using CLC NGS Cell v.10. Data analysis was performed using online tools from the Center of Genomic Epidemiology.

RESULTS

The genome size was calculated at 4966856bp, containing a total of 4796 protein-coding sequences. The strain was assigned to sequence type 279 (ST279) and, besides the clinically relevant bla_CTX-M-15 and aac(6')-Ib-cr genes, it also presented resistance genes to β-lactams, aminoglycosides, phenicols, sulphonamides, tetracyclines, trimethoprim, quinolones and fosfomycin.

CONCLUSION

These data offer novel information regarding multidrug-resistant E. cloacae dissemination in wild animals and might contribute to further comparative genomic analysis.

Genomic features of a highly virulent, ceftiofur-resistant, CTX-M-8-producing Escherichia coli ST224 causing fatal infection in a domestic cat

OBJECTIVES

Escherichia coli strains producing extended-spectrum β-lactamases (ESBLs), especially CTX-M-type, have been largely described in companion animals; however, genomic data are lacking to clarify the clinical impact of ESBL-producing isolates in these hosts. The aim of this study was to present the genomic features of a highly virulent, ceftiofur-resistant, CTX-M-8-producing E. coli isolate from a case of pneumonia in a domestic cat with fatal outcome.

METHODS

Genomic DNA was sequenced using an Illumina NextSeq 500 platform and was assembled using CLC Genomic Workbench. Genomic data were analysed using online bioinformatics tools.

RESULTS

The genome size was evaluated at 5.1Mb, with 5334 protein-coding sequences. The strain was assigned to sequence type 224 (ST224) and presented genes conferring resistance to β-lactams (bla_CTX-M-8), sulphonamides (sul2), tetracycline (tetA) and trimethoprim (dfrA14) as well as chromosomal point mutations in ParC (S80I), GyrA (S83L) and GyrB (D87N). In addition, the presence of the virulence genes cba, gad, ipfA, iroN, iss, mchF and tsh was detected.

CONCLUSION

This draft genome sequence might provide important data for a better understanding of genomic aspects regarding the dissemination of CTX-M-8-producing E. coli in the human-animal-environment interface.

Extended-spectrum-β-lactamase (CTX-M)-producing Escherichia coli in wild fishes from a polluted area in the Atlantic Coast of South America

The presence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in oceanic ecosystems constitutes an emerging public health risks in the marine environment. In this study, we report for the first time the identification of ESBL (CTX-M)-producing E. coli in wild fishes from a polluted area in the South Atlantic coast of Brazil, where a genomic analysis confirm the presence of livestock and human E. coli lineages belonging to sequence types (STs) ST744 and ST746, which carried clinically relevant resistance genes for human and veterinary antibiotics, and heavy metals. These findings reveal the presence of multidrug-resistant (MDR) bacteria in the gut microbiota of wild fishes living in polluted coastal waters, alerting that microbial contamination by bacteria related directly and indirectly to human or animal activities could affect the safety of the seafood supply, as well as the commercial and recreational use of coastal marine waters.

International high-risk clonal lineages of CTX-M-producing Escherichia coli F-ST648 in free-roaming cats, South America

The dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli belonging to high-virulent pandemic lineages has become a global problem with serious consequences for public health worldwide. In this regard, E. coli lineages belonging to the sequence type ST648, which are mostly associated with human infections, have begun to be reported in animals. In this study, we report the identification and genomic characterization of international CTX-M-producing E. coli ST648/F lineages in free-roaming cats from an urban slum, in Brazil. Moreover, we have performed a comparative genomic analysis of worldwide reported E. coli ST648 strains, highlighting an epidemiologic linkage between human and companion animals.

Genome sequence analysis of a hypermucoviscous/hypervirulent and MDR CTX-M-15/K19/ST29 Klebsiella pneumoniae isolated from human infection

The emergence of hypervirulent Klebsiella pneumoniae (hvKP) with multidrug resistance (MDR) profile is a worrisome public health issue. We report the first draft genome sequence of a hypermucoviscous (positive string test) and MDR K. pneumoniae serotype K19, belonging to ST29, isolated from human infection. This strain harboured multiple antimicrobial resistance genes, including blaCTX-M-15, besides yersiniabactin and type 3 fimbriae virulence genes. In vivo experiments carried out with the Galleria mellonella infection model revealed that K. pneumoniae K19/ST29 killed 100% of the larvae at 24 h post-infection, in a similar way to the known hypermucoviscous hvKP K1/ST23 lineage.

Draft genome sequence of a blaCMY-2/IncI1-harbouring Escherichia coli D:ST457 isolated from coastal benthic organisms

OBJECTIVES

Marine bivalves can act as bioindicators of marine environment pollution by multidrug-resistant (MDR) enteric bacteria of medical interest. The aim of this study was to report the draft genome sequence of a plasmid-encoded AmpC (pAmpC) (CMY-2)-carrying Escherichia coli isolate recovered from a marine bivalve sample in the coastal shore of Southeast Brazil.

METHODS

The whole genome was sequenced on an Illumina NextSeq platform and was assembled using Velvet v.1.2.10. Data analysis was carried out using tools available from the Center of Genomic Epidemiology and Geneious R10 software.

RESULTS

The genome size was calculated at 5198055bp, comprising a total of 5316 protein-coding sequences. The strain was assigned to ST457 and presented the bla_CMY-2 pAmpC gene. In addition, the strain was clustered into the pathogenic phylogenetic group D.

CONCLUSION

The release of this draft genome sequence can provide valuable information to better understand the dissemination of MDR enteric bacteria in marine environments.

Multidrug-resistant CTX-M-15-producing Klebsiella pneumoniae ST231 associated with infection and persistent colonization of dog

Extended spectrum β-lactamase (ESBL)-producing bacterial infections in veterinary medicine are a clinical and epidemiological challenge. We report a case of CTX-M-15-producing Klebsiella pneumoniae infection followed by persistent colonization, in a dog presenting with bilateral purulent nasal discharge and dyspnea. In this regard, 5 broad-spectrum cephalosporin-resistant K. pneumoniae isolates were recovered from infection and surveillance cultures, collected during 1 year and eight months study. Genomic analysis of a representative clone of K. pneumoniae (KpPB76) revealed the presence of the human-associated lineage ST231, whereas resistome data confirmed the presence of genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones, fosfomycin, phenicols, sulfonamides, tetracyclines and trimethoprim. In the absence of therapeutic options, meropenem therapy was used, contributing to the control of infection during persistent carriage of K. pneumoniae CTX-M-15/ST231. Persistent colonization of companion animals with ESBL-producing bacteria could be result from a variety of situations, including multi introduction from the owner or household family members to pets, or from environmental exposure; whereas colonized animals may serve as an important source for the spread of ESBL-producing strains in the human-animal interface.

Novel class 1 integron (In1390) harboring blaGES-5 in a Morganella morganii strain recovered from a remote community

Antimicrobial resistance in Morganella morganii has been mainly acquired via plasmids and class 1 integrons. We hereby report acquisition of bla_GES-5 by a M. morganii isolated in a remote community from the Amazon region. Genomic analysis revealed that bla_GES-5 was harbored by a novel class 1 integron designated as In1390.

Draft genome sequence of an extensively drug-resistant Pseudomonas aeruginosa isolate belonging to ST644 isolated from a footpad infection in a Magellanic penguin (Spheniscus magellanicus)

OBJECTIVES

The incidence of multidrug-resistant bacteria in wildlife animals has been investigated to improve our knowledge of the spread of clinically relevant antimicrobial resistance genes. The aim of this study was to report the first draft genome sequence of an extensively drug-resistant (XDR) Pseudomonas aeruginosa ST644 isolate recovered from a Magellanic penguin with a footpad infection (bumblefoot) undergoing rehabilitation process.

METHODS

The genome was sequenced on an Illumina NextSeq^® platform using 150-bp paired-end reads. De novo genome assembly was performed using Velvet v.1.2.10, and the whole genome sequence was evaluated using bioinformatics approaches from the Center of Genomic Epidemiology, whereas an in-house method (mapping of raw whole genome sequence reads) was used to identify chromosomal point mutations.

RESULTS

The genome size was calculated at 6436450bp, with 6357 protein-coding sequences and the presence of genes conferring resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracyclines, quinolones and fosfomycin; in addition, mutations in the genes gyrA (Thr83Ile), parC (Ser87Leu), phoQ (Arg61His) and pmrB (Tyr345His), conferring resistance to quinolones and polymyxins, respectively, were confirmed.

CONCLUSION

This draft genome sequence can provide useful information for comparative genomic analysis regarding the dissemination of clinically significant antibiotic resistance genes and XDR bacterial species at the human-animal interface.

International high-risk clones of Klebsiella pneumoniae KPC-2/CC258 and Escherichia coli CTX-M-15/CC10 in urban lake waters

The emergence of high-risk clones of multidrug-resistant (MDR) bacteria in aquatic environments has generated an important public health problem, creating an urgent need to strengthen surveillance. This study reports the occurrence of clinically significant MDR Enterobacteriaceae and non-fermentative bacteria carrying carbapenemases (KPC-2), extended-spectrum β-lactamases (CTX-M) and plasmid-mediated quinolone resistance (PMQR) genes in urban lakes and reservoirs, in Southeastern Brazil. In this regard, the detection of hospital-associated lineages of KPC-2-producing Klebsiella pneumoniae belonging to the international clonal complex CC258 (ST11) and CTX-M-15-producing Escherichia coli belonging to the international CC10 (ST617), in an urban lake, is reported for the first time. Whole genome sequencing (WGS) analysis of KPC-2-producing K. pneumoniae ST11 revealed that bla_KPC-2 gene was carried by an IncN plasmid on a Tn4401b element. This study support that aquatic environments with public access can act as reservoirs of clinically important MDR bacteria, constituting a potential risk to human and animal health. On the other hand, the detection of high-risk clones highlights the extra-hospital spread of clinically significant bacteria into urban aquatic environments.

Draft genome sequence of a CTX-M-15-producing endophytic Klebsiella pneumoniae ST198 isolate from commercial lettuce

CTX-M-15-producing Klebsiella pneumoniae is one of the leading causes of hospital-acquired infections globally. In this study, we present the draft genome sequence of the first CTX-M-15-producing endophytic K. pneumoniae strain, belonging to sequence type 198 (ST198) and isolated from commercial lettuce, which can be used as a reference sequence for comparative analysis with clinical and environmental strains of K. pneumoniae.

Draft genome sequence of Enterobacter cloacae ST520 harbouring blaKPC-2, blaCTX-M-15 and blaOXA-17 isolated from coastal waters of the South Atlantic Ocean

OBJECTIVES

Aquatic environments have contributed to the dissemination of multidrug-resistant (MDR) bacteria, representing a risk for humans and animals. The aim of this study was to report the first draft genome sequence of a MDR Enterobacter cloacae strain recovered from seawater in a public beach in Brazil.

METHODS

The genome was sequenced on an Illumina MiSeq platform. De novo genome assembly was performed using SPAdes 3.10.1 and the whole genome sequence was analysed using bioinformatics tools from the Center of Genomic Epidemiology.

RESULTS

This draft genome resulted in 5 228 857bp with 5331 protein-coding sequences, revealing the presence of bla_KPC-2, bla_CTX-M-15 and bla_OXA-17 genes, responsible for resistance to all β-lactam antibiotics. In addition, the strain was assigned to sequenced type 520 (ST520).

CONCLUSION

These data provide useful information for comparative genomic analysis regarding the dissemination of antibiotic resistance genes.

Draft genome sequence of a multidrug-resistant KPC-2-producing Enterobacter aerogenes isolated from a hospitalised patient in Brazil

OBJECTIVES

Multidrug-resistant (MDR) Enterobacter aerogenes strains are frequently associated with nosocomial infections and high mortality rates, representing a serious public health problem. The aim of this study was to present the draft genome sequence of a MDR KPC-2-producing E. aerogenes isolated from a perineal swab of a hospitalised patient in Brazil.

METHODS

Genomic DNA was sequenced using an Illumina MiSeq platform. De novo genome assembly was carried out using the A5-Miseq pipeline, and whole-genome sequence analysis was performed using tools from the Center for Genomic Epidemiology.

RESULTS

The strain harboured resistance genes to β-lactams, aminoglycosides, sulphonamides and trimethoprim in addition to genes encoding multidrug efflux system proteins, a quaternary ammonium transporter and heavy metal efflux system proteins. In addition, the strain harboured genes encoding diverse virulence factors.

CONCLUSION

These data might allow a better understanding of the genetic basis of antimicrobial resistance and virulence in E. aerogenes strains.

Draft genome sequence of a multidrug-resistant Aeromonas hydrophila ST508 strain carrying rmtD and blaCTX-M-131 isolated from a bloodstream infection

Here we report the draft genome sequence of a multidrug-resistant (MDR) Aeromonas hydrophila strain belonging to sequence type 508 (ST508) isolated from a human bloodstream infection. Assembly and annotation of this draft genome resulted in 5028498bp and revealed the presence of 16S rRNA methylase rmtD and bla_CTX-M-131 genes encoding high-level resistance to aminoglycosides and cephalosporins, respectively, as well as multiple virulence genes. This draft genome can provide significant information for understanding mechanisms on the establishment and treatment of infections caused by this pathogen.

Draft genome sequence of an environmental multidrug-resistant Klebsiella pneumoniae ST340/CC258 harbouring blaCTX-M-15 and blaKPC-2 genes

Anthropogenic activities, including the release of wastewater and sewage from hospitals, have contributed to the contamination of aquatic environments, raising a concern to public health. In this study, we present the first draft genome sequence of a Klebsiella pneumoniae strain (Kp171, TIET-4200) belonging to the high-risk hospital-associated clonal lineage ST340/CC258, which was recovered from a water sample collected in an urban river in Brazil.

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children

The administration of antimicrobial agents leads to an ecological imbalance of the host-microorganisms relationship, and it causes a rapid and significant reduction in the microbial diversity. The aim of the current study was to evaluate the impact of antibiotic therapy on intestinal microbiota of children between 3 and 12 years of age. The fecal samples were collected from hospitalized children (n = 31) and from healthy untreated children (n = 30). The presence of bacteria and their quantities were assessed by culture-based methods and quantitative polymerase chain reaction (qPCR). By culture method, in the children receiving antibiotics, a low recovery of Bifidobacterium spp. (54.8%), Bacteroides spp./Parabacteroides spp. (54.8%), Clostridium spp. (35.5%), and Escherichia coli (74.2%) was observed compared with the children without antibiotic therapy (100%, 80%, 63.3%, and 86.6%, respectively). By qPCR, the children receiving antibiotics showed a lower copy number for all microorganisms, except to Lactobacillus spp. (p = 0.0092). In comparison to the nontreated children, the antibiotic-treated children showed a significantly lower copy number of Bifidobacterium spp. (p = 0.0002), Clostridium perfringens (p < 0.0001), E. coli (p = 0.0268), Methanobrevibacter smithii (p = 0.0444), and phylum Firmicutes (p = 0.0009). In conclusion, our results obtained through qualitative and quantitative analyses, demonstrate that antibiotic therapy affect the intestinal microbiome of children.

Silent dissemination of colistin-resistant Escherichia coli in South America could contribute to the global spread of the mcr-1 gene

During a Brazilian multicentric antimicrobial resistance surveillance study, colistin resistance was investigated in 4,620 Enterobacteriaceae isolated from human, animal, food and environmental samples collected from 2000 to 2016. We present evidence that mcr-1-positive Escherichia coli has been emerging in South America since at least 2012, supporting a previous report on the possible acquisition of mcr-1-harbouring E. coli by European travellers visiting Latin American countries.

Correlation between body mass index and faecal microbiota from children

Childhood obesity is an increasing problem at the global level and considered as a risk factor for obesity development and the associated co-morbidities in adult life. In this study, the occurrence of Bacteroides fragilis group, Clostridium spp., Bifidobacterium spp. and Escherichia coli in 84 faecal samples from 30 obese, 24 overweight and 30 lean children was verified by culture technique and quantitative determination by quantitative PCR. In addition, Lactobacillus spp. and Methanobrevibacter smithii were also analysed. A correlation between the body mass index (BMI) and these bacteria was sought. Bacteroides vulgatus, Clostridium perfringens and Bifidobacterium adolescentis were most prevalent in all samples evaluated by culture-method. The B. fragilis group were found at high concentrations in obese and overweight children when compared with the lean ones (p 0.015). The obese and overweight children harboured higher numbers of Lactobacillus spp. than lean children (p 0.022). The faecal concentrations of the B. fragilis group (r = 0.24; p 0.026) and Lactobacillus spp. (r = 0.44; p 0.002) were positively correlated with BMI. Bifidobacterium spp. were found in higher numbers in the lean group than the overweight and obese ones (p 0.042). Furthermore, a negative correlation between BMI and Bifidobacterium spp. copy number (r = -0.22; p 0.039) was observed. Our findings show some difference in the intestinal microbial ecosystem of obese children compared with the lean ones and a significant association between number of Lactobacillus spp. and B. fragilis group and BMI.

High occurrence of Fusobacterium nucleatum and Clostridium difficile in the intestinal microbiota of colorectal carcinoma patients

Colorectal carcinoma is considered the fourth leading cause of cancer deaths worldwide. Several microorganisms have been associated with carcinogenesis, including Enterococcus spp., Helicobacter pylori, enterotoxigenic Bacteroides fragilis, pathogenic E. coli strains and oral Fusobacterium. Here we qualitatively and quantitatively evaluated the presence of oral and intestinal microorganisms in the fecal microbiota of colorectal cancer patients and healthy controls. Seventeen patients (between 49 and 70 years-old) visiting the Cancer Institute of the Sao Paulo State were selected, 7 of whom were diagnosed with colorectal carcinoma. Bacterial detection was performed by qRT-PCR. Although all of the tested bacteria were detected in the majority of the fecal samples, quantitative differences between the Cancer Group and healthy controls were detected only for F. nucleatum and C. difficile. The three tested oral microorganisms were frequently observed, suggesting a need for furthers studies into a potential role for these bacteria during colorectal carcinoma pathogenesis. Despite the small number of patients included in this study, we were able to detect significantly more F. nucleatum and C. difficile in the Cancer Group patients compared to healthy controls, suggesting a possible role of these bacteria in colon carcinogenesis. This finding should be considered when screening for colorectal cancer.